Migrate project configuration and CI/CD workflows from Poetry to Pixi

.gitattributes

@@ -0,0 +1,2 @@
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true -diff

.github/workflows/ci.yaml

@@ -1,53 +1,36 @@
 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-13, ubuntu-latest]
-        python-version: ["3.9"]
 
     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: dnaapler
-          environment-file: build/environment.yaml
-          python-version: ${{ matrix.python-version }}
-          auto-activate-base: false
-          channels: conda-forge,bioconda,defaults
-          channel-priority: strict
-          auto-update-conda: true
-      - name: Install project
-        shell: bash -l {0}
-        run: |
-          conda install python=${{ 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
+          pixi-version: v0.70.2
+          cache: true
+          environments: dev
+
       - name: Check formatting
-        shell: bash -l {0}
-        run: just check-fmt
-      - name: Test and generate coverage report with pytest
-        shell: bash -l {0}
-        run: just test-ci
+        run: pixi run check-fmt
+
+      - name: Lint
+        run: pixi run lint
+
+      - name: Run unit tests
+        run: pixi run coverage
+
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v4
-
-

.github/workflows/release.yaml

@@ -11,28 +11,18 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
-      - uses: conda-incubator/setup-miniconda@v3
+      - uses: actions/checkout@v4
+
+      - name: Setup Pixi
+        uses: prefix-dev/setup-pixi@v0.8.1
         with:
-          python-version: 3.9
-          activate-environment: dnaapler
-          environment-file: build/environment.yaml
-          auto-activate-base: false
-          channels: conda-forge,bioconda,defaults
-          channel-priority: strict
-          auto-update-conda: true
-      - name: Install project
-        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
+          pixi-version: v0.70.2
+          cache: true
+          environments: dev
+
       - 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@release/v1
         with:

.gitignore

@@ -110,3 +110,6 @@ ENV/
 .DS_Store
 */.DS_Store
 */*/.DS_Store
+# pixi environments
+.pixi/*
+!.pixi/config.toml

README.md

@@ -18,31 +18,22 @@ Dnaapler is a simple tool that reorients complete circular microbial genomes.
 
 ## Quick Start
 
+For local development or running directly in the cloned repository:
 ```
-# creates empty conda environment
-conda create -n dnaapler_env
+# install dependencies and setup the environment
+pixi install
 
-# activates conda environment
-conda activate dnaapler_env
+# run dnaapler all 
+pixi run dnaapler all -i input_mixed_contigs.fasta -o output_directory_path -p my_bacteria_name -t 8
 
-# installs dnaapler
-conda install -c bioconda dnaapler
-
-# runs dnaapler all 
-dnaapler all -i input_mixed_contigs.fasta -o output_directory_path -p my_bacteria_name -t 8
-
-# runs dnaapler all with a gfa file from e.g. Flye, Unicycler or Autocycler
-dnaapler all -i assembly.gfa -o output_directory_path -p my_bacteria_name -t 8
+# run dnaapler all with a gfa file
+pixi run dnaapler all -i assembly.gfa -o output_directory_path -p my_bacteria_name -t 8
 ```
 
-* If you have a MacOS machine with Apple Silicon (M1/M2/M3/M4) and are having installation issues, please try
-
+For general usage, you can also install it globally:
 ```
-conda create --platform osx-64 -n dnaapler_env dnaapler
-
-conda activate dnaapler_env
-
-dnaapler all -i input_mixed_contigs.fasta -o output_directory_path -p my_bacteria_name -t 8
+# installs dnaapler globally
+pixi global install dnaapler
 ```
 
 ## Paper
@@ -93,7 +84,7 @@ Hyatt, D., Chen, GL., LoCascio, P.F. et al. Prodigal: prokaryotic gene recogniti
 
 # v1.0
 
-* **BREAKING CHANGE** - `dnaapler` now uses `MMSeqs2 v13.45111` rather than `BLAST`. You will need to install [MMSeqs2](https://github.com/soedinglab/MMseqs2) if you upgrade (if you use conda, it should be handled for you). The CLI is identical.
+* **BREAKING CHANGE** - `dnaapler` now uses `MMSeqs2 v13.45111` rather than `BLAST`. You will need to install [MMSeqs2](https://github.com/soedinglab/MMseqs2) if you upgrade (if you use pixi or conda, it should be handled for you). The CLI is identical.
 * There are 2 reasons for this:
     1. Users reported problems installing BLAST on MacOS with Apple Silicon (see e.g. [here](https://github.com/gbouras13/pharokka/issues/368)). MMseqs2 works on all platforms and is dilligently maintained.
     2. MMSeqs2 is much much faster than BLAST (what took BLAST a few minutes takes MMSeqs2 seconds). We probably should have written `dnaapler` with `MMseqs2` to begin with. `MMSeqs2 v13.45111` was chosen to ensure interoperability with [pharokka](https://github.com/gbouras13/pharokka)
@@ -121,7 +112,7 @@ If you don't want to install `dnaapler` locally, you can run `dnaapler all` with
   - [Documentation](#documentation)
   - [Commands](#commands)
   - [Installation](#installation)
-    - [Conda](#conda)
+    - [Pixi](#pixi)
     - [Pip](#pip)
   - [Usage](#usage)
   - [Example Usage](#example-usage)
@@ -177,14 +168,14 @@ The full documentation for `dnaapler` can be found [here](https://dnaapler.readt
 
 `dnaapler` requires only `MMseqs2 v13.45111` as an external dependency. 
 
-Installation from conda is highly recommended as this will install `MMseqs2` automatically.
+Installation using `pixi` is highly recommended as this will install `MMseqs2` automatically.
 
-### Conda
+### Pixi
 
-`dnaapler` is available on bioconda.
+`dnaapler` is available on bioconda and can be installed globally using `pixi`:
 
 ```
-conda install -c bioconda dnaapler
+pixi global install dnaapler
 ```
 
 ### Pip

justfile

@@ -1,37 +1,35 @@
 PROJECT := "dnaapler"
 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
 fmt:
-    poetry run black .
-    poetry run isort .
+    pixi run fmt
 
 # check format of code with black and isort
 check-fmt:
-    poetry run black --check .
-    poetry run isort --check .
+    pixi run check-fmt
 
 # lint code with flake8
 lint:
-    poetry run flake8 .
+    pixi run lint
 
-# 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 pytest --cov={{ PROJECT }} --cov-report=xml --cov-branch tests/
 
 # prints out the commands to run to tag the release and push it
 tag:
@@ -40,4 +38,4 @@ tag:
 
 # build a python release
 build:
-    poetry build --no-interaction
+    pixi run build