SECURITY-47: Add GHA workflows by Xiangs18 · Pull Request #24 · kbase/file_cache_server

Xiangs18 · 2025-03-14T21:04:15Z

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github-advanced-security · 2025-03-14T21:05:06Z

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MrCreosote · 2025-03-14T22:07:55Z

.github/codeql.yml

Again I'm assuming these are the same workflows we're using everywhere else?

MrCreosote · 2025-03-14T22:08:42Z

.github/workflows/test.yml

+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.9.19


Why such a low version?

Most of the other repos where we have done the Mongo upgrade are using this version. I'm trying to make it consistent here. If you prefer 3.11.x, that's fine. I don't have a strong opinion on this.

I don't remember off the top of my head, but I think there were specific reasons why we used lower versions. If it's just as easy to go to a higher version go ahead and do it. Also make sure the test version and build version are aligned

If we change the build version to 3.9.19, 19/39 tests would fail. If we want to git them fixed, I prefer to do them in the next PR. If we upgrade python version to 3.11.x, we need more dep changes because of build error.

Just leave it as 3.9 in that case, don't bother upgrading for now

yes, so we need to create an issue for that as well.

no, it needs to be updated in the build in this PR - the build and tests need to be aligned

E.g. https://github.com/kbase/file_cache_server/blob/develop/Dockerfile#L1 and maybe other placees

I commented out the mypy check to allow the tests to run. Let me know if you know how to fix 945b204

In my experience mypy isn't worth the trouble as long as you have reasonable tests. I like what it's trying to do but it seems too clunky (although I haven't tried it recently, maybe it's better now)

MrCreosote · 2025-03-14T22:09:24Z

.github/workflows/test.yml

+        shell: bash
+        run: |
+          docker compose up -d
+          sleep 10


yuck but ok, that's what's in travis.yml

MrCreosote · 2025-03-14T22:10:12Z

.github/workflows/test.yml

+          pip install -r requirements.txt
+          pip install -r dev-requirements.txt


Can you make an issue to upgrade to pipenv or something later?

MrCreosote · 2025-03-14T22:14:15Z

scripts/run_tests.sh

+coverage run --source=src/caching_service -m unittest discover src/test/caching_service
+coverage report


Could you also add a ticket to convert to pytest?

Do you mean just this line, or the entire test codebase, from unittest to pytest?

These 2 lines. pytest is compatible with unittest

converted to pytest

It's still using coverage to run the tests though?

Actually I just realized that there hasn't been a post from codecov so it seems that's not working yet...?

I'm not sure; it seems like it cannot process the upload.

Are you setting the right format for the coverage report? https://github.com/kbase/cdm-task-service/blob/main/.github/workflows/test.yml#L76

yeah, that's what I thought. Let's see if it passes this time.

codecov · 2025-03-17T20:49:56Z

Welcome to Codecov 🎉

Once you merge this PR into your default branch, you're all set! Codecov will compare coverage reports and display results in all future pull requests.

Thanks for integrating Codecov - We've got you covered ☂️

MrCreosote

LGTM. @bio-boris do you want to review?

Xiangs18 · 2025-03-17T22:47:06Z

I'm curious why the Makefile requires docker compose run web sh scripts/run_tests.sh instead of just sh scripts/run_tests.sh.

MrCreosote · 2025-03-17T23:01:33Z

I'm just guessing but I assume the docker file is installing test dependencies that may not exist on the system.

bio-boris

lgtm

Xiangs18 added 2 commits March 14, 2025 13:21

run pass tests locally

8931e03

add GHA files

d48f48e

Xiangs18 added 3 commits March 14, 2025 14:33

upgrade python version in GHA

fd5d1aa

change to docker compose

b5494fe

add coverage support

d148f61

Xiangs18 requested review from MrCreosote and bio-boris March 14, 2025 22:06

remove travis file

d0b0657

MrCreosote reviewed Mar 14, 2025

View reviewed changes

Xiangs18 mentioned this pull request Mar 14, 2025

Upgrade to pipenv #25

Open

Xiangs18 added 5 commits March 14, 2025 16:06

conver to pytest and update python version in GHA

9d09a8f

keep python version as 3.9.19

0d117dc

convert to pytest

decde53

fix codecov display error

3275e09

upload coverage.xml

9b4eeb9

Xiangs18 added 2 commits March 17, 2025 15:15

upgrade build python version to 3.9.19

945b204

comment mypy to allow tests pass

f516823

Xiangs18 requested a review from MrCreosote March 17, 2025 22:31

MrCreosote reviewed Mar 17, 2025

View reviewed changes

bio-boris approved these changes Mar 18, 2025

View reviewed changes

MrCreosote changed the title ~~Add GHA workflows~~ SECURITY-47: Add GHA workflows Mar 18, 2025

Xiangs18 merged commit 37ef46b into develop Mar 18, 2025
11 checks passed

Xiangs18 deleted the dev-add_gha branch March 18, 2025 17:12

		pip install -r requirements.txt
		pip install -r dev-requirements.txt

		coverage run --source=src/caching_service -m unittest discover src/test/caching_service
		coverage report

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Xiangs18 Mar 14, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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Xiangs18 Mar 17, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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codecov bot commented Mar 17, 2025

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Xiangs18 commented Mar 17, 2025

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Xiangs18 Mar 14, 2025 •

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