From cdab53b8bd8e4f5eef58a18a58201cbb9d249d3f Mon Sep 17 00:00:00 2001
From: clintval <valentine.clint@gmail.com>
Date: Thu, 8 Aug 2024 08:57:47 -0700
Subject: [PATCH 01/11] chore: update the release process to leverage GitHub
 Actions

---
 .github/workflows/publish.yml       | 132 ++++++++++++++++++++++++++++
 .github/workflows/pythonpackage.yml |  93 --------------------
 .github/workflows/tests.yml         | 104 ++++++++++++++++++++++
 .github/workflows/wheels.yml        |  31 ++++---
 pyproject.toml                      |  30 +++++++
 5 files changed, 281 insertions(+), 109 deletions(-)
 create mode 100644 .github/workflows/publish.yml
 delete mode 100644 .github/workflows/pythonpackage.yml
 create mode 100644 .github/workflows/tests.yml

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
new file mode 100644
index 0000000..a1321ca
--- /dev/null
+++ b/.github/workflows/publish.yml
@@ -0,0 +1,132 @@
+name: publish
+
+on:
+  push:
+    tags: '\d+.\d+.\d+'
+
+env:
+  POETRY_VERSION: 1.6
+
+jobs:
+  on-main-branch-check:
+    runs-on: ubuntu-latest
+    outputs:
+      on_main: ${{ steps.contains_tag.outputs.retval }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - uses: rickstaa/action-contains-tag@v1
+        id: contains_tag
+        with:
+          reference: "main"
+          tag: "${{ github.ref_name }}"
+
+  tests:
+    name: tests
+    needs: on-main-branch-check
+    if: ${{ needs.on-main-branch-check.outputs.on_main == 'true' }}
+    uses: "./.github/workflows/tests.yml"
+
+  build-wheels:
+    name: build wheels
+    needs: tests
+    uses: "./.github/workflows/wheels.yml"
+
+  build-sdist:
+    name: build source distribution
+    needs: tests
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          submodules: true
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
+
+      - name: Install poetry
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install poetry==${{env.POETRY_VERSION}}
+
+      - name: Configure poetry
+        shell: bash
+        run: poetry config virtualenvs.in-project true
+
+      - name: Install dependencies
+        run: poetry install --no-interaction --no-root --without=dev
+
+      - name: Install project
+        run: poetry install --no-interaction --without=dev
+
+      - name: Build package
+        run: poetry build --format=sdist
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: pybedlite-sdist
+          path: dist/*.tar.gz
+
+  publish-to-pypi:
+    runs-on: ubuntu-latest
+    needs: [build-wheels, build-sdist]
+    environment: pypi
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          path: packages
+          pattern: 'pybedlite-*'
+          merge-multiple: true
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: packages/
+          skip-existing: true
+          verbose: true
+
+  make-changelog:
+    runs-on: ubuntu-latest
+    needs: publish-to-pypi
+    outputs:
+      release_body: ${{ steps.git-cliff.outputs.content }}
+    steps:
+      - name: Checkout the Repository at the Tagged Commit
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          ref: ${{ github.ref_name }}
+
+      - name: Generate a Changelog
+        uses: orhun/git-cliff-action@v3
+        id: git-cliff
+        with:
+          config: pyproject.toml
+          args: --latest --verbose
+        env:
+          GITHUB_REPO: ${{ github.repository }}
+
+  make-github-release:
+    runs-on: ubuntu-latest
+    environment: github
+    permissions:
+      contents: write
+      pull-requests: read
+    needs: make-changelog
+    steps:
+      - name: Create Draft Release
+        id: create_release
+        uses: softprops/action-gh-release@v2
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          name: ${{ github.ref_name }}
+          body: |
+            ${{ needs.draft-changelog.outputs.release_body }}
+          draft: false
+          prerelease: false
diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml
deleted file mode 100644
index fe3b9cc..0000000
--- a/.github/workflows/pythonpackage.yml
+++ /dev/null
@@ -1,93 +0,0 @@
-name: Python package
-
-on: [push]
-env:
-  POETRY_VERSION: 1.6.1
-
-jobs:
-  testing:
-    runs-on: ubuntu-20.04
-    environment: github-action-ci
-    strategy:
-      matrix:
-        PYTHON_VERSION: ["3.8", "3.9", "3.10", "3.11"]
-    steps:
-    - uses: actions/checkout@v2
-      with:
-        submodules: 'true'
-
-    - name: Set up Python ${{matrix.PYTHON_VERSION}}
-      uses: actions/setup-python@v4
-      with:
-        python-version: ${{matrix.PYTHON_VERSION}}
-
-    - name: Get full Python version
-      id: full-python-version
-      shell: bash
-      run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
-
-    - name: Install poetry
-      shell: bash
-      run: |
-        pip install poetry==${{env.POETRY_VERSION}}
-
-    - name: Configure poetry
-      shell: bash
-      run: poetry config virtualenvs.in-project true
-
-    - name: Set up cache
-      uses: actions/cache@v2
-      id: cache
-      with:
-        path: .venv
-        key: venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('**/poetry.lock') }}
-
-    - name: Ensure cache is healthy
-      if: steps.cache.outputs.cache-hit == 'true'
-      shell: bash
-      run: poetry run pip --version >/dev/null 2>&1 || rm -rf .venv
-
-    - name: Install deps
-      shell: bash
-      run: |
-        poetry install --only dev
-        poetry build
-        poetry install --extras docs
-
-    - name: Run pytest
-      shell: bash
-      run: |
-        poetry run python -m pytest --cov=pybedlite --cov-report=xml --cov-branch 
-
-    - name: Style checking
-      shell: bash
-      run: |
-        poetry run black --line-length 99 --check pybedlite
-
-    - name: Import sorting
-      shell: bash
-      run: |
-        poetry run isort --force-single-line-imports --profile black --check pybedlite
-
-    - name: Run lint
-      shell: bash
-      run: |
-        poetry run flake8 --config=ci/flake8.cfg pybedlite
-
-    - name: Run mypy
-      shell: bash
-      run: |
-        poetry run mypy -p pybedlite --config=ci/mypy.ini
-
-    - name: Run docs
-      shell: bash
-      run: |
-        set -euo pipefail
-        pushd docs
-        poetry run make html
-        popd
-
-    - name: Upload code coverage
-      uses: codecov/codecov-action@v4.5.0
-      with:
-        token: ${{ secrets.CODECOV_TOKEN }}
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
new file mode 100644
index 0000000..425e112
--- /dev/null
+++ b/.github/workflows/tests.yml
@@ -0,0 +1,104 @@
+name: tests
+
+on:
+  push:
+    branches:
+      - "**"
+    tags:
+      - "!**"
+  workflow_call:
+
+env:
+  POETRY_VERSION: 1.6
+
+jobs:
+  unit-tests:
+    runs-on: ubuntu-latest
+    environment: github-action-ci
+    strategy:
+      matrix:
+        PYTHON_VERSION: ["3.8", "3.9", "3.10", "3.11"]
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: "true"
+
+      - name: Set up Python ${{ matrix.PYTHON_VERSION }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.PYTHON_VERSION }}
+
+      - name: Get full Python version
+        id: full-python-version
+        shell: bash
+        run: echo "version=$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")" >> $GITHUB_OUTPUT
+
+      - name: Install poetry
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install poetry==${{env.POETRY_VERSION}}
+
+      - name: Configure poetry
+        shell: bash
+        run: poetry config virtualenvs.in-project true
+
+      - name: Set up cache
+        uses: actions/cache@v4
+        id: cache
+        with:
+          path: .venv
+          key: venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('**/poetry.lock') }}
+
+      - name: Ensure cache is healthy
+        if: steps.cache.outputs.cache-hit == 'true'
+        shell: bash
+        run: poetry run pip --version >/dev/null 2>&1 || rm -rf .venv
+
+      - name: Test the lock file is up to date
+        run: python -m poetry check --lock
+
+      - name: Install dependencies and package
+        shell: bash
+        run: |
+          poetry install --only dev
+          poetry build
+          poetry install --extras docs
+  
+      - name: Run pytest
+        shell: bash
+        run: |
+          poetry run python -m pytest --cov=pybedlite --cov-report=xml --cov-branch 
+  
+      - name: Style checking
+        shell: bash
+        run: |
+          poetry run black --line-length 99 --check pybedlite
+  
+      - name: Import sorting
+        shell: bash
+        run: |
+          poetry run isort --force-single-line-imports --profile black --check pybedlite
+  
+      - name: Run lint
+        shell: bash
+        run: |
+          poetry run flake8 --config=ci/flake8.cfg pybedlite
+  
+      - name: Run mypy
+        shell: bash
+        run: |
+          poetry run mypy -p pybedlite --config=ci/mypy.ini
+  
+      - name: Run docs
+        shell: bash
+        run: |
+          set -euo pipefail
+          pushd docs
+          poetry run make html
+          popd
+  
+      - name: Upload code coverage
+        uses: codecov/codecov-action@v4.5.0
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml
index f555d6c..3cfa839 100644
--- a/.github/workflows/wheels.yml
+++ b/.github/workflows/wheels.yml
@@ -1,12 +1,12 @@
-name: Build wheels for multiple platforms
+name: build wheels
 
 on:
-  push:
-    branches: [main]
+  pull_request:
+  workflow_call:
   workflow_dispatch:
 
 jobs:
-  build_wheels:
+  build-wheels:
     name: Build wheels for ${{ matrix.python }}-${{ matrix.platform.target }}_${{ matrix.platform.arch }} on ${{ matrix.platform.os }}
     runs-on: ${{ matrix.platform.os }}
     strategy:
@@ -22,12 +22,12 @@ jobs:
           # These don't work right now - they just hang while pulling the build image from quay.
           # If this doesn't resolve itself, we could try to configure different images:
           # https://cibuildwheel.readthedocs.io/en/stable/options/.
-          #- os: ubuntu-latest
-          #  target: manylinux
-          #  arch: aarch64
-          #- os: ubuntu-latest
-          #  target: musllinux
-          #  arch: aarch64
+          # - os: ubuntu-latest
+          #   target: manylinux
+          #   arch: aarch64
+          # - os: ubuntu-latest
+          #   target: musllinux
+          #   arch: aarch64
           - os: macos-latest
             target: macosx
             arch: x86_64
@@ -40,13 +40,12 @@ jobs:
         with:
           submodules: "true"
 
-      # Used to host cibuildwheel
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.12
 
       - name: Install cibuildwheel
-        run: python -m pip install cibuildwheel==2.15.0
+        run: python -m pip install cibuildwheel==2.20.0
 
       - name: Build wheels
         run: python -m cibuildwheel --output-dir wheelhouse
@@ -55,8 +54,8 @@ jobs:
           CIBW_BUILD: ${{ matrix.python }}-${{ matrix.platform.target }}_${{ matrix.platform.arch }}
           CIBW_BUILD_VERBOSITY: 1
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
-          name: wheels
+          name: pybedlite-wheels-${{ matrix.python }}-${{ matrix.platform.target }}_${{ matrix.platform.arch }}
           path: ./wheelhouse/*.whl
           if-no-files-found: error
diff --git a/pyproject.toml b/pyproject.toml
index 06402b2..cb5ec11 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -50,3 +50,33 @@ generate-setup-file = true
 [build-system]
 requires = ["poetry-core", "setuptools", "cython"]
 build-backend = "poetry.core.masonry.api"
+
+[tool.git-cliff.changelog]
+header = ""
+trim = true
+body = """
+{% for group, commits in commits | group_by(attribute="group") %}
+    ## {{ group | upper_first }}
+    {% for commit in commits %}
+        - {{ commit.message | upper_first }} ({{ commit.id | truncate(length=8, end="") }})\
+    {% endfor %}
+{% endfor %}\n
+"""
+
+[tool.git-cliff.git]
+conventional_commits = true
+commit_parsers = [
+    { message = "^.+!:*", group = "Breaking"},
+    { message = "^feat*", group = "Features"},
+    { message = "^fix*", group = "Bug Fixes"},
+    { message = "^[cC]i*", group = "CI/CD"},
+    { message = "^docs*", group = "Documentation"},
+    { message = "^perf*", group = "Performance"},
+    { message = "^refactor*", group = "Refactor"},
+    { message = "^style*", group = "Styling"},
+    { message = "^test*", group = "Testing"},
+    { message = "^chore\\(release\\):*", skip = true},
+    { message = "^chore*", group = "Miscellaneous Tasks"},
+    { body = ".*security", group = "Security"}
+]
+filter_commits = false

From 8db28b6e32a12e789d972da807edc8674b238b29 Mon Sep 17 00:00:00 2001
From: clintval <valentine.clint@gmail.com>
Date: Thu, 8 Aug 2024 09:20:23 -0700
Subject: [PATCH 02/11] chore: downgrade cibuildwheel

---
 .github/workflows/wheels.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml
index 3cfa839..f4c403b 100644
--- a/.github/workflows/wheels.yml
+++ b/.github/workflows/wheels.yml
@@ -45,7 +45,7 @@ jobs:
           python-version: 3.12
 
       - name: Install cibuildwheel
-        run: python -m pip install cibuildwheel==2.20.0
+        run: python -m pip install cibuildwheel==2.15.0
 
       - name: Build wheels
         run: python -m cibuildwheel --output-dir wheelhouse

From d80ef903a0c20dd8092d38367d2682cf93871aa1 Mon Sep 17 00:00:00 2001
From: clintval <valentine.clint@gmail.com>
Date: Thu, 8 Aug 2024 09:20:46 -0700
Subject: [PATCH 03/11] chore: downgrade Python for building wheels

---
 .github/workflows/wheels.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml
index f4c403b..fb8b8cf 100644
--- a/.github/workflows/wheels.yml
+++ b/.github/workflows/wheels.yml
@@ -42,7 +42,7 @@ jobs:
 
       - uses: actions/setup-python@v5
         with:
-          python-version: 3.12
+          python-version: 3.8
 
       - name: Install cibuildwheel
         run: python -m pip install cibuildwheel==2.15.0

From 83c859276b55245ec78e8f5b980917e669e2a26c Mon Sep 17 00:00:00 2001
From: clintval <valentine.clint@gmail.com>
Date: Thu, 8 Aug 2024 09:22:37 -0700
Subject: [PATCH 04/11] chore: try removing the environment to make less noisy

---
 .github/workflows/tests.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 425e112..b85287d 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -14,7 +14,6 @@ env:
 jobs:
   unit-tests:
     runs-on: ubuntu-latest
-    environment: github-action-ci
     strategy:
       matrix:
         PYTHON_VERSION: ["3.8", "3.9", "3.10", "3.11"]

From 3f92a96dceb24e0f7f012770b1b8f00e1e28402e Mon Sep 17 00:00:00 2001
From: clintval <valentine.clint@gmail.com>
Date: Thu, 8 Aug 2024 09:44:41 -0700
Subject: [PATCH 05/11] chore: address @nh13 review

---
 .github/workflows/publish.yml | 2 --
 .github/workflows/tests.yml   | 2 +-
 .github/workflows/wheels.yml  | 2 +-
 README.md                     | 9 ++++++---
 4 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index a1321ca..6888582 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -122,8 +122,6 @@ jobs:
       - name: Create Draft Release
         id: create_release
         uses: softprops/action-gh-release@v2
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
           name: ${{ github.ref_name }}
           body: |
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index b85287d..b8a68a5 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -16,7 +16,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        PYTHON_VERSION: ["3.8", "3.9", "3.10", "3.11"]
+        PYTHON_VERSION: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 
     steps:
       - uses: actions/checkout@v4
diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml
index fb8b8cf..39bf75c 100644
--- a/.github/workflows/wheels.yml
+++ b/.github/workflows/wheels.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ${{ matrix.platform.os }}
     strategy:
       matrix:
-        python: [cp38, cp39, cp310, cp311]
+        python: [cp38, cp39, cp310, cp311, cp312]
         platform:
           - os: ubuntu-latest
             target: manylinux
diff --git a/README.md b/README.md
index cfc230e..8c3db64 100644
--- a/README.md
+++ b/README.md
@@ -8,7 +8,8 @@
 
 ---
 
-[![Python package][python-package-badge]][python-package-link]
+[![Unit tests][tests-badge]][tests-link]
+[![Python versions][python-version-badge]](https://github.com/fulcrumgenomics/python-template)
 [![PyPI version][pypi-badge]][pypi-link]
 [![PyPI download total][pypi-downloads-badge]][pypi-downloads-link]
 
@@ -26,12 +27,14 @@
 [code-coverage-link]:   https://codecov.io/gh/fulcrumgenomics/pybedlite
 [license-badge]:        http://img.shields.io/badge/license-MIT-blue.svg
 [license-link]:         https://github.com/fulcrumgenomics/pybedlite/blob/main/LICENSE
-[python-package-badge]: https://github.com/fulcrumgenomics/pybedlite/workflows/Python%20package/badge.svg
-[python-package-link]:  https://github.com/fulcrumgenomics/pybedlite/actions?query=workflow%3A%22Python+package%22
 [pypi-badge]:           https://badge.fury.io/py/pybedlite.svg
 [pypi-link]:            https://pypi.python.org/pypi/pybedlite
 [pypi-downloads-badge]: https://img.shields.io/pypi/dm/pybedlite
 [pypi-downloads-link]:  https://pypi.python.org/pypi/pybedlite
+[python-version-badge]: https://img.shields.io/badge/python-3.8_|_3.9_|_3.10_|_3.11_|_3.12-blue
+[python-version-link]:  https://codecov.io/gh/fulcrumgenomics/pybedlite
+[tests-badge]:          https://github.com/fulcrumgenomics/pybedlite/workflows/tests/badge.svg
+[tests-link]:           https://github.com/fulcrumgenomics/pybedlite/actions/workflows/tests.yml?query=branch%3Amain
 
 # pybedlite
 

From 6a41783a4ea5fdb569860e1dfa54c59352f311a7 Mon Sep 17 00:00:00 2001
From: clintval <valentine.clint@gmail.com>
Date: Thu, 8 Aug 2024 09:50:21 -0700
Subject: [PATCH 06/11] chore: silence false positive flake8 lint

---
 pybedlite/tests/test_overlap_detector.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pybedlite/tests/test_overlap_detector.py b/pybedlite/tests/test_overlap_detector.py
index 4208fe2..4bc801e 100644
--- a/pybedlite/tests/test_overlap_detector.py
+++ b/pybedlite/tests/test_overlap_detector.py
@@ -213,7 +213,7 @@ def test_construction_from_ucsc_with_strand(strand: str) -> None:
     `Interval.from_ucsc()` should correctly parse UCSC position-formatted strings with strands.
     """
     expected_interval = Interval("chr1", 100, 200, negative=(strand == "-"))
-    assert Interval.from_ucsc(f"chr1:101-200({strand})") == expected_interval
+    assert Interval.from_ucsc(f"chr1:101-200({strand})") == expected_interval  # noqa: E231  # false positive lint with flake8
 
 
 @pytest.mark.parametrize(
@@ -223,7 +223,7 @@ def test_construction_from_ucsc_other_contigs(contig: str) -> None:
     """
     `Interval.from_ucsc()` should accommodate non-human, decoy, custom, and other contig names.
     """
-    assert Interval.from_ucsc(f"{contig}:101-200") == Interval(contig, 100, 200)
+    assert Interval.from_ucsc(f"{contig}:101-200") == Interval(contig, 100, 200)  # noqa: E231  # false positive lint with flake8
 
 
 def test_that_overlap_detector_allows_generic_parameterization() -> None:

From 39fc70d17ee3fe7e3c0b2ed6049f3b2ff6890d14 Mon Sep 17 00:00:00 2001
From: clintval <valentine.clint@gmail.com>
Date: Thu, 8 Aug 2024 09:52:09 -0700
Subject: [PATCH 07/11] chore: style code

---
 pybedlite/tests/test_overlap_detector.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/pybedlite/tests/test_overlap_detector.py b/pybedlite/tests/test_overlap_detector.py
index 4bc801e..4aed439 100644
--- a/pybedlite/tests/test_overlap_detector.py
+++ b/pybedlite/tests/test_overlap_detector.py
@@ -213,7 +213,9 @@ def test_construction_from_ucsc_with_strand(strand: str) -> None:
     `Interval.from_ucsc()` should correctly parse UCSC position-formatted strings with strands.
     """
     expected_interval = Interval("chr1", 100, 200, negative=(strand == "-"))
-    assert Interval.from_ucsc(f"chr1:101-200({strand})") == expected_interval  # noqa: E231  # false positive lint with flake8
+    assert (
+        Interval.from_ucsc(f"chr1:101-200({strand})") == expected_interval
+    )  # noqa: E231  # false positive lint with flake8
 
 
 @pytest.mark.parametrize(
@@ -223,7 +225,9 @@ def test_construction_from_ucsc_other_contigs(contig: str) -> None:
     """
     `Interval.from_ucsc()` should accommodate non-human, decoy, custom, and other contig names.
     """
-    assert Interval.from_ucsc(f"{contig}:101-200") == Interval(contig, 100, 200)  # noqa: E231  # false positive lint with flake8
+    assert Interval.from_ucsc(f"{contig}:101-200") == Interval(
+        contig, 100, 200
+    )  # noqa: E231  # false positive lint with flake8
 
 
 def test_that_overlap_detector_allows_generic_parameterization() -> None:

From 0779fd5ae169e94f5f026dc29b44f5b09a031851 Mon Sep 17 00:00:00 2001
From: clintval <valentine.clint@gmail.com>
Date: Thu, 8 Aug 2024 09:54:52 -0700
Subject: [PATCH 08/11] chore: appease black and flake8 at the same time

---
 pybedlite/tests/test_overlap_detector.py | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/pybedlite/tests/test_overlap_detector.py b/pybedlite/tests/test_overlap_detector.py
index 4aed439..dcaac58 100644
--- a/pybedlite/tests/test_overlap_detector.py
+++ b/pybedlite/tests/test_overlap_detector.py
@@ -212,10 +212,9 @@ def test_construction_from_ucsc_with_strand(strand: str) -> None:
     """
     `Interval.from_ucsc()` should correctly parse UCSC position-formatted strings with strands.
     """
+    # false positive lint with flake8 below
     expected_interval = Interval("chr1", 100, 200, negative=(strand == "-"))
-    assert (
-        Interval.from_ucsc(f"chr1:101-200({strand})") == expected_interval
-    )  # noqa: E231  # false positive lint with flake8
+    assert Interval.from_ucsc(f"chr1:101-200({strand})") == expected_interval  # noqa: E231
 
 
 @pytest.mark.parametrize(
@@ -225,9 +224,8 @@ def test_construction_from_ucsc_other_contigs(contig: str) -> None:
     """
     `Interval.from_ucsc()` should accommodate non-human, decoy, custom, and other contig names.
     """
-    assert Interval.from_ucsc(f"{contig}:101-200") == Interval(
-        contig, 100, 200
-    )  # noqa: E231  # false positive lint with flake8
+    # false positive lint with flake8 below
+    assert Interval.from_ucsc(f"{contig}:101-200") == Interval(contig, 100, 200)  # noqa: E231
 
 
 def test_that_overlap_detector_allows_generic_parameterization() -> None:

From 6e7c52b93f078060e021c268408877219167531a Mon Sep 17 00:00:00 2001
From: clintval <valentine.clint@gmail.com>
Date: Thu, 8 Aug 2024 15:24:30 -0700
Subject: [PATCH 09/11] chore: document the release process in a
 CONTRIBUTING.md

---
 CONTRIBUTING.md | 69 +++++++++++++++++++++++++++++++++++++++++++++++++
 README.md       | 47 ++++-----------------------------
 pyproject.toml  |  2 +-
 3 files changed, 75 insertions(+), 43 deletions(-)
 create mode 100644 CONTRIBUTING.md

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
new file mode 100644
index 0000000..e204371
--- /dev/null
+++ b/CONTRIBUTING.md
@@ -0,0 +1,69 @@
+# Contributing to pybedlite
+
+## Getting Setup for Development Work
+
+Clone the repository to your local machine.
+Note that pybedlite includes [cgranges][cgranges-link] as a submodule, so you must use the `--recurse-submodules` option:
+
+```
+git clone --recurse-submodules https://github.com/fulcrumgenomics/pybedlite.git
+```
+
+[Poetry][poetry-link] is used to manage the python development environment.
+
+A simple way to create an environment with the desired version of python and poetry is to use [conda][conda-link].  E.g.:
+
+```bash
+conda create -n pybedlite python=3.8 poetry=1.6
+conda activate pybedlite
+poetry install
+```
+
+If the methods listed above do not work try the following:
+
+```bash
+mamba create -n pybedlite -c conda-forge "python=3.9.16" "poetry=1.6.1"
+mamba activate pybedlite
+poetry install
+```
+
+[poetry-link]: https://github.com/python-poetry/poetry
+[conda-link]:  https://docs.conda.io/en/latest/miniconda.html
+[cgranges-link]: https://github.com/lh3/cgranges
+
+## Checking the Build
+
+Check the library with:
+
+```bash
+poetry run ./ci/check.sh
+```
+
+## Building the Documentation
+
+Build the documentation with:
+
+```bash
+(cd docs/ && poetry run make html)
+```
+
+## Creating a Release on PyPi
+
+1. Clone the repository recursively and ensure you are on the `main` (un-dirty) branch
+2. Checkout a new branch to prepare the library for release
+3. Bump the version of the library to the desired SemVer with `poetry version #.#.#`
+4. Commit the version bump changes with a Git commit message like `chore(release): bump to #.#.#`
+5. Push the commit to the upstream remote, open a PR, ensure tests pass, and seek reviews
+6. Squash merge the PR
+7. Tag the new commit on the main branch of the repository with the new SemVer
+
+GitHub Actions will take care of the remainder of the deploy and release process with:
+
+1. Unit tests will be run for safety-sake
+2. A source distribution will be built
+3. Many multi-arch multi-Python binary distributions will be built
+4. Assets will be deployed to PyPi with the new SemVer
+5. A [Conventional Commit](https://www.conventionalcommits.org/en/v1.0.0/)-aware changelog will be drafted
+6. A GitHub release will be created with the new SemVer and the drafted changelog
+
+Consider editing the changelog if there are any errors or necessary enhancements.
diff --git a/README.md b/README.md
index 8c3db64..b9722ec 100644
--- a/README.md
+++ b/README.md
@@ -40,58 +40,21 @@
 
 See documentation on [pybedlite.readthedocs.org][rtd-link].
 
-```
+```bash
 pip install pybedlite
 ```
 OR
-```
+```bash
 conda install -c bioconda pybedlite
 ```
 OR
-```
+```bash
 conda create -n pybedlite pybedlite
 conda activate pybedlite
 ```
 
 [rtd-link]:    http://pybedlite.readthedocs.org/en/stable
 
-**Requires python 3.8+** (for python < 3.8, please use pybedlite <= 0.0.3)
-
-# Getting Setup for Development Work
-
-Clone the repository to your local machine. Note that pybedlite >= 0.0.4 includes [cgranges][cgranges-link] as a submodule, so you must use the `--recurse-submodules` option:
-```
-git clone --recurse-submodules https://github.com/fulcrumgenomics/pybedlite.git
-```
-
-[Poetry][poetry-link] is used to manage the python development environment.
-
-A simple way to create an environment with the desired version of python and poetry is to use [conda][conda-link].  E.g.:
+## Development and Testing
 
-```bash
-conda create -n pybedlite python=3.8 poetry
-conda activate pybedlite
-poetry install
-```
-
-If the methods listed above do not work try the following:
-```bash
-mamba create -n pybedlite -c conda-forge "python=3.9.16" "poetry=1.6.1"
-mamba activate pybedlite
-poetry install
-```
-
-If, during `poetry install` on Mac OS X errors are encountered running gcc/clang to build `pybedtools` or other packages with native code, try setting the following and re-running `poetry install`:
-```bash
-export CFLAGS="-stdlib=libc++"
-``` 
-
-[poetry-link]: https://github.com/python-poetry/poetry
-[conda-link]:  https://docs.conda.io/en/latest/miniconda.html
-[cgranges-link]: https://github.com/lh3/cgranges
-
-## Checking the Build
-### Run all checks with:
-```bash
-./ci/check.sh
-```
+See the [contributing guide](./CONTRIBUTING.md) for more information.
diff --git a/pyproject.toml b/pyproject.toml
index cb5ec11..dda9687 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -24,7 +24,7 @@ classifiers = [
 	"Topic :: Software Development :: Documentation",
 	"Topic :: Software Development :: Libraries :: Python Modules",
 ]
-include = ["LICENSE"]
+include = ["LICENSE", "CONTRIBUTING.md"]
 packages = [{ include = "pybedlite" }, { include = "cgranges" }]
 
 [tool.poetry.dependencies]

From 69c8340b9e19c67bfb28d0f60970240c848595ed Mon Sep 17 00:00:00 2001
From: clintval <valentine.clint@gmail.com>
Date: Thu, 8 Aug 2024 15:25:41 -0700
Subject: [PATCH 10/11] chore: remove temp CI group

---
 pyproject.toml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index dda9687..c45af0f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -69,7 +69,6 @@ commit_parsers = [
     { message = "^.+!:*", group = "Breaking"},
     { message = "^feat*", group = "Features"},
     { message = "^fix*", group = "Bug Fixes"},
-    { message = "^[cC]i*", group = "CI/CD"},
     { message = "^docs*", group = "Documentation"},
     { message = "^perf*", group = "Performance"},
     { message = "^refactor*", group = "Refactor"},

From b949f6d3fe88875b93cd8373f16c974a38ee11f0 Mon Sep 17 00:00:00 2001
From: clintval <valentine.clint@gmail.com>
Date: Wed, 18 Sep 2024 13:54:29 -0700
Subject: [PATCH 11/11] chore: make the workflow named pybedlite-specific

---
 .github/workflows/{publish.yml => publish_pybedlite.yml} | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)
 rename .github/workflows/{publish.yml => publish_pybedlite.yml} (97%)

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish_pybedlite.yml
similarity index 97%
rename from .github/workflows/publish.yml
rename to .github/workflows/publish_pybedlite.yml
index 6888582..f85d1d7 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish_pybedlite.yml
@@ -1,4 +1,4 @@
-name: publish
+name: publish pybedlite
 
 on:
   push:
@@ -124,7 +124,6 @@ jobs:
         uses: softprops/action-gh-release@v2
         with:
           name: ${{ github.ref_name }}
-          body: |
-            ${{ needs.draft-changelog.outputs.release_body }}
+          body: ${{ needs.make-changelog.outputs.release_body }}
           draft: false
           prerelease: false