Drop python 3.7, 3.8

.github/workflows/run-tests.yml

@@ -12,10 +12,9 @@ jobs:
       fail-fast: false
       matrix:
         python-version:
-          - '3.7'
-          - '3.8'
           - '3.9'
           - '3.10'
+          - '3.11'
         igraph: ["igraph", "no-igraph"]
     steps:
     #   # This cancels any such job that is still runnning
@@ -42,6 +41,8 @@ jobs:
       run: pip install -e .
     - run: pip install python-igraph
       if: ${{ matrix.igraph == 'igraph' }}
+    - name: Report dependency versions
+      run: pip freeze -r requirements.txt
     - name: Test
       run: |
         pytest --cov=./ --verbose

docs/source/whats_new.rst

@@ -12,6 +12,7 @@ What's new?
      -
    * - Next
      - n/a
+     - BREAKING: Drop python 3.7 support.
      - - :class:`pymaid.neuron_label.NeuronLabeller` added for labelling neurons
          like in the CATMAID frontend.
    * - 2.4.0

pymaid/cluster.py

@@ -400,7 +400,7 @@ def _calc_connectivity_matching_index(neuronA, neuronB, connectivity,
 
     if vertex_score:
         # We only need the columns for neuronA and neuronB
-        this_cn = total[[neuronA, neuronB]]
+        this_cn = total[[neuronA, neuronB]].astype(float)
 
         # Get min and max between both neurons
         this_max = np.max(this_cn, axis=1)

pymaid/fetch/__init__.py

@@ -918,9 +918,9 @@ def get_node_details(x, chunk_size=10000, convert_ts=True, remote_instance=None)
     df.rename({'user': 'creator'}, axis='columns', inplace=True)
 
     if convert_ts:
-        df['creation_time'] = pd.to_datetime(df.creation_time)
-        df['edition_time'] = pd.to_datetime(df.edition_time)
-        df['review_times'] = df.review_times.apply(lambda x: [pd.to_datetime(d)
+        df['creation_time'] = pd.to_datetime(df.creation_time, format="ISO8601")
+        df['edition_time'] = pd.to_datetime(df.edition_time, format="ISO8601")
+        df['review_times'] = df.review_times.apply(lambda x: [pd.to_datetime(d, format="ISO8601")
                                                               for d in x])
 
     return df
@@ -1360,8 +1360,8 @@ def get_connector_links(x, with_tags=False, chunk_size=50,
         df = df[df.connector_id.isin(x.connectors.connector_id)]
 
     # Convert to timestamps
-    df['creation_time'] = pd.to_datetime(df.creation_time)
-    df['edition_time'] = pd.to_datetime(df.edition_time)
+    df['creation_time'] = pd.to_datetime(df.creation_time, format="ISO8601")
+    df['edition_time'] = pd.to_datetime(df.edition_time, format="ISO8601")
 
     if with_tags:
         return df, tags
@@ -4613,7 +4613,7 @@ def get_sampler(x=None, remote_instance=None):
 
     # Convert timestamps
     df['creation_time'] = pd.to_datetime(df.creation_time, unit='s', utc=True)
-    df['edition_time'] = pd.to_datetime(df.creaedition_timetion_time, unit='s', utc=True)
+    df['edition_time'] = pd.to_datetime(df.edition_time, unit='s', utc=True)
 
     return df
 
@@ -4646,7 +4646,7 @@ def get_sampler_domains(sampler, remote_instance=None):
 
     # Convert timestamps
     df['creation_time'] = pd.to_datetime(df.creation_time, unit='s', utc=True)
-    df['edition_time'] = pd.to_datetime(df.creaedition_timetion_time, unit='s', utc=True)
+    df['edition_time'] = pd.to_datetime(df.edition_time, unit='s', utc=True)
 
     return df
 

pymaid/tests/test_pymaid.py

@@ -698,6 +698,10 @@ def test_node_sorting(self):
         self.assertIsInstance(ns.graph.node_label_sorting(self.n),
                               list)
 
+    @try_conditions
+    def test_geodesic_matrix(self):
+        geo = ns.geodesic_matrix(self.n)
+
 
 class TestConnectivity(unittest.TestCase):
     """Test connectivity-related functions."""

pymaid/user_stats.py

@@ -365,7 +365,7 @@ def get_team_contributions(teams, neurons=None, remote_instance=None):
 
         # Add column with just the date and make it the index
         all_ts['date'] = all_ts.timestamp.values.astype('datetime64[D]')
-        all_ts.index = pd.to_datetime(all_ts.date)
+        all_ts.index = pd.to_datetime(all_ts.date, format="ISO8601")
 
         # Fill in teams for each timestamp based on user + date
         all_ts['team'] = None

setup.py

@@ -41,14 +41,13 @@
         'License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)',
 
         'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.6',
-        'Programming Language :: Python :: 3.7',
-        'Programming Language :: Python :: 3.8',
         'Programming Language :: Python :: 3.9',
+        'Programming Language :: Python :: 3.10',
+        'Programming Language :: Python :: 3.11',
     ],
     install_requires=requirements,
     extras_require={'extras': ['fuzzywuzzy[speedup]~=0.17.0',
                                'ujson~=1.35']},
-    python_requires='>=3.6',
+    python_requires='>=3.9',
     zip_safe=False
 )