Merge branch 'master' into ref/pybedtools-pysam

.coveragerc

@@ -1,5 +1,5 @@
 [run]
-omit = *test*,setup.py
+omit = *test*
 
 [report]
 exclude_lines =

.github/pull_request_template.md

@@ -0,0 +1,11 @@
+## Checklist
+
+* [ ] I've checked to ensure there aren't already other open [pull requests](../../../pulls) for the same update/change
+* [ ] I've prefixed the title of my PR according to [the conventional commits specification](https://www.conventionalcommits.org/). If your PR fixes a bug, please prefix the PR with `fix: `. Otherwise, if it introduces a new feature, please prefix it with `feat: `. If it introduces a breaking change, please add an exclamation before the colon, like `feat!: `. If the scope of the PR changes because of a revision to it, please update the PR title, since the title will be used in our CHANGELOG.
+* [ ] At the top of the PR, I've [listed any open issues that this PR will resolve](https://docs.github.com/en/issues/tracking-your-work-with-issues/linking-a-pull-request-to-an-issue#linking-a-pull-request-to-an-issue-using-a-keyword). For example, "resolves #0" if this PR resolves issue #0
+- [ ] I've explained my changes in a manner that will make it possible for both users and maintainers of TRTools to understand them
+* [ ] I've added tests for any new functionality. Or, if this PR fixes a bug, I've added test(s) that replicate it
+* [ ] I've updated the relevant REAMDEs with any new usage information and checked that the newly built documentation is formatted properly
+* [ ] All functions, modules, classes etc. still conform to [numpy docstring standards](https://numpydoc.readthedocs.io/en/latest/format.html)
+* [ ] (if applicable) I've updated the pyproject.toml file with any changes I've made to TRTools's dependencies
+* [ ] In the body of this PR, I've included a short address to the reviewer highlighting one or two items that might deserve their focus

.github/workflows/conventional-prs.yml

@@ -0,0 +1,23 @@
+name: Title
+on:
+  pull_request_target:
+    types:
+      - opened
+      - reopened
+      - edited
+      - synchronize
+  workflow_call:
+
+permissions:
+  contents: read
+
+jobs:
+  title-format:
+    permissions:
+      pull-requests: read  # for amannn/action-semantic-pull-request to analyze PRs
+      statuses: write  # for amannn/action-semantic-pull-request to mark status of analyzed PR
+    runs-on: ubuntu-latest
+    steps:
+      - uses: amannn/[email protected]
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/release.yml

@@ -0,0 +1,47 @@
+name: Release
+
+on:
+  push:
+    branches:
+      - master
+
+jobs:
+  release:
+    name: Release
+    runs-on: ubuntu-latest
+    steps:
+      - uses: GoogleCloudPlatform/release-please-action@v3
+        id: release
+        with:
+          release-type: python
+          package-name: trtools
+
+      - uses: actions/checkout@v3
+        if: ${{ steps.release.outputs.release_created }}
+        with:
+          fetch-depth: 2
+
+      - name: Set up Python
+        if: ${{ steps.release.outputs.release_created }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.8'
+
+      - name: Upgrade pip
+        if: ${{ steps.release.outputs.release_created }}
+        run: |
+          pip install --upgrade pip
+          pip install build
+          pip --version
+
+      - name: Build package
+        if: ${{ steps.release.outputs.release_created }}
+        run: |
+          python -m build
+
+      - name: Publish package on PyPI
+        if: ${{ steps.release.outputs.release_created }}
+        uses: pypa/[email protected]
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_TOKEN }}

.github/workflows/tests.yml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
 
     steps:
       - uses: actions/checkout@v4
@@ -33,12 +33,12 @@ jobs:
       - name: Upgrade pip and install our package
         shell: bash -el {0}
         run: |
-          python -m pip install --upgrade pip setuptools wheel setuptools-scm
+          python -m pip install --upgrade pip setuptools wheel
           pip install -e .
       - name: Test with pytest
         shell: bash -el {0}
         run: |
-          python -m pytest --cov=. --cov-report term-missing --cov-fail-under 89 --doctest-modules --junitxml=junit/test-results-${{ matrix.python-version }}.xml
+          python -m pytest --cov=. --cov-report term-missing --cov-fail-under 90 --doctest-modules --junitxml=junit/test-results-${{ matrix.python-version }}.xml
       - name: Test command line
         shell: bash -el {0}
         run: |