Merge pull request #29 from haessar/feature-macos

macOS compatibility

.github/workflows/ci.yml

@@ -12,24 +12,29 @@ on:
 jobs:
   build:
 
-    runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
         python-version: ["3.8", "3.9", "3.10", "3.11"]
+        os: [ubuntu-latest, macos-latest]
+    runs-on: ${{ matrix.os }}
 
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v3
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Cache APT Packages
+    - name: Cache APT Packages (Linux)
       uses: awalsh128/[email protected]
       with:
         packages: bedtools genometools
         version: 1.0
-    - name: Install dependencies
+      if: matrix.os == 'ubuntu-latest'
+    - name: Install dependencies (macOS)
+      run: brew install bedtools genometools
+      if: matrix.os == 'macos-latest'
+    - name: Install Python dependencies
       run: |
         python -m pip install --upgrade pip
         python -m pip install flake8 pytest

peaks2utr/__init__.py

@@ -78,7 +78,8 @@ def main():
     from .constants import PERC_ALLOCATED_VRAM
     from .utils import limit_memory
 
-    limit_memory(PERC_ALLOCATED_VRAM * virtual_memory().total / 100)
+    if platform != "darwin":
+        limit_memory(PERC_ALLOCATED_VRAM * virtual_memory().total / 100)
     argparser = prepare_argparser()
     args = argparser.parse_args()
     asyncio.run(_main(args))

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = peaks2utr
-version = 1.2.2
+version = 1.2.3
 author = William Haese-Hill
 author_email = [email protected]
 description = A robust, parallelized Python CLI for annotating three_prime_UTR

tests/test_entrypoint.py

@@ -0,0 +1,25 @@
+import multiprocessing
+from sys import platform
+import unittest
+from unittest.mock import patch
+
+from peaks2utr import main
+
+
+class TestEntryPoint(unittest.TestCase):
+    def test_main(self):
+        with patch('asyncio.run') as mock_run:
+            with patch('peaks2utr.prepare_argparser') as mock_argparser:
+                with patch('peaks2utr.utils.limit_memory') as mock_limit_memory:
+                    main()
+                    self.assertEqual(mock_run.call_count, 1)
+                    self.assertEqual(mock_argparser.call_count, 1)
+                    self.assertEqual(multiprocessing.get_start_method(), 'fork')
+                    if platform == "darwin":
+                        self.assertEqual(mock_limit_memory.call_count, 0)
+                    else:
+                        self.assertEqual(mock_limit_memory.call_count, 1)
+
+
+if __name__ == '__main__':
+    unittest.main()