Autodoc by jeanjacquemier · Pull Request #39 · LSSTDESC/CLPipe

jeanjacquemier · 2026-10-06T07:54:21Z

Add the documentation with Sphinx and the corresponding mechanisms
- Add a logo to the README
- Add clp_covariance and clp_firecrown confirguration options
- Add an overview
- Add an installation doc:
- Add doc generation with CI
- Use github Pages withgithub actions to publish the docs
- add deployment on autodoc branch before merging
- Add some github badges
- Add LSST DESC software dependencie to doc

jeanjacquemier · 2026-10-06T13:08:01Z

+
+  deploy:
+    needs: build
+    if: github.event_name != 'pull_request' && (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/autodoc')


Here, you can choose when the publication of the document is triggered.

I think this could be triggered inside a PR once it is marked READY FOR REVIEW. Also we can add another condition for the deploy which is: it has to eb ready for review and we trigger a button in the github actions, so it is not done all the time:

deploy: needs: build if: > (github.event_name != 'pull_request' && (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/autodoc')) || (github.event_name == 'workflow_dispatch' && inputs.deploy == true)

Copilot

Copilot review overview

🟡 Changes recommended

The documentation contains invalid configuration guidance, lacks functional autodoc, and includes build and deployment defects.

Review effort: Balanced
Findings: 1 · 6 · 6

Open (13)

Keep checked-in documentation out of make clean · New
Restrict production publishing to the main branch · New
Use O instead of zero for Make options · New
Enable autodoc extensions and add API documentation · New
Remove unsupported cosmo configuration from CLPCovariance · New
Document the correct default HMF model · New
Replace copied CLPCovariance options with Firecrown options · New
Use descriptive alt text for the logo · New
Correct the spelling of publicly · New
Reference merge_data_covariance for mixed covariance blocks · New
Remove Markdown fences from the reStructuredText literal block · New
Remove the literal Markdown fence from the test command · New
Fix line wrapping and opening article in overview · New

What changed in this PR

Introduces a Sphinx documentation site, configuration guides, and automated validation/deployment.

Changes:

Adds overview, installation, covariance, and Firecrown documentation.
Adds Sphinx configuration and dependencies.
Adds documentation CI, GitHub Pages deployment, and README branding.

File	Description
`README.md`	Adds the CLPipe logo.
`docs/source/overview.rst`	Adds the project overview.
`docs/source/installation.rst`	Adds installation and testing instructions.
`docs/source/clp_firecrown.rst`	Documents Firecrown configuration.
`docs/source/clp_covariance.rst`	Documents covariance configuration.
`docs/requirements.txt`	Declares documentation dependencies.
`docs/Makefile`	Adds Sphinx build targets.
`docs/index.rst`	Defines documentation navigation.
`docs/conf.py`	Configures Sphinx and its theme.
`.gitignore`	Ignores generated documentation.
`.github/workflows/docs.yml`	Builds and deploys documentation.
`.github/workflows/ci.yml`	Adds documentation validation.

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jeanjacquemier · 2026-10-06T13:15:16Z

+
+  deploy:
+    needs: build
+    if: github.event_name != 'pull_request' && (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/autodoc')


This is fine for now, once this doc mechanism will be valided we will remove the autodoc banch

Lets just not forget to go back to main for publishing the docs before merging this PR

jeanjacquemier · 2026-10-06T13:16:41Z

+release = "0.0.1"
+
+root_doc = "index"
+extensions = []


jeanjacquemier · 2026-10-06T13:17:04Z

+cosmo (str)
+    Defines how cosmology is provided.
+
+    Options:
+        - "set": use parameters from config


@eduardojsbarroso. Do you confirm ?

Yes this was changed. Copilot is right

jeanjacquemier · 2026-10-06T13:18:11Z

+This is handled by:
+    extract_data_covariance()


@eduardojsbarroso ?

+  ```bash
+  git clone https://github.com/LSSTDESC/CLPipe.git 
+  cd CLPipe
+  conda env update -f txpipe_environment.yml
+  conda activate txpipe_clp
+  pip install .
+  conda deactivate
+
+
+  conda env update -f firecrown_environment.yml
+  conda activate firecrown_clp
+  pip install .
+  conda env config vars set CSL_DIR=${CONDA_PREFIX}/cosmosis-standard-library
+  conda deactivate
+  conda activate firecrown_clp
+
+  cd ${CONDA_PREFIX}
+  source ${CONDA_PREFIX}/bin/cosmosis-configure
+  cosmosis-build-standard-library main
+  ```


jeanjacquemier · 2026-10-06T13:20:18Z

+  ```bash
+  pytest
+  ```


jeanjacquemier · 2026-10-06T13:25:51Z

+clpipe is a automated framework developed within the Legacy
+Survey of Space and Time Dark Energy Science Collaboration (LSST DESC) for galaxy cluster cos-
+mology, in preparation for the first Rubin LSST Data releases. This cluster cosmology pipeline in-
+tegrates DESC-developed tools spanning galaxy/cluster catalog ingestion, cluster number count and


coveralls · 2026-10-07T11:37:14Z

Coverage Report for CI Build 37614240398

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No base build found for commit 3a6cd70 on main.
Coverage changes can't be calculated without a base build.
If a base build is processing, this comment will update automatically when it completes.

Coverage: 42.255%

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Patch coverage: No coverable lines changed in this PR.

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Requires a base build to compare against. How to fix this →

Coverage Stats


Relevant Lines:	1020
Covered Lines:	431
Line Coverage:	42.25%
Coverage Strength:	0.85 hits per line

💛 - Coveralls

codecov-commenter · 2026-10-07T12:02:48Z

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 ☂️

- Add a logo to the README - Add clp_covariance and clp_firecrown confirguration options - Add an overview - Add an installation doc: - Add doc generation with CI - Use github Pages withgithub actions to publish the docs - add deployment on autodoc branch before merging - Add some github badges - Add LSST DESC software dependencie to doc - Add sphinx copy button extension - Add coveralls command - Add API doc

eduardojsbarroso · 2026-10-08T12:49:25Z

+
+on:
+  push:
+    branches: [autodoc, main]


We have to change this to be only main later? Or any PR once ready for review?

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jeanjacquemier requested a review from eduardojsbarroso October 6, 2026 13:07

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eduardojsbarroso reviewed Oct 8, 2026

View reviewed changes

Modified docs, fixed leftover configurations and test

49cde33

eduardojsbarroso deployed to github-pages October 8, 2026 14:08 — with GitHub Actions View deployment

Fixed Equations out of margin

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eduardojsbarroso deployed to github-pages October 8, 2026 14:15 — with GitHub Actions View deployment

eduardojsbarroso mentioned this pull request Oct 9, 2026

Update cluster_theory_pred to match CLPFirecrown and add a tutorial #40

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