Merge pull request #684 from gammasim/linter

Linter updates

.github/workflows/CI-linter.yml

@@ -0,0 +1,136 @@
+---
+name: CI-linting
+
+on:
+  pull_request:
+    types: [opened, synchronize]
+  schedule:
+    - cron: "0 0 * * *"
+
+jobs:
+
+  linting:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -leo pipefail {0}
+
+    permissions:
+      contents: read
+      packages: read
+      statuses: write
+
+    steps:
+      - name: checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+
+      - name: Check for non-ASCII characters
+        run: |
+          output=$(find . -type f \
+          \( -name "*.py" -o -name "*.rst" -o -name "*.yml" -o -name "*.toml" \) \
+          -exec perl -ne 'print if /[^[:ascii:]]/' {} \;)
+          if [ -n "$output" ]; then
+            echo "Non-ASCII characters found in documentation."
+            exit 1
+          fi
+
+      - name: install packages not included in super-linter
+        run: |
+          pip install validate-pyproject restructuredtext-lint
+
+      - name: pyproject.toml
+        run: |
+          validate-pyproject pyproject.toml
+
+      # RST linter
+      # Note: unclear how to suppress error messages
+      # (use grep -v in this case)
+    #  - name: restructuredtext-lint
+    #    run: |
+    #      rst-lint README.rst docs/source |
+    #       grep -v "Unknown directive type" |
+    #       grep -v "Unknown interpreted text role" |
+    #       grep -v "Cannot analyze code. Pygments package not found."
+
+      - name: Check whether the citation metadata from CITATION.cff is valid
+        uses: citation-file-format/[email protected]
+        with:
+          args: "--validate"
+
+      - name: yaml_config used by super-linter
+        run: |
+          # TODO - very large line length
+          echo 'rules:' > yaml_config.yaml
+          echo '  line-length:' >> yaml_config.yaml
+          echo '    max: 250' >> yaml_config.yaml
+
+      # Dependencies required to avoid errors
+      # reported by linters
+      - name: Install mamba dependencies
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: environment.yml
+          init-shell: bash
+
+      - name: Python dependencies
+        run: |
+          pip install -e '.[tests,dev,doc]'
+          pip install pylint
+
+      - name: pylint
+        run: |
+          pylint $(git ls-files 'simtools/*.py')
+
+
+      - name: Lint Code Base
+        uses: super-linter/super-linter@v5
+        env:
+          VALIDATE_ALL_CODEBASE: false
+          # github actions
+          VALIDATE_GITHUB_ACTIONS: true
+          # yaml
+          VALIDATE_YAML: true
+          YAML_CONFIG_FILE: yaml_config.yaml
+          YAML_ERROR_ON_WARNING: false
+          # isort
+          VALIDATE_PYTHON_ISORT: true
+          PYTHON_ISORT_CONFIG_FILE: pyproject.toml
+          # flake8
+          VALIDATE_PYTHON_FLAKE8: true
+          # black
+          VALIDATE_PYTHON_BLACK: true
+          PYTHON_BLACK_CONFIG_FILE: pyproject.toml
+          # markdown
+          VALIDATE_MARKDOWN: true
+          # docker
+          VALIDATE_DOCKERFILE_HADOLINT: true
+          # copy and paste
+          VALIDATE_JSCPD_ALL_CODEBASE: true
+          # .env file
+          VALIDATE_ENV: true
+          # language
+          VALIDATE_NATURAL_LANGUAGE: true
+          # bash
+          VALIDATE_BASH: true
+          # path for linter rules
+          LINTER_RULES_PATH: ./
+          # create a log file
+          CREATE_LOG_FILE: true
+          LOG_FILE: superlinter.log
+          DEFAULT_BRANCH: main
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      # Upload super-linter log file
+      # and keep it for 5 days
+      - name: Archive production artifacts
+        uses: actions/upload-artifact@v3
+        with:
+          name: super-linter reports
+          path: |
+             superlinter.log
+             retention-days: 5

.github/workflows/CI-unittests.yml

@@ -46,7 +46,7 @@ jobs:
       - name: checkout
         uses: actions/checkout@v4
 
-      - name: Set up Python ${{ matrix.python-version }}
+      - name: Set up Python
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ repos:
       - id: isort
         args: ["--profile", "black", "--filter-files"]
   - repo: https://github.com/psf/black
-    rev: 23.7.0
+    rev: 23.11.0
     hooks:
       - id: black
         args: ["--line-length=100"]
@@ -18,7 +18,7 @@ repos:
         args: ["--max-line-length=100"]
   # https://github.com/pre-commit/pre-commit-hooks
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
@@ -28,3 +28,8 @@ repos:
     hooks:
       - id: docstr-coverage
         args: ["--verbose", "2", "--fail-under", "70.", "simtools"]
+  # gitup action
+  - repo: https://github.com/rhysd/actionlint
+    rev: v1.6.26
+    hooks:
+      - id: actionlint

README.rst

@@ -101,4 +101,4 @@ Please cite this software if it use used for a publication, see the `Zenodo reco
 Acknowledgements
 ================
 
-This project is supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – project number 460248186 (PUNCH4NFDI).
+This project is supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - project number 460248186 (PUNCH4NFDI).

docker/README.md

@@ -8,7 +8,7 @@ Types of dockerfiles and containers available:
 
 - [simtools users](#container-for-simtools-users): a container with all software installed (CORSIKA, sim\_telarray, simtools python environment, simtools). Pull latest release with: `docker pull ghcr.io/gammasim/simtools-prod:latest`
 - [simtools developers](#container-for-simtools-developers): a container with CORSIKA, sim\_telarray, and simtools conda environment installed. Pull latest release with: `docker pull ghcr.io/gammasim/simtools-dev:latest`
-- [sim\_telarray](#container-for-simulation-software-corsika--sim_telarray): provides a container with the CORSIKA and sim\_telarray installed. This provides the base image for the previously listed containers. Pull latest release with: `docker pull ghcr.io/gammasim/simtools-simtelarray:latest`
+- [sim_telarray](#container-for-corsika-and-simtelarray): provides a container with the CORSIKA and sim\_telarray installed. This provides the base image for the previously listed containers. Pull latest release with: `docker pull ghcr.io/gammasim/simtools-simtelarray:latest`
 
 ## Container for simtools Users
 
@@ -95,7 +95,7 @@ docker build -f Dockerfile-dev -t simtools-dev .
 
 Use the docker container in the same way as above, replacing `ghcr.io/gammasim/simtools-dev:latest` by `simtools-dev`.
 
-## Container for simulation software CORSIKA / sim\_telarray
+## Container for CORSIKA and sim\_telarray
 
 Provide a container including the following the CORSIKA and sim\_telarray simulation software packages.
 
@@ -118,7 +118,7 @@ docker build -f Dockerfile-simtelarray  -t simtelarray .
 ```
 
 Building expects that a tar ball of corsika/sim\_telarray (named corsika7.7\_simtelarray.tar.gz) is available in the building directory.
-Download the tar package from the MPIK website (password applies) with
+Download the tar package from MPIK (password applies) with
 
 ```bash
 ./download_simulationsoftware.sh

docs/source/coding_guidelines.rst

@@ -37,6 +37,16 @@ In rare cases, one might want to skip pre-commit checks with
 
     git commit --no-verify
 
+Code Linting
+============
+
+Linters of almost all file types are run by the CI-linter workflow.
+
+To run pylint locally, use:
+
+.. code-block::
+
+    pylint $(git ls-files 'simtools/*.py')
 
 API documentation
 -----------------

docs/source/conf.py

@@ -13,12 +13,11 @@
 
 import os
 import sys
+from pathlib import Path
 
 import toml
 import yaml
 
-from pathlib import Path
-
 import simtools.version
 
 sys.path.insert(0, os.path.abspath("../../simtools"))
@@ -31,20 +30,17 @@ def get_authors_from_citation_file():
     Read list of authors from CITATION.cff file
 
     """
-    try:
-        with open(Path(__file__).parent / "../../CITATION.cff") as file:
-            citation = yaml.safe_load(file)
-    except FileNotFoundError:
-        raise
+    with open(Path(__file__).parent / "../../CITATION.cff", encoding="utf-8") as file:
+        citation = yaml.safe_load(file)
 
-    author = ""
+    tmp_author = ""
     try:
         for person in citation["authors"]:
-            author = author + person["given-names"] + " " + person["family-names"]
-            author += " (" + person["affiliation"] + "), "
+            tmp_author = tmp_author + person["given-names"] + " " + person["family-names"]
+            tmp_author += " (" + person["affiliation"] + "), "
     except KeyError:
         pass
-    return author[:-2]
+    return tmp_author[:-2]
 
 
 def get_python_version_from_pyproject():