Dropped excel export. Closes #113

Author: MichaelClerx

.github/workflows/tests.yml

@@ -41,7 +41,7 @@ jobs:
     - name: Extract test data
       run: |
         wget https://cardiac.nottingham.ac.uk/syncropatch_export/test_data.tar.xz -P tests/
-        tar xvf tests/test_data.tar.xz -C tests/
+        tar xvf test_data.tar.xz -C tests/
 
     - name: Install TeX dependencies for run_herg_qc test
       timeout-minutes: 5

README.md

@@ -34,9 +34,9 @@ To run the tests you must first download some test data.
 Test data is available at [cardiac.nottingham.ac.uk/syncropatch\_export](https://cardiac.nottingham.ac.uk/syncropatch_export)
 
 ```sh
-wget https://cardiac.nottingham.ac.uk/syncropatch_export/test_data.tar.xz -P tests/
-tar xvf tests/test_data.tar.xz -C tests/
-rm tests/test_data.tar.xz
+wget https://cardiac.nottingham.ac.uk/syncropatch_export/test_data.tar.xz
+tar xvf test_data.tar.xz
+rm test_data.tar.xz
 ```
 
 Then you can run the tests.

pcpostprocess/scripts/run_herg_qc.py

@@ -452,7 +452,6 @@ def run(data_path, output_path, qc_map, wells=None,
 
     qc_styled_df = create_qc_table(qc_df)
     logging.info(qc_styled_df)
-    # qc_styled_df.to_excel(os.path.join(output_path, 'qc_table.xlsx'))
     qc_styled_df.to_latex(os.path.join(output_path, 'qc_table.tex'))
 
     # Save in csv format

pcpostprocess/scripts/summarise_herg_export.py

@@ -84,7 +84,6 @@ def run(data_path, output_path, experiment_name, reversal_potential=None,
 
     qc_styled_df = create_qc_table(qc_df)
     qc_styled_df = qc_styled_df.pivot(columns='protocol', index='crit')
-    # qc_styled_df.to_excel(os.path.join(output_path, 'qc_table.xlsx'))
     qc_styled_df.to_latex(os.path.join(output_path, 'qc_table.tex'))
 
     qc_df.protocol = ['staircaseramp1' if protocol == 'staircaseramp' else protocol

pyproject.toml

@@ -38,7 +38,6 @@ dependencies = [
     'pandas>=1.3',
     'regex>=2023.12.25',
     'seaborn>=0.12.2',
-    'openpyxl>=3.1.2',
     'jinja2>=3.1.0',
     'syncropatch_export @ git+https://github.com/CardiacModelling/syncropatch_export.git'
 ]