release: create release-0.0.1a0 branch

Author: github-actions[bot]

.github/workflows/deploy_docs.yaml

@@ -0,0 +1,36 @@
+name: documentation
+
+on:
+  push:
+    branches: [main]
+
+permissions:
+  contents: write
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    container:
+       image: python:3.10.12-slim-bullseye
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install dependencies
+        run: |
+          apt-get update && apt-get install -y coreutils
+          POETRY_VERSION=1.8.4
+          pip install -U pip setuptools
+          pip install poetry==${POETRY_VERSION}
+          poetry install
+
+      - name: Sphinx build
+        run: |
+          poetry run sphinx-build -b html docs/source _build
+
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: _build/
+          force_orphan: true

.github/workflows/publish.yaml

@@ -0,0 +1,30 @@
+name: Package publishing
+
+on:
+  push:
+    branches: [main]
+
+jobs:
+  publish-new-mlip-release:
+    runs-on: ubuntu-latest
+
+    container:
+       image: python:3.10.12-slim-bullseye
+
+    steps:
+      - name: checkout
+        uses: actions/checkout@v4
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: install poetry
+        run: |
+          POETRY_VERSION=1.8.4
+          pip install -U pip setuptools
+          pip install poetry==${POETRY_VERSION}
+
+      # - name: build and publish
+      #   run: |
+      #     export POETRY_PYPI_TOKEN_PYPI=${{secrets.POETRY_PYPI_TOKEN}}
+      #     poetry build
+      #     poetry publish

.github/workflows/tests_and_linters.yaml

@@ -0,0 +1,84 @@
+name: Open-source Tests and Linters 🧪
+
+on:
+  push:
+    branches:
+      - 'main'
+      - 'new-release*'
+
+jobs:
+  linters:
+    runs-on: ubuntu-latest
+    container:
+       image: python:3.10.12-slim-bullseye
+    steps:
+      - name: checkout code 📦
+        uses: actions/checkout@v4
+
+      # Workaround for https://github.com/actions/checkout/issues/1169
+      - name: setup
+        run: |
+          apt-get update && apt-get install -y \
+          coreutils \
+          git
+          git config --system --add safe.directory $GITHUB_WORKSPACE
+
+      - name: install poetry
+        run: |
+          POETRY_VERSION=1.8.4
+          pip install -U pip setuptools
+          pip install poetry==${POETRY_VERSION}
+          poetry install
+
+      - name: run linters 🖌️
+        run: |
+          git init
+          poetry run pre-commit run --all-files --verbose
+
+  tests:
+    runs-on: ubuntu-latest
+    container:
+       image: python:3.10.12-slim-bullseye
+    steps:
+      - name: checkout code 📂
+        uses: actions/checkout@v4
+
+      - name: setup
+        run: |
+          apt-get update && apt-get install -y \
+          coreutils \
+          git
+
+      - name: install poetry
+        run: |
+          POETRY_VERSION=1.8.4
+          pip install -U pip setuptools
+          pip install poetry==${POETRY_VERSION}
+          poetry install
+          poetry add git+https://github.com/jax-md/jax-md.git
+
+      - name: run tests 🧪
+        run: |
+          poetry run pytest --ignore tests/experiments --verbose \
+                                            --cov-report xml:coverage.xml \
+                                            --cov-report term-missing \
+                                            --junitxml=pytest.xml \
+                                            --cov=mlip tests/
+
+      - name: pytest coverage comment
+        id: coverageComment
+        uses: MishaKav/pytest-coverage-comment@main
+        with:
+          pytest-xml-coverage-path: ./coverage.xml
+          junitxml-path: ./pytest.xml
+
+      - name: Create the Badge
+        uses: schneegans/[email protected]
+        with:
+          auth: ${{ secrets.BOT_ACCESS_TOKEN }}
+          gistID: b6e4bf384215e60775699a83c3c00aef
+          filename: pytest-coverage-comment.json
+          label: Test Coverage
+          message: ${{ steps.coverageComment.outputs.coverage }}
+          color: ${{ steps.coverageComment.outputs.color }}
+          namedLogo: python

.pre-commit-config.yaml

@@ -0,0 +1,63 @@
+default_stages: [ "pre-commit", "commit-msg", "pre-push" ]
+default_language_version:
+  python: python3.10
+
+repos:
+  - repo: https://github.com/timothycrosley/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+
+  - repo: https://github.com/psf/black
+    rev: 24.2.0
+    hooks:
+      - id: black
+        name: "Code formatter"
+        exclude: notebooks/
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.1.0
+    hooks:
+      - id: end-of-file-fixer
+        name: "End of file fixer"
+        exclude: docker/template.env *.fasta
+      - id: debug-statements
+        name: "Debug imports and breakpoints checker"
+      - id: requirements-txt-fixer
+        name: "Requirements txt fixer"
+      - id: mixed-line-ending
+        name: "Mixed line ending fixer"
+      - id: check-yaml
+        name: "Yaml checker"
+        args: [ '--unsafe' ]
+      - id: trailing-whitespace
+        name: "Trailing whitespace fixer"
+
+  - repo: https://github.com/PyCQA/flake8
+    rev: 4.0.1
+    hooks:
+      - id: flake8
+        # E203 - ":" with whitespace before it
+        # W503 - line break before binary operator (conflicts with other pre-commit hooks).
+        # CCR001 - Cognitive complexity (it's too annoying - write the functions you want ;)).
+        # C408 - allow to write dict() instead of rewriting as literal
+        name: "Linter"
+        args:
+          - --config=setup.cfg
+          - --ignore=E203,W503,CCR001,C408
+          - --max-line-length=88
+        additional_dependencies:
+          - pep8-naming
+          - flake8-builtins
+          - flake8-comprehensions
+          - flake8-bugbear
+          - flake8-pytest-style
+          - flake8-cognitive-complexity
+
+  - repo: https://github.com/compilerla/conventional-pre-commit
+    rev: v2.3.0
+    hooks:
+      - id: conventional-pre-commit
+        name: "Commit linter"
+        stages: [ commit-msg ]
+        args: [ ci, build, docs, feat, fix, perf, refactor, style, test, EXP, revert, chore, config, release]

CHANGELOG

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+# Changelog
+
+## Release 1.0.0
+
+To be added upon release...

Dockerfile.release

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+FROM python:3.10-slim
+
+RUN apt-get update && apt-get install -y \
+    coreutils \
+    git \
+    curl \
+    build-essential \
+    gh \
+    && rm -rf /var/lib/apt/lists/*
+
+WORKDIR /app
+
+COPY . /app/
+
+ENTRYPOINT ["/bin/bash"]