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Merge pull request #47 from Tieqiong/cookie
Refactor: Cookiecut (merge the other ones first)
2 parents 3ce7204 + 178507a commit fdceb92

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‎.codecov.yml

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fixes:
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- ".*/site-packages/::src/"
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coverage:
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status:
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project: # more options at https://docs.codecov.com/docs/commit-status
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default:
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target: auto # use the coverage from the base commit, fail if coverage is lower
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threshold: 0% # allow the coverage to drop by
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comment:
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layout: " diff, flags, files"
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behavior: default
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require_changes: false
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require_base: false # [true :: must have a base report to post]
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require_head: false # [true :: must have a head report to post]
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hide_project_coverage: false # [true :: only show coverage on the git diff aka patch coverage]

‎.codespell/ignore_words.txt

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;; Frobenius norm used in np.linalg.norm
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fro
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;; abbreviation for "structure"
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struc
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;; method name within JournalPanel class
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onText
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;; a method name within JournalPanel class
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delt
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;; structure file format
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discus
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‎.coveragerc

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‎.gitarchive.cfg

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‎.gitattributes

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‎.github/workflows/build-wheel-release-upload.yml

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name: Release (GitHub/PyPI) and Deploy Docs
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on:
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workflow_dispatch:
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push:
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tags:
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- "*" # Trigger on all tags initially, but tag and release privilege are verified in _build-wheel-release-upload.yml
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jobs:
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release:
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uses: Billingegroup/release-scripts/.github/workflows/_build-wheel-release-upload.yml@v0
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with:
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project: diffpy.srreal
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c_extension: true
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github_admin_username: sbillinge
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secrets:
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PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
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PAT_TOKEN: ${{ secrets.PAT_TOKEN }}

‎.github/workflows/check-news-item.yml

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name: Check for News
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on:
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pull_request_target:
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branches:
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- main
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jobs:
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check-news-item:
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uses: Billingegroup/release-scripts/.github/workflows/_check-news-item.yml@v0
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with:
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project: diffpy.srreal

‎.github/workflows/matrix-and-codecov-on-merge-to-main.yml

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name: CI
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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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jobs:
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matrix-coverage:
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uses: Billingegroup/release-scripts/.github/workflows/_matrix-and-codecov-on-merge-to-main.yml@v0
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with:
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project: diffpy.srreal
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c_extension: true
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headless: false
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secrets:
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CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

‎.github/workflows/publish-docs-on-release.yml

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name: Deploy Documentation on Release
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on:
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workflow_dispatch:
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jobs:
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docs:
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uses: Billingegroup/release-scripts/.github/workflows/_publish-docs-on-release.yml@v0
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with:
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project: diffpy.srreal
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c_extension: true
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headless: false

‎.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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# 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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.settings
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# SCons build files
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.gdb_history
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.sconf_temp/
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.sconsign.dblite
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config.log
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/sconscript.local
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/sconsvars.py
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# version information
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setup.cfg
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/src/diffpy/*/version.cfg
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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

‎AUTHORS.rst

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Authors
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=======
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Pavol Juhas,
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Chris Farrow,
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Simon J.L. Billinge
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Contributors
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------------
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For a list of contributors, visit
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https://github.com/diffpy/diffpy.srreal/graphs/contributors

‎AUTHORS.txt

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‎CHANGELOG.md

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‎CHANGELOG.rst

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=============
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Release Notes
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=============
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.. current developments
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Version 1.3.0 2019-03-13
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=========================
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Main differences from version 1.2.
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**Added:**
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* Support for Python 3.7, 3.6, 3.5 in addition to 2.7.
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* Validation of compiler options from `python-config`.
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* Make scons scripts compatible with Python 3 and Python 2.
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* `ConstantPeakWidth` attributes `uisowidth`, `bisowidth` to ease
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PDF simulation with uniform isotropic atom displacements.
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**Changed:**
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* Require libdiffpy 1.4 or later.
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* Build Anaconda package with Anaconda C++ compiler.
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* Allow language standard c++11.
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* Pickle format for `PDFCalculator`, `DebyePDFCalculator`,
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`OverlapCalculator`, `PeakWidthModel`, `PeakProfile`, `PDFEnvelope`,
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`PDFBaseline`, and `ScatteringFactorTable` objects.
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**Deprecated:**
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* Variable `__gitsha__` in the `version` module renamed to `__git_commit__`.
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* `libdiffpy_version_info` attribute `git_sha` renamed to `git_commit`.
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**Removed**
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* Unused method `BVParam.__hash__`.
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* Disable pickling of `BasePairQuantity` as it is in effect abstract.
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* Pickling of Python-added attributes to exported C++ classes.
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* Function `get_libdiffpy_version_info` from the `version` module.
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**Fixed**
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* Return value conversion of `CrystalStructureAdapter` methods
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`expandLatticeAtom` and `getEquivalentAtoms` methods.
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Make them return a `list` of `Atom` objects.
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* Name suffix resolution of `boost_python` shared library.

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