Merge pull request #471 from NLeSC/458_citation

fdiblen · web-flow · commit aa7326f5d5cf · 2024-08-21T16:55:19.000+02:00
458-Add question for citation files
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,7 @@
 
 ### Added
 
+* Make citation optional [#471](https://github.com/NLeSC/python-template/pull/471)
 * Make online documentation optional [#476](https://github.com/NLeSC/python-template/pull/476)
 * Added Python 3.12 support [#356](https://github.com/NLeSC/python-template/issues/356)
 * Template unit tests for documentation generation, linting and version bumping
diff --git a/README.md b/README.md
@@ -19,7 +19,7 @@ Use this [Copier](https://copier.readthedocs.io) template to generate an empty P
   - [Contributing guidelines](template/CONTRIBUTING.md.jinja),
 - Continuous code quality and code coverage reporting using [Sonarcloud](https://sonarcloud.io/),
 - Automatic creation of [issues](template/.github/next_steps) with instructions how to pass all GitHub action workflows and integrate with services like Zenodo and Read the Docs,
-- Instructions how to make package [citable](template/.github/next_steps/02_citation.md.jinja)
+- Instructions how to make package [citable](.github/next_steps/%7B%25%20if%20AddCitation%20%25%7D02_citation.md%7B%25%20endif%20%25%7D.jinja)
 - FAIR software recommendation badge,
 - Optional [pre commit hook](template/README.dev.md.jinja#running-linters-locally) to catch lint errors early
 
diff --git a/copier.yml b/copier.yml
@@ -83,6 +83,12 @@ AddGitHubActions:
   default: "{{ template_profile != 'minimum' }}"
   help: GitHub actions to test the package and the documentation
 
+AddCitation:
+  when: "{{ template_profile == 'ask' }}"
+  type: bool
+  default: "{{ template_profile != 'minimum' }}"
+  help: Citation file and cffconvert workflow which validates the citation file
+
 AddChangeLog:
   when: "{{ template_profile == 'ask' }}"
   type: bool
diff --git a/profiles.md b/profiles.md
@@ -2,16 +2,16 @@
 - package_name:
 - version:
 - template_profile:
-  - minumum --> DONE  
-  - recommeded --> all questions - excluded with the defaults  
+  - minumum --> DONE
+  - recommeded --> all questions - excluded with the defaults
   - optional --> all questions with answers off
 
 - github_organization:
 - full_name:
 - email:
 - copyright_holder:
 - licence (exist)
-  
+
 - community:
   - code of conduct --> if TRUE ask for email
   - contributing guidelines
@@ -20,7 +20,7 @@
   - developer documentation
   - online documentation (read the docs)
   - project_setup.md
-    
+
 - code quality:
   - sonarcloud
   - ruff and lint workflow
@@ -30,7 +30,7 @@
 
 - publishing and release
   - zenodo
-  - keywords 
+  - keywords
   - changelog.md
   - cffconvert workflow and citation file
 
diff --git a/template/.github/next_steps/{% if AddCitation %}02_citation.md{% endif %}.jinja b/template/.github/next_steps/{% if AddCitation %}02_citation.md{% endif %}.jinja
diff --git a/template/.github/workflows/next_steps.yml b/template/.github/workflows/next_steps.yml
@@ -11,39 +11,30 @@ jobs:
       - name: Create Sonarcloud integration issue
         uses: JasonEtco/create-an-issue@v2
         env:
-          GITHUB_TOKEN: ${{ '{{ ' -}} secrets.GITHUB_TOKEN }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
           filename: .github/next_steps/01_sonarcloud_integration.md
         id: sonarcloud
-
-      - name: Create citation data issue
-        uses: JasonEtco/create-an-issue@v2
-        env:
-          GITHUB_TOKEN: ${{ '{{ ' -}} secrets.GITHUB_TOKEN }}
-        with:
-          filename: .github/next_steps/02_citation.md
-        id: citation
       - name: Create Zenodo integration issue
         uses: JasonEtco/create-an-issue@v2
         env:
-          GITHUB_TOKEN: ${{ '{{ ' -}} secrets.GITHUB_TOKEN }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
           filename: .github/next_steps/04_zenodo_integration.md
         id: zenodo
       - name: Create linting issue
         uses: JasonEtco/create-an-issue@v2
         env:
-          GITHUB_TOKEN: ${{ '{{ ' -}} secrets.GITHUB_TOKEN }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
           filename: .github/next_steps/05_linting.md
         id: linting
       - name: List created issues
         run: |
           echo 'Created issues that must be completed to have fully working Python package:
-          * Sonarcloud integration ${{ '{{ ' -}} steps.sonarcloud.outputs.url }}
-          * Zenodo integration ${{ '{{ ' -}} steps.zenodo.outputs.url }}
-          * Citation data ${{ '{{ ' -}} steps.citation.outputs.url }}
-          * Linting fixes ${{ '{{ ' -}} steps.linting.outputs.url }}'
+          * Sonarcloud integration ${{ steps.sonarcloud.outputs.url }}
+          * Zenodo integration ${{ steps.zenodo.outputs.url }}
+          * Linting fixes ${{ steps.linting.outputs.url }}'
       - name: Cleanup files needed to create next steps issues
         run: |
           git config --global user.name 'NLeSC Python template'
diff --git a/template/.github/workflows/{% if AddCitation %}cffconvert.yml{% endif %} b/template/.github/workflows/{% if AddCitation %}cffconvert.yml{% endif %}
diff --git a/template/.github/workflows/{% if AddCitation %}next_steps_citation.yml{% endif %} b/template/.github/workflows/{% if AddCitation %}next_steps_citation.yml{% endif %}
@@ -0,0 +1,29 @@
+on: [push]
+permissions:
+  contents: write
+  issues: write
+name: Create an issue for citation
+jobs:
+  next_steps:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Create citation data issue
+        uses: JasonEtco/create-an-issue@v2
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          filename: .github/next_steps/02_citation.md
+        id: citation
+      - name: List created issues
+        run: |
+          echo 'Created issues that must be completed to have fully working Python package:
+          * Citation data ${{ steps.citation.outputs.url }}'
+      - name: Cleanup files needed to create next steps issues
+        run: |
+          git config --global user.name 'NLeSC Python template'
+          git config --global user.email 'nlesc-python-template@users.noreply.github.com'
+          git rm .github/workflows/next_steps_citation.yml
+          git rm -r .github/next_steps
+          git commit -am "Cleanup automated next steps issue generator"
+          git push
diff --git a/template/CONTRIBUTING.md.jinja b/template/CONTRIBUTING.md.jinja
@@ -47,8 +47,8 @@ In case you feel like you've made a valuable contribution, but you don't know ho
 
 To create a release you need write permission on the repository.
 
-1. Check the author list in [`CITATION.cff`](CITATION.cff)
-1. Bump the version using `bump-my-version bump <major|minor|patch>`. For example, `bump-my-version bump major` will increase major version numbers everywhere it's needed (code, meta, etc.) in the repo. Alternatively the version can be manually changed in {{ package_name }}/__init__.py, pyproject.toml, CITATION.cff and docs/conf.py (and other places it was possibly added).
+{% if AddCitation -%}1. Check the author list in [`CITATION.cff`](CITATION.cff){%- endif %}
+1. Bump the version using `bump-my-version bump <major|minor|patch>`. For example, `bump-my-version bump major` will increase major version numbers everywhere it's needed (code, meta, etc.) in the repo. Alternatively the version can be manually changed in {{ package_name }}/__init__.py, pyproject.toml, {% if AddCitation %}CITATION.cff{%- endif -%} and docs/conf.py (and other places it was possibly added).
 {% if AddChangeLog -%}
 1. Update the `CHANGELOG.md` to include changes made
 {%- endif %}
diff --git a/template/MANIFEST.in b/template/MANIFEST.in
diff --git a/template/MANIFEST.in.jinja b/template/MANIFEST.in.jinja
@@ -0,0 +1,4 @@
+{% if AddCitation -%}include CITATION.cff{%- endif %}
+include LICENSE
+include NOTICE
+include README.md
diff --git a/template/README.dev.md.jinja b/template/README.dev.md.jinja
@@ -133,10 +133,8 @@ This section describes how to make a release in 3 parts:
 
 ### (1/3) Preparation
 
-{% if AddChangeLog -%}
-1. Update the <CHANGELOG.md> (don't forget to update links at bottom of page)
-{%- endif %}
-1. Verify that the information in [`CITATION.cff`](CITATION.cff) is correct.
+{% if AddChangeLog -%}1. Update the <CHANGELOG.md> (don't forget to update links at bottom of page).{%- endif %}
+{% if AddCitation -%}1. Verify that the information in [`CITATION.cff`](CITATION.cff) is correct.{%- endif %}
 1. Make sure the [version has been updated](#versioning).
 1. Run the unit tests with `pytest -v`
 
diff --git a/template/README.md.jinja b/template/README.md.jinja
@@ -18,7 +18,9 @@
 {%- endif -%}
 | **GitHub Actions**                 | &nbsp; |
 | Build                              | [![build]({{repository_url}}/actions/workflows/build.yml/badge.svg)]({{repository_url}}/actions/workflows/build.yml) |
+{% if AddCitation -%}
 | Citation data consistency          | [![cffconvert]({{repository_url}}/actions/workflows/cffconvert.yml/badge.svg)]({{repository_url}}/actions/workflows/cffconvert.yml) |
+{%- endif -%}
 | SonarCloud                         | [![sonarcloud]({{repository_url}}/actions/workflows/sonarcloud.yml/badge.svg)]({{repository_url}}/actions/workflows/sonarcloud.yml) |
 | MarkDown link checker              | [![markdown-link-check]({{repository_url}}/actions/workflows/markdown-link-check.yml/badge.svg)]({{repository_url}}/actions/workflows/markdown-link-check.yml) |
 
diff --git a/template/project_setup.md.jinja b/template/project_setup.md.jinja
@@ -92,11 +92,13 @@ help you decide which tool to use for packaging.
 - [Relevant section in the guide](https://guide.esciencecenter.nl/#/best_practices/releases?id=changelogmd)
 {%- endif %}
 
+{% if AddCitation -%}
 ## CITATION.cff
 
 - To allow others to cite your software, add a `CITATION.cff` file
 - It only makes sense to do this once there is something to cite (e.g., a software release with a DOI).
 - Follow the [making software citable](https://guide.esciencecenter.nl/#/citable_software/making_software_citable) section in the guide.
+{%- endif -%}
 
 ## CODE_OF_CONDUCT.md
 
diff --git a/template/pyproject.toml.jinja b/template/pyproject.toml.jinja
@@ -151,8 +151,10 @@ filename = "src/{{ package_name }}/__init__.py"
 [[tool.bumpversion.files]]
 filename = "pyproject.toml"
 
+{% if AddCitation -%}
 [[tool.bumpversion.files]]
 filename = "CITATION.cff"
+{%- endif %}
 
 [[tool.bumpversion.files]]
 filename = "docs/conf.py"
diff --git a/template/{% if AddCitation %}CITATION.cff{% endif %}.jinja b/template/{% if AddCitation %}CITATION.cff{% endif %}.jinja
