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Cookie (#179)
* copy .github directory * nest inside .github * update for pdfgui * test tests (#131) * pin numpy to 1.x for now * add environment.yml * test tests * trigger * try again with requirements * try again with requirements * now update test reqs * try and handle xwindow display issue * try using xfvb action * refactor xvfb action commands * source activate? * different tack, generate error and work on test? * again * again * chatgpt method * supress running qc of meta.yaml in conda-forge by renaming * try new pyproject.toml * again2 * forgot to install diffpy.pdfgui! * back to setup.py * copyright fixes (#134) * Flake8v1 (#137) * move modules to top * remove extra #s * line length and extra #s * extra #s * modules to top * replace lambda function and line length * add # noqa: E501 * modules to top * fix lambda func * Flake8v2 (#138) * fix not in * fix lambda functions * remove # * remove lambda func * modules to top * mod to top * line length and import and #s * fix line length and #s * comment unused var, fix imports and #s * modules to top and inline comment fix * def functions within function to pass tests * move functions outside of class * Flake8v4 (#140) * capitalize Trustees * Exception on errorwrapper * wx.PyObjectError in except * ValueError and Exception * Exception * remove import * pre-commit errors in comments (#141) * wx12 and bonlengthdialog (#142) * wx12 and bonlengthdialog * devutils/makedist import order * news (#143) * cookiecutter: untracked files (#149) * untracked files * [pre-commit.ci] auto fixes from pre-commit hooks * update LICENSE.rst * update AUTHORS.rst and remove AUTHORS.txt * tipping our hat * Remove BSD 3-Clause, leaving Columbia copyright * remove README from requirements * replace requirements * adding wxpython back * adding back freezegun --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Simon Billinge <sbillinge@users.noreply.github.com> * Files in doc directory (#157) * move images to _static * move files in .../doc/manual into doc/source * move .gitignore file * move rest of files to doc/ * move makefile from doc/source to doc/ * remove Makefile from doc/source * update Makefile in doc * add rest of cookiecutter files into doc/source * add make.bat file * moving .py files into doc/manual * move files into manual * moving images into manual * add TUTORIAL.rst * convert .txt to .rst in TUTORIAL * fix formating * formating * formating * reference formating * move TUTORIAL.rst to manual * move tutorial.rst from manual to source * rm extra tutorial.rst * add tutorial section to index.rst * index.rst formating * files (#158) * Replace Caden's PR (#160) Minor copyright fixes and news update * try workflow for testing (#161) * workflow for testing * test unittest * try Xvfb * try to remove no test ran line * [pre-commit.ci] auto fixes from pre-commit hooks * try to remove no test ran line * try pytest --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * remove unused files (#166) * update requirements/run.txt (#165) * update requirements/run.txt, include right package * use matplotlib-base * remove dependency tests (#169) * fix deprecation warning when test (#170) * fix pkg_resources deprecation warning * use __name__ * daemon deprecation * rst file changes (#171) * Use the original license * other file changes * add a bit more in readme * remove epydoc (#173) * build doc (#174) * build doc * pre commit * Apply the new workflow (#168) * Apply the new workflow * remove prerelease from docs workflow * rename to main --------- Co-authored-by: Caden Myers <cjm2304@columbia.edu> Co-authored-by: Caden Myers <158210249+cadenmyers13@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Tieqiong <123656525+Tieqiong@users.noreply.github.com>
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‎.codecov.yml‎

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fixes:
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- ".*/site-packages/::src/"
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# codecov can find this file anywhere in the repo, so we don't need to clutter
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# the root folder.
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#comment: false
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codecov:
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notify:
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require_ci_to_pass: no
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coverage:
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status:
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patch:
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default:
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target: '70'
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if_no_uploads: error
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if_not_found: success
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if_ci_failed: failure
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project:
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default: false
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library:
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target: auto
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if_no_uploads: error
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if_not_found: success
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if_ci_failed: error
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paths: '!*/tests/.*'
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tests:
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target: 97.9%
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paths: '*/tests/.*'
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if_not_found: success
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flags:
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tests:
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paths:
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- tests/

‎.coveragerc‎

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# Configuration of the coverage.py tool for reporting test coverage.
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[report]
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# RE patterns for lines to be excluded from consideration.
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exclude_lines =
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## Have to re-enable the standard pragma
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pragma: no cover
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## Don't complain if tests don't hit defensive assertion code:
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raise AssertionError
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raise NotImplementedError
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^[ ]*assert False
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## Don't complain if non-runnable code isn't run:
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^[ ]*@unittest.skip\b
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^[ ]{4}unittest.main()
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if __name__ == .__main__.:
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[run]
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source =
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diffpy.pdfgui
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[report]
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omit =
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## exclude debug.py from codecov report
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*/tests/debug.py
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*/python?.?/*
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*/site-packages/nose/*
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# ignore _version.py and versioneer.py
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.*version.*
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*_version.py
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exclude_lines =
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if __name__ == '__main__':

‎.gitattributes‎

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/.gitattributes export-ignore
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/.gitignore export-ignore
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/.travis.yml export-ignore
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/conda-recipe/ export-ignore
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/devutils export-ignore
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.gitarchive.cfg export-subst
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*.bat text eol=crlf
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diffpy.pdfgui/_version.py export-subst

‎.github/workflows/codecov.yml‎

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name: Gather coverage report and upload to codecov
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on:
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push:
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branches:
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- main
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release:
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types:
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- prereleased
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- published
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workflow_dispatch:
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defaults:
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run:
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shell: bash -l {0}
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jobs:
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coverage:
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runs-on: ubuntu-latest
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steps:
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- name: Check out diffpy.pdfgui
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uses: actions/checkout@v4
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- name: Initialize miniconda
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uses: conda-incubator/setup-miniconda@v3
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with:
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activate-environment: test
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auto-update-conda: true
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environment-file: environment.yml
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auto-activate-base: false
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- name: Conda config
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run: >-
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conda config --set always_yes yes
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--set changeps1 no
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- name: Install diffpy.pdfgui and requirements
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run: |
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conda install --file requirements/run.txt
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conda install --file requirements/test.txt
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python -m pip install -r requirements/pip.txt
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python -m pip install . --no-deps
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- name: Install Xvfb
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run: sudo apt-get install -y xvfb
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- name: Start Xvfb
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run: |
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export DISPLAY=:99
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Xvfb :99 -screen 0 1024x768x16 &
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- name: Validate diffpy.pdfgui
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run: |
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export DISPLAY=:99
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coverage run -m pytest -vv -s
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coverage report -m
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codecov
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- name: Upload coverage to Codecov
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uses: codecov/codecov-action@v4
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env:
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CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

‎.github/workflows/docs.yml‎

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name: Build and Deploy Documentation
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on:
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release:
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types:
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- published
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workflow_dispatch:
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defaults:
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run:
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shell: bash -l {0}
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jobs:
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docs:
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runs-on: ubuntu-latest
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steps:
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- name: Check out diffpy.pdfgui
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uses: actions/checkout@v4
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- name: Initialize miniconda
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uses: conda-incubator/setup-miniconda@v3
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with:
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activate-environment: build
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auto-update-conda: true
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environment-file: environment.yml
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auto-activate-base: false
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- name: Conda config
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run: >-
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conda config --set always_yes yes
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--set changeps1 no
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- name: Install diffpy.pdfgui and build requirements
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run: |
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conda install --file requirements/build.txt
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conda install --file requirements/run.txt
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conda install --file requirements/docs.txt
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python -m pip install -r requirements/pip.txt
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python -m pip install . --no-deps
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- name: build documents
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run: make -C doc html
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- name: Deploy
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uses: peaceiris/actions-gh-pages@v4
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: ./doc/build/html

‎.github/workflows/main.yml‎

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name: Test
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on:
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push:
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branches:
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- main
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pull_request:
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workflow_dispatch:
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defaults:
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run:
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shell: bash -l {0}
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jobs:
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validate:
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runs-on: ubuntu-latest
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steps:
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- name: Check out diffpy.pdfgui
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uses: actions/checkout@v4
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- name: Initialize miniconda
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uses: conda-incubator/setup-miniconda@v3
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with:
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activate-environment: test
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auto-update-conda: true
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environment-file: environment.yml
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auto-activate-base: false
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- name: Conda config
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run: >-
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conda config --set always_yes yes
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--set changeps1 no
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- name: Install diffpy.pdfgui and requirements
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run: |
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conda install --file requirements/run.txt
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conda install --file requirements/test.txt
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python -m pip install -r requirements/pip.txt
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python -m pip install . --no-deps
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- name: Install Xvfb
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run: sudo apt-get install -y xvfb
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- name: Start Xvfb
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run: |
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export DISPLAY=:99
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Xvfb :99 -screen 0 1024x768x16 &
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- name: Validate diffpy.pdfgui
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run: |
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export DISPLAY=:99
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python -m pytest

‎.gitignore‎

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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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# C extensions
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*.so
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# Packages
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*.egg
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*.egg-info
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dist
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build
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eggs
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parts
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bin
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var
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sdist
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temp
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develop-eggs
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# Distribution / packaging
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.Python
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env/
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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venv/
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*.egg-info/
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.installed.cfg
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lib
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lib64
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tags
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*.egg
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bin/
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temp/
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tags/
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errors.err
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.idea
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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MANIFEST
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.coverage
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.tox
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*,cover
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.hypothesis/
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# Translations
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*.mo
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*.pot
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# Mr Developer
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.mr.developer.cfg
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.project
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.pydevproject
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# Django stuff:
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*.log
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# Sphinx documentation
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docs/build/
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docs/source/generated/
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# pytest
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.pytest_cache/
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# PyBuilder
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target/
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# Editor files
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# mac
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.DS_Store
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*~
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# vim
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*.swp
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*.swo
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# pycharm
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.idea/
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# VSCode
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.vscode/
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# Ipython Notebook
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.ipynb_checkpoints
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# version information
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setup.cfg
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/src/diffpy/*/version.cfg
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# Rever
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rever/

‎.isort.cfg‎

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[settings]
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line_length = 115
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multi_line_output = 3
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include_trailing_comma = True

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