From e5f96ad7ac7a82907865059669a23d995604a8d6 Mon Sep 17 00:00:00 2001
From: Malte Benedikt Kuehl <malte.kuehl@clin.au.dk>
Date: Thu, 30 May 2024 22:24:31 +0200
Subject: [PATCH] Add workflow

---
 .github/workflows/ci.yml     | 62 ++++++++++++++++++++++++++++++++++++
 README.md                    |  1 +
 docs/source/start.md         |  1 +
 pytximport/core/_tximport.py |  3 +-
 4 files changed, 65 insertions(+), 2 deletions(-)
 create mode 100644 .github/workflows/ci.yml

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
new file mode 100644
index 0000000..d5c6e8f
--- /dev/null
+++ b/.github/workflows/ci.yml
@@ -0,0 +1,62 @@
+name: Test & lint package & deploy documentation
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: true
+      matrix:
+        python-version: [3.11.4]
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+      - uses: actions/cache@v3
+        with:
+          path: ${{ env.pythonLocation }}
+          key: ${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
+      - name: Install dependencies
+        run: |
+          export FLIT_ROOT_INSTALL=1
+          python -m pip install --upgrade pip
+          python -m pip install flit
+          python -m flit install --deps production
+          python -m pip install git+https://github.com/complextissue/xpysom.git
+          python -m pip install black flake8 flake8-docstrings isort flake8-comprehensions mypy
+          python -m pip install coverage pytest bandit sphinx sphinx-autoapi \
+            myst-parser pygments sphinx-autodoc-typehints sphinx-rtd-theme furo sphinx_design \
+            sphinx-copybutton sphinxcontrib-bibtex sphinxcontrib-mermaid nbsphinx pandoc
+          sudo apt-get update
+          sudo apt-get install -y pandoc
+      - name: Format with black
+        run: |
+          python -m black .
+      - name: Lint with flake8
+        run: |
+          python -m flake8 pytximport
+      - name: Check imports with isort
+        run: |
+          python -m isort --check-only --diff --recursive pytximport
+      - name: Type check with mypy
+        run: |
+          python -m mypy -p pytximport
+      - name: Check security with bandit
+        run: |
+          python -m bandit --verbose --ini .bandit.ini -ll --recursive pytximport
+      - name: Test with pytest
+        run: |
+          coverage run -m pytest --maxfail=10
+          coverage xml
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v4.0.1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
diff --git a/README.md b/README.md
index bc69d08..a3728d1 100755
--- a/README.md
+++ b/README.md
@@ -6,6 +6,7 @@
 [![Python Version Required](https://img.shields.io/pypi/pyversions/pytximport)](https://pypi.org/project/pytximport/)
 [![License](https://img.shields.io/pypi/l/pytximport)](https://github.com/complextissue/pytximport)
 [![Documentation Status](https://readthedocs.org/projects/pytximport/badge/?version=latest)](https://pytximport.readthedocs.io/en/latest/?badge=latest)
+[![codecov](https://codecov.io/gh/complextissue/pytximport/graph/badge.svg?token=M9JEHJVXYI)](https://codecov.io/gh/complextissue/pytximport)
 
 `pytximport` is a Python package for fast gene count estimation based on transcript abundance, inspired by the `tximport` R package.
 
diff --git a/docs/source/start.md b/docs/source/start.md
index 1ab497d..e58527b 100755
--- a/docs/source/start.md
+++ b/docs/source/start.md
@@ -6,6 +6,7 @@
 [![Python Version Required](https://img.shields.io/pypi/pyversions/pytximport)](https://pypi.org/project/pytximport/)
 [![License](https://img.shields.io/pypi/l/pytximport)](https://github.com/complextissue/pytximport)
 [![Documentation Status](https://readthedocs.org/projects/pytximport/badge/?version=latest)](https://pytximport.readthedocs.io/en/latest/?badge=latest)
+[![codecov](https://codecov.io/gh/complextissue/pytximport/graph/badge.svg?token=M9JEHJVXYI)](https://codecov.io/gh/complextissue/pytximport)
 
 `pytximport` is a Python package for fast gene count estimation based on transcript abundance, inspired by the `tximport` R package.
 
diff --git a/pytximport/core/_tximport.py b/pytximport/core/_tximport.py
index 32c64db..891d6f1 100644
--- a/pytximport/core/_tximport.py
+++ b/pytximport/core/_tximport.py
@@ -43,8 +43,7 @@ def tximport(
     return_data: bool = True,
     biotype_filter: Optional[List[str]] = None,
 ) -> Union[xr.Dataset, ad.AnnData, None]:
-    """Import transcript-level quantification files and convert them to gene-level expression estimates, correcting
-    for transcript length differences.
+    """Import transcript-level quantification files and convert them to gene-level expression estimates.
 
     Args:
         file_paths (List[Union[str, Path]]): The paths to the quantification files.