Merge pull request #20 from metagenlab/dev

Update macos test to latest

.github/workflows/unit-tests.yml

@@ -20,25 +20,20 @@ permissions:
   contents: read
 
 jobs:
-  tests:
-    name: "Python ${{ matrix.python-version }} on ${{ matrix.os }}"
-    runs-on: ${{ matrix.os }}
-
+  linux:
+    runs-on: "ubuntu-latest"
     defaults:
       run:
         shell: bash -el {0}
-
     strategy:
-      fail-fast: false
       matrix:
-        os: [macos-13, ubuntu-latest]
         python-version: ["3.12"]
-
+      fail-fast: false
+    name: Linux Python ${{ matrix.python-version }}
     steps:
-      - uses: "actions/checkout@v3"
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-
       - uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
@@ -51,8 +46,41 @@ jobs:
           activate-environment: assembly_finder
           python-version: ${{ matrix.python-version }}
           auto-activate-base: false
+      - name: "Test and generate coverage report for Linux python ${{ matrix.python-version }}"
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install pytest coverage
+          python -m pip install .
+          coverage run -m pytest
 
-      - name: "Test and generate coverage report on ${{ matrix.os }} for Python ${{ matrix.python-version }}"
+  osx:
+    runs-on: "macos-latest"
+    defaults:
+      run:
+        shell: bash -el {0}
+    strategy:
+      matrix:
+        python-version: ["3.12"]
+        architecture: ["x64"]
+      fail-fast: false
+    name: OSX Python ${{ matrix.python-version }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          miniforge-version: "latest"
+          miniforge-variant: Mambaforge
+          use-mamba: true
+          mamba-version: "*"
+          channels: conda-forge,bioconda,defaults
+          channel-priority: strict
+          activate-environment: assembly_finder
+          python-version: ${{ matrix.python-version }}
+          auto-activate-base: false
+      - name: "Test and generate coverage report for Linux python ${{ matrix.python-version }}"
         run: |
           python -m pip install --upgrade pip
           python -m pip install pytest coverage

assembly_finder/config/config.yaml

@@ -1,20 +1,31 @@
 args:
+  annotated:
+  api_key:
+  assembly_level:
+  atypical:
+  compressed:
+  conda_prefix:
+  configfile:
+  include:
   input:
-  output:
-  taxonkit:
   limit:
+  log:
+  mag:
+  nrank:
+  output:
+  print_versions:
+  profile:
+  rank:
+  reference:
   requests:
-  compressed:
-  include:
+  snake_args:
+  snake_default:
   source:
+  system_config:
   taxon:
-  reference:
-  assembly_level:
-  annotated:
-  atypical:
-  mag:
-  rank:
-  nrank:
+  taxonkit:
+  threads:
+  use_conda:
 
 links:
   taxdump: https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz

assembly_finder/workflow/envs/unzip.yml

@@ -3,4 +3,4 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - unzip =6.0
+  - p7zip =16.02

assembly_finder/workflow/rules/download.smk

@@ -225,7 +225,7 @@ rule unzip_archive:
         os.path.join(dir.env, "unzip.yml")
     shell:
         """
-        unzip {input} -d {output} &> {log}
+        7z x -o{output} {input} &> {log}
         """
 
 

setup.py

@@ -32,7 +32,6 @@ def get_data_files():
     "Natural Language :: English",
     "Operating System :: POSIX :: Linux",
     "Operating System :: MacOS :: MacOS X",
-    "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
@@ -42,7 +41,7 @@ def get_data_files():
     name="assembly_finder",
     packages=find_namespace_packages(),
     url="https://github.com/metagenlab/assembly_finder",
-    python_requires=">=3.10",
+    python_requires=">=3.11",
     description="Snakemake-powered cli to download genomes using NCBI datasets",
     long_description=get_description(),
     long_description_content_type="text/markdown",