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fix p3 (#12)
* DOC: remove trailing white space from README * DOC: fix download link for Anaconda Python * add .github directory, add requirements, and other setup files. * added back blank line in main.yml * inserting precommit and other testing yamls * [pre-commit.ci] auto fixes from pre-commit hooks --------- Co-authored-by: Pavol Juhas <[email protected]> Co-authored-by: stevenhua0320 <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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Diff for: ‎.codecov.yml

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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/

Diff for: ‎.coveragerc

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[run]
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source =
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diffpy.srmise
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[report]
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omit =
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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__':

Diff for: ‎.flake8

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[flake8]
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exclude =
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.git,
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__pycache__,
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build,
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dist,
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doc/source/conf.py
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max-line-length = 115
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# Ignore some style 'errors' produced while formatting by 'black'
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# https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#labels-why-pycodestyle-warnings
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extend-ignore = E203

Diff for: ‎.github/workflows/docs.yml

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name: Build Documentation
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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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jobs:
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test:
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runs-on: ubuntu-latest
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defaults:
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run:
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shell: bash -l {0}
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steps:
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- uses: actions/checkout@v3
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with:
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fetch-depth: 0
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- uses: conda-incubator/setup-miniconda@v2
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with:
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activate-environment: build
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auto-update-conda: true
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- name: install requirements
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run: >-
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conda install -n build -c conda-forge
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--file requirements/build.txt
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--file requirements/run.txt
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--file requirements/docs.txt
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--quiet --yes
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- name: install the package
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run: 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@v3
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: ./doc/build/html

Diff for: ‎.github/workflows/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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- CI
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pull_request:
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workflow_dispatch:
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jobs:
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miniconda:
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name: Miniconda ${{ matrix.os }}
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: ["ubuntu-latest"]
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steps:
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- name: check out diffpy.srmise
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uses: actions/checkout@v3
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with:
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repository: diffpy/diffpy.srmise
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path: .
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fetch-depth: 0 # avoid shallow clone with no tags
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- name: initialize miniconda
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# this uses a marketplace action that sets up miniconda in a way that makes
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# it easier to use. I tried setting it up without this and it was a pain
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uses: conda-incubator/setup-miniconda@v2
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with:
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activate-environment: test
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# environment.yml file is needed by this action. Because I don't want
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# maintain this but rather maintain the requirements files it just has
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# basic things in it like conda and pip
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environment-file: ./environment.yml
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python-version: 3
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auto-activate-base: false
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- name: install diffpy.srmise requirements
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shell: bash -l {0}
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run: |
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conda config --set always_yes yes --set changeps1 no
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conda config --add channels conda-forge
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conda activate test
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conda install --file requirements/run.txt
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conda install --file requirements/test.txt
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pip install .
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- name: Validate diffpy.srmise
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shell: bash -l {0}
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run: |
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conda activate test
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coverage run -m pytest -vv -s
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coverage report -m
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codecov

Diff for: ‎.github/workflows/pre-commit.yml

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name: pre-commit
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on:
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pull_request:
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push:
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workflow_dispatch:
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jobs:
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pre-commit:
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# pull requests are a duplicate of a branch push if within the same repo.
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if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.repository
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/setup-python@v4
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- uses: pre-commit/[email protected]
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with:
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extra_args: --all-files

Diff for: ‎.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

Diff for: ‎.pre-commit-config.yaml

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default_language_version:
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python: python3
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ci:
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autofix_commit_msg: |
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[pre-commit.ci] auto fixes from pre-commit hooks
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autofix_prs: true
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autoupdate_branch: 'pre-commit-autoupdate'
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autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
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autoupdate_schedule: monthly
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skip: [no-commit-to-branch]
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submodules: false
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.6.0
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hooks:
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- id: check-yaml
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- id: end-of-file-fixer
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- id: trailing-whitespace
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exclude: '\.(rst|txt)$'
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- repo: https://github.com/psf/black
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rev: 24.4.2
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hooks:
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- id: black
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- repo: https://github.com/pycqa/flake8
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rev: 7.0.0
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hooks:
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- id: flake8
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- repo: https://github.com/pycqa/isort
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rev: 5.13.2
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hooks:
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- id: isort
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args: ["--profile", "black"]
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- repo: https://github.com/kynan/nbstripout
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rev: 0.7.1
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hooks:
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- id: nbstripout
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.4.0
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hooks:
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- id: no-commit-to-branch
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name: Prevent Commit to Main Branch
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args: ["--branch", "main"]
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stages: [pre-commit]

Diff for: ‎MANIFEST.in

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recursive-include doc/manual/source *.rst *.txt
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include doc/manual/source/conf.py
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include doc/manual/Makefile
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Diff for: ‎README.rst

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`DiffPy project <http://www.diffpy.org>`_ tool for unbiased peak extraction from
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atomic pair distribution functions.
77

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SrMise is an implementation of the `ParSCAPE algorithm
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<https://dx.doi.org/10.1107/S2053273315005276>`_ for peak extraction from
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atomic pair distribution functions (PDFs). It is designed to function even
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when *a priori* knowledge of the physical sample is limited, utilizing the
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Akaike Information Criterion (AIC) to estimate whether peaks are
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statistically justified relative to alternate models. Three basic use cases
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are anticipated for SrMise. The first is peak fitting a user-supplied
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collections of peaks. The second is peak extraction from a PDF with no (or
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only partial) user-supplied peaks. The third is an AIC-driven multimodeling
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analysis where the output of multiple SrMise trials are ranked.
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The framework for peak extraction defines peak-like clusters within the data,
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extracts a single peak within each cluster, and iteratively combines nearby
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clusters while performing a recursive search on the residual to identify
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occluded peaks. Eventually this results in a single global cluster
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containing many peaks fit over all the data. Over- and underfitting are
8+
SrMise is an implementation of the `ParSCAPE algorithm
9+
<https://dx.doi.org/10.1107/S2053273315005276>`_ for peak extraction from
10+
atomic pair distribution functions (PDFs). It is designed to function even
11+
when *a priori* knowledge of the physical sample is limited, utilizing the
12+
Akaike Information Criterion (AIC) to estimate whether peaks are
13+
statistically justified relative to alternate models. Three basic use cases
14+
are anticipated for SrMise. The first is peak fitting a user-supplied
15+
collections of peaks. The second is peak extraction from a PDF with no (or
16+
only partial) user-supplied peaks. The third is an AIC-driven multimodeling
17+
analysis where the output of multiple SrMise trials are ranked.
18+
19+
The framework for peak extraction defines peak-like clusters within the data,
20+
extracts a single peak within each cluster, and iteratively combines nearby
21+
clusters while performing a recursive search on the residual to identify
22+
occluded peaks. Eventually this results in a single global cluster
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containing many peaks fit over all the data. Over- and underfitting are
2424
discouraged by use of the AIC when adding or, during a pruning step, removing
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peaks. Termination effects, which can lead to physically spurious peaks in
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the PDF, are incorporated in the mathematical peak model and the pruning step
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attempts to remove peaks which are fit better as termination ripples due to
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another peak.
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Where possible, SrMise provides physically reasonable default values
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for extraction parameters. However, the PDF baseline should be estimated by
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the user before extraction, or by performing provisional peak extraction with
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varying baseline parameters. The package defines a linear (crystalline)
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baseline, arbitrary polynomial baseline, a spherical nanoparticle baseline,
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and an arbitrary baseline interpolated from a list of user-supplied values.
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In addition, PDFs with accurate experimentally-determined uncertainties are
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necessary to provide the most reliable results, but historically such PDFs
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are rare. In the absence of accurate uncertainties an *ad hoc* uncertainty
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must be specified.
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peaks. Termination effects, which can lead to physically spurious peaks in
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the PDF, are incorporated in the mathematical peak model and the pruning step
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attempts to remove peaks which are fit better as termination ripples due to
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another peak.
29+
30+
Where possible, SrMise provides physically reasonable default values
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for extraction parameters. However, the PDF baseline should be estimated by
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the user before extraction, or by performing provisional peak extraction with
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varying baseline parameters. The package defines a linear (crystalline)
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baseline, arbitrary polynomial baseline, a spherical nanoparticle baseline,
35+
and an arbitrary baseline interpolated from a list of user-supplied values.
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In addition, PDFs with accurate experimentally-determined uncertainties are
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necessary to provide the most reliable results, but historically such PDFs
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are rare. In the absence of accurate uncertainties an *ad hoc* uncertainty
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must be specified.
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For more information about SrMise, see the users manual at
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http://diffpy.github.io/diffpy.srmise.
@@ -65,7 +65,7 @@ individual and/or academic use, but some also have commercial version. Links to
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executables, installation instructions, and licensing information
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for some popular options are listed below.
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* `Anaconda <http://www.continuum.io/downloads>`_
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* `Anaconda <https://www.anaconda.com/download>`_
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* `Enthought Canopy <https://www.enthought.com/products/canopy/>`_
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* `Python(x,y) <https://code.google.com/p/pythonxy/>`_
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* `WinPython <http://winpython.github.io>`_
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The simplest way to obtain diffpy.srmise on Mac OS X systems
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is using ``pip`` to download and install the latest release from
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`PyPI <https://pypi.python.org>`_. ::
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`PyPI <https://pypi.python.org>`_. ::
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sudo pip install diffpy.srmise
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sudo python setup.py install
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This installs diffpy.srmise for all users in the default system location. If
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administrator (root) access is not available, see the usage info from
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``python setup.py install --help`` for options to install to user-writable
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This installs diffpy.srmise for all users in the default system location. If
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administrator (root) access is not available, see the usage info from
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``python setup.py install --help`` for options to install to user-writable
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directories.
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The simplest way to obtain diffpy.srmise on Linux systems
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is using ``pip`` to download and install the latest release from the
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`PyPI <https://pypi.python.org>`_. ::
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`PyPI <https://pypi.python.org>`_. ::
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sudo pip install diffpy.srmise
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sudo python setup.py install
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This installs diffpy.srmise for all users in the default system location. If
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administrator (root) access is not available, see the usage info from
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``python setup.py install --help`` for options to install to user-writable
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directories.
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This installs diffpy.srmise for all users in the default system location. If
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administrator (root) access is not available, see the usage info from
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``python setup.py install --help`` for options to install to user-writable
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directories.
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DEVELOPMENT
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===========
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diffpy.srmise is open-source software developed with support of the Center of
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Research Excellence in Complex Materials at Michigan State University, in
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cooperation with the DiffPy-CMI complex modeling initiative at the Brookhaven
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National Laboratory. The diffpy.srmise sources are hosted at
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https://github.com/diffpy/diffpy.srmise.
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diffpy.srmise is open-source software developed with support of the Center of
178+
Research Excellence in Complex Materials at Michigan State University, in
179+
cooperation with the DiffPy-CMI complex modeling initiative at the Brookhaven
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National Laboratory. The diffpy.srmise sources are hosted at
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https://github.com/diffpy/diffpy.srmise.
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Feel free to fork the project and contribute. To install diffpy.srmise in a
184-
development mode, with its sources being directly used by Python rather than
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copied to a package directory, use ::
183+
Feel free to fork the project and contribute. To install diffpy.srmise in a
184+
development mode, with its sources being directly used by Python rather than
185+
copied to a package directory, use ::
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python setup.py develop --user
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