Inference data loader

.github/workflows/coverage.yaml

@@ -0,0 +1,31 @@
+name: Post coverage comment
+
+on:
+  workflow_run:
+    workflows: ["unit-tests"]
+    types:
+      - completed
+
+jobs:
+  test:
+    name: Run tests & display coverage
+    runs-on: ubuntu-latest
+    if: github.event.workflow_run.event == 'pull_request' && github.event.workflow_run.conclusion == 'success'
+    permissions:
+      # Gives the action the necessary permissions for publishing new
+      # comments in pull requests.
+      pull-requests: write
+      # Gives the action the necessary permissions for editing existing comments
+      contents: write
+      # Gives the action the necessary permissions for looking up the
+      # workflow that launched this workflow, and download the related
+      # artifact that contains the comment to be published
+      actions: read
+    steps:
+      # DO NOT run actions/checkout here, for security reasons
+      # For details, refer to https://securitylab.github.com/research/github-actions-preventing-pwn-requests/
+      - name: Post comment
+        uses: py-cov-action/python-coverage-comment-action@v3
+        with:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_PR_RUN_ID: ${{ github.event.workflow_run.id }}

.github/workflows/docs.yaml

@@ -13,15 +13,11 @@ jobs:
       uses: actions/setup-python@v5
       with:
         python-version: '3.10'
-    - name: Install Poetry
-      uses: snok/install-poetry@v1
-      with:
-        virtualenvs-create: false
-        virtualenvs-in-project: false
-        installer-parallel: true
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
     - name: Install and Build Docs
       run: |
-        poetry install
+        uv sync
         cd docs
         make clean
         make html

.github/workflows/publish.yaml

@@ -9,10 +9,19 @@ jobs:
     runs-on: ubuntu-latest
     environment: PyPI
     steps:
-    - uses: actions/checkout@v2
-    - 
-      name: Build and publish to pypi
-      uses: JRubics/[email protected]
+    - uses: actions/checkout@v4
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v3
       with:
-        python_version: "3.10.9"
-        pypi_token: ${{ secrets.PYPI_TOKEN }}
+        enable-cache: true
+        cache-dependency-glob: uv.lock
+
+    - name: Set up Python
+      run: uv python install 3.12
+
+    - name: Build
+      run: uv build
+
+    - name: Publish
+      run: uv publish -t ${{ secrets.PYPI_TOKEN }}

.github/workflows/unit-tests.yaml

@@ -12,9 +12,9 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     # set up our environment
     - 
@@ -33,4 +33,48 @@ jobs:
       name: run tests
       env:
         pyver: ${{ matrix.python-version }}
-      run: tox -e py${pyver//./}
+        COVERAGE_FILE: .coverage.${{ matrix.python-version }}
+      run: |
+        tox -e py${pyver//./}
+
+    - name: Store coverage file
+      uses: actions/upload-artifact@v4
+      with:
+        name: coverage-${{ matrix.python-version }}
+        path: .coverage.${{ matrix.python-version }}
+        include-hidden-files: true
+
+  coverage:
+    name: Coverage
+    runs-on: ubuntu-latest
+    needs: test
+    permissions:
+      # Gives the action the necessary permissions for publishing new
+      # comments in pull requests.
+      pull-requests: write
+      # Gives the action the necessary permissions for pushing data to the
+      # python-coverage-comment-action branch, and for editing existing
+      # comments (to avoid publishing multiple comments in the same PR)
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/download-artifact@v4
+        id: download
+        with:
+          pattern: coverage-*
+          merge-multiple: true
+
+      - name: Coverage comment
+        id: coverage_comment
+        uses: py-cov-action/python-coverage-comment-action@v3
+        with:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          MERGE_COVERAGE_FILES: true
+
+      - name: Store Pull Request comment to be posted
+        uses: actions/upload-artifact@v4
+        if: steps.coverage_comment.outputs.COMMENT_FILE_WRITTEN == 'true'
+        with:
+          name: python-coverage-comment-action
+          path: python-coverage-comment-action.txt

.pre-commit-config.yaml

@@ -1,26 +1,23 @@
 repos:
-- repo: https://github.com/pycqa/isort
-  rev: 5.12.0
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.9.6
   hooks:
-  - id: isort
-    name: isort (python)
-- repo: https://github.com/psf/black
-  rev: 22.3.0
+    - id: ruff
+      args: [ --fix ]
+    - id: ruff-format
+
+- repo: https://github.com/astral-sh/uv-pre-commit
+  # uv version
+  rev: 0.6.0
   hooks:
-  - id: black
-    additional_dependencies: ["click==8.0.4"]
-    language_version: python3
-- repo: https://github.com/pycqa/flake8
-  rev: 3.9.2
-  hooks:
-  - id: flake8
+    - id: uv-lock
+
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v2.3.0
   hooks:
   - id: end-of-file-fixer
-- repo: https://github.com/python-poetry/poetry
-  rev: 1.2.2
+
+- repo: https://github.com/dhruvmanila/remove-print-statements
+  rev: v0.5.2  
   hooks:
-  - id: poetry-check
-  - id: poetry-lock
-    args: [--check, --no-update]
+  - id: remove-print-statements

.readthedocs.yaml

@@ -0,0 +1,36 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+
+  jobs:
+    post_create_environment:
+      # Install uv
+      - pip install uv
+    post_install:
+      # Install dependencies
+      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH uv sync --all-extras
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#    - pdf
+#    - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+# python:
+#    install:
+#    - requirements: docs/requirements.txt

CITATION.cff

@@ -0,0 +1,37 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: ml4gw
+message: >-
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
+authors:
+  - given-names: Ethan
+    family-names: Marx
+    email: [email protected]
+    affiliation: MIT
+    orcid: 'https://orcid.org/0009-0000-4183-7876'
+  - given-names: William
+    family-names: Benoit
+    email: [email protected]
+    affiliation: University of Minnesota
+    orcid: 'https://orcid.org/0000-0003-4750-9413'
+  - given-names: Deep
+    family-names: Chatterjee
+    email: [email protected]
+    affiliation: MIT
+    orcid: 'https://orcid.org/0000-0003-0038-5468'
+  - given-names: Ravi
+    family-names: Kumar
+    email: [email protected]
+    affiliation: Indian Institute of Technology Bombay
+  - given-names: Alec
+    family-names: Gunny
+repository-code: 'https://github.com/ML4GW/ml4gw'
+abstract: >-
+  Torch utilities for doing machine learning in gravitational wave physics
+keywords:
+  - Gravitational waves
+  - Machine learning