Merge pull request #882 from kedhammar/ci

CI pt. 1: Configuration

.github/workflows/lint-code.yml

@@ -0,0 +1,38 @@
+name: Lint code
+on: [push, pull_request]
+
+jobs:
+  # Use ruff to check for code style violations
+  ruff-check:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.12"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install ruff
+      - name: ruff --> Check for style violations
+        # Configured in pyproject.toml
+        run: ruff check .
+
+  # Use ruff to check code formatting
+  ruff-format:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.12"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install ruff
+      - name: ruff --> Check code formatting
+        run: ruff format --check .

.gitignore

@@ -1,17 +1,20 @@
-d3/
-jquery/
+__pycache__/
+.DS_Store
+.ruff_cache/
+.vscode/
+*.orig
 *.pyc
+*.swp
 *~
 build/
+d3/
 dist/
-status.egg-info/
-run_dir/settings.yaml
-tests/test_items.yaml
-.DS_Store
-run_dir/qc_reports/
+jquery/
 Pipfile
 Pipfile.lock
-run_dir/settings/
-*.swp
-*.orig
 run_dir/genosqlrc.yaml
+run_dir/qc_reports/
+run_dir/settings.yaml
+run_dir/settings/
+status.egg-info/
+tests/test_items.yaml

conda_requirements.yml

@@ -1,9 +1,13 @@
+channels:
+  - conda-forge
 dependencies:
   - python=3.12
-  - 'conda-forge::pango>=1.42.0'
-  - 'conda-forge::pandas>=1.3.2'
-  - conda-forge::psycopg2
-  - conda-forge::open-fonts
-  - conda-forge::xorg-libxrender
-  - conda-forge::xorg-libxext
-  - conda-forge::xorg-libxau
+  - pango>=1.42.0
+  - pandas>=1.3.2
+  - psycopg2
+  - open-fonts
+  - xorg-libxrender
+  - xorg-libxext
+  - xorg-libxau
+  - pip:
+    - '-r requirements.txt'

pyproject.toml

@@ -0,0 +1,21 @@
+# === LINTING ================================================================
+
+[tool.ruff.lint]
+select = [
+    #         Ruff default rules
+    # ------------------------------
+    "E4", # pycodestyle Imports
+    "E7", # pycodestyle Statements
+    "E9", # pycodestyle Runtime
+    "F",  # Pyflakes
+
+    #         Additional    Comment
+    # ------------------------------------------------------
+    "I",  # isort         Best-practice sorting of imports
+    "UP", # pyupgrade     Make sure syntax is up-to-date
+]
+ignore = [
+    "E402", # Module level import not at top of file
+    "E722", # Do not use bare 'except'
+    "E741", # Ambiguous variable name
+]

requirements.txt

@@ -1,24 +1,26 @@
+atlassian-python-api
 backports.ssl-match-hostname>=3.5.0.1
+cffi
 CouchDB==1.1
 ecdsa>=0.13
 genologics @ git+https://github.com/SciLifeLab/genologics.git
 genologics_sql @ git+https://github.com/SciLifeLab/genologics_sql.git
 httplib2>=0.10.3
 ibmcloudant>=0.9.1
-cffi
-matplotlib>=2.0.0
 markdown
+matplotlib>=2.0.0
 nest_asyncio
 numpy>=1.12.1
 oauth2>=1.9.0.post1
 openpyxl
-atlassian-python-api
 pycryptodome>=3.6.1
 pyparsing>=2.2.0
 python-dateutil>=2.7.5
 pytz>=2018.9
 PyYAML
 requests>=2.14.2
+selenium
+setuptools
 simplejson>=3.10.0
 six>=1.10.0
 slack_sdk

requirements_dev.txt

@@ -1 +1,3 @@
+ipdb
+ruff
 selenium