Cookiecuting - git add untracked files

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

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+name: Check News Item
+
+on:
+  pull_request_target:
+    branches:
+    - main
+
+permissions:
+  pull-requests: write
+  contents: read
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    name: Check News item
+    steps:
+
+      # note: the checkout will pull code from the base branch. This step should not pull code from the merge commit
+      - uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+          cache: 'pip'
+          cache-dependency-path: 'pyproject.toml'
+      - run: pip install PyGithub
+      - run: python .github/workflows/check-news.py
+        env:
+          PR_NUMBER: "${{ github.event.number }}"
+          GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
+          GITHUB_REPOSITORY: "${{ env.GITHUB_REPOSITORY }}"

.github/workflows/check-news.py

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+"""Check if the PR has a news item.
+
+Put a warning comment if it doesn't.
+"""
+
+import os
+from fnmatch import fnmatch
+
+from github import Github, PullRequest
+
+
+def get_added_files(pr: PullRequest.PullRequest):
+    print(pr, pr.number)
+    for file in pr.get_files():
+        if file.status == "added":
+            yield file.filename
+
+
+def check_news_file(pr):
+    return any(map(lambda file_name: fnmatch(file_name, "news/*.rst"), get_added_files(pr)))
+
+
+def get_pr_number():
+    number = os.environ["PR_NUMBER"]
+    if not number:
+        raise Exception(f"Pull request number is not found `PR_NUMBER={number}")
+    return int(number)
+
+
+def get_old_comment(pr: PullRequest.PullRequest):
+    for comment in pr.get_issue_comments():
+        if ("github-actions" in comment.user.login) and ("No news item is found" in comment.body):
+            return comment
+
+
+def main():
+    # using an access token
+    gh = Github(os.environ["GITHUB_TOKEN"])
+    repo = gh.get_repo(os.environ["GITHUB_REPOSITORY"])
+    pr = repo.get_pull(get_pr_number())
+    has_news_added = check_news_file(pr)
+    old_comment = get_old_comment(pr)
+
+    if old_comment:
+        print("Found an existing comment from bot")
+        if has_news_added:
+            print("Delete warning from bot, since news items is added.")
+            old_comment.delete()
+    elif not has_news_added:
+        print("No news item found")
+
+        pr.create_issue_comment(
+            """\
+**Warning!** No news item is found for this PR. If this is an user facing change/feature/fix,
+ please add a news item by copying the format from `news/TEMPLATE.rst`.
+"""
+        )
+        assert False
+
+
+if __name__ == "__main__":
+    main()

.github/workflows/codecov.yml

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

.github/workflows/docs.yml

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

.github/workflows/main.yml

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+name: Test
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+jobs:
+  validate:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out diffpy.srfit
+        uses: actions/checkout@v4
+
+      - name: Initialize miniconda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: test
+          auto-update-conda: true
+          environment-file: environment.yml
+          auto-activate-base: false
+
+      - name: Conda config
+        run: >-
+          conda config --set always_yes yes
+          --set changeps1 no
+
+      - name: Install diffpy.srfit and requirements
+        run: |
+          conda install --file requirements/run.txt
+          conda install --file requirements/build.txt
+          conda install --file requirements/test.txt
+          python -m pip install -r requirements/pip.txt
+          python -m pip install . --no-deps
+
+      - name: Validate diffpy.srfit
+        run: python -m pytest

.isort.cfg

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

AUTHORS.rst

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+Authors
+=======
+
+Billinge Group and community contibutors.
+
+Contributors
+------------
+
+For a list of contributors, visit
+https://github.com/diffpy/diffpy.srfit/graphs/contributors

CHANGELOG.rst

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+=============
+Release Notes
+=============
+
+.. current developments

CODE_OF_CONDUCT.rst

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+=====================================
+ Contributor Covenant Code of Conduct
+=====================================
+
+Our Pledge
+----------
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+Our Standards
+-------------
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+Enforcement Responsibilities
+----------------------------
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+Scope
+-----
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official email address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+Enforcement
+-----------
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+sb2896@columbia.edu. All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+Enforcement Guidelines
+----------------------
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+1. Correction
+****************
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+2. Warning
+*************
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+3. Temporary Ban
+******************
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+4. Permanent Ban
+******************
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+Attribution
+-----------
+
+This Code of Conduct is adapted from the `Contributor Covenant <https://www.contributor-covenant.org/version/2/1/code_of_conduct.html>`_.
+
+Community Impact Guidelines were inspired by `Mozilla's code of conduct enforcement ladder <https://github.com/mozilla/inclusion>`_.
+
+For answers to common questions about this code of conduct, see the `FAQ <https://www.contributor-covenant.org/faq>`_. `Translations are available <https://www.contributor-covenant.org/translations>`_