v2.8.0 #68

IAlibay · 2024-11-22T21:54:38Z

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 @conda-forge-admin, please rerender in a comment in this PR for automated rerendering)
Ensured the license file is being packaged.

IAlibay · 2024-11-22T21:55:28Z

@conda-forge-admin, please rerender

conda-forge-admin · 2024-11-22T21:56:54Z

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

I wanted to let you know that I linted all conda-recipes in your PR (recipe/meta.yaml) and found some lint.

Here's what I've got...

For recipe/meta.yaml:

❌ This recipe is using a compiler, which now requires adding a build dependence on {{ stdlib("c") }} as well. Note that this rule applies to each output of the recipe using a compiler. For further details, please see META: {{ stdlib("c") }} migration conda-forge.github.io#2102.

For recipe/meta.yaml:

ℹ️ No valid build backend found for Python recipe for package mdanalysis using pip. Python recipes using pip need to explicitly specify a build backend in the host section. If your recipe has built with only pip in the host section in the past, you likely should add setuptools to the host section of your recipe.
ℹ️ The recipe is not parsable by parser conda-souschef (grayskull). Your recipe may not receive automatic updates and/or may not be compatible with conda-forge's infrastructure. Please check the logs for more information and ensure your recipe can be parsed.
ℹ️ PyPI default URL is now pypi.org, and not pypi.io. You may want to update the default source url.

_{This message was generated by GitHub Actions workflow run https://github.com/conda-forge/conda-forge-webservices/actions/runs/11980776031. Examine the logs at this URL for more detail.}

…nda-forge-pinning 2024.11.22.21.06.17

… v2.8.0

IAlibay · 2024-11-22T22:01:14Z

@conda-forge-admin, please rerender

conda-forge-admin · 2024-11-22T22:01:58Z

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/meta.yaml) and found it was in an excellent condition.

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

For recipe/meta.yaml:

ℹ️ The recipe is not parsable by parser conda-souschef (grayskull). Your recipe may not receive automatic updates and/or may not be compatible with conda-forge's infrastructure. Please check the logs for more information and ensure your recipe can be parsed.

_{This message was generated by GitHub Actions workflow run https://github.com/conda-forge/conda-forge-webservices/actions/runs/12037303447. Examine the logs at this URL for more detail.}

…nda-forge-pinning 2024.11.22.21.06.17

… v2.8.0

IAlibay · 2024-11-22T22:16:23Z

@conda-forge-admin, please rerender

conda-forge-admin · 2024-11-22T22:18:50Z

Hi! This is the friendly automated conda-forge-webservice.

I tried to rerender for you, but it looks like there was nothing to do.

_{This message was generated by GitHub Actions workflow run https://github.com/conda-forge/conda-forge-webservices/actions/runs/11980985833. Examine the logs at this URL for more detail.}

IAlibay · 2024-11-22T22:24:27Z

@conda-forge-admin, please rerender

conda-forge-admin · 2024-11-22T22:27:48Z

Hi! This is the friendly automated conda-forge-webservice.

I tried to rerender for you, but it looks like there was nothing to do.

_{This message was generated by GitHub Actions workflow run https://github.com/conda-forge/conda-forge-webservices/actions/runs/11981087520. Examine the logs at this URL for more detail.}

IAlibay · 2024-11-22T22:36:21Z

@conda-forge-admin, please rerender

conda-forge-admin · 2024-11-22T22:39:44Z

Hi! This is the friendly automated conda-forge-webservice.

I tried to rerender for you, but it looks like there was nothing to do.

_{This message was generated by GitHub Actions workflow run https://github.com/conda-forge/conda-forge-webservices/actions/runs/11981221367. Examine the logs at this URL for more detail.}

orbeckst

LICENSE was properly updated.
numpy 2.0 migration looks good

LGTM, thanks for the update.

orbeckst · 2024-11-22T22:53:50Z

recipe/meta.yaml

    - matplotlib-base >=1.5.1
    - seaborn    # [not ppc64le]
    - netcdf4 >=1.0
-    - biopython >=1.80
+    - biopython >=1.80  # [not py>312]


Does biopython not work for 3.13 yet?

Not as far as I can tell, their migrator is currently up.

orbeckst · 2024-11-22T22:54:18Z

recipe/meta.yaml

-    - {{ pin_compatible('numpy', lower_bound='1.22.3') }}
+    - numpy >=1.23.2


nice — I read the npy 2.0 migrator notes

orbeckst · 2024-11-22T22:54:45Z

recipe/meta.yaml

+  license: LGPL-3.0-or-later
+  license_family: LGPL


big step forward!

orbeckst · 2024-11-22T22:56:48Z

Obviously, we shouldn't merge until all runners build correctly.

IAlibay · 2024-11-22T23:13:23Z

Thanks @orbeckst - the main thing we need to do is make a new release of mdahole2, waterdynamics, and pathsimanalysis.

The former is most important because it has a py<3.13 pin on.

IAlibay · 2024-11-25T15:38:02Z

@conda-forge-admin, please rerender

…nda-forge-pinning 2024.11.25.08.53.39

IAlibay · 2024-11-25T15:52:15Z

@orbeckst we have a weird cycling dependency going on - I'm going to not add python 3.13 support for now and do it as a separate build.

IAlibay · 2024-11-25T15:52:59Z

recipe/meta.yaml

@@ -56,6 +56,9 @@ requirements:
    - pytng >=0.2.3    # [not ppc64le]
    - pyedr >=0.7.1
    - mda-xdrlib
+    - waterdynamics


We need to put a lower pin once we merge the LGPL PR & update the feedstock upstream.

Waterdynamics is now LGPL MDAnalysis/waterdynamics#41

Thanks, just waiting on the waterdynamics feedstock to update and we should be good.

orbeckst · 2024-11-25T17:21:24Z

we have a weird cycling dependency going on - I'm going to not add python 3.13 support for now and do it as a separate build.

Ok – I wouldn't know how to.

Is the issue that the kits depend on MDA and MDA depends on the kits?

IAlibay · 2024-11-25T17:25:07Z

Is the issue that the kits depend on MDA and MDA depends on the kits?

Yup exactly, it's a problematic cyclic dependency - we might need to hurry up a v3.0 release.

orbeckst · 2024-11-25T17:44:50Z

Then perhaps we drop the dependency on kits in MDAnalysis and tell users in an error message that they need to install the kit? I know that this is not how SemVer works but it would fix the problem and be in the spirit of "deprecations".

orbeckst · 2024-11-25T17:46:51Z

Basically, the installation instructions would be

mamba install mdanalysis waterdynamics mdahole2 pathsimanalysis ## did not look up package names

instead of

mamba install mdanalysis

IAlibay · 2024-11-25T17:51:21Z

@orbeckst the issue is that the mdakits themselves need MDAnalysis... so it's just weird packaging wise.

That being said - I think it works for now, at least the checks are passing. The issue was that py3.13 didn't work because it was attempting to first look for a compatible MDA version with py3.13 (for that mdakit) and then failing to resolve. Once 2.8.0, we can create a new build that should work.

orbeckst · 2024-11-25T18:45:20Z

You're in charge here — merge when ready. 🚀

IAlibay · 2024-11-25T22:45:09Z

/azp run

azure-pipelines · 2024-11-25T22:45:17Z

Azure Pipelines successfully started running 1 pipeline(s).

IAlibay · 2024-11-25T22:59:43Z

@conda-forge-admin, please rerender

conda-forge-admin · 2024-11-25T23:02:11Z

Hi! This is the friendly automated conda-forge-webservice.

I tried to rerender for you, but it looks like there was nothing to do.

_{This message was generated by GitHub Actions workflow run https://github.com/conda-forge/conda-forge-webservices/actions/runs/12020308304. Examine the logs at this URL for more detail.}

IAlibay · 2024-11-25T23:07:00Z

Looks like we're hitting this bug now.. conda/conda-build#5416

IAlibay · 2024-11-25T23:22:47Z

@conda-forge-admin, please rerender

…onda-forge-pinning 2024.11.25.17.21.37

IAlibay · 2024-11-26T00:03:30Z

Having to drop windows too...

wshanks · 2024-11-26T17:08:30Z

If you don't want to drop Windows, consider pinning conda-build until the issue is fixed:

conda/conda-build#5416 (comment)

IAlibay · 2024-11-26T18:59:52Z

@conda-forge-admin, please rerender

…onda-forge-pinning 2024.11.26.07.33.56

IAlibay · 2024-11-26T19:24:19Z

@wshanks you are my hero 🚀

orbeckst · 2024-11-26T21:10:28Z

Thank you @IAlibay !!

IAlibay · 2024-11-26T21:11:17Z

Py13 support will have to be done elsewhere.. that might be a lot harder.

orbeckst · 2024-11-26T21:27:52Z

Can you please add a footnote to the release blog post MDAnalysis/MDAnalysis.github.io#411 if there are some conda-forge packages missing?

v2.8.0

bd04e67

IAlibay requested review from kain88-de, orbeckst and richardjgowers as code owners November 22, 2024 21:54

reset build number to 0

84b35e3

IAlibay and others added 3 commits November 22, 2024 21:59

fixing some things

2e6c7e9

MNT: Re-rendered with conda-build 24.9.0, conda-smithy 3.44.7, and co…

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…nda-forge-pinning 2024.11.22.21.06.17

Merge branch 'v2.8.0' of github.com:IAlibay/mdanalysis-feedstock into…

3f5252d

… v2.8.0

conda-forge-webservices[bot] and others added 3 commits November 22, 2024 22:03

MNT: Re-rendered with conda-build 24.9.0, conda-smithy 3.44.7, and co…

ec9c98c

…nda-forge-pinning 2024.11.22.21.06.17

update source

5af7d60

Merge branch 'v2.8.0' of github.com:IAlibay/mdanalysis-feedstock into…

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… v2.8.0

Update meta.yaml

343fef0

update recipe

dadd192

orbeckst approved these changes Nov 22, 2024

View reviewed changes

IAlibay mentioned this pull request Nov 23, 2024

mdanalysis v2.8.0 #69

Closed

3 tasks

IAlibay added 2 commits November 25, 2024 15:04

Update meta.yaml

272265f

Delete .ci_support/migrations/python313.yaml

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MNT: Re-rendered with conda-build 24.9.0, conda-smithy 3.44.7, and co…

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…nda-forge-pinning 2024.11.25.08.53.39

IAlibay commented Nov 25, 2024

View reviewed changes

Update meta.yaml

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Update meta.yaml

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MNT: Re-rendered with conda-build 24.11.1, conda-smithy 3.44.7, and c…

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…onda-forge-pinning 2024.11.25.17.21.37

pin conda-build

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MNT: Re-rendered with conda-build 24.11.1, conda-smithy 3.44.8, and c…

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…onda-forge-pinning 2024.11.26.07.33.56

IAlibay merged commit 6ab988d into conda-forge:main Nov 26, 2024
21 checks passed

IAlibay deleted the v2.8.0 branch November 26, 2024 19:42

		- {{ pin_compatible('numpy', lower_bound='1.22.3') }}
		- numpy >=1.23.2

v2.8.0 #68

v2.8.0 #68

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