Use GitHub Actions for CI #776

bdice · 2022-06-19T20:52:07Z

Description

This PR overhauls our CI configurations to build and test signac with GitHub Actions. We've been planning to move to GitHub Actions for a long time and the breakage of our Windows builds (limited monthly minutes) and limited parallel runners are finally motivating a change here.

Depends on #777.

I'm going to leave CircleCI active (except for the failing Windows jobs) for a little while to ensure a smooth transition.

Before merging:

Ensure we have builds for all supported platforms (Linux, macOS, Windows) and configurations (Python versions, oldest/newest dependencies). I have the following:
- Linux, Python 3.10
- Linux, Python 3.10 "minimal" (no optional dependencies)
- Linux, Python 3.9
- Linux, Python 3.8
- Linux, Python 3.8 "oldest" (minimum versions of supported dependencies)
- macOS, some supported Python version
- Windows, some supported Python version
- ❌ PyPy. I don't really think we need to keep testing PyPy. If another maintainer would like to add that to the CI, feel free.
- ❌ Benchmarks. I haven't attempted to port these over from CircleCI. We deleted the CI script for benchmarks from signac 2.0 anyway, because it's not reliable and we want to use asv instead.
❌ Make an attempt at the "deploy to PyPI" logic that should release a source distribution (tarball) and a wheel tagged py3-none-any uploaded from one of those test configurations mentioned above. See https://github.com/pypa/gh-action-pypi-publish
- I'm going to revisit this at a later time using the wonderful template from @matthewfeickert linked below.
- We will need to port the check-metadata job and the deploy.bash script.

Motivation and Context

I don't think an issue exists for this but we've been discussing moving to GitHub Actions for a while. Supersedes previous attempt in #773.

Checklist:

I am familiar with the Contributing Guidelines.
I agree with the terms of the Contributor Agreement.
My name is on the list of contributors.
The changes introduced by this pull request are covered by existing or newly introduced tests.
The package documentation and framework documentation in signac-docs are up to date with these changes.
I have updated the changelog and added any related issue and pull request numbers for future reference.

… of numpy. Instead, this is covered by the system-independent `longdouble` where supported.

matthewfeickert · 2022-06-19T22:27:41Z

Make an attempt at the "deploy to PyPI" logic that should release a source distribution (tarball) and a wheel tagged py3-none-any uploaded from one of those test configurations mentioned above. See https://github.com/pypa/gh-action-pypi-publish

@bdice Would highly recommend taking advantage of the idea that GHA supports many workflows and make this a separate workflow that is triggered either on a release and/or workflow_dispatch. c.f. pyhf's worfkflow for an example.

… of numpy. Instead, this is covered by the system-independent `longdouble` where supported.

for more information, see https://pre-commit.ci

bdice · 2022-06-20T01:49:01Z

I confirmed that the number of tests that pass/skip is the same between CircleCI and GitHub Actions for the Linux tests (newest, oldest, minimal dependencies). This confirms that we're correctly testing what we intend to test with respect to optional dependencies (MongoDB, Redis, etc.).

codecov · 2022-06-20T01:57:13Z

Codecov Report

Merging #776 (360b898) into master (a9c75e0) will increase coverage by 0.17%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           master     #776      +/-   ##
==========================================
+ Coverage   78.27%   78.45%   +0.17%     
==========================================
  Files          66       66              
  Lines        7267     7267              
  Branches     1590     1590              
==========================================
+ Hits         5688     5701      +13     
+ Misses       1262     1253       -9     
+ Partials      317      313       -4

Impacted Files	Coverage Δ
signac/contrib/project.py	`85.18% <0.00%> (+0.36%)`	⬆️
signac/__main__.py	`72.08% <0.00%> (+0.44%)`	⬆️
...nac/synced_collections/backends/collection_json.py	`100.00% <0.00%> (+1.42%)`	⬆️
...ed_collections/buffers/file_buffered_collection.py	`99.17% <0.00%> (+1.65%)`	⬆️
signac/core/utility.py	`77.27% <0.00%> (+4.54%)`	⬆️

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bdice · 2022-06-20T02:04:43Z

Tagging @mikemhenry and @cbkerr for review since you've had some interest in CI in the past.

mikemhenry · 2022-06-20T20:16:18Z

.github/workflows/run-pytest.yml

+
+on:
+  # trigger on pull requests
+  pull_request:


Do we want this to run on all PRs or ones that target a given branch?

All PRs? 🤷‍♂️

.github/workflows/run-pytest.yml

joaander · 2022-06-20T20:24:07Z

Make an attempt at the "deploy to PyPI" logic that should release a source distribution (tarball) and a wheel tagged py3-none-any uploaded from one of those test configurations mentioned above. See https://github.com/pypa/gh-action-pypi-publish

@bdice Would highly recommend taking advantage of the idea that GHA supports many workflows and make this a separate workflow that is triggered either on a release and/or workflow_dispatch. c.f. pyhf's worfkflow for an example.

This is what gsd does: https://github.com/glotzerlab/gsd/blob/ca4f7c133594dd88f46d33b6e99c34a31b5706e8/.github/workflows/build_wheels.yml#L65-L96

joaander · 2022-06-20T20:25:50Z

.github/workflows/run-pytest.yml

+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.config.python }}
+    - name: Install newest dependencies


You can use actions/cache to cache the files pip downloads and reduce the CI run time slightly: https://github.com/actions/cache

I think this is a good idea but I'm going to leave it out-of-scope for this PR. Looks like this explains how to set it up for pip caching: https://github.com/actions/cache/blob/main/examples.md#simple-example

Caching works fine on multi-platform CI. You include the platform and any other relevant system specific quantities (like python version) in the cache key.

Your "install newest" dependencies step takes ~3 m 18 s (out of 10m 56 s total test time). Caching would remove the download times from that 3m 18s, but not the install times.

.github/workflows/run-pytest.yml

mikemhenry

Just a few notes!

cbkerr

I only had time for a quick look, but I didn't see any obvious problems.
Thanks!

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>

bdice added 11 commits June 19, 2022 15:51

Create run-pytest.yml

15c3f4d

Fix requirements.

ed587b2

Use conditionals.

e5da565

Use single quotes.

8af97ce

Bump to minimum requirement of h5py 2.10.0 for macOS py38 wheels.

ad0b34d

Fix names of dependencies.

c1f3c47

Remove float128 from tests because it doesn't exist on Windows builds…

09b734d

… of numpy. Instead, this is covered by the system-independent `longdouble` where supported.

Use "latest" os images.

a8bc1d2

Fix deprecation ignore for next().

931ad29

Use safe relative paths.

79e488e

Use safe relative paths.

f21b2b3

bdice mentioned this pull request Jun 19, 2022

Improve Windows compatibility (safe relative paths, no float128). #777

Merged

6 tasks

bdice and others added 11 commits June 19, 2022 17:51

Fix message.

0aa23eb

Remove float128 from tests because it doesn't exist on Windows builds…

c6565da

… of numpy. Instead, this is covered by the system-independent `longdouble` where supported.

Permit a ValueError if no relative path exists.

6d9eb6c

[pre-commit.ci] auto fixes from pre-commit.com hooks

a675a22

for more information, see https://pre-commit.ci

Fix Windows platform detection, disable more failing tests.

4ae33fe

[pre-commit.ci] auto fixes from pre-commit.com hooks

1191c9d

for more information, see https://pre-commit.ci

Update changelog.

6bbc6f0

Merge branch 'safe-relpath' into github-actions

46a1e34

Always skip test_multithreaded. Don't skip buffered multithreaded tests.

8e0d131

Remove failing Windows jobs from CircleCI.

abaf092

Exclude macOS, Python 3.10.

3234e46

bdice force-pushed the github-actions branch from ba0821a to 3234e46 Compare June 20, 2022 01:29

bdice added 2 commits June 19, 2022 20:29

Merge branch 'safe-relpath' into github-actions

bb37cc7

Fix conditional for MongoDB / Redis.

1f5578d

bdice marked this pull request as ready for review June 20, 2022 02:03

bdice requested review from a team as code owners June 20, 2022 02:03

bdice requested review from csadorf and jennyfothergill and removed request for a team June 20, 2022 02:03

bdice self-assigned this Jun 20, 2022

bdice added the enhancement New feature or request label Jun 20, 2022

bdice added this to the v1.8.0 milestone Jun 20, 2022

bdice requested review from cbkerr and mikemhenry June 20, 2022 02:04

matthewfeickert mentioned this pull request Jun 20, 2022

research: time metrics with honeycomb scikit-hep/pyhf#1115

Open

mikemhenry reviewed Jun 20, 2022

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joaander reviewed Jun 20, 2022

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mikemhenry reviewed Jun 20, 2022

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mikemhenry approved these changes Jun 20, 2022

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cbkerr approved these changes Jun 21, 2022

View reviewed changes

bdice and others added 3 commits July 4, 2022 20:41

Exit early if a new commit is pushed.

fefa48b

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>

Merge branch 'master' into github-actions

faff779

xfail all multithreaded tests.

360b898

bdice merged commit 3d546da into master Jul 5, 2022

bdice deleted the github-actions branch July 5, 2022 02:16

bdice mentioned this pull request Jul 5, 2022

Disable CircleCI #788

Merged

6 tasks

vyasr mentioned this pull request Nov 3, 2022

Reenable multithreading tests #850

Merged

6 tasks

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Use GitHub Actions for CI #776

Use GitHub Actions for CI #776

bdice commented Jun 19, 2022 •

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Use GitHub Actions for CI #776

Use GitHub Actions for CI #776

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bdice commented Jun 19, 2022 • edited Loading

Description

Motivation and Context

Checklist:

matthewfeickert commented Jun 19, 2022 • edited Loading

bdice commented Jun 20, 2022

codecov bot commented Jun 20, 2022 • edited Loading

Codecov Report

bdice commented Jun 20, 2022

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bdice commented Jun 19, 2022 •

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