Merge pull request #18 from bodegalab/python_tests

Enhance compatibility with different versions of python

.github/workflows/pytest-workflow.yml

@@ -17,14 +17,18 @@ jobs:
   test:
     runs-on: ubuntu-22.04
     name: test
+    strategy:
+      matrix:
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
     steps:
       - name: Checkout
         uses: actions/[email protected]
 
       - name: Setup conda
-        uses: conda-incubator/setup-miniconda@v2.2.0
+        uses: conda-incubator/setup-miniconda@v3
         with:
           environment-file: tests/config/environment.yml
+          python-version: ${{ matrix.python-version }}
           condarc-file: tests/config/condarc.yml
           auto-update-conda: true
 
@@ -58,4 +62,4 @@ jobs:
             /home/runner/pytest_workflow_*/*/log.out
             /home/runner/pytest_workflow_*/*/log.err
             /home/runner/pytest_workflow_*/*/IRescue_out
-            /home/runner/pytest_workflow_*/*/IRescue_tmp
+            /home/runner/pytest_workflow_*/*/IRescue_tmp

README.md

@@ -34,7 +34,7 @@ conda create -n irescue -c conda-forge -c bioconda irescue
 
 ### <a name="pip"></a>Using pip
 
-If for any reason it's not possible or desiderable to use conda, it can be installed with pip and the following requirements must be installed manually: `python>=3.7`, `samtools>=1.12`, `bedtools>=2.30.0`, and fairly recent versions of the GNU utilities are required, specifically `gawk>=5.0.1`, `coreutils>=8.30` and `gzip>=1.10` (older versions are untested).
+If for any reason it's not possible or desiderable to use conda, it can be installed with pip and the following requirements must be installed manually: `python>=3.8`, `samtools>=1.12`, `bedtools>=2.30.0`, and fairly recent versions of the GNU utilities are required, specifically `gawk>=5.0.1`, `coreutils>=8.30` and `gzip>=1.10` (older versions are untested).
 
 ```bash
 pip install irescue

irescue/count.py

@@ -238,9 +238,9 @@ def run_count(maps_file, features_index, tmpdir, dumpEC, verbose,
     taskn, barcodes = barcodes_set
     matrix_file = os.path.join(tmpdir, f'{taskn}_matrix.mtx.gz')
     dump_file = os.path.join(tmpdir, f'{taskn}_EqCdump.tsv.gz')
-    with (gzip.open(matrix_file, 'wb') as f,
-          gzip.open(dump_file, 'wb') if dumpEC
-          else gzip.open(os.devnull) as df):
+    with gzip.open(matrix_file, 'wb') as f, \
+            gzip.open(dump_file, 'wb') if dumpEC \
+            else gzip.open(os.devnull) as df:
         for cellbarcode, cellmaps in parse_maps(maps_file, features_index):
             if cellbarcode not in barcodes:
                 continue

pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 name = "IRescue"
 description = "Interspersed Repeats singl-cell quantifier"
 readme = "README.md"
-requires-python = ">=3.7"
+requires-python = ">=3.8"
 license = { file = "LICENSE" }
 authors = [
     { name = "Benedetto Polimeni", email = "[email protected]" },
@@ -22,10 +22,11 @@ classifiers = [
     "Intended Audience :: Science/Research",
     "License :: OSI Approved :: MIT License",
     "Operating System :: OS Independent",
-    "Programming Language :: Python :: 3.7",
     "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
 ]
 dependencies = [

tests/config/environment.yml

@@ -4,6 +4,6 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - python>=3.7
+  - python>=3.8
   - samtools>=1.12
   - bedtools>=2.30.0