publish to Pypi (#260)

.github/workflows/ci-cd.yml

@@ -0,0 +1,135 @@
+name: CI/CD
+on:
+  push:
+    branches: [ "master", "develop" ]
+  pull_request:
+    branches: [ "master", "develop" ]
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  ci_pip:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+
+    - name: Cleanup build folder 🧹
+      run: |
+        ls -la ./
+        rm -rf ./* || true
+        rm -rf ./.??* || true
+        ls -la ./
+
+    - name: Setup Python 3.12 🐍
+      uses: actions/setup-python@v5
+      with:
+        python-version: 3.12
+
+    - name: Setup backend 🏗️
+      run: |
+        pip install uv
+        uv pip install --system hatch pytest pytest-rerunfailures autoflake==1.7 isort==6.0 black==25.1
+
+    - name: Checkout 🛎️
+      uses: actions/checkout@v4
+
+    # Builds a wheel needed for the CD
+    - name: Build wheel 🎡
+      run: hatch build -t wheel
+
+    # Store the wheel in GitHub Actions
+    - name: Upload artifact ❄️
+      uses: actions/upload-artifact@v4
+      with:
+        name: genomepy_wheel
+        path: dist/
+
+    # Test if the created wheel can be installed
+    - name: Install 🛠️
+      run: uv pip install --system dist/*.whl --force-reinstall
+
+    - name: Unit tests 📜
+      run: pytest -vvv --reruns 1 --reruns-delay 10 tests/test_01_basic.py
+
+    - name: Integration tests 📚
+      run: |
+        genomepy --help
+        genomepy annotation --help
+        genomepy install --help
+        genomepy search --help
+
+  ci_conda:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+
+    - name: Cleanup build folder 🧹
+      run: |
+        ls -la ./
+        rm -rf ./* || true
+        rm -rf ./.??* || true
+        ls -la ./
+
+    - name: Checkout 🛎️
+      uses: actions/checkout@v4
+
+    - name: Setup backend 🏗️
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        environment-file: environment.yml
+        miniforge-version: latest
+
+    - name: Install 🛠️
+      run: pip install . --no-deps --ignore-installed
+
+    - name: Unit tests 📜
+      run: pytest -vvv --reruns 1 --reruns-delay 10 tests/test_01_basic.py
+
+    - name: Integration tests 📚
+      run: |
+        genomepy --help
+        genomepy annotation --help
+        genomepy install --help
+        genomepy search --help
+
+  cd:
+    needs: ci_pip
+    runs-on: ubuntu-latest
+    # Only run this job if new work is pushed to "master"
+    if: github.event_name == 'push' && github.ref == 'refs/heads/master'
+#    # Only run this job on a tagged commit
+#    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+
+    steps:
+
+    - name: Cleanup build folder 🧹
+      run: |
+        ls -la ./
+        rm -rf ./* || true
+        rm -rf ./.??* || true
+        ls -la ./
+
+    - name: Setup Python 3.12 🐍
+      uses: actions/setup-python@v5
+      with:
+        python-version: 3.12
+
+    - run: mkdir -p dist
+
+    - name: Download artifact ❄️
+      uses: actions/download-artifact@v4
+      with:
+        name: genomepy_wheel
+        path: dist/
+
+    - name: Publish to PyPI 🚀
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/docs.yml

@@ -1,16 +1,16 @@
-name: Build and Deploy
+name: Documentation
 on:
   push:
-    branches:
-      - master
-      - docs # backdoor branch to update docs
+    branches: [ "master" ]
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
 
 jobs:
   build-and-deploy:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout 🛎️
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install & Build 📜
         run: |

.travis.yml

@@ -17,8 +17,8 @@ env:
 
 before_install:
   # setup mambaforge
-  - wget -q -O Mambaforge.sh "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh"
-  - bash Mambaforge.sh -b -p "${HOME}/conda" > /dev/null
+  - wget -O Miniforge3.sh "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
+  - bash Miniforge3.sh -b -p "${HOME}/conda" > /dev/null
   - source "${HOME}/conda/etc/profile.d/conda.sh"
   - source "${HOME}/conda/etc/profile.d/mamba.sh"
   - mamba activate

environment.yml

@@ -10,7 +10,7 @@ dependencies:
   - click
   - colorama
   - filelock >=3.5
-  - libsqlite <3.49  # v3.49.1: no column "size" (this is a diskcache requirement)
+  # - libsqlite <3.49  # v3.49.1: no column "size" (this is a diskcache requirement)
   - loguru
   - mygene
   - mysql <=8.4  # 9.3: 'mysql_native_password' cannot be loaded
@@ -49,8 +49,8 @@ dependencies:
   # Testing
   - autoflake =1.7
   - black =25.1
-  - flake8 =4.0
-  - flake8-bugbear =23.3
+#  - flake8 =4.0
+#  - flake8-bugbear =23.3
 #  - flakeheaven  # v3.3.0 does not work with python 3.12
   - isort =6.0
   - pytest

pyproject.toml

@@ -24,6 +24,7 @@ dependencies = [
     "mygene",
     "mysql-connector-python",
     "norns >=0.1.6",
+    "setuptools; python_version >= '3.12'",  # norns uses pkg_resources
     "numpy",
     "pandas",
     "pyfaidx >=0.7.2.1",