Add more base precommit hooks

.git_archival.txt

@@ -1,4 +1,4 @@
 node: $Format:%H$
 node-date: $Format:%cI$
 describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
-ref-names: $Format:%D$
+ref-names: $Format:%D$

.gitattributes

@@ -21,4 +21,4 @@
 # png image files
 # *.png	filter=lfs diff=lfs merge=lfs -text
 
-.git_archival.txt export-subst
+.git_archival.txt export-subst

.github/workflows/smoke-test.yml

@@ -10,7 +10,7 @@ on:
   # Runs this workflow automatically
   schedule:
     - cron: 45 6 * * *
-    
+
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
 

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 
 repos:
     # Compare the local template version to the latest remote template version
-    # This hook should always pass. It will print a message if the local version 
+    # This hook should always pass. It will print a message if the local version
     # is out of date.
   - repo: https://github.com/lincc-frameworks/pre-commit-hooks
     rev: 439dda8bd784f4aa721851ecec03877df286f6b5
@@ -21,9 +21,14 @@ repos:
         stages: [pre-commit]
         language: system
         entry: jupyter nbconvert --clear-output
-    # Prevents committing directly branches named 'main' and 'master'.
+    # Run a series of standard precommit checks, including:
+    #  - no commits to branches named 'main' and 'master'.
+    #  - No large files (>= 500kb)
+    #  - All YAML and TOML files are valid.
+    #  - No whitespace at the end of lines and a single newline at end of file.
+    #  - No outstanding merge conflict markers in the codebase.
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: 3e8a8703264a2f4a69428a0aa4dcb512790b2c8c
+    rev: 3e8a8703264a2f4a69428a0aa4dcb512790b2c8c  # v6.0.0
     hooks:
       - id: no-commit-to-branch
         name: Prevent main branch commits
@@ -32,6 +37,18 @@ repos:
         name: Check for large files
         description: Prevent the user from committing very large files.
         args: ['--maxkb=500']
+      - id: trailing-whitespace
+        exclude: \.(rst|md|txt|html)$  # Skip rst, md, txt, and html files
+        name: Fix trailing whitespace
+      - id: end-of-file-fixer
+        name: Files end with a newline
+      - id: check-toml
+        name: Validate TOML files
+      - id: check-yaml
+        args: [--allow-multiple-documents]  # Allow multiple document format
+        name: Validate YAML files
+      - id: check-merge-conflict
+        name: Check for merge conflicts
     # Verify that pyproject.toml is well formed
   - repo: https://github.com/abravalheri/validate-pyproject
     rev: 17e12779811926f000bdfa1795f9e3735dd71ac3
@@ -79,7 +96,9 @@ repos:
         # supported by your project here, or alternatively use
         # pre-commit's default_language_version, see
         # https://pre-commit.com/#top_level-default_language_version
-        language_version: python3.11
+        # This currently uses the default language version. Uncomment
+        # the following line to use the max version.
+        # language_version: python{{ py.max(python_versions) }}
     # Run unit tests, verify that they pass. Note that coverage is run against
     # the ./src directory here because that is what will be committed. In the
     # github workflow script, the coverage is run against the installed package

docs/practices/issue_pr_templating.rst

@@ -60,4 +60,4 @@ provides generic fields for:
 
 As well as a set of additional project and issue-specific fields. This template
 only serves as an initial framework, and you should feel free to modify this as
-you see fit by directly modifying the template file.
+you see fit by directly modifying the template file.

docs/source/update_project.rst

@@ -141,4 +141,4 @@ For all the details about updating with Copier checkout the
 Still have questions?
 -------------------------------------
 
-:doc:`/source/contact`
+:doc:`/source/contact`

python-project-template/.git_archival.txt

@@ -1,4 +1,4 @@
 node: $Format:%H$
 node-date: $Format:%cI$
 describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
-ref-names: $Format:%D$
+ref-names: $Format:%D$

python-project-template/.gitattributes

@@ -21,4 +21,4 @@
 # png image files
 # *.png	filter=lfs diff=lfs merge=lfs -text
 
-.git_archival.txt export-subst
+.git_archival.txt export-subst

python-project-template/.github/workflows/README.md

@@ -6,4 +6,4 @@ or when you create a new PR.
 
 For more information about CI and workflows, look here: https://lincc-ppt.readthedocs.io/en/latest/practices/ci.html
 
-Or if you still have questions contact us: https://lincc-ppt.readthedocs.io/en/latest/source/contact.html
+Or if you still have questions contact us: https://lincc-ppt.readthedocs.io/en/latest/source/contact.html

python-project-template/.github/workflows/pre-commit-ci.yml.jinja

@@ -39,4 +39,4 @@ jobs:
       env:
         SKIP: "check-lincc-frameworks-template-version,no-commit-to-branch,check-added-large-files,validate-pyproject,sphinx-build,pytest-check"
     - uses: pre-commit-ci/lite-action@062bca0919bc9d6e66755cc05074b70c77e111fc  # v1.2.0
-      if: failure() && github.event_name == 'pull_request' && github.event.pull_request.draft == false
+      if: failure() && github.event_name == 'pull_request' && github.event.pull_request.draft == false

python-project-template/.github/workflows/{% if contains_code %}smoke-test.yml{% endif %}.jinja

@@ -122,4 +122,4 @@ jobs:
             ]
           }
     {%- endraw %}
-{%- endif %}
+{%- endif %}

python-project-template/.github/workflows/{% if contains_code %}testing-and-coverage.yml{% endif %}.jinja

@@ -83,4 +83,4 @@ jobs:
       run: |
         source venv/bin/activate
         python -m pytest
-{%- endif %}
+{%- endif %}

python-project-template/.github/workflows/{% if include_benchmarks %}asv-main.yml{% endif %}.jinja

@@ -73,4 +73,5 @@ jobs:
       with:
         branch: gh-pages
         folder: ${{env.WORKING_DIR}}/_html
-{%- endraw -%}
+
+{%- endraw -%}

python-project-template/.github/workflows/{% if include_benchmarks %}asv-nightly.yml{% endif %}.jinja

@@ -79,4 +79,5 @@ jobs:
       with:
         path: ${{env.WORKING_DIR}}
         key: nightly-results-${{steps.nightly-dates.outputs.today}}
-{%- endraw -%}
+
+{%- endraw -%}

python-project-template/.github/workflows/{% if include_benchmarks %}asv-pr.yml{% endif %}.jinja

@@ -78,4 +78,5 @@ jobs:
       with:
         name: benchmark-artifacts
         path: ${{env.ARTIFACTS_DIR}}
-{%- endraw -%}
+
+{%- endraw -%}

python-project-template/.github/workflows/{% if include_benchmarks %}publish-benchmarks-pr.yml{% endif %}.jinja

@@ -55,4 +55,5 @@ jobs:
         issue-number: ${{ steps.pr-info.outputs.pr }}
         body-path: output
         edit-mode: replace
+
 {%- endraw -%}

python-project-template/.pre-commit-config.yaml.jinja

@@ -21,7 +21,12 @@ repos:
         stages: [pre-commit]
         language: system
         entry: jupyter nbconvert --clear-output
-    # Prevents committing directly branches named 'main' and 'master'.
+    # Run a series of standard precommit checks, including:
+    #  - no commits to branches named 'main' and 'master'.
+    #  - No large files (>= 500kb)
+    #  - All YAML and TOML files are valid.
+    #  - No whitespace at the end of lines and a single newline at end of file.
+    #  - No outstanding merge conflict markers in the codebase.
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: 3e8a8703264a2f4a69428a0aa4dcb512790b2c8c  # v6.0.0
     hooks:
@@ -32,6 +37,18 @@ repos:
         name: Check for large files
         description: Prevent the user from committing very large files.
         args: ['--maxkb=500']
+      - id: trailing-whitespace
+        exclude: \.(rst|md|txt|html)$  # Skip rst, md, txt, and html files
+        name: Fix trailing whitespace
+      - id: end-of-file-fixer
+        name: Files end with a newline
+      - id: check-toml
+        name: Validate TOML files
+      - id: check-yaml
+        args: [--allow-multiple-documents]  # Allow multiple document format
+        name: Validate YAML files
+      - id: check-merge-conflict
+        name: Check for merge conflicts
     # Verify that pyproject.toml is well formed
   - repo: https://github.com/abravalheri/validate-pyproject
     rev: 17e12779811926f000bdfa1795f9e3735dd71ac3  # v0.26

python-project-template/README.md.jinja

@@ -15,13 +15,13 @@
 [![Benchmarks](https://img.shields.io/github/actions/workflow/status/{{project_organization}}/{{project_name}}/asv-main.yml?label=benchmarks)](https://{{project_organization}}.github.io/{{project_name}}/)
 {%- endif %}
 
-This project was automatically generated using the LINCC-Frameworks 
+This project was automatically generated using the LINCC-Frameworks
 [python-project-template](https://github.com/lincc-frameworks/python-project-template).
 
 A repository badge was added to show that this project uses the python-project-template, however it's up to
 you whether or not you'd like to display it!
 
-For more information about the project template see the 
+For more information about the project template see the
 [documentation](https://lincc-ppt.readthedocs.io/en/latest/).
 
 ## Dev Guide - Getting Started
@@ -47,7 +47,7 @@ development using the following commands:
 Notes:
 1. `./.setup_dev.sh` will initialize pre-commit for this local repository, so
    that a set of tests will be run prior to completing a local commit. For more
-   information, see the Python Project Template documentation on 
+   information, see the Python Project Template documentation on
    [pre-commit](https://lincc-ppt.readthedocs.io/en/latest/practices/precommit.html)
 {%- if include_notebooks %}
 2. Install `pandoc` allows you to verify that automatic rendering of Jupyter notebooks

python-project-template/{% if include_dev_guide %}DEVELOPMENT_GUIDE.md{% endif %}.jinja

@@ -65,4 +65,3 @@ benchmarks/                       ASV performance benchmarks
 - **File naming:** `tests/{{package_name}}/<SUBDIR>/test_<name>.py`, mirroring the `src/{{package_name}}/` layout.
 - **Fixtures:** defined in `tests/conftest.py`. Use existing fixtures, do not duplicate test data.
 - Default test run: `python -m pytest`
-

python-project-template/{% if project_license == 'GPL3' %}LICENSE{% endif%}.jinja

@@ -671,4 +671,4 @@ into proprietary programs.  If your program is a subroutine library, you
 may consider it more useful to permit linking proprietary applications with
 the library.  If this is what you want to do, use the GNU Lesser General
 Public License instead of this License.  But first, please read
-<https://www.gnu.org/licenses/why-not-lgpl.html>.
+<https://www.gnu.org/licenses/why-not-lgpl.html>.