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Migrate package to hatch - #166

Merged
jkanche merged 5 commits into
masterfrom
update-hatchit
Sep 3, 2026
Merged

Migrate package to hatch#166
jkanche merged 5 commits into
masterfrom
update-hatchit

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@jkanche

@jkanche jkanche commented Sep 3, 2026

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@jkanche jkanche self-assigned this Sep 3, 2026
Comment on lines +12 to +18
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v7
- uses: actions/setup-python@v5
with:
python-version: '3.12'
- uses: pre-commit/action@v3.0.1
- uses: actions/setup-python@v5
with:
python-version: '3.12'
- uses: pre-commit/action@v3.0.1
Comment on lines +9 to +34
name: Build and Test
runs-on: ubuntu-latest
permissions:
id-token: write
repository-projects: write
contents: write
pages: write

steps:
- uses: actions/checkout@v4
- uses: actions/checkout@v7

- name: Set up Python 3.12
uses: actions/setup-python@v5
with:
python-version: 3.12

- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install tox
- name: Install tox
run: python -m pip install tox

- name: Test with tox
run: |
tox
- name: Test
run: tox -e default

- name: Build Project and Publish
run: |
python -m tox -e clean,build
- name: Build Project
run: tox -e build

# This uses the trusted publisher workflow so no token is required.
- name: Publish to PyPI
uses: pypa/gh-action-pypi-publish@release/v1
- name: Store the distribution packages
uses: actions/upload-artifact@v4
with:
name: python-package-distributions
path: dist/

build-docs:
Comment on lines +35 to +59
name: Build Documentation
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v7

- name: Set up Python 3.12
uses: actions/setup-python@v5
with:
python-version: 3.12

- name: Install tox
run: python -m pip install tox

- name: Build docs
run: |
tox -e docs
run: tox -e docs

- run: touch ./docs/_build/html/.nojekyll
- name: Add .nojekyll
run: touch ./docs/_build/html/.nojekyll

- name: GH Pages Deployment
uses: JamesIves/github-pages-deploy-action@v4
- name: Upload Pages artifact
uses: actions/upload-pages-artifact@v5
with:
branch: gh-pages # The branch the action should deploy to.
folder: ./docs/_build/html
clean: true # Automatically remove deleted files from the deploy branch
path: ./docs/_build/html

publish-pypi:
path: dist/

- name: Publish package to PyPI
uses: pypa/gh-action-pypi-publish@release/v1

- name: Upload coverage reports to Codecov with GitHub Action
uses: codecov/codecov-action@v5
uses: codecov/codecov-action@v7
@codecov

codecov Bot commented Sep 3, 2026

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Codecov Report

❌ Patch coverage is 0% with 89 lines in your changes missing coverage. Please review.
✅ Project coverage is 0.00%. Comparing base (593dc80) to head (b80e639).
⚠️ Report is 1 commits behind head on master.

Files with missing lines Patch % Lines
src/genomicranges/sequence_info.py 0.00% 31 Missing ⚠️
src/genomicranges/GenomicRanges.py 0.00% 25 Missing ⚠️
src/genomicranges/utils.py 0.00% 15 Missing ⚠️
src/genomicranges/io/gtf.py 0.00% 9 Missing ⚠️
src/genomicranges/grangeslist.py 0.00% 5 Missing ⚠️
src/genomicranges/io/ucsc.py 0.00% 4 Missing ⚠️

❗ There is a different number of reports uploaded between BASE (593dc80) and HEAD (b80e639). Click for more details.

HEAD has 8 uploads less than BASE
Flag BASE (593dc80) HEAD (b80e639)
8 0
Additional details and impacted files
@@            Coverage Diff             @@
##           master    #166       +/-   ##
==========================================
- Coverage   65.23%   0.00%   -65.24%     
==========================================
  Files           8       8               
  Lines        1717    1730       +13     
  Branches      310       0      -310     
==========================================
- Hits         1120       0     -1120     
- Misses        465    1730     +1265     
+ Partials      132       0      -132     
Flag Coverage Δ
macos-latest - py3.10 0.00% <0.00%> (?)
macos-latest - py3.11 0.00% <0.00%> (?)
macos-latest - py3.12 0.00% <0.00%> (?)
macos-latest - py3.13 0.00% <0.00%> (?)
macos-latest - py3.14 0.00% <0.00%> (?)
ubuntu-latest - py3.10 0.00% <0.00%> (?)
ubuntu-latest - py3.11 0.00% <0.00%> (?)
ubuntu-latest - py3.12 0.00% <0.00%> (?)
ubuntu-latest - py3.13 0.00% <0.00%> (?)
ubuntu-latest - py3.14 0.00% <0.00%> (?)

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@jkanche
jkanche merged commit 46a64f8 into master Sep 3, 2026
15 of 17 checks passed
@jkanche
jkanche deleted the update-hatchit branch September 3, 2026 07:23
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2 participants