diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml index 055155c..950cc03 100644 --- a/.github/workflows/python-package-conda.yml +++ b/.github/workflows/python-package-conda.yml @@ -18,28 +18,33 @@ jobs: strategy: fail-fast: true matrix: - os: ["ubuntu-latest", "macos-latest"] - python-version: ["3.8"] + os: ['ubuntu-latest', 'macos-latest'] + python-version: ['3.8'] steps: - uses: actions/checkout@v2 - - uses: conda-incubator/setup-miniconda@v2 + - uses: mamba-org/setup-micromamba@v1 with: - auto-update-conda: false - python-version: ${{ matrix.python-version }} - miniconda-version: "latest" - mamba-version: "*" - channels: conda-forge,bioconda - channel-priority: true - auto-activate-base: false - environment-file: environment.yml - activate-environment: platon + micromamba-version: 'latest' + environment-name: 'platon' + environment-file: 'environment.yml' + create-args: python=${{ matrix.python-version }} + condarc: | + channels: + - conda-forge + - bioconda + init-shell: bash + cache-environment: true + cache-downloads: true + post-cleanup: 'all' - name: Install PyTest - run: conda install pytest - - name: Conda info + run: micromamba install pytest + shell: bash -l {0} + - name: Mamba info run: | - conda info - conda list - conda config --show + micromamba info + micromamba list printenv | sort + shell: bash -l {0} - name: Run PyTest run: pytest + shell: bash -l {0} diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml index b5736f5..8507e62 100644 --- a/.github/workflows/pythonpackage.yml +++ b/.github/workflows/pythonpackage.yml @@ -14,8 +14,8 @@ jobs: runs-on: ${{ matrix.os }} strategy: matrix: - os: [ubuntu-18.04, ubuntu-20.04, macos-latest] - python-version: [3.8, 3.9] + os: ['ubuntu-latest', 'macos-latest'] + python-version: ['3.8', '3.10'] steps: - uses: actions/checkout@v2 diff --git a/CITATION.cff b/CITATION.cff index 0597bb1..4e9dbff 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -29,7 +29,7 @@ authors: affiliation: Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, 35392, Germany title: "Platon: identification and characterization of bacterial plasmid contigs in short-read draft assemblies exploiting protein sequence-based replicon distribution scores" doi: "10.1099/mgen.0.000398" -version: 1.6 +version: 1.7 keywords: - bioinformatics - assembly diff --git a/platon.cwl b/platon.cwl index e5dc98d..239b4d7 100644 --- a/platon.cwl +++ b/platon.cwl @@ -17,7 +17,7 @@ hints: SoftwareRequirement: packages: platon: - version: [ "1.3.0" ] + version: [ "1.7.0" ] requirements: ResourceRequirement: diff --git a/platon/__init__.py b/platon/__init__.py index 6d5e09d..218f431 100644 --- a/platon/__init__.py +++ b/platon/__init__.py @@ -1 +1 @@ -__version__ = '1.6' +__version__ = '1.7' diff --git a/pytest.ini b/pytest.ini index cc74663..4aea3fd 100644 --- a/pytest.ini +++ b/pytest.ini @@ -1,4 +1,2 @@ [pytest] addopts = --strict-markers -markers = - slow: mark tests as slow. \ No newline at end of file diff --git a/test/conftest.py b/test/conftest.py index 12fbb01..0faef86 100644 --- a/test/conftest.py +++ b/test/conftest.py @@ -1,5 +1,3 @@ -from _pytest.mark import Mark - global FILES @@ -10,14 +8,3 @@ 'test.plasmid.fasta', 'test.tsv' ] - - -empty_mark = Mark('', [], {}) - - -def by_slow_marker(item): - return item.get_closest_marker('slow', default=empty_mark) - - -def pytest_collection_modifyitems(items): - items.sort(key=by_slow_marker, reverse=False) \ No newline at end of file diff --git a/test/test_platon.py b/test/test_platon.py index 6681a5f..ddbb386 100644 --- a/test/test_platon.py +++ b/test/test_platon.py @@ -6,7 +6,6 @@ from .conftest import FILES -@pytest.mark.slow def test_platon_db_parameter(tmpdir): # full test on draft assembly containing plasmid contigs proc = run(['bin/platon', '--db', 'test/db', '--output', tmpdir, '--prefix', 'test', 'test/data/mock-sample.fna']) @@ -18,7 +17,6 @@ def test_platon_db_parameter(tmpdir): assert Path.exists(output_path) -@pytest.mark.slow def test_platon_db_env(tmpdir): # full test on draft assembly containing plasmid contigs @@ -33,7 +31,6 @@ def test_platon_db_env(tmpdir): assert Path.exists(output_path) -@pytest.mark.slow def test_platon_w_plasmids(tmpdir): # full test on draft assembly containing plasmid contigs proc = run(['bin/platon', '--db', 'test/db', '--output', tmpdir, '--prefix', 'test', 'test/data/draft-w-plasmids.fna']) @@ -46,7 +43,6 @@ def test_platon_w_plasmids(tmpdir): assert output_path.stat().st_size > 0 -@pytest.mark.slow def test_platon_wo_plasmids(tmpdir): # full test on draft assembly containing no plasmid contigs proc = run(['bin/platon', '--db', 'test/db', '--output', tmpdir, '--prefix', 'test', 'test/data/draft-wo-plasmids.fna'])