diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..997504b --- /dev/null +++ b/.gitattributes @@ -0,0 +1,2 @@ +# SCM syntax highlighting & preventing 3-way merges +pixi.lock merge=binary linguist-language=YAML linguist-generated=true -diff diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index bb1c808..611b48d 100644 --- a/.github/workflows/ci.yaml +++ b/.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 - - diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml index 0618cf8..9390f3e 100644 --- a/.github/workflows/release.yaml +++ b/.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: diff --git a/.gitignore b/.gitignore index 279fa4a..4a9c36c 100644 --- a/.gitignore +++ b/.gitignore @@ -110,3 +110,6 @@ ENV/ .DS_Store */.DS_Store */*/.DS_Store +# pixi environments +.pixi/* +!.pixi/config.toml diff --git a/README.md b/README.md index f81d332..d798d0d 100644 --- a/README.md +++ b/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 diff --git a/build/environment.yaml b/build/environment.yaml deleted file mode 100644 index bffb51e..0000000 --- a/build/environment.yaml +++ /dev/null @@ -1,11 +0,0 @@ -name: dnaapler_env -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - mmseqs2 >=13.45111 - - just - - poetry - - python >=3.8,<4.0 - - ripgrep \ No newline at end of file diff --git a/justfile b/justfile index a4cf1a5..de63021 100644 --- a/justfile +++ b/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 \ No newline at end of file + pixi run build \ No newline at end of file diff --git a/pixi.lock b/pixi.lock new file mode 100644 index 0000000..35fe144 --- /dev/null +++ b/pixi.lock @@ -0,0 +1,2095 @@ +version: 7 +platforms: +- name: linux-64 +environments: + default: + channels: + - url: https://conda.anaconda.org/conda-forge/ + - url: https://conda.anaconda.org/bioconda/ + indexes: + - https://pypi.org/simple + packages: + linux-64: + - conda: https://conda.anaconda.org/bioconda/linux-64/mmseqs2-18.8cc5c-hd6d6fdc_0.tar.bz2 + - 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"HISTORY.md" +requires-python = ">=3.8,<4.0" +dependencies = [ + "click>=8.0.0", + "loguru>=0.5.3", + "pyyaml>=6.0", + "pandas>=1.4.2", + "biopython>=1.76", + "pyrodigal>=3.0.0", ] -[tool.poetry.scripts] -dnaapler = 'dnaapler:main' +[project.urls] +homepage = "https://github.com/gbouras13/dnaapler" +repository = "https://github.com/gbouras13/dnaapler" + +[project.scripts] +dnaapler = "dnaapler:main" + +[tool.isort] +profile = "black" + +[tool.pixi.workspace] +channels = ["conda-forge", "bioconda"] +platforms = ["linux-64"] -[tool.poetry.dependencies] +[tool.pixi.dependencies] python = ">=3.8,<4.0" click = ">=8.0.0" loguru = ">=0.5.3" @@ -23,23 +44,33 @@ pyyaml = ">=6.0" pandas = ">=1.4.2" biopython = ">=1.76" pyrodigal = ">=3.0.0" +mmseqs2 = ">=13.45111" +[tool.pixi.pypi-dependencies] +dnaapler = { path = ".", editable = true } -[tool.poetry.dev-dependencies] -black = ">=22.3.0" -isort = ">=5.10.1" +[tool.pixi.feature.test.dependencies] pytest = ">=6.2.5" pytest-cov = ">=3.0.0" + +[tool.pixi.feature.lint.dependencies] +black = ">=22.3.0" +isort = ">=5.10.1" flake8 = ">=3.0.1" +hatch = "*" -[[tool.poetry.source]] -name = "pypi-test" -url = "https://test.pypi.org/simple/" -priority = "primary" +[tool.pixi.feature.dev-tools.dependencies] +just = "*" +ripgrep = "*" -[build-system] -requires = ["poetry-core>=1.0.0"] -build-backend = "poetry.core.masonry.api" +[tool.pixi.environments] +default = { solve-group = "default" } +dev = { features = ["test", "lint", "dev-tools"], solve-group = "default" } -[tool.isort] -profile = "black" +[tool.pixi.tasks] +fmt = { cmd = "black src tests && isort src tests", default-environment = "dev" } +check-fmt = { cmd = "black --check src tests && isort --check src tests", default-environment = "dev" } +lint = { cmd = "flake8 src tests", default-environment = "dev" } +test = { cmd = "pytest -vv tests/", default-environment = "dev" } +coverage = { cmd = "pytest --cov-report term --cov-report html --cov=dnaapler --cov-branch tests/", default-environment = "dev" } +build = { cmd = "hatch build", default-environment = "dev" } diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 1a31be7..0000000 --- a/requirements.txt +++ /dev/null @@ -1,9 +0,0 @@ -pyyaml >=6.0 -pytest-runner >= 5.0.0 -biopython >=1.76 -pytest >=6.2.5 -pandas >=1.4.1 -loguru >=0.5.3 -Click >=8.0.0 -pytest-cov >=3.0.0 -pyrodigal >=2.0.0 diff --git a/src/dnaapler/utils/all.py b/src/dnaapler/utils/all.py index e7703ae..9091e7b 100644 --- a/src/dnaapler/utils/all.py +++ b/src/dnaapler/utils/all.py @@ -172,7 +172,7 @@ def all_process_MMseqs2_output_and_reorient( else: message = f"autocomplete_method_{autocomplete}" - (start, strand) = run_autocomplete_record( + start, strand = run_autocomplete_record( record, autocomplete, reoriented_output_file, seed_value )