Use GitHub actions for unit testing by peanutfun · Pull Request #745 · CLIMADA-project/climada_python

peanutfun · 2023-07-04T12:20:09Z

Changes proposed in this PR:

Define allowed Python versions in setup.py and environment file
Allow Python 3.10 and 3.11 for Climada
Add a GitHub workflow for CI
- Build new conda environments for every branch. Environments are cached over one calendar day, meaning that they do not have to be rebuilt during that period if the environment files don't change.
- Test CLIMADA with Python 3.9, 3.10, 3.11
- Run unit tests and report test results
- Upload coverage reports as artifacts
Fix some tests
- Two nightlight tests are actually integration tests, as they require that some files have been downloaded
- Adjust accuracy on some tests which fail otherwise
- Use default_factory to initialize mutable default values for dataclass

PR Author Checklist

PR Reviewer Checklist

This reverts commit dc37cec.

This reverts commit 9be8632. The command does not actually use multiprocessing but makes coverage aware of multiprocessing used by the called tests.

* Move file checks to integration tests. They require file downloads. * Fix assertion for almost equal arrays.

The unsequa module throws segmentation faults while unit testing.

peanutfun · 2023-08-17T12:54:59Z

I tried to achieve compatibility also with Python 3.11, but the unsequa module causes segmentation faults there, see https://github.com/CLIMADA-project/climada_python/actions/runs/5890648735/job/15976187422. I think this is due to the process pool. Maybe #763 will resolve these issues, but we will have to look out.

chahank · 2023-08-17T13:27:35Z

The build in 3.10 also fails, but because of another module. Can this be easily fixed?

peanutfun · 2023-08-17T13:29:14Z

All checks have passed for the latest commit. What are you referring to? 🤔

chahank · 2023-08-17T13:30:38Z

I was referring to the link https://github.com/CLIMADA-project/climada_python/actions/runs/5890648735/job/15976187422

peanutfun · 2023-08-17T13:37:37Z

This was the test result of an earlier commit. The particular error was resolved by 109d994

chahank · 2023-08-18T08:48:18Z

.github/workflows/ci.yml

+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10"]


Is this something we then have to update manually for each release?

For each Python release, yes.

chahank · 2023-08-18T08:56:18Z

Looks good to me if this does what it should do which I cannot tell from looking at the code only. Maybe @emanuel-schmid can confirm?

peanutfun · 2023-08-21T08:46:11Z

@chahank @emanuel-schmid How and where should I document this? (topics: What does the pipeline do, how to inspect results and coverage reports, etc)

…limada_python into github-actions

peanutfun · 2023-08-28T13:54:26Z

I tried to achieve compatibility also with Python 3.11, but the unsequa module causes segmentation faults there, see https://github.com/CLIMADA-project/climada_python/actions/runs/5890648735/job/15976187422. I think this is due to the process pool.

This apparently was resolved by #763. Excellent work, @chahank!

peanutfun · 2023-09-13T13:32:38Z

@chahank @emanuel-schmid How and where should I document this? (topics: What does the pipeline do, how to inspect results and coverage reports, etc)

I would highly appreciate your comments on this. Apart from that, the branch is ready to be merged.

emanuel-schmid · 2023-09-13T14:19:17Z

Well - there is https://github.com/CLIMADA-project/climada_python/blob/main/doc/guide/Guide_Continuous_Integration_and_Testing.ipynb where it wouldn't be completely out of place.
But atm I'd suggest to keep it basic - let's see whether it's sustainable before making a full-fledged documentation about it.

peanutfun · 2023-09-14T09:28:24Z

From personal discussion: I'll add a documentation of the pipeline itself but not make it part of the guides for testing yet.

* Add introduction to GitHub Actions to the docs. * Add information to the CI guide. * Improve comments in the ci.yml workflow definition.

peanutfun added 30 commits January 12, 2023 16:57

Add GitHub Actions and Dockerfile for test environment

11a9eb8

Fix env var query in github workflow

dc37cec

Revert "Fix env var query in github workflow"

7a880a3

This reverts commit dc37cec.

Try specifying Docker tag with variables

8eb75e2

Hardcode Docker Hub namespace

dfefe7b

Conditionally run jobs and try to fix unittest job

bec8823

Fix syntax error in github workflow

f5ef2d5

Do not call make in github workflow

a4806c0

Try fixing the shell inside Docker container for github workflow

84223c4

Call micromamba directly in github workflow

d9b3696

Use 'micromamba install' because 'update' does not update pip deps

9bf1054

Split GitHub workflows

b9e9c25

Consolidate GitHub Workflows

9302bf2

Try fixing syntax for GitHub workflow expression

bb320bb

Fix typo in docker workflow

e43e582

Fix list input for docker.yml workflow

0022546

Run all tests in GitHub workflow

36c5cd1

Do not use 'defaults' in workflow

e38a835

Fix stray 'defaults' in workflow

9e3b15b

Rename testing steps

089ba8e

Do not use multiprocessing for integration tests

9be8632

Revert climada.conf to 9302bf2

ad5cb0f

Revert "Do not use multiprocessing for integration tests"

58601ed

This reverts commit 9be8632. The command does not actually use multiprocessing but makes coverage aware of multiprocessing used by the called tests.

Skip failing integration tests for now

ab73601

Add action to publish test results

3fb11cc

Run pipeline on branches and pull requests

c6e8949

Grant permissions from top-level job

b68c4a3

Use other XML test reports for displaying results

bc5499b

Merge branch 'develop' into github-actions

d8d2bda

Add new workflow using micromamba directly

7bf2c5e

peanutfun added 5 commits August 17, 2023 13:53

Fix Nightlight and LitPop tests

4335e22

* Move file checks to integration tests. They require file downloads. * Fix assertion for almost equal arrays.

Merge branch 'develop' into github-actions

6f1da97

Fix accuracy in default Emanuel impact func test

109d994

Improve names in Github CI

c18cb76

Disallow Python 3.11 for Climada

d55e0ea

The unsequa module throws segmentation faults while unit testing.

peanutfun marked this pull request as ready for review August 17, 2023 12:51

peanutfun requested review from chahank and emanuel-schmid August 17, 2023 12:52

chahank reviewed Aug 18, 2023

View reviewed changes

peanutfun added 3 commits August 28, 2023 15:18

Merge branch 'develop' into github-actions

aff5f05

Merge branch 'github-actions' of https://github.com/CLIMADA-project/c…

a9a0914

…limada_python into github-actions

Try testing Python v3.11 again

ceab933

peanutfun added 3 commits September 19, 2023 16:19

Improve GitHub Actions documentation

f42da0a

* Add introduction to GitHub Actions to the docs. * Add information to the CI guide. * Improve comments in the ci.yml workflow definition.

Merge branch 'develop' into github-actions

f00bf3e

Merge branch 'develop' into github-actions

d06051d

emanuel-schmid merged commit d8eaf55 into develop Sep 20, 2023

emanuel-schmid deleted the github-actions branch September 20, 2023 11:16

emanuel-schmid restored the github-actions branch July 18, 2024 08:26

emanuel-schmid deleted the github-actions branch July 18, 2024 08:26

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peanutfun commented Aug 17, 2023

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peanutfun commented Jul 4, 2023 •

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