Merge pull request #85 from gbouras13/migrate-poetry-to-pixi

Migrate poetry to pixi

Author: gbouras13

.flake8

@@ -1,58 +1,37 @@
 name: CI
 
-on: [push,pull_request]
+on: [push, pull_request]
 
 jobs:
   tests:
-    name: "Python ${{ matrix.python-version }}"
+    name: "Tests (${{ matrix.os }})"
     runs-on: ${{ matrix.os }}
 
-    defaults:
-      run:
-        shell: bash -el {0}
-
     strategy:
       matrix:
-        os: [macos-latest, ubuntu-latest] #macos-latest/macos-14 is M1 - some deps fail it due to not having M1 build (MMSeqs2)
-        python-version: ["3.12"]
+        os: [macos-latest, ubuntu-latest]
 
     steps:
-      - uses: "actions/checkout@v3"
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
-      # Setup env
-      - uses: "conda-incubator/setup-miniconda@v3"
+      - name: Setup Pixi
+        uses: prefix-dev/setup-pixi@v0.8.1
         with:
-          activate-environment: plassembler
-          environment-file: build/environment.yaml
-          python-version: ${{ matrix.python-version }}
-          auto-activate-base: false
-          channels: conda-forge,bioconda,defaults
-          channel-priority: strict
-          auto-update-conda: true
-          
-      - name: Install plassembler
-        shell: bash -l {0}
-        run: |
-          conda install python=${{ matrix.python-version }}
-          python -m pip install --upgrade pip
-          pip install -e .
-          pip install black
-          pip install isort
-          pip install pytest
-          pip install pytest-cov
-          pip install git+https://github.com/rrwick/Unicycler.git
-          unicycler --help
-      - name: Check formatting
-        shell: bash -l {0}
-        run: just check-fmt
-      - name: Test and generate coverage report with pytest
-        shell: bash -l {0}
-        # need to set TERM to linux for some reason,kept getting a nasty error that was breaking unicycler 
+          pixi-version: v0.71.2
+          cache: true
+          environments: dev
+
+      - name: Check formatting and lint
+        run: pixi run check-fmt
+
+      - name: Run unit tests
+        # TERM is set to avoid tput/terminal noise breaking Unicycler
         # https://github.com/cypress-io/cypress/issues/15679
-        run: |
-          export TERM=linux
-          unicycler --version
-          just test-ci
+        env:
+          TERM: linux
+        run: pixi run test-ci
 
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v4

.github/workflows/ci.yaml

@@ -11,32 +11,20 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
-      - uses: conda-incubator/setup-miniconda@v3
+      - uses: actions/checkout@v4
+
+      - name: Setup Pixi
+        uses: prefix-dev/setup-pixi@v0.8.1
         with:
-          python-version: 3.12
-          activate-environment: plassembler
-          environment-file: build/environment.yaml
-          auto-activate-base: false
-          channels: conda-forge,bioconda,defaults
-          channel-priority: strict
-          auto-update-conda: true 
+          pixi-version: v0.71.2
+          cache: true
+          environments: dev
 
-      - name: Install plassembler
-        shell: bash -l {0}
-        run: |
-          python -m pip install -U pip
-          pip install -e .
-          pip install black
-          pip install isort
-          pip install pytest
-          pip install pytest-cov
-          pip install git+https://github.com/rrwick/Unicycler.git
       - name: Build a binary wheel and a source tarball
-        shell: bash -l {0}
-        run: just build
+        run: pixi run build
+
       - name: Publish to PyPI
-        uses: pypa/gh-action-pypi-publish@master
+        uses: pypa/gh-action-pypi-publish@release/v1
         with:
           user: __token__
           password: ${{ secrets.PYPI_TOKEN }}

.github/workflows/release.yaml

@@ -3,6 +3,9 @@ __pycache__/
 *.py[cod]
 *$py.class
 
+# Pixi
+.pixi/
+
 # C extensions
 *.so
 

.gitignore

@@ -1,5 +1,12 @@
 # History
 
+1.8.3 (2026-07-05)
+------------------
+
+* Migrates the build and development tooling from Poetry to Pixi
+* Switches the build backend to hatchling and linting/formatting to ruff
+* Single-sources the package version via `importlib.metadata`
+
 1.8.1 (2025-09-27)
 ------------------
 

HISTORY.md

@@ -14,7 +14,5 @@ dependencies:
   - samtools >=0.15.0
   - canu >=2.2
   - dnaapler >=0.4.0
-  - just
-  - poetry
+  - pip
   - python >=3.8,<3.14
-  - ripgrep

build/environment.yaml

@@ -26,7 +26,7 @@ You can install the Python components of `plassembler` using pip.
 pip install plassembler
 ```
 
-You will then need to install the external dependencies separately, which can be found in `build/environment.yml`
+You will then need to install the external dependencies separately, which can be found in `build/environment.yaml`
 
 * [Flye](https://github.com/fenderglass/Flye) >=2.9
 * [Unicycler](https://github.com/rrwick/Unicycler) >=0.4.8

docs/install.md

@@ -1,34 +1,31 @@
 PROJECT := "plassembler"
 OPEN := if os() == "macos" { "open" } else { "xdg-open" }
-VERSION := `poetry version | rg -o '\d+\.\d+\.\d+'`
+VERSION := `pixi workspace version get`
 
-# format code with black and isort
+# format code with ruff
 fmt:
-    poetry run black .
-    poetry run isort .
+    pixi run fmt
 
-# check format of code with black and isort
+# check formatting and lint with ruff
 check-fmt:
-    poetry run black --check .
-    poetry run isort --check .
+    pixi run check-fmt
 
-
-# install latest version with poetry
+# install environment with pixi
 install:
-    poetry install --no-interaction
+    pixi install
 
 # run all tests
 test opts="":
-    poetry run pytest -vv {{opts}} tests/
+    pixi run test {{opts}}
 
 # run tests with coverage report
 coverage:
-    poetry run pytest --cov-report term --cov-report html --cov={{ PROJECT }} --cov-branch tests/
+    pixi run coverage
     {{ OPEN }} htmlcov/index.html
 
 # run tests on the CI
 test-ci:
-    poetry run pytest --cov={{ PROJECT }} --cov-report=xml --cov-branch tests/
+    pixi run test-ci
 
 # prints out the commands to run to tag the release and push it
 tag:
@@ -37,4 +34,4 @@ tag:
 
 # build a python release
 build:
-    poetry build --no-interaction
+    pixi run build