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aiidateam / aiida-common-workflows

A repository for the implementation of common workflow interfaces across materials-science codes and plugins
https://aiida-common-workflows.readthedocs.io
MIT License
52 stars 30 forks source link

Docs on readthedocs don't seem to be updated #231

Closed giovannipizzi closed 2 years ago

giovannipizzi commented 2 years ago

See e.g. the bottom of the homepage, where in the code there is the correct citation, but it's not visible in the HTML rendered version.

If I login in RTD, I think the most recent error log is this, if it helps:

Processing /home/docs/checkouts/readthedocs.org/user_builds/aiida-common-workflows/checkouts/stable
  DEPRECATION: A future pip version will change local packages to be built in-place without first copying to a temporary directory. We recommend you use --use-feature=in-tree-build to test your packages with this new behavior before it becomes the default.
   pip 21.3 will remove support for this functionality. You can find discussion regarding this at https://github.com/pypa/pip/issues/7555.
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Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/aiida-common-workflows/envs/stable/lib/python3.8/site-packages (from sphinx~=3.2->aiida-common-workflows==0.1.0) (1.1.5)
Collecting elementpath<3.0.0,>=2.2.2
  Downloading elementpath-2.3.2-py3-none-any.whl (155 kB)
Collecting abipy
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Collecting pydispatcher>=2.0.5
  Downloading PyDispatcher-2.0.5.zip (47 kB)
Collecting apscheduler==2.1.0
  Downloading APScheduler-2.1.0.tar.gz (42 kB)
Collecting netCDF4
  Downloading netCDF4-1.5.7-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.7 MB)
Collecting cclib>=1.6.1
  Downloading cclib-1.7.1.tar.gz (278 kB)
Collecting periodictable
  Downloading periodictable-1.6.0.tar.gz (686 kB)
Collecting pymatgen<=2021.3.3
  Downloading pymatgen-2020.12.3.tar.gz (2.8 MB)
Collecting parsevasp>=2.0.1
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Collecting subprocess32
  Downloading subprocess32-3.5.4.tar.gz (97 kB)
Collecting zipp>=3.1.0
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Collecting cftime
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Collecting mpmath>=0.19
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Collecting multidict>=4.0
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Building wheels for collected packages: aiida-bigdft, aiida-cp2k, aiida-siesta, click-completion, configobj, ete3, pgsu, PyCifRW, sqlalchemy-utils, wrapt, apscheduler, pydispatcher, aiida-common-workflows, aiida-gaussian, cclib, pymatgen, periodictable, pyhull, sisl, subprocess32, voluptuous
  Building wheel for aiida-bigdft (setup.py): started
  Building wheel for aiida-bigdft (setup.py): finished with status 'done'
  Created wheel for aiida-bigdft: filename=aiida_bigdft-0.2.6-py3-none-any.whl size=215779 sha256=26f67732b1b5bf02a57cc5acd48844d5ab5c4064a0299a016ca25a5db2e231fe
  Stored in directory: /tmp/pip-ephem-wheel-cache-36h5bb53/wheels/db/7d/66/ad7233b44b56b80868e0e3564fdb29f1d6ed74e1a34f07f3b8
  Building wheel for aiida-cp2k (setup.py): started
  Building wheel for aiida-cp2k (setup.py): finished with status 'done'
  Created wheel for aiida-cp2k: filename=aiida_cp2k-1.3.0-py3-none-any.whl size=24064 sha256=13d0146527bfc843a7c735fed2d082e8802c7cbc580ffad17238c05413924cbb
  Stored in directory: /tmp/pip-ephem-wheel-cache-36h5bb53/wheels/84/1a/c4/49b1d19bc8c6bea0e52e7bbd48ae336acada34dbf237fd970f
  Building wheel for aiida-siesta (setup.py): started
  Building wheel for aiida-siesta (setup.py): finished with status 'done'
  Created wheel for aiida-siesta: filename=aiida_siesta-1.2.0-py3-none-any.whl size=1583730 sha256=82326b4ad7da5a978fec847ccdf5b6fae67c0b2268965e2d0f76e22126bcdc5a
  Stored in directory: /tmp/pip-ephem-wheel-cache-36h5bb53/wheels/0c/1a/3b/b2fa1c837a206fb1bd45d69d17b6249eb4968c04e8f8f1ff3d
  Building wheel for click-completion (setup.py): started
  Building wheel for click-completion (setup.py): finished with status 'done'
  Created wheel for click-completion: filename=click_completion-0.5.2-py3-none-any.whl size=11202 sha256=b5bbb418ad3e91d8048307c29c73d1d6b9876104e6d655a67c09e12fa6c57d9e
  Stored in directory: /tmp/pip-ephem-wheel-cache-36h5bb53/wheels/5e/b7/ff/813f27cecf9a5054c19b566d2b4b2d8588ce46671f3d1821ce
  Building wheel for configobj (setup.py): started
  Building wheel for configobj (setup.py): finished with status 'done'
  Created wheel for configobj: filename=configobj-5.0.6-py3-none-any.whl size=34546 sha256=cf09dba8b54858c36cfd56538ee1417c475f27032ed695c8b361a4fecc069f5b
  Stored in directory: /tmp/pip-ephem-wheel-cache-36h5bb53/wheels/34/2a/24/a490264ae9041fd48f778ff393526572c80bb498ddecb07ea5
  Building wheel for ete3 (setup.py): started
  Building wheel for ete3 (setup.py): finished with status 'done'
  Created wheel for ete3: filename=ete3-3.1.2-py3-none-any.whl size=2273013 sha256=db458ed7d20f28b238066b5baaf6a8aa164e8908b467f0628dd45d565a6dde8b
  Stored in directory: /tmp/pip-ephem-wheel-cache-36h5bb53/wheels/78/96/a0/973292c4813e6b39b611bec535521655088425516959768f46
  Building wheel for pgsu (PEP 517): started
  Building wheel for pgsu (PEP 517): finished with status 'done'
  Created wheel for pgsu: filename=pgsu-0.2.1-py3-none-any.whl size=8708 sha256=cee486956fa9af4af194d68b128667bf27d1f0a1344d42e866f781edadad64c5
  Stored in directory: /tmp/pip-ephem-wheel-cache-36h5bb53/wheels/c6/21/44/c3bf9674a10743dbe1513e8d157b3a4390df686f8ba56f1006
  Building wheel for PyCifRW (setup.py): started
  Building wheel for PyCifRW (setup.py): finished with status 'done'
  Created wheel for PyCifRW: filename=PyCifRW-4.4.3-cp38-cp38-linux_x86_64.whl size=163333 sha256=86d7436273daff7fae918f5a348ffc914c48856d6d65a9489a3a80397c083f4f
  Stored in directory: /tmp/pip-ephem-wheel-cache-36h5bb53/wheels/d3/2a/90/c6700f618a0630c91b4c6d8ba6eb95fcc64369c5d94a27721b
  Building wheel for sqlalchemy-utils (setup.py): started
  Building wheel for sqlalchemy-utils (setup.py): finished with status 'done'
  Created wheel for sqlalchemy-utils: filename=SQLAlchemy_Utils-0.36.5-py2.py3-none-any.whl size=93149 sha256=5391f90662ccecba6b3e0d18c511cb1af9588448c4920e8b9676a46bc743c4b4
  Stored in directory: /tmp/pip-ephem-wheel-cache-36h5bb53/wheels/d6/cd/c7/3a3f8a4e28092c76183ac5b346facfb4f736810a71f66d629a
  Building wheel for wrapt (setup.py): started
  Building wheel for wrapt (setup.py): finished with status 'done'
  Created wheel for wrapt: filename=wrapt-1.11.2-cp38-cp38-linux_x86_64.whl size=77865 sha256=f0863a01e565b727533b2307f0f5a1f53b5306fb6f16d2f2fe8b1853937a0930
  Stored in directory: /tmp/pip-ephem-wheel-cache-36h5bb53/wheels/52/25/16/7e228f52ee876e9c9c66dfd6eaf6fb2f73f18629a74dcf7045
  Building wheel for apscheduler (setup.py): started
  Building wheel for apscheduler (setup.py): finished with status 'done'
  Created wheel for apscheduler: filename=APScheduler-2.1.0-py3-none-any.whl size=25544 sha256=6dab3b0048cd009df034493ae9aa59b159d6b3e792c2c3b2a0a1b3f294118290
  Stored in directory: /tmp/pip-ephem-wheel-cache-36h5bb53/wheels/15/b9/90/08893043c0e3ccfcb61854b3b01a4f2495456b3776a19a8665
  Building wheel for pydispatcher (setup.py): started
  Building wheel for pydispatcher (setup.py): finished with status 'done'
  Created wheel for pydispatcher: filename=PyDispatcher-2.0.5-py3-none-any.whl size=11515 sha256=d8ee3741c255c011e804059e5d7e98a2cedafbcde38edbf220a48d71ddbdf495
  Stored in directory: /tmp/pip-ephem-wheel-cache-36h5bb53/wheels/3c/31/7f/d7d7b5f0b9bad841ed856138ff0c5ee2bf2e04dbeb413097c8
  Building wheel for aiida-common-workflows (setup.py): started
  Building wheel for aiida-common-workflows (setup.py): finished with status 'done'
  Created wheel for aiida-common-workflows: filename=aiida_common_workflows-0.1.0-py3-none-any.whl size=628400 sha256=5169a6c7d59e69b16019cfca22243b6349b3b6fa51fb98f96f58a26944b66de6
  Stored in directory: /tmp/pip-ephem-wheel-cache-36h5bb53/wheels/d5/63/97/cf60387282e09d8521fb9b1156df5f94dcf75ecd20ec0b2406
  Building wheel for aiida-gaussian (setup.py): started
  Building wheel for aiida-gaussian (setup.py): finished with status 'done'
  Created wheel for aiida-gaussian: filename=aiida_gaussian-1.4.1-py3-none-any.whl size=22254 sha256=0a146b3995d73de4b4a521f38ded4d97d016cbb76141b91f997d101f329dad1a
  Stored in directory: /tmp/pip-ephem-wheel-cache-36h5bb53/wheels/1e/50/62/8dee9b547f3e1d58d77f6014b11aee06084edc112d227f12cd
  Building wheel for cclib (setup.py): started
  Building wheel for cclib (setup.py): finished with status 'done'
  Created wheel for cclib: filename=cclib-1.7.1-py3-none-any.whl size=313116 sha256=8294e1459e83ed0c306b55cb4d5d342ae1c47552939d514c9d8e7f9bb6004c78
  Stored in directory: /tmp/pip-ephem-wheel-cache-36h5bb53/wheels/1c/05/1b/6a5cc9ab8eac7f4de427eb94f70f8cdc2eb3019baeac909ba4
  Building wheel for pymatgen (setup.py): started
  Building wheel for pymatgen (setup.py): finished with status 'done'
  Created wheel for pymatgen: filename=pymatgen-2020.12.3-cp38-cp38-linux_x86_64.whl size=3766166 sha256=45a26ca2c8db097cc9a74db77e620b6fab7ff405f0868d9254549fcd67b4d66f
  Stored in directory: /tmp/pip-ephem-wheel-cache-36h5bb53/wheels/6e/f9/ef/31c3538f5f5cf303956cb40067b1ef8299b4623761d7a724a9
  Building wheel for periodictable (setup.py): started
  Building wheel for periodictable (setup.py): finished with status 'done'
  Created wheel for periodictable: filename=periodictable-1.6.0-py3-none-any.whl size=749751 sha256=869db4ce33f0477f1c71e10f18dc58f879319d0524fb59c31d4713db1def79ef
  Stored in directory: /tmp/pip-ephem-wheel-cache-36h5bb53/wheels/42/fd/65/8cacc08d4786953b91cf2c8d5f309a1cc1039c2bf1727390a1
  Building wheel for pyhull (setup.py): started
  Building wheel for pyhull (setup.py): finished with status 'done'
  Created wheel for pyhull: filename=pyhull-2015.2.1-cp38-cp38-linux_x86_64.whl size=465119 sha256=b8d8b037caf9833c4992162cf58fb822779f69144f7e1e60b44857a6af65964b
  Stored in directory: /tmp/pip-ephem-wheel-cache-36h5bb53/wheels/da/f2/56/d932911d4d882263b8b14822ce3c01aee5dd3b95253168518e
  Building wheel for sisl (PEP 517): started
  Building wheel for sisl (PEP 517): finished with status 'error'
  ERROR: Command errored out with exit status 1:
   command: /home/docs/checkouts/readthedocs.org/user_builds/aiida-common-workflows/envs/stable/bin/python /home/docs/checkouts/readthedocs.org/user_builds/aiida-common-workflows/envs/stable/lib/python3.8/site-packages/pip/_vendor/pep517/in_process/_in_process.py build_wheel /tmp/tmp50enem_q
       cwd: /tmp/pip-install-v4owotne/sisl_23af8289d35d410bbb492c23e19d44dd
  Complete output (698 lines):
  sisl-install: using internal shipped revisions
  running bdist_wheel
  running build
  running config_cc
  unifing config_cc, config, build_clib, build_ext, build commands --compiler options
  running config_fc
  unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
  running build_src
  build_src
  building extension "sisl.io.siesta._siesta" sources
  f2py options: []
    adding 'build/src.linux-x86_64-3.8/build/src.linux-x86_64-3.8/sisl/io/siesta/fortranobject.c' to sources.
    adding 'build/src.linux-x86_64-3.8/build/src.linux-x86_64-3.8/sisl/io/siesta' to include_dirs.
    adding 'build/src.linux-x86_64-3.8/sisl/io/siesta/_siesta-f2pywrappers2.f90' to sources.
  building extension "sisl._indices" sources
  building extension "sisl._math_small" sources
  building extension "sisl._sparse" sources
  building extension "sisl._supercell" sources
  building extension "sisl.physics._bloch" sources
  building extension "sisl.physics._phase" sources
  building extension "sisl.physics._matrix_utils" sources
  building extension "sisl.physics._matrix_k" sources
  building extension "sisl.physics._matrix_dk" sources
  building extension "sisl.physics._matrix_ddk" sources
  building extension "sisl.physics._matrix_phase3" sources
  building extension "sisl.physics._matrix_phase3_nc" sources
  building extension "sisl.physics._matrix_phase3_so" sources
  building extension "sisl.physics._matrix_phase" sources
  building extension "sisl.physics._matrix_phase_nc_diag" sources
  building extension "sisl.physics._matrix_phase_nc" sources
  building extension "sisl.physics._matrix_phase_so" sources
  building extension "sisl.physics._matrix_sc_phase" sources
  building extension "sisl.physics._matrix_sc_phase_nc_diag" sources
  building extension "sisl.physics._matrix_sc_phase_nc" sources
  building extension "sisl.physics._matrix_sc_phase_so" sources
  build_src: building npy-pkg config files
  running build_py
  creating build/lib.linux-x86_64-3.8
  creating build/lib.linux-x86_64-3.8/sisl
  copying sisl/orbital.py -> build/lib.linux-x86_64-3.8/sisl
  copying sisl/quaternion.py -> build/lib.linux-x86_64-3.8/sisl
  copying sisl/_category.py -> build/lib.linux-x86_64-3.8/sisl
  copying sisl/_internal.py -> build/lib.linux-x86_64-3.8/sisl
  copying sisl/grid.py -> build/lib.linux-x86_64-3.8/sisl
  copying sisl/atom.py -> build/lib.linux-x86_64-3.8/sisl
  copying sisl/supercell.py -> build/lib.linux-x86_64-3.8/sisl
  copying sisl/conftest.py -> build/lib.linux-x86_64-3.8/sisl
  copying sisl/_help.py -> build/lib.linux-x86_64-3.8/sisl
  copying sisl/__main__.py -> build/lib.linux-x86_64-3.8/sisl
  copying sisl/sparse.py -> build/lib.linux-x86_64-3.8/sisl
  copying sisl/_array.py -> build/lib.linux-x86_64-3.8/sisl
  copying sisl/sparse_geometry.py -> build/lib.linux-x86_64-3.8/sisl
  copying sisl/geometry.py -> build/lib.linux-x86_64-3.8/sisl
  copying sisl/_plot.py -> build/lib.linux-x86_64-3.8/sisl
  copying sisl/messages.py -> build/lib.linux-x86_64-3.8/sisl
  copying sisl/_namedindex.py -> build/lib.linux-x86_64-3.8/sisl
  copying sisl/_environ.py -> build/lib.linux-x86_64-3.8/sisl
  copying sisl/_dispatcher.py -> build/lib.linux-x86_64-3.8/sisl
  copying sisl/constant.py -> build/lib.linux-x86_64-3.8/sisl
  copying sisl/__init__.py -> build/lib.linux-x86_64-3.8/sisl
  copying sisl/oplist.py -> build/lib.linux-x86_64-3.8/sisl
  copying sisl/selector.py -> build/lib.linux-x86_64-3.8/sisl
  copying sisl/info.py -> build/lib.linux-x86_64-3.8/sisl
  creating build/lib.linux-x86_64-3.8/sisl/io
  copying sisl/io/pdb.py -> build/lib.linux-x86_64-3.8/sisl/io
  copying sisl/io/xsf.py -> build/lib.linux-x86_64-3.8/sisl/io
  copying sisl/io/ham.py -> build/lib.linux-x86_64-3.8/sisl/io
  copying sisl/io/molden.py -> build/lib.linux-x86_64-3.8/sisl/io
  copying sisl/io/sile.py -> build/lib.linux-x86_64-3.8/sisl/io
  copying sisl/io/_help.py -> build/lib.linux-x86_64-3.8/sisl/io
  copying sisl/io/cube.py -> build/lib.linux-x86_64-3.8/sisl/io
  copying sisl/io/xyz.py -> build/lib.linux-x86_64-3.8/sisl/io
  copying sisl/io/table.py -> build/lib.linux-x86_64-3.8/sisl/io
  copying sisl/io/__init__.py -> build/lib.linux-x86_64-3.8/sisl/io
  creating build/lib.linux-x86_64-3.8/sisl/shape
  copying sisl/shape/base.py -> build/lib.linux-x86_64-3.8/sisl/shape
  copying sisl/shape/ellipsoid.py -> build/lib.linux-x86_64-3.8/sisl/shape
  copying sisl/shape/prism4.py -> build/lib.linux-x86_64-3.8/sisl/shape
  copying sisl/shape/__init__.py -> build/lib.linux-x86_64-3.8/sisl/shape
  creating build/lib.linux-x86_64-3.8/sisl/utils
  copying sisl/utils/cmd.py -> build/lib.linux-x86_64-3.8/sisl/utils
  copying sisl/utils/ranges.py -> build/lib.linux-x86_64-3.8/sisl/utils
  copying sisl/utils/mathematics.py -> build/lib.linux-x86_64-3.8/sisl/utils
  copying sisl/utils/misc.py -> build/lib.linux-x86_64-3.8/sisl/utils
  copying sisl/utils/__init__.py -> build/lib.linux-x86_64-3.8/sisl/utils
  copying sisl/utils/_sisl_cmd.py -> build/lib.linux-x86_64-3.8/sisl/utils
  creating build/lib.linux-x86_64-3.8/sisl/geom
  copying sisl/geom/special.py -> build/lib.linux-x86_64-3.8/sisl/geom
  copying sisl/geom/nanoribbon.py -> build/lib.linux-x86_64-3.8/sisl/geom
  copying sisl/geom/flat.py -> build/lib.linux-x86_64-3.8/sisl/geom
  copying sisl/geom/basic.py -> build/lib.linux-x86_64-3.8/sisl/geom
  copying sisl/geom/bilayer.py -> build/lib.linux-x86_64-3.8/sisl/geom
  copying sisl/geom/nanotube.py -> build/lib.linux-x86_64-3.8/sisl/geom
  copying sisl/geom/__init__.py -> build/lib.linux-x86_64-3.8/sisl/geom
  creating build/lib.linux-x86_64-3.8/sisl/mixing
  copying sisl/mixing/diis.py -> build/lib.linux-x86_64-3.8/sisl/mixing
  copying sisl/mixing/base.py -> build/lib.linux-x86_64-3.8/sisl/mixing
  copying sisl/mixing/linear.py -> build/lib.linux-x86_64-3.8/sisl/mixing
  copying sisl/mixing/__init__.py -> build/lib.linux-x86_64-3.8/sisl/mixing
  creating build/lib.linux-x86_64-3.8/sisl/linalg
  copying sisl/linalg/base.py -> build/lib.linux-x86_64-3.8/sisl/linalg
  copying sisl/linalg/__init__.py -> build/lib.linux-x86_64-3.8/sisl/linalg
  creating build/lib.linux-x86_64-3.8/sisl/physics
  copying sisl/physics/self_energy.py -> build/lib.linux-x86_64-3.8/sisl/physics
  copying sisl/physics/bloch.py -> build/lib.linux-x86_64-3.8/sisl/physics
  copying sisl/physics/hamiltonian.py -> build/lib.linux-x86_64-3.8/sisl/physics
  copying sisl/physics/state.py -> build/lib.linux-x86_64-3.8/sisl/physics
  copying sisl/physics/brillouinzone.py -> build/lib.linux-x86_64-3.8/sisl/physics
  copying sisl/physics/energydensitymatrix.py -> build/lib.linux-x86_64-3.8/sisl/physics
  copying sisl/physics/electron.py -> build/lib.linux-x86_64-3.8/sisl/physics
  copying sisl/physics/sparse.py -> build/lib.linux-x86_64-3.8/sisl/physics
  copying sisl/physics/overlap.py -> build/lib.linux-x86_64-3.8/sisl/physics
  copying sisl/physics/spin.py -> build/lib.linux-x86_64-3.8/sisl/physics
  copying sisl/physics/distribution.py -> build/lib.linux-x86_64-3.8/sisl/physics
  copying sisl/physics/_brillouinzone_apply.py -> build/lib.linux-x86_64-3.8/sisl/physics
  copying sisl/physics/densitymatrix.py -> build/lib.linux-x86_64-3.8/sisl/physics
  copying sisl/physics/dynamicalmatrix.py -> build/lib.linux-x86_64-3.8/sisl/physics
  copying sisl/physics/__init__.py -> build/lib.linux-x86_64-3.8/sisl/physics
  copying sisl/physics/phonon.py -> build/lib.linux-x86_64-3.8/sisl/physics
  creating build/lib.linux-x86_64-3.8/sisl/unit
  copying sisl/unit/siesta.py -> build/lib.linux-x86_64-3.8/sisl/unit
  copying sisl/unit/base.py -> build/lib.linux-x86_64-3.8/sisl/unit
  copying sisl/unit/__init__.py -> build/lib.linux-x86_64-3.8/sisl/unit
  creating build/lib.linux-x86_64-3.8/sisl/viz
  copying sisl/viz/_plotables.py -> build/lib.linux-x86_64-3.8/sisl/viz
  copying sisl/viz/__init__.py -> build/lib.linux-x86_64-3.8/sisl/viz
  creating build/lib.linux-x86_64-3.8/sisl/tests
  copying sisl/tests/test_help.py -> build/lib.linux-x86_64-3.8/sisl/tests
  copying sisl/tests/test_geometry.py -> build/lib.linux-x86_64-3.8/sisl/tests
  copying sisl/tests/test_atoms.py -> build/lib.linux-x86_64-3.8/sisl/tests
  copying sisl/tests/test_orbital.py -> build/lib.linux-x86_64-3.8/sisl/tests
  copying sisl/tests/test_namedindex.py -> build/lib.linux-x86_64-3.8/sisl/tests
  copying sisl/tests/test_package.py -> build/lib.linux-x86_64-3.8/sisl/tests
  copying sisl/tests/test_messages.py -> build/lib.linux-x86_64-3.8/sisl/tests
  copying sisl/tests/test_sgeom.py -> build/lib.linux-x86_64-3.8/sisl/tests
  copying sisl/tests/test_plot.py -> build/lib.linux-x86_64-3.8/sisl/tests
  copying sisl/tests/test_geometry_return.py -> build/lib.linux-x86_64-3.8/sisl/tests
  copying sisl/tests/test_quaternion.py -> build/lib.linux-x86_64-3.8/sisl/tests
  copying sisl/tests/test_sparse_orbital.py -> build/lib.linux-x86_64-3.8/sisl/tests
  copying sisl/tests/test_selector.py -> build/lib.linux-x86_64-3.8/sisl/tests
  copying sisl/tests/test_grid.py -> build/lib.linux-x86_64-3.8/sisl/tests
  copying sisl/tests/test_sparse_geometry.py -> build/lib.linux-x86_64-3.8/sisl/tests
  copying sisl/tests/test_sparse.py -> build/lib.linux-x86_64-3.8/sisl/tests
  copying sisl/tests/test_atom.py -> build/lib.linux-x86_64-3.8/sisl/tests
  copying sisl/tests/test_supercell.py -> build/lib.linux-x86_64-3.8/sisl/tests
  copying sisl/tests/test_sgrid.py -> build/lib.linux-x86_64-3.8/sisl/tests
  copying sisl/tests/test_oplist.py -> build/lib.linux-x86_64-3.8/sisl/tests
  copying sisl/tests/__init__.py -> build/lib.linux-x86_64-3.8/sisl/tests
  creating build/lib.linux-x86_64-3.8/sisl/io/scaleup
  copying sisl/io/scaleup/orbocc.py -> build/lib.linux-x86_64-3.8/sisl/io/scaleup
  copying sisl/io/scaleup/sile.py -> build/lib.linux-x86_64-3.8/sisl/io/scaleup
  copying sisl/io/scaleup/rham.py -> build/lib.linux-x86_64-3.8/sisl/io/scaleup
  copying sisl/io/scaleup/ref.py -> build/lib.linux-x86_64-3.8/sisl/io/scaleup
  copying sisl/io/scaleup/__init__.py -> build/lib.linux-x86_64-3.8/sisl/io/scaleup
  creating build/lib.linux-x86_64-3.8/sisl/io/siesta
  copying sisl/io/siesta/fdf.py -> build/lib.linux-x86_64-3.8/sisl/io/siesta
  copying sisl/io/siesta/out.py -> build/lib.linux-x86_64-3.8/sisl/io/siesta
  copying sisl/io/siesta/sile.py -> build/lib.linux-x86_64-3.8/sisl/io/siesta
  copying sisl/io/siesta/bands.py -> build/lib.linux-x86_64-3.8/sisl/io/siesta
  copying sisl/io/siesta/binaries.py -> build/lib.linux-x86_64-3.8/sisl/io/siesta
  copying sisl/io/siesta/eig.py -> build/lib.linux-x86_64-3.8/sisl/io/siesta
  copying sisl/io/siesta/_help.py -> build/lib.linux-x86_64-3.8/sisl/io/siesta
  copying sisl/io/siesta/fc.py -> build/lib.linux-x86_64-3.8/sisl/io/siesta
  copying sisl/io/siesta/siesta_nc.py -> build/lib.linux-x86_64-3.8/sisl/io/siesta
  copying sisl/io/siesta/fa.py -> build/lib.linux-x86_64-3.8/sisl/io/siesta
  copying sisl/io/siesta/kp.py -> build/lib.linux-x86_64-3.8/sisl/io/siesta
  copying sisl/io/siesta/transiesta_grid.py -> build/lib.linux-x86_64-3.8/sisl/io/siesta
  copying sisl/io/siesta/pdos.py -> build/lib.linux-x86_64-3.8/sisl/io/siesta
  copying sisl/io/siesta/siesta_grid.py -> build/lib.linux-x86_64-3.8/sisl/io/siesta
  copying sisl/io/siesta/basis.py -> build/lib.linux-x86_64-3.8/sisl/io/siesta
  copying sisl/io/siesta/__init__.py -> build/lib.linux-x86_64-3.8/sisl/io/siesta
  copying sisl/io/siesta/orb_indx.py -> build/lib.linux-x86_64-3.8/sisl/io/siesta
  copying sisl/io/siesta/xv.py -> build/lib.linux-x86_64-3.8/sisl/io/siesta
  creating build/lib.linux-x86_64-3.8/sisl/io/openmx
  copying sisl/io/openmx/sile.py -> build/lib.linux-x86_64-3.8/sisl/io/openmx
  copying sisl/io/openmx/omx.py -> build/lib.linux-x86_64-3.8/sisl/io/openmx
  copying sisl/io/openmx/__init__.py -> build/lib.linux-x86_64-3.8/sisl/io/openmx
  creating build/lib.linux-x86_64-3.8/sisl/io/vasp
  copying sisl/io/vasp/out.py -> build/lib.linux-x86_64-3.8/sisl/io/vasp
  copying sisl/io/vasp/eigenval.py -> build/lib.linux-x86_64-3.8/sisl/io/vasp
  copying sisl/io/vasp/sile.py -> build/lib.linux-x86_64-3.8/sisl/io/vasp
  copying sisl/io/vasp/car.py -> build/lib.linux-x86_64-3.8/sisl/io/vasp
  copying sisl/io/vasp/doscar.py -> build/lib.linux-x86_64-3.8/sisl/io/vasp
  copying sisl/io/vasp/locpot.py -> build/lib.linux-x86_64-3.8/sisl/io/vasp
  copying sisl/io/vasp/chg.py -> build/lib.linux-x86_64-3.8/sisl/io/vasp
  copying sisl/io/vasp/__init__.py -> build/lib.linux-x86_64-3.8/sisl/io/vasp
  creating build/lib.linux-x86_64-3.8/sisl/io/wannier90
  copying sisl/io/wannier90/sile.py -> build/lib.linux-x86_64-3.8/sisl/io/wannier90
  copying sisl/io/wannier90/seedname.py -> build/lib.linux-x86_64-3.8/sisl/io/wannier90
  copying sisl/io/wannier90/__init__.py -> build/lib.linux-x86_64-3.8/sisl/io/wannier90
  creating build/lib.linux-x86_64-3.8/sisl/io/tests
  copying sisl/io/tests/test_object.py -> build/lib.linux-x86_64-3.8/sisl/io/tests
  copying sisl/io/tests/test_table.py -> build/lib.linux-x86_64-3.8/sisl/io/tests
  copying sisl/io/tests/test_xyz.py -> build/lib.linux-x86_64-3.8/sisl/io/tests
  copying sisl/io/tests/test_cube.py -> build/lib.linux-x86_64-3.8/sisl/io/tests
  copying sisl/io/tests/test_xsf.py -> build/lib.linux-x86_64-3.8/sisl/io/tests
  copying sisl/io/tests/test_tb.py -> build/lib.linux-x86_64-3.8/sisl/io/tests
  copying sisl/io/tests/__init__.py -> build/lib.linux-x86_64-3.8/sisl/io/tests
  creating build/lib.linux-x86_64-3.8/sisl/io/gulp
  copying sisl/io/gulp/sile.py -> build/lib.linux-x86_64-3.8/sisl/io/gulp
  copying sisl/io/gulp/fc.py -> build/lib.linux-x86_64-3.8/sisl/io/gulp
  copying sisl/io/gulp/got.py -> build/lib.linux-x86_64-3.8/sisl/io/gulp
  copying sisl/io/gulp/__init__.py -> build/lib.linux-x86_64-3.8/sisl/io/gulp
  creating build/lib.linux-x86_64-3.8/sisl/io/bigdft
  copying sisl/io/bigdft/sile.py -> build/lib.linux-x86_64-3.8/sisl/io/bigdft
  copying sisl/io/bigdft/ascii.py -> build/lib.linux-x86_64-3.8/sisl/io/bigdft
  copying sisl/io/bigdft/__init__.py -> build/lib.linux-x86_64-3.8/sisl/io/bigdft
  creating build/lib.linux-x86_64-3.8/sisl/io/tbtrans
  copying sisl/io/tbtrans/sile.py -> build/lib.linux-x86_64-3.8/sisl/io/tbtrans
  copying sisl/io/tbtrans/binaries.py -> build/lib.linux-x86_64-3.8/sisl/io/tbtrans
  copying sisl/io/tbtrans/phtproj.py -> build/lib.linux-x86_64-3.8/sisl/io/tbtrans
  copying sisl/io/tbtrans/delta.py -> build/lib.linux-x86_64-3.8/sisl/io/tbtrans
  copying sisl/io/tbtrans/pht.py -> build/lib.linux-x86_64-3.8/sisl/io/tbtrans
  copying sisl/io/tbtrans/tbtproj.py -> build/lib.linux-x86_64-3.8/sisl/io/tbtrans
  copying sisl/io/tbtrans/tbt.py -> build/lib.linux-x86_64-3.8/sisl/io/tbtrans
  copying sisl/io/tbtrans/_cdf.py -> build/lib.linux-x86_64-3.8/sisl/io/tbtrans
  copying sisl/io/tbtrans/__init__.py -> build/lib.linux-x86_64-3.8/sisl/io/tbtrans
  copying sisl/io/tbtrans/se.py -> build/lib.linux-x86_64-3.8/sisl/io/tbtrans
  creating build/lib.linux-x86_64-3.8/sisl/io/siesta/tests
  copying sisl/io/siesta/tests/test_kp.py -> build/lib.linux-x86_64-3.8/sisl/io/siesta/tests
  copying sisl/io/siesta/tests/test_fc.py -> build/lib.linux-x86_64-3.8/sisl/io/siesta/tests
  copying sisl/io/siesta/tests/test_bands.py -> build/lib.linux-x86_64-3.8/sisl/io/siesta/tests
  copying sisl/io/siesta/tests/test_hsx.py -> build/lib.linux-x86_64-3.8/sisl/io/siesta/tests
  copying sisl/io/siesta/tests/test_orb_indx.py -> build/lib.linux-x86_64-3.8/sisl/io/siesta/tests
  copying sisl/io/siesta/tests/test_eig.py -> build/lib.linux-x86_64-3.8/sisl/io/siesta/tests
  copying sisl/io/siesta/tests/test_fdf.py -> build/lib.linux-x86_64-3.8/sisl/io/siesta/tests
  copying sisl/io/siesta/tests/test_siesta.py -> build/lib.linux-x86_64-3.8/sisl/io/siesta/tests
  copying sisl/io/siesta/tests/test_grid.py -> build/lib.linux-x86_64-3.8/sisl/io/siesta/tests
  copying sisl/io/siesta/tests/test_pdos.py -> build/lib.linux-x86_64-3.8/sisl/io/siesta/tests
  copying sisl/io/siesta/tests/test_basis.py -> build/lib.linux-x86_64-3.8/sisl/io/siesta/tests
  copying sisl/io/siesta/tests/test_xv.py -> build/lib.linux-x86_64-3.8/sisl/io/siesta/tests
  copying sisl/io/siesta/tests/test_dm.py -> build/lib.linux-x86_64-3.8/sisl/io/siesta/tests
  copying sisl/io/siesta/tests/test_tsde.py -> build/lib.linux-x86_64-3.8/sisl/io/siesta/tests
  copying sisl/io/siesta/tests/test_fa.py -> build/lib.linux-x86_64-3.8/sisl/io/siesta/tests
  copying sisl/io/siesta/tests/test_tshs.py -> build/lib.linux-x86_64-3.8/sisl/io/siesta/tests
  copying sisl/io/siesta/tests/__init__.py -> build/lib.linux-x86_64-3.8/sisl/io/siesta/tests
  copying sisl/io/siesta/tests/test_out.py -> build/lib.linux-x86_64-3.8/sisl/io/siesta/tests
  copying sisl/io/siesta/tests/test_gf.py -> build/lib.linux-x86_64-3.8/sisl/io/siesta/tests
  creating build/lib.linux-x86_64-3.8/sisl/io/vasp/tests
  copying sisl/io/vasp/tests/test_chg.py -> build/lib.linux-x86_64-3.8/sisl/io/vasp/tests
  copying sisl/io/vasp/tests/test_doscar.py -> build/lib.linux-x86_64-3.8/sisl/io/vasp/tests
  copying sisl/io/vasp/tests/test_car.py -> build/lib.linux-x86_64-3.8/sisl/io/vasp/tests
  copying sisl/io/vasp/tests/test_eigenval.py -> build/lib.linux-x86_64-3.8/sisl/io/vasp/tests
  copying sisl/io/vasp/tests/test_locpot.py -> build/lib.linux-x86_64-3.8/sisl/io/vasp/tests
  copying sisl/io/vasp/tests/__init__.py -> build/lib.linux-x86_64-3.8/sisl/io/vasp/tests
  copying sisl/io/vasp/tests/test_out.py -> build/lib.linux-x86_64-3.8/sisl/io/vasp/tests
  creating build/lib.linux-x86_64-3.8/sisl/io/wannier90/tests
  copying sisl/io/wannier90/tests/test_seedname.py -> build/lib.linux-x86_64-3.8/sisl/io/wannier90/tests
  copying sisl/io/wannier90/tests/__init__.py -> build/lib.linux-x86_64-3.8/sisl/io/wannier90/tests
  creating build/lib.linux-x86_64-3.8/sisl/io/gulp/tests
  copying sisl/io/gulp/tests/test_gout.py -> build/lib.linux-x86_64-3.8/sisl/io/gulp/tests
  copying sisl/io/gulp/tests/__init__.py -> build/lib.linux-x86_64-3.8/sisl/io/gulp/tests
  creating build/lib.linux-x86_64-3.8/sisl/io/tbtrans/tests
  copying sisl/io/tbtrans/tests/test_tbtproj.py -> build/lib.linux-x86_64-3.8/sisl/io/tbtrans/tests
  copying sisl/io/tbtrans/tests/test_delta.py -> build/lib.linux-x86_64-3.8/sisl/io/tbtrans/tests
  copying sisl/io/tbtrans/tests/test_tbt.py -> build/lib.linux-x86_64-3.8/sisl/io/tbtrans/tests
  copying sisl/io/tbtrans/tests/__init__.py -> build/lib.linux-x86_64-3.8/sisl/io/tbtrans/tests
  creating build/lib.linux-x86_64-3.8/sisl/shape/tests
  copying sisl/shape/tests/test_prism4.py -> build/lib.linux-x86_64-3.8/sisl/shape/tests
  copying sisl/shape/tests/test_shape.py -> build/lib.linux-x86_64-3.8/sisl/shape/tests
  copying sisl/shape/tests/__init__.py -> build/lib.linux-x86_64-3.8/sisl/shape/tests
  copying sisl/shape/tests/test_ellipsoid.py -> build/lib.linux-x86_64-3.8/sisl/shape/tests
  creating build/lib.linux-x86_64-3.8/sisl/utils/tests
  copying sisl/utils/tests/test_ranges.py -> build/lib.linux-x86_64-3.8/sisl/utils/tests
  copying sisl/utils/tests/test_mathematics.py -> build/lib.linux-x86_64-3.8/sisl/utils/tests
  copying sisl/utils/tests/test_misc.py -> build/lib.linux-x86_64-3.8/sisl/utils/tests
  copying sisl/utils/tests/test_cmd.py -> build/lib.linux-x86_64-3.8/sisl/utils/tests
  copying sisl/utils/tests/__init__.py -> build/lib.linux-x86_64-3.8/sisl/utils/tests
  creating build/lib.linux-x86_64-3.8/sisl/geom/category
  copying sisl/geom/category/_coord.py -> build/lib.linux-x86_64-3.8/sisl/geom/category
  copying sisl/geom/category/_kind.py -> build/lib.linux-x86_64-3.8/sisl/geom/category
  copying sisl/geom/category/base.py -> build/lib.linux-x86_64-3.8/sisl/geom/category
  copying sisl/geom/category/_neighbours.py -> build/lib.linux-x86_64-3.8/sisl/geom/category
  copying sisl/geom/category/__init__.py -> build/lib.linux-x86_64-3.8/sisl/geom/category
  creating build/lib.linux-x86_64-3.8/sisl/geom/tests
  copying sisl/geom/tests/test_geom.py -> build/lib.linux-x86_64-3.8/sisl/geom/tests
  copying sisl/geom/tests/__init__.py -> build/lib.linux-x86_64-3.8/sisl/geom/tests
  creating build/lib.linux-x86_64-3.8/sisl/geom/category/tests
  copying sisl/geom/category/tests/test_geom_category.py -> build/lib.linux-x86_64-3.8/sisl/geom/category/tests
  copying sisl/geom/category/tests/__init__.py -> build/lib.linux-x86_64-3.8/sisl/geom/category/tests
  creating build/lib.linux-x86_64-3.8/sisl/mixing/tests
  copying sisl/mixing/tests/test_diis.py -> build/lib.linux-x86_64-3.8/sisl/mixing/tests
  copying sisl/mixing/tests/test_linear.py -> build/lib.linux-x86_64-3.8/sisl/mixing/tests
  copying sisl/mixing/tests/__init__.py -> build/lib.linux-x86_64-3.8/sisl/mixing/tests
  creating build/lib.linux-x86_64-3.8/sisl/linalg/tests
  copying sisl/linalg/tests/test_solve.py -> build/lib.linux-x86_64-3.8/sisl/linalg/tests
  copying sisl/linalg/tests/test_eig.py -> build/lib.linux-x86_64-3.8/sisl/linalg/tests
  copying sisl/linalg/tests/test_inv.py -> build/lib.linux-x86_64-3.8/sisl/linalg/tests
  copying sisl/linalg/tests/__init__.py -> build/lib.linux-x86_64-3.8/sisl/linalg/tests
  creating build/lib.linux-x86_64-3.8/sisl/physics/tests
  copying sisl/physics/tests/test_dynamical_matrix.py -> build/lib.linux-x86_64-3.8/sisl/physics/tests
  copying sisl/physics/tests/test_self_energy.py -> build/lib.linux-x86_64-3.8/sisl/physics/tests
  copying sisl/physics/tests/test_density_matrix.py -> build/lib.linux-x86_64-3.8/sisl/physics/tests
  copying sisl/physics/tests/test_overlap.py -> build/lib.linux-x86_64-3.8/sisl/physics/tests
  copying sisl/physics/tests/test_state.py -> build/lib.linux-x86_64-3.8/sisl/physics/tests
  copying sisl/physics/tests/test_hamiltonian.py -> build/lib.linux-x86_64-3.8/sisl/physics/tests
  copying sisl/physics/tests/test_spin.py -> build/lib.linux-x86_64-3.8/sisl/physics/tests
  copying sisl/physics/tests/test_brillouinzone.py -> build/lib.linux-x86_64-3.8/sisl/physics/tests
  copying sisl/physics/tests/test_distribution.py -> build/lib.linux-x86_64-3.8/sisl/physics/tests
  copying sisl/physics/tests/test_physics_sparse.py -> build/lib.linux-x86_64-3.8/sisl/physics/tests
  copying sisl/physics/tests/__init__.py -> build/lib.linux-x86_64-3.8/sisl/physics/tests
  copying sisl/physics/tests/test_energy_density_matrix.py -> build/lib.linux-x86_64-3.8/sisl/physics/tests
  copying sisl/physics/tests/test_bloch.py -> build/lib.linux-x86_64-3.8/sisl/physics/tests
  creating build/lib.linux-x86_64-3.8/sisl/unit/tests
  copying sisl/unit/tests/test_unit.py -> build/lib.linux-x86_64-3.8/sisl/unit/tests
  copying sisl/unit/tests/test_unit_siesta.py -> build/lib.linux-x86_64-3.8/sisl/unit/tests
  copying sisl/unit/tests/__init__.py -> build/lib.linux-x86_64-3.8/sisl/unit/tests
  creating build/lib.linux-x86_64-3.8/sisl/viz/plotly
  copying sisl/viz/plotly/_templates.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly
  copying sisl/viz/plotly/_input_field.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly
  copying sisl/viz/plotly/configurable.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly
  copying sisl/viz/plotly/session.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly
  copying sisl/viz/plotly/_user_customs.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly
  copying sisl/viz/plotly/_plotables.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly
  copying sisl/viz/plotly/_presets.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly
  copying sisl/viz/plotly/_doc_updater.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly
  copying sisl/viz/plotly/_shortcuts.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly
  copying sisl/viz/plotly/plot.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly
  copying sisl/viz/plotly/_express.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly
  copying sisl/viz/plotly/__init__.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly
  copying sisl/viz/plotly/splot.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly
  copying sisl/viz/plotly/plotutils.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly
  creating build/lib.linux-x86_64-3.8/sisl/viz/plotly/plots
  copying sisl/viz/plotly/plots/bands.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/plots
  copying sisl/viz/plotly/plots/grid.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/plots
  copying sisl/viz/plotly/plots/bond_length.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/plots
  copying sisl/viz/plotly/plots/fatbands.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/plots
  copying sisl/viz/plotly/plots/forces.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/plots
  copying sisl/viz/plotly/plots/geometry.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/plots
  copying sisl/viz/plotly/plots/pdos.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/plots
  copying sisl/viz/plotly/plots/__init__.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/plots
  creating build/lib.linux-x86_64-3.8/sisl/viz/plotly/input_fields
  copying sisl/viz/plotly/input_fields/rangeslider.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/input_fields
  copying sisl/viz/plotly/input_fields/array.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/input_fields
  copying sisl/viz/plotly/input_fields/aiida_node.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/input_fields
  copying sisl/viz/plotly/input_fields/text.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/input_fields
  copying sisl/viz/plotly/input_fields/list.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/input_fields
  copying sisl/viz/plotly/input_fields/dropdown.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/input_fields
  copying sisl/viz/plotly/input_fields/sisl_obj.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/input_fields
  copying sisl/viz/plotly/input_fields/range.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/input_fields
  copying sisl/viz/plotly/input_fields/number.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/input_fields
  copying sisl/viz/plotly/input_fields/queries.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/input_fields
  copying sisl/viz/plotly/input_fields/programatic.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/input_fields
  copying sisl/viz/plotly/input_fields/color.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/input_fields
  copying sisl/viz/plotly/input_fields/switch.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/input_fields
  copying sisl/viz/plotly/input_fields/__init__.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/input_fields
  creating build/lib.linux-x86_64-3.8/sisl/viz/plotly/tests
  copying sisl/viz/plotly/tests/test_session.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/tests
  copying sisl/viz/plotly/tests/test_plot.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/tests
  copying sisl/viz/plotly/tests/test_namedhistory.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/tests
  copying sisl/viz/plotly/tests/__init__.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/tests
  creating build/lib.linux-x86_64-3.8/sisl/viz/plotly/sessions
  copying sisl/viz/plotly/sessions/blank.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/sessions
  copying sisl/viz/plotly/sessions/__init__.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/sessions
  creating build/lib.linux-x86_64-3.8/sisl/viz/plotly/plots/experimental
  copying sisl/viz/plotly/plots/experimental/ldos.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/plots/experimental
  copying sisl/viz/plotly/plots/experimental/__init__.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/plots/experimental
  creating build/lib.linux-x86_64-3.8/sisl/viz/plotly/plots/tests
  copying sisl/viz/plotly/plots/tests/test_plots.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/plots/tests
  copying sisl/viz/plotly/plots/tests/test_geometry.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/plots/tests
  copying sisl/viz/plotly/plots/tests/test_bands.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/plots/tests
  copying sisl/viz/plotly/plots/tests/conftest.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/plots/tests
  copying sisl/viz/plotly/plots/tests/test_grid.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/plots/tests
  copying sisl/viz/plotly/plots/tests/test_fatbands.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/plots/tests
  copying sisl/viz/plotly/plots/tests/test_pdos.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/plots/tests
  copying sisl/viz/plotly/plots/tests/test_bondlengthmap.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/plots/tests
  copying sisl/viz/plotly/plots/tests/__init__.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/plots/tests
  creating build/lib.linux-x86_64-3.8/sisl/viz/plotly/sessions/tests
  copying sisl/viz/plotly/sessions/tests/test_sessions.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/sessions/tests
  copying sisl/viz/plotly/sessions/tests/__init__.py -> build/lib.linux-x86_64-3.8/sisl/viz/plotly/sessions/tests
  creating build/lib.linux-x86_64-3.8/sisl_toolbox
  creating build/lib.linux-x86_64-3.8/sisl_toolbox/siesta
  copying toolbox/siesta/__init__.py -> build/lib.linux-x86_64-3.8/sisl_toolbox/siesta
  creating build/lib.linux-x86_64-3.8/sisl_toolbox/cli
  copying toolbox/cli/__init__.py -> build/lib.linux-x86_64-3.8/sisl_toolbox/cli
  creating build/lib.linux-x86_64-3.8/sisl_toolbox/transiesta
  copying toolbox/transiesta/__init__.py -> build/lib.linux-x86_64-3.8/sisl_toolbox/transiesta
  creating build/lib.linux-x86_64-3.8/sisl_toolbox/siesta/atom
  copying toolbox/siesta/atom/_atom.py -> build/lib.linux-x86_64-3.8/sisl_toolbox/siesta/atom
  copying toolbox/siesta/atom/__init__.py -> build/lib.linux-x86_64-3.8/sisl_toolbox/siesta/atom
  creating build/lib.linux-x86_64-3.8/sisl_toolbox/siesta/minimizer
  copying toolbox/siesta/minimizer/_runner.py -> build/lib.linux-x86_64-3.8/sisl_toolbox/siesta/minimizer
  copying toolbox/siesta/minimizer/_minimize.py -> build/lib.linux-x86_64-3.8/sisl_toolbox/siesta/minimizer
  copying toolbox/siesta/minimizer/_atom_basis.py -> build/lib.linux-x86_64-3.8/sisl_toolbox/siesta/minimizer
  copying toolbox/siesta/minimizer/_metric.py -> build/lib.linux-x86_64-3.8/sisl_toolbox/siesta/minimizer
  copying toolbox/siesta/minimizer/_path.py -> build/lib.linux-x86_64-3.8/sisl_toolbox/siesta/minimizer
  copying toolbox/siesta/minimizer/_metric_siesta.py -> build/lib.linux-x86_64-3.8/sisl_toolbox/siesta/minimizer
  copying toolbox/siesta/minimizer/_minimize_siesta.py -> build/lib.linux-x86_64-3.8/sisl_toolbox/siesta/minimizer
  copying toolbox/siesta/minimizer/__init__.py -> build/lib.linux-x86_64-3.8/sisl_toolbox/siesta/minimizer
  copying toolbox/siesta/minimizer/_atom_pseudo.py -> build/lib.linux-x86_64-3.8/sisl_toolbox/siesta/minimizer
  copying toolbox/siesta/minimizer/_variable.py -> build/lib.linux-x86_64-3.8/sisl_toolbox/siesta/minimizer
  creating build/lib.linux-x86_64-3.8/sisl_toolbox/transiesta/poisson
  copying toolbox/transiesta/poisson/fftpoisson_fix.py -> build/lib.linux-x86_64-3.8/sisl_toolbox/transiesta/poisson
  copying toolbox/transiesta/poisson/__init__.py -> build/lib.linux-x86_64-3.8/sisl_toolbox/transiesta/poisson
  running build_ext
  customize UnixCCompiler
  customize UnixCCompiler using EnsureBuildExt
  CCompilerOpt.cc_test_flags[1013] : testing flags (-march=native)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  creating /tmp/tmpm38z9bwh/tmp
  creating /tmp/tmpm38z9bwh/tmp/pip-build-env-q5hr_x1u
  creating /tmp/tmpm38z9bwh/tmp/pip-build-env-q5hr_x1u/overlay
  creating /tmp/tmpm38z9bwh/tmp/pip-build-env-q5hr_x1u/overlay/lib
  creating /tmp/tmpm38z9bwh/tmp/pip-build-env-q5hr_x1u/overlay/lib/python3.8
  creating /tmp/tmpm38z9bwh/tmp/pip-build-env-q5hr_x1u/overlay/lib/python3.8/site-packages
  creating /tmp/tmpm38z9bwh/tmp/pip-build-env-q5hr_x1u/overlay/lib/python3.8/site-packages/numpy
  creating /tmp/tmpm38z9bwh/tmp/pip-build-env-q5hr_x1u/overlay/lib/python3.8/site-packages/numpy/distutils
  creating /tmp/tmpm38z9bwh/tmp/pip-build-env-q5hr_x1u/overlay/lib/python3.8/site-packages/numpy/distutils/checks
  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-march=native'
  CCompilerOpt.cc_test_flags[1013] : testing flags (-O3)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-O3'
  CCompilerOpt.cc_test_flags[1013] : testing flags (-Werror)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-Werror'
  CCompilerOpt.__init__[1701] : check requested baseline
  CCompilerOpt.cc_test_flags[1013] : testing flags (-msse)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-msse'
  CCompilerOpt.cc_test_flags[1013] : testing flags (-msse2)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-msse2'
  CCompilerOpt.feature_test[1466] : testing feature 'SSE' with flags (-msse -msse2)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-msse -msse2 -Werror'
  CCompilerOpt.feature_test[1466] : testing feature 'SSE2' with flags (-msse -msse2)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-msse -msse2 -Werror'
  CCompilerOpt.cc_test_flags[1013] : testing flags (-msse3)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-msse3'
  CCompilerOpt.feature_test[1466] : testing feature 'SSE3' with flags (-msse -msse2 -msse3)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-msse -msse2 -msse3 -Werror'
  CCompilerOpt.__init__[1710] : check requested dispatch-able features
  CCompilerOpt.cc_test_flags[1013] : testing flags (-mssse3)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-mssse3'
  CCompilerOpt.feature_test[1466] : testing feature 'SSSE3' with flags (-msse -msse2 -msse3 -mssse3)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-msse -msse2 -msse3 -mssse3 -Werror'
  CCompilerOpt.cc_test_flags[1013] : testing flags (-msse4.1)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-msse4.1'
  CCompilerOpt.cc_test_flags[1013] : testing flags (-mpopcnt)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-mpopcnt'
  CCompilerOpt.cc_test_flags[1013] : testing flags (-msse4.2)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-msse4.2'
  CCompilerOpt.cc_test_flags[1013] : testing flags (-mavx)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-mavx'
  CCompilerOpt.cc_test_flags[1013] : testing flags (-mf16c)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-mf16c'
  CCompilerOpt.cc_test_flags[1013] : testing flags (-mfma)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-mfma'
  CCompilerOpt.cc_test_flags[1013] : testing flags (-mavx2)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-mavx2'
  CCompilerOpt.cc_test_flags[1013] : testing flags (-mavx512f)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-mavx512f'
  CCompilerOpt.cc_test_flags[1013] : testing flags (-mavx512cd)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-mavx512cd'
  CCompilerOpt.feature_test[1466] : testing feature 'AVX512CD' with flags (-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mavx512cd)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mavx512cd -Werror'
  CCompilerOpt.feature_test[1466] : testing feature 'FMA3' with flags (-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -Werror'
  CCompilerOpt.feature_test[1466] : testing feature 'AVX' with flags (-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -Werror'
  CCompilerOpt.feature_test[1466] : testing feature 'SSE41' with flags (-msse -msse2 -msse3 -mssse3 -msse4.1)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -Werror'
  CCompilerOpt.cc_test_flags[1013] : testing flags (-mavx512er -mavx512pf)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-mavx512er -mavx512pf'
  CCompilerOpt.feature_test[1466] : testing feature 'AVX512_KNL' with flags (-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mavx512cd -mavx512er -mavx512pf)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mavx512cd -mavx512er -mavx512pf -Werror'
  CCompilerOpt.feature_test[1466] : testing feature 'F16C' with flags (-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -Werror'
  CCompilerOpt.feature_test[1466] : testing feature 'AVX2' with flags (-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mavx2)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mavx2 -Werror'
  CCompilerOpt.feature_test[1466] : testing feature 'AVX512F' with flags (-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -Werror'
  CCompilerOpt.feature_test[1466] : testing feature 'SSE42' with flags (-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -Werror'
  CCompilerOpt.feature_test[1466] : testing feature 'POPCNT' with flags (-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -Werror'
  CCompilerOpt.cc_test_flags[1013] : testing flags (-mavx5124fmaps -mavx5124vnniw -mavx512vpopcntdq)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-mavx5124fmaps -mavx5124vnniw -mavx512vpopcntdq'
  CCompilerOpt.feature_test[1466] : testing feature 'AVX512_KNM' with flags (-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mavx512cd -mavx512er -mavx512pf -mavx5124fmaps -mavx5124vnniw -mavx512vpopcntdq)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mavx512cd -mavx512er -mavx512pf -mavx5124fmaps -mavx5124vnniw -mavx512vpopcntdq -Werror'
  CCompilerOpt.cc_test_flags[1013] : testing flags (-mavx512vl -mavx512bw -mavx512dq)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-mavx512vl -mavx512bw -mavx512dq'
  CCompilerOpt.cc_test_flags[1013] : testing flags (-mavx512ifma -mavx512vbmi)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-mavx512ifma -mavx512vbmi'
  CCompilerOpt.feature_test[1466] : testing feature 'AVX512_CNL' with flags (-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq -mavx512ifma -mavx512vbmi)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq -mavx512ifma -mavx512vbmi -Werror'
  CCompilerOpt.cc_test_flags[1013] : testing flags (-mavx512vnni)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-mavx512vnni'
  CCompilerOpt.dist_test[581] : CCompilerOpt._dist_test_spawn[716] : Command (gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c /tmp/pip-build-env-q5hr_x1u/overlay/lib/python3.8/site-packages/numpy/distutils/checks/test_flags.c -o /tmp/tmpm38z9bwh/tmp/pip-build-env-q5hr_x1u/overlay/lib/python3.8/site-packages/numpy/distutils/checks/test_flags.o -MMD -MF /tmp/tmpm38z9bwh/tmp/pip-build-env-q5hr_x1u/overlay/lib/python3.8/site-packages/numpy/distutils/checks/test_flags.o.d -mavx512vnni) failed with exit status 1 output ->
  gcc: error: unrecognized command line option ‘-mavx512vnni’; did you mean ‘-mavx5124vnniw’?

  CCompilerOpt.cc_test_flags[1017] : testing failed
  CCompilerOpt.feature_test[1466] : testing feature 'AVX512_CLX' with flags (-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq -Werror'
  CCompilerOpt.dist_test[581] : CCompilerOpt._dist_test_spawn[716] : Command (gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c /tmp/pip-build-env-q5hr_x1u/overlay/lib/python3.8/site-packages/numpy/distutils/checks/cpu_avx512_clx.c -o /tmp/tmpm38z9bwh/tmp/pip-build-env-q5hr_x1u/overlay/lib/python3.8/site-packages/numpy/distutils/checks/cpu_avx512_clx.o -MMD -MF /tmp/tmpm38z9bwh/tmp/pip-build-env-q5hr_x1u/overlay/lib/python3.8/site-packages/numpy/distutils/checks/cpu_avx512_clx.o.d -msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq -Werror) failed with exit status 1 output ->
  /tmp/pip-build-env-q5hr_x1u/overlay/lib/python3.8/site-packages/numpy/distutils/checks/cpu_avx512_clx.c: In function ‘main’:
  /tmp/pip-build-env-q5hr_x1u/overlay/lib/python3.8/site-packages/numpy/distutils/checks/cpu_avx512_clx.c:20:17: error: implicit declaration of function ‘_mm512_dpbusd_epi32’; did you mean ‘_mm512_4dpwssd_epi32’? [-Werror=implicit-function-declaration]
               a = _mm512_dpbusd_epi32(a, _mm512_setzero_si512(), a);
                   ^~~~~~~~~~~~~~~~~~~
                   _mm512_4dpwssd_epi32
  /tmp/pip-build-env-q5hr_x1u/overlay/lib/python3.8/site-packages/numpy/distutils/checks/cpu_avx512_clx.c:20:15: error: incompatible types when assigning to type ‘__m512i {aka __vector(8) long long int}’ from type ‘int’
               a = _mm512_dpbusd_epi32(a, _mm512_setzero_si512(), a);
                 ^
  cc1: all warnings being treated as errors

  CCompilerOpt.feature_test[1482] : testing failed
  CCompilerOpt.feature_test[1466] : testing feature 'AVX512_SKX' with flags (-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq -Werror'
  CCompilerOpt.__init__[1722] : skip features (SSE2 SSE3 SSE) since its part of baseline
  CCompilerOpt.__init__[1726] : initialize targets groups
  CCompilerOpt.__init__[1728] : parse target group simd_test
  CCompilerOpt._parse_target_tokens[1939] : skip targets (VSX2 FMA4 XOP NEON VSX3 ASIMD VSX) not part of baseline or dispatch-able features
  CCompilerOpt._parse_policy_not_keepbase[2051] : skip baseline features (SSE2)
  CCompilerOpt.generate_dispatch_header[2272] : generate CPU dispatch header: (build/src.linux-x86_64-3.8/numpy/distutils/include/npy_cpu_dispatch_config.h)
  CCompilerOpt.generate_dispatch_header[2281] : dispatch header dir build/src.linux-x86_64-3.8/numpy/distutils/include does not exist, creating it
  CCompilerOpt.feature_extra_checks[1546] : Testing extra checks for feature 'AVX512F' (AVX512F_REDUCE)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -Werror'
  CCompilerOpt.feature_extra_checks[1546] : Testing extra checks for feature 'AVX512_SKX' (AVX512BW_MASK AVX512DQ_MASK)
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq -Werror'
  C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

  compile options: '-I/home/docs/.pyenv/versions/3.8.6/include/python3.8 -c'
  extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq -Werror'
  get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'nv', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor', 'fujitsu']'
  customize Gnu95FCompiler
  Could not locate executable gfortran
  Could not locate executable f95
  customize IntelFCompiler
  Could not locate executable ifort
  Could not locate executable ifc
  customize LaheyFCompiler
  Could not locate executable lf95
  customize PGroupFCompiler
  Could not locate executable pgfortran
  customize NVHPCFCompiler
  Could not locate executable nvfortran
  customize AbsoftFCompiler
  Could not locate executable f90
  Could not locate executable f77
  customize NAGFCompiler
  customize VastFCompiler
  customize CompaqFCompiler
  Could not locate executable fort
  customize IntelItaniumFCompiler
  Could not locate executable efort
  Could not locate executable efc
  customize IntelEM64TFCompiler
  customize GnuFCompiler
  Could not locate executable g77
  customize G95FCompiler
  Could not locate executable g95
  customize PathScaleFCompiler
  Could not locate executable pathf95
  customize NAGFORCompiler
  Could not locate executable nagfor
  customize FujitsuFCompiler
  Could not locate executable frt
  don't know how to compile Fortran code on platform 'posix'
  warning: EnsureBuildExt: f77_compiler=None is not available.

  building 'sisl.io.siesta._siesta' extension
  /tmp/pip-build-env-q5hr_x1u/overlay/lib/python3.8/site-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead
    warnings.warn(

  ########### EXT COMPILER OPTIMIZATION ###########
  Platform      :
    Architecture: x64
    Compiler    : gcc

  CPU baseline  :
    Requested   : 'min'
    Enabled     : SSE SSE2 SSE3
    Flags       : -msse -msse2 -msse3
    Extra checks: none

  CPU dispatch  :
    Requested   : 'max -xop -fma4'
    Enabled     : SSSE3 SSE41 POPCNT SSE42 AVX F16C FMA3 AVX2 AVX512F AVX512CD AVX512_KNL AVX512_KNM AVX512_SKX AVX512_CNL
    Generated   : none
  CCompilerOpt.cache_flush[809] : write cache to path -> /tmp/pip-install-v4owotne/sisl_23af8289d35d410bbb492c23e19d44dd/build/temp.linux-x86_64-3.8/ccompiler_opt_cache_ext.py
  error: extension 'sisl.io.siesta._siesta' has Fortran sources but no Fortran compiler found
  ----------------------------------------
  ERROR: Failed building wheel for sisl
  Building wheel for subprocess32 (setup.py): started
  Building wheel for subprocess32 (setup.py): finished with status 'done'
  Created wheel for subprocess32: filename=subprocess32-3.5.4-py3-none-any.whl size=6502 sha256=195254d190df7159f63a7d2619bdbe9fd3a1b43195a67d1b003a31983e2f2afc
  Stored in directory: /tmp/pip-ephem-wheel-cache-36h5bb53/wheels/9f/69/d1/50b39b308a87998eaf5c1d9095e5a5bd2ad98501e2b7936d36
  Building wheel for voluptuous (setup.py): started
  Building wheel for voluptuous (setup.py): finished with status 'done'
  Created wheel for voluptuous: filename=voluptuous-0.12.2-py3-none-any.whl size=29562 sha256=caf1d8e8fb5ad720cf569d8ac744c6d7c6bec56127180d08f4ffc6ee6643e7ba
  Stored in directory: /tmp/pip-ephem-wheel-cache-36h5bb53/wheels/63/c0/d7/d09babb5ec150707e09d6cabd2850c2ab322b3fb37b3081511
Successfully built aiida-bigdft aiida-cp2k aiida-siesta click-completion configobj ete3 pgsu PyCifRW sqlalchemy-utils wrapt apscheduler pydispatcher aiida-common-workflows aiida-gaussian cclib pymatgen periodictable pyhull subprocess32 voluptuous
Failed to build sisl
ERROR: Could not build wheels for sisl which use PEP 517 and cannot be installed directly
giovannipizzi commented 2 years ago

Maybe @bosonie you have some idea (I guess SISL is a dependency of aiida-siesta?) Seems it cannot build: error: extension 'sisl.io.siesta._siesta' has Fortran sources but no Fortran compiler found, probably we just need to instruct RTD to install Fortran (or have a way to install sisl without compiling, that's going to be even faster?)

Also, when did this change?

giovannipizzi commented 2 years ago

(The first PR where it fails is #205, but most probably it's due to a dependency change in some dependency, between 3 and 5 months ago (the two builds that resp. failed and succeeded))

sphuber commented 2 years ago

We had already encountered this problem before with sisl requiring a fortran compiler to be built, which I think is not ideal for a Python package, but apparently it is not easy to change for them or at least they don't want to: https://github.com/zerothi/sisl/issues/348

sphuber commented 2 years ago

Looking at the docs of RTD, it doesn't seem that it is possible to install custom system requirements. Here they say that you cannot even install C-libraries, which is typically needed for Python code containing C-extensions. I take that to mean that installing a Fortran compiler is definitely not supported.

sphuber commented 2 years ago

Maybe we can use this Sphinx feature though: https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html#confval-autodoc_mock_imports Not sure if mocking the imports for either sisl or aiida-siesta will prevent the setup from trying to build sisl.

giovannipizzi commented 2 years ago

The mocking feature seems nice! I'd be confident that sisl is not required for the docs, but @bosonie can confirm (and it seems easy to setup and test?)