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update project template
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‎.gitignore

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# Jupyter Notebook
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.ipynb_checkpoints
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# Dask worker cache
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dask-worker-space/
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# pyenv
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.python-version
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.vscode/
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.idea/
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#
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tests/data/*
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*.h5
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*.hdf
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*DS_Store
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*.tif
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*.png

‎CODE_OF_CONDUCT.rst

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====================================
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Contributor Covenant Code of Conduct
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====================================
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Our Pledge
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----------
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In the interest of fostering an open and welcoming environment, we as
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contributors and maintainers pledge to make participation in our project and
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our community a harassment-free experience for everyone, regardless of age, body
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size, disability, ethnicity, sex characteristics, gender identity and expression,
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level of experience, education, socio-economic status, nationality, personal
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appearance, race, religion, or sexual identity and orientation.
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Our Standards
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-------------
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Examples of behavior that contributes to creating a positive environment
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include:
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* Using welcoming and inclusive language
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* Being respectful of differing viewpoints and experiences
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* Gracefully accepting constructive criticism
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* Focusing on what is best for the community
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* Showing empathy towards other community members
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Examples of unacceptable behavior by participants include:
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* The use of sexualized language or imagery and unwelcome sexual attention or
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advances
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* Trolling, insulting/derogatory comments, and personal or political attacks
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* Public or private harassment
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* Publishing others' private information, such as a physical or electronic
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address, without explicit permission
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* Other conduct which could reasonably be considered inappropriate in a
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professional setting
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Our Responsibilities
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--------------------
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Project maintainers are responsible for clarifying the standards of acceptable
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behavior and are expected to take appropriate and fair corrective action in
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response to any instances of unacceptable behavior.
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Project maintainers have the right and responsibility to remove, edit, or
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reject comments, commits, code, wiki edits, issues, and other contributions
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that are not aligned to this Code of Conduct, or to ban temporarily or
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permanently any contributor for other behaviors that they deem inappropriate,
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threatening, offensive, or harmful.
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Scope
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-----
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This Code of Conduct applies within all project spaces, and it also applies when
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an individual is representing the project or its community in public spaces.
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Examples of representing a project or community include using an official
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project e-mail address, posting via an official social media account, or acting
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as an appointed representative at an online or offline event. Representation of
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a project may be further defined and clarified by project maintainers.
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Enforcement
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-----------
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Instances of abusive, harassing, or otherwise unacceptable behavior may be
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reported by contacting the project team at [INSERT EMAIL ADDRESS]. All
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complaints will be reviewed and investigated and will result in a response that
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is deemed necessary and appropriate to the circumstances. The project team is
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obligated to maintain confidentiality with regard to the reporter of an incident.
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Further details of specific enforcement policies may be posted separately.
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Project maintainers who do not follow or enforce the Code of Conduct in good
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faith may face temporary or permanent repercussions as determined by other
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members of the project's leadership.
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Attribution
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-----------
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This Code of Conduct is adapted from the `Contributor Covenant`_, version 1.4,
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available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
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For answers to common questions about this code of conduct, see
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https://www.contributor-covenant.org/faq
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.. _`Contributor Covenant`: https://www.contributor-covenant.org

‎CONTRIBUTING.rst

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5. When you're done making changes, check that your changes pass flake8 and the
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tests, including testing other Python versions with tox::
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$ flake8 pysimplemask tests
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$ python setup.py test or pytest
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$ tox
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$ make lint
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$ make test
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Or
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$ make test-all
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To get flake8 and tox, just pip install them into your virtualenv.
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$ git push --tags
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Travis will then deploy to PyPI if tests pass.
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Code of Conduct
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---------------
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Please note that this project is released with a `Contributor Code of Conduct`_.
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By participating in this project you agree to abide by its terms.
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.. _`Contributor Code of Conduct`: CODE_OF_CONDUCT.rst

‎HISTORY.rst

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History
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=======
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5-
0.0.1 (2021-10-22)
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0.1.0 (2024-12-19)
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------------------
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* First release on PyPI.

‎LICENSE

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MIT License
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Copyright (c) 2021, Miaoqi Chu
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Copyright (c) 2024, Miaoqi Chu
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal

‎Makefile

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.PHONY: clean clean-test clean-pyc clean-build docs help
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.PHONY: clean clean-build clean-pyc clean-test coverage dist docs help install lint lint/flake8
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.DEFAULT_GOAL := help
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define BROWSER_PYSCRIPT
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lint/flake8: ## check style with flake8
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flake8 pysimplemask tests
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lint: lint/flake8 ## check style
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test: ## run tests quickly with the default Python

‎README.rst

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A GUI tool to create mask and qmap for xarea detectors used in xray experiments
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A GUI for creating mask and q-partition maps for scattering patterns in preparation for SAXS/WAXS/XPCS data reduction
2020

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* Free software: MIT license
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* Documentation: https://pysimplemask.readthedocs.io.
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Installation
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--------
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Step 1. create your virtual environement::
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conda create -n YOUR_ENV_NAME python==3.9.7
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Step 2. activate your newly created environment::
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conda activate YOUR_ENV_NAME
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Step 3. clone pysimple to your local disk::
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git clone https://github.com/AdvancedPhotonSource/pySimpleMask.git
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Step 4. install it::
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cd pySimpleMask
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pip install .
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You may also need to install magic-bin on windows systems,
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pip install python-magic-bin
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Step 5. run simplemask, open a terminal and activate your virtual environment, ::
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pysimplemask
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pysimplemask --path YOUR_HDF_PATH
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Features
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--------
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Main layout
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.. image:: docs/figures/main.png
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Create a mask by importing a blemish file or masks from other files
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.. image:: docs/figures/mask_files.png
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Create a mask by drawing on the scattering pattern.
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.. image:: docs/figures/mask_draw.png
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Set a threshold to make the scattering image binary.
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.. image:: docs/figures/mask_binary.png
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Manually set the the coordinates of bad pixels on the area detector. This can be done in 3 ways now. 1. import from a file (either CSV or white space separated). 2. mannaul input the coordinates. 3. use the mouse the double clicke the bad pixels. Other pixels with similar counts can also be selected.
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.. image:: docs/figures/mask_manual.png
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Some bad pixels can be hard to detect. By doing azimuthal grouping, we can compute the statistics of photon counts on the pixels that have similar momentum transfer. The pixels that deviate from the average more than the cutoff will be masked out.
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.. image:: docs/figures/mask_outlier.png
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Create a qmap partition for SAXS and XPCS analysis.
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.. image:: docs/figures/qpartition.png
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* TODO
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Credits
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-------

‎docs/conf.py

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# General information about the project.
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project = 'pySimpleMask'
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copyright = "2021, Miaoqi Chu"
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copyright = "2024, Miaoqi Chu"
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author = "Miaoqi Chu"
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# The version info for the project you're documenting, acts as replacement

‎docs/figures/after_masking.png

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‎docs/figures/main.png

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‎docs/figures/mask_binary.png

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‎docs/figures/mask_draw.png

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‎docs/figures/mask_files.png

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‎docs/figures/readme

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‎docs/make.bat

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

‎pyproject.toml

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[build-system]
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requires = ["setuptools>=61.0"]
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build-backend = "setuptools.build_meta"
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[project]
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name = "pysimplemask"
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version = "0.1.0"
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description = "A GUI for creating mask and q-partition maps for scattering patterns in preparation for SAXS/WAXS/XPCS data reduction"
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readme = "README.rst"
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authors = [
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{name = "Miaoqi Chu", email = "[email protected]"}
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]
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maintainers = [
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{name = "Miaoqi Chu", email = "[email protected]"}
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]
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classifiers = [
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]
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license = {text = "MIT license"}
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dependencies = [
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]
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[project.optional-dependencies]
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dev = [
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"coverage", # testing
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"mypy", # linting
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"pytest", # testing
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"ruff" # linting
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]
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[project.scripts]
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pysimplemask = "pysimplemask.cli:main"
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[project.urls]
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bugs = "https://github.com/AZjk/pysimplemask/issues"
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changelog = "https://github.com/AZjk/pysimplemask/blob/master/changelog.md"
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homepage = "https://github.com/AZjk/pysimplemask"
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[tool.setuptools]
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package-dir = {"" = "src"}
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[tool.setuptools.package-data]
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"*" = ["*.*"]
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# Mypy
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# ----
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[tool.mypy]
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files = "."
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# Use strict defaults
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strict = true
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warn_unreachable = true
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warn_no_return = true
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[[tool.mypy.overrides]]
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# Don't require test functions to include types
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module = "tests.*"
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allow_untyped_defs = true
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disable_error_code = "attr-defined"
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‎requirements.txt

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