Complete release v2.1.0

[IAlibay]

Fixes #3446

Please do review but don't merge yet. This PR ties off version 2.1.0, but we want to make sure that testpypi looks fine.

@MDAnalysis/coredevs this means that we are completely commit frozen until after this PR is completed, tags are created and the PR starting 2.2.0-dev0 is merged. Should be ~ day or so.

Changes made in this Pull Request:

• Ties off the changelog and version numbers of the 2.1.0 release.
• Fixes userguide dev0 link in the docs.

PR Checklist

• Tests?
• Docs?
• CHANGELOG updated?
• Issue raised/referenced?

[codecov]

Codecov Report

Merging #3553 (3487a5d) into develop (8835ab7) will increase coverage by 0.01%.
The diff coverage is 100.00%.

@@             Coverage Diff             @@
##           develop    #3553      +/-   ##
===========================================
+ Coverage    94.10%   94.11%   +0.01%     
===========================================
  Files          190      190              
  Lines        24656    24656              
  Branches      3309     3309              
===========================================
+ Hits         23202    23206       +4     
+ Misses        1408     1404       -4     
  Partials        46       46              

Impacted Files	Coverage Δ
package/MDAnalysis/version.py	100.00% <100.00%> (ø)
package/MDAnalysis/coordinates/H5MD.py	97.60% <0.00%> (+0.71%)	⬆️
...sis/analysis/encore/clustering/ClusteringMethod.py	96.96% <0.00%> (+1.51%)	⬆️

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[IAlibay]

Test versions of 2.1.0 are now on testpypi, if you have spare time please pip install them and run tests (particularly if you have a macOS machine since I can't test that).

Instructions are:

# install MDA 2.1.0
pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple MDAnalysis

# install MDAtests 2.1.0
pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple MDAnalysisTests

# Run tests
pytest --pyargs MDAnalysisTests 2>&1 | tee mda-test-release.logs

Please report any failures and relevant log bits as required.

[IAlibay]

Versions to check before we merge

• Windows py3.7 - failures: known OSErrors with symlink creation in HOLE2
• Windows py3.10 - failures: as above
• Linux py3.7
• Linux py3.10
• Linux py3.9 all dependencies
• MacOS py3.7
• MacOS py3.10

extras:

• MacOS 11.6 py3.9
• MacOS 12.2 py3.9

[IAlibay]

/azp run

[azure-pipelines]

Azure Pipelines successfully started running 1 pipeline(s).

[hmacdope]

@IAlibay I can do py3.10 and py 3.17 MacOS if that would help?

[IAlibay]

@IAlibay I can do py3.10 and py 3.17 MacOS if that would help?

please that would be useful

[hmacdope]

@IAlibay I assume you mean 3.7 for "3.17"?

EDIT:
3.10 is done, logs on discord.

EDIT:
3.7 is done logs on discord

[IAlibay]

Things to do:

• Need to check that the maintainer yaml files need updating
• Need to run that final "all deps" test

Then we should be good to go

[IAlibay]

Ok that should be everything. @richardjgowers can you review as previous / maybe still current lord of the releases?

[richardjgowers]

@IAlibay lgtm. The only thing I sometimes did for releases was regenerate all .c files from their .pyx equivalent, but now we're depending on Cython this isn't necessary.

[IAlibay]

@IAlibay lgtm. The only thing I sometimes did for releases was regenerate all .c files from their .pyx equivalent, but now we're depending on Cython this isn't necessary.

So Cython isn't a core dependency as far as I'm aware, maybe we need to re-discuss this.

[IAlibay]

Ok so it turns out we probably want to keep the C/C++ files somewhere on github so we have a record of them somewhere.

Current plan is to do:

1. Merge the current PR
2. Create a release tag
3. Create a feature branch from this tag (i.e. release-2.1.0)
4. In that branch call python setup.py sdist, commit the C/C++ files
5. Upload the sdist generated tarballs to pypi

Thoughts @MDAnalysis/coredevs ? (@jbarnoud probably had some views on this?)

In the future the aim would be to just make Cython a core dependency hopefully?

[jbarnoud]

It might be better to tag the commit that has the C files if it is the one from which the packages will be produced. But that is really nothing but a "might".

[orbeckst]

I thought @jbarnoud 's comment made sense: branch release-2.1.0, create everything that goes into the package, then tag the package stuff (and because the tag is associated with the release on GitHub, one can also download a tarball from GH that contains "everything").

[orbeckst]

Following up from discord: Having a tag on develop is really useful for benchmarking and other diff-based operations such as bisection. Perhaps we can instead

• introduce a new tag package-2.1.0 that gets attached to the released files
• use the release-2.1.0 tag as before on develop to mark the feature-complete release

(Or something along these lines — the main point is that we have the freedom to introduce different tags and that we can choose them as to disrupt procedures as little as possible.)

[orbeckst]

This is good to sit on develop with an appropriate tag to mark the 0.2.1-feature complete state.

See ongoing discussion on how to tag this merge commit.