caskade 0.6.1__tar.gz

caskade-0.6.1/.github/workflows/cd.yml

@@ -0,0 +1,99 @@
+name: CD
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+      - dev
+  release:
+    types:
+      - published
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  FORCE_COLOR: 3
+
+jobs:
+  dist:
+    name: Distribution build
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Build sdist and wheel
+        run: pipx run build
+
+      - uses: actions/upload-artifact@v4
+        with:
+          path: dist
+
+      - name: Check products
+        run: pipx run twine check dist/*
+
+  test-built-dist:
+    needs: [dist]
+    name: Test built distribution
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/setup-python@v5
+        name: Install Python
+        with:
+          python-version: "3.10"
+      - uses: actions/download-artifact@v4
+        with:
+          name: artifact
+          path: dist
+      - name: List contents of built dist
+        run: |
+          ls -ltrh
+          ls -ltrh dist
+      - name: Publish to Test PyPI
+        uses: pypa/gh-action-pypi-publish@v1.12.3
+        with:
+          repository-url: https://test.pypi.org/legacy/
+          verbose: true
+          skip-existing: true
+      - name: Check pypi packages
+        run: |
+          sleep 3
+          python -m pip install --upgrade pip
+
+          echo "=== Testing wheel file ==="
+          # Install wheel to get dependencies and check import
+          python -m pip install --extra-index-url https://test.pypi.org/simple --upgrade --pre caskade
+          python -c "import caskade; print(caskade.__version__); caskade.test()"
+          echo "=== Done testing wheel file ==="
+
+          echo "=== Testing source tar file ==="
+          # Install tar gz and check import
+          python -m pip uninstall --yes caskade
+          python -m pip install --extra-index-url https://test.pypi.org/simple --upgrade --pre --no-binary=:all: caskade
+          python -c "import caskade; print(caskade.__version__); caskade.test()"
+          echo "=== Done testing source tar file ==="
+
+  publish:
+    needs: [dist, test-built-dist]
+    name: Publish to PyPI
+    environment: pypi
+    permissions:
+      id-token: write
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release' && github.event.action == 'published'
+
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: artifact
+          path: dist
+
+      - uses: pypa/gh-action-pypi-publish@v1.12.3
+        if: startsWith(github.ref, 'refs/tags')

caskade-0.6.1/.github/workflows/ci.yml

@@ -0,0 +1,83 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: CI
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - main
+      - dev
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  FORCE_COLOR: 3
+  PROJECT_NAME: "caskade"
+
+jobs:
+  build:
+    runs-on: ${{matrix.os}}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+        os: [ubuntu-latest, windows-latest, macOS-latest]
+
+    steps:
+      - name: Checkout caskade
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          allow-prereleases: true
+
+      - name: Record State
+        run: |
+          pwd
+          echo github.ref is: ${{ github.ref }}
+          echo GITHUB_SHA is: $GITHUB_SHA
+          echo github.event_name is: ${{ github.event_name }}
+          echo github workspace: ${{ github.workspace }}
+          pip --version
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install pytest pytest-cov torch wheel pydantic
+
+      # We only want to install this on one run, because otherwise we'll have
+      # duplicate annotations.
+      - name: Install error reporter
+        if: ${{ matrix.python-version == '3.10' }}
+        run: |
+          python -m pip install pytest-github-actions-annotate-failures
+
+      - name: Install caskade
+        run: |
+          pip install -e ".[dev]"
+          pip show ${{ env.PROJECT_NAME }}
+
+      - name: Test with pytest
+        run: |
+          pytest -vvv --cov=${{ env.PROJECT_NAME }} --cov-report=xml --cov-report=term tests/
+
+      - name: Upload coverage reports to Codecov with GitHub Action
+        if:
+          ${{ matrix.python-version == '3.10' && matrix.os == 'ubuntu-latest'}}
+        uses: codecov/codecov-action@v4
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+        with:
+          files: ./coverage.xml
+          flags: unittests
+          name: codecov-umbrella
+          fail_ci_if_error: true

caskade-0.6.1/.gitignore

@@ -0,0 +1,163 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+src/caskade/_version.py
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

caskade-0.6.1/.readthedocs.yml

@@ -0,0 +1,43 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/source/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
+# Specify dependencies to be installed
+# Define the system dependencies
+build:
+  os: "ubuntu-20.04"
+  tools:
+    python: "3.10"
+  apt_packages:
+    - pandoc # Specify pandoc to be installed via apt-get
+    - graphviz # Specify graphviz to be installed via apt-get
+  jobs:
+    pre_build:
+      # Generate the Sphinx configuration for this Jupyter Book so it builds.
+      - "jupyter-book config sphinx docs/source/"
+      # Create font cache ahead of jupyter book
+      - 'python -c "import matplotlib.pyplot as plt"'
+      # Get the API documentation dynamically
+      - "sphinx-apidoc -f -o docs/source/ src/caskade/"
+
+python:
+  install:
+    - requirements: docs/requirements.txt # Path to your requirements.txt file
+    - requirements: requirements.txt # Path to your requirements.txt file
+    - method: pip
+      path: . # Install the package itself

caskade-0.6.1/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Connor Stone, PhD
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

caskade-0.6.1/PKG-INFO

@@ -0,0 +1,113 @@
+Metadata-Version: 2.4
+Name: caskade
+Version: 0.6.1
+Summary: Package for building scientific simulators, with dynamic arguments arranged in a directed acyclic graph.
+Project-URL: Homepage, https://github.com/ConnorStoneAstro/caskade
+Project-URL: Documentation, https://github.com/ConnorStoneAstro/caskade
+Project-URL: Repository, https://github.com/ConnorStoneAstro/caskade
+Project-URL: Issues, https://github.com/ConnorStoneAstro/caskade/issues
+Author-email: Connor Stone <connorstone628@gmail.com>, Alexandre Adam <alexandre.adam@mila.quebec>
+License: MIT License
+        
+        Copyright (c) 2024 Connor Stone, PhD
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+License-File: LICENSE
+Keywords: DAG,caskade,differentiable programming,pytorch,scientific python
+Classifier: Development Status :: 1 - Planning
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.9
+Requires-Dist: torch
+Provides-Extra: dev
+Requires-Dist: graphviz<1,>=0.17; extra == 'dev'
+Requires-Dist: pre-commit<4,>=3.6; extra == 'dev'
+Requires-Dist: pytest-cov<5,>=4.1; extra == 'dev'
+Requires-Dist: pytest-mock<4,>=3.12; extra == 'dev'
+Requires-Dist: pytest<9,>=8.0; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# caskade
+
+[![CI](https://github.com/ConnorStoneAstro/caskade/actions/workflows/ci.yml/badge.svg)](https://github.com/ConnorStoneAstro/caskade/actions/workflows/ci.yml)
+[![CD](https://github.com/ConnorStoneAstro/caskade/actions/workflows/cd.yml/badge.svg)](https://github.com/ConnorStoneAstro/caskade/actions/workflows/cd.yml)
+[![codecov](https://codecov.io/gh/ConnorStoneAstro/caskade/graph/badge.svg?token=7YAEJJZ4GM)](https://codecov.io/gh/ConnorStoneAstro/caskade)
+[![PyPI - Version](https://img.shields.io/pypi/v/caskade)](https://pypi.org/project/caskade/)
+[![Documentation Status](https://readthedocs.org/projects/caskade/badge/?version=latest)](https://caskade.readthedocs.io/en/latest/?badge=latest)
+
+Build scientific simulators, treating them as a directed acyclic graph. Handles
+argument passing for complex nested simulators.
+
+## Install
+
+``` bash
+pip install caskade
+```
+
+## Usage
+
+Make a `Module` object which may have some `Param`s. Define a `forward` method
+using the decorator.
+
+``` python
+from caskade import Module, Param, forward
+
+class MySim(Module):
+    def __init__(self, a, b=None):
+        super().__init__()
+        self.a = a
+        self.b = Param("b", b)
+
+    @forward
+    def myfun(self, x, b=None):
+        return x + self.a + b
+```
+
+We may now create instances of the simulator and pass the dynamic parameters.
+
+``` python
+import torch
+
+sim = MySim(1.0)
+
+params = [torch.tensor(2.0)]
+
+print(sim.myfun(3.0, params=params))
+```
+
+Which will print `6` by automatically filling `b` with the value from `params`.
+
+### Why do this?
+
+The above example is not very impressive, the real power comes from the fact
+that `Module` objects can be nested arbitrarily making a much more complicated
+analysis graph. Further, the `Param` objects can be linked or have other complex
+relationships. All of the complexity of the nested structure and argument
+passing is abstracted away so that at the top one need only pass a list of
+tensors for each parameter, a single large 1d tensor, or a dictionary with the
+same structure as the graph.
+
+## Documentation
+
+The `caskade` interface has lots of flexibility, check out the
+[docs](https://caskade.readthedocs.io) to learn more. For a quick start, jump
+right to the [Jupyter notebook
+tutorial](https://caskade.readthedocs.io/en/latest/notebooks/BeginnersGuide.html)!

caskade-0.6.1/README.md

@@ -0,0 +1,66 @@
+# caskade
+
+[![CI](https://github.com/ConnorStoneAstro/caskade/actions/workflows/ci.yml/badge.svg)](https://github.com/ConnorStoneAstro/caskade/actions/workflows/ci.yml)
+[![CD](https://github.com/ConnorStoneAstro/caskade/actions/workflows/cd.yml/badge.svg)](https://github.com/ConnorStoneAstro/caskade/actions/workflows/cd.yml)
+[![codecov](https://codecov.io/gh/ConnorStoneAstro/caskade/graph/badge.svg?token=7YAEJJZ4GM)](https://codecov.io/gh/ConnorStoneAstro/caskade)
+[![PyPI - Version](https://img.shields.io/pypi/v/caskade)](https://pypi.org/project/caskade/)
+[![Documentation Status](https://readthedocs.org/projects/caskade/badge/?version=latest)](https://caskade.readthedocs.io/en/latest/?badge=latest)
+
+Build scientific simulators, treating them as a directed acyclic graph. Handles
+argument passing for complex nested simulators.
+
+## Install
+
+``` bash
+pip install caskade
+```
+
+## Usage
+
+Make a `Module` object which may have some `Param`s. Define a `forward` method
+using the decorator.
+
+``` python
+from caskade import Module, Param, forward
+
+class MySim(Module):
+    def __init__(self, a, b=None):
+        super().__init__()
+        self.a = a
+        self.b = Param("b", b)
+
+    @forward
+    def myfun(self, x, b=None):
+        return x + self.a + b
+```
+
+We may now create instances of the simulator and pass the dynamic parameters.
+
+``` python
+import torch
+
+sim = MySim(1.0)
+
+params = [torch.tensor(2.0)]
+
+print(sim.myfun(3.0, params=params))
+```
+
+Which will print `6` by automatically filling `b` with the value from `params`.
+
+### Why do this?
+
+The above example is not very impressive, the real power comes from the fact
+that `Module` objects can be nested arbitrarily making a much more complicated
+analysis graph. Further, the `Param` objects can be linked or have other complex
+relationships. All of the complexity of the nested structure and argument
+passing is abstracted away so that at the top one need only pass a list of
+tensors for each parameter, a single large 1d tensor, or a dictionary with the
+same structure as the graph.
+
+## Documentation
+
+The `caskade` interface has lots of flexibility, check out the
+[docs](https://caskade.readthedocs.io) to learn more. For a quick start, jump
+right to the [Jupyter notebook
+tutorial](https://caskade.readthedocs.io/en/latest/notebooks/BeginnersGuide.html)!

caskade-0.6.1/docs/Makefile

@@ -0,0 +1,19 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+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)

caskade-0.6.1/docs/requirements.txt

@@ -0,0 +1,7 @@
+ipywidgets
+jupyter-book
+matplotlib
+sphinx
+sphinx_rtd_theme
+sphinx-automodapi
+graphviz

caskade-0.6.1/docs/source/_config.yml

@@ -0,0 +1,57 @@
+# Book settings
+# Learn more at https://jupyterbook.org/customize/config.html
+
+title: caskade
+author: Connor Stone and Alexandre Adam
+# logo: ../../media/caustics_logo.png
+
+# Force re-execution of notebooks on each build.
+# See https://jupyterbook.org/content/execute.html
+execute:
+  execute_notebooks: force
+  allow_errors: false
+  # Per-cell notebook execution limit (seconds)
+  timeout: 300
+
+# Define the name of the latex output file for PDF builds
+# latex:
+#   latex_documents:
+#     targetname: book.tex
+
+# Add a bibtex file so that we can create citations
+# bibtex_bibfiles:
+#   - references.bib
+
+# Information about where the book exists on the web
+repository:
+  url: https://github.com/ConnorStoneAstro/caskade # Online location of your book
+  path_to_book: docs/source # Optional path to your book, relative to the repository root
+  branch: main # Which branch of the repository should be used when creating links (optional)
+
+# Add GitHub buttons to your book
+# See https://jupyterbook.org/customize/config.html#add-a-link-to-your-repository
+html:
+  # favicon: ../../media/caustics_favicon.ico
+  use_issues_button: true
+  use_repository_button: true
+
+sphinx:
+  extra_extensions:
+    # - "sphinx_automodapi.automodapi"
+    - "sphinx.ext.autodoc"
+    - "sphinx.ext.napoleon"
+    - "sphinx.ext.viewcode"
+    - "sphinx.ext.autosummary"
+    - "sphinx.ext.doctest"
+    - "sphinx.ext.coverage"
+    - "sphinx.ext.mathjax"
+    - "sphinx.ext.ifconfig"
+  config:
+    autosummary_generate: True
+#   config:
+#     numpydoc_show_class_members: False
+  # config:
+  #   html_theme_options:
+  #     logo:
+  #       image_light: ../../media/caustics_logo_white.png
+  #       image_dark: ../../media/caustics_logo.png

caskade-0.6.1/docs/source/_toc.yml

@@ -0,0 +1,15 @@
+# Table of contents
+# Learn more at https://jupyterbook.org/customize/toc.html
+
+format: jb-book
+root: intro
+chapters:
+  - file: notebooks/BeginnersGuide
+  - file: install
+  - file: modules
+  # - file: contributing
+  # - file: frequently_asked_questions
+  # - file: citation
+  # - file: license
+  # - file: glossary
+  # - file: genindex