ptychi 1.0.0__tar.gz

ptychi-1.0.0/.github/pull_request_template.md

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+# Features/fixes
+
+Describe new features or bugs fixed.
+
+# Related issues (optional)
+
+Add links to issues related to this pull request, if any.
+
+# Mentions
+
+Mention team members responsible for reviewing this change. 
+
+# Checklist
+
+Have you...
+- [ ] Formatted your code properly adhering to PEP-8? Considering using RUFF to format your code automatically.
+- [ ] Merged or rebased the main branch in your branch?

ptychi-1.0.0/.github/workflows/pypi_publish.yml

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+name: Upload Python Package to PyPI when a Release is Created
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  pypi-publish:
+    name: Publish release to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/ptychi
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip build
+      - name: Build package
+        run: |
+          python -m build
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}

ptychi-1.0.0/.github/workflows/python-app.yml

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+# 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: Python application
+
+on:
+  push:
+    branches: [ "main", "ci" ]
+  pull_request:
+    branches: [ "main" ]
+  workflow_dispatch:
+
+env:
+  PTYCHO_CI_DATA_DIR: /local/ptycho_aux_data/ci_data
+  CONDA_EXE: /local/actions-env/miniconda3/condabin/conda
+  CONDA_ROOT: /local/actions-env/miniconda3/
+
+permissions:
+  contents: read
+
+jobs:
+  lint:
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    runs-on: self-hosted
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Activate environment
+        id: activate_env
+        run: |
+          source $CONDA_ROOT/bin/activate ci_py311_base
+
+      - name: Install Ruff
+        run: pip install ruff
+
+      - name: Run Ruff
+        run: ruff check src/ --output-format=github
+
+  linux-x86-gpu:
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    runs-on: self-hosted
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Update test data
+      id: update_test_data
+      run: |
+        PACKAGE_DIR=$(pwd)
+        cd $PTYCHO_CI_DATA_DIR
+        git pull origin main
+        cd $PACKAGE_DIR
+
+    - name: Create environment
+      id: create_env
+      run: |
+        export ENVNAME=ci_py311_$(date +%s)
+        $CONDA_EXE create --quiet --yes --force -n $ENVNAME --clone ci_py311_base
+        echo "ENVNAME=$ENVNAME" >> $GITHUB_ENV
+      
+    - name: Install dependencies
+      run: |
+        $CONDA_EXE env list
+        source $CONDA_ROOT/bin/activate $ENVNAME
+        $CONDA_ROOT/envs/$ENVNAME/bin/pip install --upgrade pip
+        $CONDA_ROOT/envs/$ENVNAME/bin/pip install pytest
+        if [ -f requirements.txt ]; then $CONDA_ROOT/envs/$ENVNAME/bin/pip install -r requirements.txt; fi
+        $CONDA_ROOT/envs/$ENVNAME/bin/pip install -e .
+        $CONDA_ROOT/envs/$ENVNAME/bin/pip install torch==2.4.1 torchvision==0.19.1 numpy==2.1.2
+
+    - name: List build environment
+      run: $CONDA_EXE list -n $ENVNAME
+
+    - name: Test with pytest
+      run: |
+        source $CONDA_ROOT/bin/activate $ENVNAME
+        echo $(which python)
+        cd tests
+        pytest -s --high-tol --save-timing
+
+    - name: Remove environment
+      if: always()
+      run: |
+        $CONDA_EXE remove -n $ENVNAME --all --yes --force
+  

ptychi-1.0.0/.gitignore

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+# 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
+
+# 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
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__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/
+
+# Workspace stuff
+workspace/
+
+# Binaries
+*.tiff
+*.tif
+*.pdf
+*.date
+*.png
+*.npy
+*.mat
+*.hdf5
+*.h5
+
+# 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/

ptychi-1.0.0/LICENSE

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+Apache License
+                           Version 2.0, January 2004
+                
+Copyright © 2025 UChicago Argonne, LLC All right reserved
+
+Title: Pty-chi: a multi-engine ptychography reconstruction library
+
+ARGONNE NATIONAL LABORATORY, WITH A FACILITY IN THE STATE OF ILLINOIS, IS OWNED BY THE UNITED STATES GOVERNMENT, AND OPERATED BY UCHICAGO ARGONNE, LLC UNDER PROVISION OF A CONTRACT WITH THE DEPARTMENT OF ENERGY.
+
+
+ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
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+      any Contribution intentionally submitted for inclusion in the Work
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+      the terms of any separate license agreement you may have executed
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+      whether in tort (including negligence), contract, or otherwise,
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+   END OF TERMS AND CONDITIONS
+
+ 

ptychi-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: ptychi
+Version: 1.0.0
+Summary: Pty-chi is a package of ptychography reconstruction engines
+Requires-Python: >=3.11
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+Requires-Dist: h5py
+Requires-Dist: matplotlib
+Requires-Dist: mypy
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: ruff
+Requires-Dist: scikit-image
+Requires-Dist: scikit-learn
+Requires-Dist: scipy
+Requires-Dist: torch>=2.4.1
+Requires-Dist: torchvision
+Requires-Dist: tqdm
+Provides-Extra: movies
+Requires-Dist: opencv-python; extra == "movies"
+Dynamic: license-file
+
+.. image:: docs/source/img/logo.png
+   :alt: Pty-chi Logo
+   :align: center
+   :width: 200px
+
+
+Welcome to the repository of Pty-chi, a PyTorch-based ptychography reconstruction library!
+
+
+============
+Installation
+============
+
+Clone the repository to your workspace, and create a new conda environment
+using::
+
+    conda create -n ptychi -c conda-forge -c nvidia --file requirements-dev.txt
+
+Then install the package using::
+
+    pip install -e .
+
+
+=======================
+How to run test scripts 
+=======================
+
+1. Contact the developers to be given access to the APS GitLab repository
+   that holds test data. 
+2. After gaining access, clone the GitLab data repository to your
+   hard drive. 
+3. Set ``PTYCHO_CI_DATA_DIR`` to the ``ci_data`` directory of the data
+   repository: ``export PTYCHO_CI_DATA_DIR="path_to_data_repo/ci_data"``.
+4. Run any test scripts in ``tests`` with Python.
+
+
+=====================
+How to build the docs
+=====================
+
+To build the docs, install the dependencies as the first step::
+
+   pip install -e .[docs]
+
+Then::
+
+   cd docs
+   make html
+
+You can then view the docs by opening ``docs/build/html/index.html`` in your browser.
+
+
+=================
+Developer's Guide
+=================
+
+Please refer to the developer's guide for more information on how to contribute
+to the project. The developer's guide is hosted on the
+`Wiki <https://git.aps.anl.gov/ptycho_software/pty-chi/-/wikis/Developer's-guide/home>`_ page of Pty-Chi's 
+APS GitLab repository.
+To gain access to the APS GitLab repository, please contact the developers.

ptychi-1.0.0/README.rst

@@ -0,0 +1,61 @@
+.. image:: docs/source/img/logo.png
+   :alt: Pty-chi Logo
+   :align: center
+   :width: 200px
+
+
+Welcome to the repository of Pty-chi, a PyTorch-based ptychography reconstruction library!
+
+
+============
+Installation
+============
+
+Clone the repository to your workspace, and create a new conda environment
+using::
+
+    conda create -n ptychi -c conda-forge -c nvidia --file requirements-dev.txt
+
+Then install the package using::
+
+    pip install -e .
+
+
+=======================
+How to run test scripts 
+=======================
+
+1. Contact the developers to be given access to the APS GitLab repository
+   that holds test data. 
+2. After gaining access, clone the GitLab data repository to your
+   hard drive. 
+3. Set ``PTYCHO_CI_DATA_DIR`` to the ``ci_data`` directory of the data
+   repository: ``export PTYCHO_CI_DATA_DIR="path_to_data_repo/ci_data"``.
+4. Run any test scripts in ``tests`` with Python.
+
+
+=====================
+How to build the docs
+=====================
+
+To build the docs, install the dependencies as the first step::
+
+   pip install -e .[docs]
+
+Then::
+
+   cd docs
+   make html
+
+You can then view the docs by opening ``docs/build/html/index.html`` in your browser.
+
+
+=================
+Developer's Guide
+=================
+
+Please refer to the developer's guide for more information on how to contribute
+to the project. The developer's guide is hosted on the
+`Wiki <https://git.aps.anl.gov/ptycho_software/pty-chi/-/wikis/Developer's-guide/home>`_ page of Pty-Chi's 
+APS GitLab repository.
+To gain access to the APS GitLab repository, please contact the developers.

ptychi-1.0.0/docs/Makefile

@@ -0,0 +1,19 @@
+# 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     = source
+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) 

ptychi-1.0.0/docs/source/api/enums.rst

@@ -0,0 +1,7 @@
+Enumerations
+============
+
+.. automodule:: ptychi.api.enums
+   :members:
+   :undoc-members:
+   :show-inheritance: 

ptychi-1.0.0/docs/source/api/index.rst

@@ -0,0 +1,10 @@
+API Reference
+=============
+
+.. toctree::
+   :maxdepth: 2
+
+   options
+   enums 
+   task
+   utils