Merge pull request #111 from GoekeLab/m6anet_setup_patch

M6anet setup patch

.github/workflows/merge_test.yaml

@@ -25,11 +25,11 @@ jobs:
         # Install pip and pytest
       - name: Install dependencies
         run: |
-          python setup.py install
+          pip install .
       - name: Install m6anet-package
         run: |
           python -m pip install --upgrade pip
-          pip install pytest
+          pip install pytest pytest-dependency
       - name: Test with pytest
         run: pytest --junitxml=junit/test-results-${{ matrix.python-version }}.xml
       - name: Upload pytest test results
@@ -38,4 +38,4 @@ jobs:
           name: pytest-results-${{ matrix.python-version }}
           path: junit/test-results-${{ matrix.python-version }}.xml
         # Use always() to always run this step to publish test results when there are test failures
-        if: ${{ always() }}
+        if: ${{ always() }}

docs/source/installation.rst

@@ -17,4 +17,4 @@ Installation from our GitHub repository
 
     git clone https://github.com/GoekeLab/m6anet.git
     cd m6anet
-    python setup.py install
+    pip install .

m6anet/__init__.py

@@ -5,7 +5,7 @@
 
 modules = ['dataprep', 'inference', 'train', 'compute_norm_factors', 'convert']
 
-__version__ = "2.0.1"
+__version__ = "2.0.2"
 
 
 def main():

m6anet/tests/test_dataprep.py

@@ -22,7 +22,7 @@ def test_parallel_index(dataprep_args, tmp_path, eventalign_index):
 
     assert((index_df == index_test).all().all())
 
-@pytest.mark.depends(on=['test_parallel_index'])
+@pytest.mark.dependency(depends=['test_parallel_index'])
 def test_parallel_parallel_preprocess_tx(dataprep_args, eventalign_index, data_info, data_json, dataprep_helpers):
     eventalign_filepath = dataprep_args['eventalign']
     out_dir = dataprep_args['out_dir']

setup.py

@@ -26,17 +26,19 @@
     url='https://github.com/GoekeLab/m6anet',
     packages=find_packages(),
     package_data={'m6anet.model': ['model_states/human_hct116.pt', 'configs/model_configs/m6anet.toml', 'norm_factors/norm_factors_hct116.joblib']},
-    python_requires=">=3.7",
+    python_requires=">=3.7, <3.9",
     install_requires=[
-            'numpy==1.18.0',
-            'pandas==0.25.3',
-            'scikit-learn==0.24.1',
-            'scipy==1.4.1',
-            'ujson',
-            'torch==1.6.0',
-            'toml==0.10.2',
-            'tqdm',
-            'typing-extensions'
+            "numpy>=1.18.0",
+            "pandas>=0.25.3",
+            "scikit-learn>=0.24.0, <1.1.0; python_version=='3.7'",
+            "scikit-learn>=0.24.0; python_version=='3.8'",
+            "scipy>=1.4.1, <1.8.0; python_version=='3.7'",
+            "scipy>=1.4.1; python_version=='3.8'",
+            "ujson",
+            "torch==1.6.0",
+            "toml>=0.10.2",
+            "tqdm",
+            "typing-extensions"
             ],
     entry_points = {
         'console_scripts': [