search

OpenTreeOfLife / python-opentree

Python package for working with Open Tree of Life webservices and artifacts. Importable as opentree
BSD 2-Clause "Simplified" License
5 stars 5 forks source link

put opentree on conda-forge #23

Open harmsm opened 2 years ago

harmsm commented 2 years ago

This library is extraordinarily useful. Would you be willing to make it installable by conda as well as pip? My lab is working on an ancestral sequence reconstruction pipeline that relies on opentree, as well as some conda-only packages. It would be useful to be able to give users an option to install the whole pipeline with conda.

I would be happy to take point on submitting to conda-forge if helpful and okay with you.

Thanks!

harmsm commented 2 years ago

I just submitted a PR with a draft meta.yaml file, if helpful.

snacktavish commented 2 years ago

Thanks! I merged it to development and updated it. https://github.com/OpenTreeOfLife/python-opentree/blob/development/meta.yaml

I have started walking through the steps at https://conda-forge.org/docs/maintainer/adding_pkgs.html

Was there a reason you used v0.0.3 for the meta.yml? I figured I would just submit it with v1.0.1, (honestly it reminds me that we should submit a newer release to pypi... but one thing at time) but if there is a reason to start with the 0.0.3 that is fine too.

harmsm commented 2 years ago

Oops, copied in wrong version number when making the template. No reason at all, in other words….

On Aug 15, 2022, at 11:51 AM, Emily Jane McTavish @.***> wrote:

Thanks! I merged it to development and updated it. https://github.com/OpenTreeOfLife/python-opentree/blob/development/meta.yaml https://github.com/OpenTreeOfLife/python-opentree/blob/development/meta.yaml I have started walking through the steps at https://conda-forge.org/docs/maintainer/adding_pkgs.html https://conda-forge.org/docs/maintainer/adding_pkgs.html Was there a reason you used v0.0.3 for the meta.yml? I figured I would just submit it with v1.0.1, (honestly it reminds me that we should submit a newer release to pypi... but one thing at time) but if there is a reason to start with the 0.0.3 that is fine too.

— Reply to this email directly, view it on GitHub https://github.com/OpenTreeOfLife/python-opentree/issues/23#issuecomment-1215607410, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABFZA6VLDEL5YY57R2HTD53VZKGR5ANCNFSM555K47KQ. You are receiving this because you authored the thread.

snacktavish commented 2 years ago

Ah - it's because we tagged it but never created a new release on GitHub! I just fixed that.

harmsm commented 2 years ago

👍

On Aug 15, 2022, at 12:53 PM, Emily Jane McTavish @.***> wrote:

Ah - it's because we tagged it but never created a new release on GitHub! I just fixed that.

— Reply to this email directly, view it on GitHub https://github.com/OpenTreeOfLife/python-opentree/issues/23#issuecomment-1215713029, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABFZA6R2I2XJ2MRYPORI2LTVZKN35ANCNFSM555K47KQ. You are receiving this because you authored the thread.

snacktavish commented 2 years ago

I am trying to locally test my recipe before submitting a PR to staged recipes (as described in https://conda-forge.org/docs/maintainer/adding_pkgs.html#staging-test-locally). I have forked the repo, and updated the recipe in /recipes in https://github.com/snacktavish/staged-recipes

However, when I try to run the tests using python build-locally.py from the top level dir, a bunch of stuff runs (I could share output), but at the end I get "There are no tempfile(s) to remove. There are no logfile(s) to remove. Found no recipes to build".

Any ideas?

snacktavish commented 2 years ago

gave up on local testing, submitted a PR and am letting the CI test it! https://github.com/conda-forge/staged-recipes/pull/20097

harmsm commented 2 years ago

🤞 Thanks for working on it!

On Aug 16, 2022, at 3:01 PM, Emily Jane McTavish @.***> wrote:

gave up on local testing, submitted a PR and am letting the CI test it! conda-forge/staged-recipes#20097 https://github.com/conda-forge/staged-recipes/pull/20097 — Reply to this email directly, view it on GitHub https://github.com/OpenTreeOfLife/python-opentree/issues/23#issuecomment-1217214275, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABFZA6SY5XKVRWNTYT7P7A3VZQFTLANCNFSM555K47KQ. You are receiving this because you authored the thread.

harmsm commented 2 years ago

I noticed this is stalled out on conda-forge. When I requested the conda-forge repo I did not realize that all dependencies had to be on conda-forge, rather than just visible on conda via some channel. It seems like bioconda will be a more flexible option given dendropy is already on bioconda, not conda-forge.

I created a recipe file for bioconda and have a fork ready for a PR against bioconda master. If you like, I can do the PR. (I tried to test locally, but bioconda-utils seems to be very, very broken. It relies on an apparently abandoned GO program to interface with docker???)

Thanks!

snacktavish commented 2 years ago

Ah nice! I will take a look this week. I was away last week and am digging out!

harmsm commented 1 year ago

Unfortunately, I’m my package is also my first conda-forge submission. I didn’t even get to that step before I hit the snag of having a few non-conda packages in my dependency tree.

I’ve done a fair amount in conda, so maybe I would have ideas seeing output. Could you post output spew?

Thanks!

On Aug 15, 2022, at 12:58 PM, Emily Jane McTavish @.***> wrote:

I am trying to locally test my recipe before submitting a PR to staged recipes (as described in https://conda-forge.org/docs/maintainer/adding_pkgs.html#staging-test-locally https://conda-forge.org/docs/maintainer/adding_pkgs.html#staging-test-locally). I have forked the repo, and updated the recipe in /recipes in https://github.com/snacktavish/staged-recipes https://github.com/snacktavish/staged-recipes However, when I try to run the tests using python build-locally.py from the top level dir, a bunch of stuff runs (I could share output), but at the end I get "There are no tempfile(s) to remove. There are no logfile(s) to remove. Found no recipes to build".

Any ideas?

— Reply to this email directly, view it on GitHub https://github.com/OpenTreeOfLife/python-opentree/issues/23#issuecomment-1215723420, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABFZA6T4UJQNATKBOQPH3X3VZKONDANCNFSM555K47KQ. You are receiving this because you authored the thread.

snacktavish commented 1 year ago

Hi Mike, Sorry for dropping the ball on this! I suspect there is just an issue with my setup that it isn't even trying to build this recipe when I run build-locally.py, but here's all the output.

It doesn't seem like it is even trying any of the recipes :thinking: (the other ones happened to be in staged-recipes when I forked it)

$ ls recipes/
example  perl-file-chdir  perl-mime-base64  python-opentree
Click to expand verbose output ``` $ python build-locally.py valid configs are {'win64', 'linux64_cuda102', 'linux64', 'osx64', 'linux64_cuda110', 'linux64_cuda111', 'linux64_cuda112'} config not selected, please choose from the following: 1. linux64 2. linux64_cuda102 3. linux64_cuda110 4. linux64_cuda111 5. linux64_cuda112 6. osx64 7. win64 > 1 selected linux64 Client: Context: default Debug Mode: false Server: Containers: 16 Running: 0 Paused: 0 Stopped: 16 Images: 97 Server Version: 20.10.12 Storage Driver: overlay2 Backing Filesystem: extfs Supports d_type: true Native Overlay Diff: true userxattr: false Logging Driver: json-file Cgroup Driver: systemd Cgroup Version: 2 Plugins: Volume: local Network: bridge host ipvlan macvlan null overlay Log: awslogs fluentd gcplogs gelf journald json-file local logentries splunk syslog Swarm: inactive Runtimes: io.containerd.runtime.v1.linux runc io.containerd.runc.v2 Default Runtime: runc Init Binary: docker-init containerd version: runc version: init version: Security Options: apparmor seccomp Profile: default cgroupns Kernel Version: 5.15.0-48-generic Operating System: Ubuntu 22.04.1 LTS OSType: linux Architecture: x86_64 CPUs: 8 Total Memory: 15.31GiB Name: byatt ID: YN25:ULNR:5DVO:HSYD:WVKW:FMBM:ZEZ2:YQZE:R6QW:BL5U:KHSD:BFEY Docker Root Dir: /var/lib/docker Debug Mode: false Username: mctavishlab Registry: https://index.docker.io/v1/ Labels: Experimental: false Insecure Registries: 127.0.0.0/8 Live Restore Enabled: false .scripts/run_docker_build.sh: line 24: shyaml: command not found WARNING: DOCKER_IMAGE variable not set and shyaml not installed. Trying to parse with coreutils Using default tag: latest latest: Pulling from condaforge/linux-anvil-cos7-x86_64 2d473b07cdd5: Already exists dadc05df4b32: Pull complete Digest: sha256:1c1b355ecab912c157741dcd971f1db9d6d6fe9f0393f13e0b54828e6f85bb57 Status: Downloaded newer image for quay.io/condaforge/linux-anvil-cos7-x86_64:latest quay.io/condaforge/linux-anvil-cos7-x86_64:latest useradd: warning: the home directory already exists. Not copying any file from skel directory into it. + export PYTHONUNBUFFERED=1 + PYTHONUNBUFFERED=1 + cat + cp -r /home/conda/staged-recipes /home/conda/staged-recipes-copy + find /home/conda/staged-recipes-copy/recipes -maxdepth 1 -name .DS_Store -delete + echo 'Pending recipes.' Pending recipes. + ls -la /home/conda/staged-recipes-copy/recipes total 24 drwxr-xr-x 6 conda conda 4096 Oct 11 17:13 . drwxr-xr-x 10 conda conda 4096 Oct 11 17:13 .. drwxr-xr-x 2 conda conda 4096 Oct 11 17:13 example drwxr-xr-x 2 conda conda 4096 Oct 11 17:13 perl-file-chdir drwxr-xr-x 2 conda conda 4096 Oct 11 17:13 perl-mime-base64 drwxr-xr-x 2 conda conda 4096 Oct 11 17:13 python-opentree + echo 'Finding recipes merged in main and removing them from the build.' Finding recipes merged in main and removing them from the build. + pushd /home/conda/staged-recipes/recipes + '[' False == True ']' + git ls-tree --name-only main -- . + xargs -I '{}' sh -c 'rm -rf ~/staged-recipes-copy/recipes/{} && echo Removing recipe: {}' Removing recipe: example Removing recipe: perl-file-chdir Removing recipe: perl-mime-base64 Removing recipe: python-opentree + popd + conda index /home/conda/staged-recipes/build_artifacts + mamba install --yes --quiet 'conda>4.7.12' 'conda-forge-ci-setup=3.*' conda-forge-pinning networkx=2.4 'conda-build>=3.16' boa __ __ __ __ / \ / \ / \ / \ / \/ \/ \/ \ ███████████████/ /██/ /██/ /██/ /████████████████████████ / / \ / \ / \ / \ \____ / / \_/ \_/ \_/ \ o \__, / _/ \_____/ ` |/ ███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗ ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗ ██╔████╔██║███████║██╔████╔██║██████╔╝███████║ ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║ ██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║ ╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝ mamba (0.27.0) supported by @QuantStack GitHub: https://github.com/mamba-org/mamba Twitter: https://twitter.com/QuantStack █████████████████████████████████████████████████████████████ Package Version Build Channel Size ────────────────────────────────────────────────────────────────────────────────────────────────── Install: ────────────────────────────────────────────────────────────────────────────────────────────────── + click 8.1.3 py310hff52083_0 conda-forge/linux-64 152kB + conda-env 2.6.0 1 conda-forge/noarch 2kB + conda-forge-ci-setup 3.21.0 py310hce54274_100 conda-forge/linux-64 44kB + conda-forge-pinning 2022.10.11.03.04.53 hd8ed1ab_0 conda-forge/noarch 22kB + decorator 5.1.1 pyhd8ed1ab_0 conda-forge/noarch 12kB + jq 1.6 h36c2ea0_1000 conda-forge/linux-64 354kB + networkx 2.4 py_1 conda-forge/noarch 1MB + oniguruma 6.9.8 h166bdaf_0 conda-forge/linux-64 440kB + shyaml 0.6.2 pyhd3deb0d_0 conda-forge/noarch 22kB Summary: Install: 9 packages Total download: 2MB ────────────────────────────────────────────────────────────────────────────────────────────────── Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done + export FEEDSTOCK_ROOT=/home/conda/staged-recipes + FEEDSTOCK_ROOT=/home/conda/staged-recipes + export CI_SUPPORT=/home/conda/staged-recipes-copy/.ci_support + CI_SUPPORT=/home/conda/staged-recipes-copy/.ci_support + setup_conda_rc /home/conda/staged-recipes /home/conda/staged-recipes-copy/recipes /home/conda/staged-recipes-copy/.ci_support/linux64.yaml + source run_conda_forge_build_setup ++ export PYTHONUNBUFFERED=1 ++ PYTHONUNBUFFERED=1 ++ conda config --env --set show_channel_urls true ++ conda config --env --set auto_update_conda false ++ conda config --env --set add_pip_as_python_dependency false ++ conda config --env --append aggressive_update_packages ca-certificates ++ conda config --env --remove-key aggressive_update_packages ++ conda config --env --append aggressive_update_packages ca-certificates ++ conda config --env --append aggressive_update_packages certifi ++ export CONDA_BLD_PATH=/home/conda/staged-recipes/build_artifacts ++ CONDA_BLD_PATH=/home/conda/staged-recipes/build_artifacts ++ set +u ++ [[ '' == \d\r\o\n\e ]] ++ [[ '' == \g\i\t\h\u\b\_\a\c\t\i\o\n\s ]] ++ export CPU_COUNT=2 ++ CPU_COUNT=2 +++ cat /home/conda/staged-recipes/conda-forge.yml +++ shyaml get-value channel_priority strict ++ conda config --env --set channel_priority strict ++ [[ ! -z '' ]] ++ '[' '!' -z linux64 ']' ++ '[' '!' -z '' ']' ++ cat /home/conda/staged-recipes-copy/.ci_support/linux64.yaml c_compiler: - gcc cxx_compiler: - gxx fortran_compiler: - gfortran target_platform: - linux-64 channel_sources: - conda-forge docker_image: - quay.io/condaforge/linux-anvil-cos7-x86_64 cuda_compiler_version: - None ++ set -u ++ mkdir -p /opt/conda/etc/conda/activate.d ++ echo 'export CONDA_BLD_PATH='\''/home/conda/staged-recipes/build_artifacts'\''' ++ '[' -n 2 ']' ++ echo 'export CPU_COUNT='\''2'\''' ++ echo 'export PYTHONUNBUFFERED='\''1'\''' +++ cat /home/conda/staged-recipes-copy/.ci_support/linux64.yaml +++ shyaml get-value cuda_compiler_version.0 None ++ CUDA_VERSION=None ++ [[ None != \N\o\n\e ]] ++++ dirname /opt/conda/bin/run_conda_forge_build_setup +++ cd /opt/conda/bin +++ pwd ++ SCRIPT_DIR=/opt/conda/bin ++ source /opt/conda/bin/cross_compile_support.sh ++++ conda info --json ++++ jq -r .platform +++ BUILD_PLATFORM=linux-64 +++ '[' -f /home/conda/staged-recipes-copy/.ci_support/linux64.yaml ']' ++++ cat /home/conda/staged-recipes-copy/.ci_support/linux64.yaml ++++ shyaml get-value target_platform.0 linux-64 +++ HOST_PLATFORM=linux-64 +++ HOST_PLATFORM=linux-64 +++ [[ linux-64 != \l\i\n\u\x\-\6\4 ]] ++ '[' -f /home/conda/staged-recipes-copy/.ci_support/linux64.yaml ']' +++ cat /home/conda/staged-recipes-copy/.ci_support/linux64.yaml +++ shyaml get-value MACOSX_DEPLOYMENT_TARGET.0 0 ++ need_osx_sdk=0 ++ [[ 0 != \0 ]] ++ conda info active environment : base active env location : /opt/conda shell level : 1 user config file : /home/conda/.condarc populated config files : /opt/conda/.condarc /home/conda/.condarc conda version : 22.9.0 conda-build version : 3.22.0 python version : 3.10.6.final.0 virtual packages : __linux=5.15.0=0 __glibc=2.17=0 __unix=0=0 __archspec=1=x86_64 base environment : /opt/conda (writable) conda av data dir : /opt/conda/etc/conda conda av metadata url : None channel URLs : https://conda.anaconda.org/conda-forge/linux-64 https://conda.anaconda.org/conda-forge/noarch package cache : /home/conda/staged-recipes/build_artifacts/pkg_cache /opt/conda/pkgs envs directories : /opt/conda/envs /home/conda/.conda/envs platform : linux-64 user-agent : conda/22.9.0 requests/2.28.1 CPython/3.10.6 Linux/5.15.0-48-generic centos/7.9.2009 glibc/2.17 UID:GID : 1000:1000 netrc file : None offline mode : False ++ conda config --env --show-sources ==> /opt/conda/.condarc <== add_pip_as_python_dependency: False auto_update_conda: False aggressive_update_packages: - ca-certificates - certifi channel_priority: strict channels: - conda-forge show_channel_urls: True ==> /home/conda/.condarc <== pkgs_dirs: - /home/conda/staged-recipes/build_artifacts/pkg_cache - /opt/conda/pkgs channels: - conda-forge show_channel_urls: True conda-build: root-dir: /home/conda/staged-recipes/build_artifacts ==> envvars <== bld_path: /home/conda/staged-recipes/build_artifacts ++ conda list --show-channel-urls # packages in environment at /opt/conda: # # Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge anaconda-client 1.8.0 pyhd8ed1ab_0 conda-forge anyio 3.6.1 pyhd8ed1ab_1 conda-forge attrs 22.1.0 pyh71513ae_1 conda-forge backports 1.0 py_2 conda-forge backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge beautifulsoup4 4.11.1 pyha770c72_0 conda-forge boa 0.12.0 pyha770c72_4 conda-forge brotlipy 0.7.0 py310h5764c6d_1004 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.18.1 h7f98852_0 conda-forge ca-certificates 2022.9.24 ha878542_0 conda-forge certifi 2022.9.24 pyhd8ed1ab_0 conda-forge cffi 1.15.1 py310h255011f_0 conda-forge chardet 5.0.0 py310hff52083_0 conda-forge charset-normalizer 2.1.1 pyhd8ed1ab_0 conda-forge click 8.1.3 py310hff52083_0 conda-forge clyent 1.2.2 py_1 conda-forge colorama 0.4.5 pyhd8ed1ab_0 conda-forge commonmark 0.9.1 py_0 conda-forge conda 22.9.0 py310hff52083_1 conda-forge conda-build 3.22.0 py310hff52083_2 conda-forge conda-env 2.6.0 1 conda-forge conda-forge-ci-setup 3.21.0 py310hce54274_100 conda-forge conda-forge-pinning 2022.10.11.03.04.53 hd8ed1ab_0 conda-forge conda-package-handling 1.9.0 py310h5764c6d_0 conda-forge cryptography 38.0.1 py310h597c629_0 conda-forge curl 7.85.0 h7bff187_0 conda-forge dataclasses 0.8 pyhc8e2a94_3 conda-forge decorator 5.1.1 pyhd8ed1ab_0 conda-forge expat 2.4.9 h27087fc_0 conda-forge filelock 3.8.0 pyhd8ed1ab_0 conda-forge future 0.18.2 py310hff52083_5 conda-forge gettext 0.19.8.1 h27087fc_1009 conda-forge git 2.38.0 pl5321h5fbbf19_0 conda-forge glob2 0.7 py_0 conda-forge icu 70.1 h27087fc_0 conda-forge idna 3.4 pyhd8ed1ab_0 conda-forge importlib-metadata 4.11.4 py310hff52083_0 conda-forge importlib_resources 5.10.0 pyhd8ed1ab_0 conda-forge jinja2 3.1.2 pyhd8ed1ab_1 conda-forge joblib 1.2.0 pyhd8ed1ab_0 conda-forge jq 1.6 h36c2ea0_1000 conda-forge json5 0.9.5 pyh9f0ad1d_0 conda-forge jsonschema 4.16.0 pyhd8ed1ab_0 conda-forge jupyter_core 4.11.1 py310hff52083_0 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge krb5 1.19.3 h3790be6_0 conda-forge ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge libarchive 3.5.2 hb890918_3 conda-forge libcurl 7.85.0 h7bff187_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 h516909a_1 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc-ng 12.1.0 h8d9b700_16 conda-forge libgomp 12.1.0 h8d9b700_16 conda-forge libiconv 1.17 h166bdaf_0 conda-forge liblief 0.12.2 h27087fc_0 conda-forge libmamba 0.27.0 h0dd8ff0_0 conda-forge libmambapy 0.27.0 py310hab0e683_0 conda-forge libnghttp2 1.47.0 hdcd2b5c_1 conda-forge libnsl 2.0.0 h7f98852_0 conda-forge libsolv 0.7.22 h6239696_0 conda-forge libsqlite 3.39.4 h753d276_0 conda-forge libssh2 1.10.0 haa6b8db_3 conda-forge libstdcxx-ng 12.1.0 ha89aaad_16 conda-forge libuuid 2.32.1 h7f98852_1000 conda-forge libxml2 2.9.14 h22db469_4 conda-forge libzlib 1.2.12 h166bdaf_4 conda-forge lz4-c 1.9.3 h9c3ff4c_1 conda-forge lzo 2.10 h516909a_1000 conda-forge mamba 0.27.0 py310hf87f941_0 conda-forge markupsafe 2.1.1 py310h5764c6d_1 conda-forge nbformat 5.6.1 pyhd8ed1ab_0 conda-forge ncurses 6.3 h27087fc_1 conda-forge networkx 2.4 py_1 conda-forge oniguruma 6.9.8 h166bdaf_0 conda-forge openssl 1.1.1q h166bdaf_0 conda-forge patch 2.7.6 h7f98852_1002 conda-forge patchelf 0.15.0 h58526e2_0 conda-forge pcre2 10.37 hc3806b6_1 conda-forge perl 5.32.1 2_h7f98852_perl5 conda-forge pip 22.2.2 pyhd8ed1ab_0 conda-forge pkginfo 1.8.3 pyhd8ed1ab_0 conda-forge pkgutil-resolve-name 1.3.10 pyhd8ed1ab_0 conda-forge prompt-toolkit 3.0.31 pyha770c72_0 conda-forge prompt_toolkit 3.0.31 hd8ed1ab_0 conda-forge psutil 5.9.2 py310h5764c6d_0 conda-forge py-lief 0.12.2 py310hd8f1fbe_0 conda-forge pybind11-abi 4 hd8ed1ab_3 conda-forge pycosat 0.6.3 py310h5764c6d_1010 conda-forge pycparser 2.21 pyhd8ed1ab_0 conda-forge pygments 2.13.0 pyhd8ed1ab_0 conda-forge pyopenssl 22.0.0 pyhd8ed1ab_1 conda-forge pyrsistent 0.18.1 py310h5764c6d_1 conda-forge pysocks 1.7.1 pyha2e5f31_6 conda-forge python 3.10.6 h582c2e5_0_cpython conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python-fastjsonschema 2.16.2 pyhd8ed1ab_0 conda-forge python-libarchive-c 4.0 py310hff52083_1 conda-forge python_abi 3.10 2_cp310 conda-forge pytz 2022.4 pyhd8ed1ab_0 conda-forge pyyaml 6.0 py310h5764c6d_4 conda-forge readline 8.1.2 h0f457ee_0 conda-forge reproc 14.2.3 h7f98852_0 conda-forge reproc-cpp 14.2.3 h9c3ff4c_0 conda-forge requests 2.28.1 pyhd8ed1ab_1 conda-forge rich 12.6.0 pyhd8ed1ab_0 conda-forge ripgrep 13.0.0 h2f28480_2 conda-forge ruamel.yaml 0.17.21 py310h5764c6d_1 conda-forge ruamel.yaml.clib 0.2.6 py310h5764c6d_1 conda-forge ruamel_yaml 0.15.80 py310h5764c6d_1007 conda-forge setuptools 65.4.1 pyhd8ed1ab_0 conda-forge shyaml 0.6.2 pyhd3deb0d_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge sniffio 1.3.0 pyhd8ed1ab_0 conda-forge soupsieve 2.3.2.post1 pyhd8ed1ab_0 conda-forge su-exec 0.2 h166bdaf_1003 conda-forge tini 0.19.0 h166bdaf_1 conda-forge tk 8.6.12 h27826a3_0 conda-forge toml 0.10.2 pyhd8ed1ab_0 conda-forge toolz 0.12.0 pyhd8ed1ab_0 conda-forge tqdm 4.64.1 pyhd8ed1ab_0 conda-forge traitlets 5.4.0 pyhd8ed1ab_0 conda-forge typing_extensions 4.4.0 pyha770c72_0 conda-forge tzdata 2022d h191b570_0 conda-forge urllib3 1.26.11 pyhd8ed1ab_0 conda-forge watchgod 0.8.2 pyhd8ed1ab_0 conda-forge wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge wheel 0.37.1 pyhd8ed1ab_0 conda-forge xz 5.2.6 h166bdaf_0 conda-forge yaml 0.2.5 h7f98852_2 conda-forge yaml-cpp 0.7.0 h27087fc_2 conda-forge zipp 3.8.1 pyhd8ed1ab_0 conda-forge zstd 1.5.2 h6239696_4 conda-forge + find /home/conda/staged-recipes-copy/recipes -mindepth 2 -maxdepth 2 -type f -name yum_requirements.txt + xargs -n1 cat + grep -v -e '^#' -e '^$' + xargs -r /usr/bin/sudo -n yum install -y + test 1 == 1 + python /home/conda/staged-recipes-copy/.ci_support/build_all.py Updating build index: /home/conda/staged-recipes/build_artifacts Will remove 9 (2.2 MB) tarball(s). Will remove 1 index cache(s). Will remove 26 (495.5 MB) package(s). There are no tempfile(s) to remove. There are no logfile(s) to remove. Found no recipes to build + touch /home/conda/staged-recipes/build_artifacts/conda-forge-build-done ```
snacktavish commented 1 year ago

Aha! Progress. Verbose below, but the key part is:

Unsatisfiable dependencies for platform linux-64: {'nosetests', 'm2r', "dendropy[version='>=4.4.0'] m2r is just for the docs, and nose is for testing which presumably doesn't have to happen on conda, but dendropy is pivotal.

Nose and dendropy can be installed using: conda install -c bioconda dendropy conda install -c conda-forge nose

But on a quick google I don't see how to add channels to the meta.yml

Click to expand verbose output ``` conda build python-opentree/ No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.16 WARNING:conda_build.metadata:No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.16 Adding in variants from internal_defaults INFO:conda_build.variants:Adding in variants from internal_defaults Attempting to finalize metadata for python-opentree INFO:conda_build.metadata:Attempting to finalize metadata for python-opentree Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done BUILD START: ['python-opentree-1.0.1-py_0.tar.bz2'] Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/ejmctavish/.conda/envs/testenv/conda-bld/python-opentree_1665510019295/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p The following NEW packages will be INSTALLED: _libgcc_mutex: 0.1-main _openmp_mutex: 5.1-1_gnu ca-certificates: 2022.07.19-h06a4308_0 certifi: 2022.9.24-py37h06a4308_0 ld_impl_linux-64: 2.38-h1181459_1 libffi: 3.3-he6710b0_2 libgcc-ng: 11.2.0-h1234567_1 libgomp: 11.2.0-h1234567_1 libstdcxx-ng: 11.2.0-h1234567_1 ncurses: 6.3-h5eee18b_3 openssl: 1.1.1q-h7f8727e_0 pip: 22.2.2-py37h06a4308_0 python: 3.7.13-h12debd9_0 readline: 8.1.2-h7f8727e_1 setuptools: 63.4.1-py37h06a4308_0 sqlite: 3.39.3-h5082296_0 tk: 8.6.12-h1ccaba5_0 wheel: 0.37.1-pyhd3eb1b0_0 xz: 5.2.6-h5eee18b_0 zlib: 1.2.12-h5eee18b_3 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... failed Leaving build/test directories: Work: /home/ejmctavish/.conda/envs/testenv/conda-bld/work Test: /home/ejmctavish/.conda/envs/testenv/conda-bld/test_tmp Leaving build/test environments: Test: source activate /home/ejmctavish/.conda/envs/testenv/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh Build: source activate /home/ejmctavish/.conda/envs/testenv/conda-bld/_build_env Traceback (most recent call last): File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda_build/environ.py", line 799, in get_install_actions actions = install_actions(prefix, index, specs, force=True) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/common/io.py", line 86, in decorated return f(*args, **kwds) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/plan.py", line 476, in install_actions txn = solver.solve_for_transaction(prune=prune, ignore_pinned=not pinned) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/core/solve.py", line 159, in solve_for_transaction should_retry_solve) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/core/solve.py", line 200, in solve_for_diff force_remove, should_retry_solve) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/core/solve.py", line 317, in solve_final_state ssc = self._add_specs(ssc) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/core/solve.py", line 607, in _add_specs explicit_pool = ssc.r._get_package_pool(self.specs_to_add) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/resolve.py", line 556, in _get_package_pool pool = self.get_reduced_index(specs) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/common/io.py", line 86, in decorated return f(*args, **kwds) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/resolve.py", line 577, in get_reduced_index explicit_specs, features = self.verify_specs(explicit_specs) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/resolve.py", line 289, in verify_specs raise ResolvePackageNotFound(bad_deps) conda.exceptions.ResolvePackageNotFound: - nosetests - m2r - dendropy[version='>=4.4.0'] During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/ejmctavish/.conda/envs/testenv/bin/conda-build", line 11, in sys.exit(main()) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda_build/cli/main_build.py", line 496, in main execute(sys.argv[1:]) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda_build/cli/main_build.py", line 487, in execute verify=args.verify, variants=args.variants, cache_dir=args.cache_dir) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda_build/api.py", line 195, in build variants=variants File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda_build/build.py", line 3096, in build_tree notest=notest, File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda_build/build.py", line 2131, in build create_build_envs(top_level_pkg, notest) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda_build/build.py", line 2009, in create_build_envs raise e File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda_build/build.py", line 1999, in create_build_envs channel_urls=tuple(m.config.channel_urls)) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda_build/environ.py", line 801, in get_install_actions raise DependencyNeedsBuildingError(exc, subdir=subdir) conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {'nosetests', 'm2r', "dendropy[version='>=4.4.0']"} ```
harmsm commented 1 year ago

Thanks for working on this! (This stuff is no fun, so I really appreciate it).

One question: are you trying to get this up on conda-forge or on bioconda? I originally suggested conda-forge, but that only allows dependencies on conda-forge, which is basically impossible on my end as well.

Bioconda lists the following for their dependencies (https://bioconda.github.io/contributor/guidelines.html#bioconda-recipe-checklist)

There is currently no mechanism to define, in the meta.yaml file, that a particular dependency should come from a particular channel. This means that a recipe must have its dependencies in one of the following: as-yet-unbuilt recipes in the repo but that will be included in the PR conda-forge channel bioconda channel default Anaconda channel

Mike

On Oct 11, 2022, at 10:54 AM, Emily Jane McTavish @.***> wrote:

Aha! Progress. Verbose below, but the key part is:

Unsatisfiable dependencies for platform linux-64: {'nosetests', 'm2r', "dendropy[version='>=4.4.0'] m2r is just for the docs, and nose is for testing which presumably doesn't have to happen on conda, but dendropy is pivotal.

Nose and dendropy can be installed using: conda install -c bioconda dendropy conda install -c conda-forge nose

But on a quick google I don't see how to add channels to the meta.yml

conda build python-opentree/ No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.16 WARNING:conda_build.metadata:No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.16 Adding in variants from internal_defaults INFO:conda_build.variants:Adding in variants from internal_defaults Attempting to finalize metadata for python-opentree INFO:conda_build.metadata:Attempting to finalize metadata for python-opentree Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done BUILD START: ['python-opentree-1.0.1-py_0.tar.bz2'] Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done

Package Plan

environment location: /home/ejmctavish/.conda/envs/testenv/conda-bld/python-opentree_1665510019295/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p

The following NEW packages will be INSTALLED:

_libgcc_mutex:    0.1-main                
_openmp_mutex:    5.1-1_gnu               
ca-certificates:  2022.07.19-h06a4308_0   
certifi:          2022.9.24-py37h06a4308_0
ld_impl_linux-64: 2.38-h1181459_1         
libffi:           3.3-he6710b0_2          
libgcc-ng:        11.2.0-h1234567_1       
libgomp:          11.2.0-h1234567_1       
libstdcxx-ng:     11.2.0-h1234567_1       
ncurses:          6.3-h5eee18b_3          
openssl:          1.1.1q-h7f8727e_0       
pip:              22.2.2-py37h06a4308_0   
python:           3.7.13-h12debd9_0       
readline:         8.1.2-h7f8727e_1        
setuptools:       63.4.1-py37h06a4308_0   
sqlite:           3.39.3-h5082296_0       
tk:               8.6.12-h1ccaba5_0       
wheel:            0.37.1-pyhd3eb1b0_0     
xz:               5.2.6-h5eee18b_0        
zlib:             1.2.12-h5eee18b_3

Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... failed

Leaving build/test directories: Work: /home/ejmctavish/.conda/envs/testenv/conda-bld/work Test: /home/ejmctavish/.conda/envs/testenv/conda-bld/test_tmp Leaving build/test environments: Test: source activate /home/ejmctavish/.conda/envs/testenv/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh Build: source activate /home/ejmctavish/.conda/envs/testenv/conda-bld/_build_env

Traceback (most recent call last): File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda_build/environ.py", line 799, in get_install_actions actions = install_actions(prefix, index, specs, force=True) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/common/io.py", line 86, in decorated return f(*args, *kwds) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/plan.py", line 476, in install_actions txn = solver.solve_for_transaction(prune=prune, ignore_pinned=not pinned) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/core/solve.py", line 159, in solve_for_transaction should_retry_solve) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/core/solve.py", line 200, in solve_for_diff force_remove, should_retry_solve) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/core/solve.py", line 317, in solve_final_state ssc = self._add_specs(ssc) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/core/solve.py", line 607, in _add_specs explicit_pool = ssc.r._get_package_pool(self.specs_to_add) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/resolve.py", line 556, in _get_package_pool pool = self.get_reduced_index(specs) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/common/io.py", line 86, in decorated return f(args, **kwds) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/resolve.py", line 577, in get_reduced_index explicit_specs, features = self.verify_specs(explicit_specs) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda/resolve.py", line 289, in verify_specs raise ResolvePackageNotFound(bad_deps) conda.exceptions.ResolvePackageNotFound:

  • nosetests
  • m2r
  • dendropy[version='>=4.4.0']

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/ejmctavish/.conda/envs/testenv/bin/conda-build", line 11, in sys.exit(main()) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda_build/cli/main_build.py", line 496, in main execute(sys.argv[1:]) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda_build/cli/main_build.py", line 487, in execute verify=args.verify, variants=args.variants, cache_dir=args.cache_dir) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda_build/api.py", line 195, in build variants=variants File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda_build/build.py", line 3096, in build_tree notest=notest, File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda_build/build.py", line 2131, in build create_build_envs(top_level_pkg, notest) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda_build/build.py", line 2009, in create_build_envs raise e File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda_build/build.py", line 1999, in create_build_envs channel_urls=tuple(m.config.channel_urls)) File "/home/ejmctavish/.conda/envs/testenv/lib/python3.7/site-packages/conda_build/environ.py", line 801, in get_install_actions raise DependencyNeedsBuildingError(exc, subdir=subdir) conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {'nosetests', 'm2r', "dendropy[version='>=4.4.0']"} — Reply to this email directly, view it on GitHub https://github.com/OpenTreeOfLife/python-opentree/issues/23#issuecomment-1275066722, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABFZA6RQZ4CHCFDYX6TRULTWCWSU5ANCNFSM555K47KQ. You are receiving this because you authored the thread.