Merge pull request #258 from anilbey/pandas2.0

Pandas2.0 support

bluepymm/select_combos/reporting.py

@@ -374,12 +374,21 @@ def create_final_db_and_write_report(pdf_filename,
                     emodel_megate_passed_all, emodel_median_scores, \
                     emodel_passed_combos = \
                     emodel_info
-                ext_neurondb = ext_neurondb.append(emodel_ext_neurondb_rows)
+                ext_neurondb = pandas.concat(
+                    [ext_neurondb, emodel_ext_neurondb_rows], axis=0
+                ).reset_index(drop=True)
 
-                megate_passed_all = megate_passed_all.append(
-                    emodel_megate_passed_all)
-                median_scores = median_scores.append(emodel_median_scores)
-                passed_combos = passed_combos.append(emodel_passed_combos)
+                megate_passed_all = pandas.concat(
+                    [megate_passed_all, emodel_megate_passed_all], axis=0
+                ).reset_index(drop=True)
+
+                median_scores = pandas.concat(
+                    [median_scores, emodel_median_scores], axis=0
+                ).reset_index(drop=True)
+
+                passed_combos = pandas.concat(
+                    [passed_combos, emodel_passed_combos], axis=0
+                ).reset_index(drop=True)
 
                 # Reporting per e-model
                 add_plot_to_report(

bluepymm/select_combos/table_processing.py

@@ -377,7 +377,7 @@ def process_emodel(args):
     emodel_mtype_etype_thresholds['megate_feature_threshold'] = None
 
     print('Getting megating thresholds for emodel %s' % emodel)
-    emodel_mtype_etype_thresholds.apply(
+    emodel_mtype_etype_thresholds = emodel_mtype_etype_thresholds.apply(
         lambda row: row_threshold_transform(row, megate_patterns),
         axis=1)
 

setup.py

@@ -27,8 +27,17 @@ setuptools.setup(
     name="bluepymm",
     version=versioneer.get_version(),
     cmdclass=versioneer.get_cmdclass(),
-    install_requires=['sh', 'bluepyopt', 'matplotlib', 'pandas', 'numpy',
-                      'ipyparallel', 'lxml', 'h5py', 'pyyaml'],
+    install_requires=[
+        "sh",
+        "bluepyopt",
+        "matplotlib",
+        "pandas>=2.0.0",
+        "numpy",
+        "ipyparallel",
+        "lxml",
+        "h5py",
+        "pyyaml",
+    ],
     packages=setuptools.find_packages(exclude=('notebook',)),
     author="BlueBrain Project, EPFL",
     author_email="werner.vangeit@epfl.ch",