jaimergp
commented
3 months ago As a workaround, can you use grayskull instead of conda skeleton?
Open Mathias-Boulanger opened 3 months ago
Mathias-Boulanger
commented
3 months ago Yes, I tried grayskull and I succeeded to create the recipe (and went through local test) for one of the dependency
of the pod5 package called: vbz-h5py-plugin.
But the recipe for the pod5 package failed upon testing mainly due to a dependency called lib-pod5 that is not available on conda-forge.
When I try to use grayskull to create lib-pod5 that is available on PyPi I got this error:
(condaforge) [boulange@seneca recipes]$ grayskull pypi lib-pod5
#### Initializing recipe for lib-pod5 (pypi) ####
Recovering metadata from pypi...
Traceback (most recent call last):
File "/g/krebs/boulanger/miniconda3/envs/condaforge/bin/grayskull", line 10, in <module>
sys.exit(main())
^^^^^^
File "/g/krebs/boulanger/miniconda3/envs/condaforge/lib/python3.12/site-packages/grayskull/main.py", line 277, in main
generate_recipes_from_list(args.pypi_packages, args)
File "/g/krebs/boulanger/miniconda3/envs/condaforge/lib/python3.12/site-packages/grayskull/main.py", line 300, in generate_recipes_from_list
recipe, config = create_python_recipe(
^^^^^^^^^^^^^^^^^^^^^
File "/g/krebs/boulanger/miniconda3/envs/condaforge/lib/python3.12/site-packages/grayskull/main.py", line 335, in create_python_recipe
GrayskullFactory.create_recipe(
File "/g/krebs/boulanger/miniconda3/envs/condaforge/lib/python3.12/site-packages/grayskull/base/factory.py", line 46, in create_recipe
GrayskullFactory.REGISTERED_STRATEGY[repo_type.lower()].fetch_data(
File "/g/krebs/boulanger/miniconda3/envs/condaforge/lib/python3.12/site-packages/grayskull/strategy/pypi.py", line 62, in fetch_data
update_recipe(recipe, config, sections or ALL_SECTIONS)
File "/g/krebs/boulanger/miniconda3/envs/condaforge/lib/python3.12/site-packages/grayskull/strategy/pypi.py", line 499, in update_recipe
metadata = get_metadata(recipe, config)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/g/krebs/boulanger/miniconda3/envs/condaforge/lib/python3.12/site-packages/grayskull/strategy/pypi.py", line 350, in get_metadata
sdist_metadata, pypi_metadata = get_origin_wise_metadata(config)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/g/krebs/boulanger/miniconda3/envs/condaforge/lib/python3.12/site-packages/grayskull/strategy/pypi.py", line 234, in get_origin_wise_metadata
pypi_metadata = get_pypi_metadata(config)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/g/krebs/boulanger/miniconda3/envs/condaforge/lib/python3.12/site-packages/grayskull/strategy/pypi.py", line 277, in get_pypi_metadata
raise AttributeError(f"There is no sdist package on pypi for {config.name}.")
AttributeError: There is no sdist package on pypi for lib-pod5.Thank you for your idea!
jaimergp
commented
3 months ago You can try to use the GH repo for lib-pod5 as a the source. That said, it looks like a C++ heavy package so it won't be one of those trivial packaging tasks :P
Mathias-Boulanger
commented
3 months ago Indeed, my first experience trying make conda package is not smooth as I though it would be...
The pod5 project is also located on GH here Do you think I will have more chance to create recipe from this URL?
Thank you the suggestion.
Checklist
What happened?
Dear conda devs,
It's my first time trying to contribute to conda framework by creating a conda package. The idea is to just create a package for the Nanopore
pod5python tool kit available on PyPi.For this purpose I used this command:
conda skeleton pypi --version 0.3.10 pod5but I got this error:If I understood correctly this is the
setuptoolspackage that using a deprecated syntaxyaml.safe_dump()from theruamel/yamlpackage.Do you have any idea how to fix this? Please let me know if I posted this on the wrong repo or if I should address this issue to anyone else...
Thank you for your help.
Full error log:
Conda Info
Conda Config
Conda list
Additional Context
No response