Pypi

.github/release.yml

@@ -0,0 +1,25 @@
+changelog:
+  exclude:
+    labels:
+      - skip-changelog
+  categories:
+    - title: Breaking Changes
+      labels:
+        - breaking
+        - breaking-change
+    - title: Features
+      labels:
+        - enhancement
+        - feature
+    - title: Fixes
+      labels:
+        - bug
+        - fix
+    - title: CI and Tooling
+      labels:
+        - ci
+        - dependencies
+        - tooling
+    - title: Other Changes
+      labels:
+        - "*"

.github/workflows/ci.yml

@@ -0,0 +1,70 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - dev
+  pull_request:
+
+permissions:
+  contents: read
+
+jobs:
+  tests:
+    name: Tests (Python ${{ matrix.python-version }})
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install uv
+        run: python -m pip install uv
+
+      - name: Install dependencies
+        run: uv sync --group dev --locked
+
+      - name: Run tests
+        run: uv run pytest
+
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+    needs:
+      - tests
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install uv
+        run: python -m pip install uv
+
+      - name: Install dependencies
+        run: uv sync --group dev --locked
+
+      - name: Build distributions
+        run: uv run python -m build
+
+      - name: Validate distribution metadata
+        run: uv run python -m twine check dist/*
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/

.github/workflows/publish-testpypi.yml

@@ -0,0 +1,65 @@
+name: Publish to TestPyPI
+
+on:
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install uv
+        run: python -m pip install uv
+
+      - name: Install dependencies
+        run: uv sync --group dev --locked
+
+      - name: Run tests
+        run: uv run pytest
+
+      - name: Build distributions
+        run: uv run python -m build
+
+      - name: Validate distribution metadata
+        run: uv run python -m twine check dist/*
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+  publish:
+    name: Publish to TestPyPI
+    runs-on: ubuntu-latest
+    needs:
+      - build
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/adagio-cli
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Download distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+      - name: Publish distribution to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/

.github/workflows/publish.yml

@@ -0,0 +1,75 @@
+name: Publish to PyPI
+
+on:
+  push:
+    tags:
+      - "v*"
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install uv
+        run: python -m pip install uv
+
+      - name: Install dependencies
+        run: uv sync --group dev --locked
+
+      - name: Run tests
+        run: uv run pytest
+
+      - name: Verify tag matches package version
+        run: |
+          PACKAGE_VERSION=$(grep '^version = ' pyproject.toml | head -n 1 | cut -d '"' -f 2)
+          TAG_VERSION="${GITHUB_REF_NAME#v}"
+
+          if [ "$PACKAGE_VERSION" != "$TAG_VERSION" ]; then
+            echo "Tag version $TAG_VERSION does not match pyproject version $PACKAGE_VERSION"
+            exit 1
+          fi
+
+      - name: Build distributions
+        run: uv run python -m build
+
+      - name: Validate distribution metadata
+        run: uv run python -m twine check dist/*
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+  publish:
+    name: Publish to PyPI
+    runs-on: ubuntu-latest
+    needs:
+      - build
+    environment:
+      name: pypi
+      url: https://pypi.org/p/adagio-cli
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Download distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+      - name: Publish distribution to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.gitignore

@@ -9,14 +9,13 @@ venv/
 
 # Distribution / packaging
 *.egg-info/
+build/
+dist/
 
 # Local test / coverage files
 .coverage
 .pytest_cache/
 
-# Project lock file
-uv.lock
-
 # OS junk
 .DS_Store
 Thumbs.db
@@ -30,4 +29,5 @@ Thumbs.db
 
 .ipynb_checkpoints/
 .mypy_cache/
-runinfo/
+.uv-cache/
+runinfo/

CHANGELOG.md

@@ -0,0 +1,15 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project follows [Semantic Versioning](https://semver.org/spec/v2.0.0.html)
+using [PEP 440](https://packaging.python.org/en/latest/specifications/version-specifiers/) version strings for Python releases.
+
+## [Unreleased]
+
+### Added
+
+- GitHub Actions CI for linting, tests, and build verification.
+- Trusted Publishing workflows for manual TestPyPI validation and tagged PyPI releases.
+- A release playbook covering changelog, tags, and publish steps.

Dockerfile

@@ -1,36 +1,22 @@
-ARG QIIME_BASE_IMAGE=quay.io/qiime2/amplicon:2024.5
-FROM ${QIIME_BASE_IMAGE} as base
+ARG QIIME_BASE_IMAGE=quay.io/qiime2/amplicon:2026.1
+FROM ${QIIME_BASE_IMAGE} AS base
 
 ENV PYTHONUNBUFFERED=1
 WORKDIR /app
+FROM base AS dev
 
-COPY --from=ghcr.io/astral-sh/uv:0.5.11 /uv /uvx /bin/
-
-ENV UV_COMPILE_BYTECODE=1
-ENV UV_LINK_MODE=copy
-
-# Development stage
-FROM base as dev
-
-RUN --mount=type=cache,target=/root/.cache/uv \
-    --mount=type=bind,source=uv.lock,target=uv.lock \
-    --mount=type=bind,source=pyproject.toml,target=pyproject.toml \
-    uv sync --frozen --no-install-project
-
-ENV PYTHONPATH=/app/src
-
-COPY ./pyproject.toml ./uv.lock /app/
+COPY ./pyproject.toml /app/
 COPY ./README.md /app/
 COPY ./src /app/src
 
-RUN --mount=type=cache,target=/root/.cache/uv \
-    uv sync --frozen
+# Skip UV and use QIIME conda env
+RUN pip install .
+
+RUN pip uninstall pyOpenSSL -y || true
 
-# is this needed still?
-RUN pip3 uninstall pyOpenSSL -y || true
 
-# We can extend this if needed
-FROM dev as production
+FROM dev AS production
+WORKDIR /app
+
+CMD ["adagio", "--help"]
 
-# Set default command
-CMD ["uv", "run", "adagio", "--help"]

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Cymis
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.