Fix/relax parmed pins - Githubissues

conda-forge / ambertools-feedstock

A conda-smithy repository for ambertools.

BSD 3-Clause "New" or "Revised" License

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Fix/relax parmed pins #105

Closed mikemhenry closed 1 year ago

mikemhenry commented 1 year ago

Checklist

[ ] Used a personal fork of the feedstock to propose changes
[ ] Bumped the build number (if the version is unchanged)
[ ] Reset the build number to 0 (if the version changed)
[ ] Re-rendered with the latest conda-smithy (Use the phrase code>@<space/conda-forge-admin, please rerender in a comment in this PR for automated rerendering)
[ ] Ensured the license file is being packaged.

conda-forge-webservices[bot] commented 1 year ago

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipe) and found it was in an excellent condition.

I do have some suggestions for making it better though...

For recipe:

License is not an SPDX identifier (or a custom LicenseRef) nor an SPDX license expression.

Documentation on acceptable licenses can be found here.

mikemhenry commented 1 year ago

Traceback (most recent call last):
  File "/home/conda/feedstock_root/build_artifacts/ambertools_1680042506198/test_tmp/run_test.py", line 14, in <module>
    import sander
  File "/home/conda/feedstock_root/build_artifacts/ambertools_1680042506198/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/python3.10/site-packages/sander/__init__.py", line 5, in <module>
    from parmed.utils.six import string_types
ModuleNotFoundError: No module named 'parmed.utils.six'

Going to see if I can patch this or fix upstream

mattwthompson commented 1 year ago

Commenting because I'm curious how this works.

I thought the vendored version wasn't built? https://github.com/conda-forge/ambertools-feedstock/blob/ed56ef1fd7158c287d6374342dde9ff09e89032f/recipe/patches/do_not_install_vendored_parmed.patch

ijpulidos commented 1 year ago

@mattwthompson You are right, the issue here is that you can get conflicting environments if you try to install parmed 4 in them. An old version of ambertools with the vendored parmed will get pulled (such as 20.9 in our case in https://github.com/choderalab/perses/actions/runs/4550979162/jobs/8024534545#step:7:51

jaimergp commented 1 year ago

Is AT 22 known to be compatible with parmed 4? Otherwise this cannot be accepted.

swails commented 1 year ago

Unfortunately there is an import of parmed.utils.six inside pysander that renders pysander incompatible with ParmEd 4.

I'll prepare an update to AmberTools 22 that will fix this incompatibility (although it may be helpful to note that AmberTools 23 should be released this week and actually vendors ParmEd 4.0.0 and will be fully compatible with ParmEd >4.0.0,<5.0.0a.

jaimergp commented 1 year ago

I updated the parmed pins on #102, thanks @swails

mikemhenry commented 1 year ago

Closing in favor of https://github.com/conda-forge/ambertools-feedstock/pull/108