8 add pipeline (#9)

Author: JosePizarro3

.github/workflows/actions.yml

@@ -0,0 +1,72 @@
+name: Installing and Testing
+on: [push]
+
+# https://docs.github.com/en/actions/using-jobs/assigning-permissions-to-jobs
+# `contents` is for permission to the contents of the repository.
+# `pull-requests` is for permission to pull request
+permissions:
+  contents: write
+  checks: write
+  pull-requests: write
+
+env:
+  UV_SYSTEM_PYTHON: true
+
+jobs:
+  install-and-test:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python_version: ["3.9", "3.10", "3.11", "3.12"]
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{matrix.python_version}}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{matrix.python_version}}
+    - name: Install uv
+      run: |
+        curl -LsSf https://astral.sh/uv/install.sh | sh
+    - name: Install dependencies
+      run: |
+        pip install --upgrade pip
+        uv pip install -e '.[dev]'
+    - name: mypy
+      run: |
+        python -m mypy --ignore-missing-imports --follow-imports=silent --no-strict-optional --exclude dependencies bam_data_store tests
+    - name: Test with pytest
+      run: |
+        python -m pytest -sv --ignore=bam_data_store/dependencies tests
+  build-and-install:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v5
+      with:
+        python-version: 3.12
+    - name: Install uv
+      run: |
+        curl -LsSf https://astral.sh/uv/install.sh | sh
+    - name: Build the package
+      run: |
+        uv pip install build
+        python -m build --sdist
+    - name: Install the package
+      run: |
+        uv pip install dist/*.tar.gz
+  ruff-linting:
+      runs-on: ubuntu-latest
+      steps:
+        - uses: actions/checkout@v4
+        - uses: chartboost/ruff-action@v1
+          with:
+            args: "check . --exclude bam_data_store/dependencies"
+  ruff-formatting:
+      runs-on: ubuntu-latest
+      steps:
+        - uses: actions/checkout@v4
+        - uses: chartboost/ruff-action@v1
+          with:
+            args: "format . --check --verbose --exclude bam_data_store/dependencies"

.github/workflows/mkdocs-deploy.yml

@@ -0,0 +1,29 @@
+name: Deploy MkDocs Site
+
+on:
+  push:
+    branches:
+      - main # Triggers deployment on push to the main branch
+
+permissions:
+  contents: write
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v4
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+      - name: Install Documentation Dependencies
+        run: |
+          pip install --upgrade pip
+          pip install .[docu]
+      - name: Deploy docs
+        uses: mhausenblas/mkdocs-deploy-gh-pages@master
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          CONFIG_FILE: mkdocs.yml

.github/workflows/publish.yml

@@ -0,0 +1,43 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Build and Publish Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+env:
+  UV_SYSTEM_PYTHON: true
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v5
+      with:
+        python-version: 3.11
+    - name: Install uv
+      run: |
+        curl -LsSf https://astral.sh/uv/install.sh | sh
+    - name: Install dependencies
+      run: |
+        pip install --upgrade pip
+        uv pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

.gitlab-ci.yml

@@ -26,10 +26,11 @@ maintainers = [
 ]
 license = { file = "LICENSE" }
 dependencies = [
-  "pybis",
+  "pybis<=1.36.3",
   "pandas",
   "openpyxl",
   "click",
+  "pydantic",
 ]
 
 [project.urls]
@@ -43,6 +44,7 @@ dev = [
   "pytest",
   "pytest-timeout",
   "pytest-cov",
+  "python-decouple",
 ]
 jupy = [
   "jupyterlab",
@@ -135,13 +137,10 @@ follow_imports = "silent"
 no_strict_optional = true
 disable_error_code = "import, annotation-unchecked"
 
-[tool.setuptools]
-package-dir = { "" = "bam_data_store" }
-
 [tool.setuptools.packages.find]
-where = ["bam_data_store"]
+where = ["."]
 exclude = ["dependencies*"]
 namespaces = false
 
 [tool.setuptools_scm]
-write_to = "bam_data_store/_version.py"
+write_to = "bam_data_store/_version.py"

pyproject.toml

@@ -0,0 +1,3 @@
+from setuptools import setup
+
+setup()

requirements.txt

@@ -10,4 +10,4 @@ def pytest_exception_interact(call):
 
     @pytest.hookimpl(tryfirst=True)
     def pytest_internalerror(excinfo):
-        raise excinfo.value
+        raise excinfo.value

setup.py

@@ -0,0 +1,2 @@
+def test_dummy():
+    assert True