GH #2744 Fix installation and tests for Python 3.10-3.13

Three pinned dependencies blocked installation on 3.12+:
- numpy<1.24: no cp312 wheels; now uncapped (numpy 2.x supported)
- pandas==1.5.3: no cp312 wheels; now >=1.5.3
- scipy<1.11: requires_python<3.12; now uncapped
- pynwb<3: cap to avoid breaking API changes
- xarray<2023.2.0: unpinned (pure Python, no breakage)
- pytz: added (was transitive via pandas 1.x, now needed explicitly)
- setuptools<81: cap (pkg_resources removed in 81+)

Source fixes for removed/changed APIs:
- scipy.interpolate.interp2d → RectBivariateSpline (removed in 1.14)
- ConfigParser.readfp → read_string (removed in Python 3.12)
- DataFrame.iteritems() → items() (removed in pandas 2.0)
- np.int() → int() (removed in numpy 1.24)
- np.NaN/np.NAN → np.nan (removed in numpy 2.0)
- np.Inf → np.inf, np.string_ → np.bytes_ (removed in numpy 2.0)
- np.product → np.prod, np.in1d → np.isin (removed in numpy 2.0)
- np.ediff1d to_begin dtype must match array dtype in numpy 2.0
- np.VisibleDeprecationWarning → try/except import (removed in 2.0)
- nwbfile.modules → .processing (pynwb 2.x deprecation)
- IndexSeries unit='None' → 'N/A' (pynwb 2.5+ validation)
- np.linalg.norm([array, scalar]) → np.vstack (numpy 1.24+ rejects)
- aiohttp.ClientSession → lazy property (aiohttp 3.9+ event loop)
- groupby().apply() → select column first (pandas 2.2+ behavior)
- demixer: add np.isfinite guard after linalg.solve (some LAPACK
  implementations return inf instead of raising LinAlgError for
  singular matrices)

Test fixes:
- pytest.warns(None) → warnings.catch_warnings (pytest 8)
- mock.called_once_with → assert_called_once() (proper assertion)
- Add res.x to MagicMock for scipy.optimize result
- rng.choice(inhomogeneous) → rng.integers + index (numpy 1.24+)
- Widen curve-fit tolerances for platform variance
- Cast dtypes for pynwb 2.x roundtrip and pandas 2.x index changes
- subprocess 'python' → sys.executable for venv correctness
- Replace flaky test_demix_raises_warning_for_singular_matrix with
  a result-based assertion in test_demix_point
- from mock import → from unittest.mock import (69 test files)
- Uncap/modernize test dependency bounds, remove dead weight

CI:
- Update to actions/checkout@v4, actions/setup-python@v5
- Slim matrix to min/max Python (3.10, 3.13) on ubuntu, 3.13 on
  macOS/windows
- Add pip caching, coverage on single matrix element only
- Modernize notebook_runner.yml to Python 3.13
- Update nightly.yml to checkout@v4

Fixes #2747, #2744, #2746, #2754

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: galenlynch

.github/workflows/github-actions-ci.yml

@@ -26,7 +26,7 @@ jobs:
     name: Lint
     runs-on: "ubuntu-latest"
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: flake8 linting
         run: |
           pip install flake8
@@ -43,28 +43,30 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: ["macos-latest", "windows-latest", "ubuntu-latest"]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        os: ["ubuntu-latest"]
+        python-version: ["3.10", "3.13"]
+        include:
+          - os: "macos-latest"
+            python-version: "3.13"
+          - os: "windows-latest"
+            python-version: "3.13"
       fail-fast: false
-    defaults:
-      run:
-        shell: bash -l {0}
     steps:
-      - uses: actions/checkout@v2
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
-          auto-update-conda: true
           python-version: ${{ matrix.python-version }}
-          activate-environment: test-env
+          cache: pip
+          cache-dependency-path: |
+            requirements.txt
+            test_requirements.txt
       - name: Install
         run: |
-          conda activate test-env
-          pip install codecov
           pip install -r test_requirements.txt
           pip install .
       - name: Test
         run: |
-          py.test --cov=allensdk -n 4
+          python -m pytest -n 4 ${{ (matrix.os == 'ubuntu-latest' && matrix.python-version == '3.13') && '--cov=allensdk' || '' }}
 
   onprem:
     name: python ${{ matrix.image }} on-prem test
@@ -73,7 +75,7 @@ jobs:
       matrix:
         image: ["allensdk_local_py38:latest"]
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: run test in docker
         run: |
           docker run \

.github/workflows/nightly.yml

@@ -13,7 +13,7 @@ jobs:
         image: ["allensdk_local_py38:latest"]
         branch: ["master", "rc/**"]
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           ref: ${{ matrix.branch }}
       - name: run test in docker

.github/workflows/notebook_runner.yml

@@ -9,15 +9,20 @@ jobs:
     strategy:
       matrix:
         os: ["ubuntu-latest"]
-        python-version: ["3.8"]
+        python-version: ["3.13"]
       fail-fast: false
     runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+          cache: pip
+          cache-dependency-path: |
+            requirements.txt
+            dev_requirements.txt
+            notebook_requirements.txt
       - name: Install
         run: |
           pip install -r requirements.txt

allensdk/brain_observatory/behavior/data_objects/cell_specimens/cell_specimens.py

@@ -857,13 +857,13 @@ def _validate_traces(
             if traces is None:
                 continue
             # validate traces contain expected roi ids
-            if not np.in1d(traces.value.index, cell_roi_ids).all():
+            if not np.isin(traces.value.index, cell_roi_ids).all():
                 raise RuntimeError(
                     f"{traces.name} contains ROI IDs that "
                     f"are not in "
                     f"cell_specimen_table.cell_roi_id"
                 )
-            if not np.in1d(cell_roi_ids, traces.value.index).all():
+            if not np.isin(cell_roi_ids, traces.value.index).all():
                 raise RuntimeError(
                     f"cell_specimen_table contains ROI IDs "
                     f"that are not in {traces.name}"

allensdk/brain_observatory/behavior/data_objects/metadata/behavior_metadata/behavior_metadata.py

@@ -149,7 +149,7 @@ def get_task_parameters(data: Dict) -> Dict:
     # displayed stimuli (no flashes).
 
     if stim_duration is None:
-        stim_duration = np.NaN
+        stim_duration = np.nan
     else:
         stim_duration = stim_duration[0]
 

allensdk/brain_observatory/behavior/data_objects/running_speed/running_acquisition.py

@@ -129,7 +129,7 @@ def from_nwb(
         cls,
         nwbfile: NWBFile
     ) -> "RunningAcquisition":
-        running_module = nwbfile.modules['running']
+        running_module = nwbfile.processing['running']
         dx_interface = running_module.get_data_interface('dx')
 
         dx = dx_interface.data

allensdk/brain_observatory/behavior/data_objects/running_speed/running_speed.py

@@ -188,7 +188,7 @@ def from_nwb(
         nwbfile: NWBFile,
         filtered=True
     ) -> "RunningSpeed":
-        running_module = nwbfile.modules['running']
+        running_module = nwbfile.processing['running']
         interface_name = 'speed' if filtered else 'speed_unfiltered'
         running_interface = running_module.get_data_interface(interface_name)
 

allensdk/brain_observatory/behavior/data_objects/stimuli/templates.py

@@ -208,7 +208,7 @@ def _add_image_index_to_nwb(
         image_index = IndexSeries(
             name=nwb_template.name,
             data=stimulus_index['image_index'].values,
-            unit='None',
+            unit='N/A',
             indexed_timeseries=nwb_template,
             timestamps=stimulus_index['start_time'].values)
         nwbfile.add_stimulus(image_index)

allensdk/brain_observatory/behavior/data_objects/task_parameters.py

@@ -223,7 +223,7 @@ def _parse_stimulus_key():
         # displayed stimuli (no flashes).
 
         if stim_duration is None:
-            stim_duration = np.NaN
+            stim_duration = np.nan
         else:
             stim_duration = stim_duration[0]
         return stim_duration

allensdk/brain_observatory/behavior/data_objects/trials/trial.py

@@ -415,7 +415,7 @@ def add_change_time(self, trial_dict: dict) -> Tuple[dict, float]:
         """
         change_frame = trial_dict['change_frame']
         if np.isnan(change_frame):
-            change_time = np.NaN
+            change_time = np.nan
         else:
             change_frame = int(change_frame)
             change_time = self._stimulus_timestamps.value[change_frame]