add linting and tests workflow + update precommit hook

.githooks/pre-commit

@@ -41,8 +41,8 @@ then
   exit 0
 fi
 
-PY_FILES=$(git diff --cached --name-only --diff-filter=ACMR | sed 's| |\\ |g' | { grep -E "\.py$" || test $? = 1; })
-YAML_FILES=$(git diff --cached --name-only --diff-filter=ACMR | sed 's| |\\ |g' | { grep -E "\.ya?ml$" || test $? = 1; })
+PY_FILES=$(git ls-files --cached --modified --other --exclude-standard | { grep -E "\.py$" || test $? = 1; })
+YAML_FILES=$(git ls-files --cached --modified --other --exclude-standard | { grep -E "\.ya?ml$" || test $? = 1; })
 
 if [ -n "$PY_FILES" ]; then
     command_available "mypy"
@@ -54,19 +54,19 @@ if [ -n "$PY_FILES" ]; then
 
     command_available "black"
     print_message "running Black formatting" 1 "" true
-    echo "$PY_FILES" | xargs black --stdin-filename "{}"
+    black .
 
     command_available "ruff"
     print_message "running ruff  linting" 1 "" true
-    echo "$PY_FILES" | xargs ruff --fix
+    ruff --fix .
 
-    echo "$PY_FILES" | xargs git add
+    echo "$PY_FILES"  | xargs git add
 fi
 
 if [ -n "$YAML_FILES" ]; then
     command_available "prettier"
     print_message "running prettier yaml formatting" 1 "" true
-    echo "$YAML_FILES" | xargs prettier --ignore-unknown --stdin-filepath
+    echo "$YAML_FILES" | xargs prettier --ignore-unknown --stdin-filepath --write > /dev/null
     echo "$YAML_FILES" | xargs git add
 fi
 

.github/workflows/codeql.yaml

@@ -0,0 +1,80 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: ["main"]
+  schedule:
+    - cron: "28 8 * * 3"
+
+jobs:
+  analyze:
+    name: Analyze
+    # Runner size impacts CodeQL analysis time. To learn more, please see:
+    #   - https://gh.io/recommended-hardware-resources-for-running-codeql
+    #   - https://gh.io/supported-runners-and-hardware-resources
+    #   - https://gh.io/using-larger-runners
+    # Consider using larger runners for possible analysis time improvements.
+    runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }}
+    timeout-minutes: ${{ (matrix.language == 'swift' && 120) || 360 }}
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: ["python"]
+        # CodeQL supports [ 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'swift' ]
+        # Use only 'java-kotlin' to analyze code written in Java, Kotlin or both
+        # Use only 'javascript-typescript' to analyze code written in JavaScript, TypeScript or both
+        # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      # Initializes the CodeQL tools for scanning.
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v2
+        with:
+          languages: ${{ matrix.language }}
+          # If you wish to specify custom queries, you can do so here or in a config file.
+          # By default, queries listed here will override any specified in a config file.
+          # Prefix the list here with "+" to use these queries and those in the config file.
+
+          # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+          # queries: security-extended,security-and-quality
+
+      # Autobuild attempts to build any compiled languages (C/C++, C#, Go, Java, or Swift).
+      # If this step fails, then you should remove it and run the build manually (see below)
+      - name: Autobuild
+        uses: github/codeql-action/autobuild@v2
+
+      # ℹ️ Command-line programs to run using the OS shell.
+      # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+
+      #   If the Autobuild fails above, remove it and uncomment the following three lines.
+      #   modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance.
+
+      # - run: |
+      #     echo "Run, Build Application using script"
+      #     ./location_of_script_within_repo/buildscript.sh
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v2
+        with:
+          category: "/language:${{matrix.language}}"

.github/workflows/linting-and-tests.yaml

@@ -0,0 +1,46 @@
+name: Run linting and unit tests
+
+on:
+  pull_request:
+
+jobs:
+  linting_and_tests:
+    name: Linting and Tests | python=${{ matrix.python-version }}
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: ["3.11"]
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0 # to fetch all history for all branches and tags; required because we derive app version from latest tag
+          fetch-tags: true
+      - name: Setup conda
+        uses: s-weigand/setup-conda@v1
+        with:
+          update-conda: true
+          python-version: ${{ matrix.python-version }}
+          conda-channels: anaconda, conda-forge
+
+      - name: Conda install dependencies
+        run: conda install -c conda-forge pyproj==3.6.0
+
+      - name: Install dependencies
+        run: |
+          python${{ matrix.python-version }} -m pip install --upgrade pip
+          python${{ matrix.python-version }} -m pip install --force-reinstall -e ".[dev]"
+
+      - name: Lint with black
+        run: |
+          python${{ matrix.python-version }} -m black --check .
+
+      - name: Lint with ruff
+        run: |
+          python${{ matrix.python-version }} -m ruff -v .
+
+      - name: Test with pytest and generate coverage report
+        run: |
+          python${{ matrix.python-version }} -m coverage run --source=src/coordinate_transformation_api -m pytest -v tests

.markdownlint.yaml

@@ -3,4 +3,4 @@ MD013: false
 MD004:
   style: "sublist"
 MD007:
-  indent: 4
+  indent: 4

pyproject.toml

@@ -10,7 +10,7 @@ classifiers = [
 ]
 readme = { file = "./README.md", content-type = "text/markdown" }
 dependencies = [
-    "fastapi == 0.104.1",
+    "fastapi[all] == 0.104.1",
     "uvicorn == 0.24.0.post1",
     "pyyaml == 6.0.1",
     "geojson_pydantic == 1.0.1",
@@ -29,6 +29,8 @@ dev = [
     "mypy == 1.7.1",
     "pytest == 7.4.3",
     "ruff == 0.1.7",
+    "types-ujson == 5.8.0.1",
+    "types-PyYAML == 6.0.12.12",
 ]
 
 [build-system]
@@ -119,6 +121,7 @@ exclude = [
     "dist",
     "node_modules",
     "venv",
+    "build"
 ]
 
 line-length = 120