put opentree on conda-forge #23
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Merged
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I just submitted a PR with a draft meta.yaml file, if helpful. |
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Thanks! I merged it to development and updated it. 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. |
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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.
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Ah - it's because we tagged it but never created a new release on GitHub! I just fixed that. |
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👍
… 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.
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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). However, when I try to run the tests using Any ideas? |
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gave up on local testing, submitted a PR and am letting the CI test it! conda-forge/staged-recipes#20097 |
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🤞 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 <conda-forge/staged-recipes#20097>
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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! |
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Ah nice! I will take a look this week. I was away last week and am digging out! |
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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?
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Hi Mike, It doesn't seem like it is even trying any of the recipes 🤔 (the other ones happened to be in staged-recipes when I forked it) Click to expand verbose output |
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Aha! Progress. Verbose below, but the key part is:
Nose and dendropy can be installed using: But on a quick google I don't see how to add channels to the meta.yml Click to expand verbose output |
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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)
<paste>
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
</paste>
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 <module>
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']"}
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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!
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