Merge pull request #5 from jbloomAus/clean_up_repo

Add CI/CD, black formatting, pre-commit with flake8 linting. Fix some bugs.

.flake8

@@ -0,0 +1,7 @@
+[flake8]
+ignore = E203, E266, E501, W503
+max-line-length = 79
+max-complexity = 10
+select = E9, F63, F7, F82
+show-source = true
+statistics = true

.github/workflows/tests.yml

@@ -0,0 +1,59 @@
+name: build
+
+on:
+  push:
+    branches:
+      - main
+      - clean_up_repo
+    paths-ignore:
+      - '.devcontainer/**'
+      - '.github/**'
+      - '.vscode/**'
+      - '.gitignore'
+      - '*.md'
+  pull_request:
+    branches:
+      - main
+    paths-ignore:
+      - '.devcontainer/**'
+      - '.github/**'
+      - '.vscode/**'
+      - '.gitignore'
+      - '*.md'
+  # Allow this workflow to be called from other workflows
+  workflow_call:
+    inputs:
+      #  Requires at least one input to be valid, but in practice we don't need any
+      dummy:
+        type: string
+        required: false
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11"]
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8 pytest
+          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: Run Unit Tests
+        run: |
+          make unit-test

.gitignore

@@ -170,4 +170,4 @@ activations/
 *.DS_Store
 
 feature_dashboards/
-research/
+research/

.pre-commit-config.yaml

@@ -0,0 +1,25 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.2.0
+    hooks:
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    -   id: check-added-large-files
+        args: [--maxkb=250000]
+-   repo: https://github.com/psf/black
+    rev: 23.3.0
+    hooks:
+    -   id: black
+-   repo: https://github.com/PyCQA/flake8
+    rev: 6.0.0
+    hooks:
+    -   id: flake8
+        additional_dependencies: [
+            'flake8-blind-except',
+            'flake8-docstrings',
+            'flake8-bugbear',
+            'flake8-comprehensions',
+            'flake8-docstrings',
+            'flake8-implicit-str-concat',
+            'pydocstyle>=5.0.0',
+        ]

.pylintrc

@@ -16,4 +16,4 @@ default-docstring-type = numpy
 max-line-length = 100
 
 [MESSAGES CONTROL]
-disable = C0330, C0326, C0199, C0411, C103, C0303, C0304
+disable = C0330, C0326, C0199, C0411, C103, C0303, C0304

.vscode/settings.json

@@ -17,4 +17,4 @@
         "black"
     ],
     "editor.defaultFormatter": "mikoz.black-py",
-}
+}

requirements.txt

@@ -11,4 +11,5 @@ pylint==3.0.2
 black==23.11.0
 pytest==7.4.3
 pytest-cov==4.1.0
-git+https://github.com/callummcdougall/eindex.git
+pre-commit==3.6.0
+git+https://github.com/callummcdougall/eindex.git