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Update instance repo (PR 457 -- Enable OIDC in Codecov action) #246

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Update instance repo (PR 457 -- Enable OIDC in Codecov action) #246

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4 changes: 2 additions & 2 deletions .cruft.json
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@@ -1,6 +1,6 @@
{
"template": "/home/runner/work/cookiecutter-scverse/cookiecutter-scverse",
"commit": "cd4676edc794359c10500cb4edfd98ce9fc2c2a3",
"commit": "e2f65bec773faa32ed290e9242adb09246974c1c",
"checkout": null,
"context": {
"cookiecutter": {
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"trim_blocks": true
},
"_template": "/home/runner/work/cookiecutter-scverse/cookiecutter-scverse",
"_commit": "cd4676edc794359c10500cb4edfd98ce9fc2c2a3"
"_commit": "e2f65bec773faa32ed290e9242adb09246974c1c"
}
},
"directory": null
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5 changes: 5 additions & 0 deletions .github/workflows/test.yaml
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Expand Up @@ -46,6 +46,8 @@ jobs:
# Run tests through hatch. Spawns a separate runner for each environment defined in the hatch matrix obtained above.
test:
needs: get-environments
permissions:
id-token: write # for codecov OIDC

strategy:
fail-fast: false
Expand Down Expand Up @@ -82,6 +84,9 @@ jobs:
uvx hatch run ${{ matrix.env.name }}:coverage xml # create report for upload
- name: Upload coverage
uses: codecov/codecov-action@v5
with:
fail_ci_if_error: true
use_oidc: true

# Check that all tests defined above pass. This makes it easy to set a single "required" test in branch
# protection instead of having to update it frequently. See https://github.com/re-actors/alls-green#why.
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43 changes: 6 additions & 37 deletions docs/template_usage.md
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Expand Up @@ -86,52 +86,21 @@ line-length = 120

### Coverage tests with _Codecov_

Coverage tells what fraction of the code is "covered" by unit tests, thereby encouraging contributors to [write tests](contributing.md#writing-tests).
Coverage tells what fraction of the code is "covered" by unit tests,
thereby encouraging contributors to [write tests](contributing.md#writing-tests).
To enable coverage checks, head over to [codecov][] and sign in with your GitHub account.
You'll find more information in "getting started" section of the [codecov docs][].
You'll find more information in "quick start" section of the [codecov docs][].

In the `Actions` tab of your projects' GitHub repository, you can see that the workflows are failing due to the **Upload coverage** step.
The error message in the workflow should display something like:

```
...
Retrying 5/5 in 2s..
{'detail': ErrorDetail(string='Could not find a repository, try using repo upload token', code='not_found')}
Error: 404 Client Error: Not Found for url:
...
```

While [codecov docs][] has a very extensive documentation on how to get started,
_if_ you are using the default settings of this template we can assume that you are using [codecov][] in a GitHub action workflow and hence you can make use of the [codecov bot][].
Codecov uses [OpenID connect][] to authenticate, therefore, specifying a token should not be necessary.

If you want codecov to comment on pull requests, you can make use of the [codecov bot][].
To set it up, simply go to the [codecov app][] page and follow the instructions to activate it for your repository.
Once the activation is completed, go back to the `Actions` tab and re-run the failing workflows.

The workflows should now succeed, and you will be able to find the code coverage at this link:
`https://app.codecov.io/gh/scverse/cookiecutter-scverse-instance`.
You might have to wait a couple of minutes and the coverage of this repository should be ~60%.

If your repository is private, you will have to specify an additional token in the repository secrets.
In brief, you need to:

1. Generate a Codecov Token by clicking _setup repo_ in the codecov dashboard.
- If you have already set up codecov in the repository by following the previous steps, you can directly go to the codecov repo webpage.
2. Go to _Settings_ and copy **only** the token `_______-____-...`.
3. Go to _Settings_ of your newly created repository on GitHub.
4. Go to _Security > Secrets > Actions_.
5. Create new repository secret with name `CODECOV_TOKEN` and paste the token generated by codecov.
6. Paste these additional lines in `/.github/workflows.test.yaml` under the **Upload coverage** step:
```bash
- name: Upload coverage
uses: codecov/codecov-action@v3
with:
token: ${{ secrets.CODECOV_TOKEN }} ```
7. Go back to GitHub `Actions` page an re-run previously failed jobs.

[codecov]: https://about.codecov.io/sign-up/
[codecov app]: https://github.com/apps/codecov
[codecov bot]: https://docs.codecov.com/docs/team-bot
[codecov docs]: https://docs.codecov.com/docs
[OpenID connect]: https://docs.github.com/en/actions/concepts/security/openid-connect

### Documentation on _readthedocs_

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