ml4gw 0.7.2__tar.gz → 0.7.4__tar.gz

ml4gw-0.7.4/.gitattributes

@@ -0,0 +1,2 @@
+# use lf line endings for all text files
+* text=auto

ml4gw-0.7.4/.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 }}

ml4gw-0.7.4/.github/workflows/docs.yaml

@@ -0,0 +1,29 @@
+name: Build and publish docs
+on:
+  push:
+    branches:
+      - main
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v1
+    - name: Setup python
+      id: setup-python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.10'
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
+    - name: Install and Build Docs
+      run: |
+        uv sync
+        cd docs
+        uv run make clean
+        uv run make html
+    - 
+      name: Deploy pages
+      uses: JamesIves/github-pages-deploy-action@v4.2.5
+      with:
+        branch: gh-pages
+        folder: docs/_build/html

ml4gw-0.7.4/.github/workflows/pre-commit.yaml

@@ -0,0 +1,17 @@
+name: pre-commit
+
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - uses: actions/setup-python@v2
+      with:
+        python-version: "3.9"
+    - uses: pre-commit/action@v2.0.3

ml4gw-0.7.4/.github/workflows/publish.yaml

@@ -0,0 +1,27 @@
+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    environment: PyPI
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v3
+      with:
+        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 }}

ml4gw-0.7.4/.github/workflows/unit-tests.yaml

@@ -0,0 +1,80 @@
+name: unit-tests
+
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.9', '3.10', '3.11', '3.12']
+    steps:
+    - uses: actions/checkout@v4
+
+    # set up our environment
+    - 
+      name: Install Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    -
+      name: Install tox
+      run: |
+        python -m pip install --upgrade pip
+        pip install tox tox-gh-actions
+
+    # run the library's tests
+    -
+      name: run tests
+      env:
+        pyver: ${{ matrix.python-version }}
+        COVERAGE_FILE: .coverage.${{ 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

ml4gw-0.7.4/.gitignore

@@ -0,0 +1,3 @@
+**/__pycache__
+**/.ipynb_checkpoints
+**/.tox

ml4gw-0.7.4/.pre-commit-config.yaml

@@ -0,0 +1,23 @@
+repos:
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.9.6
+  hooks:
+    - id: ruff
+      args: [ --fix ]
+    - id: ruff-format
+
+- repo: https://github.com/astral-sh/uv-pre-commit
+  # uv version
+  rev: 0.6.0
+  hooks:
+    - 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/dhruvmanila/remove-print-statements
+  rev: v0.5.2  
+  hooks:
+  - id: remove-print-statements

ml4gw-0.7.4/.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

ml4gw-0.7.4/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: emarx@mit.edu
+    affiliation: MIT
+    orcid: 'https://orcid.org/0009-0000-4183-7876'
+  - given-names: William
+    family-names: Benoit
+    email: benoi090@umn.edu
+    affiliation: University of Minnesota
+    orcid: 'https://orcid.org/0000-0003-4750-9413'
+  - given-names: Deep
+    family-names: Chatterjee
+    email: deep1018@mit.edu
+    affiliation: MIT
+    orcid: 'https://orcid.org/0000-0003-0038-5468'
+  - given-names: Ravi
+    family-names: Kumar
+    email: ravi.kr@iitb.ac.in
+    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

ml4gw-0.7.2/README.md → ml4gw-0.7.4/PKG-INFO

@@ -1,3 +1,17 @@
+Metadata-Version: 2.4
+Name: ml4gw
+Version: 0.7.4
+Summary: Tools for training torch models on gravitational wave data
+Author-email: Ethan Marx <emarx@mit.edu>, Will Benoit <benoi090@umn.edu>, Deep Chatterjee <deep1018@mit.edu>, Alec Gunny <alec.gunny@ligo.org>
+License-File: LICENSE
+Requires-Python: <3.13,>=3.9
+Requires-Dist: jaxtyping<0.3,>=0.2
+Requires-Dist: numpy<2.0.0
+Requires-Dist: scipy<1.15,>=1.9.0
+Requires-Dist: torchaudio~=2.0
+Requires-Dist: torch~=2.0
+Description-Content-Type: text/markdown
+
 # ML4GW
 ![PyPI - Version](https://img.shields.io/pypi/v/ml4gw)
 ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/ml4gw) 
@@ -25,29 +39,6 @@ To build with a specific version of PyTorch/CUDA, please see the PyTorch install
 pip install ml4gw torch==2.5.1--extra-index-url=https://download.pytorch.org/whl/cu118
 ```
 
-### Poetry installation
-`ml4gw` is also fully compatible with use in Poetry, with your `pyproject.toml` set up like
-
-```toml
-[tool.poetry.dependencies]
-python = "^3.9"  # python versions 3.9-3.12 are supported
-ml4gw = "^0.6"
-```
-
-To build against a specific PyTorch/CUDA combination, consult the PyTorch installation documentation above and specify the `extra-index-url` via the `tool.poetry.source` table in your `pyproject.toml`. For example, to build against CUDA 11.6, you would do something like:
-
-```toml
-[tool.poetry.dependencies]
-python = "^3.9"
-ml4gw = "^0.6"
-torch = {version = "^2.0", source = "torch"}
-
-[[tool.poetry.source]]
-name = "torch"
-url = "https://download.pytorch.org/whl/cu118"
-priority = "explicit"
-```
-
 ## Contributing
 If you come across errors in the code, have difficulties using this software, or simply find that the current version doesn't cover your use case, please file an issue on our GitHub page, and we'll be happy to offer support.
 We encourage users who encounter these difficulties to file issues on GitHub, and we'll be happy to offer support to extend our coverage to new or improved functionality.

ml4gw-0.7.2/PKG-INFO → ml4gw-0.7.4/README.md

@@ -1,21 +1,3 @@
-Metadata-Version: 2.3
-Name: ml4gw
-Version: 0.7.2
-Summary: Tools for training torch models on gravitational wave data
-Author: Alec Gunny
-Author-email: alec.gunny@ligo.org
-Requires-Python: >=3.9,<3.13
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Requires-Dist: jaxtyping (>=0.2,<0.3)
-Requires-Dist: numpy (<2.0.0)
-Requires-Dist: torch (>=2.0,<3.0)
-Requires-Dist: torchaudio (>=2.0,<3.0)
-Description-Content-Type: text/markdown
-
 # ML4GW
 ![PyPI - Version](https://img.shields.io/pypi/v/ml4gw)
 ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/ml4gw) 
@@ -43,29 +25,6 @@ To build with a specific version of PyTorch/CUDA, please see the PyTorch install
 pip install ml4gw torch==2.5.1--extra-index-url=https://download.pytorch.org/whl/cu118
 ```
 
-### Poetry installation
-`ml4gw` is also fully compatible with use in Poetry, with your `pyproject.toml` set up like
-
-```toml
-[tool.poetry.dependencies]
-python = "^3.9"  # python versions 3.9-3.12 are supported
-ml4gw = "^0.6"
-```
-
-To build against a specific PyTorch/CUDA combination, consult the PyTorch installation documentation above and specify the `extra-index-url` via the `tool.poetry.source` table in your `pyproject.toml`. For example, to build against CUDA 11.6, you would do something like:
-
-```toml
-[tool.poetry.dependencies]
-python = "^3.9"
-ml4gw = "^0.6"
-torch = {version = "^2.0", source = "torch"}
-
-[[tool.poetry.source]]
-name = "torch"
-url = "https://download.pytorch.org/whl/cu118"
-priority = "explicit"
-```
-
 ## Contributing
 If you come across errors in the code, have difficulties using this software, or simply find that the current version doesn't cover your use case, please file an issue on our GitHub page, and we'll be happy to offer support.
 We encourage users who encounter these difficulties to file issues on GitHub, and we'll be happy to offer support to extend our coverage to new or improved functionality.
@@ -75,4 +34,3 @@ By bringing in new users with new use cases, we hope to develop this library int
 
 ## Funding
 We are grateful for the support of the U.S. National Science Foundation (NSF) Harnessing the Data Revolution (HDR) Institute for <a href="https://a3d3.ai">Accelerating AI Algorithms for Data Driven Discovery (A3D3)</a> under Cooperative Agreement No. <a href="https://www.nsf.gov/awardsearch/showAward?AWD_ID=2117997">PHY-2117997</a>.
-

ml4gw-0.7.4/docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

ml4gw-0.7.4/docs/conf.py

@@ -0,0 +1,65 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+
+sys.path.insert(0, os.path.abspath("../"))
+
+
+# -- Project information -----------------------------------------------------
+
+project = "ml4gw"
+copyright = "2024, Alec Gunny, Ethan Marx, William Benoit, Deep Chatterjee"
+author = "Alec Gunny, Ethan Marx, William Benoit, Deep Chatterjee"
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.napoleon",
+    "sphinx_autodoc_typehints",
+    "sphinx.ext.githubpages",
+]
+
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = "python"
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "sphinx_rtd_theme"
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ["_static"]

ml4gw-0.7.4/docs/index.rst

@@ -0,0 +1,50 @@
+.. ml4gw documentation master file, created by
+   sphinx-quickstart on Mon Feb 19 09:02:43 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to ml4gw's documentation!
+=================================
+
+.. note:: 
+   This documentation is a work in progress!
+   If you have any questions or suggestions, please feel free to reach out to ml4gw@ligo.mit.edu
+
+ml4gw
+=====
+ml4gw is a library of `pytorch  <https://pytorch.org/docs/stable/index.html>`_ utilities 
+for training neural networks in service of gravitational wave physics applications.
+
+The code can be found on github at `<https://github.com/ml4gw/ml4gw>`_
+
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Contents:
+
+   installation
+   modules
+
+Projects
+========
+Currently, the following projects are using ml4gw to support their research:
+
+* `Aframe <https://github.com/ml4gw/aframev2>`_ - Gravitational wave detection of binary black hole mergers
+* `PE <https://github.com/ml4gw/aframev2>`_ - Parameter estimation of gravitational wave signals
+
+
+Development
+===========
+As this library is still very much a work in progress, 
+we anticipate that novel use cases will encounter errors stemming from a lack of robustness. 
+We encourage users who encounter these difficulties to file issues on GitHub, and we'll be happy to offer 
+support to extend our coverage to new or improved functionality. 
+We also strongly encourage ML users in the GW physics space to try their hand at working on these issues and joining on as collaborators! 
+For more information about how to get involved, feel free to reach out to ml4gw@ligo.mit.edu. 
+By bringing in new users with new use cases, we hope to develop this library into a truly general-purpose tool which makes 
+DL more accessible for gravitational wave physicists everywhere.
+   
+
+Funding
+=======
+We are grateful for the support of the U.S. National Science Foundation (NSF) Harnessing the Data Revolution (HDR) Institute for `Accelerating AI Algorithms for Data Driven Discovery (A3D3) <https://a3d3.ai">`_ under Cooperative Agreement No. `PHY-2117997 <https://www.nsf.gov/awardsearch/showAward?AWD_ID=2117997>`_.

ml4gw-0.7.4/docs/installation.rst

@@ -0,0 +1,19 @@
+============
+Installation
+============
+
+Pip
+===
+ml4gw is installable with pip:
+
+.. code-block:: console
+       
+    $ pip install ml4gw
+
+
+To build with a specific version of PyTorch/CUDA, please see the PyTorch installation `instructions <https://pytorch.org/get-started/previous-versions/>`_
+to see how to specify the desired torch version and :code:`--extra-index-url` flag. For example, to install with PyTorch 1.12 and CUDA 11.6, use the following command:
+
+.. code-block:: console
+    
+        $ pip install ml4gw torch==1.12.0 --extra-index-url=https://download.pytorch.org/whl/cu116

ml4gw-0.7.4/docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

ml4gw-0.7.4/docs/ml4gw.dataloading.rst

@@ -0,0 +1,37 @@
+ml4gw.dataloading package
+=========================
+
+Submodules
+----------
+
+ml4gw.dataloading.chunked\_dataset module
+-----------------------------------------
+
+.. automodule:: ml4gw.dataloading.chunked_dataset
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ml4gw.dataloading.hdf5\_dataset module
+--------------------------------------
+
+.. automodule:: ml4gw.dataloading.hdf5_dataset
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ml4gw.dataloading.in\_memory\_dataset module
+--------------------------------------------
+
+.. automodule:: ml4gw.dataloading.in_memory_dataset
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: ml4gw.dataloading
+   :members:
+   :undoc-members:
+   :show-inheritance:

ml4gw-0.7.4/docs/ml4gw.nn.autoencoder.rst

@@ -0,0 +1,45 @@
+ml4gw.nn.autoencoder package
+============================
+
+Submodules
+----------
+
+ml4gw.nn.autoencoder.base module
+--------------------------------
+
+.. automodule:: ml4gw.nn.autoencoder.base
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ml4gw.nn.autoencoder.convolutional module
+-----------------------------------------
+
+.. automodule:: ml4gw.nn.autoencoder.convolutional
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ml4gw.nn.autoencoder.skip\_connection module
+--------------------------------------------
+
+.. automodule:: ml4gw.nn.autoencoder.skip_connection
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ml4gw.nn.autoencoder.utils module
+---------------------------------
+
+.. automodule:: ml4gw.nn.autoencoder.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: ml4gw.nn.autoencoder
+   :members:
+   :undoc-members:
+   :show-inheritance: