From 9a4fa4ac4086d7b63d6540f0e9f1513f59b4c933 Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 27 Jun 2024 11:07:40 +0200
Subject: [PATCH] add CI stuff from scilifelab/scilifelab_epps

---
 .editorconfig                   |  12 +++
 .github/workflows/lint-code.yml | 130 ++++++++++++++++++++++++++++++++
 pyproject.toml                  |  27 +++++++
 3 files changed, 169 insertions(+)
 create mode 100644 .editorconfig
 create mode 100644 .github/workflows/lint-code.yml
 create mode 100644 pyproject.toml

diff --git a/.editorconfig b/.editorconfig
new file mode 100644
index 0000000..70c7a9a
--- /dev/null
+++ b/.editorconfig
@@ -0,0 +1,12 @@
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+indent_size = 4
+indent_style = space
+
+[*.{md,yml,yaml,cff}]
+indent_size = 2
diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
new file mode 100644
index 0000000..84cf192
--- /dev/null
+++ b/.github/workflows/lint-code.yml
@@ -0,0 +1,130 @@
+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: "3.10"
+      - 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: "3.10"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install ruff
+      - name: ruff --> Check code formatting
+        run: ruff format --check .
+
+  # Use mypy for static type checking
+  mypy-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: "3.10"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install mypy
+      # Start by installing type stubs
+      - name: mypy --> Install stubs
+        run: echo -e "y" | mypy --install-types . || exit 0
+      - name: mypy --> Static type checking
+        # Configured in pyprojet.toml
+        run: mypy .
+
+  # Use pipreqs to check for missing dependencies
+  pipreqs-check:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+
+      - name: Install pipreqs
+        run: pip install pipreqs
+
+      - name: Install requirements
+        run: pip install -r requirements.txt
+
+      - name: Run pipreqs
+        run: pipreqs --savepath pipreqs.txt
+
+      - name: Compare requirements
+        run: |
+          # Extract and sort package names
+          awk '{print $1}' $1 | sort -u > "$1".compare
+          awk -F'==' '{print $1}' $2 | sort -u > "$2".compare
+
+          # Compare package lists
+          if cmp -s "$1".compare "$2".compare
+          then
+            echo "Requirements are the same"
+            exit 0
+          else
+            echo "Requirements are different"
+            exit 1
+          fi
+
+    # Use Prettier to check various file formats
+  prettier:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Setup node
+        uses: actions/setup-node@v4
+        with:
+          node-version: "20"
+
+      - name: Install Prettier
+        run: npm install -g prettier
+
+      - name: Run Prettier --check
+        run: prettier --check .
+
+  # Use editorconfig to check all remaining file formats
+  editorconfig:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+
+      - name: Setup node
+        uses: actions/setup-node@v4
+        with:
+          node-version: "20"
+
+      - name: Install editorconfig-checker
+        run: npm install -g editorconfig-checker
+
+      - name: editorconfig --> Lint files
+        run: editorconfig-checker $(git ls-files | grep -v '.py\|.md\|.json\|.yml\|.yaml\|.html')
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..4bb3c6a
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,27 @@
+title = "scilifelab_epps"
+
+
+[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
+]
+
+
+[tool.mypy]
+ignore_missing_imports = true
+follow_imports = 'skip'