Merge pull request #1 from DuncDennis/develop_CICD_workflow

Develop cicd workflow

.github/workflows/pre-commit.yml

@@ -0,0 +1,13 @@
+name: pre-commit
+on: [pull_request, push, workflow_dispatch]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.9"
+          architecture: "x64"
+      - uses: pre-commit/[email protected]

.github/workflows/testing.yml → .github/workflows/test_and_coverage.yml

@@ -1,14 +1,8 @@
-name: Testing lorenzpy
-on:
-  push:
-    branches:
-      - main
-  pull_request:
-    branches:
-      - main
+name: test and coverage
+on: [pull_request, push, workflow_dispatch]
 
 jobs:
-  install-test:
+  test:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
@@ -26,12 +20,6 @@ jobs:
         run: pip --version
       - name: installation of package in dev mode
         run: pip install .[dev]
-      - name: checking with black
-        run: black --check .
-      - name: checking with ruff
-        run: ruff check --format=github .
-      - name: checking with mypy
-        run: mypy
       - name: running pytest
         run: pytest
       - name: Upload coverage reports to Codecov

.pre-commit-config.yaml

@@ -0,0 +1,20 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.2.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: check-added-large-files
+-   repo: https://github.com/psf/black
+    rev: "23.1.0"
+    hooks:
+    -   id: black
+        language_version: python3
+-   repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: 'v0.0.245'
+    hooks:
+    -   id: ruff
+-   repo: https://github.com/pre-commit/mirrors-mypy
+    rev: 'v1.1.1'
+    hooks:
+    -   id: mypy
+        args: [--config-file=pyproject.toml]

CHANGELOG.md

@@ -1,57 +1,73 @@
 # Changelog:
 
 ---
+### Pre-release status (13.03.2023):
+- Now using [pre-commit](https://pre-commit.com/) as an automatic CI tool.
+- pre-commit runs some standard hooks, black, ruff and mypy.
+- The config for black, ruff and mypy is still in `pyproject.toml`
+- To run the pre-commit manual, run `pre-commit run --all-files`
+- To reinstall the pre-commits, run `pre-commit install`
+- My pre-commit GH action is running on ubuntu on python3.9
+- **Note:** There is some redundancy, as I have to specify the versions of
+    black, ruff and mypy twice. Once in the `.pre-commit-config.yaml` and once in the
+    `pyproject.toml`.
+  Maybe I am only specifying which *hook* to use in the `.pre-commit-config.yaml`.
+- Q:
+  - Should I add the tests also to pre-commit?
+  - When to test?
 
 
-### Pre-release status (12.03.2023): 
+### Pre-release status (12.03.2023):
 
-**Development features:** 
+**Development features:**
 
-1. Use [Black](https://github.com/psf/black) for formatting the code. 
+1. Use [Black](https://github.com/psf/black) for formatting the code.
     - Local terminal usage: `black .`
     - Config in `pyproject.toml`
       - Set line-length to `88`, set python versions to `py8`to `py11`
-    - GitHub Actions: 
+    - GitHub Actions:
       - Just check with black by running: `black --check .`
-      
+
 2. Use [Ruff](https://github.com/charliermarsh/ruff) as the Python linter.
    - Local terminal usage: `ruff check .`
    - Config in `pyproject.toml`
-     - set line-length, the Rules (*pycodestyle*, *pyflakes*, *pydocstyle*, *isort*), 
-      the source files, and to ignore rule *F401* to not complain about unused imports 
-      in `__init__` files. 
-   - GitHub Actions: 
+     - set line-length, the Rules (*pycodestyle*, *pyflakes*, *pydocstyle*, *isort*),
+      the source files, and to ignore rule *F401* to not complain about unused imports
+      in `__init__` files.
+   - GitHub Actions:
      - run `ruff check --format=github .`
-     
-3. Use [MyPy](https://github.com/python/mypy) as for type checking. 
+
+3. Use [MyPy](https://github.com/python/mypy) as for type checking.
    - Local terminal usage: `mypy`
    - Config in `pyproject.toml`
      - Specify files: `src/lorenzpy/`
      - Ignore missing imports for `plotly`
-   - GitHub Actions: 
+   - GitHub Actions:
      - Just running `mypy`
 
 4. Testing with [pytest-cov](https://github.com/pytest-dev/pytest-cov)
    - Local terminal usage: `pytest`
    - Config in `pyproject.toml`
-     - automatically add the following options when `pytest` is run: 
+     - automatically add the following options when `pytest` is run:
        - `--verbose --cov-config=pyproject.toml --cov-report term-missing --cov=lorenzpy`
        - Note: This is somehow important for GitHub actions to work fine...
-     - Omit the `plot` folder for the coverage. 
-   - GitHub Actions: 
+     - Omit the `plot` folder for the coverage.
+   - GitHub Actions:
      - simply running `pytest` and then uploading the coverage reports to [Codecov](https://about.codecov.io/)
      using the GitHub action: [codecov-action](https://github.com/codecov/codecov-action)
-   
+
 5. Generating docs with [mkdocs](https://github.com/mkdocs/mkdocs):
    - Following [this tutorial](https://realpython.com/python-project-documentation-with-mkdocs/)
    - Generate the docs with `mkdocs gh-deploy`
    - Use the plugin [mkdocstrings](https://github.com/mkdocstrings/mkdocstrings) to
    automatically use the code-docstrings in the documentation.
 
-**Deployment on PyPI**:
+**Deployment on PyPI with GitHub Actions**:
 - Following the [PyPA tutorial](https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/)
+- Also use [this PyPA tutorial](https://packaging.python.org/en/latest/tutorials/packaging-projects/) to manually upload the package to test PyPI.
+    - This uses `build` and `twine`
 
-**Resources**: 
-Taking inspiration from: 
- https://github.com/dkmiller/modern-python-package, and 
-https://github.com/denkiwakame/py-tiny-pkg. 
+**Resources**:
+Taking inspiration from:
+ https://github.com/dkmiller/modern-python-package, and
+https://github.com/denkiwakame/py-tiny-pkg.

README.md

@@ -7,23 +7,23 @@
 [![Python versions](https://img.shields.io/badge/python-3.8+-blue.svg)](https://www.python.org/downloads/)
 
 ## 🚧 Under construction 🚧
-There is no release of the package yet and most of the functionalities are missing. 
-For now only the basic functionalities are implemented in order to build up the 
-developing workflow. 
+There is no release of the package yet and most of the functionalities are missing.
+For now only the basic functionalities are implemented in order to build up the
+developing workflow.
 
-## Documentation: 
+## Documentation:
 The documentation can be found here: https://duncdennis.github.io/lorenzpy/
 
-## Installation: 
+## Installation:
 
-#### User installation: 
-Only the core LorenzPy functionality: 
+#### User installation:
+Only the core LorenzPy functionality:
 
 ``
 pip install .
 ``
 
-With plotting functionalities: 
+With plotting functionalities:
 
 ``
 pip install .[plot]
@@ -35,6 +35,6 @@ pip install -e .[dev,plot]
 ``
 
 
-## Resources: 
+## Resources:
 #### Similar package: *pynamical*
 https://github.com/gboeing/pynamical

docs/index.md

@@ -1,12 +1,12 @@
 # Welcome to LorenzPy
 
-This site contains the documentation for the `LorenzPy` Python package 
-that can be used to simulate and measure discrete and continuous chaotic dynamical 
+This site contains the documentation for the `LorenzPy` Python package
+that can be used to simulate and measure discrete and continuous chaotic dynamical
 systems.
 
-## Contents: 
+## Contents:
 
-1. [Reference](reference.md) The API reference. 
+1. [Reference](reference.md) The API reference.
 
-## Project Overview: 
+## Project Overview:
 ::: lorenzpy

docs/reference.md

@@ -1,8 +1,8 @@
 ### LorenzPy package:
 ::: lorenzpy
 
-### simulations module: 
+### simulations module:
 ::: lorenzpy.simulations
 
-### measures module: 
+### measures module:
 ::: lorenzpy.measures

pyproject.toml

@@ -25,12 +25,13 @@ dependencies = [
 dev = [
     "pytest==7.2.0",
     "pytest-cov==4.0",
-    "black==22.12.0",
+    "black==23.1.0",
     "mypy==1.1.1",
     "ruff==0.0.254",
-    "mkdocs",
-    "mkdocstrings[python]",
-    "mkdocs-material"
+    "mkdocs",  # add version?
+    "mkdocstrings[python]",  # add version?
+    "mkdocs-material",  # add version?
+    "pre-commit==3.1.1",  # add version?
 ]
 plot = [
     "plotly==5.13.1",
@@ -50,7 +51,7 @@ line-length = 88
 files = "src/lorenzpy/"
 
 [[tool.mypy.overrides]]
-module = ['plotly.*']   # ignore missing imports from the plotly package.
+module = ['plotly.*', 'numpy', 'pytest']   # ignore missing imports from the plotly package.
 ignore_missing_imports = true
 
 [tool.ruff]

src/lorenzpy/__init__.py

@@ -8,4 +8,4 @@
 
 from . import measures, simulations
 
-__version__ = "0.1.0"
+__version__ = "0.0.1"

src/lorenzpy/simulations.py

@@ -91,7 +91,7 @@ class _SimBase(ABC):
 
     @abstractmethod
     def iterate(self, x: np.ndarray) -> np.ndarray:
-        """The abstract iterate function."""
+        """Generate the next time step when the previous one is given."""
 
     def simulate(
         self, time_steps: int, starting_point: np.ndarray | None = None
@@ -124,10 +124,10 @@ class _SimBaseRungeKutta(_SimBase):
 
     @abstractmethod
     def flow(self, x: np.ndarray) -> np.ndarray:
-        """The abstract flow function."""
+        """Return the flow of the continuous dynamical system."""
 
     def iterate(self, x: np.ndarray) -> np.ndarray:
-        """Calculates next timestep x(t+dt) with given x(t) using runge kutta.
+        """Calculate the next timestep x(t+dt) with given x(t) using runge kutta.
 
         Args:
             x: the previous point x(t).
@@ -178,7 +178,7 @@ def __init__(
         self.dt = self.default_parameters["dt"] if dt is None else dt
 
     def flow(self, x: np.ndarray) -> np.ndarray:
-        """Calculates (dx/dt, dy/dt, dz/dt) with given (x,y,z) for RK4.
+        """Calculate (dx/dt, dy/dt, dz/dt) with given (x,y,z) for RK4.
 
         Args:
             x: (x,y,z) coordinates. Needs to have shape (3,).