Refactor to begin aligning with femto (#67)

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,12 +1,6 @@
 ## Description
-Provide a brief description of the PR's purpose here.
 
-## Todos
-Notable points that this PR has either accomplished or will accomplish.
-  - [ ] TODO 1
-
-## Questions
-- [ ] Question1
+<!--- Provide a brief description of the PR's purpose here. -->
 
 ## Status
-- [ ] Ready to go
+- [ ] Ready to go

.github/workflows/ci.yaml

@@ -5,83 +5,29 @@ concurrency:
   cancel-in-progress: true
 
 on:
-  push:
-    branches: [ "main" ]
-  pull_request:
-    branches: [ "main" ]
-
+  push: { branches: [ "main" ] }
+  pull_request: { branches: [ "main" ] }
 
 jobs:
-
-  lint:
-    runs-on: ubuntu-latest
-    strategy:
-      fail-fast: false
-    steps:
-      - uses: actions/checkout@v2
-      - uses: actions/[email protected]
-        with:
-          python-version: '3.10'
-      - name: Install the package
-        run: |
-          pip install -e .
-
-      - name: Install isort / flake8 / black
-        run: |
-          pip install isort flake8 black
-
-      - name: Run isort
-        run: |
-          isort --check-only absolv
-
-      - name: Run black
-        run: |
-          black absolv --check
-
-      - name: Run flake8
-        run: |
-          flake8 absolv
-
   test:
 
-    name: ${{ matrix.os }} python=${{ matrix.python-version }}
-    runs-on: ${{ matrix.os }}
-
-    strategy:
-      fail-fast: false
-      matrix:
-        os: [ "ubuntu-latest" ]
-        python-version: [ "3.10" ]
+    runs-on: ubuntu-latest
+    container: condaforge/mambaforge:latest
 
     steps:
-    - uses: actions/checkout@v2.4.0
+    - uses: actions/checkout@v3.3.0
 
     - name: Setup Conda Environment
-      uses: mamba-org/provision-with-micromamba@main
-      with:
-        environment-file: devtools/envs/base.yaml
-        extra-specs: |
-          python=${{ matrix.python-version }}
-
-    - name: Install Package
-      shell: bash -l {0}
-      run: |
-        pip install -e .
-
-    - name: Conda Environment Information
-      shell: bash -l {0}
       run: |
-        conda info
-        conda list
+        apt update && apt install -y git make
 
-    - name: Run Tests
-      shell: bash -l {0}
-      run: |
-        pytest -v --cov=absolv --cov-report=xml --cov-report=term --color=yes absolv/tests/
+        make env
+        make lint
+        make test
+        make docs-build
 
     - name: CodeCov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v3.1.1
       with:
         file: ./coverage.xml
         flags: unittests
-        name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}

.github/workflows/docs.yaml

@@ -1,51 +1,53 @@
-name: docs
+name: Publish Documentation
 
 on:
   push:
     branches:
-      - "main"
-  pull_request:
-    branches:
-      - "main"
+      - main
+    tags:
+      - '*'
 
 jobs:
-  docs:
+  deploy-docs:
 
     runs-on: ubuntu-latest
+    container: condaforge/mambaforge:latest
 
     steps:
-    - uses: actions/[email protected]
+    - name: Prepare container
+      run: |
+        apt update && apt install -y git make
 
-    - name: Setup Conda Environment
-      uses: mamba-org/provision-with-micromamba@main
-      with:
-        environment-file: docs/environment.yml
-        extra-specs: |
-          python=${{ matrix.python-version }}
+    - name: Checkout
+      uses: actions/[email protected]
 
-    - name: Install Package
-      shell: bash -l {0}
+    - name: Determine Version
+      shell: bash
       run: |
-        pip install -e .
-
-    - name: Environment Information
-      shell: bash -l {0}
+        if [ "$GITHUB_REF" = "refs/heads/main" ]; then
+          echo "VERSION=latest" >> $GITHUB_ENV
+        elif [ "${GITHUB_REF#refs/tags/}" != "$GITHUB_REF" ]; then
+          VERSION=$(echo $GITHUB_REF | sed 's/refs\/tags\///')
+          echo "VERSION=$VERSION stable" >> $GITHUB_ENV
+        else
+          echo "Invalid ref: $GITHUB_REF"
+          exit 1
+        fi
+
+    - name: Build and Deploy Documentation
+      env:
+        INSIDER_DOCS_TOKEN: ${{ secrets.INSIDER_DOCS_TOKEN }}
       run: |
-        conda info
-        conda list
+        git config --global user.name 'GitHub Actions'
+        git config --global user.email '[email protected]'
+        git config --global --add safe.directory "$PWD"
+        git remote set-url origin https://x-access-token:${{ secrets.GITHUB_TOKEN }}@github.com/${{ github.repository }}
 
-    - name: Build 🔧
-      shell: bash -l {0}
-      run: |
+        git fetch --all --prune
 
-        cd docs
+        make env
 
-        python compile-sass.py
-        make html
+        sed -i 's/# extensions/extensions/' mkdocs.yml
 
-    - name: Deploy 🚀
-      if: github.ref == 'refs/heads/main'
-      uses: JamesIves/[email protected]
-      with:
-        branch: gh-pages
-        folder: docs/_build/html
+        make docs-insiders INSIDER_DOCS_TOKEN="${INSIDER_DOCS_TOKEN}"
+        make docs-deploy VERSION="$VERSION"

.gitignore

@@ -109,4 +109,6 @@ ENV/
 .idea
 
 # OSX
-.DS_Store
+.DS_Store
+
+.ruff_cache

.pre-commit-config.yaml

@@ -1,19 +1,15 @@
-files: \.py$
 repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.2.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
 
-- repo: local
-  hooks:
-    - id: isort
-      name: Import formatting
-      language: system
-      entry: isort
-
-    - id: black
-      name: Code formatting
-      language: system
-      entry: black
-
-    - id: flake8
-      name: Linting
-      language: system
-      entry: flake8
+-   repo: local
+    hooks:
+    -   id: ruff
+        name: Autoformat python code
+        language: system
+        entry: ruff
+        args: [check]
+        files: \.py$

LICENSE

@@ -1,7 +1,7 @@
 
 MIT License
 
-Copyright (c) 2021 Simon Boothroyd
+Copyright (c) 2023 Simon Boothroyd
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

MANIFEST.in

@@ -1,6 +1 @@
-include LICENSE
-include MANIFEST.in
-include versioneer.py
-
-graft absolv
-global-exclude *.py[cod] __pycache__ *.so
+global-exclude *.py[cod] __pycache__ *.so

Makefile

@@ -1,10 +1,36 @@
-.PHONY: env
+PACKAGE_NAME := absolv
+
+CONDA_ENV_RUN=conda run --no-capture-output --name $(PACKAGE_NAME)
+
+TEST_ARGS := -v --cov=$(PACKAGE_NAME) --cov-report=term --cov-report=xml --junitxml=unit.xml --color=yes
+
+.PHONY: env lint format test docs-build docs-deploy docs-insiders
+
 env:
-	mamba create -n absolv
-	mamba env update -n absolv --file devtools/envs/base.yaml
-	conda run --no-capture-output --name absolv pip install --no-deps -e .
-	conda run --no-capture-output --name absolv pre-commit install
+	mamba create     --name $(PACKAGE_NAME)
+	mamba env update --name $(PACKAGE_NAME) --file devtools/envs/base.yaml
+	$(CONDA_ENV_RUN) pip install --no-deps -e .
+	$(CONDA_ENV_RUN) pre-commit install || true
+
+lint:
+	$(CONDA_ENV_RUN) ruff check $(PACKAGE_NAME)
 
-.PHONY: format
 format:
-	pre-commit run --all-files
+	$(CONDA_ENV_RUN) ruff format $(PACKAGE_NAME)
+	$(CONDA_ENV_RUN) ruff check --fix --select I $(PACKAGE_NAME)
+
+test:
+	$(CONDA_ENV_RUN) pytest -v $(TEST_ARGS) $(PACKAGE_NAME)/tests/
+
+docs-build:
+	$(CONDA_ENV_RUN) mkdocs build
+
+docs-deploy:
+ifndef VERSION
+	$(error VERSION is not set)
+endif
+	$(CONDA_ENV_RUN) mike deploy --push --update-aliases $(VERSION)
+
+docs-insiders:
+	$(CONDA_ENV_RUN) pip install git+https://$(INSIDER_DOCS_TOKEN)@github.com/SimonBoothroyd/mkdocstrings-python.git \
+                    			 git+https://$(INSIDER_DOCS_TOKEN)@github.com/SimonBoothroyd/griffe-pydantic.git@fix-inheritence-static