Remove Poetry

Author: evilkermit

.github/workflows/build-test.yml

@@ -36,15 +36,16 @@ jobs:
         with:
           file: dockerfiles/Dockerfile
           load: true
+          target: source
       - name: Run ruff check
-        run: docker run --rm ${{ steps.build.outputs.imageid }} poetry run ruff check
+        run: docker run --rm ${{ steps.build.outputs.imageid }} ruff check
       - name: Run format check
-        run: docker run --rm ${{ steps.build.outputs.imageid }} poetry run ruff format --check
+        run: docker run --rm ${{ steps.build.outputs.imageid }} ruff format --check
       - name: Run mypy
-        run: docker run --rm ${{ steps.build.outputs.imageid }} poetry run mypy .
+        run: docker run --rm ${{ steps.build.outputs.imageid }} mypy .
       - name: Unit tests
-        run: docker run -e NOVA_GALAXY_TEST_GALAXY_KEY=${{ env.GALAXY_KEY }} -e NOVA_GALAXY_TEST_GALAXY_URL=${{ env.GALAXY_URL }} --rm ${{ steps.build.outputs.imageid }} poetry run pytest
+        run: docker run -e NOVA_GALAXY_TEST_GALAXY_KEY=${{ env.GALAXY_KEY }} -e NOVA_GALAXY_TEST_GALAXY_URL=${{ env.GALAXY_URL }} --rm ${{ steps.build.outputs.imageid }} pytest
       - name: Run coverage
-        run: docker run -e NOVA_GALAXY_TEST_GALAXY_KEY=${{ env.GALAXY_KEY }} -e NOVA_GALAXY_TEST_GALAXY_URL=${{ env.GALAXY_URL }} --rm ${{ steps.build.outputs.imageid }} sh -c "poetry run coverage run && poetry run coverage report"
+        run: docker run -e NOVA_GALAXY_TEST_GALAXY_KEY=${{ env.GALAXY_KEY }} -e NOVA_GALAXY_TEST_GALAXY_URL=${{ env.GALAXY_URL }} --rm ${{ steps.build.outputs.imageid }} sh -c "coverage run && coverage report"
       - name: Docs test
         run: docker run --rm ${{ steps.build.outputs.imageid }} bash build_docs.sh

.github/workflows/nova-galaxy.yml

@@ -58,4 +58,4 @@ jobs:
           file: dockerfiles/Dockerfile
           load: true
       - name: Publish
-        run: docker run --rm ${{ steps.build.outputs.imageid }} poetry publish -u __token__ -p ${PYPI_API_TOKEN}
+        run: docker run --rm ${{ steps.build.outputs.imageid }} sh -c "hatch build && hatch publish -u __token__ -a ${PYPI_API_TOKEN}"

.gitignore

@@ -164,3 +164,5 @@ cython_debug/
 
 
 junit.xml
+
+.pixi

.pre-commit-config.yaml

@@ -20,7 +20,7 @@ repos:
   hooks:
     - id: mypy
       name: mypy
-      entry: poetry run mypy .
+      entry: pixi run mypy .
       language: system
       types: [python]
       verbose: true

.readthedocs.yaml

@@ -11,7 +11,7 @@ build:
     python: "3.13"
   jobs:
     post_create_environment:
-      - pip install altair sphinx-rtd-theme==3.0.0rc3
+      - pip install altair sphinx-rtd-theme==3.0.0rc3 tomli
       - pip install .
 
 # Build documentation in the "docs/" directory with Sphinx

README.md

@@ -16,37 +16,36 @@ You can install this package directly with
 pip install nova-galaxy
 ```
 
-or with Poetry by placing the following in your pyproject.toml file (you can version lock with typical Semantic Versioning syntax)
+or with [Pixi](https://pixi.sh/latest/):
 
 
-```
-[tool.poetry.dependencies]
-nova-galaxy = "*"
+```commandline
+pixi add --pypi nova-galaxy
 ```
 
 ## Formatting
 ```commandline
-poetry run ruff format
+pixi run ruff format
 ```
 
 ## Linting
 ```commandline
-poetry run ruff check
-poetry run mypy .
+pixi run ruff check
+pixi run mypy .
 ```
 
 ## Testing
 You can run the tests for this package with the following command from the base directory:
 ```commandline
-NOVA_GALAXY_TEST_GALAXY_URL=galaxy-url NOVA_GALAXY_TEST_GALAXY_KEY=key poetry run pytest tests/
+NOVA_GALAXY_TEST_GALAXY_URL=galaxy-url NOVA_GALAXY_TEST_GALAXY_KEY=key pixi run pytest tests/
 ```
 with `NOVA_GALAXY_TEST_GALAXY_URL` being the url of your Galaxy instance and `NOVA_GALAXY_TEST_GALAXY_KEY` being your
 Galaxy API Key.
 
 To run tests with coverage (include the above environment variables):
 ```commandline
-poetry run coverage run
-poetry run coverage report
+pixi run coverage run
+pixi run coverage report
 ```
 
 ## CI/CD in GitHub

build_docs.sh

@@ -1 +1 @@
-poetry run sphinx-build -M html docs docs/_build
+sphinx-build -M html docs docs/_build

dockerfiles/Dockerfile

@@ -1,16 +1,27 @@
 FROM --platform=amd64 python:3.10-slim AS source
 
-# make sure image can run as non-root user
-ENV POETRY_CACHE_DIR=/poetry/.cache
-ENV POETRY_CONFIG_DIR=/poetry/.config
-ENV POETRY_HOME=/poetry
+RUN apt update && apt install -y curl wget
 
-RUN pip install poetry
 COPY . /src
 WORKDIR /src
 
-RUN poetry install
-RUN poetry build --format=wheel
+RUN curl -fsSL https://pixi.sh/install.sh | sh
+ENV PATH="/root/.pixi/bin:${PATH}"
+RUN pixi install
+SHELL [ "pixi", "run" ]
+ENTRYPOINT [ "pixi", "run" ]
 
-RUN chmod og+rwX -R /poetry
-RUN chmod og+rwX -R /src
+RUN chmod og+rwX -R /src /.cache
+
+FROM --platform=amd64 python:3.10-slim AS package
+
+RUN apt update && apt install -y curl
+
+COPY . /src
+WORKDIR /src
+
+RUN curl -fsSL https://pixi.sh/install.sh | sh
+ENV PATH="/root/.pixi/bin:${PATH}"
+RUN pixi install -e production
+SHELL [ "pixi", "run" ]
+ENTRYPOINT [ "pixi", "run" ]

docs/conf.py

@@ -7,7 +7,7 @@
 author = "Andrew Ayres"
 with open("../pyproject.toml", "rb") as toml_file:
     toml_dict = tomli.load(toml_file)
-    release = toml_dict["tool"]["poetry"]["version"]
+    release = toml_dict["project"]["version"]
 
 extensions = ["sphinx.ext.autodoc", "sphinx.ext.napoleon", "sphinx.ext.viewcode", "sphinx_rtd_theme"]
 

docs/core_concepts/parameters.rst

@@ -62,4 +62,4 @@ Use `add_step_param` to set parameters for specific steps within the workflow. T
     list_of_datasets = [Dataset(id="ds1"), Dataset(id="ds2")]
     workflow_params.add_step_param("4", "multiple_inputs", list_of_datasets)
 
-When running a workflow, you pass an instance of `WorkflowParameters` to the `Workflow.run()` method.
+When running a workflow, you pass an instance of `WorkflowParameters` to the `Workflow.run()` method.