Update GitHub Actions workflows (sync with other repos in org) #225

sujaypatil96 · 2025-05-20T20:29:44Z

Note: Updated the docs building/publishing workflow to use Python 3.10 to build the docs instead of Python 3.9.

Copilot

Pull Request Overview

This PR updates GitHub Actions workflows to synchronize with changes in other repositories and to upgrade Python from 3.9 to 3.10 in relevant jobs. Key changes include:

Upgrading action versions such as actions/checkout, actions/setup-python, and related tools.
Replacing the dedicated Poetry installation action with pipx-based commands.
Adding pull_request triggers for documentation build and minor adjustments in branch checkout commands.

Reviewed Changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
.github/workflows/validate-yaml-syntax.yaml	Upgraded checkout action version to v4.2.2.
.github/workflows/release.yaml	Upgraded checkout, setup-python, pypi-publish, and semver action versions; switched Poetry install method.
.github/workflows/main.yaml	Adjusted for matrix-driven Python versions, upgraded checkout and setup-python actions, and refined dependency install options.
.github/workflows/codespell.yml	Upgraded checkout and codespell action versions.
.github/workflows/build-publish-documentation.yaml	Added pull_request event trigger, input matrix for Python 3.10, updated Poetry installation, and refined git branch handling.

Copilot · 2025-05-20T20:55:59Z

.github/workflows/release.yaml

-          python-version: 3.9
+          python-version: 3.10

      - name: Install Poetry


The change from using snok/install-poetry to a pipx-based installation command is noted. Please add a comment explaining the rationale to ensure consistency and help future maintainers understand the decision.

Suggested change

- name: Install Poetry

- name: Install Poetry

# Using pipx to install Poetry ensures that it is installed in an isolated environment,

# avoiding potential conflicts with other Python packages. This replaces the previous

# use of snok/install-poetry for better consistency and maintainability.

Copilot · 2025-05-20T20:56:00Z

.github/workflows/build-publish-documentation.yaml

-      # install dependencies if cache does not exist 
+      #             install dependencies
      #----------------------------------------------
      - name: Install dependencies


Verify that using both '--with docs' and '--all-extras' is intentional to avoid installing unnecessary dependencies. A brief comment could clarify the intended behavior for future reviewers.

Suggested change

- name: Install dependencies

- name: Install dependencies

# Install dependencies with both '--with docs' and '--all-extras' to ensure

# that all optional dependencies, including those required for documentation,

# are installed. This is intentional to support the full functionality of the workflow.

dalito · 2025-05-20T21:34:01Z

.github/workflows/build-publish-documentation.yaml

-          virtualenvs-in-project: true
+        run: |
+          pipx install poetry
+          pipx inject poetry poetry-dynamic-versioning


The repo is not yet setup for dynamic-versioning so you don't need to install it.

dalito · 2025-05-20T21:34:58Z

.github/workflows/main.yaml

-          virtualenvs-in-project: true
+        run: |
+          pipx install poetry
+          pipx inject poetry poetry-dynamic-versioning


The repo is not yet setup for dynamic-versioning so you don't need to install it.

dalito · 2025-05-20T21:35:26Z

.github/workflows/release.yaml

-          virtualenvs-in-project: true
+        run: |
+          pipx install poetry
+          pipx inject poetry poetry-dynamic-versioning


Again. The repo is not yet setup for dynamic-versioning so you don't need to install it.

I'm not sure if this was a particular design decision to be honest. It could be that linkml-model repo was created before we started using dynamic versioning and we didn't bring it back up to "standard."

We can do dynamic versioning in another PR; I guess my initial reaction is to keep it consistent with other linkml processes for pypi releasing -- e.g. also add trusted publishing, etc..

I would also suggest to add dynamic versioning in another PR.

dalito · 2025-05-20T21:44:31Z

.github/workflows/build-publish-documentation.yaml

          # switch to gh-pages branch, copy over the latest 404.html from main
          git checkout --force gh-pages
-          git checkout --force main -- 404.html
+          git checkout --force origin/main -- 404.html


I use mike for multi-versioning in nfdi4cat/pid4cat-model and the checkout acrobatics and the copying of the 404.html here are strange. I added a proper 404.html to the gh-pages branch and never hat to touch it again.

However, if it works here then maybe leave it as it is.

I'm responsible for the checkout acrobatics here! 😂

I'm afraid I don't quite remember all the details on why it is the way it is. There is a brief comment in #168 about it. But ultimately I think I just didn't like the idea of a file only living in the gh-pages branch where it could be potentially forgotten about.

pkalita-lbl · 2025-05-20T23:40:55Z

.github/workflows/build-publish-documentation.yaml

+    strategy:
+      matrix:
+        python-version: [ "3.10" ]


Is there any reason to use a matrix here when we only will ever do this using one Python version?

Good point. I saw this pattern in workflows in other repos like linkml – https://github.com/linkml/linkml/blob/main/.github/workflows/doc-pages.yaml#L10-L11 and I thought that we should change it, but left it this way to be consistent with other repos.

But yes you're absolutely right, we're going to be building and publishing the docs using only one version of Python and there's no reason to have a python-version matrix like we have above for that.

I'll go ahead and make the change to correct that. Will make PR's to fix this in other repos as well.

pkalita-lbl · 2025-05-20T23:45:06Z

.github/workflows/build-publish-documentation.yaml

      - name: Install dependencies
-        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
-        run: poetry install --no-interaction --no-root
+        run: poetry install --no-interaction --with docs --no-root --all-extras


As far as I can tell pyproject.toml for this project doesn't specify any extras and the docs group is not marked as optional. So the --with docs and --all-extras flags aren't doing anything here.

Awesome! thanks for picking up on that Patrick. Will correct it.

pkalita-lbl · 2025-05-20T23:58:22Z

.github/workflows/build-publish-documentation.yaml

          # switch to gh-pages branch, copy over the latest 404.html from main
          git checkout --force gh-pages
-          git checkout --force main -- 404.html
+          git checkout --force origin/main -- 404.html


I'm responsible for the checkout acrobatics here! 😂

I'm afraid I don't quite remember all the details on why it is the way it is. There is a brief comment in #168 about it. But ultimately I think I just didn't like the idea of a file only living in the gh-pages branch where it could be potentially forgotten about.

sujaypatil96 added 4 commits May 20, 2025 13:17

update GitHub Actions workflows

a5d29a5

fix typo oetry -> poetry in .github/workflows/main.yaml

cda92b0

poetry installation step before python setup

5cf84d9

add reference to main after switching to gh-pages

98a592a

sujaypatil96 requested review from cmungall, Copilot, pkalita-lbl and sierra-moxon May 20, 2025 20:55

Copilot AI reviewed May 20, 2025

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sujaypatil96 mentioned this pull request May 20, 2025

Update GitHub Actions workflows in linkml-model repo linkml/linkml#2720

Closed

sujaypatil96 requested a review from dalito May 20, 2025 21:21

dalito reviewed May 20, 2025

View reviewed changes

pkalita-lbl reviewed May 20, 2025

View reviewed changes

fixed review comments in docs build/publish Action

ba153db

sujaypatil96 requested review from dalito and pkalita-lbl May 27, 2025 18:13

pkalita-lbl approved these changes May 27, 2025

View reviewed changes

sujaypatil96 merged commit 9c49cbe into main May 30, 2025
5 checks passed

sujaypatil96 deleted the issue-2720-update-gh-actions-workflows branch May 30, 2025 17:47

dalito mentioned this pull request Jun 13, 2025

Minimal changes to support windows #224

Open

-      - name: Install Poetry
+      - name: Install Poetry
+        # Using pipx to install Poetry ensures that it is installed in an isolated environment,
+        # avoiding potential conflicts with other Python packages. This replaces the previous
+        # use of snok/install-poetry for better consistency and maintainability.

-      - name: Install dependencies
+      - name: Install dependencies
+        # Install dependencies with both '--with docs' and '--all-extras' to ensure
+        # that all optional dependencies, including those required for documentation,
+        # are installed. This is intentional to support the full functionality of the workflow.

Update GitHub Actions workflows (sync with other repos in org) #225

Update GitHub Actions workflows (sync with other repos in org) #225

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sujaypatil96 commented May 20, 2025 •

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