Improve code quality

.github/workflows/README.md

@@ -1,7 +1,9 @@
 # GitHub Actions CI workflows
+
 Definitions for GitHub Actions (continuous integration) workflows
 
 ## Publishing
+
 To publish a new version of the `pymap3d` package to PyPI, create and publish a
 release in GitHub (preferrably from a Git tag) for the version; the workflow
 will automatically build and publish an sdist and wheel from the tag.

.github/workflows/ci.yml

@@ -3,41 +3,41 @@ name: ci
 on:
   push:
     paths:
-    - "**.py"
-    - .github/workflows/ci.yml
-    - "!scripts/"
-    pull-request:
-    - "**.py"
-    - .github/workflows/ci.yml
+      - "**.py"
+      - .github/workflows/ci.yml
+      - "!scripts/"
+  pull_request:
+    paths:
+      - "**.py"
+      - .github/workflows/ci.yml
 
 jobs:
-
   full:
     runs-on: ${{ matrix.os }}
 
     name: ${{ matrix.os }} Python ${{ matrix.python-version }}
     strategy:
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
         os: [ubuntu-latest]
         include:
-        - os: macos-latest
-          python-version: '3.11'
-        - os: windows-latest
-          python-version: '3.11'
+          - os: macos-latest
+            python-version: "3.11"
+          - os: windows-latest
+            python-version: "3.11"
 
     steps:
-    - uses: actions/checkout@v3
-    - uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
+      - uses: actions/checkout@v3
 
-    - run: pip install .[full,tests,lint]
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
 
-    - run: flake8
-    - run: mypy
+      - name: Install tests dependencies
+        run: pip install .[full,tests]
 
-    - run: pytest
+      - run: pytest
 
   coverage:
     runs-on: ubuntu-latest
@@ -55,7 +55,7 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Install tests and lint dependencies
+      - name: Install tests and coverage dependencies
         run: pip install -e .[tests,coverage]
 
       - name: Collect coverage without NumPy

.github/workflows/ci_stdlib_only.yml

@@ -3,35 +3,35 @@ name: ci_stdlib_only
 on:
   push:
     paths:
-    - "**.py"
-    - .github/workflows/ci_stdlib_only.yml
-    - "!scripts/"
-    pull-request:
-    - "**.py"
-    - .github/workflows/ci_stdlib_only.yml
+      - "**.py"
+      - .github/workflows/ci_stdlib_only.yml
+      - "!scripts/"
+  pull_request:
+    paths:
+      - "**.py"
+      - .github/workflows/ci_stdlib_only.yml
 
 jobs:
-
   stdlib_only:
     runs-on: ${{ matrix.os }}
 
     name: ${{ matrix.os }} Python ${{ matrix.python-version }}
     strategy:
       matrix:
-        python-version: [ '3.7', '3.8', '3.9', '3.10', '3.11']
-        os: ['ubuntu-latest']
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+        os: ["ubuntu-latest"]
         include:
-        - os: macos-latest
-          python-version: '3.11'
-        - os: windows-latest
-          python-version: '3.11'
+          - os: macos-latest
+            python-version: "3.11"
+          - os: windows-latest
+            python-version: "3.11"
 
     steps:
-    - uses: actions/checkout@v3
-    - uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
 
-    - run: pip install .[tests]
+      - run: pip install .[tests]
 
-    - run: pytest
+      - run: pytest

.github/workflows/publish-python-package.yml

@@ -8,25 +8,21 @@ jobs:
   release:
     runs-on: ubuntu-latest
     steps:
+      - uses: actions/checkout@v3
 
-    - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
 
-    - name: Set up Python
-      uses: actions/setup-python@v4
-      with:
-        python-version: '3.x'
+      - name: Install builder
+        run: pip install build
 
-    - name: Update pip
-      run: pip install -U pip
+      - name: Build package
+        run: pyproject-build --outdir dist/ .
 
-    - name: Install builder
-      run: pip install build
-
-    - name: Build package
-      run: pyproject-build --outdir dist/ .
-
-    - name: Publish package
-      uses: pypa/gh-action-pypi-publish@release/v1
-      with:
-        user: __token__
-        password: ${{ secrets.PYPI_API_TOKEN }}
+      - name: Publish package
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}

.lgtm.yml

@@ -1,6 +1,6 @@
 path_classifiers:
   test:
-  - exclude: scripts
+    - exclude: scripts
 
 extraction:
   python:

.pre-commit-config.yaml

@@ -0,0 +1,62 @@
+repos:
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.2.2
+    hooks:
+      - id: pyupgrade
+        args: ["--py37-plus"]
+
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.0.121
+    hooks:
+      - id: ruff
+        args:
+          - --fix
+
+  - repo: https://github.com/pycqa/isort
+    rev: 5.10.1
+    hooks:
+      - id: isort
+
+  - repo: https://github.com/psf/black
+    rev: 22.10.0
+    hooks:
+      - id: black
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v0.991
+    hooks:
+      - id: mypy
+        additional_dependencies:
+          - numpy
+          - pytest
+          - types-python-dateutil
+          - types-requests
+          - xarray
+
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v3.0.0-alpha.4
+    hooks:
+      - id: prettier
+
+  - repo: https://github.com/markdownlint/markdownlint
+    rev: v0.12.0
+    hooks:
+      - id: markdownlint
+        args: ["--rules", "~MD013,~MD032"]
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.3.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-yaml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+        args: ["--fix=lf"]
+      - id: trailing-whitespace
+
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.9.0
+    hooks:
+      - id: python-check-blanket-type-ignore
+      - id: python-no-eval

CONTRIBUTING.md

@@ -0,0 +1,90 @@
+# Contributing
+
+## Setting up an environment
+
+Clone the `PyMap3D`.
+
+Inside the repository, create a virtual environment.
+
+```bash
+python3 -m venv env
+```
+
+Activate the virtual environment.
+
+```bash
+source ./env/bin/activate
+```
+
+Upgrade `pip`.
+
+```bash
+pip install --upgrade pip
+```
+
+Install the development dependencies.
+
+```bash
+pip install -e .[full,tests,lint,format]
+```
+
+Install [pre-commit](https://pre-commit.com/) so that your code is formatted and checked when you are doing a commit.
+
+```bash
+pip install pre-commit
+pre-commit install
+```
+
+### Visual Studio Code
+
+If you are using VSCode, here are the settings to activate on save,
+
+- `black` and `isort` to format.
+- `mypy` to lint.
+- Install [charliermarsh.ruff](https://marketplace.visualstudio.com/items?itemName=charliermarsh.ruff) extension to lint (`ruff` is a fast equivalent to `flake8`)
+
+```json
+{
+  "[python]": {
+    "editor.formatOnSave": true,
+    "editor.codeActionsOnSave": {
+      "source.organizeImports": true
+    }
+  },
+  "python.formatting.provider": "black",
+  "python.linting.mypyEnabled": true
+}
+```
+
+## Testing
+
+To test the code use [pytest](https://docs.pytest.org/en/7.1.x/).
+
+```bash
+pytest
+```
+
+To do the full coverage of `PyMap3d`, you must combine the coverage of the tests with,
+
+- Vanilla Python
+- NumPy installed
+- Full dependencies installed
+
+Here is how to do it with a newly created environment,
+
+```bash
+pip install -e .[tests]
+pytest --cov=src --cov-report=html
+pip install numpy
+pytest --cov=src --cov-report=html --cov-append
+pip install -e .[full]
+pytest --cov=src --cov-report=html --cov-append
+```
+
+## Committing
+
+After doing `git commit`, `pre-commit` will check the committed code.
+The check can be passed, skipped or failed.
+If the check failed, it is possible it auto-fixed the code, so you will only need to stage and commit again for it to pass.
+If it did not auto-fixed the code, you will need to do it manually.
+`pre-commit` will only check the code that is staged, the unstaged code will be stashed during the checks.