Merge pull request #1 from VectorInstitute/initial_port

Initial commit, porting from cyclops repo
VectorInstitute · Oct 20, 2023 · 6dbd67a · 6dbd67a
2 parents 82631b0 + 7e99242
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diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -0,0 +1,26 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+### Describe the bug
+A clear and concise description of what the bug is.
+
+### To Reproduce
+Code snippet or clear steps to reproduce behaviour.
+
+### Expected behavior
+A clear and concise description of what you expected to happen.
+
+### Screenshots
+If applicable, add screenshots to help explain your problem.
+
+### Version
+ - Version info such as v0.1.5
+
+### Additional context
+Add any other context about the problem here.
diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml
@@ -0,0 +1 @@
+blank_issues_enabled: false
diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md
@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+### Is your feature request related to a problem? Please describe.
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+### Describe the solution you'd like
+A clear and concise description of what you want to happen.
+
+### Describe alternatives you've considered
+A clear and concise description of any alternative solutions or features you've considered.
+
+### Additional context
+Add any other context or screenshots about the feature request here.
diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -0,0 +1,7 @@
+# PR Type ([Feature | Fix | Documentation | Test])
+
+## Short Description
+...
+
+## Tests Added
+...
diff --git a/.github/workflows/code_checks.yml b/.github/workflows/code_checks.yml
@@ -0,0 +1,41 @@
+name: code checks
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - .pre-commit-config.yaml
+      - .github/workflows/code_checks.yml
+      - '**.py'
+      - poetry.lock
+      - pyproject.toml
+      - '**.ipynb'
+  pull_request:
+    branches:
+      - main
+    paths:
+      - .pre-commit-config.yaml
+      - .github/workflows/code_checks.yml
+      - '**.py'
+      - poetry.lock
+      - pyproject.toml
+      - '**.ipynb'
+
+jobs:
+  run-code-check:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Install poetry
+        run: python3 -m pip install --upgrade pip && python3 -m pip install poetry
+      - uses: actions/[email protected]
+        with:
+          python-version: '3.10'
+          cache: 'poetry'
+      - name: Install dependencies and check code
+        run: |
+          poetry env use '3.10'
+          source $(poetry env info --path)/bin/activate
+          poetry install --without docs
+          pre-commit run --all-files
diff --git a/.github/workflows/docs_build.yml b/.github/workflows/docs_build.yml
@@ -0,0 +1,48 @@
+name: docs (build)
+
+on:
+  pull_request:
+    branches:
+      - main
+    paths:
+      - .pre-commit-config.yaml
+      - .github/workflows/docs_build.yml
+      - '**.py'
+      - '**.ipynb'
+      - poetry.lock
+      - pyproject.toml
+      - '**.rst'
+      - '**.md'
+
+jobs:
+  build:
+    runs-on: [self-hosted, db]
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          submodules: 'true'
+      - name: Install dependencies, build docs and coverage report
+        run: python3 -m pip install --upgrade pip && python3 -m pip install poetry
+      - uses: actions/[email protected]
+        with:
+          python-version: '3.10'
+          cache: 'poetry'
+      - run: |
+          python3 -m pip install --upgrade pip && python3 -m pip install poetry
+          poetry env use '3.10'
+          source $(poetry env info --path)/bin/activate
+          poetry install
+          # pandoc README.md -f markdown -t rst -s -o docs/source/intro.rst
+          cd docs && rm -rf source/reference/api/_autosummary && make html
+          cd .. && coverage run -m pytest -m "not integration_test" && coverage xml && coverage report -m
+      - name: Upload coverage to Codecov
+        uses: Wandalen/[email protected]
+        with:
+          action: codecov/[email protected]
+          with: |
+            token: ${{ secrets.CODECOV_TOKEN }}
+            file: ./coverage.xml
+            name: codecov-umbrella
+            fail_ci_if_error: true
+          attempt_limit: 5
+          attempt_delay: 30000
diff --git a/.github/workflows/docs_deploy.yml b/.github/workflows/docs_deploy.yml
@@ -0,0 +1,56 @@
+name: docs
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - .pre-commit-config.yaml
+      - .github/workflows/code_checks.yml
+      - .github/workflows/docs_build.yml
+      - .github/workflows/docs_deploy.yml
+      - .github/workflows/integration_tests.yml
+      - '**.py'
+      - '**.ipynb'
+      - poetry.lock
+      - pyproject.toml
+      - '**.rst'
+      - '**.md'
+
+jobs:
+  deploy:
+    runs-on: [self-hosted, db]
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          submodules: 'true'
+      - name: Install dependencies, build docs and coverage report
+        run: python3 -m pip install --upgrade pip && python3 -m pip install poetry
+      - uses: actions/[email protected]
+        with:
+          python-version: '3.10'
+          cache: 'poetry'
+      - run: |
+          poetry env use '3.10'
+          source $(poetry env info --path)/bin/activate
+          poetry install
+          # pandoc README.md -f markdown -t rst -s -o docs/source/intro.rst
+          cd docs && rm -rf source/reference/api/_autosummary && make html
+          cd .. && coverage run -m pytest -m "not integration_test" && coverage xml && coverage report -m
+      - name: Upload coverage to Codecov
+        uses: Wandalen/[email protected]
+        with:
+          action: codecov/[email protected]
+          with: |
+            token: ${{ secrets.CODECOV_TOKEN }}
+            file: ./coverage.xml
+            name: codecov-umbrella
+            fail_ci_if_error: true
+          attempt_limit: 5
+          attempt_delay: 30000
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_branch: github_pages
+          publish_dir: docs/build
diff --git a/.github/workflows/integration_tests.yml b/.github/workflows/integration_tests.yml
@@ -0,0 +1,61 @@
+name: integration tests
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - .pre-commit-config.yaml
+      - .github/workflows/code_checks.yml
+      - .github/workflows/docs_build.yml
+      - .github/workflows/docs_deploy.yml
+      - .github/workflows/integration_tests.yml
+      - '**.py'
+      - '**.ipynb'
+      - poetry.lock
+      - pyproject.toml
+      - '**.rst'
+      - '**.md'
+  pull_request:
+    branches:
+      - main
+    paths:
+      - .pre-commit-config.yaml
+      - .github/workflows/code_checks.yml
+      - .github/workflows/docs_build.yml
+      - .github/workflows/docs_deploy.yml
+      - .github/workflows/integration_tests.yml
+      - '**.py'
+      - '**.ipynb'
+      - poetry.lock
+      - pyproject.toml
+      - '**.rst'
+      - '**.md'
+
+jobs:
+  integration-tests:
+    runs-on: [self-hosted, db]
+    steps:
+      - uses: actions/checkout@v3
+      - name: Install poetry
+        run: pip install poetry
+      - uses: actions/[email protected]
+        with:
+          python-version: '3.10'
+      - name: Install dependencies and check code
+        run: |
+          poetry env use '3.10'
+          source $(poetry env info --path)/bin/activate
+          poetry install --without docs
+          coverage run -m pytest -m integration_test && coverage xml && coverage report -m
+      - name: Upload coverage to Codecov
+        uses: Wandalen/[email protected]
+        with:
+          action: codecov/[email protected]
+          with: |
+            token: ${{ secrets.CODECOV_TOKEN }}
+            file: ./coverage.xml
+            name: codecov-umbrella
+            fail_ci_if_error: true
+          attempt_limit: 5
+          attempt_delay: 30000
diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
@@ -0,0 +1,27 @@
+name: publish package
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Install apt dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install libcurl4-openssl-dev libssl-dev
+      - uses: actions/checkout@v3
+      - name: Install poetry
+        run: python3 -m pip install --upgrade pip && python3 -m pip install poetry
+      - uses: actions/[email protected]
+        with:
+          python-version: '3.10'
+      - name: Build package
+        run: poetry build
+      - name: Publish package
+        uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,30 @@
+*__pycache__*
+*.log
+docs/build
+.python-version
+*.DS_Store
+htmlcov
+.coverage
+venv
+.ipynb_checkpoints
+*.pt
+*.csv
+mlruns
+.profile
+.env
+*.html
+_extract
+*.gzip
+*checkpoint*
+*.parquet
+*.npy
+*.pkl
+*.npz
+*.csv
+*.pickle
+dist/
+outputs/
+multirun/
+_autosummary
+*cyclops_reports*
+*dummy_reports*
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,61 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0  # Use the ref you want to point at
+    hooks:
+    - id: trailing-whitespace
+    - id: check-ast
+    - id: check-builtin-literals
+    - id: check-docstring-first
+    - id: check-executables-have-shebangs
+    - id: debug-statements
+    - id: end-of-file-fixer
+    - id: mixed-line-ending
+      args: [--fix=lf]
+    - id: requirements-txt-fixer
+    - id: check-yaml
+    - id: check-toml
+
+  - repo: https://github.com/psf/black
+    rev: 23.7.0
+    hooks:
+    - id: black
+
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: 'v0.1.0'
+    hooks:
+    - id: ruff
+      args: [--fix, --exit-non-zero-on-fix]
+      types_or: [python, jupyter]
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.5.1
+    hooks:
+    - id: mypy
+      entry: python3 -m mypy --config-file pyproject.toml
+      language: system
+      types: [python]
+      exclude: "tests"
+
+  - repo: local
+    hooks:
+    - id: nbstripout
+      name: nbstripout
+      language: python
+      entry: nbstripout
+      exclude: ^docs/source/tutorials/gemini.ipynb
+
+  - repo: https://github.com/nbQA-dev/nbQA
+    rev: 1.7.0
+    hooks:
+    - id: nbqa-black
+    - id: nbqa-ruff
+      args: [--fix, --exit-non-zero-on-fix]
+
+  - repo: local
+    hooks:
+    - id: pytest
+      name: pytest
+      entry: python3 -m pytest -m "not integration_test"
+      language: system
+      pass_filenames: false
+      always_run: true