From 5d46b14fd28473b42c4e26198fbde3153e348f73 Mon Sep 17 00:00:00 2001
From: Mike Huang <huangjmike@gmail.com>
Date: Thu, 20 Jul 2023 19:57:24 -0700
Subject: [PATCH 01/15] poetry dependency setup for py3.8 to 3.10

---
 poetry.lock               | 2902 +++++++++++++++++++++++++++++++++++++
 pyproject.toml            |   47 +
 requirements_py38-310.txt |   33 +
 3 files changed, 2982 insertions(+)
 create mode 100644 poetry.lock
 create mode 100644 pyproject.toml
 create mode 100644 requirements_py38-310.txt

diff --git a/poetry.lock b/poetry.lock
new file mode 100644
index 000000000..9e1abf3b5
--- /dev/null
+++ b/poetry.lock
@@ -0,0 +1,2902 @@
+# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand.
+
+[[package]]
+name = "aiohttp"
+version = "3.8.5"
+description = "Async http client/server framework (asyncio)"
+optional = false
+python-versions = ">=3.6"
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+[metadata]
+lock-version = "2.0"
+python-versions = ">=3.8,<=3.11"
+content-hash = "91ec54d6d7018a08f60de2b9fb7b9e9a0ece3caf2f3502d9ccf32b004f15daca"
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 000000000..4232af91b
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,47 @@
+[tool.poetry]
+name = "allensdk"
+version = "2.15.2"
+description = "core libraries for the allensdk."
+authors = ["Allen Institute for Brain Science"]
+readme = "README.md"
+
+[tool.poetry.dependencies]
+python = ">=3.8,<=3.11"
+psycopg2-binary = "^2.9.6"
+hdmf = "^3.7.0"
+h5py = "^3.9.0"
+matplotlib = "^3.7.2"
+numpy = "<1.25"
+pandas = "^2.0.3"
+jinja2 = "^3.1.2"
+scipy = "<1.11"
+six = "^1.16.0"
+pynrrd = "^1.0.0"
+future = "^0.18.3"
+requests = "^2.31.0"
+requests-toolbelt = "^1.0.0"
+simplejson = "^3.19.1"
+scikit-image = "^0.21.0"
+scikit-build = "^0.17.6"
+statsmodels = "^0.14.0"
+simpleitk = "^2.2.1"
+argschema = "^3.0.4"
+glymur = "^0.12.8"
+xarray = "<2023.2.0"
+pynwb = "^2.3.3"
+tables = "^3.8.0"
+seaborn = "^0.12.2"
+aiohttp = "^3.8.5"
+nest-asyncio = "^1.5.6"
+tqdm = "^4.65.0"
+ndx-events = "^0.2.0"
+boto3 = "^1.28.8"
+semver = "^3.0.1"
+cachetools = "^5.3.1"
+sqlalchemy = "^2.0.19"
+python-dateutil = "^2.8.2"
+
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
diff --git a/requirements_py38-310.txt b/requirements_py38-310.txt
new file mode 100644
index 000000000..ec2c3d21b
--- /dev/null
+++ b/requirements_py38-310.txt
@@ -0,0 +1,33 @@
+psycopg2-binary
+hdmf
+h5py
+matplotlib
+numpy<1.25
+pandas
+jinja2
+scipy<1.11
+six
+pynrrd
+future
+requests
+requests-toolbelt
+simplejson
+scikit-image
+scikit-build
+statsmodels
+simpleitk
+argschema
+glymur
+xarray<2023.2.0
+pynwb
+tables
+seaborn
+aiohttp
+nest_asyncio
+tqdm
+ndx-events
+boto3
+semver
+cachetools
+sqlalchemy
+python-dateutil

From 971d5788313acc13e4c194f7957d1ee141a12b98 Mon Sep 17 00:00:00 2001
From: Mike Huang <huangjmike@gmail.com>
Date: Thu, 20 Jul 2023 19:58:04 -0700
Subject: [PATCH 02/15] fix deprecated np.bool

---
 .../data_objects/cell_specimens/cell_specimens.py    |  2 +-
 allensdk/brain_observatory/behavior/dprime.py        | 12 ++++++------
 allensdk/brain_observatory/chisquare_categorical.py  |  4 ++--
 .../ecephys_project_warehouse_api.py                 |  2 +-
 .../receptive_field_analysis/chisquarerf.py          |  4 ++--
 .../receptive_field_analysis/eventdetection.py       |  2 +-
 .../receptive_field_analysis/postprocessing.py       |  2 +-
 .../receptive_field_analysis/receptive_field.py      |  4 ++--
 .../receptive_field_analysis/utilities.py            |  4 ++--
 allensdk/core/json_utilities.py                      |  2 +-
 .../interval_unionize/data_utilities.py              |  4 ++--
 11 files changed, 21 insertions(+), 21 deletions(-)

diff --git a/allensdk/brain_observatory/behavior/data_objects/cell_specimens/cell_specimens.py b/allensdk/brain_observatory/behavior/data_objects/cell_specimens/cell_specimens.py
index d17226379..dad81f32e 100644
--- a/allensdk/brain_observatory/behavior/data_objects/cell_specimens/cell_specimens.py
+++ b/allensdk/brain_observatory/behavior/data_objects/cell_specimens/cell_specimens.py
@@ -820,7 +820,7 @@ def _postprocess(
             curr_roi.width = table_row["width"]
             curr_roi.height = table_row["height"]
             curr_roi.mask = np.array(table_row["roi_mask"])
-            roi_mask_list.append(curr_roi.get_mask_plane().astype(np.bool))
+            roi_mask_list.append(curr_roi.get_mask_plane().astype(bool))
 
         cell_specimen_table["roi_mask"] = roi_mask_list
         cell_specimen_table = cell_specimen_table[
diff --git a/allensdk/brain_observatory/behavior/dprime.py b/allensdk/brain_observatory/behavior/dprime.py
index 9519cd703..13cbe80cb 100644
--- a/allensdk/brain_observatory/behavior/dprime.py
+++ b/allensdk/brain_observatory/behavior/dprime.py
@@ -9,9 +9,9 @@
 
 def get_go_responses(hit=None, miss=None, aborted=None):
     assert len(hit) == len(miss) == len(aborted)
-    not_aborted = np.logical_not(np.array(aborted, dtype=np.bool))
-    hit = np.array(hit, dtype=np.bool)[not_aborted]
-    miss = np.array(miss, dtype=np.bool)[not_aborted]
+    not_aborted = np.logical_not(np.array(aborted, dtype=bool))
+    hit = np.array(hit, dtype=bool)[not_aborted]
+    miss = np.array(miss, dtype=bool)[not_aborted]
 
     # Go responses are nan when catch (aborted are masked out); 0 for miss, 1 for hit
     # This allows pd.Series.rolling to ignore non-go trial data
@@ -38,9 +38,9 @@ def get_trial_count_corrected_hit_rate(hit=None, miss=None, aborted=None, slidin
 
 def get_catch_responses(correct_reject=None, false_alarm=None, aborted=None):
     assert len(correct_reject) == len(false_alarm) == len(aborted)
-    not_aborted = np.logical_not(np.array(aborted, dtype=np.bool))
-    correct_reject = np.array(correct_reject, dtype=np.bool)[not_aborted]
-    false_alarm = np.array(false_alarm, dtype=np.bool)[not_aborted]
+    not_aborted = np.logical_not(np.array(aborted, dtype=bool))
+    correct_reject = np.array(correct_reject, dtype=bool)[not_aborted]
+    false_alarm = np.array(false_alarm, dtype=bool)[not_aborted]
 
     # Catch responses are nan when go (aborted are masked out); 0 for correct-rejection, 1 for false-alarm
     # This allows pd.Series.rolling to ignore non-catch trial data
diff --git a/allensdk/brain_observatory/chisquare_categorical.py b/allensdk/brain_observatory/chisquare_categorical.py
index 4400cdc88..42edf8e17 100644
--- a/allensdk/brain_observatory/chisquare_categorical.py
+++ b/allensdk/brain_observatory/chisquare_categorical.py
@@ -89,7 +89,7 @@ def stim_table_to_categories(stim_table,
     all_tried = False
     while not all_tried:
         
-        matches_combination = np.ones((num_sweeps,),dtype=np.bool)
+        matches_combination = np.ones((num_sweeps,),dtype=bool)
         for i_col,column in enumerate(columns):
             param = unique_params[i_col][curr_combination[i_col]]
             matches_param = stim_table[column].values == param
@@ -140,7 +140,7 @@ def make_category_dummy(sweep_categories):
     categories = np.unique(sweep_categories)
     num_categories = len(categories)
     
-    sweep_category_mat = np.zeros((num_sweeps,num_categories),dtype=np.bool)
+    sweep_category_mat = np.zeros((num_sweeps,num_categories),dtype=bool)
     for i_cat,category in enumerate(categories):
         category_idx = np.argwhere(sweep_categories==category)[:,0]
         sweep_category_mat[category_idx,i_cat] = True
diff --git a/allensdk/brain_observatory/ecephys/ecephys_project_api/ecephys_project_warehouse_api.py b/allensdk/brain_observatory/ecephys/ecephys_project_api/ecephys_project_warehouse_api.py
index bad7c764c..c219a5de2 100644
--- a/allensdk/brain_observatory/ecephys/ecephys_project_api/ecephys_project_warehouse_api.py
+++ b/allensdk/brain_observatory/ecephys/ecephys_project_api/ecephys_project_warehouse_api.py
@@ -288,7 +288,7 @@ def get_unit_analysis_metrics(self, unit_ids=None, ecephys_session_ids=None, ses
         columns = set(output.columns.values.tolist())
         if "p_value_rf" in columns and "on_screen_rf" in columns:
 
-            pv_is_bool = np.issubdtype(output["p_value_rf"].values[0], np.bool)
+            pv_is_bool = np.issubdtype(output["p_value_rf"].values[0], bool)
             on_screen_is_float = np.issubdtype(output["on_screen_rf"].values[0].dtype, np.floating)
 
             # this is not a good test, but it avoids the case where we fix
diff --git a/allensdk/brain_observatory/receptive_field_analysis/chisquarerf.py b/allensdk/brain_observatory/receptive_field_analysis/chisquarerf.py
index 97647b9c6..8fa1094c7 100644
--- a/allensdk/brain_observatory/receptive_field_analysis/chisquarerf.py
+++ b/allensdk/brain_observatory/receptive_field_analysis/chisquarerf.py
@@ -146,9 +146,9 @@ def get_peak_significance(chi_square_grid_NLL,
         best_p[n] = p_value_corrected_per_pixel[y,x]
         if best_p[n] < alpha:
             significant_cells[n] = True
-            best_exclusion_region_list.append(disc_masks[y, x, :,:].astype(np.bool))
+            best_exclusion_region_list.append(disc_masks[y, x, :,:].astype(bool))
         else:
-            best_exclusion_region_list.append(np.zeros((disc_masks.shape[0], disc_masks.shape[1]), dtype=np.bool))
+            best_exclusion_region_list.append(np.zeros((disc_masks.shape[0], disc_masks.shape[1]), dtype=bool))
 
     return significant_cells, best_p, corrected_p_value_array_list, best_exclusion_region_list
 
diff --git a/allensdk/brain_observatory/receptive_field_analysis/eventdetection.py b/allensdk/brain_observatory/receptive_field_analysis/eventdetection.py
index 93b56d6f9..b7b25f50a 100644
--- a/allensdk/brain_observatory/receptive_field_analysis/eventdetection.py
+++ b/allensdk/brain_observatory/receptive_field_analysis/eventdetection.py
@@ -128,7 +128,7 @@ def detect_events(data, cell_index, stimulus, debug_plots=False):
 
 
     assert len(var_dict) == len(stimulus_table)
-    b = np.zeros(len(stimulus_table), dtype=np.bool)
+    b = np.zeros(len(stimulus_table), dtype=bool)
     for yi in yes_set:
         b[yi] = True
 
diff --git a/allensdk/brain_observatory/receptive_field_analysis/postprocessing.py b/allensdk/brain_observatory/receptive_field_analysis/postprocessing.py
index ebb294b4f..aacab6d25 100644
--- a/allensdk/brain_observatory/receptive_field_analysis/postprocessing.py
+++ b/allensdk/brain_observatory/receptive_field_analysis/postprocessing.py
@@ -106,7 +106,7 @@ def run_postprocessing(data, rf):
     cell_index = rf['attrs']['cell_index']
     locally_sparse_noise_template = data.get_stimulus_template(stimulus)
 
-    event_array = np.zeros((rf['event_vector']['data'].shape[0], 1), dtype=np.bool)
+    event_array = np.zeros((rf['event_vector']['data'].shape[0], 1), dtype=bool)
     event_array[:,0] = rf['event_vector']['data']
 
     chi_squared_grid = chi_square_binary(event_array, locally_sparse_noise_template)
diff --git a/allensdk/brain_observatory/receptive_field_analysis/receptive_field.py b/allensdk/brain_observatory/receptive_field_analysis/receptive_field.py
index a122293ff..7939e1fde 100644
--- a/allensdk/brain_observatory/receptive_field_analysis/receptive_field.py
+++ b/allensdk/brain_observatory/receptive_field_analysis/receptive_field.py
@@ -93,13 +93,13 @@ def compute_receptive_field(data, cell_index, stimulus, **kwargs):
 
     fdr_corrected_pvalues_on = fdr_corrected_pvalues[
                                :number_of_pixels].reshape(s1, s2)
-    _fdr_mask_on = np.zeros_like(pvalues_on, dtype=np.bool)
+    _fdr_mask_on = np.zeros_like(pvalues_on, dtype=bool)
     _fdr_mask_on[fdr_corrected_pvalues_on < alpha] = True
     components_on, number_of_components_on = get_components(_fdr_mask_on)
 
     fdr_corrected_pvalues_off = fdr_corrected_pvalues[
                                 number_of_pixels:].reshape(s1, s2)
-    _fdr_mask_off = np.zeros_like(pvalues_off, dtype=np.bool)
+    _fdr_mask_off = np.zeros_like(pvalues_off, dtype=bool)
     _fdr_mask_off[fdr_corrected_pvalues_off < alpha] = True
     components_off, number_of_components_off = get_components(_fdr_mask_off)
 
diff --git a/allensdk/brain_observatory/receptive_field_analysis/utilities.py b/allensdk/brain_observatory/receptive_field_analysis/utilities.py
index bbef432f3..187af810d 100644
--- a/allensdk/brain_observatory/receptive_field_analysis/utilities.py
+++ b/allensdk/brain_observatory/receptive_field_analysis/utilities.py
@@ -130,7 +130,7 @@ def get_shuffle_matrix(data, event_vector, A, number_of_shuffles=5000, response_
         size = number_of_events + int(np.round(response_detection_error_std_dev*number_of_events*np.random.randn()))
         shuffled_event_inds = np.random.choice(evr, size=size, replace=False)
 
-        b_tmp = np.zeros(len(event_vector), dtype=np.bool)
+        b_tmp = np.zeros(len(event_vector), dtype=bool)
         b_tmp[shuffled_event_inds] = True
         shuffle_data[:, ii] = A[:,b_tmp].sum(axis=1)/float(size)
 
@@ -270,7 +270,7 @@ def get_components(receptive_field_data):
         return_array = np.zeros((len(component_list), receptive_field_data.shape[0], receptive_field_data.shape[1]))
 
     for ii, component in enumerate(component_list):
-        curr_component_mask = np.zeros_like(receptive_field_data, dtype=np.bool).flatten()
+        curr_component_mask = np.zeros_like(receptive_field_data, dtype=bool).flatten()
         curr_component_mask[component] = True
         return_array[ii,:,:] = curr_component_mask.reshape(receptive_field_data.shape)
 
diff --git a/allensdk/core/json_utilities.py b/allensdk/core/json_utilities.py
index 8c195c6e3..e85649516 100644
--- a/allensdk/core/json_utilities.py
+++ b/allensdk/core/json_utilities.py
@@ -164,7 +164,7 @@ def json_handler(obj):
         return float(obj)
     elif isinstance(obj, np.integer):
         return int(obj)
-    elif (isinstance(obj, np.bool) or
+    elif (isinstance(obj, bool) or
           isinstance(obj, np.bool_)):
         return bool(obj)
     elif hasattr(obj, 'isoformat'):
diff --git a/allensdk/internal/mouse_connectivity/interval_unionize/data_utilities.py b/allensdk/internal/mouse_connectivity/interval_unionize/data_utilities.py
index 89e5c123c..aabbc971a 100755
--- a/allensdk/internal/mouse_connectivity/interval_unionize/data_utilities.py
+++ b/allensdk/internal/mouse_connectivity/interval_unionize/data_utilities.py
@@ -93,11 +93,11 @@ def get_projection_data(projection_density_path, projection_energy_path,
         logging.info('getting aav exclusion fraction')
         aav_exclusion_fraction = read(aav_exclusion_fraction_path)
         aav_exclusion_fraction[aav_exclusion_fraction > 0] = 1
-        aav_exclusion_fraction = aav_exclusion_fraction.astype(np.bool_, order='C')
+        aav_exclusion_fraction = aav_exclusion_fraction.astype(bool_, order='C')
     
     except (IOError, OSError, RuntimeError):
         logging.info('skipping aav exclusion fraction')
-        aav_exclusion_fraction = np.zeros(projection_density.shape, dtype=np.bool_, order='C')
+        aav_exclusion_fraction = np.zeros(projection_density.shape, dtype=bool_, order='C')
     
     return {'projection_density': projection_density, 
             'projection_energy': projection_energy, 

From 43a4094e12e43d5f044031d4ffb4d79e7001711c Mon Sep 17 00:00:00 2001
From: Mike Huang <huangjmike@gmail.com>
Date: Fri, 21 Jul 2023 09:18:17 -0700
Subject: [PATCH 03/15] fix Int64Index deprecation and explicit requirement for
 regex boolean on str.replace

---
 .../behavior/data_objects/stimuli/presentations.py     | 10 ++++++----
 .../ecephys/stimulus_table/naming_utilities.py         |  2 +-
 .../test/brain_observatory/ecephys/test_write_nwb.py   |  2 +-
 requirements_py38-310.txt                              |  2 +-
 4 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/allensdk/brain_observatory/behavior/data_objects/stimuli/presentations.py b/allensdk/brain_observatory/behavior/data_objects/stimuli/presentations.py
index 91cc8a99a..3d313bbee 100644
--- a/allensdk/brain_observatory/behavior/data_objects/stimuli/presentations.py
+++ b/allensdk/brain_observatory/behavior/data_objects/stimuli/presentations.py
@@ -246,10 +246,12 @@ def from_stimulus_file(
         stim_pres_df = \
             stim_pres_df[sorted(stim_pres_df)].dropna(axis=1, how='all')
         if limit_to_images is not None:
-            stim_pres_df = \
-                stim_pres_df[stim_pres_df['image_name'].isin(limit_to_images)]
-            stim_pres_df.index = pd.Int64Index(
-                range(stim_pres_df.shape[0]), name=stim_pres_df.index.name)
+            stim_pres_df = stim_pres_df[
+                stim_pres_df["image_name"].isin(limit_to_images)
+            ]
+            stim_pres_df.index = pd.Index(
+                range(stim_pres_df.shape[0]), name=stim_pres_df.index.name
+            )
 
         stim_pres_df['stimulus_block'] = 0
         # Match the Ecephys VBN stimulus name convention.
diff --git a/allensdk/brain_observatory/ecephys/stimulus_table/naming_utilities.py b/allensdk/brain_observatory/ecephys/stimulus_table/naming_utilities.py
index 8b06cd83b..bb49953b6 100644
--- a/allensdk/brain_observatory/ecephys/stimulus_table/naming_utilities.py
+++ b/allensdk/brain_observatory/ecephys/stimulus_table/naming_utilities.py
@@ -154,7 +154,7 @@ def replace(match_obj):
 
     movie_rows = table[stim_colname].str.contains(movie_re, na=False)
     table.loc[movie_rows, stim_colname] = \
-        table.loc[movie_rows, stim_colname].str.replace(numeral_re, replace)
+        table.loc[movie_rows, stim_colname].str.replace(numeral_re, replace, regex=True)
 
     return table
 
diff --git a/allensdk/test/brain_observatory/ecephys/test_write_nwb.py b/allensdk/test/brain_observatory/ecephys/test_write_nwb.py
index 28aa8c9e3..3b9488bd2 100644
--- a/allensdk/test/brain_observatory/ecephys/test_write_nwb.py
+++ b/allensdk/test/brain_observatory/ecephys/test_write_nwb.py
@@ -563,7 +563,7 @@ def test_add_raw_running_data_to_nwbfile(
 def test_read_stimulus_table(tmpdir_factory, presentations,
                              column_renames_map, columns_to_drop, expected):
     expected = expected.set_index(
-        pd.Int64Index(range(expected.shape[0]),
+        pd.Index(range(expected.shape[0]),
                       name='stimulus_presentations_id'))
     dirname = str(tmpdir_factory.mktemp("ecephys_nwb_test"))
     stim_table_path = os.path.join(dirname, "stim_table.csv")
diff --git a/requirements_py38-310.txt b/requirements_py38-310.txt
index ec2c3d21b..159ed36d9 100644
--- a/requirements_py38-310.txt
+++ b/requirements_py38-310.txt
@@ -1,5 +1,5 @@
 psycopg2-binary
-hdmf
+hdmf<=3.6.1
 h5py
 matplotlib
 numpy<1.25

From d6b4a80abed943de2f306e0e79105912403ef5da Mon Sep 17 00:00:00 2001
From: Mike Huang <huangjmike@gmail.com>
Date: Fri, 21 Jul 2023 13:04:03 -0700
Subject: [PATCH 04/15] fix pandas reindex change

---
 .../tables/util/prior_exposure_processing.py                     | 1 +
 1 file changed, 1 insertion(+)

diff --git a/allensdk/brain_observatory/behavior/behavior_project_cache/tables/util/prior_exposure_processing.py b/allensdk/brain_observatory/behavior/behavior_project_cache/tables/util/prior_exposure_processing.py
index a5f710a84..78e8e1f43 100644
--- a/allensdk/brain_observatory/behavior/behavior_project_cache/tables/util/prior_exposure_processing.py
+++ b/allensdk/brain_observatory/behavior/behavior_project_cache/tables/util/prior_exposure_processing.py
@@ -168,4 +168,5 @@ def cumsum(x):
         raise ValueError(f'agg method {agg_method} not supported')
 
     # reindex to original index
+    counts.reset_index(drop=True, inplace=True)
     return counts.reindex(index)

From 7e9a67e4008883333cdd3a7da7e7bd95e57ba99f Mon Sep 17 00:00:00 2001
From: Mike Huang <huangjmike@gmail.com>
Date: Mon, 24 Jul 2023 05:05:19 -0700
Subject: [PATCH 05/15] change check_less_precise to rtol in
 assert_series_equal

---
 .../ecephys/stimulus_analysis/test_stimulus_analysis.py         | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/allensdk/test/brain_observatory/ecephys/stimulus_analysis/test_stimulus_analysis.py b/allensdk/test/brain_observatory/ecephys/stimulus_analysis/test_stimulus_analysis.py
index 4e59e62c4..0cab53812 100644
--- a/allensdk/test/brain_observatory/ecephys/stimulus_analysis/test_stimulus_analysis.py
+++ b/allensdk/test/brain_observatory/ecephys/stimulus_analysis/test_stimulus_analysis.py
@@ -185,7 +185,7 @@ def test_conditionwise_statistics(ecephys_api):
         ["spike_count", "stimulus_presentation_count", "spike_mean", "spike_std", "spike_sem"]
     )
     obtained = stim_analysis.conditionwise_statistics.loc[(0, 1)]
-    pd.testing.assert_series_equal(expected, obtained[expected.index], check_less_precise=5, check_names=False)
+    pd.testing.assert_series_equal(expected, obtained[expected.index], check_dtype=True, check_names=False, rtol=1e-5, atol=1e-8)
 
 
 def test_presentationwise_spike_times(ecephys_api):

From bd8016c2689e0fa817591bdc067b46486ec7213f Mon Sep 17 00:00:00 2001
From: Mike Huang <huangjmike@gmail.com>
Date: Mon, 24 Jul 2023 05:06:00 -0700
Subject: [PATCH 06/15] fix attempt to reindex a MultiIndex

---
 .../tables/util/prior_exposure_processing.py    | 17 ++++++++---------
 1 file changed, 8 insertions(+), 9 deletions(-)

diff --git a/allensdk/brain_observatory/behavior/behavior_project_cache/tables/util/prior_exposure_processing.py b/allensdk/brain_observatory/behavior/behavior_project_cache/tables/util/prior_exposure_processing.py
index 78e8e1f43..d0e5a7774 100644
--- a/allensdk/brain_observatory/behavior/behavior_project_cache/tables/util/prior_exposure_processing.py
+++ b/allensdk/brain_observatory/behavior/behavior_project_cache/tables/util/prior_exposure_processing.py
@@ -142,9 +142,8 @@ def __get_prior_exposure_count(df: pd.DataFrame, to: pd.Series,
     exposure counts
     """
     index = df.index
-    df = df.sort_values('date_of_acquisition')
-    df = df[df['session_type'].notnull()]
-
+    df = df.sort_values("date_of_acquisition")
+    df = df[df["session_type"].notnull()]
     # reindex "to" to df
     to = to.loc[df.index]
 
@@ -154,19 +153,19 @@ def __get_prior_exposure_count(df: pd.DataFrame, to: pd.Series,
     # reindex df to match "to" index with missing values removed
     df = df.loc[to.index]
 
-    if agg_method == 'cumcount':
-        counts = df.groupby(['mouse_id', to]).cumcount()
-    elif agg_method == 'cumsum':
-        df['to'] = to
-
+    if agg_method == "cumcount":
+        counts = df.groupby(["mouse_id", to]).cumcount()
+    elif agg_method == "cumsum":
+        df["to"] = to
+        df_index_name = df.index.name
         def cumsum(x):
             return x.cumsum().shift(fill_value=0).astype('int64')
 
         counts = df.groupby(['mouse_id'])['to'].apply(cumsum)
         counts.name = None
+        counts.index = counts.index.get_level_values(df_index_name)
     else:
         raise ValueError(f'agg method {agg_method} not supported')
 
     # reindex to original index
-    counts.reset_index(drop=True, inplace=True)
     return counts.reindex(index)

From 2d864017eee607f985fb92df12e6c9d23333f56b Mon Sep 17 00:00:00 2001
From: Mike Huang <huangjmike@gmail.com>
Date: Mon, 24 Jul 2023 11:10:26 -0700
Subject: [PATCH 07/15] fix deprecated np.float and np.int

---
 .../behavior/data_objects/stimuli/stimulus_templates.py      | 2 +-
 allensdk/brain_observatory/behavior/dprime.py                | 4 ++--
 allensdk/brain_observatory/behavior/swdb/summary_figures.py  | 2 +-
 allensdk/brain_observatory/chisquare_categorical.py          | 4 ++--
 allensdk/brain_observatory/stimulus_info.py                  | 5 +----
 5 files changed, 7 insertions(+), 10 deletions(-)

diff --git a/allensdk/brain_observatory/behavior/data_objects/stimuli/stimulus_templates.py b/allensdk/brain_observatory/behavior/data_objects/stimuli/stimulus_templates.py
index 2493f4b3a..ee1185c68 100644
--- a/allensdk/brain_observatory/behavior/data_objects/stimuli/stimulus_templates.py
+++ b/allensdk/brain_observatory/behavior/data_objects/stimuli/stimulus_templates.py
@@ -73,7 +73,7 @@ def _exclude_unseen_pixels(self, arr: np.ndarray):
         """After warping, some pixels are not visible on the screen.
         This sets those pixels to nan to make downstream analysis easier."""
         mask = self._monitor.get_mask()
-        arr = arr.astype(np.float)
+        arr = arr.astype('float')
         arr *= mask
         arr[mask == 0] = np.nan
         return arr
diff --git a/allensdk/brain_observatory/behavior/dprime.py b/allensdk/brain_observatory/behavior/dprime.py
index 13cbe80cb..d731a8b98 100644
--- a/allensdk/brain_observatory/behavior/dprime.py
+++ b/allensdk/brain_observatory/behavior/dprime.py
@@ -15,7 +15,7 @@ def get_go_responses(hit=None, miss=None, aborted=None):
 
     # Go responses are nan when catch (aborted are masked out); 0 for miss, 1 for hit
     # This allows pd.Series.rolling to ignore non-go trial data
-    go_responses = np.empty_like(hit, dtype=np.float)
+    go_responses = np.empty_like(hit, dtype='float')
     go_responses.fill(float('nan'))
     go_responses[hit] = 1
     go_responses[miss] = 0
@@ -44,7 +44,7 @@ def get_catch_responses(correct_reject=None, false_alarm=None, aborted=None):
 
     # Catch responses are nan when go (aborted are masked out); 0 for correct-rejection, 1 for false-alarm
     # This allows pd.Series.rolling to ignore non-catch trial data
-    catch_responses = np.empty_like(correct_reject, dtype=np.float)
+    catch_responses = np.empty_like(correct_reject, dtype='float')
     catch_responses.fill(float('nan'))
     catch_responses[false_alarm] = 1
     catch_responses[correct_reject] = 0
diff --git a/allensdk/brain_observatory/behavior/swdb/summary_figures.py b/allensdk/brain_observatory/behavior/swdb/summary_figures.py
index 080536f49..91fabdc47 100644
--- a/allensdk/brain_observatory/behavior/swdb/summary_figures.py
+++ b/allensdk/brain_observatory/behavior/swdb/summary_figures.py
@@ -381,7 +381,7 @@ def plot_max_proj_and_roi_masks(session, save_dir=None):
     ax[2].set_title(str(session.metadata['ophys_experiment_id']))
 
     tmp = session.segmentation_mask_image.data.copy()
-    mask = np.empty(session.segmentation_mask_image.data.shape, dtype=np.float)
+    mask = np.empty(session.segmentation_mask_image.data.shape, dtype='float')
     mask[:] = np.nan
     mask[tmp > 0] = 1
     cax = ax[2].imshow(mask, cmap='hsv', alpha=0.4, vmin=0, vmax=1)
diff --git a/allensdk/brain_observatory/chisquare_categorical.py b/allensdk/brain_observatory/chisquare_categorical.py
index 42edf8e17..9b0725f5c 100644
--- a/allensdk/brain_observatory/chisquare_categorical.py
+++ b/allensdk/brain_observatory/chisquare_categorical.py
@@ -84,8 +84,8 @@ def stim_table_to_categories(stim_table,
 
     category = 0
     sweep_categories = -1*np.ones((num_sweeps,))
-    curr_combination = np.zeros((num_params,),dtype=np.int)
-    options_per_column = np.array(options_per_column).astype(np.int)
+    curr_combination = np.zeros((num_params,),dtype='int')
+    options_per_column = np.array(options_per_column).astype('int')
     all_tried = False
     while not all_tried:
         
diff --git a/allensdk/brain_observatory/stimulus_info.py b/allensdk/brain_observatory/stimulus_info.py
index 595510c56..e37f2a0d9 100755
--- a/allensdk/brain_observatory/stimulus_info.py
+++ b/allensdk/brain_observatory/stimulus_info.py
@@ -518,9 +518,6 @@ def lsn_image_to_screen(self, img, stimulus_type, origin='lower', background_col
 
     def natural_scene_image_to_screen(self, img, origin='lower', translation=(0,0)):
 
-        # assert img.dtype == np.float32
-        # img = img.astype(np.uint8)
-
         full_image = np.full((self.n_pixels_r, self.n_pixels_c), 127, dtype=np.uint8)
         mr, mc = natural_scene_coordinate_to_monitor_coordinate((0, 0), (self.n_pixels_r, self.n_pixels_c))
         Mr, Mc = natural_scene_coordinate_to_monitor_coordinate((img.shape[0], img.shape[1]), (self.n_pixels_r, self.n_pixels_c))
@@ -756,7 +753,7 @@ def warp_stimulus_coords(vertices,
     distance = float(distance)
     mon_res_x, mon_res_y = float(mon_res[0]), float(mon_res[1])
 
-    vertices = vertices.astype(np.float)
+    vertices = vertices.astype('float')
 
     # from pixels (-1920/2 -> 1920/2) to stimulus space (-0.5->0.5)
     vertices[:, 0] = vertices[:, 0] / mon_res_x

From 85a97c4dd7c4356048812d9f087f47a20094584d Mon Sep 17 00:00:00 2001
From: Mike Huang <huangjmike@gmail.com>
Date: Mon, 24 Jul 2023 14:09:10 -0700
Subject: [PATCH 08/15] downgrade pandas=1.53, hdmf=3.4.7, pynwb=2.3.3

---
 allensdk/core/mouse_connectivity_cache.py     |   2 +-
 poetry.lock                                   | 309 ++++++++----------
 ...ements_py38-310.txt => poetry_py38-311.txt |   8 +-
 pyproject.toml                                |  13 +-
 requirements.txt                              | 119 +++++--
 5 files changed, 234 insertions(+), 217 deletions(-)
 rename requirements_py38-310.txt => poetry_py38-311.txt (85%)

diff --git a/allensdk/core/mouse_connectivity_cache.py b/allensdk/core/mouse_connectivity_cache.py
index 041db7724..9a94692db 100644
--- a/allensdk/core/mouse_connectivity_cache.py
+++ b/allensdk/core/mouse_connectivity_cache.py
@@ -481,7 +481,7 @@ def rank_structures(self, experiment_ids, is_injection, structure_ids=None, hemi
             this_experiment_unionizes = this_experiment_unionizes.sort_values(by=rank_on, ascending=False)
             this_experiment_unionizes = this_experiment_unionizes.loc[:, output_keys]
 
-            records = this_experiment_unionizes.to_dict('record')
+            records = this_experiment_unionizes.to_dict('records')
             if len(records) > n:
                 records = records[:n]
             results.append(records)
diff --git a/poetry.lock b/poetry.lock
index 9e1abf3b5..9fede1dc1 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -205,17 +205,17 @@ msgpack = "*"
 
 [[package]]
 name = "boto3"
-version = "1.28.8"
+version = "1.28.10"
 description = "The AWS SDK for Python"
 optional = false
 python-versions = ">= 3.7"
 files = [
-    {file = "boto3-1.28.8-py3-none-any.whl", hash = "sha256:7132ac3f3a9c28b84dcc344cfb439d37d2c5ab45f6b577358fc9aeba5d5aab63"},
-    {file = "boto3-1.28.8.tar.gz", hash = "sha256:cf88309d9b8cd9a2fb0c8049cb4b217b4e9dcb55bf670d6054b0bbe2eef25e57"},
+    {file = "boto3-1.28.10-py3-none-any.whl", hash = "sha256:67001b3f512cbe2e00e352c65fb443b504e5e388fee39d73bcc42da1ae87d9e3"},
+    {file = "boto3-1.28.10.tar.gz", hash = "sha256:cb8af03f553f1c7db7137bc897785baeeaa97b8fde483eb1cdb1f1ef3cec9cb7"},
 ]
 
 [package.dependencies]
-botocore = ">=1.31.8,<1.32.0"
+botocore = ">=1.31.10,<1.32.0"
 jmespath = ">=0.7.1,<2.0.0"
 s3transfer = ">=0.6.0,<0.7.0"
 
@@ -224,13 +224,13 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"]
 
 [[package]]
 name = "botocore"
-version = "1.31.8"
+version = "1.31.10"
 description = "Low-level, data-driven core of boto 3."
 optional = false
 python-versions = ">= 3.7"
 files = [
-    {file = "botocore-1.31.8-py3-none-any.whl", hash = "sha256:61ba7efaa6305c1928b9b3fbb6f780cbfbd762e19008d20c11ba52b47f20e1b0"},
-    {file = "botocore-1.31.8.tar.gz", hash = "sha256:092baa2168ae78080b0c28011527bfc11d8debd3767aa1e9a4ce8a91fd9943a2"},
+    {file = "botocore-1.31.10-py3-none-any.whl", hash = "sha256:a3bfd3627a490faedf37d79373d6957936d7720888ca85466e0471cb921e4557"},
+    {file = "botocore-1.31.10.tar.gz", hash = "sha256:736a9412f405d6985570c4a87b533c2396dd8d4042d8c7a0ca14e73d4f1bcf9d"},
 ]
 
 [package.dependencies]
@@ -254,13 +254,13 @@ files = [
 
 [[package]]
 name = "certifi"
-version = "2023.5.7"
+version = "2023.7.22"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "certifi-2023.5.7-py3-none-any.whl", hash = "sha256:c6c2e98f5c7869efca1f8916fed228dd91539f9f1b444c314c06eef02980c716"},
-    {file = "certifi-2023.5.7.tar.gz", hash = "sha256:0f0d56dc5a6ad56fd4ba36484d6cc34451e1c6548c61daad8c320169f91eddc7"},
+    {file = "certifi-2023.7.22-py3-none-any.whl", hash = "sha256:92d6037539857d8206b8f6ae472e8b77db8058fec5937a1ef3f54304089edbb9"},
+    {file = "certifi-2023.7.22.tar.gz", hash = "sha256:539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082"},
 ]
 
 [[package]]
@@ -507,45 +507,45 @@ files = [
 
 [[package]]
 name = "fonttools"
-version = "4.41.0"
+version = "4.41.1"
 description = "Tools to manipulate font files"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "fonttools-4.41.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:ba2a367ff478cd108d5319c0dc4fd4eb4ea3476dbfc45b00c45718e889cd9463"},
-    {file = "fonttools-4.41.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:69178674505ec81adf4af2a3bbacd0cb9a37ba7831bc3fca307f80e48ab2767b"},
-    {file = "fonttools-4.41.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:86edb95c4d1fe4fae2111d7e0c10c6e42b7790b377bcf1952303469eee5b52bb"},
-    {file = "fonttools-4.41.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:50f8bdb421270f71b54695c62785e300fab4bb6127be40bf9f3084962a0c3adb"},
-    {file = "fonttools-4.41.0-cp310-cp310-musllinux_1_1_aarch64.whl", hash = "sha256:c890061915e95b619c1d3cc3c107c6fb021406b701c0c24b03e74830d522f210"},
-    {file = "fonttools-4.41.0-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:b329ae7ce971b5c4148d6cdb8119c0ce4587265b2330d4f2f3776ef851bee020"},
-    {file = "fonttools-4.41.0-cp310-cp310-win32.whl", hash = "sha256:bc9e7b1e268be7a23fc66471b615c324e99c5db39ce8c49dd6dd8e962c7bc1b8"},
-    {file = "fonttools-4.41.0-cp310-cp310-win_amd64.whl", hash = "sha256:f3fe90dfb297bd8265238c06787911cd81c2cb89ac5b13e1c911928bdabfce0f"},
-    {file = "fonttools-4.41.0-cp311-cp311-macosx_10_9_universal2.whl", hash = "sha256:e38bd91eae257f36c2b7245c0278e9cd9d754f3a66b8d2b548c623ba66e387b6"},
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 [[package]]
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 ]
 
 [[package]]
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 [[package]]
 name = "pandas"
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 description = "Powerful data structures for data analysis, time series, and statistics"
 optional = false
 python-versions = ">=3.8"
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+    {file = "pandas-1.5.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:9f69c4029613de47816b1bb30ff5ac778686688751a5e9c99ad8c7031f6508e5"},
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+    {file = "pandas-1.5.3-cp39-cp39-win_amd64.whl", hash = "sha256:dfd681c5dc216037e0b0a2c821f5ed99ba9f03ebcf119c7dac0e9a7b960b9ec9"},
+    {file = "pandas-1.5.3.tar.gz", hash = "sha256:74a3fd7e5a7ec052f183273dc7b0acd3a863edf7520f5d3a1765c04ffdb3b0b1"},
 ]
 
 [package.dependencies]
@@ -1608,32 +1605,11 @@ numpy = [
     {version = ">=1.21.0", markers = "python_version >= \"3.10\""},
     {version = ">=1.23.2", markers = "python_version >= \"3.11\""},
 ]
-python-dateutil = ">=2.8.2"
+python-dateutil = ">=2.8.1"
 pytz = ">=2020.1"
-tzdata = ">=2022.1"
 
 [package.extras]
-all = ["PyQt5 (>=5.15.1)", "SQLAlchemy (>=1.4.16)", "beautifulsoup4 (>=4.9.3)", "bottleneck (>=1.3.2)", "brotlipy (>=0.7.0)", "fastparquet (>=0.6.3)", "fsspec (>=2021.07.0)", "gcsfs (>=2021.07.0)", "html5lib (>=1.1)", "hypothesis (>=6.34.2)", "jinja2 (>=3.0.0)", "lxml (>=4.6.3)", "matplotlib (>=3.6.1)", "numba (>=0.53.1)", "numexpr (>=2.7.3)", "odfpy (>=1.4.1)", "openpyxl (>=3.0.7)", "pandas-gbq (>=0.15.0)", "psycopg2 (>=2.8.6)", "pyarrow (>=7.0.0)", "pymysql (>=1.0.2)", "pyreadstat (>=1.1.2)", "pytest (>=7.3.2)", "pytest-asyncio (>=0.17.0)", "pytest-xdist (>=2.2.0)", "python-snappy (>=0.6.0)", "pyxlsb (>=1.0.8)", "qtpy (>=2.2.0)", "s3fs (>=2021.08.0)", "scipy (>=1.7.1)", "tables (>=3.6.1)", "tabulate (>=0.8.9)", "xarray (>=0.21.0)", "xlrd (>=2.0.1)", "xlsxwriter (>=1.4.3)", "zstandard (>=0.15.2)"]
-aws = ["s3fs (>=2021.08.0)"]
-clipboard = ["PyQt5 (>=5.15.1)", "qtpy (>=2.2.0)"]
-compression = ["brotlipy (>=0.7.0)", "python-snappy (>=0.6.0)", "zstandard (>=0.15.2)"]
-computation = ["scipy (>=1.7.1)", "xarray (>=0.21.0)"]
-excel = ["odfpy (>=1.4.1)", "openpyxl (>=3.0.7)", "pyxlsb (>=1.0.8)", "xlrd (>=2.0.1)", "xlsxwriter (>=1.4.3)"]
-feather = ["pyarrow (>=7.0.0)"]
-fss = ["fsspec (>=2021.07.0)"]
-gcp = ["gcsfs (>=2021.07.0)", "pandas-gbq (>=0.15.0)"]
-hdf5 = ["tables (>=3.6.1)"]
-html = ["beautifulsoup4 (>=4.9.3)", "html5lib (>=1.1)", "lxml (>=4.6.3)"]
-mysql = ["SQLAlchemy (>=1.4.16)", "pymysql (>=1.0.2)"]
-output-formatting = ["jinja2 (>=3.0.0)", "tabulate (>=0.8.9)"]
-parquet = ["pyarrow (>=7.0.0)"]
-performance = ["bottleneck (>=1.3.2)", "numba (>=0.53.1)", "numexpr (>=2.7.1)"]
-plot = ["matplotlib (>=3.6.1)"]
-postgresql = ["SQLAlchemy (>=1.4.16)", "psycopg2 (>=2.8.6)"]
-spss = ["pyreadstat (>=1.1.2)"]
-sql-other = ["SQLAlchemy (>=1.4.16)"]
-test = ["hypothesis (>=6.34.2)", "pytest (>=7.3.2)", "pytest-asyncio (>=0.17.0)", "pytest-xdist (>=2.2.0)"]
-xml = ["lxml (>=4.6.3)"]
+test = ["hypothesis (>=5.5.3)", "pytest (>=6.0)", "pytest-xdist (>=1.31)"]
 
 [[package]]
 name = "patsy"
@@ -1833,21 +1809,21 @@ typing-extensions = "*"
 
 [[package]]
 name = "pynwb"
-version = "2.3.3"
+version = "2.2.0"
 description = "Package for working with Neurodata stored in the NWB format"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "pynwb-2.3.3-py3-none-any.whl", hash = "sha256:28b7448b627483e64cf5efaa066735c9b6944045507b7e117e05bee59e9bd9f2"},
-    {file = "pynwb-2.3.3.tar.gz", hash = "sha256:a072815277912fdacdd67f10edfd763e05fe6016a5353b67dcc837d525daee14"},
+    {file = "pynwb-2.2.0-py3-none-any.whl", hash = "sha256:d6a640efa3bf2614be88e44b35e788392d0b7a86f9d6d0719809ba374243b90f"},
+    {file = "pynwb-2.2.0.tar.gz", hash = "sha256:7a1a08688237cd7ff41daa43b625903b3068f7327a928d379b1c43bbdf37555d"},
 ]
 
 [package.dependencies]
-h5py = ">=2.10"
-hdmf = ">=3.5.4"
-numpy = ">=1.16"
-pandas = ">=1.1.5"
-python-dateutil = ">=2.7.3"
+h5py = ">=2.10,<4"
+hdmf = ">=3.4.2,<4"
+numpy = ">=1.16,<1.24"
+pandas = ">=1.1.5,<2"
+python-dateutil = ">=2.7.3,<3"
 setuptools = "*"
 
 [[package]]
@@ -2729,17 +2705,6 @@ files = [
     {file = "typing_extensions-4.7.1.tar.gz", hash = "sha256:b75ddc264f0ba5615db7ba217daeb99701ad295353c45f9e95963337ceeeffb2"},
 ]
 
-[[package]]
-name = "tzdata"
-version = "2023.3"
-description = "Provider of IANA time zone data"
-optional = false
-python-versions = ">=2"
-files = [
-    {file = "tzdata-2023.3-py2.py3-none-any.whl", hash = "sha256:7e65763eef3120314099b6939b5546db7adce1e7d6f2e179e3df563c70511eda"},
-    {file = "tzdata-2023.3.tar.gz", hash = "sha256:11ef1e08e54acb0d4f95bdb1be05da659673de4acbd21bf9c69e94cc5e907a3a"},
-]
-
 [[package]]
 name = "urllib3"
 version = "1.26.16"
@@ -2758,17 +2723,17 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
 
 [[package]]
 name = "wheel"
-version = "0.40.0"
+version = "0.41.0"
 description = "A built-package format for Python"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "wheel-0.40.0-py3-none-any.whl", hash = "sha256:d236b20e7cb522daf2390fa84c55eea81c5c30190f90f29ae2ca1ad8355bf247"},
-    {file = "wheel-0.40.0.tar.gz", hash = "sha256:cd1196f3faee2b31968d626e1731c94f99cbdb67cf5a46e4f5656cbee7738873"},
+    {file = "wheel-0.41.0-py3-none-any.whl", hash = "sha256:7e9be3bbd0078f6147d82ed9ed957e323e7708f57e134743d2edef3a7b7972a9"},
+    {file = "wheel-0.41.0.tar.gz", hash = "sha256:55a0f0a5a84869bce5ba775abfd9c462e3a6b1b7b7ec69d72c0b83d673a5114d"},
 ]
 
 [package.extras]
-test = ["pytest (>=6.0.0)"]
+test = ["pytest (>=6.0.0)", "setuptools (>=65)"]
 
 [[package]]
 name = "xarray"
@@ -2899,4 +2864,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.8,<=3.11"
-content-hash = "91ec54d6d7018a08f60de2b9fb7b9e9a0ece3caf2f3502d9ccf32b004f15daca"
+content-hash = "8cc854451fa4be372ba6661605aaff072d94f6054ada51572281e0fef4ff100b"
diff --git a/requirements_py38-310.txt b/poetry_py38-311.txt
similarity index 85%
rename from requirements_py38-310.txt
rename to poetry_py38-311.txt
index 159ed36d9..2de15f8ab 100644
--- a/requirements_py38-310.txt
+++ b/poetry_py38-311.txt
@@ -1,9 +1,9 @@
 psycopg2-binary
-hdmf<=3.6.1
+hdmf<=3.4.7
 h5py
 matplotlib
-numpy<1.25
-pandas
+numpy<1.24
+pandas==1.5.3
 jinja2
 scipy<1.11
 six
@@ -19,7 +19,7 @@ simpleitk
 argschema
 glymur
 xarray<2023.2.0
-pynwb
+pynwb<=2.3.3
 tables
 seaborn
 aiohttp
diff --git a/pyproject.toml b/pyproject.toml
index 4232af91b..35924388c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -6,13 +6,13 @@ authors = ["Allen Institute for Brain Science"]
 readme = "README.md"
 
 [tool.poetry.dependencies]
-python = ">=3.8,<=3.11"
+python = ">=3.8,<3.12"
 psycopg2-binary = "^2.9.6"
-hdmf = "^3.7.0"
+hdmf = "<=3.4.7"
 h5py = "^3.9.0"
 matplotlib = "^3.7.2"
-numpy = "<1.25"
-pandas = "^2.0.3"
+numpy = "<1.24"
+pandas = "1.5.3"
 jinja2 = "^3.1.2"
 scipy = "<1.11"
 six = "^1.16.0"
@@ -28,20 +28,19 @@ simpleitk = "^2.2.1"
 argschema = "^3.0.4"
 glymur = "^0.12.8"
 xarray = "<2023.2.0"
-pynwb = "^2.3.3"
+pynwb = "<=2.3.3"
 tables = "^3.8.0"
 seaborn = "^0.12.2"
 aiohttp = "^3.8.5"
 nest-asyncio = "^1.5.6"
 tqdm = "^4.65.0"
 ndx-events = "^0.2.0"
-boto3 = "^1.28.8"
+boto3 = "^1.28.10"
 semver = "^3.0.1"
 cachetools = "^5.3.1"
 sqlalchemy = "^2.0.19"
 python-dateutil = "^2.8.2"
 
-
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"
diff --git a/requirements.txt b/requirements.txt
index 8e1ed26e9..14c6f1b08 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,33 +1,86 @@
-psycopg2-binary
-hdmf<=3.4.7
-h5py
-matplotlib>=1.4.3,<3.4.3
-numpy
-pandas>=1.1.5
-jinja2>=3.0.0
-scipy>=1.4.0,<2.0.0
-six>=1.9.0,<2.0.0
-pynrrd>=0.2.1,<1.0.0
-future >= 0.14.3,<1.0.0
-requests<3.0.0
-requests-toolbelt<1.0.0
-simplejson>=3.10.0,<4.0.0
-scikit-image>=0.14.0
-scikit-build<1.0.0
-statsmodels
-simpleitk>=2.0.2,<3.0.0
-argschema>=3.0.1,<4.0.0
-glymur==0.8.19
-xarray
-pynwb
-tables
-seaborn<1.0.0
-aiohttp==3.7.4
-nest_asyncio
-tqdm>=4.27
-ndx-events<=0.2.0
-boto3==1.17.21
-semver
-cachetools>=4.2.1,<5.0.0
-sqlalchemy
-python-dateutil
+aiohttp==3.8.5 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+aiosignal==1.3.1 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+argschema==3.0.4 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+async-timeout==4.0.2 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+attrs==23.1.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+blosc2==2.0.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+boto3==1.28.10 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+botocore==1.31.10 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+cachetools==5.3.1 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+certifi==2023.7.22 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+charset-normalizer==3.2.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+colorama==0.4.6 ; python_version >= "3.8" and python_full_version <= "3.11.0" and platform_system == "Windows"
+contourpy==1.1.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+cycler==0.11.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+cython==3.0.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+distro==1.8.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+fonttools==4.41.1 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+frozenlist==1.4.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+future==0.18.3 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+glymur==0.12.8 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+greenlet==2.0.2 ; python_version >= "3.8" and python_full_version <= "3.11.0" and (platform_machine == "win32" or platform_machine == "WIN32" or platform_machine == "AMD64" or platform_machine == "amd64" or platform_machine == "x86_64" or platform_machine == "ppc64le" or platform_machine == "aarch64")
+h5py==3.9.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+hdmf==3.4.7 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+idna==3.4 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+imageio==2.31.1 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+importlib-resources==6.0.0 ; python_version >= "3.8" and python_version < "3.10"
+jinja2==3.1.2 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+jmespath==1.0.1 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+jsonschema-specifications==2023.7.1 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+jsonschema==4.18.4 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+kiwisolver==1.4.4 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+lazy-loader==0.3 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+lxml==4.9.3 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+markupsafe==2.1.3 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+marshmallow==3.20.1 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+matplotlib==3.7.2 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+msgpack==1.0.5 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+multidict==6.0.4 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+ndx-events==0.2.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+nest-asyncio==1.5.6 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+networkx==3.1 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+nptyping==2.5.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+numexpr==2.8.4 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+numpy==1.23.5 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+packaging==23.1 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+pandas==1.5.3 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+patsy==0.5.3 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+pillow==10.0.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+pkgutil-resolve-name==1.3.10 ; python_version >= "3.8" and python_version < "3.9"
+psycopg2-binary==2.9.6 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+py-cpuinfo==9.0.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+pynrrd==1.0.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+pynwb==2.2.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+pyparsing==3.0.9 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+python-dateutil==2.8.2 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+pytz==2023.3 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+pywavelets==1.4.1 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+pyyaml==6.0.1 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+referencing==0.30.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+requests-toolbelt==1.0.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+requests==2.31.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+rpds-py==0.9.2 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+ruamel-yaml-clib==0.2.7 ; platform_python_implementation == "CPython" and python_full_version <= "3.11.0" and python_version >= "3.8"
+ruamel-yaml==0.17.32 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+s3transfer==0.6.1 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+scikit-build==0.17.6 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+scikit-image==0.21.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+scipy==1.10.1 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+seaborn==0.12.2 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+semver==3.0.1 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+setuptools==68.0.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+simpleitk==2.2.1 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+simplejson==3.19.1 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+six==1.16.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+sqlalchemy==2.0.19 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+statsmodels==0.14.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+tables==3.8.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+tifffile==2023.7.10 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11"
+tqdm==4.65.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+typing-extensions==4.7.1 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+urllib3==1.26.16 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+wheel==0.41.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+xarray==2023.1.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+yarl==1.9.2 ; python_version >= "3.8" and python_full_version <= "3.11.0"
+zipp==3.16.2 ; python_version >= "3.8" and python_version < "3.10"

From 88c8c044ecd7b48cd946e89d34d69c368a5dcf2e Mon Sep 17 00:00:00 2001
From: Mike Huang <huangjmike@gmail.com>
Date: Mon, 24 Jul 2023 16:25:25 -0700
Subject: [PATCH 09/15] add python 3.11 to github actions

---
 .github/workflows/github-actions-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/github-actions-ci.yml b/.github/workflows/github-actions-ci.yml
index 887d1ce86..c4f656027 100644
--- a/.github/workflows/github-actions-ci.yml
+++ b/.github/workflows/github-actions-ci.yml
@@ -44,7 +44,7 @@ jobs:
     strategy:
       matrix:
         os: ["macos-latest", "windows-latest", "ubuntu-latest"]
-        python-version: ["3.7", "3.8", "3.9"]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
       fail-fast: false
     defaults:
       run:

From 844f5dd3f528cf4e45394b6149e61aa3021e0c7d Mon Sep 17 00:00:00 2001
From: Mike Huang <huangjmike@gmail.com>
Date: Mon, 24 Jul 2023 16:26:51 -0700
Subject: [PATCH 10/15] add Python 3.11 in setup.py

---
 setup.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/setup.py b/setup.py
index 452134ef8..dccb6e316 100644
--- a/setup.py
+++ b/setup.py
@@ -90,6 +90,8 @@ def prepend_find_packages(*roots):
         "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",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
     ],
 )

From c1915de2a16d8894f8f3021ed04755cf38d603f7 Mon Sep 17 00:00:00 2001
From: Mike Huang <huangjmike@gmail.com>
Date: Wed, 9 Aug 2023 14:57:38 -0700
Subject: [PATCH 11/15] remove python3.7 from setup metadata

---
 setup.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/setup.py b/setup.py
index dccb6e316..5dda2bbb0 100644
--- a/setup.py
+++ b/setup.py
@@ -87,7 +87,6 @@ def prepend_find_packages(*roots):
         "License :: Other/Proprietary License", # Allen Institute License
         "Natural Language :: English",
         "Operating System :: OS Independent",
-        "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",

From f17b449ce96a4898784f9596cd9bec00f67c0a16 Mon Sep 17 00:00:00 2001
From: Mike Huang <huangjmike@gmail.com>
Date: Wed, 9 Aug 2023 23:07:57 -0700
Subject: [PATCH 12/15] remove poetry related setup config

---
 poetry.lock         | 2867 -------------------------------------------
 poetry_py38-311.txt |   33 -
 pyproject.toml      |   46 -
 requirements.txt    |  119 +-
 setup.cfg           |    9 -
 setup.py            |    3 +
 6 files changed, 36 insertions(+), 3041 deletions(-)
 delete mode 100644 poetry.lock
 delete mode 100644 poetry_py38-311.txt
 delete mode 100644 pyproject.toml

diff --git a/poetry.lock b/poetry.lock
deleted file mode 100644
index 9fede1dc1..000000000
--- a/poetry.lock
+++ /dev/null
@@ -1,2867 +0,0 @@
-# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand.
-
-[[package]]
-name = "aiohttp"
-version = "3.8.5"
-description = "Async http client/server framework (asyncio)"
-optional = false
-python-versions = ">=3.6"
-files = [
-    {file = "aiohttp-3.8.5-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:a94159871304770da4dd371f4291b20cac04e8c94f11bdea1c3478e557fbe0d8"},
-    {file = "aiohttp-3.8.5-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:13bf85afc99ce6f9ee3567b04501f18f9f8dbbb2ea11ed1a2e079670403a7c84"},
-    {file = "aiohttp-3.8.5-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:2ce2ac5708501afc4847221a521f7e4b245abf5178cf5ddae9d5b3856ddb2f3a"},
-    {file = "aiohttp-3.8.5-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:96943e5dcc37a6529d18766597c491798b7eb7a61d48878611298afc1fca946c"},
-    {file = "aiohttp-3.8.5-cp310-cp310-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:2ad5c3c4590bb3cc28b4382f031f3783f25ec223557124c68754a2231d989e2b"},
-    {file = "aiohttp-3.8.5-cp310-cp310-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:0c413c633d0512df4dc7fd2373ec06cc6a815b7b6d6c2f208ada7e9e93a5061d"},
-    {file = "aiohttp-3.8.5-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:df72ac063b97837a80d80dec8d54c241af059cc9bb42c4de68bd5b61ceb37caa"},
-    {file = "aiohttp-3.8.5-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:c48c5c0271149cfe467c0ff8eb941279fd6e3f65c9a388c984e0e6cf57538e14"},
-    {file = "aiohttp-3.8.5-cp310-cp310-musllinux_1_1_aarch64.whl", hash = "sha256:368a42363c4d70ab52c2c6420a57f190ed3dfaca6a1b19afda8165ee16416a82"},
-    {file = "aiohttp-3.8.5-cp310-cp310-musllinux_1_1_i686.whl", hash = "sha256:7607ec3ce4993464368505888af5beb446845a014bc676d349efec0e05085905"},
-    {file = "aiohttp-3.8.5-cp310-cp310-musllinux_1_1_ppc64le.whl", hash = "sha256:0d21c684808288a98914e5aaf2a7c6a3179d4df11d249799c32d1808e79503b5"},
-    {file = "aiohttp-3.8.5-cp310-cp310-musllinux_1_1_s390x.whl", hash = "sha256:312fcfbacc7880a8da0ae8b6abc6cc7d752e9caa0051a53d217a650b25e9a691"},
-    {file = "aiohttp-3.8.5-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:ad093e823df03bb3fd37e7dec9d4670c34f9e24aeace76808fc20a507cace825"},
-    {file = "aiohttp-3.8.5-cp310-cp310-win32.whl", hash = "sha256:33279701c04351a2914e1100b62b2a7fdb9a25995c4a104259f9a5ead7ed4802"},
-    {file = "aiohttp-3.8.5-cp310-cp310-win_amd64.whl", hash = "sha256:6e4a280e4b975a2e7745573e3fc9c9ba0d1194a3738ce1cbaa80626cc9b4f4df"},
-    {file = "aiohttp-3.8.5-cp311-cp311-macosx_10_9_universal2.whl", hash = "sha256:ae871a964e1987a943d83d6709d20ec6103ca1eaf52f7e0d36ee1b5bebb8b9b9"},
-    {file = "aiohttp-3.8.5-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:461908b2578955045efde733719d62f2b649c404189a09a632d245b445c9c975"},
-    {file = "aiohttp-3.8.5-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:72a860c215e26192379f57cae5ab12b168b75db8271f111019509a1196dfc780"},
-    {file = "aiohttp-3.8.5-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:cc14be025665dba6202b6a71cfcdb53210cc498e50068bc088076624471f8bb9"},
-    {file = "aiohttp-3.8.5-cp311-cp311-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:8af740fc2711ad85f1a5c034a435782fbd5b5f8314c9a3ef071424a8158d7f6b"},
-    {file = "aiohttp-3.8.5-cp311-cp311-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:841cd8233cbd2111a0ef0a522ce016357c5e3aff8a8ce92bcfa14cef890d698f"},
-    {file = "aiohttp-3.8.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:5ed1c46fb119f1b59304b5ec89f834f07124cd23ae5b74288e364477641060ff"},
-    {file = "aiohttp-3.8.5-cp311-cp311-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:84f8ae3e09a34f35c18fa57f015cc394bd1389bce02503fb30c394d04ee6b938"},
-    {file = "aiohttp-3.8.5-cp311-cp311-musllinux_1_1_aarch64.whl", hash = "sha256:62360cb771707cb70a6fd114b9871d20d7dd2163a0feafe43fd115cfe4fe845e"},
-    {file = "aiohttp-3.8.5-cp311-cp311-musllinux_1_1_i686.whl", hash = "sha256:23fb25a9f0a1ca1f24c0a371523546366bb642397c94ab45ad3aedf2941cec6a"},
-    {file = "aiohttp-3.8.5-cp311-cp311-musllinux_1_1_ppc64le.whl", hash = "sha256:b0ba0d15164eae3d878260d4c4df859bbdc6466e9e6689c344a13334f988bb53"},
-    {file = "aiohttp-3.8.5-cp311-cp311-musllinux_1_1_s390x.whl", hash = "sha256:5d20003b635fc6ae3f96d7260281dfaf1894fc3aa24d1888a9b2628e97c241e5"},
-    {file = "aiohttp-3.8.5-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:0175d745d9e85c40dcc51c8f88c74bfbaef9e7afeeeb9d03c37977270303064c"},
-    {file = "aiohttp-3.8.5-cp311-cp311-win32.whl", hash = "sha256:2e1b1e51b0774408f091d268648e3d57f7260c1682e7d3a63cb00d22d71bb945"},
-    {file = "aiohttp-3.8.5-cp311-cp311-win_amd64.whl", hash = "sha256:043d2299f6dfdc92f0ac5e995dfc56668e1587cea7f9aa9d8a78a1b6554e5755"},
-    {file = "aiohttp-3.8.5-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:cae533195e8122584ec87531d6df000ad07737eaa3c81209e85c928854d2195c"},
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-    {file = "yarl-1.9.2.tar.gz", hash = "sha256:04ab9d4b9f587c06d801c2abfe9317b77cdf996c65a90d5e84ecc45010823571"},
-]
-
-[package.dependencies]
-idna = ">=2.0"
-multidict = ">=4.0"
-
-[[package]]
-name = "zipp"
-version = "3.16.2"
-description = "Backport of pathlib-compatible object wrapper for zip files"
-optional = false
-python-versions = ">=3.8"
-files = [
-    {file = "zipp-3.16.2-py3-none-any.whl", hash = "sha256:679e51dd4403591b2d6838a48de3d283f3d188412a9782faadf845f298736ba0"},
-    {file = "zipp-3.16.2.tar.gz", hash = "sha256:ebc15946aa78bd63458992fc81ec3b6f7b1e92d51c35e6de1c3804e73b799147"},
-]
-
-[package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
-
-[metadata]
-lock-version = "2.0"
-python-versions = ">=3.8,<=3.11"
-content-hash = "8cc854451fa4be372ba6661605aaff072d94f6054ada51572281e0fef4ff100b"
diff --git a/poetry_py38-311.txt b/poetry_py38-311.txt
deleted file mode 100644
index 2de15f8ab..000000000
--- a/poetry_py38-311.txt
+++ /dev/null
@@ -1,33 +0,0 @@
-psycopg2-binary
-hdmf<=3.4.7
-h5py
-matplotlib
-numpy<1.24
-pandas==1.5.3
-jinja2
-scipy<1.11
-six
-pynrrd
-future
-requests
-requests-toolbelt
-simplejson
-scikit-image
-scikit-build
-statsmodels
-simpleitk
-argschema
-glymur
-xarray<2023.2.0
-pynwb<=2.3.3
-tables
-seaborn
-aiohttp
-nest_asyncio
-tqdm
-ndx-events
-boto3
-semver
-cachetools
-sqlalchemy
-python-dateutil
diff --git a/pyproject.toml b/pyproject.toml
deleted file mode 100644
index 35924388c..000000000
--- a/pyproject.toml
+++ /dev/null
@@ -1,46 +0,0 @@
-[tool.poetry]
-name = "allensdk"
-version = "2.15.2"
-description = "core libraries for the allensdk."
-authors = ["Allen Institute for Brain Science"]
-readme = "README.md"
-
-[tool.poetry.dependencies]
-python = ">=3.8,<3.12"
-psycopg2-binary = "^2.9.6"
-hdmf = "<=3.4.7"
-h5py = "^3.9.0"
-matplotlib = "^3.7.2"
-numpy = "<1.24"
-pandas = "1.5.3"
-jinja2 = "^3.1.2"
-scipy = "<1.11"
-six = "^1.16.0"
-pynrrd = "^1.0.0"
-future = "^0.18.3"
-requests = "^2.31.0"
-requests-toolbelt = "^1.0.0"
-simplejson = "^3.19.1"
-scikit-image = "^0.21.0"
-scikit-build = "^0.17.6"
-statsmodels = "^0.14.0"
-simpleitk = "^2.2.1"
-argschema = "^3.0.4"
-glymur = "^0.12.8"
-xarray = "<2023.2.0"
-pynwb = "<=2.3.3"
-tables = "^3.8.0"
-seaborn = "^0.12.2"
-aiohttp = "^3.8.5"
-nest-asyncio = "^1.5.6"
-tqdm = "^4.65.0"
-ndx-events = "^0.2.0"
-boto3 = "^1.28.10"
-semver = "^3.0.1"
-cachetools = "^5.3.1"
-sqlalchemy = "^2.0.19"
-python-dateutil = "^2.8.2"
-
-[build-system]
-requires = ["poetry-core"]
-build-backend = "poetry.core.masonry.api"
diff --git a/requirements.txt b/requirements.txt
index 14c6f1b08..2de15f8ab 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,86 +1,33 @@
-aiohttp==3.8.5 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-aiosignal==1.3.1 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-argschema==3.0.4 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-async-timeout==4.0.2 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-attrs==23.1.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-blosc2==2.0.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-boto3==1.28.10 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-botocore==1.31.10 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-cachetools==5.3.1 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-certifi==2023.7.22 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-charset-normalizer==3.2.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-colorama==0.4.6 ; python_version >= "3.8" and python_full_version <= "3.11.0" and platform_system == "Windows"
-contourpy==1.1.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-cycler==0.11.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-cython==3.0.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-distro==1.8.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-fonttools==4.41.1 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-frozenlist==1.4.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-future==0.18.3 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-glymur==0.12.8 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-greenlet==2.0.2 ; python_version >= "3.8" and python_full_version <= "3.11.0" and (platform_machine == "win32" or platform_machine == "WIN32" or platform_machine == "AMD64" or platform_machine == "amd64" or platform_machine == "x86_64" or platform_machine == "ppc64le" or platform_machine == "aarch64")
-h5py==3.9.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-hdmf==3.4.7 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-idna==3.4 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-imageio==2.31.1 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-importlib-resources==6.0.0 ; python_version >= "3.8" and python_version < "3.10"
-jinja2==3.1.2 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-jmespath==1.0.1 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-jsonschema-specifications==2023.7.1 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-jsonschema==4.18.4 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-kiwisolver==1.4.4 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-lazy-loader==0.3 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-lxml==4.9.3 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-markupsafe==2.1.3 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-marshmallow==3.20.1 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-matplotlib==3.7.2 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-msgpack==1.0.5 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-multidict==6.0.4 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-ndx-events==0.2.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-nest-asyncio==1.5.6 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-networkx==3.1 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-nptyping==2.5.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-numexpr==2.8.4 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-numpy==1.23.5 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-packaging==23.1 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-pandas==1.5.3 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-patsy==0.5.3 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-pillow==10.0.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-pkgutil-resolve-name==1.3.10 ; python_version >= "3.8" and python_version < "3.9"
-psycopg2-binary==2.9.6 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-py-cpuinfo==9.0.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-pynrrd==1.0.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-pynwb==2.2.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-pyparsing==3.0.9 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-python-dateutil==2.8.2 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-pytz==2023.3 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-pywavelets==1.4.1 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-pyyaml==6.0.1 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-referencing==0.30.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-requests-toolbelt==1.0.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-requests==2.31.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-rpds-py==0.9.2 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-ruamel-yaml-clib==0.2.7 ; platform_python_implementation == "CPython" and python_full_version <= "3.11.0" and python_version >= "3.8"
-ruamel-yaml==0.17.32 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-s3transfer==0.6.1 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-scikit-build==0.17.6 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-scikit-image==0.21.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-scipy==1.10.1 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-seaborn==0.12.2 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-semver==3.0.1 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-setuptools==68.0.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-simpleitk==2.2.1 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-simplejson==3.19.1 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-six==1.16.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-sqlalchemy==2.0.19 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-statsmodels==0.14.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-tables==3.8.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-tifffile==2023.7.10 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11"
-tqdm==4.65.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-typing-extensions==4.7.1 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-urllib3==1.26.16 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-wheel==0.41.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-xarray==2023.1.0 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-yarl==1.9.2 ; python_version >= "3.8" and python_full_version <= "3.11.0"
-zipp==3.16.2 ; python_version >= "3.8" and python_version < "3.10"
+psycopg2-binary
+hdmf<=3.4.7
+h5py
+matplotlib
+numpy<1.24
+pandas==1.5.3
+jinja2
+scipy<1.11
+six
+pynrrd
+future
+requests
+requests-toolbelt
+simplejson
+scikit-image
+scikit-build
+statsmodels
+simpleitk
+argschema
+glymur
+xarray<2023.2.0
+pynwb<=2.3.3
+tables
+seaborn
+aiohttp
+nest_asyncio
+tqdm
+ndx-events
+boto3
+semver
+cachetools
+sqlalchemy
+python-dateutil
diff --git a/setup.cfg b/setup.cfg
index 1d0afbece..52102fb8b 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -4,15 +4,6 @@ author = David Feng
 author-email = davidf@alleninstitute.org
 summary = Core libraries for the allensdk.
 description-file = README.md
-classifier = 
-	Development Status :: 3 - Alpha',
-	Intended Audience :: Science/Research',
-	Natural Language :: English',
-	Operating System :: OS Independent',
-	Programming Language :: Python
-	Programming Language :: Python :: 2
-	Programming Language :: Python :: 2.7
-	Topic :: Scientific/Engineering :: Bio-Informatics
 
 [build_sphinx]
 source-dir = .
diff --git a/setup.py b/setup.py
index 5dda2bbb0..a9d7508c2 100644
--- a/setup.py
+++ b/setup.py
@@ -87,6 +87,9 @@ def prepend_find_packages(*roots):
         "License :: Other/Proprietary License", # Allen Institute License
         "Natural Language :: English",
         "Operating System :: OS Independent",
+        "Programming Language :: Python",
+        "Programming Language :: Python :: 3",
+        'Programming Language :: Python :: 3 :: Only',
         "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",

From a20e811ceb4c5f8c954d1d1567bd60aab0be2bd7 Mon Sep 17 00:00:00 2001
From: Mike Huang <huangjmike@gmail.com>
Date: Thu, 10 Aug 2023 09:09:58 -0700
Subject: [PATCH 13/15] remove scikit-learn from test-requirements

---
 test_requirements.txt | 1 -
 1 file changed, 1 deletion(-)

diff --git a/test_requirements.txt b/test_requirements.txt
index dbacc24a6..eca280c5c 100644
--- a/test_requirements.txt
+++ b/test_requirements.txt
@@ -6,7 +6,6 @@ pytest-xdist>=1.14,<2.0.0
 pytest-mock>=1.5.0,<3.0.0
 mock>=1.0.1,<5.0.0
 coverage>=3.7.1,<6.0.0
-scikit-learn<1.0.0
 moto==3.0.7
 # these overlap with requirements specified in doc_requirements. As long as they are needed, these specifications must be kept in sync
 # TODO: see if we can avoid duplicating these requirements - this will involved surveying CI

From ec8765cbc5b8f21b97be4d71ef0b37598cb9ac34 Mon Sep 17 00:00:00 2001
From: Mike Huang <huangjmike@gmail.com>
Date: Thu, 10 Aug 2023 09:17:32 -0700
Subject: [PATCH 14/15] unpin test dependencies

---
 test_requirements.txt | 33 ++++++++++++++++-----------------
 1 file changed, 16 insertions(+), 17 deletions(-)

diff --git a/test_requirements.txt b/test_requirements.txt
index eca280c5c..86fc36127 100644
--- a/test_requirements.txt
+++ b/test_requirements.txt
@@ -1,19 +1,18 @@
-pytest>=4.4.0,<6.0.0
-pytest-cov>=2.6.1,<3.0.0
-pytest-cover>=3.0.0,<4.0.0
-pytest-pep8>=1.0.6,<2.0.0
-pytest-xdist>=1.14,<2.0.0
-pytest-mock>=1.5.0,<3.0.0
-mock>=1.0.1,<5.0.0
-coverage>=3.7.1,<6.0.0
-moto==3.0.7
+pytest
+pytest-cov
+pytest-cover
+pytest-pep8
+pytest-xdist
+pytest-mock
+mock
+coverage
+moto
 # these overlap with requirements specified in doc_requirements. As long as they are needed, these specifications must be kept in sync
 # TODO: see if we can avoid duplicating these requirements - this will involved surveying CI
-pep8==1.7.0,<2.0.0
-flake8>=1.5.0,<4.0.0
-pylint>=1.5.4,<3.0.0
-jinja2>=2.7.3,<2.12.0
-numpydoc>=0.6.0,<1.0.0
-jupyter>=1.0.0,<2.0.0
-markupsafe==2.0.1
-pywinpty==2.0.2; python_version <= '3.6' and sys_platform == 'win32'
\ No newline at end of file
+pep8
+flake8
+pylint
+jinja2>=2.7.3
+numpydoc
+jupyter
+markupsafe
\ No newline at end of file

From 86b8c5732ea03e26475bedebbf900b6ce0273d3f Mon Sep 17 00:00:00 2001
From: Mike Huang <huangjmike@gmail.com>
Date: Thu, 10 Aug 2023 09:25:53 -0700
Subject: [PATCH 15/15] repin some test dependencies

---
 test_requirements.txt | 23 ++++++++++++-----------
 1 file changed, 12 insertions(+), 11 deletions(-)

diff --git a/test_requirements.txt b/test_requirements.txt
index 86fc36127..31fafefad 100644
--- a/test_requirements.txt
+++ b/test_requirements.txt
@@ -3,16 +3,17 @@ pytest-cov
 pytest-cover
 pytest-pep8
 pytest-xdist
-pytest-mock
-mock
-coverage
-moto
+pytest-mock>=1.5.0,<3.0.0
+mock>=1.0.1,<5.0.0
+coverage>=3.7.1,<6.0.0
+moto==3.0.7
 # these overlap with requirements specified in doc_requirements. As long as they are needed, these specifications must be kept in sync
 # TODO: see if we can avoid duplicating these requirements - this will involved surveying CI
-pep8
-flake8
-pylint
-jinja2>=2.7.3
-numpydoc
-jupyter
-markupsafe
\ No newline at end of file
+pep8==1.7.0,<2.0.0
+flake8>=1.5.0,<4.0.0
+pylint>=1.5.4,<3.0.0
+jinja2>=2.7.3,<2.12.0
+numpydoc>=0.6.0,<1.0.0
+jupyter>=1.0.0,<2.0.0
+markupsafe==2.0.1
+pywinpty==2.0.2; python_version <= '3.6' and sys_platform == 'win32'
\ No newline at end of file