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theislab / cellrank

CellRank: dynamics from multi-view single-cell data
https://cellrank.org
BSD 3-Clause "New" or "Revised" License
342 stars 47 forks source link

Developer installation #628

Closed WeilerP closed 3 years ago

WeilerP commented 3 years ago

Description

Running pip install -e '.[dev]' does not install all packages required for a full development cycle. For example, any modules related to testing are not installed. IMO, a developer installation should allow running the entire codebase as well as unit tests without having to install additional libraries. What do you think @Marius1311, @michalk8?

michalk8 commented 3 years ago

It installs all the necessary things - tox and pre-commit (the latter is just for convenience of not running tox -e lint), think it's fine as it is.

WeilerP commented 3 years ago

It installs all the necessary things - tox and pre-commit (the latter is just for convenience of not running tox -e lint), think it's fine as it is.

Running

pip install -e '.[dev]'
pre-commit install
tox -e py38-linux

failed for me since, e.g., pytest wasn't installed.

michalk8 commented 3 years ago

Thanks for catching this, indeed, the required packages are not listed in tox.ini, will fix it soon.

michalk8 commented 3 years ago

Thanks for catching this, indeed, the required packages are not listed in tox.ini, will fix it soon.

Hmm, upon further inspection, it seems correct, the test requirements are still in setup.py and also used in tox.ini. Furthermore, I wasn't able to reproduce this or the warning in #627 (let's move the discussion here).

michalk8 commented 3 years ago

@Marius1311 can you reproduce this on your Mac?

Marius1311 commented 3 years ago

I'll check this out, however, it's a bit tight before the release - I'll look into it afterwards, we can exclude this from the release.

Marius1311 commented 3 years ago

Is this still an issue?

michalk8 commented 3 years ago

Is this still an issue?

Did you try locally on your machine with a fresh conda environment whether you get the same issues as mentioned above? If yes, let's discuss tomorrow.

Marius1311 commented 3 years ago

I tried:

See below for the output I got. Is this what you guys wanted me to run?

Traceback ```python (test_cr_dev) ➜ cellrank git:(dev) tox covclean create: /Users/marius/Projects/cellrank/.tox/covclean covclean installdeps: coverage covclean installed: coverage==5.5 covclean run-test-pre: PYTHONHASHSEED='3393242636' covclean run-test: commands[0] | coverage erase lint create: /Users/marius/Projects/cellrank/.tox/lint lint installdeps: pre-commit>=2.9.3 lint installed: appdirs==1.4.4,cfgv==3.3.0,distlib==0.3.2,filelock==3.0.12,identify==2.2.10,nodeenv==1.6.0,pre-commit==2.13.0,PyYAML==5.4.1,six==1.16.0,toml==0.10.2,virtualenv==20.4.7 lint run-test-pre: PYTHONHASHSEED='3393242636' lint run-test: commands[0] | pre-commit run --all-files --show-diff-on-failure black....................................................................Passed isort....................................................................Passed Strip unnecessary `# noqa`s..............................................Passed Pretty format YAML.......................................................Passed Detect Private Key.......................................................Passed Check for merge conflicts................................................Passed Check python ast.........................................................Passed Check for broken symlinks............................(no files to check)Skipped Check for added large files..............................................Passed Check that executables have shebangs.....................................Passed Fix python encoding pragma...............................................Passed Fix End of Files.........................................................Passed Mixed line ending........................................................Passed Trim Trailing Whitespace.................................................Passed Check for case conflicts.................................................Passed Check docstring is first.................................................Passed Check Yaml...............................................................Passed Check Toml...............................................................Passed Fix requirements.txt.....................................................Passed autoflake................................................................Passed flake8...................................................................Passed Check executable files use .sh extension.................................Passed rstcheck.................................................................Passed blacken-docs.............................................................Passed pyupgrade................................................................Passed check for eval().........................................................Passed type annotations not comments............................................Passed rst ``code`` is two backticks............................................Passed rst directives end with two colons.......................................Passed rst ``inline code`` next to normal text..................................Passed doc8.....................................................................Passed py37-macos create: /Users/marius/Projects/cellrank/.tox/py37-macos py37-macos installdeps: adjustText ERROR: invocation failed (exit code 1), logfile: /Users/marius/Projects/cellrank/.tox/py37-macos/log/py37-macos-1.log ============================================== log start ============================================== WARNING: pip is configured with locations that require TLS/SSL, however the ssl module in Python is not available. WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError("Can't connect to HTTPS URL because the SSL module is not available.")': /simple/adjusttext/ WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError("Can't connect to HTTPS URL because the SSL module is not available.")': /simple/adjusttext/ WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError("Can't connect to HTTPS URL because the SSL module is not available.")': /simple/adjusttext/ WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError("Can't connect to HTTPS URL because the SSL module is not available.")': /simple/adjusttext/ WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError("Can't connect to HTTPS URL because the SSL module is not available.")': /simple/adjusttext/ Could not fetch URL https://pypi.org/simple/adjusttext/: There was a problem confirming the ssl certificate: HTTPSConnectionPool(host='pypi.org', port=443): Max retries exceeded with url: /simple/adjusttext/ (Caused by SSLError("Can't connect to HTTPS URL because the SSL module is not available.")) - skipping ERROR: Could not find a version that satisfies the requirement adjustText (from versions: none) ERROR: No matching distribution found for adjustText WARNING: pip is configured with locations that require TLS/SSL, however the ssl module in Python is not available. Could not fetch URL https://pypi.org/simple/pip/: There was a problem confirming the ssl certificate: HTTPSConnectionPool(host='pypi.org', port=443): Max retries exceeded with url: /simple/pip/ (Caused by SSLError("Can't connect to HTTPS URL because the SSL module is not available.")) - skipping =============================================== log end =============================================== ERROR: could not install deps [adjustText]; v = InvocationError('/Users/marius/Projects/cellrank/.tox/py37-macos/bin/python -m pip install adjustText', 1) py38-macos create: /Users/marius/Projects/cellrank/.tox/py38-macos py38-macos installdeps: adjustText py38-macos develop-inst: /Users/marius/Projects/cellrank ERROR: invocation failed (exit code 1), logfile: /Users/marius/Projects/cellrank/.tox/py38-macos/log/py38-macos-2.log ============================================== log start ============================================== Obtaining file:///Users/marius/Projects/cellrank Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing wheel metadata: started Preparing wheel metadata: finished with status 'done' Collecting pandas>=1.2.0 Using cached pandas-1.2.5-cp38-cp38-macosx_10_9_x86_64.whl (10.5 MB) Collecting scvelo>=0.2.3 Using cached scvelo-0.2.3-py3-none-any.whl (177 kB) Collecting scipy>=1.2.0 Using cached scipy-1.7.0-cp38-cp38-macosx_10_9_x86_64.whl (31.9 MB) Requirement already satisfied: numpy>=1.2.0 in ./.tox/py38-macos/lib/python3.8/site-packages (from cellrank==1.3.2.dev73+ge5c6191) (1.21.0) Collecting seaborn>=0.10.0 Using cached seaborn-0.11.1-py3-none-any.whl (285 kB) Collecting joblib>=0.13.1 Using cached joblib-1.0.1-py3-none-any.whl (303 kB) Requirement already satisfied: setuptools>=41.0.1 in ./.tox/py38-macos/lib/python3.8/site-packages (from cellrank==1.3.2.dev73+ge5c6191) (57.0.0) Collecting wrapt>=1.12.1 Using cached wrapt-1.12.1-cp38-cp38-macosx_10_9_x86_64.whl Requirement already satisfied: matplotlib>=3.3.0 in ./.tox/py38-macos/lib/python3.8/site-packages (from cellrank==1.3.2.dev73+ge5c6191) (3.4.2) Collecting pygpcca>=1.0.2 Using cached pygpcca-1.0.2-py3-none-any.whl (68 kB) Collecting typing-extensions Using cached typing_extensions-3.10.0.0-py3-none-any.whl (26 kB) Collecting scanpy>=1.7.2 Using cached scanpy-1.8.0-py3-none-any.whl (11.3 MB) Collecting docrep>=0.3.0 Using cached docrep-0.3.2-py3-none-any.whl Collecting scikit-learn>=0.24.0 Using cached scikit_learn-0.24.2-cp38-cp38-macosx_10_13_x86_64.whl (7.2 MB) Collecting networkx>=2.2 Using cached networkx-2.5.1-py3-none-any.whl (1.6 MB) Collecting numba<0.53.0,>=0.51.0 Using cached numba-0.52.0-cp38-cp38-macosx_10_14_x86_64.whl (2.2 MB) Collecting pygam>=0.8.0 Using cached pygam-0.8.0-py2.py3-none-any.whl (1.8 MB) Collecting python-igraph Downloading python_igraph-0.9.6-cp38-cp38-macosx_10_9_x86_64.whl (2.0 MB) Collecting leidenalg Using cached leidenalg-0.8.4-cp38-cp38-macosx_10_9_x86_64.whl (230 kB) Collecting pytest-cov Downloading pytest_cov-2.12.1-py2.py3-none-any.whl (20 kB) Collecting jaxlib Downloading jaxlib-0.1.68-cp38-none-macosx_10_9_x86_64.whl (44.1 MB) Requirement already satisfied: Pillow in ./.tox/py38-macos/lib/python3.8/site-packages (from cellrank==1.3.2.dev73+ge5c6191) (8.3.0) Collecting jax Downloading jax-0.2.16.tar.gz (680 kB) Collecting bezier Using cached bezier-2021.2.12-cp38-cp38-macosx_10_9_x86_64.whl (1.7 MB) Collecting pytest-xdist>=2.1.0 Downloading pytest_xdist-2.3.0-py3-none-any.whl (37 kB) Collecting filelock Using cached filelock-3.0.12-py3-none-any.whl (7.6 kB) Collecting pytest-mock>=3.5.1 Downloading pytest_mock-3.6.1-py3-none-any.whl (12 kB) Collecting louvain!=0.6.2,>=0.6 Using cached louvain-0.7.0-cp38-cp38-macosx_10_9_x86_64.whl (736 kB) Collecting pytest>=6.1.1 Downloading pytest-6.2.4-py3-none-any.whl (280 kB) Collecting statot>=0.0.14 Downloading statot-0.0.14-py3-none-any.whl (11 kB) Collecting wot Downloading wot-1.0.8.post2-py2.py3-none-any.whl (60 kB) Collecting POT Using cached POT-0.7.0-cp38-cp38-macosx_10_9_x86_64.whl (146 kB) Requirement already satisfied: six in ./.tox/py38-macos/lib/python3.8/site-packages (from docrep>=0.3.0->cellrank==1.3.2.dev73+ge5c6191) (1.16.0) Requirement already satisfied: cycler>=0.10 in ./.tox/py38-macos/lib/python3.8/site-packages (from matplotlib>=3.3.0->cellrank==1.3.2.dev73+ge5c6191) (0.10.0) Requirement already satisfied: python-dateutil>=2.7 in ./.tox/py38-macos/lib/python3.8/site-packages (from matplotlib>=3.3.0->cellrank==1.3.2.dev73+ge5c6191) (2.8.1) Requirement already satisfied: kiwisolver>=1.0.1 in ./.tox/py38-macos/lib/python3.8/site-packages (from matplotlib>=3.3.0->cellrank==1.3.2.dev73+ge5c6191) (1.3.1) Requirement already satisfied: pyparsing>=2.2.1 in ./.tox/py38-macos/lib/python3.8/site-packages (from matplotlib>=3.3.0->cellrank==1.3.2.dev73+ge5c6191) (2.4.7) Collecting decorator<5,>=4.3 Using cached decorator-4.4.2-py2.py3-none-any.whl (9.2 kB) Collecting llvmlite<0.36,>=0.35.0 Using cached llvmlite-0.35.0-cp38-cp38-macosx_10_9_x86_64.whl (18.5 MB) Collecting pytz>=2017.3 Using cached pytz-2021.1-py2.py3-none-any.whl (510 kB) Collecting future Using cached future-0.18.2-py3-none-any.whl Collecting progressbar2 Using cached progressbar2-3.53.1-py2.py3-none-any.whl (25 kB) Collecting py>=1.8.2 Using cached py-1.10.0-py2.py3-none-any.whl (97 kB) Collecting pluggy<1.0.0a1,>=0.12 Using cached pluggy-0.13.1-py2.py3-none-any.whl (18 kB) Collecting packaging Using cached packaging-20.9-py2.py3-none-any.whl (40 kB) Collecting iniconfig Using cached iniconfig-1.1.1-py2.py3-none-any.whl (5.0 kB) Collecting toml Using cached toml-0.10.2-py2.py3-none-any.whl (16 kB) Collecting attrs>=19.2.0 Using cached attrs-21.2.0-py2.py3-none-any.whl (53 kB) Collecting pytest-forked Using cached pytest_forked-1.3.0-py2.py3-none-any.whl (4.7 kB) Collecting execnet>=1.1 Downloading execnet-1.9.0-py2.py3-none-any.whl (39 kB) Collecting texttable>=1.6.2 Using cached texttable-1.6.3-py2.py3-none-any.whl (10 kB) Collecting patsy Using cached patsy-0.5.1-py2.py3-none-any.whl (231 kB) Collecting h5py>=2.10.0 Using cached h5py-3.3.0-cp38-cp38-macosx_10_9_x86_64.whl (2.9 MB) Collecting legacy-api-wrap Using cached legacy_api_wrap-1.2-py3-none-any.whl (37 kB) Collecting natsort Using cached natsort-7.1.1-py3-none-any.whl (35 kB) Collecting anndata>=0.7.4 Using cached anndata-0.7.6-py3-none-any.whl (127 kB) Collecting umap-learn>=0.3.10 Using cached umap-learn-0.5.1.tar.gz (80 kB) Collecting tqdm Using cached tqdm-4.61.1-py2.py3-none-any.whl (75 kB) Collecting sinfo Using cached sinfo-0.3.4-py3-none-any.whl Collecting statsmodels>=0.10.0rc2 Using cached statsmodels-0.12.2-cp38-cp38-macosx_10_15_x86_64.whl (9.5 MB) Collecting tables Using cached tables-3.6.1-cp38-cp38-macosx_10_9_x86_64.whl (4.3 MB) Collecting xlrd<2.0 Using cached xlrd-1.2.0-py2.py3-none-any.whl (103 kB) Collecting threadpoolctl>=2.0.0 Using cached threadpoolctl-2.1.0-py3-none-any.whl (12 kB) Collecting umap-learn>=0.3.10 Using cached umap_learn-0.4.6-py3-none-any.whl Collecting loompy>=2.0.12 Using cached loompy-3.0.6-py3-none-any.whl Collecting click Using cached click-8.0.1-py3-none-any.whl (97 kB) Collecting numpy-groupies Using cached numpy_groupies-0.9.13-py3-none-any.whl Collecting absl-py Downloading absl_py-0.13.0-py3-none-any.whl (132 kB) Collecting opt_einsum Downloading opt_einsum-3.3.0-py3-none-any.whl (65 kB) Collecting flatbuffers<3.0,>=1.12 Downloading flatbuffers-2.0-py2.py3-none-any.whl (26 kB) Collecting get-version>=2.0.4 Using cached get_version-3.2-py3-none-any.whl (16 kB) Collecting dunamai Using cached dunamai-1.5.5-py3-none-any.whl (16 kB) Collecting cython>=0.23 Downloading Cython-0.29.23-cp38-cp38-macosx_10_9_x86_64.whl (1.9 MB) Collecting python-utils>=2.3.0 Using cached python_utils-2.5.6-py2.py3-none-any.whl (12 kB) Collecting slepc4py<3.14,>=3.13 Downloading slepc4py-3.13.0.tar.gz (815 kB) Collecting mpi4py<3.1,>=3.0.3 Downloading mpi4py-3.0.3.tar.gz (1.4 MB) Collecting petsc4py<3.14,>=3.13 Downloading petsc4py-3.13.0.tar.gz (1.9 MB) Collecting petsc<3.14,>=3.13 Downloading petsc-3.13.5.tar.gz (14.9 MB) Collecting slepc<3.14,>=3.13 Downloading slepc-3.13.2.tar.gz (4.8 MB) Collecting coverage>=5.2.1 Using cached coverage-5.5-cp38-cp38-macosx_10_9_x86_64.whl (207 kB) Collecting stdlib-list Using cached stdlib_list-0.8.0-py3-none-any.whl (63 kB) Collecting numexpr>=2.6.2 Using cached numexpr-2.7.3-cp38-cp38-macosx_10_9_x86_64.whl (99 kB) Building wheels for collected packages: jax, mpi4py, petsc, petsc4py, slepc, slepc4py Building wheel for jax (setup.py): started Building wheel for jax (setup.py): finished with status 'done' Created wheel for jax: filename=jax-0.2.16-py3-none-any.whl size=784392 sha256=779d82a6cb7ed2e81a428730e627f419413b0680908a0d674368f40cb24bea69 Stored in directory: /Users/marius/Library/Caches/pip/wheels/1d/bd/78/aaa554c33eb6d6e44454fdddbddb67c74a4455f648f1cdedb7 Building wheel for mpi4py (setup.py): started Building wheel for mpi4py (setup.py): finished with status 'error' ERROR: Command errored out with exit status 1: command: /Users/marius/Projects/cellrank/.tox/py38-macos/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/mx/0hyv8t2s26jdj79f55kvc_b80000gn/T/pip-install-0c7ialkz/mpi4py_13644ce5c597452fad3b5d585147c818/setup.py'"'"'; __file__='"'"'/private/var/folders/mx/0hyv8t2s26jdj79f55kvc_b80000gn/T/pip-install-0c7ialkz/mpi4py_13644ce5c597452fad3b5d585147c818/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/mx/0hyv8t2s26jdj79f55kvc_b80000gn/T/pip-wheel-qsdjfr8v cwd: /private/var/folders/mx/0hyv8t2s26jdj79f55kvc_b80000gn/T/pip-install-0c7ialkz/mpi4py_13644ce5c597452fad3b5d585147c818/ Complete output (162 lines): running bdist_wheel running build running build_src running build_py creating build creating build/lib.macosx-10.9-x86_64-3.8 creating build/lib.macosx-10.9-x86_64-3.8/mpi4py copying src/mpi4py/run.py -> build/lib.macosx-10.9-x86_64-3.8/mpi4py copying src/mpi4py/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/mpi4py copying src/mpi4py/bench.py -> build/lib.macosx-10.9-x86_64-3.8/mpi4py copying src/mpi4py/__main__.py -> build/lib.macosx-10.9-x86_64-3.8/mpi4py creating build/lib.macosx-10.9-x86_64-3.8/mpi4py/futures copying src/mpi4py/futures/_base.py -> build/lib.macosx-10.9-x86_64-3.8/mpi4py/futures copying src/mpi4py/futures/server.py -> build/lib.macosx-10.9-x86_64-3.8/mpi4py/futures copying src/mpi4py/futures/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/mpi4py/futures copying src/mpi4py/futures/pool.py -> build/lib.macosx-10.9-x86_64-3.8/mpi4py/futures copying src/mpi4py/futures/aplus.py -> build/lib.macosx-10.9-x86_64-3.8/mpi4py/futures copying src/mpi4py/futures/__main__.py -> build/lib.macosx-10.9-x86_64-3.8/mpi4py/futures copying src/mpi4py/futures/_lib.py -> build/lib.macosx-10.9-x86_64-3.8/mpi4py/futures copying src/mpi4py/__init__.pxd -> build/lib.macosx-10.9-x86_64-3.8/mpi4py copying src/mpi4py/libmpi.pxd -> build/lib.macosx-10.9-x86_64-3.8/mpi4py copying src/mpi4py/MPI.pxd -> build/lib.macosx-10.9-x86_64-3.8/mpi4py creating build/lib.macosx-10.9-x86_64-3.8/mpi4py/include creating build/lib.macosx-10.9-x86_64-3.8/mpi4py/include/mpi4py copying src/mpi4py/include/mpi4py/mpi4py.MPI.h -> build/lib.macosx-10.9-x86_64-3.8/mpi4py/include/mpi4py copying src/mpi4py/include/mpi4py/mpi4py.MPI_api.h -> build/lib.macosx-10.9-x86_64-3.8/mpi4py/include/mpi4py copying src/mpi4py/include/mpi4py/mpi4py.h -> build/lib.macosx-10.9-x86_64-3.8/mpi4py/include/mpi4py copying src/mpi4py/include/mpi4py/mpi4py.i -> build/lib.macosx-10.9-x86_64-3.8/mpi4py/include/mpi4py copying src/mpi4py/include/mpi4py/mpi.pxi -> build/lib.macosx-10.9-x86_64-3.8/mpi4py/include/mpi4py running build_clib MPI configuration: [mpi] from 'mpi.cfg' MPI C compiler: /usr/local/Cellar/mpich/3.3.2/bin/mpicc MPI C++ compiler: /usr/local/Cellar/mpich/3.3.2/bin/mpicxx MPI F compiler: /usr/local/Cellar/mpich/3.3.2/bin/mpifort MPI F90 compiler: /usr/local/Cellar/mpich/3.3.2/bin/mpif90 MPI F77 compiler: /usr/local/Cellar/mpich/3.3.2/bin/mpif77 checking for library 'lmpe' ... /usr/local/Cellar/mpich/3.3.2/bin/mpicc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -c _configtest.c -o _configtest.o /usr/local/Cellar/mpich/3.3.2/bin/mpicc -flat_namespace -undefined suppress -arch x86_64 _configtest.o -llmpe -o _configtest ld: library not found for -llmpe clang: error: linker command failed with exit code 1 (use -v to see invocation) failure. removing: _configtest.c _configtest.o building 'mpe' dylib library creating build/temp.macosx-10.9-x86_64-3.8 creating build/temp.macosx-10.9-x86_64-3.8/src creating build/temp.macosx-10.9-x86_64-3.8/src/lib-pmpi /usr/local/Cellar/mpich/3.3.2/bin/mpicc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -c src/lib-pmpi/mpe.c -o build/temp.macosx-10.9-x86_64-3.8/src/lib-pmpi/mpe.o creating build/lib.macosx-10.9-x86_64-3.8/mpi4py/lib-pmpi /usr/local/Cellar/mpich/3.3.2/bin/mpicc -shared -undefined dynamic_lookup -L/Users/marius/miniconda3/envs/test_cr_dev/lib -arch x86_64 -L/Users/marius/miniconda3/envs/test_cr_dev/lib -arch x86_64 -arch x86_64 -install_name libmpe.dylib build/temp.macosx-10.9-x86_64-3.8/src/lib-pmpi/mpe.o -o build/lib.macosx-10.9-x86_64-3.8/mpi4py/lib-pmpi/libmpe.dylib ld: file not found: /usr/local/opt/gcc/lib/gcc/9/libgfortran.5.dylib for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) warning: build_clib: command '/usr/local/Cellar/mpich/3.3.2/bin/mpicc' failed with exit status 1 warning: build_clib: building optional library "mpe" failed checking for library 'vt-mpi' ... /usr/local/Cellar/mpich/3.3.2/bin/mpicc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -c _configtest.c -o _configtest.o /usr/local/Cellar/mpich/3.3.2/bin/mpicc -flat_namespace -undefined suppress -arch x86_64 _configtest.o -lvt-mpi -o _configtest ld: library not found for -lvt-mpi clang: error: linker command failed with exit code 1 (use -v to see invocation) failure. removing: _configtest.c _configtest.o checking for library 'vt.mpi' ... /usr/local/Cellar/mpich/3.3.2/bin/mpicc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -c _configtest.c -o _configtest.o /usr/local/Cellar/mpich/3.3.2/bin/mpicc -flat_namespace -undefined suppress -arch x86_64 _configtest.o -lvt.mpi -o _configtest ld: library not found for -lvt.mpi clang: error: linker command failed with exit code 1 (use -v to see invocation) failure. removing: _configtest.c _configtest.o building 'vt' dylib library /usr/local/Cellar/mpich/3.3.2/bin/mpicc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -c src/lib-pmpi/vt.c -o build/temp.macosx-10.9-x86_64-3.8/src/lib-pmpi/vt.o /usr/local/Cellar/mpich/3.3.2/bin/mpicc -shared -undefined dynamic_lookup -L/Users/marius/miniconda3/envs/test_cr_dev/lib -arch x86_64 -L/Users/marius/miniconda3/envs/test_cr_dev/lib -arch x86_64 -arch x86_64 -install_name libvt.dylib build/temp.macosx-10.9-x86_64-3.8/src/lib-pmpi/vt.o -o build/lib.macosx-10.9-x86_64-3.8/mpi4py/lib-pmpi/libvt.dylib ld: file not found: /usr/local/opt/gcc/lib/gcc/9/libgfortran.5.dylib for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) warning: build_clib: command '/usr/local/Cellar/mpich/3.3.2/bin/mpicc' failed with exit status 1 warning: build_clib: building optional library "vt" failed checking for library 'vt-mpi' ... /usr/local/Cellar/mpich/3.3.2/bin/mpicc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -c _configtest.c -o _configtest.o /usr/local/Cellar/mpich/3.3.2/bin/mpicc -flat_namespace -undefined suppress -arch x86_64 _configtest.o -lvt-mpi -o _configtest ld: library not found for -lvt-mpi clang: error: linker command failed with exit code 1 (use -v to see invocation) failure. removing: _configtest.c _configtest.o checking for library 'vt.mpi' ... /usr/local/Cellar/mpich/3.3.2/bin/mpicc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -c _configtest.c -o _configtest.o /usr/local/Cellar/mpich/3.3.2/bin/mpicc -flat_namespace -undefined suppress -arch x86_64 _configtest.o -lvt.mpi -o _configtest ld: library not found for -lvt.mpi clang: error: linker command failed with exit code 1 (use -v to see invocation) failure. removing: _configtest.c _configtest.o building 'vt-mpi' dylib library /usr/local/Cellar/mpich/3.3.2/bin/mpicc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -c src/lib-pmpi/vt-mpi.c -o build/temp.macosx-10.9-x86_64-3.8/src/lib-pmpi/vt-mpi.o /usr/local/Cellar/mpich/3.3.2/bin/mpicc -shared -undefined dynamic_lookup -L/Users/marius/miniconda3/envs/test_cr_dev/lib -arch x86_64 -L/Users/marius/miniconda3/envs/test_cr_dev/lib -arch x86_64 -arch x86_64 -install_name libvt-mpi.dylib build/temp.macosx-10.9-x86_64-3.8/src/lib-pmpi/vt-mpi.o -o build/lib.macosx-10.9-x86_64-3.8/mpi4py/lib-pmpi/libvt-mpi.dylib ld: file not found: /usr/local/opt/gcc/lib/gcc/9/libgfortran.5.dylib for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) warning: build_clib: command '/usr/local/Cellar/mpich/3.3.2/bin/mpicc' failed with exit status 1 warning: build_clib: building optional library "vt-mpi" failed checking for library 'vt-hyb' ... /usr/local/Cellar/mpich/3.3.2/bin/mpicc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -c _configtest.c -o _configtest.o /usr/local/Cellar/mpich/3.3.2/bin/mpicc -flat_namespace -undefined suppress -arch x86_64 _configtest.o -lvt-hyb -o _configtest ld: library not found for -lvt-hyb clang: error: linker command failed with exit code 1 (use -v to see invocation) failure. removing: _configtest.c _configtest.o checking for library 'vt.ompi' ... /usr/local/Cellar/mpich/3.3.2/bin/mpicc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -c _configtest.c -o _configtest.o /usr/local/Cellar/mpich/3.3.2/bin/mpicc -flat_namespace -undefined suppress -arch x86_64 _configtest.o -lvt.ompi -o _configtest ld: library not found for -lvt.ompi clang: error: linker command failed with exit code 1 (use -v to see invocation) failure. removing: _configtest.c _configtest.o building 'vt-hyb' dylib library /usr/local/Cellar/mpich/3.3.2/bin/mpicc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -c src/lib-pmpi/vt-hyb.c -o build/temp.macosx-10.9-x86_64-3.8/src/lib-pmpi/vt-hyb.o /usr/local/Cellar/mpich/3.3.2/bin/mpicc -shared -undefined dynamic_lookup -L/Users/marius/miniconda3/envs/test_cr_dev/lib -arch x86_64 -L/Users/marius/miniconda3/envs/test_cr_dev/lib -arch x86_64 -arch x86_64 -install_name libvt-hyb.dylib build/temp.macosx-10.9-x86_64-3.8/src/lib-pmpi/vt-hyb.o -o build/lib.macosx-10.9-x86_64-3.8/mpi4py/lib-pmpi/libvt-hyb.dylib ld: file not found: /usr/local/opt/gcc/lib/gcc/9/libgfortran.5.dylib for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) warning: build_clib: command '/usr/local/Cellar/mpich/3.3.2/bin/mpicc' failed with exit status 1 warning: build_clib: building optional library "vt-hyb" failed running build_ext MPI configuration: [mpi] from 'mpi.cfg' MPI C compiler: /usr/local/Cellar/mpich/3.3.2/bin/mpicc MPI C++ compiler: /usr/local/Cellar/mpich/3.3.2/bin/mpicxx MPI F compiler: /usr/local/Cellar/mpich/3.3.2/bin/mpifort MPI F90 compiler: /usr/local/Cellar/mpich/3.3.2/bin/mpif90 MPI F77 compiler: /usr/local/Cellar/mpich/3.3.2/bin/mpif77 checking for dlopen() availability ... checking for header 'dlfcn.h' ... gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -I/Users/marius/Projects/cellrank/.tox/py38-macos/include -I/Users/marius/miniconda3/envs/test_cr_dev/include/python3.8 -c _configtest.c -o _configtest.o success! removing: _configtest.c _configtest.o success! checking for library 'dl' ... gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -I/Users/marius/Projects/cellrank/.tox/py38-macos/include -I/Users/marius/miniconda3/envs/test_cr_dev/include/python3.8 -c _configtest.c -o _configtest.o gcc -flat_namespace -undefined suppress -arch x86_64 _configtest.o -Lbuild/temp.macosx-10.9-x86_64-3.8 -ldl -o _configtest success! removing: _configtest.c _configtest.o _configtest checking for function 'dlopen' ... gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -I/Users/marius/Projects/cellrank/.tox/py38-macos/include -I/Users/marius/miniconda3/envs/test_cr_dev/include/python3.8 -c _configtest.c -o _configtest.o gcc -arch x86_64 _configtest.o -Lbuild/temp.macosx-10.9-x86_64-3.8 -ldl -o _configtest success! removing: _configtest.c _configtest.o _configtest building 'mpi4py.dl' extension gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -DHAVE_DLFCN_H=1 -DHAVE_DLOPEN=1 -I/Users/marius/Projects/cellrank/.tox/py38-macos/include -I/Users/marius/miniconda3/envs/test_cr_dev/include/python3.8 -c src/dynload.c -o build/temp.macosx-10.9-x86_64-3.8/src/dynload.o gcc -bundle -undefined dynamic_lookup -L/Users/marius/miniconda3/envs/test_cr_dev/lib -arch x86_64 -L/Users/marius/miniconda3/envs/test_cr_dev/lib -arch x86_64 -arch x86_64 build/temp.macosx-10.9-x86_64-3.8/src/dynload.o -Lbuild/temp.macosx-10.9-x86_64-3.8 -ldl -o build/lib.macosx-10.9-x86_64-3.8/mpi4py/dl.cpython-38-darwin.so checking for MPI compile and link ... /usr/local/Cellar/mpich/3.3.2/bin/mpicc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -I/Users/marius/Projects/cellrank/.tox/py38-macos/include -I/Users/marius/miniconda3/envs/test_cr_dev/include/python3.8 -c _configtest.c -o _configtest.o success! removing: _configtest.c _configtest.o /usr/local/Cellar/mpich/3.3.2/bin/mpicc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -I/Users/marius/Projects/cellrank/.tox/py38-macos/include -I/Users/marius/miniconda3/envs/test_cr_dev/include/python3.8 -c _configtest.c -o _configtest.o /usr/local/Cellar/mpich/3.3.2/bin/mpicc -arch x86_64 _configtest.o -Lbuild/temp.macosx-10.9-x86_64-3.8 -o _configtest ld: file not found: /usr/local/opt/gcc/lib/gcc/9/libgfortran.5.dylib for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) failure. removing: _configtest.c _configtest.o error: Cannot link MPI programs. Check your configuration!!! ---------------------------------------- ERROR: Failed building wheel for mpi4py Running setup.py clean for mpi4py Building wheel for petsc (setup.py): started Building wheel for petsc (setup.py): finished with status 'error' ERROR: Command errored out with exit status 1: command: /Users/marius/Projects/cellrank/.tox/py38-macos/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/mx/0hyv8t2s26jdj79f55kvc_b80000gn/T/pip-install-0c7ialkz/petsc_e84ec31d200d465281c352ed1b3e9719/setup.py'"'"'; __file__='"'"'/private/var/folders/mx/0hyv8t2s26jdj79f55kvc_b80000gn/T/pip-install-0c7ialkz/petsc_e84ec31d200d465281c352ed1b3e9719/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/mx/0hyv8t2s26jdj79f55kvc_b80000gn/T/pip-wheel-imbvjykx cwd: /private/var/folders/mx/0hyv8t2s26jdj79f55kvc_b80000gn/T/pip-install-0c7ialkz/petsc_e84ec31d200d465281c352ed1b3e9719/ Complete output (1 lines): petsc: this package cannot be built as a wheel ---------------------------------------- ERROR: Failed building wheel for petsc Running setup.py clean for petsc Building wheel for petsc4py (setup.py): started Building wheel for petsc4py (setup.py): finished with status 'error' ERROR: Command errored out with exit status 1: command: /Users/marius/Projects/cellrank/.tox/py38-macos/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/mx/0hyv8t2s26jdj79f55kvc_b80000gn/T/pip-install-0c7ialkz/petsc4py_021ad2ca40d54fcfa2cc85152483e4a2/setup.py'"'"'; __file__='"'"'/private/var/folders/mx/0hyv8t2s26jdj79f55kvc_b80000gn/T/pip-install-0c7ialkz/petsc4py_021ad2ca40d54fcfa2cc85152483e4a2/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/mx/0hyv8t2s26jdj79f55kvc_b80000gn/T/pip-wheel-2yircs6m cwd: /private/var/folders/mx/0hyv8t2s26jdj79f55kvc_b80000gn/T/pip-install-0c7ialkz/petsc4py_021ad2ca40d54fcfa2cc85152483e4a2/ Complete output (587 lines): running bdist_wheel running build running build_src running build_py creating build creating build/lib.macosx-10.9-x86_64-3.8 creating build/lib.macosx-10.9-x86_64-3.8/petsc4py copying src/PETSc.py -> build/lib.macosx-10.9-x86_64-3.8/petsc4py copying src/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/petsc4py copying src/__main__.py -> build/lib.macosx-10.9-x86_64-3.8/petsc4py creating build/lib.macosx-10.9-x86_64-3.8/petsc4py/lib copying src/lib/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/petsc4py/lib creating build/lib.macosx-10.9-x86_64-3.8/petsc4py/include creating build/lib.macosx-10.9-x86_64-3.8/petsc4py/include/petsc4py copying src/include/petsc4py/numpy.h -> build/lib.macosx-10.9-x86_64-3.8/petsc4py/include/petsc4py copying src/include/petsc4py/petsc4py.h -> build/lib.macosx-10.9-x86_64-3.8/petsc4py/include/petsc4py copying src/include/petsc4py/petsc4py.PETSc.h -> build/lib.macosx-10.9-x86_64-3.8/petsc4py/include/petsc4py copying src/include/petsc4py/petsc4py.PETSc_api.h -> build/lib.macosx-10.9-x86_64-3.8/petsc4py/include/petsc4py copying src/include/petsc4py/petsc4py.i -> build/lib.macosx-10.9-x86_64-3.8/petsc4py/include/petsc4py copying src/include/petsc4py/PETSc.pxd -> build/lib.macosx-10.9-x86_64-3.8/petsc4py/include/petsc4py copying src/include/petsc4py/__init__.pxd -> build/lib.macosx-10.9-x86_64-3.8/petsc4py/include/petsc4py copying src/include/petsc4py/__init__.pyx -> build/lib.macosx-10.9-x86_64-3.8/petsc4py/include/petsc4py copying src/PETSc.pxd -> build/lib.macosx-10.9-x86_64-3.8/petsc4py copying src/lib/petsc.cfg -> build/lib.macosx-10.9-x86_64-3.8/petsc4py/lib running build_ext PETSC_DIR: /Users/marius/petsc-3.13.0 PETSC_ARCH: macx version: 3.13.0 release integer-size: 32-bit scalar-type: real precision: double language: CONLY compiler: /Users/marius/petsc-3.13.0/macx/bin/mpicc linker: /Users/marius/petsc-3.13.0/macx/bin/mpicc building 'PETSc' extension creating build/temp.macosx-10.9-x86_64-3.8 creating build/temp.macosx-10.9-x86_64-3.8/macx creating build/temp.macosx-10.9-x86_64-3.8/macx/src /Users/marius/petsc-3.13.0/macx/bin/mpicc -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fno-stack-check -Qunused-arguments -g3 -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -I/Users/marius/petsc-3.13.0/macx/include -I/Users/marius/petsc-3.13.0/include -Isrc/include -I/Users/marius/Projects/cellrank/.tox/py38-macos/lib/python3.8/site-packages/numpy/core/include -I/Users/marius/Projects/cellrank/.tox/py38-macos/include -I/Users/marius/miniconda3/envs/test_cr_dev/include/python3.8 -c src/PETSc.c -o build/temp.macosx-10.9-x86_64-3.8/macx/src/PETSc.o In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:302985:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:303284:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:303408:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:303541:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:303741:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:303880:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:304012:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:304436:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:304531:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:304620:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:304722:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:304867:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:305310:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:305407:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:305595:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:305993:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:306453:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:306865:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:307135:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:307230:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:307447:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:307550:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:307645:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:307735:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:307872:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:308009:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:308136:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:308295:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:308526:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:308673:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:308868:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:308977:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:309080:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:309304:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:309507:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:309732:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:309826:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:310014:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:310170:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:310346:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:310439:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:310544:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:310665:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:310854:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:310973:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:311234:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:311380:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:333201:5: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ 48 warnings generated. /Users/marius/petsc-3.13.0/macx/bin/mpicc -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fno-stack-check -Qunused-arguments -g3 -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -I/Users/marius/petsc-3.13.0/macx/include -I/Users/marius/petsc-3.13.0/include -Isrc/include -I/Users/marius/Projects/cellrank/.tox/py38-macos/lib/python3.8/site-packages/numpy/core/include -I/Users/marius/Projects/cellrank/.tox/py38-macos/include -I/Users/marius/miniconda3/envs/test_cr_dev/include/python3.8 -c src/libpetsc4py.c -o build/temp.macosx-10.9-x86_64-3.8/macx/src/libpetsc4py.o In file included from src/libpetsc4py.c:6: src/libpetsc4py/libpetsc4py.c:29354:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/libpetsc4py.c:6: src/libpetsc4py/libpetsc4py.c:29433:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/libpetsc4py.c:6: src/libpetsc4py/libpetsc4py.c:29512:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/libpetsc4py.c:6: src/libpetsc4py/libpetsc4py.c:29591:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/libpetsc4py.c:6: src/libpetsc4py/libpetsc4py.c:29670:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/libpetsc4py.c:6: src/libpetsc4py/libpetsc4py.c:29749:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ 6 warnings generated. creating build/lib.macosx-10.9-x86_64-3.8/petsc4py/lib/macx /Users/marius/petsc-3.13.0/macx/bin/mpicc -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs -Wl,-search_paths_first -Wl,-no_compact_unwind -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs -Wl,-search_paths_first -Wl,-no_compact_unwind -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fno-stack-check -Qunused-arguments -g3 -bundle -undefined dynamic_lookup -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -L/Users/marius/miniconda3/envs/test_cr_dev/lib -arch x86_64 -L/Users/marius/miniconda3/envs/test_cr_dev/lib -arch x86_64 -arch x86_64 build/temp.macosx-10.9-x86_64-3.8/macx/src/PETSc.o build/temp.macosx-10.9-x86_64-3.8/macx/src/libpetsc4py.o -L/Users/marius/petsc-3.13.0/macx/lib -L/Users/marius/petsc-3.13.0/macx/lib -lpetsc -o build/lib.macosx-10.9-x86_64-3.8/petsc4py/lib/macx/PETSc.cpython-38-darwin.so ld: file not found: /usr/local/opt/gcc/lib/gcc/9/libgfortran.5.dylib for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) error: command '/Users/marius/petsc-3.13.0/macx/bin/mpicc' failed with exit status 1 ---------------------------------------- ERROR: Failed building wheel for petsc4py Running setup.py clean for petsc4py Building wheel for slepc (setup.py): started Building wheel for slepc (setup.py): finished with status 'error' ERROR: Command errored out with exit status 1: command: /Users/marius/Projects/cellrank/.tox/py38-macos/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/mx/0hyv8t2s26jdj79f55kvc_b80000gn/T/pip-install-0c7ialkz/slepc_7369694c127545d298d73e5cbee629cc/setup.py'"'"'; __file__='"'"'/private/var/folders/mx/0hyv8t2s26jdj79f55kvc_b80000gn/T/pip-install-0c7ialkz/slepc_7369694c127545d298d73e5cbee629cc/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/mx/0hyv8t2s26jdj79f55kvc_b80000gn/T/pip-wheel-l91o2ll8 cwd: /private/var/folders/mx/0hyv8t2s26jdj79f55kvc_b80000gn/T/pip-install-0c7ialkz/slepc_7369694c127545d298d73e5cbee629cc/ Complete output (1 lines): slepc: this package cannot be built as a wheel ---------------------------------------- ERROR: Failed building wheel for slepc Running setup.py clean for slepc Building wheel for slepc4py (setup.py): started Building wheel for slepc4py (setup.py): finished with status 'error' ERROR: Command errored out with exit status 1: command: /Users/marius/Projects/cellrank/.tox/py38-macos/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/mx/0hyv8t2s26jdj79f55kvc_b80000gn/T/pip-install-0c7ialkz/slepc4py_dfeec3854c6d4a0dbdb6700555f4acf3/setup.py'"'"'; __file__='"'"'/private/var/folders/mx/0hyv8t2s26jdj79f55kvc_b80000gn/T/pip-install-0c7ialkz/slepc4py_dfeec3854c6d4a0dbdb6700555f4acf3/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/mx/0hyv8t2s26jdj79f55kvc_b80000gn/T/pip-wheel-3z12de0x cwd: /private/var/folders/mx/0hyv8t2s26jdj79f55kvc_b80000gn/T/pip-install-0c7ialkz/slepc4py_dfeec3854c6d4a0dbdb6700555f4acf3/ Complete output (165 lines): running bdist_wheel running build running build_src running build_py creating build creating build/lib.macosx-10.9-x86_64-3.8 creating build/lib.macosx-10.9-x86_64-3.8/slepc4py copying src/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/slepc4py copying src/SLEPc.py -> build/lib.macosx-10.9-x86_64-3.8/slepc4py copying src/__main__.py -> build/lib.macosx-10.9-x86_64-3.8/slepc4py creating build/lib.macosx-10.9-x86_64-3.8/slepc4py/lib copying src/lib/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/slepc4py/lib creating build/lib.macosx-10.9-x86_64-3.8/slepc4py/include creating build/lib.macosx-10.9-x86_64-3.8/slepc4py/include/slepc4py copying src/include/slepc4py/slepc4py.h -> build/lib.macosx-10.9-x86_64-3.8/slepc4py/include/slepc4py copying src/include/slepc4py/slepc4py.SLEPc.h -> build/lib.macosx-10.9-x86_64-3.8/slepc4py/include/slepc4py copying src/include/slepc4py/slepc4py.SLEPc_api.h -> build/lib.macosx-10.9-x86_64-3.8/slepc4py/include/slepc4py copying src/include/slepc4py/slepc4py.i -> build/lib.macosx-10.9-x86_64-3.8/slepc4py/include/slepc4py copying src/include/slepc4py/__init__.pxd -> build/lib.macosx-10.9-x86_64-3.8/slepc4py/include/slepc4py copying src/include/slepc4py/SLEPc.pxd -> build/lib.macosx-10.9-x86_64-3.8/slepc4py/include/slepc4py copying src/include/slepc4py/__init__.pyx -> build/lib.macosx-10.9-x86_64-3.8/slepc4py/include/slepc4py copying src/SLEPc.pxd -> build/lib.macosx-10.9-x86_64-3.8/slepc4py copying src/lib/slepc.cfg -> build/lib.macosx-10.9-x86_64-3.8/slepc4py/lib running build_ext SLEPC_DIR: /Users/marius/slepc-3.13.1 PETSC_DIR: /Users/marius/petsc-3.13.0 PETSC_ARCH: macx version: 3.13.0 release integer-size: 32-bit scalar-type: real precision: double language: CONLY compiler: /Users/marius/petsc-3.13.0/macx/bin/mpicc linker: /Users/marius/petsc-3.13.0/macx/bin/mpicc building 'SLEPc' extension creating build/temp.macosx-10.9-x86_64-3.8 creating build/temp.macosx-10.9-x86_64-3.8/macx creating build/temp.macosx-10.9-x86_64-3.8/macx/src /Users/marius/petsc-3.13.0/macx/bin/mpicc -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fno-stack-check -Qunused-arguments -g3 -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -I/Users/marius/slepc-3.13.1/include -I/Users/marius/slepc-3.13.1/macx/include -I/Users/marius/petsc-3.13.0/macx/include -I/Users/marius/petsc-3.13.0/include -Isrc/include -I/Users/marius/Projects/cellrank/.tox/py38-macos/include -I/Users/marius/miniconda3/envs/test_cr_dev/include/python3.8 -c src/SLEPc.c -o build/temp.macosx-10.9-x86_64-3.8/macx/src/SLEPc.o In file included from src/SLEPc.c:3: src/slepc4py.SLEPc.c:58818:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/SLEPc.c:3: src/slepc4py.SLEPc.c:58966:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/SLEPc.c:3: src/slepc4py.SLEPc.c:59101:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/SLEPc.c:3: src/slepc4py.SLEPc.c:59225:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/SLEPc.c:3: src/slepc4py.SLEPc.c:59349:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/SLEPc.c:3: src/slepc4py.SLEPc.c:59671:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/SLEPc.c:3: src/slepc4py.SLEPc.c:59901:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/SLEPc.c:3: src/slepc4py.SLEPc.c:60081:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/SLEPc.c:3: src/slepc4py.SLEPc.c:60231:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/SLEPc.c:3: src/slepc4py.SLEPc.c:60365:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/SLEPc.c:3: src/slepc4py.SLEPc.c:60470:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/SLEPc.c:3: src/slepc4py.SLEPc.c:60565:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ 12 warnings generated. creating build/lib.macosx-10.9-x86_64-3.8/slepc4py/lib/macx /Users/marius/petsc-3.13.0/macx/bin/mpicc -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs -Wl,-search_paths_first -Wl,-no_compact_unwind -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs -Wl,-search_paths_first -Wl,-no_compact_unwind -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fno-stack-check -Qunused-arguments -g3 -bundle -undefined dynamic_lookup -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -L/Users/marius/miniconda3/envs/test_cr_dev/lib -arch x86_64 -L/Users/marius/miniconda3/envs/test_cr_dev/lib -arch x86_64 -arch x86_64 build/temp.macosx-10.9-x86_64-3.8/macx/src/SLEPc.o -L/Users/marius/slepc-3.13.1/lib -L/Users/marius/slepc-3.13.1/macx/lib -L/Users/marius/petsc-3.13.0/macx/lib -L/Users/marius/slepc-3.13.1/lib -L/Users/marius/slepc-3.13.1/macx/lib -L/Users/marius/petsc-3.13.0/macx/lib -lslepc -lpetsc -o build/lib.macosx-10.9-x86_64-3.8/slepc4py/lib/macx/SLEPc.cpython-38-darwin.so ld: file not found: /usr/local/opt/gcc/lib/gcc/9/libgfortran.5.dylib for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) error: command '/Users/marius/petsc-3.13.0/macx/bin/mpicc' failed with exit status 1 ---------------------------------------- ERROR: Failed building wheel for slepc4py Running setup.py clean for slepc4py Successfully built jax Failed to build mpi4py petsc petsc4py slepc slepc4py Installing collected packages: threadpoolctl, scipy, pytz, llvmlite, joblib, dunamai, xlrd, stdlib-list, scikit-learn, patsy, pandas, packaging, numexpr, numba, natsort, h5py, get-version, decorator, umap-learn, tqdm, toml, tables, statsmodels, sinfo, seaborn, python-utils, py, pluggy, numpy-groupies, networkx, legacy-api-wrap, iniconfig, click, attrs, anndata, texttable, scanpy, pytest, progressbar2, petsc4py, mpi4py, loompy, future, docrep, cython, wrapt, typing-extensions, slepc4py, slepc, scvelo, python-igraph, pytest-forked, pygpcca, pygam, POT, petsc, opt-einsum, flatbuffers, execnet, coverage, absl-py, wot, statot, pytest-xdist, pytest-mock, pytest-cov, louvain, leidenalg, jaxlib, jax, filelock, cellrank, bezier Running setup.py install for petsc4py: started Running setup.py install for petsc4py: finished with status 'error' ERROR: Command errored out with exit status 1: command: /Users/marius/Projects/cellrank/.tox/py38-macos/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/mx/0hyv8t2s26jdj79f55kvc_b80000gn/T/pip-install-0c7ialkz/petsc4py_021ad2ca40d54fcfa2cc85152483e4a2/setup.py'"'"'; __file__='"'"'/private/var/folders/mx/0hyv8t2s26jdj79f55kvc_b80000gn/T/pip-install-0c7ialkz/petsc4py_021ad2ca40d54fcfa2cc85152483e4a2/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/mx/0hyv8t2s26jdj79f55kvc_b80000gn/T/pip-record-b0ixmx7y/install-record.txt --single-version-externally-managed --compile --install-headers /Users/marius/Projects/cellrank/.tox/py38-macos/include/site/python3.8/petsc4py cwd: /private/var/folders/mx/0hyv8t2s26jdj79f55kvc_b80000gn/T/pip-install-0c7ialkz/petsc4py_021ad2ca40d54fcfa2cc85152483e4a2/ Complete output (587 lines): running install running build running build_src running build_py creating build creating build/lib.macosx-10.9-x86_64-3.8 creating build/lib.macosx-10.9-x86_64-3.8/petsc4py copying src/PETSc.py -> build/lib.macosx-10.9-x86_64-3.8/petsc4py copying src/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/petsc4py copying src/__main__.py -> build/lib.macosx-10.9-x86_64-3.8/petsc4py creating build/lib.macosx-10.9-x86_64-3.8/petsc4py/lib copying src/lib/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/petsc4py/lib creating build/lib.macosx-10.9-x86_64-3.8/petsc4py/include creating build/lib.macosx-10.9-x86_64-3.8/petsc4py/include/petsc4py copying src/include/petsc4py/numpy.h -> build/lib.macosx-10.9-x86_64-3.8/petsc4py/include/petsc4py copying src/include/petsc4py/petsc4py.h -> build/lib.macosx-10.9-x86_64-3.8/petsc4py/include/petsc4py copying src/include/petsc4py/petsc4py.PETSc.h -> build/lib.macosx-10.9-x86_64-3.8/petsc4py/include/petsc4py copying src/include/petsc4py/petsc4py.PETSc_api.h -> build/lib.macosx-10.9-x86_64-3.8/petsc4py/include/petsc4py copying src/include/petsc4py/petsc4py.i -> build/lib.macosx-10.9-x86_64-3.8/petsc4py/include/petsc4py copying src/include/petsc4py/PETSc.pxd -> build/lib.macosx-10.9-x86_64-3.8/petsc4py/include/petsc4py copying src/include/petsc4py/__init__.pxd -> build/lib.macosx-10.9-x86_64-3.8/petsc4py/include/petsc4py copying src/include/petsc4py/__init__.pyx -> build/lib.macosx-10.9-x86_64-3.8/petsc4py/include/petsc4py copying src/PETSc.pxd -> build/lib.macosx-10.9-x86_64-3.8/petsc4py copying src/lib/petsc.cfg -> build/lib.macosx-10.9-x86_64-3.8/petsc4py/lib running build_ext PETSC_DIR: /Users/marius/petsc-3.13.0 PETSC_ARCH: macx version: 3.13.0 release integer-size: 32-bit scalar-type: real precision: double language: CONLY compiler: /Users/marius/petsc-3.13.0/macx/bin/mpicc linker: /Users/marius/petsc-3.13.0/macx/bin/mpicc building 'PETSc' extension creating build/temp.macosx-10.9-x86_64-3.8 creating build/temp.macosx-10.9-x86_64-3.8/macx creating build/temp.macosx-10.9-x86_64-3.8/macx/src /Users/marius/petsc-3.13.0/macx/bin/mpicc -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fno-stack-check -Qunused-arguments -g3 -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -I/Users/marius/petsc-3.13.0/macx/include -I/Users/marius/petsc-3.13.0/include -Isrc/include -I/Users/marius/Projects/cellrank/.tox/py38-macos/lib/python3.8/site-packages/numpy/core/include -I/Users/marius/Projects/cellrank/.tox/py38-macos/include -I/Users/marius/miniconda3/envs/test_cr_dev/include/python3.8 -c src/PETSc.c -o build/temp.macosx-10.9-x86_64-3.8/macx/src/PETSc.o In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:302985:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:303284:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:303408:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:303541:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:303741:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:303880:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:304012:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:304436:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:304531:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:304620:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:304722:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:304867:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:305310:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:305407:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:305595:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:305993:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:306453:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:306865:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:307135:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:307230:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:307447:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:307550:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:307645:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:307735:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:307872:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:308009:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:308136:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:308295:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:308526:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:308673:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:308868:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:308977:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:309080:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:309304:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:309507:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:309732:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:309826:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:310014:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:310170:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:310346:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:310439:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:310544:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:310665:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:310854:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:310973:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:311234:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:311380:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/PETSc.c:4: src/petsc4py.PETSc.c:333201:5: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ 48 warnings generated. /Users/marius/petsc-3.13.0/macx/bin/mpicc -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fno-stack-check -Qunused-arguments -g3 -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -I/Users/marius/petsc-3.13.0/macx/include -I/Users/marius/petsc-3.13.0/include -Isrc/include -I/Users/marius/Projects/cellrank/.tox/py38-macos/lib/python3.8/site-packages/numpy/core/include -I/Users/marius/Projects/cellrank/.tox/py38-macos/include -I/Users/marius/miniconda3/envs/test_cr_dev/include/python3.8 -c src/libpetsc4py.c -o build/temp.macosx-10.9-x86_64-3.8/macx/src/libpetsc4py.o In file included from src/libpetsc4py.c:6: src/libpetsc4py/libpetsc4py.c:29354:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/libpetsc4py.c:6: src/libpetsc4py/libpetsc4py.c:29433:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/libpetsc4py.c:6: src/libpetsc4py/libpetsc4py.c:29512:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/libpetsc4py.c:6: src/libpetsc4py/libpetsc4py.c:29591:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/libpetsc4py.c:6: src/libpetsc4py/libpetsc4py.c:29670:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from src/libpetsc4py.c:6: src/libpetsc4py/libpetsc4py.c:29749:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /Users/marius/miniconda3/envs/test_cr_dev/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ 6 warnings generated. creating build/lib.macosx-10.9-x86_64-3.8/petsc4py/lib/macx /Users/marius/petsc-3.13.0/macx/bin/mpicc -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs -Wl,-search_paths_first -Wl,-no_compact_unwind -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs -Wl,-search_paths_first -Wl,-no_compact_unwind -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fno-stack-check -Qunused-arguments -g3 -bundle -undefined dynamic_lookup -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -I/Users/marius/miniconda3/envs/test_cr_dev/include -arch x86_64 -L/Users/marius/miniconda3/envs/test_cr_dev/lib -arch x86_64 -L/Users/marius/miniconda3/envs/test_cr_dev/lib -arch x86_64 -arch x86_64 build/temp.macosx-10.9-x86_64-3.8/macx/src/PETSc.o build/temp.macosx-10.9-x86_64-3.8/macx/src/libpetsc4py.o -L/Users/marius/petsc-3.13.0/macx/lib -L/Users/marius/petsc-3.13.0/macx/lib -lpetsc -o build/lib.macosx-10.9-x86_64-3.8/petsc4py/lib/macx/PETSc.cpython-38-darwin.so ld: file not found: /usr/local/opt/gcc/lib/gcc/9/libgfortran.5.dylib for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) error: command '/Users/marius/petsc-3.13.0/macx/bin/mpicc' failed with exit status 1 ---------------------------------------- ERROR: Command errored out with exit status 1: /Users/marius/Projects/cellrank/.tox/py38-macos/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/mx/0hyv8t2s26jdj79f55kvc_b80000gn/T/pip-install-0c7ialkz/petsc4py_021ad2ca40d54fcfa2cc85152483e4a2/setup.py'"'"'; __file__='"'"'/private/var/folders/mx/0hyv8t2s26jdj79f55kvc_b80000gn/T/pip-install-0c7ialkz/petsc4py_021ad2ca40d54fcfa2cc85152483e4a2/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/mx/0hyv8t2s26jdj79f55kvc_b80000gn/T/pip-record-b0ixmx7y/install-record.txt --single-version-externally-managed --compile --install-headers /Users/marius/Projects/cellrank/.tox/py38-macos/include/site/python3.8/petsc4py Check the logs for full command output. WARNING: You are using pip version 21.0.1; however, version 21.1.3 is available. You should consider upgrading via the '/Users/marius/Projects/cellrank/.tox/py38-macos/bin/python -m pip install --upgrade pip' command. =============================================== log end =============================================== py39-macos create: /Users/marius/Projects/cellrank/.tox/py39-macos SKIPPED: InterpreterNotFound: python3.9 docs create: /Users/marius/Projects/cellrank/.tox/docs docs installdeps: -r/Users/marius/Projects/cellrank/docs/requirements.txt docs installed: alabaster==0.7.12,anndata==0.7.6,appnope==0.1.2,argon2-cffi==20.1.0,async-generator==1.10,attrs==21.2.0,Babel==2.9.1,backcall==0.2.0,bezier==2021.2.12,bleach==3.3.0,certifi==2021.5.30,cffi==1.14.5,chardet==4.0.0,click==8.0.1,cycler==0.10.0,debugpy==1.3.0,decorator==4.4.2,defusedxml==0.7.1,docrep==0.3.2,docutils==0.16,dunamai==1.5.5,entrypoints==0.3,future==0.18.2,get-version==3.2,h5py==3.3.0,idna==2.10,imagesize==1.2.0,ipykernel==6.0.0,ipython==7.25.0,ipython-genutils==0.2.0,ipywidgets==7.6.3,jedi==0.18.0,Jinja2==3.0.1,joblib==1.0.1,jsonschema==3.2.0,jupyter-client==6.1.12,jupyter-core==4.7.1,jupyterlab-pygments==0.1.2,jupyterlab-widgets==1.0.0,kiwisolver==1.3.1,latexcodec==2.0.1,legacy-api-wrap==1.2,llvmlite==0.35.0,loompy==3.0.6,louvain==0.7.0,MarkupSafe==2.0.1,matplotlib==3.4.2,matplotlib-inline==0.1.2,memory-profiler==0.58.0,mistune==0.8.4,natsort==7.1.1,nbclient==0.5.3,nbconvert==6.1.0,nbformat==5.1.3,nbsphinx==0.8.6,nest-asyncio==1.5.1,networkx==2.5.1,notebook==6.4.0,numba==0.52.0,numexpr==2.7.3,numpy==1.21.0,numpy-groupies==0.9.13,packaging==20.9,pandas==1.2.5,pandocfilters==1.4.3,parso==0.8.2,patsy==0.5.1,pexpect==4.8.0,pickleshare==0.7.5,Pillow==8.3.0,progressbar2==3.53.1,prometheus-client==0.11.0,prompt-toolkit==3.0.19,psutil==5.8.0,ptyprocess==0.7.0,pybtex==0.24.0,pybtex-docutils==1.0.0,pycparser==2.20,pygam==0.8.0,Pygments==2.9.0,pygpcca==1.0.2,pypandoc==1.5,pyparsing==2.4.7,pyrsistent==0.18.0,python-dateutil==2.8.1,python-igraph==0.9.6,python-utils==2.5.6,pytz==2021.1,PyYAML==5.4.1,pyzmq==22.1.0,requests==2.25.1,scanpy==1.8.0,scikit-learn==0.24.2,scipy==1.7.0,scvelo==0.2.3,seaborn==0.11.1,Send2Trash==1.7.1,sinfo==0.3.4,six==1.16.0,snowballstemmer==2.1.0,Sphinx==4.0.2,sphinx-autodoc-annotation==1.0.post1,sphinx-autodoc-typehints==1.12.0,sphinx-copybutton==0.3.3,sphinx-gallery==0.9.0,sphinx-last-updated-by-git==0.3.0,sphinx-rtd-theme==0.5.2,sphinxcontrib-applehelp==1.0.2,sphinxcontrib-bibtex==2.3.0,sphinxcontrib-devhelp==1.0.2,sphinxcontrib-htmlhelp==2.0.0,sphinxcontrib-jsmath==1.0.1,sphinxcontrib-qthelp==1.0.3,sphinxcontrib-serializinghtml==1.1.5,statsmodels==0.12.2,stdlib-list==0.8.0,tables==3.6.1,terminado==0.10.1,testpath==0.5.0,texttable==1.6.3,threadpoolctl==2.1.0,tornado==6.1,tqdm==4.61.1,traitlets==5.0.5,typing-extensions==3.10.0.0,umap-learn==0.4.6,urllib3==1.26.6,wcwidth==0.2.5,webencodings==0.5.1,widgetsnbextension==3.5.1,wrapt==1.12.1,xlrd==1.2.0 docs run-test-pre: PYTHONHASHSEED='3393242636' docs run-test: commands[0] | sphinx-build --color -b html /Users/marius/Projects/cellrank/docs/source /Users/marius/Projects/cellrank/docs/build/html Running Sphinx v4.0.2 loading pickled environment... failed failed: __new__() missing 1 required positional argument: 'aliased' checking for /Users/marius/Projects/cellrank/docs/source/references.bib in bibtex cache... not found parsing bibtex file /Users/marius/Projects/cellrank/docs/source/references.bib... parsed 33 entries loading intersphinx inventory from https://anndata.readthedocs.io/en/stable/objects.inv... loading intersphinx inventory from https://scanpy.readthedocs.io/en/stable/objects.inv... loading intersphinx inventory from https://squidpy.readthedocs.io/en/latest/objects.inv... loading intersphinx inventory from https://scvelo.readthedocs.io/objects.inv... loading intersphinx inventory from https://docs.python.org/3/objects.inv... loading intersphinx inventory from https://docs.scipy.org/doc/numpy/objects.inv... loading intersphinx inventory from https://docs.scipy.org/doc/scipy/reference/objects.inv... loading intersphinx inventory from https://networkx.org/documentation/stable/objects.inv... loading intersphinx inventory from https://pandas.pydata.org/pandas-docs/stable/objects.inv... loading intersphinx inventory from https://www.statsmodels.org/stable/objects.inv... loading intersphinx inventory from https://matplotlib.org/objects.inv... loading intersphinx inventory from https://joblib.readthedocs.io/en/latest/objects.inv... loading intersphinx inventory from https://scikit-learn.org/stable/objects.inv... loading intersphinx inventory from https://seaborn.pydata.org/objects.inv... loading intersphinx inventory from https://pygam.readthedocs.io/en/latest/objects.inv... intersphinx inventory has moved: https://docs.scipy.org/doc/numpy/objects.inv -> https://numpy.org/doc/stable/objects.inv loading intersphinx inventory from https://jax.readthedocs.io/en/latest/objects.inv... loading intersphinx inventory from https://pygpcca.readthedocs.io/en/latest/objects.inv... loading intersphinx inventory from https://pythonot.github.io/objects.inv... [autosummary] generating autosummary for: api.rst, api/cellrank.datasets.lung.rst, api/cellrank.datasets.pancreas.rst, api/cellrank.datasets.pancreas_preprocessed.rst, api/cellrank.datasets.reprogramming.rst, api/cellrank.datasets.zebrafish.rst, api/cellrank.external.kernels.OTKernel.adata.rst, api/cellrank.external.kernels.OTKernel.backward.rst, api/cellrank.external.kernels.OTKernel.compute_projection.rst, api/cellrank.external.kernels.OTKernel.compute_transition_matrix.rst, ..., classes.rst, creating_new_kernel.ipynb, external_api.rst, index.rst, installation.rst, kernels_and_estimators.ipynb, latest_additions.rst, real_time.ipynb, references.rst, release_notes.rst WARNING: [autosummary] failed to import 'cellrank.external.kernels.OTKernel.adata': no module named cellrank.external.kernels.OTKernel.adata WARNING: [autosummary] failed to import 'cellrank.external.kernels.OTKernel.backward': no module named cellrank.external.kernels.OTKernel.backward WARNING: [autosummary] failed to import 'cellrank.external.kernels.OTKernel.compute_projection': no module named cellrank.external.kernels.OTKernel.compute_projection WARNING: [autosummary] failed to import 'cellrank.external.kernels.OTKernel.compute_transition_matrix': no module named cellrank.external.kernels.OTKernel.compute_transition_matrix WARNING: [autosummary] failed to import 'cellrank.external.kernels.OTKernel.condition_number': no module named cellrank.external.kernels.OTKernel.condition_number WARNING: [autosummary] failed to import 'cellrank.external.kernels.OTKernel.copy': no module named cellrank.external.kernels.OTKernel.copy WARNING: [autosummary] failed to import 'cellrank.external.kernels.OTKernel.kernels': no module named cellrank.external.kernels.OTKernel.kernels WARNING: [autosummary] failed to import 'cellrank.external.kernels.OTKernel.params': no module named cellrank.external.kernels.OTKernel.params WARNING: [autosummary] failed to import 'cellrank.external.kernels.OTKernel.plot_random_walks': no module named cellrank.external.kernels.OTKernel.plot_random_walks WARNING: [autosummary] failed to import 'cellrank.external.kernels.OTKernel.read': no module named cellrank.external.kernels.OTKernel.read WARNING: [autosummary] failed to import 'cellrank.external.kernels.OTKernel.transition_matrix': no module named cellrank.external.kernels.OTKernel.transition_matrix WARNING: [autosummary] failed to import 'cellrank.external.kernels.OTKernel.write': no module named cellrank.external.kernels.OTKernel.write WARNING: [autosummary] failed to import 'cellrank.external.kernels.OTKernel.write_to_adata': no module named cellrank.external.kernels.OTKernel.write_to_adata [autosummary] generating autosummary for: /Users/marius/Projects/cellrank/docs/source/api/cellrank.datasets.reprogramming_morris.rst, /Users/marius/Projects/cellrank/docs/source/api/cellrank.datasets.reprogramming_schiebinger.rst, /Users/marius/Projects/cellrank/docs/source/api/cellrank.external.kernels.StationaryOTKernel.rst, /Users/marius/Projects/cellrank/docs/source/api/cellrank.external.kernels.WOTKernel.rst, /Users/marius/Projects/cellrank/docs/source/api/cellrank.pl.log_odds.rst, /Users/marius/Projects/cellrank/docs/source/api/cellrank.tl.estimators.CFLARE.rst, /Users/marius/Projects/cellrank/docs/source/api/cellrank.tl.estimators.GPCCA.rst, /Users/marius/Projects/cellrank/docs/source/api/cellrank.tl.kernels.ConnectivityKernel.rst, /Users/marius/Projects/cellrank/docs/source/api/cellrank.tl.kernels.CytoTRACEKernel.rst, /Users/marius/Projects/cellrank/docs/source/api/cellrank.tl.kernels.PrecomputedKernel.rst, /Users/marius/Projects/cellrank/docs/source/api/cellrank.tl.kernels.PseudotimeKernel.rst, /Users/marius/Projects/cellrank/docs/source/api/cellrank.tl.kernels.VelocityKernel.rst, /Users/marius/Projects/cellrank/docs/source/api/cellrank.ul.models.FailedModel.rst, /Users/marius/Projects/cellrank/docs/source/api/cellrank.ul.models.FittedModel.rst, /Users/marius/Projects/cellrank/docs/source/api/cellrank.ul.models.GAM.rst, /Users/marius/Projects/cellrank/docs/source/api/cellrank.ul.models.GAMR.rst, /Users/marius/Projects/cellrank/docs/source/api/cellrank.ul.models.SKLearnModel.rst [autosummary] generating autosummary for: /Users/marius/Projects/cellrank/docs/source/api/cellrank.external.kernels.StationaryOTKernel.adata.rst, /Users/marius/Projects/cellrank/docs/source/api/cellrank.external.kernels.StationaryOTKernel.backward.rst, /Users/marius/Projects/cellrank/docs/source/api/cellrank.external.kernels.StationaryOTKernel.compute_projection.rst, /Users/marius/Projects/cellrank/docs/source/api/cellrank.external.kernels.StationaryOTKernel.compute_transition_matrix.rst, /Users/marius/Projects/cellrank/docs/source/api/cellrank.external.kernels.StationaryOTKernel.condition_number.rst, /Users/marius/Projects/cellrank/docs/source/api/cellrank.external.kernels.StationaryOTKernel.copy.rst, /Users/marius/Projects/cellrank/docs/source/api/cellrank.external.kernels.StationaryOTKernel.kernels.rst, /Users/marius/Projects/cellrank/docs/source/api/cellrank.external.kernels.StationaryOTKernel.params.rst, /Users/marius/Projects/cellrank/docs/source/api/cellrank.external.kernels.StationaryOTKernel.plot_random_walks.rst, /Users/marius/Projects/cellrank/docs/source/api/cellrank.external.kernels.StationaryOTKernel.plot_single_flow.rst, ..., /Users/marius/Projects/cellrank/docs/source/api/cellrank.external.kernels.WOTKernel.write.rst, /Users/marius/Projects/cellrank/docs/source/api/cellrank.external.kernels.WOTKernel.write_to_adata.rst, /Users/marius/Projects/cellrank/docs/source/api/cellrank.tl.estimators.CFLARE.plot_lineage_drivers_correlation.rst, /Users/marius/Projects/cellrank/docs/source/api/cellrank.tl.estimators.GPCCA.plot_lineage_drivers_correlation.rst, /Users/marius/Projects/cellrank/docs/source/api/cellrank.tl.estimators.GPCCA.plot_macrostate_composition.rst, /Users/marius/Projects/cellrank/docs/source/api/cellrank.tl.kernels.ConnectivityKernel.plot_single_flow.rst, /Users/marius/Projects/cellrank/docs/source/api/cellrank.tl.kernels.CytoTRACEKernel.plot_single_flow.rst, /Users/marius/Projects/cellrank/docs/source/api/cellrank.tl.kernels.PrecomputedKernel.plot_single_flow.rst, /Users/marius/Projects/cellrank/docs/source/api/cellrank.tl.kernels.PseudotimeKernel.plot_single_flow.rst, /Users/marius/Projects/cellrank/docs/source/api/cellrank.tl.kernels.VelocityKernel.plot_single_flow.rst generating gallery... WARNING: optipng binaries not found, PNG images and thumbnails will not be optimized Maybe try: brew install pandoc See http://johnmacfarlane.net/pandoc/installing.html for installation options --------------------------------------------------------------- WARNING: 'pypandoc' not available. Using Sphinx-Gallery to convert rst text blocks to markdown for .ipynb files. WARNING: Creating empty `AnnData` objectnels... [100%] compute_kernel_tricks.py WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`s.py WARNING: For `method='brandts'`, dense matrix is required. Densifying WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`y WARNING: For `method='brandts'`, dense matrix is required. Densifying WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`tates_gpcca.py WARNING: For `method='brandts'`, dense matrix is required. Densifying WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`py WARNING: For `method='brandts'`, dense matrix is required. Densifying WARNING: Unable to import petsc4py. For installation, please refer to: https://petsc4py.readthedocs.io/en/stable/install.html. Defaulting to `'gmres'` solver. WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`ivers.py WARNING: For `method='brandts'`, dense matrix is required. Densifying WARNING: For 1 macrostate, stationary distribution is computednitial_states.py WARNING: Did not detect percentile for stationary distribution. Setting `perc=[0, 95]` WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`.py WARNING: For `method='brandts'`, dense matrix is required. Densifying WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'` WARNING: For `method='brandts'`, dense matrix is required. Densifying WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`.py WARNING: For `method='brandts'`, dense matrix is required. Densifying WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`y WARNING: For `method='brandts'`, dense matrix is required. Densifying WARNING: For 1 macrostate, stationary distribution is computed WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`ing.py WARNING: For `method='brandts'`, dense matrix is required. Densifying WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'` WARNING: For `method='brandts'`, dense matrix is required. Densifying WARNING: Unable to fit `2` models. WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'` WARNING: For `method='brandts'`, dense matrix is required. Densifying WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`.py WARNING: For `method='brandts'`, dense matrix is required. Densifying WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`y WARNING: For `method='brandts'`, dense matrix is required. Densifying generating gallery for auto_examples/plotting... [100%] plot_graph.py WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'` WARNING: For `method='brandts'`, dense matrix is required. Densifying generating gallery for auto_examples/other... [100%] compute_lineage_tricks.py computation time summary: - ../../examples/other/plot_model.py: 61.62 sec 958.4 MB - ../../examples/other/compute_lineage_tricks.py: 61.56 sec 6.4 MB - ../../examples/estimators/compute_macrostates.py: 60.46 sec 891.4 MB - ../../examples/kernels/compute_kernel_tricks.py: 60.01 sec 430.5 MB - ../../examples/estimators/compute_abs_probs.py: 54.57 sec 952.3 MB - ../../examples/kernels/plot_projection.py: 50.00 sec 453.8 MB - ../../examples/estimators/compute_terminal_states_gpcca.py: 47.56 sec 949.2 MB - ../../examples/plotting/plot_cluster_fates.py: 45.91 sec 811.3 MB - ../../examples/plotting/plot_lineages.py: 44.35 sec 987.2 MB - ../../examples/plotting/plot_terminal_states.py: 43.56 sec 987.6 MB - ../../examples/estimators/compute_lineage_drivers.py: 40.19 sec 975.1 MB - ../../examples/plotting/plot_gene_trends.py: 40.09 sec 821.3 MB - ../../examples/plotting/plot_cluster_lineage.py: 38.11 sec 767.2 MB - ../../examples/plotting/plot_directed_paga.py: 36.63 sec 857.5 MB - ../../examples/plotting/plot_graph.py: 36.11 sec 495.7 MB - ../../examples/estimators/compute_coarse_T.py: 35.27 sec 988.5 MB - ../../examples/plotting/plot_lineage_drivers.py: 34.73 sec 987.7 MB - ../../examples/plotting/plot_heatmap.py: 31.69 sec 976.8 MB - ../../examples/plotting/plot_circular_embedding.py: 30.30 sec 899.6 MB - ../../examples/plotting/plot_initial_states.py: 26.70 sec 391.1 MB - ../../examples/kernels/plot_random_walks.py: 21.77 sec 367.6 MB building [mo]: targets for 0 po files that are out of date building [html]: targets for 347 source files that are out of date updating environment: [new config] 397 added, 0 changed, 0 removed WARNING: autodoc: failed to import function 'reprogramming' from module 'cellrank.datasets'; the following exception was raised: Traceback (most recent call last): File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/util/inspect.py", line 412, in safe_getattr return getattr(obj, name, *defargs) AttributeError: module 'cellrank.datasets' has no attribute 'reprogramming' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/importer.py", line 110, in import_object obj = attrgetter(obj, mangled_name) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/__init__.py", line 318, in get_attr return autodoc_attrgetter(self.env.app, obj, name, *defargs) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/__init__.py", line 2606, in autodoc_attrgetter return safe_getattr(obj, name, *defargs) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/util/inspect.py", line 428, in safe_getattr raise AttributeError(name) from exc AttributeError: reprogramming WARNING: autodoc: failed to import class 'OTKernel' from module 'cellrank.external.kernels'; the following exception was raised: Traceback (most recent call last): File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/util/inspect.py", line 412, in safe_getattr return getattr(obj, name, *defargs) AttributeError: module 'cellrank.external.kernels' has no attribute 'OTKernel' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/importer.py", line 110, in import_object obj = attrgetter(obj, mangled_name) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/__init__.py", line 318, in get_attr return autodoc_attrgetter(self.env.app, obj, name, *defargs) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/__init__.py", line 2606, in autodoc_attrgetter return safe_getattr(obj, name, *defargs) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/util/inspect.py", line 428, in safe_getattr raise AttributeError(name) from exc AttributeError: OTKernel WARNING: autodoc: failed to import property 'OTKernel.adata' from module 'cellrank.external.kernels'; the following exception was raised: Traceback (most recent call last): File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/util/inspect.py", line 412, in safe_getattr return getattr(obj, name, *defargs) AttributeError: module 'cellrank.external.kernels' has no attribute 'OTKernel' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/importer.py", line 110, in import_object obj = attrgetter(obj, mangled_name) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/__init__.py", line 318, in get_attr return autodoc_attrgetter(self.env.app, obj, name, *defargs) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/__init__.py", line 2606, in autodoc_attrgetter return safe_getattr(obj, name, *defargs) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/util/inspect.py", line 428, in safe_getattr raise AttributeError(name) from exc AttributeError: OTKernel WARNING: autodoc: failed to import property 'OTKernel.backward' from module 'cellrank.external.kernels'; the following exception was raised: Traceback (most recent call last): File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/util/inspect.py", line 412, in safe_getattr return getattr(obj, name, *defargs) AttributeError: module 'cellrank.external.kernels' has no attribute 'OTKernel' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/importer.py", line 110, in import_object obj = attrgetter(obj, mangled_name) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/__init__.py", line 318, in get_attr return autodoc_attrgetter(self.env.app, obj, name, *defargs) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/__init__.py", line 2606, in autodoc_attrgetter return safe_getattr(obj, name, *defargs) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/util/inspect.py", line 428, in safe_getattr raise AttributeError(name) from exc AttributeError: OTKernel WARNING: autodoc: failed to import method 'OTKernel.compute_projection' from module 'cellrank.external.kernels'; the following exception was raised: Traceback (most recent call last): File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/util/inspect.py", line 412, in safe_getattr return getattr(obj, name, *defargs) AttributeError: module 'cellrank.external.kernels' has no attribute 'OTKernel' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/importer.py", line 110, in import_object obj = attrgetter(obj, mangled_name) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/__init__.py", line 318, in get_attr return autodoc_attrgetter(self.env.app, obj, name, *defargs) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/__init__.py", line 2606, in autodoc_attrgetter return safe_getattr(obj, name, *defargs) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/util/inspect.py", line 428, in safe_getattr raise AttributeError(name) from exc AttributeError: OTKernel WARNING: autodoc: failed to import method 'OTKernel.compute_transition_matrix' from module 'cellrank.external.kernels'; the following exception was raised: Traceback (most recent call last): File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/util/inspect.py", line 412, in safe_getattr return getattr(obj, name, *defargs) AttributeError: module 'cellrank.external.kernels' has no attribute 'OTKernel' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/importer.py", line 110, in import_object obj = attrgetter(obj, mangled_name) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/__init__.py", line 318, in get_attr return autodoc_attrgetter(self.env.app, obj, name, *defargs) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/__init__.py", line 2606, in autodoc_attrgetter return safe_getattr(obj, name, *defargs) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/util/inspect.py", line 428, in safe_getattr raise AttributeError(name) from exc AttributeError: OTKernel WARNING: autodoc: failed to import property 'OTKernel.condition_number' from module 'cellrank.external.kernels'; the following exception was raised: Traceback (most recent call last): File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/util/inspect.py", line 412, in safe_getattr return getattr(obj, name, *defargs) AttributeError: module 'cellrank.external.kernels' has no attribute 'OTKernel' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/importer.py", line 110, in import_object obj = attrgetter(obj, mangled_name) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/__init__.py", line 318, in get_attr return autodoc_attrgetter(self.env.app, obj, name, *defargs) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/__init__.py", line 2606, in autodoc_attrgetter return safe_getattr(obj, name, *defargs) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/util/inspect.py", line 428, in safe_getattr raise AttributeError(name) from exc AttributeError: OTKernel WARNING: autodoc: failed to import method 'OTKernel.copy' from module 'cellrank.external.kernels'; the following exception was raised: Traceback (most recent call last): File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/util/inspect.py", line 412, in safe_getattr return getattr(obj, name, *defargs) AttributeError: module 'cellrank.external.kernels' has no attribute 'OTKernel' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/importer.py", line 110, in import_object obj = attrgetter(obj, mangled_name) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/__init__.py", line 318, in get_attr return autodoc_attrgetter(self.env.app, obj, name, *defargs) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/__init__.py", line 2606, in autodoc_attrgetter return safe_getattr(obj, name, *defargs) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/util/inspect.py", line 428, in safe_getattr raise AttributeError(name) from exc AttributeError: OTKernel WARNING: autodoc: failed to import property 'OTKernel.kernels' from module 'cellrank.external.kernels'; the following exception was raised: Traceback (most recent call last): File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/util/inspect.py", line 412, in safe_getattr return getattr(obj, name, *defargs) AttributeError: module 'cellrank.external.kernels' has no attribute 'OTKernel' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/importer.py", line 110, in import_object obj = attrgetter(obj, mangled_name) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/__init__.py", line 318, in get_attr return autodoc_attrgetter(self.env.app, obj, name, *defargs) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/__init__.py", line 2606, in autodoc_attrgetter return safe_getattr(obj, name, *defargs) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/util/inspect.py", line 428, in safe_getattr raise AttributeError(name) from exc AttributeError: OTKernel WARNING: autodoc: failed to import property 'OTKernel.params' from module 'cellrank.external.kernels'; the following exception was raised: Traceback (most recent call last): File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/util/inspect.py", line 412, in safe_getattr return getattr(obj, name, *defargs) AttributeError: module 'cellrank.external.kernels' has no attribute 'OTKernel' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/importer.py", line 110, in import_object obj = attrgetter(obj, mangled_name) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/__init__.py", line 318, in get_attr return autodoc_attrgetter(self.env.app, obj, name, *defargs) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/__init__.py", line 2606, in autodoc_attrgetter return safe_getattr(obj, name, *defargs) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/util/inspect.py", line 428, in safe_getattr raise AttributeError(name) from exc AttributeError: OTKernel WARNING: autodoc: failed to import method 'OTKernel.plot_random_walks' from module 'cellrank.external.kernels'; the following exception was raised: Traceback (most recent call last): File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/util/inspect.py", line 412, in safe_getattr return getattr(obj, name, *defargs) AttributeError: module 'cellrank.external.kernels' has no attribute 'OTKernel' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/importer.py", line 110, in import_object obj = attrgetter(obj, mangled_name) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/__init__.py", line 318, in get_attr return autodoc_attrgetter(self.env.app, obj, name, *defargs) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/__init__.py", line 2606, in autodoc_attrgetter return safe_getattr(obj, name, *defargs) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/util/inspect.py", line 428, in safe_getattr raise AttributeError(name) from exc AttributeError: OTKernel WARNING: autodoc: failed to import method 'OTKernel.read' from module 'cellrank.external.kernels'; the following exception was raised: Traceback (most recent call last): File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/util/inspect.py", line 412, in safe_getattr return getattr(obj, name, *defargs) AttributeError: module 'cellrank.external.kernels' has no attribute 'OTKernel' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/importer.py", line 110, in import_object obj = attrgetter(obj, mangled_name) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/__init__.py", line 318, in get_attr return autodoc_attrgetter(self.env.app, obj, name, *defargs) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/__init__.py", line 2606, in autodoc_attrgetter return safe_getattr(obj, name, *defargs) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/util/inspect.py", line 428, in safe_getattr raise AttributeError(name) from exc AttributeError: OTKernel WARNING: autodoc: failed to import property 'OTKernel.transition_matrix' from module 'cellrank.external.kernels'; the following exception was raised: Traceback (most recent call last): File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/util/inspect.py", line 412, in safe_getattr return getattr(obj, name, *defargs) AttributeError: module 'cellrank.external.kernels' has no attribute 'OTKernel' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/importer.py", line 110, in import_object obj = attrgetter(obj, mangled_name) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/__init__.py", line 318, in get_attr return autodoc_attrgetter(self.env.app, obj, name, *defargs) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/__init__.py", line 2606, in autodoc_attrgetter return safe_getattr(obj, name, *defargs) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/util/inspect.py", line 428, in safe_getattr raise AttributeError(name) from exc AttributeError: OTKernel WARNING: autodoc: failed to import method 'OTKernel.write' from module 'cellrank.external.kernels'; the following exception was raised: Traceback (most recent call last): File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/util/inspect.py", line 412, in safe_getattr return getattr(obj, name, *defargs) AttributeError: module 'cellrank.external.kernels' has no attribute 'OTKernel' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/importer.py", line 110, in import_object obj = attrgetter(obj, mangled_name) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/__init__.py", line 318, in get_attr return autodoc_attrgetter(self.env.app, obj, name, *defargs) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/__init__.py", line 2606, in autodoc_attrgetter return safe_getattr(obj, name, *defargs) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/util/inspect.py", line 428, in safe_getattr raise AttributeError(name) from exc AttributeError: OTKernel WARNING: autodoc: failed to import method 'OTKernel.write_to_adata' from module 'cellrank.external.kernels'; the following exception was raised: Traceback (most recent call last): File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/util/inspect.py", line 412, in safe_getattr return getattr(obj, name, *defargs) AttributeError: module 'cellrank.external.kernels' has no attribute 'OTKernel' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/importer.py", line 110, in import_object obj = attrgetter(obj, mangled_name) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/__init__.py", line 318, in get_attr return autodoc_attrgetter(self.env.app, obj, name, *defargs) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/ext/autodoc/__init__.py", line 2606, in autodoc_attrgetter return safe_getattr(obj, name, *defargs) File "/Users/marius/Projects/cellrank/.tox/docs/lib/python3.8/site-packages/sphinx/util/inspect.py", line 428, in safe_getattr raise AttributeError(name) from exc AttributeError: OTKernel /Users/marius/Projects/cellrank/docs/source/auto_examples/other/compute_kernel_tricks.rst:109: WARNING: Unknown interpreted text role "paramref". Notebook error: PandocMissing in beyond_rna_velocity.ipynb: Pandoc wasn't found. Please check that pandoc is installed: https://pandoc.org/installing.html ERROR: InvocationError for command /Users/marius/Projects/cellrank/.tox/docs/bin/sphinx-build --color -b html docs/source docs/build/html (exited with code 2) _______________________________________________ summary _______________________________________________ covclean: commands succeeded lint: commands succeeded SKIPPED: py37-linux: platform mismatch ('darwin' does not match 'linux') ERROR: py37-macos: could not install deps [adjustText]; v = InvocationError('/Users/marius/Projects/cellrank/.tox/py37-macos/bin/python -m pip install adjustText', 1) SKIPPED: py38-linux: platform mismatch ('darwin' does not match 'linux') ERROR: py38-macos: InvocationError for command /Users/marius/Projects/cellrank/.tox/py38-macos/bin/python -m pip install --exists-action w -e '/Users/marius/Projects/cellrank[test,krylov,external]' (exited with code 1) SKIPPED: py39-linux: platform mismatch ('darwin' does not match 'linux') SKIPPED: py39-macos: InterpreterNotFound: python3.9 ERROR: docs: commands failed ```
WeilerP commented 3 years ago

@michalk8, I reinstalled the developer installation in a fresh charliecloud container and ran into an issue when running the unit tests the first time. I first installed all the necessary packages in a clean conda environment, i.e.

pip install -e '.[dev, external, test]'

apt-get install libopenmpi-dev
pip install --user mpi4py

pip install --user petsc
pip install --user petsc4py
pip install --user slepc
pip install --user slepc4py

and then ran

tox -e py38-linux

which threw an error caused by petsc/slepc.

Log file ```txt ================================================================================================== log start ================================================================================================== Obtaining file:///home/icb/philipp.weiler/code/cellrank Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing wheel metadata: started Preparing wheel metadata: finished with status 'done' Collecting wot@ git+https://github.com/broadinstitute/wot@master Cloning https://github.com/broadinstitute/wot (to revision master) to /home/philipp.weiler/.ch_tmp/pip-install-j0_j3wbm/wot_27d28a66d6ed48f0870200f3cd81c9fe Running command git clone -q https://github.com/broadinstitute/wot /home/philipp.weiler/.ch_tmp/pip-install-j0_j3wbm/wot_27d28a66d6ed48f0870200f3cd81c9fe Collecting seaborn>=0.10.0 Using cached seaborn-0.11.1-py3-none-any.whl (285 kB) Requirement already satisfied: matplotlib>=3.3.0 in ./.tox/py38-linux/lib/python3.8/site-packages (from cellrank==1.4.1.dev80+g0d8747d) (3.4.2) Collecting pygam>=0.8.0 Using cached pygam-0.8.0-py2.py3-none-any.whl (1.8 MB) Collecting pygpcca>=1.0.2 Using cached pygpcca-1.0.2-py3-none-any.whl (68 kB) Requirement already satisfied: setuptools>=41.0.1 in ./.tox/py38-linux/lib/python3.8/site-packages (from cellrank==1.4.1.dev80+g0d8747d) (57.1.0) Collecting wrapt>=1.12.1 Using cached wrapt-1.12.1-cp38-cp38-linux_x86_64.whl Collecting networkx>=2.2 Using cached networkx-2.5.1-py3-none-any.whl (1.6 MB) Collecting pandas>=1.2.0 Using cached pandas-1.3.0-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl (10.6 MB) Collecting joblib>=0.13.1 Using cached joblib-1.0.1-py3-none-any.whl (303 kB) Collecting scanpy>=1.7.2 Using cached scanpy-1.8.1-py3-none-any.whl (2.0 MB) Collecting scikit-learn>=0.24.0 Using cached scikit_learn-0.24.2-cp38-cp38-manylinux2010_x86_64.whl (24.9 MB) Collecting scipy>=1.2.0 Using cached scipy-1.7.0-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl (28.4 MB) Requirement already satisfied: numpy>=1.2.0 in ./.tox/py38-linux/lib/python3.8/site-packages (from cellrank==1.4.1.dev80+g0d8747d) (1.21.0) Collecting docrep>=0.3.0 Using cached docrep-0.3.2-py3-none-any.whl Collecting numba<0.53.0,>=0.51.0 Using cached numba-0.52.0-cp38-cp38-manylinux2014_x86_64.whl (3.2 MB) Collecting scvelo>=0.2.3 Using cached scvelo-0.2.3-py3-none-any.whl (177 kB) Collecting typing-extensions Using cached typing_extensions-3.10.0.0-py3-none-any.whl (26 kB) Collecting statot>=0.0.14 Using cached statot-0.0.14-py3-none-any.whl (11 kB) Collecting POT Using cached POT-0.7.0-cp38-cp38-manylinux2010_x86_64.whl (455 kB) Collecting python-igraph Using cached python_igraph-0.9.6-cp38-cp38-manylinux2010_x86_64.whl (3.3 MB) Collecting jaxlib Using cached jaxlib-0.1.69-cp38-none-manylinux2010_x86_64.whl (46.5 MB) Collecting pytest-cov Using cached pytest_cov-2.12.1-py2.py3-none-any.whl (20 kB) Collecting filelock Using cached filelock-3.0.12-py3-none-any.whl (7.6 kB) Collecting pytest-xdist>=2.1.0 Using cached pytest_xdist-2.3.0-py3-none-any.whl (37 kB) Collecting louvain!=0.6.2,>=0.6 Using cached louvain-0.7.0-cp38-cp38-manylinux2010_x86_64.whl (2.1 MB) Collecting pytest-mock>=3.5.1 Using cached pytest_mock-3.6.1-py3-none-any.whl (12 kB) Collecting jax Using cached jax-0.2.17-py3-none-any.whl Requirement already satisfied: Pillow in ./.tox/py38-linux/lib/python3.8/site-packages (from cellrank==1.4.1.dev80+g0d8747d) (8.3.1) Collecting leidenalg Using cached leidenalg-0.8.7-cp38-cp38-manylinux2010_x86_64.whl (1.4 MB) Collecting bezier Using cached bezier-2021.2.12-cp38-cp38-manylinux2010_x86_64.whl (1.4 MB) Collecting pytest>=6.1.1 Using cached pytest-6.2.4-py3-none-any.whl (280 kB) Collecting h5py Using cached h5py-3.3.0-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (4.5 MB) Collecting anndata Using cached anndata-0.7.6-py3-none-any.whl (127 kB) Requirement already satisfied: six in ./.tox/py38-linux/lib/python3.8/site-packages (from docrep>=0.3.0->cellrank==1.4.1.dev80+g0d8747d) (1.16.0) Requirement already satisfied: pyparsing>=2.2.1 in ./.tox/py38-linux/lib/python3.8/site-packages (from matplotlib>=3.3.0->cellrank==1.4.1.dev80+g0d8747d) (2.4.7) Requirement already satisfied: kiwisolver>=1.0.1 in ./.tox/py38-linux/lib/python3.8/site-packages (from matplotlib>=3.3.0->cellrank==1.4.1.dev80+g0d8747d) (1.3.1) Requirement already satisfied: cycler>=0.10 in ./.tox/py38-linux/lib/python3.8/site-packages (from matplotlib>=3.3.0->cellrank==1.4.1.dev80+g0d8747d) (0.10.0) Requirement already satisfied: python-dateutil>=2.7 in ./.tox/py38-linux/lib/python3.8/site-packages (from matplotlib>=3.3.0->cellrank==1.4.1.dev80+g0d8747d) (2.8.2) Collecting decorator<5,>=4.3 Using cached decorator-4.4.2-py2.py3-none-any.whl (9.2 kB) Collecting llvmlite<0.36,>=0.35.0 Using cached llvmlite-0.35.0-cp38-cp38-manylinux2010_x86_64.whl (25.3 MB) Requirement already satisfied: pytz>=2017.3 in ./.tox/py38-linux/lib/python3.8/site-packages (from pandas>=1.2.0->cellrank==1.4.1.dev80+g0d8747d) (2021.1) Collecting progressbar2 Using cached progressbar2-3.53.1-py2.py3-none-any.whl (25 kB) Collecting future Using cached future-0.18.2-py3-none-any.whl Collecting py>=1.8.2 Using cached py-1.10.0-py2.py3-none-any.whl (97 kB) Collecting packaging Using cached packaging-21.0-py3-none-any.whl (40 kB) Collecting toml Using cached toml-0.10.2-py2.py3-none-any.whl (16 kB) Collecting iniconfig Using cached iniconfig-1.1.1-py2.py3-none-any.whl (5.0 kB) Collecting attrs>=19.2.0 Using cached attrs-21.2.0-py2.py3-none-any.whl (53 kB) Collecting pluggy<1.0.0a1,>=0.12 Using cached pluggy-0.13.1-py2.py3-none-any.whl (18 kB) Collecting pytest-forked Using cached pytest_forked-1.3.0-py2.py3-none-any.whl (4.7 kB) Collecting execnet>=1.1 Using cached execnet-1.9.0-py2.py3-none-any.whl (39 kB) Collecting texttable>=1.6.2 Using cached texttable-1.6.4-py2.py3-none-any.whl (10 kB) Collecting natsort Using cached natsort-7.1.1-py3-none-any.whl (35 kB) Collecting sinfo Using cached sinfo-0.3.4-py3-none-any.whl Collecting umap-learn>=0.3.10 Using cached umap-learn-0.5.1.tar.gz (80 kB) Collecting statsmodels>=0.10.0rc2 Using cached statsmodels-0.12.2-cp38-cp38-manylinux1_x86_64.whl (9.4 MB) Collecting patsy Using cached patsy-0.5.1-py2.py3-none-any.whl (231 kB) Collecting tables Using cached tables-3.6.1-cp38-cp38-manylinux1_x86_64.whl (4.3 MB) Collecting tqdm Using cached tqdm-4.61.2-py2.py3-none-any.whl (76 kB) Collecting xlrd<2.0 Using cached xlrd-1.2.0-py2.py3-none-any.whl (103 kB) Collecting threadpoolctl>=2.0.0 Using cached threadpoolctl-2.2.0-py3-none-any.whl (12 kB) Collecting loompy>=2.0.12 Using cached loompy-3.0.6-py3-none-any.whl Collecting umap-learn>=0.3.10 Using cached umap_learn-0.4.6-py3-none-any.whl Collecting numpy-groupies Using cached numpy_groupies-0.9.13-py3-none-any.whl Collecting click Using cached click-8.0.1-py3-none-any.whl (97 kB) Collecting opt-einsum Using cached opt_einsum-3.3.0-py3-none-any.whl (65 kB) Collecting absl-py Using cached absl_py-0.13.0-py3-none-any.whl (132 kB) Collecting flatbuffers<3.0,>=1.12 Using cached flatbuffers-2.0-py2.py3-none-any.whl (26 kB) Collecting cython>=0.23 Using cached Cython-0.29.24-cp38-cp38-manylinux1_x86_64.whl (1.9 MB) Collecting python-utils>=2.3.0 Using cached python_utils-2.5.6-py2.py3-none-any.whl (12 kB) Collecting slepc<3.14,>=3.13 Downloading slepc-3.13.2.tar.gz (4.8 MB) Collecting petsc4py<3.14,>=3.13 Downloading petsc4py-3.13.0.tar.gz (1.9 MB) Collecting mpi4py<3.1,>=3.0.3 Using cached mpi4py-3.0.3-cp38-cp38-linux_x86_64.whl Collecting petsc<3.14,>=3.13 Downloading petsc-3.13.5.tar.gz (14.9 MB) Collecting slepc4py<3.14,>=3.13 Downloading slepc4py-3.13.0.tar.gz (815 kB) Collecting coverage>=5.2.1 Using cached coverage-5.5-cp38-cp38-manylinux2010_x86_64.whl (245 kB) Collecting stdlib-list Using cached stdlib_list-0.8.0-py3-none-any.whl (63 kB) Collecting numexpr>=2.6.2 Using cached numexpr-2.7.3-cp38-cp38-manylinux2010_x86_64.whl (473 kB) Building wheels for collected packages: wot, petsc, petsc4py, slepc, slepc4py Building wheel for wot (setup.py): started Building wheel for wot (setup.py): finished with status 'done' Created wheel for wot: filename=wot-1.0.8.post3.dev8+gca5e94f-py2.py3-none-any.whl size=60727 sha256=d14fb86df825307407ac9d96bfa86d1ba9b57f7a6c11bcef0bdf48bafb3d90ad Stored in directory: /home/philipp.weiler/.ch_tmp/pip-ephem-wheel-cache-fvw1e6bk/wheels/f7/21/20/0ad54ba745bf1dd036dd28fb2ee8256f0ec811806235959136 Building wheel for petsc (setup.py): started Building wheel for petsc (setup.py): finished with status 'error' ERROR: Command errored out with exit status 1: command: /home/icb/philipp.weiler/code/cellrank/.tox/py38-linux/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/home/philipp.weiler/.ch_tmp/pip-install-j0_j3wbm/petsc_f1b6d15d21794765b31fee93a5ed11ae/setup.py'"'"'; __file__='"'"'/home/philipp.weiler/.ch_tmp/pip-install-j0_j3wbm/petsc_f1b6d15d21794765b31fee93a5ed11ae/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /home/philipp.weiler/.ch_tmp/pip-wheel-b5hj972g cwd: /home/philipp.weiler/.ch_tmp/pip-install-j0_j3wbm/petsc_f1b6d15d21794765b31fee93a5ed11ae/ Complete output (1 lines): petsc: this package cannot be built as a wheel ---------------------------------------- ERROR: Failed building wheel for petsc Running setup.py clean for petsc Building wheel for petsc4py (setup.py): started Building wheel for petsc4py (setup.py): finished with status 'error' ERROR: Command errored out with exit status 1: command: /home/icb/philipp.weiler/code/cellrank/.tox/py38-linux/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/home/philipp.weiler/.ch_tmp/pip-install-j0_j3wbm/petsc4py_166a880de3ea4c059d800b2de7a94504/setup.py'"'"'; __file__='"'"'/home/philipp.weiler/.ch_tmp/pip-install-j0_j3wbm/petsc4py_166a880de3ea4c059d800b2de7a94504/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /home/philipp.weiler/.ch_tmp/pip-wheel-1saq6art cwd: /home/philipp.weiler/.ch_tmp/pip-install-j0_j3wbm/petsc4py_166a880de3ea4c059d800b2de7a94504/ Complete output (27 lines): running bdist_wheel PETSC_DIR not specified running build running build_src running build_py creating build creating build/lib.linux-x86_64-3.8 creating build/lib.linux-x86_64-3.8/petsc4py copying src/PETSc.py -> build/lib.linux-x86_64-3.8/petsc4py copying src/__init__.py -> build/lib.linux-x86_64-3.8/petsc4py copying src/__main__.py -> build/lib.linux-x86_64-3.8/petsc4py creating build/lib.linux-x86_64-3.8/petsc4py/lib copying src/lib/__init__.py -> build/lib.linux-x86_64-3.8/petsc4py/lib creating build/lib.linux-x86_64-3.8/petsc4py/include creating build/lib.linux-x86_64-3.8/petsc4py/include/petsc4py copying src/include/petsc4py/petsc4py.PETSc.h -> build/lib.linux-x86_64-3.8/petsc4py/include/petsc4py copying src/include/petsc4py/numpy.h -> build/lib.linux-x86_64-3.8/petsc4py/include/petsc4py copying src/include/petsc4py/petsc4py.PETSc_api.h -> build/lib.linux-x86_64-3.8/petsc4py/include/petsc4py copying src/include/petsc4py/petsc4py.h -> build/lib.linux-x86_64-3.8/petsc4py/include/petsc4py copying src/include/petsc4py/petsc4py.i -> build/lib.linux-x86_64-3.8/petsc4py/include/petsc4py copying src/include/petsc4py/__init__.pxd -> build/lib.linux-x86_64-3.8/petsc4py/include/petsc4py copying src/include/petsc4py/PETSc.pxd -> build/lib.linux-x86_64-3.8/petsc4py/include/petsc4py copying src/include/petsc4py/__init__.pyx -> build/lib.linux-x86_64-3.8/petsc4py/include/petsc4py copying src/PETSc.pxd -> build/lib.linux-x86_64-3.8/petsc4py copying src/lib/petsc.cfg -> build/lib.linux-x86_64-3.8/petsc4py/lib running build_ext error: PETSc not found ---------------------------------------- ERROR: Failed building wheel for petsc4py Running setup.py clean for petsc4py Building wheel for slepc (setup.py): started Building wheel for slepc (setup.py): finished with status 'error' ERROR: Command errored out with exit status 1: command: /home/icb/philipp.weiler/code/cellrank/.tox/py38-linux/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/home/philipp.weiler/.ch_tmp/pip-install-j0_j3wbm/slepc_9bd37530a3c9426dbb37463c96b1ddc6/setup.py'"'"'; __file__='"'"'/home/philipp.weiler/.ch_tmp/pip-install-j0_j3wbm/slepc_9bd37530a3c9426dbb37463c96b1ddc6/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /home/philipp.weiler/.ch_tmp/pip-wheel-2k5eaxna cwd: /home/philipp.weiler/.ch_tmp/pip-install-j0_j3wbm/slepc_9bd37530a3c9426dbb37463c96b1ddc6/ Complete output (1 lines): slepc: this package cannot be built as a wheel ---------------------------------------- ERROR: Failed building wheel for slepc Running setup.py clean for slepc Building wheel for slepc4py (setup.py): started Building wheel for slepc4py (setup.py): finished with status 'error' ERROR: Command errored out with exit status 1: command: /home/icb/philipp.weiler/code/cellrank/.tox/py38-linux/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/home/philipp.weiler/.ch_tmp/pip-install-j0_j3wbm/slepc4py_02afcf2884e34929825bb665b172cf61/setup.py'"'"'; __file__='"'"'/home/philipp.weiler/.ch_tmp/pip-install-j0_j3wbm/slepc4py_02afcf2884e34929825bb665b172cf61/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /home/philipp.weiler/.ch_tmp/pip-wheel-n96a777n cwd: /home/philipp.weiler/.ch_tmp/pip-install-j0_j3wbm/slepc4py_02afcf2884e34929825bb665b172cf61/ Complete output (27 lines): running bdist_wheel PETSC_DIR not specified SLEPC_DIR not specified running build running build_src running build_py creating build creating build/lib.linux-x86_64-3.8 creating build/lib.linux-x86_64-3.8/slepc4py copying src/SLEPc.py -> build/lib.linux-x86_64-3.8/slepc4py copying src/__init__.py -> build/lib.linux-x86_64-3.8/slepc4py copying src/__main__.py -> build/lib.linux-x86_64-3.8/slepc4py creating build/lib.linux-x86_64-3.8/slepc4py/lib copying src/lib/__init__.py -> build/lib.linux-x86_64-3.8/slepc4py/lib creating build/lib.linux-x86_64-3.8/slepc4py/include creating build/lib.linux-x86_64-3.8/slepc4py/include/slepc4py copying src/include/slepc4py/slepc4py.SLEPc_api.h -> build/lib.linux-x86_64-3.8/slepc4py/include/slepc4py copying src/include/slepc4py/slepc4py.SLEPc.h -> build/lib.linux-x86_64-3.8/slepc4py/include/slepc4py copying src/include/slepc4py/slepc4py.h -> build/lib.linux-x86_64-3.8/slepc4py/include/slepc4py copying src/include/slepc4py/slepc4py.i -> build/lib.linux-x86_64-3.8/slepc4py/include/slepc4py copying src/include/slepc4py/__init__.pxd -> build/lib.linux-x86_64-3.8/slepc4py/include/slepc4py copying src/include/slepc4py/SLEPc.pxd -> build/lib.linux-x86_64-3.8/slepc4py/include/slepc4py copying src/include/slepc4py/__init__.pyx -> build/lib.linux-x86_64-3.8/slepc4py/include/slepc4py copying src/SLEPc.pxd -> build/lib.linux-x86_64-3.8/slepc4py copying src/lib/slepc.cfg -> build/lib.linux-x86_64-3.8/slepc4py/lib running build_ext error: PETSc not found ---------------------------------------- ERROR: Failed building wheel for slepc4py Running setup.py clean for slepc4py Successfully built wot Failed to build petsc petsc4py slepc slepc4py Installing collected packages: threadpoolctl, scipy, llvmlite, joblib, xlrd, stdlib-list, scikit-learn, patsy, pandas, packaging, numexpr, numba, natsort, mpi4py, h5py, decorator, umap-learn, tqdm, toml, tables, statsmodels, sinfo, seaborn, python-utils, py, pluggy, petsc, numpy-groupies, networkx, iniconfig, click, attrs, anndata, texttable, slepc, scanpy, pytest, progressbar2, petsc4py, loompy, future, docrep, cython, wrapt, typing-extensions, slepc4py, scvelo, python-igraph, pytest-forked, pygpcca, pygam, POT, opt-einsum, flatbuffers, execnet, coverage, absl-py, wot, statot, pytest-xdist, pytest-mock, pytest-cov, louvain, leidenalg, jaxlib, jax, filelock, cellrank, bezier Running setup.py install for petsc: started Running setup.py install for petsc: finished with status 'error' ERROR: Command errored out with exit status 1: command: /home/icb/philipp.weiler/code/cellrank/.tox/py38-linux/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/home/philipp.weiler/.ch_tmp/pip-install-j0_j3wbm/petsc_f1b6d15d21794765b31fee93a5ed11ae/setup.py'"'"'; __file__='"'"'/home/philipp.weiler/.ch_tmp/pip-install-j0_j3wbm/petsc_f1b6d15d21794765b31fee93a5ed11ae/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /home/philipp.weiler/.ch_tmp/pip-record-j8jsueun/install-record.txt --single-version-externally-managed --compile --install-headers /home/icb/philipp.weiler/code/cellrank/.tox/py38-linux/include/site/python3.8/petsc cwd: /home/philipp.weiler/.ch_tmp/pip-install-j0_j3wbm/petsc_f1b6d15d21794765b31fee93a5ed11ae/ Complete output (32 lines): running install PETSc: configure configure options: --prefix=/home/icb/philipp.weiler/code/cellrank/.tox/py38-linux/lib/python3.8/site-packages/petsc PETSC_ARCH=arch-python-linux-x86_64 --with-shared-libraries=1 --with-debugging=0 --with-c2html=0 --with-cc=/usr/bin/mpicc --with-cxx=/usr/bin/mpicxx --with-fc=/usr/bin/mpif90 ************************************************************************ * /usr/bin/python2 is missing "distutils.sysconfig" module! Its required to build PETSc ** * Try installing (for ex: on Ubuntu) "python3-distutils" or equivalent package that is compatible with /usr/bin/python2 *** ************************************************************************ Traceback (most recent call last): File "", line 1, in File "/home/philipp.weiler/.ch_tmp/pip-install-j0_j3wbm/petsc_f1b6d15d21794765b31fee93a5ed11ae/setup.py", line 294, in setup(name='petsc', File "/home/icb/philipp.weiler/code/cellrank/.tox/py38-linux/lib/python3.8/site-packages/setuptools/__init__.py", line 153, in setup return distutils.core.setup(**attrs) File "/home/philipp.weiler/miniconda3/envs/cellrank/lib/python3.8/distutils/core.py", line 148, in setup dist.run_commands() File "/home/philipp.weiler/miniconda3/envs/cellrank/lib/python3.8/distutils/dist.py", line 966, in run_commands self.run_command(cmd) File "/home/philipp.weiler/miniconda3/envs/cellrank/lib/python3.8/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/home/philipp.weiler/.ch_tmp/pip-install-j0_j3wbm/petsc_f1b6d15d21794765b31fee93a5ed11ae/setup.py", line 230, in run config(prefix, self.dry_run) File "/home/philipp.weiler/.ch_tmp/pip-install-j0_j3wbm/petsc_f1b6d15d21794765b31fee93a5ed11ae/setup.py", line 166, in config if status != 0: raise RuntimeError(status) RuntimeError: 1024 ---------------------------------------- ERROR: Command errored out with exit status 1: /home/icb/philipp.weiler/code/cellrank/.tox/py38-linux/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/home/philipp.weiler/.ch_tmp/pip-install-j0_j3wbm/petsc_f1b6d15d21794765b31fee93a5ed11ae/setup.py'"'"'; __file__='"'"'/home/philipp.weiler/.ch_tmp/pip-install-j0_j3wbm/petsc_f1b6d15d21794765b31fee93a5ed11ae/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /home/philipp.weiler/.ch_tmp/pip-record-j8jsueun/install-record.txt --single-version-externally-managed --compile --install-headers /home/icb/philipp.weiler/code/cellrank/.tox/py38-linux/include/site/python3.8/petsc Check the logs for full command output. =================================================================================================== log end =================================================================================================== ```

Running the tests again via

tox -e py38-linux

worked fine but I still see the deprecation warning mentioned in #627. Any idea on what went wrong?

michalk8 commented 3 years ago

Based on the log, this seems to be a problem:

/usr/bin/python2 is missing "distutils.sysconfig" module! Its required to build PETSc
Try installing (for ex: on Ubuntu) "python3-distutils"  or equivalent package that is compatible with /usr/bin/python2

Maybe sudo apt-get install python3-distutils will help? Tbh, not sure why is it trying to look-up python2 (esp. in /usr/bin). Re the warning: this is because pytest is also globally installed (via [test] external requirements). Can be fixed via python -m pytest ... in tox.ini.

michalk8 commented 3 years ago

Also, could you please post the Dockerfile you're using on MM? I want to take a look to see if all dependencies are there.

michalk8 commented 3 years ago

The warning should be fixed by 395bdcc, going to try devel install on the server now.

michalk8 commented 3 years ago

@WeilerP can't reproduce the error using my container, running dpkg --list | grep python3-distutis shows that I have it installed, so installing it should fix the issue.

Marius1311 commented 3 years ago

@WeilerP, can you share your container with @michalk8 so he can reproduce this? Or what's our solution for this?

WeilerP commented 3 years ago

@WeilerP can't reproduce the error using my container, running dpkg --list | grep python3-distutis shows that I have it installed, so installing it should fix the issue.

Sorry, forgot to answer. python3-distutils is installed. Is it a problem that I am using Python 3.8 but python3-distutils is Python 3.7.3? Or should I check that it is installed in a new container?

@WeilerP, can you share your container with @michalk8 so he can reproduce this? Or what's our solution for this?

Yes, can share the container but not sure if it is worth the effort. What do you think @michalk8? I can run the tests it just doesn't work out of the box for me. I just gotta run tox -e py38-linux at least twice (the first run fails, all following run the tests).

michalk8 commented 3 years ago

Sorry, forgot to answer. python3-distutils is installed. Is it a problem that I am using Python 3.8 but python3-distutils is Python 3.7.3? Or should I check that it is installed in a new container?

That might be a problem, so I'd check.

Yes, can share the container but not sure if it is worth the effort. What do you think @michalk8?

I'd say not worth the effort - ideally, I'd like to close this soon.

WeilerP commented 3 years ago

@michalk8, everything seems to work after upgrading python3-distutils to 3.7.3.