add pixie support

.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

@@ -1,52 +1,33 @@
 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]
-        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 }} pip
-          python -m pip install --upgrade pip
-          pip install -e .
-          pip install ruff
-          pip install pytest
-          pip install pytest-cov
-      - 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
+          pixi-version: v0.71.2
+          cache: true
+          environments: dev
+
+      - name: Check formatting and lint
+        run: pixi run check-fmt
+
+      - name: Run unit tests
+        run: pixi run test-ci
+
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v4
-
-

.github/workflows/release.yaml

@@ -11,27 +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: 3.9
-          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 ruff
+          pixi-version: v0.71.2
+          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:
           user: __token__
-          password: ${{ secrets.PYPI_TOKEN }}
+          password: ${{ secrets.PYPI_TOKEN }}

.gitignore

@@ -110,3 +110,7 @@ ENV/
 .DS_Store
 */.DS_Store
 */*/.DS_Store
+
+# pixi environments
+.pixi/*
+!.pixi/config.toml

HISTORY.md

@@ -2,6 +2,7 @@
 
 # 1.4.0
 
+* Adds support for gzip-, bzip2- and xz-compressed input ([#98](https://github.com/gbouras13/dnaapler/issues/98)). `dnaapler` now transparently decompresses `.gz`, `.bz2` and `.xz` input files (detected from the file's contents, regardless of extension), so compressed FASTA or GFA files can be passed directly to any subcommand.
 * Fixes [#102](https://github.com/gbouras13/dnaapler/issues/102). `dnaapler largest`, `mystery` and `nearest` could reorient to the wrong coordinate when the chosen CDS was on the negative strand, as the lowest coordinate of the CDS was used instead of its actual start codon. The reoriented sequence now correctly begins at the start codon. A related latent bug in the negative-strand fallback of the MMseqs2-based reorientation was also fixed.
 * If you run `dnaapler` with GFA input, it now also writes a `{prefix}_reoriented.fasta` alongside the `{prefix}_reoriented.gfa`. This FASTA contains all contigs from the GFA (circular contigs reoriented with overlap trimmed, non-circular contigs passed through unchanged), so it can be fed directly to downstream tools such as polishers.
 * If a GFA input contains no circular sequences, `dnaapler` no longer exits with an error. Instead it warns, copies the input GFA to the output, and writes all sequences out as a linear `{prefix}_reoriented.fasta`. For `dnaapler all` and `dnaapler bulk`, a reorientation summary is also written with every contig marked as not reoriented.

README.md

@@ -121,6 +121,7 @@ If you don't want to install `dnaapler` locally, you can run `dnaapler all` with
   - [Documentation](#documentation)
   - [Commands](#commands)
   - [Installation](#installation)
+    - [Pixi](#pixi)
     - [Conda](#conda)
     - [Pip](#pip)
   - [Usage](#usage)
@@ -177,7 +178,15 @@ 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` or `conda` is highly recommended as this will install `MMseqs2` automatically.
+
+### Pixi
+
+`dnaapler` is available on bioconda and can be installed globally using `pixi`:
+
+```
+pixi global install dnaapler
+```
 
 ### Conda
 

docs/run.md

@@ -1,7 +1,7 @@
 
 # Running `dnaapler`
 
-For all subcommands, `dnaapler` requires an input FASTA file using the `-i` or `--input` parameters. 
+For all subcommands, `dnaapler` requires an input FASTA file using the `-i` or `--input` parameters. The input may be in FASTA or GFA format, and may be gzip (`.gz`), bzip2 (`.bz2`) or xz (`.xz`) compressed (this is detected automatically, regardless of the file extension).
 
 It is also highly recommended to specify an output directory using the `-o` or `--output` parameters, otherwise `dnaapler` will write the output to a directory named `output.dnaapler` by default.
 

justfile

@@ -1,33 +1,31 @@
 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 ruff
 fmt:
-    poetry run ruff format .
-    poetry run ruff check --fix .
+    pixi run fmt
 
 # check formatting and lint with ruff
 check-fmt:
-    poetry run ruff format --check .
-    poetry run ruff 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:
@@ -36,4 +34,4 @@ tag:
 
 # build a python release
 build:
-    poetry build --no-interaction
+    pixi run build