Update deployment CI

[michalk8]

IMPORTANT: Please search among the Pull requests before creating one.

Title

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• New feature (non-breaking change which adds functionality)

Description

Update deployment CI and CONTRIBUTING.rst based on a new branching structure.

How has this been tested?

• make sure the merge action in deployment.yml is a merge commit

Have release notes been modified?

N/A

Closes

closes #676
closes #674

[WeilerP]

@michalk8, is the release branch merged automatically immediately after creating it and if tests passed?

1. What if we still need to add changes? For example, imagine we are close to a new release and a feature is ready to be merged to cellrank@dev but should not be included in this release. In this case, I'd create the release branch, add some final touches and only then merge and add the tag.
2. What if someone random pushes a release branch? This is caught by the secret tokens?

[michalk8]

Re 1.: right now, I can't imagine any final touches that should be on the release branch and (ultimately) not on dev (maybe you can give a small example of what you've had in mind? can't think of anything so release specific). In any case, there's a way to skip CI releases (and doing stuff manually) by doing:

1. create release/vX.X.X off dev
2. optionally modify release/vX.X.X
3. tag the last commit
4. merge release/vX.X.X into dev and master
5. push all the branches (important is the one on master, since it's where PyPI release will happen)

Alt. way of doing things is to trigger new release on merging release into master through a PR, not when release is created,
which is slightly more complex (I wanted to avoid making PR from release to ... as to make making new releases as simple as possible), although it gives you more control (adding changes) + better knowledge whether CI passes.

Re 2.: shouldn't really happen (I think/hope - how likely is that you will create a release/vX.X.X branch and push it), but there's alway to stop the CI manually.

I'd say let's discuss this on Wednesday with @Marius1311 and converge on the strategy.

[WeilerP]

Re 1.: right now, I can't imagine any final touches that should be on the release branch and (ultimately) not on dev (maybe you can give a small example of what you've had in mind? can't think of anything so release specific)

Sorry, I meant adding something to dev but not yet include it into the next release. For example, open release branch release/vX.X.X but release notes have not been added. The release branch acts as a pre-release. Now we can added new features, which we do not want to include in release vX.X.X, to dev. Prior to the release we can also fix some some newly found bugs on release/vX.X.X, add release notes, etc. release/X.X.X would evidently always be merged into dev before deleting it. The diagram in the article you cited in CONTRIBUTING.rst also shows this case in their diagram.

[codecov]

Codecov Report

Merging #725 (a3c0191) into dev (76f7445) will increase coverage by 0.08%.
The diff coverage is 92.04%.

@@            Coverage Diff             @@
##              dev     #725      +/-   ##
==========================================
+ Coverage   81.61%   81.69%   +0.08%     
==========================================
  Files          59       59              
  Lines        8717     8740      +23     
  Branches     1767     1769       +2     
==========================================
+ Hits         7114     7140      +26     
+ Misses       1023     1020       -3     
  Partials      580      580              

Impacted Files	Coverage Δ
cellrank/pl/_cluster_fates.py	86.80% <ø> (ø)
cellrank/pl/_graph.py	71.30% <0.00%> (+0.24%)	⬆️
cellrank/tl/_utils.py	77.30% <92.30%> (-0.08%)	⬇️
cellrank/ul/_utils.py	85.18% <93.33%> (+2.00%)	⬆️
cellrank/pl/_cluster_lineage.py	82.05% <93.93%> (+0.31%)	⬆️
cellrank/pl/_gene_trend.py	87.37% <100.00%> (+1.80%)	⬆️
cellrank/pl/_heatmap.py	96.56% <100.00%> (+0.42%)	⬆️
cellrank/pl/_lineages.py	84.37% <100.00%> (ø)
cellrank/ul/_docs.py	100.00% <100.00%> (ø)

[michalk8]

I've switched to aut-commit-action when merging the PRs (more maintained + able to specify --no-ff). Based on today's discussion, think it can be merged.