Three pinned dependencies blocked installation on Python 3.12+:
- numpy<1.24: no cp312 wheels, distutils removal kills source build
- pandas==1.5.3: no cp312 wheels, same distutils issue
- scipy<1.11: requires_python="<3.12", resolver rejects outright

Dependency changes:
- numpy: uncap (numpy 2.x supported after source fixes below)
- pandas: relax to >=1.5.3,<3 (2.x supported; 3.0 needs further work)
- scipy: uncap (1.14+ supported after interp2d removal)
- pynwb: cap <3 to avoid breaking API changes
- xarray: unpin <2023.2.0 (pure Python, no breakage found)
- pytz: add as explicit dep (was transitive via pandas 1.x)
- setuptools: cap <81 (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)
- DataFrame.append() → pd.concat() (removed in pandas 2.0)
- pd.to_datetime: add format="ISO8601" for mixed-precision timestamps
  (pandas 2.x rejects mixed microsecond precision without explicit format)
- pd.to_datetime: fix utc="True" (string) → utc=True (bool) bug in
  behavior_project_cloud_api.py
- 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)

Notebook fixes:
- IPython.core.display → IPython.display (removed in IPython 8.x)
  in visual_behavior_compare_across_trial_types and
  visual_behavior_mouse_history notebooks

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
- Add pandas 2.x datetime regression tests (test_pandas_compat.py)

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
- Switch notebook runner to ubuntu-latest-8x (32GB RAM) for
  ecephys notebooks that peak at ~21GB RSS
- Change notebook workflow trigger to push on master (expensive job
  should not run on every pull request)

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

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

…GH-2744/bugfix/install-on-python-312

 GH AllenInstitute#2744: Fix installation on Python 3.12, 3.13

setup.py imports allensdk at build time to read __version__, breaking
clean installs. Dependencies live in five separate requirements files
instead of package metadata. 18 files use pkg_resources at runtime,
forcing a setuptools runtime dependency.

- Replace setup.py/setup.cfg/MANIFEST.in with pyproject.toml (hatchling)
- Consolidate requirements files into optional dependency groups
- Replace pkg_resources.resource_filename with importlib.resources.files
- Replace pkg_resources.parse_version with packaging.version.Version
- Read __version__ from importlib.metadata instead of hardcoding
- Convert bps bash wrapper to a [project.scripts] console entry point
- Update CI workflows, docs, and notebook cells for new install path

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

…oject.toml

Migrate from setup.py to pyproject.toml (hatchling)

Remove all Python 2 compatibility shims (six and future packages)
and replace with stdlib equivalents:

- six.iteritems(d) → d.items()
- six.itervalues(d) → d.values()
- six.string_types → str
- six.text_type → str
- six.moves.xrange → range
- six.moves.reduce → functools.reduce
- six.moves.builtins → builtins
- six.moves.cPickle → pickle
- six.raise_from(X, e) → raise X from e
- six.ensure_str(s) → s
- past.builtins.xrange → range

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

Remove Python 2 compatibility shims

Make it clear that this package is in maintenance mode.

Co-authored-by: David Feng <dyf@users.noreply.github.com>

* fix: apply safe ruff auto-fixes

* fix: E711, E731 (none-comparison and lambda assignment)

* fix: E712 (boolean comparison) with idiomatic pandas

* fix: F841 (unused variables)

After deleting variables, some bare expressions were deleted:

Bare expressions deleted (no side effects — entire line removed):

File: brain_observatory/circle_plots.py
Deleted expression: r * np.cos(angle), r * np.sin(angle)
Why: Pure arithmetic
────────────────────────────────────────
File: brain_observatory/ecephys/.../view_blocks.py
Deleted expression: recorded_blocks[0] → pass
Why: Bare index in else clause
────────────────────────────────────────
File: brain_observatory/eye_tracking/.../DLC_Ellipse_Fitting.py
Deleted expression: 1-frac_completed
Why: Pure arithmetic
────────────────────────────────────────
File: internal/brain_observatory/demix_report.py
Deleted expression: np.zeros(mask.shape)
Why: Array allocated and discarded
────────────────────────────────────────
File: internal/brain_observatory/frame_stream.py
Deleted expression: np.prod(self.frame_shape)
Why: Pure computation
────────────────────────────────────────
File: internal/brain_observatory/roi_filter.py
Deleted expression: create_feature_array(...) → pass
Why: Returns value, no mutation
────────────────────────────────────────
File: internal/ephys/plot_qc_figures.py
Deleted expression: cell_features["long_squares"]["sweeps"]
Why: Dict lookup
────────────────────────────────────────
File: internal/ephys/plot_qc_figures3.py
Deleted expression: cell_features["long_squares"]["sweeps"]
Why: Dict lookup
────────────────────────────────────────
File: internal/model/GLM.py
Deleted expression: kbasprs['b']
Why: Dict lookup
────────────────────────────────────────
File: internal/model/biophysical/fit_stage_1.py
Deleted expression: neuronal_model_data['specimen_id']
Why: Dict lookup
────────────────────────────────────────
File: internal/model/biophysical/make_deap_fit_json.py
Deleted expression: os.path.realpath(os.curdir)
Why: Pure path op
────────────────────────────────────────
File: internal/model/biophysical/passive_fitting/preprocess.py
Deleted expression: down_idxs[1] - down_idxs[0]
Why: Pure arithmetic
────────────────────────────────────────
File: internal/model/glif/error_functions.py
Deleted expression: input_data['subthreshold_long_square_voltage_variance'], np.arange(...)*experiment.neuron.dt, [e.data['interpolated_ISI']] (dead code after raise)
Why: Dict lookup, pure computation, unreachable
────────────────────────────────────────
File: internal/model/glif/preprocess_neuron.py
Deleted expression: sweep_index[...][RESTING_POTENTIAL]*1e-3, long_square_config['all'], long_square_config['subthreshold'], np.mean(El_test_list)
Why: Dict lookups, pure computation
────────────────────────────────────────
File: internal/model/glif/spike_cutting.py
Deleted expression: np.var(xdata)
Why: Pure computation
────────────────────────────────────────
File: internal/pipeline_modules/IVSCC/ephys_nwb/qc.py
Deleted expression: sweep_data['response'], sweep_data['sampling_rate']
Why: Dict lookups
────────────────────────────────────────
File: internal/pipeline_modules/run_neuropil_correction.py
Deleted expression: np.array([...]).mean()
Why: Pure computation
────────────────────────────────────────
File: internal/pipeline_modules/run_observatory_container_thumbnails.py
Deleted expression: input_file['output_json']
Why: Dict lookup
────────────────────────────────────────
File: model/glif/glif_neuron_methods.py
Deleted expression: tcs['voltage'][-1]
Why: Dict/index lookup
────────────────────────────────────────
File: brain_observatory/behavior/swdb/summary_figures.py
Deleted expression: int(session.metadata['ophys_frame_rate'])
Why: Pure type conversion

Bare expressions kept (have side effects):

┌────────────────────────────────────────────────────────┬──────────────────────────────────┐
│                       Expression                       │             Why kept             │
├────────────────────────────────────────────────────────┼──────────────────────────────────┤
│ hero_sweep.sweep_feature("adapt"/"latency"/"mean_isi") │ Forces lazy feature caching      │
├────────────────────────────────────────────────────────┼──────────────────────────────────┤
│ swp.sweep_feature("v_baseline")                        │ Same caching pattern             │
├────────────────────────────────────────────────────────┼──────────────────────────────────┤
│ i_vec.as_numpy()                                       │ NEURON vector conversion         │
├────────────────────────────────────────────────────────┼──────────────────────────────────┤
│ subprocess.check_output([...]) (3 calls)               │ Runs external fitting processes  │
├────────────────────────────────────────────────────────┼──────────────────────────────────┤
│ p.map(func, types)                                     │ Multiprocessing execution        │
├────────────────────────────────────────────────────────┼──────────────────────────────────┤
│ description.manifest.get_path(...)                     │ Manifest path resolution         │
├────────────────────────────────────────────────────────┼──────────────────────────────────┤
│ plt.subplot2grid(...)                                  │ Creates subplot in figure layout │
├────────────────────────────────────────────────────────┼──────────────────────────────────┤
│ All allensdk/test/ expressions                         │ Smoke tests exercising APIs      │
└────────────────────────────────────────────────────────┴──────────────────────────────────┘

* fix: E722, E701, F401, F507 lint errors and configure suppressions

- E722: Replace 55 bare `except:` with `except Exception:` (32 files)
- E701: Split 29 single-line compound statements onto separate lines
- F401: Add `__all__` to 5 `__init__.py` re-export files, noqa 2 keras
  availability checks
- F507: Fix format string placeholder mismatch in glif_optimizer_neuron
- Configure ruff and flake8 to suppress E402, E741, F403, F405

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

---------

Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>
Co-authored-by: David Feng <dyf@users.noreply.github.com>

Trivial change to re-trigger CI