Merge pull request #40 from CardiacModelling/dependencies

Updated dependencies and removed get_onboard_QC_df

Author: MichaelClerx

.github/workflows/pytest.yml

@@ -6,7 +6,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8, 3.9, '3.10', 3.11, 3.12, 3.13]
+        python-version: ['3.10', 3.11, 3.12, 3.13, 3.14]
     steps:
     - name: Checkout repository
       uses: actions/checkout@v4
@@ -41,5 +41,5 @@ jobs:
     - uses: codecov/codecov-action@v4
       with:
         token: ${{ secrets.CODECOV_TOKEN }} # not required for public repos
-      if: matrix.python-version == 3.13
+      if: matrix.python-version == 3.14
 

setup.py

@@ -19,18 +19,18 @@
     # Module name (lowercase)
     name='syncropatch_export',
     version=version,
-    description='Post-process high-throughput patch-clamp data',
+    description='Reads syncropatch data',
     long_description=readme,
-    long_description_content_type="text/markdown",
-    author='Frankie Patten-Elliot, Joseph Shuttleworth, Chon Lok Lei',
+    long_description_content_type='text/markdown',
+    author='Frankie Patten-Elliot, Joseph Shuttleworth, Chon Lok Lei, Michael Clerx',
     author_email='joseph.shuttleworth@nottingham.ac.uk',
     maintainer='Joseph Shuttleworth',
     maintainer_email='joseph.shuttleworth@nottingham.ac.uk',
     # url='https://github.com/CardiacModelling/markov-builder',
     classifiers=[
-        "Programming Language :: Python :: 3",
-        "License :: OSI Approved :: BSD License",
-        "Operating System :: OS Independent",
+        'Programming Language :: Python :: 3',
+        'License :: OSI Approved :: BSD License',
+        'Operating System :: OS Independent',
     ],
 
     # Packages to include
@@ -41,23 +41,18 @@
     include_package_data=True,
 
     # Required Python version
-    python_requires='>=3.7',
+    python_requires='>=3.10',
 
     # List of dependencies
     install_requires=[
-        'scipy>=1.7',
         'numpy>=1.21',
-        'matplotlib>=3.4',
-        'pandas>=1.3',
-        'regex>=2023.12.25'
     ],
     extras_require={
         'test': [
             'pytest-cov>=2.10',     # For coverage checking
             'pytest>=4.6',          # For unit tests
             'flake8>=3',            # For code style checking
             'isort',
-            'mock>=3.0.5',         # For mocking command line args etc.
             'codecov>=2.1.3',
         ],
         'docs': [

syncropatch_export/trace.py

@@ -3,7 +3,6 @@
 import string
 
 import numpy as np
-import pandas as pd
 
 from .voltage_protocols import VoltageProtocol
 
@@ -319,32 +318,3 @@ def get_onboard_QC_values(self, sweeps=None):
 
         return out_dict
 
-    def get_onboard_QC_df(self, sweeps=None):
-        """
-        Create a Pandas DataFrame containing the seal resistance, membrane
-        capacitance, and series resistance for each well and sweep.
-
-        Returns:
-            A ``pandas.DataFrame`` with the onboard QC estimates.
-
-        """
-
-        QC_dict = self.get_onboard_QC_values(sweeps)
-
-        if sweeps is None:
-            sweeps = list(range(self.NofSweeps))
-
-        df_rows = []
-        for sweep in sweeps:
-            for well in self.WELL_ID.flatten():
-                Rseal, Capacitance, Rseries = QC_dict[well][sweep]
-                df_row = {'Rseal': Rseal,
-                          'Cm': Capacitance,
-                          'Rseries': Rseries,
-                          'well': well,
-                          'sweep': sweep
-                          }
-                df_rows.append(df_row)
-
-        return pd.DataFrame.from_records(df_rows)
-

tests/test_trace_class.py

@@ -5,7 +5,6 @@
 import unittest
 
 import numpy as np
-import pandas as pd
 
 from syncropatch_export.trace import Trace
 from syncropatch_export.voltage_protocols import VoltageProtocol
@@ -89,10 +88,6 @@ def test_protocol_get_ramps(self):
     def test_get_QC(self):
         QC_values = self.trace.get_onboard_QC_values()
         self.assertGreater(len(QC_values), 0)
-        df = self.trace.get_onboard_QC_df()
-
-        self.assertGreater(df.shape[0], 0)
-        self.assertGreater(df.shape[1], 0)
 
     def test_get_traces(self):
         v = self.trace.get_voltage()
@@ -119,47 +114,6 @@ def test_get_traces(self):
         self.assertRaisesRegex(ValueError, 'Invalid sweep selection',
                                self.trace.get_trace_sweeps, [-3])
 
-        '''
-        # plot test output
-        if False:
-            d = 'test_output'
-            if not os.path.exists(d):
-                os.makedirs(d)
-
-            import matplotlib.pyplot as plt
-            fig, (ax1, ax2) = plt.subplots(2, 1)
-            ax1.set_title('Example Sweeps')
-            some_sweeps = self.trace.get_trace_sweeps([0])['A01']
-
-            ax1.plot(ts, np.transpose(some_sweeps), color='grey', alpha=0.5)
-            ax1.set_ylabel('Current')
-            ax1.set_xlabel('Time')
-            ax2.set_title('Voltage Protocol')
-            ax2.plot(ts, v)
-            ax2.set_ylabel('Voltage')
-            ax2.set_xlabel('Time')
-            plt.tight_layout()
-            plt.savefig(os.path.join(d, 'example_trace'))
-            plt.close(fig)
-        '''
-
-    def test_qc_df(self):
-        dfs = [self.trace.get_onboard_QC_df(sweeps=[0]),
-               self.trace.get_onboard_QC_df(sweeps=None)]
-        for res in dfs:
-            # Check res is a pd.DataFrame
-            self.assertIsInstance(res, pd.DataFrame)
-
-            # Check it contains data (number of rows>0)
-            self.assertGreater(res.shape[0], 0)
-
-            # Check it contains all quality control parameters
-            for qcParam in ['Rseal', 'Cm', 'Rseries', 'well', 'sweep']:
-                self.assertIn(qcParam, res)
-
-        # Check restricting number of sweeps returns less data
-        self.assertLess(dfs[0].shape[0], dfs[1].shape[0])
-
 
 if __name__ == '__main__':
     unittest.main()  # pragma: no cover