Repo clean-up

.github/workflows/ci.yml

@@ -0,0 +1,54 @@
+name: CI
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - main
+
+jobs:
+  pre-commit:
+    name: Format + lint code
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+      - uses: pre-commit/[email protected]
+        with:
+          extra_args: --hook-stage manual --all-files
+
+  checks:
+    name: Run tests for Python ${{ matrix.python-version }} on ${{ matrix.runs-on }}
+    runs-on: ${{ matrix.runs-on }}
+    needs: [pre-commit]
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.12"] # test oldest and latest supported versions
+        runs-on: [ubuntu-latest, macos-latest] # can be extended to other OSes, e.g. [ubuntu-latest, macos-latest, windows-latest]
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          allow-prereleases: true
+
+      - name: Install package
+        run: python -m pip install .[dev]
+
+      - name: Test package
+        run: >-
+          python -m pytest -ra --cov --cov-report=xml --cov-report=term
+          --durations=20
+
+      - name: Upload coverage report
+        uses: codecov/[email protected]

.gitignore

@@ -5,7 +5,7 @@ __pycache__/
 
 # C extensions
 *.so
-.idea/
+
 # Distribution / packaging
 .Python
 build/
@@ -20,7 +20,6 @@ parts/
 sdist/
 var/
 wheels/
-pip-wheel-metadata/
 share/python-wheels/
 *.egg-info/
 .installed.cfg
@@ -50,6 +49,7 @@ coverage.xml
 *.py,cover
 .hypothesis/
 .pytest_cache/
+cover/
 
 # Translations
 *.mo
@@ -72,6 +72,7 @@ instance/
 docs/_build/
 
 # PyBuilder
+.pybuilder/
 target/
 
 # Jupyter Notebook
@@ -82,7 +83,9 @@ profile_default/
 ipython_config.py
 
 # pyenv
-.python-version
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
 
 # pipenv
 #   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
@@ -127,3 +130,29 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# setuptools_scm
+src/*/_version.py
+
+
+# ruff
+.ruff_cache/
+
+# OS specific stuff
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
+
+# Common editor files
+*~
+*.swp

.pre-commit-config.yaml

@@ -1,31 +1,32 @@
-default_language_version:
-  python: python3
-
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: "v5.0.0"
     hooks:
-      # list of supported hooks: https://pre-commit.com/hooks.html
-      - id: trailing-whitespace
-      - id: end-of-file-fixer
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-yaml
       - id: debug-statements
-      - id: detect-private-key
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: name-tests-test
+        args: ["--pytest-test-first"]
+      - id: requirements-txt-fixer
+      - id: trailing-whitespace
 
-  # python code formatting/linting
-  - repo: https://github.com/charliermarsh/ruff-pre-commit
-    # Ruff version.
-    rev: "v0.0.260"
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.9.1"
     hooks:
+      # first, lint + autofix
       - id: ruff
-        args: [--fix]
-  - repo: https://github.com/psf/black
-    rev: 23.3.0
-    hooks:
-      - id: black
-        args: [--line-length, "100"]
-  # yaml formatting
-  - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.0.0-alpha.6
+        types_or: [python, pyi, jupyter]
+        args: ["--fix", "--show-fixes"]
+      # then, format
+      - id: ruff-format
+
+  - repo: https://github.com/rbubley/mirrors-prettier
+    rev: v3.4.2
     hooks:
       - id: prettier
         types: [yaml]

CODE_OF_CONDUCT.md

@@ -0,0 +1,47 @@
+# Code of Conduct
+
+We value the participation of every member of our community and want to ensure
+that every contributor has an enjoyable and fulfilling experience. Accordingly,
+everyone who participates in the sat_pred project is expected to show respect and  courtesy to other community members at all time.
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers are dedicated to making participation in our project
+a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, sex characteristics, gender identity and expression,
+level of experience, education, socio-economic status, nationality, personal
+appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behaviour that contributes to creating a positive environment
+include:
+
+- Using welcoming and inclusive language
+- Being respectful of differing viewpoints and experiences
+- Gracefully accepting constructive criticism
+- Focusing on what is best for the community
+- Showing empathy towards other community members
+
+Examples of unacceptable behaviour by participants include:
+
+- The use of sexualized language or imagery and unwelcome sexual attention or
+ advances
+- Trolling, insulting/derogatory comments, and personal or political attacks
+- Public or private harassment
+- Publishing others' private information, such as a physical or electronic
+ address, without explicit permission
+- Other conduct which could reasonably be considered inappropriate in a
+ professional setting
+
+<!--
+Modify the following sections to the needs of your project.
+
+## Our Responsibilities
+
+## Enforcement
+-->
+
+## Attribution
+
+This Code of Conduct is adapted from the [Turing Data Stories Code of Conduct](https://github.com/alan-turing-institute/TuringDataStories/blob/main/CODE_OF_CONDUCT.md) which is based on the [scona project Code of Conduct](https://github.com/WhitakerLab/scona/blob/master/CODE_OF_CONDUCT.md)
+and the [Contributor Covenant](https://www.contributor-covenant.org), version [1.4](https://www.contributor-covenant.org/version/1/4/code-of-conduct.html)

CONTRIBUTING.md

@@ -0,0 +1,53 @@
+See the [Scientific Python Developer Guide][spc-dev-intro] for a detailed
+description of best practices for developing scientific packages.
+
+[spc-dev-intro]: https://learn.scientific-python.org/development/
+
+# Setting up a development environment manually
+
+You can set up a development environment by running:
+
+```zsh
+python3 -m venv venv          # create a virtualenv called venv
+source ./venv/bin/activate   # now `python` points to the virtualenv python
+pip install -v -e ".[dev]"    # -v for verbose, -e for editable, [dev] for dev dependencies
+```
+
+# Post setup
+
+You should prepare pre-commit, which will help you by checking that commits pass
+required checks:
+
+```bash
+pip install pre-commit # or brew install pre-commit on macOS
+pre-commit install # this will install a pre-commit hook into the git repo
+```
+
+You can also/alternatively run `pre-commit run` (changes only) or
+`pre-commit run --all-files` to check even without installing the hook.
+
+# Testing
+
+Use pytest to run the unit checks:
+
+```bash
+pytest
+```
+
+# Coverage
+
+Use pytest-cov to generate coverage reports:
+
+```bash
+pytest --cov=sat_pred
+```
+
+# Pre-commit
+
+This project uses pre-commit for all style checking. Install pre-commit and run:
+
+```bash
+pre-commit run -a
+```
+
+to check all files.