Merge pull request #78 from samclark2/cookiecutter-format-update

Updated repo structure to match cookiecutter format

.codecov.yml

@@ -0,0 +1,10 @@
+# show coverage in CI status, not as a comment.
+comment: off
+coverage:
+  status:
+    project:
+      default:
+        target: auto
+    patch:
+      default:
+        target: auto

.coveragerc

@@ -0,0 +1,13 @@
+[run]
+source =
+    pyCHX
+[report]
+omit =
+    */python?.?/*
+    */site-packages/nose/*
+    # ignore _version.py and versioneer.py
+    .*version.*
+    *_version.py
+
+exclude_lines =
+    if __name__ == '__main__':

.flake8

@@ -0,0 +1,12 @@
+[flake8]
+exclude =
+    .git,
+    __pycache__,
+    build,
+    dist,
+    versioneer.py,
+    pyCHX/_version.py,
+    docs/source/conf.py
+max-line-length = 115
+# Ignore some style 'errors' produced while formatting by 'black'
+ignore = E203, W503

.gitattributes

@@ -0,0 +1 @@
+pyCHX/_version.py export-subst

.github/workflows/docs.yml

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+name: Build Documentation
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  build_docs:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10"]
+      fail-fast: false
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - name: Set env vars
+        run: |
+          export REPOSITORY_NAME=${GITHUB_REPOSITORY#*/}  # just the repo, as opposed to org/repo
+          echo "REPOSITORY_NAME=${REPOSITORY_NAME}" >> $GITHUB_ENV
+
+      - name: Checkout the code
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 1000  # should be enough to reach the most recent tag
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install documentation-building requirements
+        run: |
+          # For reference: https://www.gnu.org/software/bash/manual/html_node/The-Set-Builtin.html.
+          set -vxeuo pipefail
+
+          # These packages are installed in the base environment but may be older
+          # versions. Explicitly upgrade them because they often create
+          # installation problems if out of date.
+          python -m pip install --upgrade pip setuptools numpy
+
+          pip install .
+          pip install -r requirements-dev.txt
+          pip list
+
+      - name: Build Docs
+        run: make -C docs/ html
+
+      - uses: actions/upload-artifact@v3
+        with:
+          name: ${{ env.REPOSITORY_NAME }}-docs
+          path: docs/build/html/

.github/workflows/pre-commit.yml

@@ -0,0 +1,15 @@
+name: pre-commit
+
+on:
+  pull_request:
+  push:
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+      - uses: pre-commit/[email protected]
+        with:
+          extra_args: --all-files

.github/workflows/publish-pypi.yml

@@ -0,0 +1,39 @@
+# This workflow will upload a Python Package using flit when a release is
+# created.  For more information see:
+# https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+name: PyPI upload
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  publish_pypi:
+    name: Publish package to PyPI
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.x'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install wheel twine setuptools
+
+    - name: Build and publish
+      env:
+        TWINE_USERNAME: __token__
+        # The PYPI_PASSWORD must be a pypi token with the "pypi-" prefix with sufficient permissions to upload this package
+        # https://pypi.org/help/#apitoken
+        TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
+      run: |
+        python setup.py sdist bdist_wheel
+        twine upload dist/*

.github/workflows/testing.yml

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+name: Unit Tests
+
+on:
+  push:
+  pull_request:
+  # schedule:
+  #   - cron: '00 4 * * *'  # daily at 4AM
+
+jobs:
+  run_tests:
+    runs-on: ${{ matrix.host-os }}
+    strategy:
+      matrix:
+        host-os: ["ubuntu-latest"]
+        # host-os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+        python-version: ["3.8", "3.9", "3.10"]
+      fail-fast: false
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - name: Set env vars
+        run: |
+          export REPOSITORY_NAME=${GITHUB_REPOSITORY#*/}  # just the repo, as opposed to org/repo
+          echo "REPOSITORY_NAME=${REPOSITORY_NAME}" >> $GITHUB_ENV
+
+      - name: Checkout the code
+        uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          # For reference: https://www.gnu.org/software/bash/manual/html_node/The-Set-Builtin.html.
+          set -vxeuo pipefail
+
+          # These packages are installed in the base environment but may be older
+          # versions. Explicitly upgrade them because they often create
+          # installation problems if out of date.
+          python -m pip install --upgrade pip setuptools numpy
+
+          pip install .
+          pip install -r requirements-dev.txt
+          pip list
+
+      - name: Test with pytest
+        run: |
+          set -vxeuo pipefail
+          coverage run -m pytest -vv -s
+          coverage report -m

.isort.cfg

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

.pre-commit-config.yaml

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+default_language_version:
+    python: python3
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+  - repo: https://github.com/ambv/black
+    rev: 23.1.0
+    hooks:
+      - id: black
+  - repo: https://github.com/pycqa/flake8
+    rev: 6.0.0
+    hooks:
+      - id: flake8
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        args: ["--profile", "black"]
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.6.1
+    hooks:
+      - id: nbstripout

AUTHORS.rst

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+=======
+Credits
+=======
+
+Maintainer
+----------
+
+* Brookhaven National Laboratory <[email protected]>
+
+Contributors
+------------
+
+None yet. Why not be the first? See: CONTRIBUTING.rst

CONTRIBUTING.rst

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+============
+Contributing
+============
+
+Contributions are welcome, and they are greatly appreciated! Every
+little bit helps, and credit will always be given.
+
+You can contribute in many ways:
+
+Types of Contributions
+----------------------
+
+Report Bugs
+~~~~~~~~~~~
+
+Report bugs at https://github.com/samclark2/pyCHX/issues.
+
+If you are reporting a bug, please include:
+
+* Any details about your local setup that might be helpful in troubleshooting.
+* Detailed steps to reproduce the bug.
+
+Fix Bugs
+~~~~~~~~
+
+Look through the GitHub issues for bugs. Anything tagged with "bug"
+is open to whoever wants to implement it.
+
+Implement Features
+~~~~~~~~~~~~~~~~~~
+
+Look through the GitHub issues for features. Anything tagged with "feature"
+is open to whoever wants to implement it.
+
+Write Documentation
+~~~~~~~~~~~~~~~~~~~
+
+pyCHX could always use more documentation, whether
+as part of the official pyCHX docs, in docstrings,
+or even on the web in blog posts, articles, and such.
+
+Submit Feedback
+~~~~~~~~~~~~~~~
+
+The best way to send feedback is to file an issue at https://github.com/samclark2/pyCHX/issues.
+
+If you are proposing a feature:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible, to make it easier to implement.
+* Remember that this is a volunteer-driven project, and that contributions
+  are welcome :)
+
+Get Started!
+------------
+
+Ready to contribute? Here's how to set up `pyCHX` for local development.
+
+1. Fork the `pyCHX` repo on GitHub.
+2. Clone your fork locally::
+
+    $ git clone [email protected]:your_name_here/pyCHX.git
+
+3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
+
+    $ mkvirtualenv pyCHX
+    $ cd pyCHX/
+    $ python setup.py develop
+
+4. Create a branch for local development::
+
+    $ git checkout -b name-of-your-bugfix-or-feature
+
+   Now you can make your changes locally.
+
+5. When you're done making changes, check that your changes pass flake8 and the tests, including testing other Python versions with tox::
+
+    $ flake8 pyCHX tests
+    $ python setup.py test
+    $ tox
+
+   To get flake8 and tox, just pip install them into your virtualenv.
+
+6. Commit your changes and push your branch to GitHub::
+
+    $ git add .
+    $ git commit -m "Your detailed description of your changes."
+    $ git push origin name-of-your-bugfix-or-feature
+
+7. Submit a pull request through the GitHub website.
+
+Pull Request Guidelines
+-----------------------
+
+Before you submit a pull request, check that it meets these guidelines:
+
+1. The pull request should include tests.
+2. If the pull request adds functionality, the docs should be updated. Put
+   your new functionality into a function with a docstring, and add the
+   feature to the list in README.rst.
+3. The pull request should work for Python 2.7, 3.3, 3.4, 3.5 and for PyPy. Check
+   https://travis-ci.org/samclark2/pyCHX/pull_requests
+   and make sure that the tests pass for all supported Python versions.