Candidate Release v1.7.0 (#42)

* bump version to v1.7.0
* use mamba-org/setup-micromamba for CI tests
* remove deprecated pytest slow Marks
* update Python Packaging CI to ubuntu-latest
* fix CI quotes

Author: oschwengers

.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}

.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

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

platon.cwl

@@ -17,7 +17,7 @@ hints:
   SoftwareRequirement:
     packages:
       platon:
-      version: [ "1.3.0" ]
+      version: [ "1.7.0" ]
 
 requirements:
   ResourceRequirement:

platon/__init__.py

@@ -1 +1 @@
-__version__ = '1.6'
+__version__ = '1.7'

pytest.ini

@@ -1,4 +1,2 @@
 [pytest]
 addopts = --strict-markers
-markers =
-    slow: mark tests as slow.

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)

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'])