figpack 0.2.15__tar.gz → 0.2.16__tar.gz

{figpack-0.2.15/figpack.egg-info → figpack-0.2.16}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: figpack
-Version: 0.2.15
+Version: 0.2.16
 Summary: A Python package for creating shareable, interactive visualizations in the browser
 Author-email: Jeremy Magland <jmagland@flatironinstitute.org>
 License: Apache-2.0
@@ -25,7 +25,7 @@ Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy
-Requires-Dist: zarr<3
+Requires-Dist: zarr
 Requires-Dist: requests
 Requires-Dist: psutil
 Provides-Extra: test
@@ -37,6 +37,25 @@ Requires-Dist: matplotlib; extra == "test"
 Requires-Dist: plotly; extra == "test"
 Requires-Dist: Pillow; extra == "test"
 Requires-Dist: pandas; extra == "test"
+Provides-Extra: test-zarr2
+Requires-Dist: pytest>=7.0; extra == "test-zarr2"
+Requires-Dist: pytest-cov>=4.0; extra == "test-zarr2"
+Requires-Dist: pytest-mock>=3.10; extra == "test-zarr2"
+Requires-Dist: spikeinterface; extra == "test-zarr2"
+Requires-Dist: matplotlib; extra == "test-zarr2"
+Requires-Dist: plotly; extra == "test-zarr2"
+Requires-Dist: Pillow; extra == "test-zarr2"
+Requires-Dist: pandas; extra == "test-zarr2"
+Requires-Dist: zarr<3; extra == "test-zarr2"
+Provides-Extra: test-zarr3
+Requires-Dist: pytest>=7.0; extra == "test-zarr3"
+Requires-Dist: pytest-cov>=4.0; extra == "test-zarr3"
+Requires-Dist: pytest-mock>=3.10; extra == "test-zarr3"
+Requires-Dist: matplotlib; extra == "test-zarr3"
+Requires-Dist: plotly; extra == "test-zarr3"
+Requires-Dist: Pillow; extra == "test-zarr3"
+Requires-Dist: pandas; extra == "test-zarr3"
+Requires-Dist: zarr>=3; extra == "test-zarr3"
 Provides-Extra: dev
 Requires-Dist: pytest>=7.0; extra == "dev"
 Requires-Dist: pytest-cov>=4.0; extra == "dev"

{figpack-0.2.15 → figpack-0.2.16}/figpack/__init__.py

@@ -2,10 +2,11 @@
 figpack - A Python package for creating shareable, interactive visualizations in the browser
 """
 
-__version__ = "0.2.15"
+__version__ = "0.2.16"
 
 from .cli import view_figure
 from .core import FigpackView, FigpackExtension, ExtensionRegistry, ExtensionView
+from .core.zarr import Group
 
 __all__ = [
     "view_figure",
@@ -13,4 +14,5 @@ __all__ = [
     "FigpackExtension",
     "ExtensionRegistry",
     "ExtensionView",
+    "Group",
 ]

{figpack-0.2.15 → figpack-0.2.16}/figpack/core/_bundle_utils.py

@@ -7,6 +7,7 @@ import zarr
 from .figpack_view import FigpackView
 from .figpack_extension import ExtensionRegistry
 from .extension_view import ExtensionView
+from .zarr import Group, _check_zarr_version
 
 thisdir = pathlib.Path(__file__).parent.resolve()
 
@@ -45,24 +46,32 @@ def prepare_figure_bundle(
                 target_sub = target / subitem.name
                 target_sub.write_bytes(subitem.read_bytes())
 
-    # Write the view data to the Zarr group
-    zarr_group = zarr.open_group(
-        pathlib.Path(tmpdir) / "data.zarr",
-        mode="w",
-        synchronizer=zarr.ThreadSynchronizer(),
-    )
-    view._write_to_zarr_group(zarr_group)
+    # If we are using zarr 3, then we set the default zarr format to 2 temporarily
+    # because we only support version 2 on the frontend right now.
 
-    # Add title and description as attributes on the top-level zarr group
-    zarr_group.attrs["title"] = title
-    if description is not None:
-        zarr_group.attrs["description"] = description
+    if _check_zarr_version() == 3:
+        old_default_zarr_format = zarr.config.get("default_zarr_format")
+        zarr.config.set({"default_zarr_format": 2})
 
-    # Discover and write extension JavaScript files
-    required_extensions = _discover_required_extensions(view)
-    _write_extension_files(required_extensions, tmpdir)
+    try:
+        # Write the view data to the Zarr group
+        zarr_group = zarr.open_group(pathlib.Path(tmpdir) / "data.zarr", mode="w")
+        zarr_group = Group(zarr_group)
+        view._write_to_zarr_group(zarr_group)
 
-    zarr.consolidate_metadata(zarr_group.store)
+        # Add title and description as attributes on the top-level zarr group
+        zarr_group.attrs["title"] = title
+        if description is not None:
+            zarr_group.attrs["description"] = description
+
+        # Discover and write extension JavaScript files
+        required_extensions = _discover_required_extensions(view)
+        _write_extension_files(required_extensions, tmpdir)
+
+        zarr.consolidate_metadata(zarr_group._zarr_group.store)
+    finally:
+        if _check_zarr_version() == 3:
+            zarr.config.set({"default_zarr_format": old_default_zarr_format})
 
 
 def _discover_required_extensions(view: FigpackView) -> Set[str]:

{figpack-0.2.15 → figpack-0.2.16}/figpack/core/_view_figure.py

@@ -109,7 +109,7 @@ def view_figure(figure_path: str, port: Union[int, None] = None) -> None:
 
         try:
             with tarfile.open(figure_path, "r:gz") as tar:
-                tar.extractall(temp_path)
+                tar.extractall(temp_path, filter="data")
 
             # Count extracted files
             extracted_files = list(temp_path.rglob("*"))

{figpack-0.2.15 → figpack-0.2.16}/figpack/core/extension_view.py

@@ -2,9 +2,9 @@
 Base class for views that use figpack extensions
 """
 
-import zarr
 from .figpack_view import FigpackView
 from .figpack_extension import ExtensionRegistry
+from ..core.zarr import Group
 
 
 class ExtensionView(FigpackView):
@@ -32,7 +32,7 @@ class ExtensionView(FigpackView):
             )
         self.extension = extension
 
-    def _write_to_zarr_group(self, group: zarr.Group) -> None:
+    def _write_to_zarr_group(self, group: Group) -> None:
         """
         Write the extension view metadata to a Zarr group.
         Subclasses should call super()._write_to_zarr_group(group) first,

{figpack-0.2.15 → figpack-0.2.16}/figpack/core/figpack_view.py

@@ -7,7 +7,7 @@ import random
 import string
 from typing import Union
 
-import zarr
+from .zarr import Group
 
 
 class FigpackView:
@@ -155,7 +155,7 @@ class FigpackView:
 
         _save_figure(self, output_path, title=title)
 
-    def _write_to_zarr_group(self, group: zarr.Group) -> None:
+    def _write_to_zarr_group(self, group: Group) -> None:
         """
         Write the view data to a Zarr group. Must be implemented by subclasses.
 

figpack-0.2.16/figpack/core/zarr.py

@@ -0,0 +1,61 @@
+from typing import Any, Dict
+import zarr
+
+
+_UNSPECIFIED = object()
+
+
+class Group:
+    def __init__(self, zarr_group: zarr.Group):
+        self._zarr_group = zarr_group
+
+    def create_group(self, name: str) -> "Group":
+        return Group(self._zarr_group.create_group(name))
+
+    def create_dataset(
+        self,
+        name: str,
+        *,
+        data=_UNSPECIFIED,
+        dtype=_UNSPECIFIED,
+        chunks=_UNSPECIFIED,
+        compressor=_UNSPECIFIED,
+    ) -> None:
+        kwargs = {}
+        if data is not _UNSPECIFIED:
+            kwargs["data"] = data
+        if dtype is not _UNSPECIFIED:
+            kwargs["dtype"] = dtype
+        if chunks is not _UNSPECIFIED:
+            kwargs["chunks"] = chunks
+        if compressor is not _UNSPECIFIED:
+            kwargs["compressor"] = compressor
+        if _check_zarr_version() == 2:
+            self._zarr_group.create_dataset(name, **kwargs)
+        elif _check_zarr_version() == 3:
+            self._zarr_group.create_array(name, **kwargs)
+        else:
+            raise RuntimeError("Unsupported Zarr version")
+
+    @property
+    def attrs(self) -> Dict[str, Any]:
+        return self._zarr_group.attrs
+
+    def __getitem__(self, key: str) -> Any:
+        return self._zarr_group[key]
+
+    # implement in operator
+    def __contains__(self, key: str) -> bool:
+        return key in self._zarr_group
+
+    def __iter__(self):
+        return iter(self._zarr_group)
+
+    def __reversed__(self):
+        return reversed(self._zarr_group)
+
+
+def _check_zarr_version():
+    version = zarr.__version__
+    major_version = int(version.split(".")[0])
+    return major_version

{figpack-0.2.15 → figpack-0.2.16}/figpack/franklab/views/TrackAnimation.py

@@ -8,6 +8,7 @@ import numpy as np
 import zarr
 
 from ...core.figpack_view import FigpackView
+from ...core.zarr import Group
 
 
 class TrackAnimation(FigpackView):
@@ -116,7 +117,7 @@ class TrackAnimation(FigpackView):
         self.track_bin_height = track_bin_height
         self.track_bin_width = track_bin_width
 
-    def _write_to_zarr_group(self, group: zarr.Group) -> None:
+    def _write_to_zarr_group(self, group: Group) -> None:
         """
         Write the track animation data to a Zarr group
 

{figpack-0.2.15 → figpack-0.2.16}/figpack/spike_sorting/views/Autocorrelograms.py

@@ -2,12 +2,12 @@
 Autocorrelograms view for figpack - displays multiple autocorrelograms
 """
 
-from typing import List, Optional
+from typing import List
 
 import numpy as np
-import zarr
 
 from ...core.figpack_view import FigpackView
+from ...core.zarr import Group
 from .AutocorrelogramItem import AutocorrelogramItem
 
 
@@ -66,7 +66,7 @@ class Autocorrelograms(FigpackView):
         view = Autocorrelograms(autocorrelograms=ac_items)
         return view
 
-    def _write_to_zarr_group(self, group: zarr.Group) -> None:
+    def _write_to_zarr_group(self, group: Group) -> None:
         """
         Write the Autocorrelograms data to a Zarr group
 
@@ -90,7 +90,6 @@ class Autocorrelograms(FigpackView):
         group.create_dataset(
             "bin_edges_sec",
             data=self.autocorrelograms[0].bin_edges_sec,
-            dtype=np.float32,
         )
 
         # Create 2D array for all bin counts
@@ -111,7 +110,6 @@ class Autocorrelograms(FigpackView):
         group.create_dataset(
             "bin_counts",
             data=bin_counts,
-            dtype=np.int32,
         )
 
         # Store the autocorrelogram metadata

{figpack-0.2.15 → figpack-0.2.16}/figpack/spike_sorting/views/AverageWaveforms.py

@@ -8,6 +8,7 @@ import numpy as np
 import zarr
 
 from ...core.figpack_view import FigpackView
+from ...core.zarr import Group
 
 
 class AverageWaveformItem:
@@ -97,7 +98,7 @@ class AverageWaveforms(FigpackView):
         view = AverageWaveforms(average_waveforms=average_waveform_items)
         return view
 
-    def _write_to_zarr_group(self, group: zarr.Group) -> None:
+    def _write_to_zarr_group(self, group: Group) -> None:
         """
         Write the AverageWaveforms data to a Zarr group
 
@@ -127,13 +128,11 @@ class AverageWaveforms(FigpackView):
             group.create_dataset(
                 f"{waveform_name}/waveform",
                 data=waveform.waveform,
-                dtype=waveform.waveform.dtype,
             )
             if waveform.waveform_std_dev is not None:
                 group.create_dataset(
                     f"{waveform_name}/waveform_std_dev",
                     data=waveform.waveform_std_dev,
-                    dtype=waveform.waveform_std_dev.dtype,
                 )
             if waveform.waveform_percentiles is not None:
                 for j, p in enumerate(waveform.waveform_percentiles):

{figpack-0.2.15 → figpack-0.2.16}/figpack/spike_sorting/views/CrossCorrelograms.py

@@ -8,6 +8,7 @@ import numpy as np
 import zarr
 
 from ...core.figpack_view import FigpackView
+from ...core.zarr import Group
 from .CrossCorrelogramItem import CrossCorrelogramItem
 
 
@@ -75,7 +76,7 @@ class CrossCorrelograms(FigpackView):
         view = CrossCorrelograms(cross_correlograms=cc_items, hide_unit_selector=False)
         return view
 
-    def _write_to_zarr_group(self, group: zarr.Group) -> None:
+    def _write_to_zarr_group(self, group: Group) -> None:
         """
         Write the CrossCorrelograms data to a Zarr group
 
@@ -103,7 +104,6 @@ class CrossCorrelograms(FigpackView):
         group.create_dataset(
             "bin_edges_sec",
             data=self.cross_correlograms[0].bin_edges_sec,
-            dtype=np.float32,
         )
 
         # Create 2D array for all bin counts
@@ -125,7 +125,6 @@ class CrossCorrelograms(FigpackView):
         group.create_dataset(
             "bin_counts",
             data=bin_counts,
-            dtype=np.int32,
         )
 
         # Store the cross-correlogram metadata

{figpack-0.2.15 → figpack-0.2.16}/figpack/spike_sorting/views/RasterPlot.py

@@ -7,6 +7,7 @@ import numpy as np
 import zarr
 
 from ...core.figpack_view import FigpackView
+from ...core.zarr import Group
 from .RasterPlotItem import RasterPlotItem
 from .UnitsTable import UnitsTable, UnitsTableColumn, UnitsTableRow
 from ...views.Box import Box, LayoutItem
@@ -105,7 +106,7 @@ class RasterPlot(FigpackView):
         else:
             return view
 
-    def _write_to_zarr_group(self, group: zarr.Group) -> None:
+    def _write_to_zarr_group(self, group: Group) -> None:
         """
         Args:
             group: Zarr group to write data into
@@ -141,25 +142,21 @@ class RasterPlot(FigpackView):
         group.create_dataset(
             "timestamps",
             data=unified_data["timestamps"],
-            dtype=np.float32,
             chunks=chunks,
         )
         group.create_dataset(
             "unit_indices",
             data=unified_data["unit_indices"],
-            dtype=np.uint16,
             chunks=chunks,
         )
         group.create_dataset(
             "reference_times",
             data=unified_data["reference_times"],
-            dtype=np.float32,
             chunks=(len(unified_data["reference_times"]),),
         )
         group.create_dataset(
             "reference_indices",
             data=unified_data["reference_indices"],
-            dtype=np.uint32,
             chunks=(len(unified_data["reference_indices"]),),
         )
 
@@ -188,7 +185,6 @@ class RasterPlot(FigpackView):
         group.create_dataset(
             "spike_counts_1sec",
             data=spike_counts,
-            dtype=np.uint16,
             chunks=(min(num_bins, 10000), min(num_units, 500)),
         )
 

{figpack-0.2.15 → figpack-0.2.16}/figpack/spike_sorting/views/SpikeAmplitudes.py

@@ -5,9 +5,9 @@ SpikeAmplitudes view for figpack - displays spike amplitudes over time
 from typing import List
 
 import numpy as np
-import zarr
 
 from ...core.figpack_view import FigpackView
+from ...core.zarr import Group
 from .SpikeAmplitudesItem import SpikeAmplitudesItem
 from .UnitsTable import UnitsTable, UnitsTableColumn, UnitsTableRow
 from ...views.Box import Box, LayoutItem
@@ -112,7 +112,7 @@ class SpikeAmplitudes(FigpackView):
         else:
             return view
 
-    def _write_to_zarr_group(self, group: zarr.Group) -> None:
+    def _write_to_zarr_group(self, group: Group) -> None:
         """
         Write the SpikeAmplitudes data to a Zarr group using unified storage format
 
@@ -151,31 +151,26 @@ class SpikeAmplitudes(FigpackView):
         group.create_dataset(
             "timestamps",
             data=unified_data["timestamps"],
-            dtype=np.float32,
             chunks=chunks,
         )
         group.create_dataset(
             "unit_indices",
             data=unified_data["unit_indices"],
-            dtype=np.uint16,
             chunks=chunks,
         )
         group.create_dataset(
             "amplitudes",
             data=unified_data["amplitudes"],
-            dtype=np.float32,
             chunks=chunks,
         )
         group.create_dataset(
             "reference_times",
             data=unified_data["reference_times"],
-            dtype=np.float32,
             chunks=(len(unified_data["reference_times"]),),
         )
         group.create_dataset(
             "reference_indices",
             data=unified_data["reference_indices"],
-            dtype=np.uint32,
             chunks=(len(unified_data["reference_indices"]),),
         )
 
@@ -202,31 +197,26 @@ class SpikeAmplitudes(FigpackView):
                 factor_group.create_dataset(
                     "timestamps",
                     data=data["timestamps"],
-                    dtype=np.float32,
                     chunks=chunks,
                 )
                 factor_group.create_dataset(
                     "unit_indices",
                     data=data["unit_indices"],
-                    dtype=np.uint16,
                     chunks=chunks,
                 )
                 factor_group.create_dataset(
                     "amplitudes",
                     data=data["amplitudes"],
-                    dtype=np.float32,
                     chunks=chunks,
                 )
                 factor_group.create_dataset(
                     "reference_times",
                     data=data["reference_times"],
-                    dtype=np.float32,
                     chunks=(len(data["reference_times"]),),
                 )
                 factor_group.create_dataset(
                     "reference_indices",
                     data=data["reference_indices"],
-                    dtype=np.uint32,
                     chunks=(len(data["reference_indices"]),),
                 )
 

{figpack-0.2.15 → figpack-0.2.16}/figpack/spike_sorting/views/UnitMetricsGraph.py

@@ -9,6 +9,7 @@ import numpy as np
 import zarr
 
 from ...core.figpack_view import FigpackView
+from ...core.zarr import Group
 
 
 class UnitMetricsGraphMetric:
@@ -97,7 +98,7 @@ class UnitMetricsGraph(FigpackView):
         self.metrics = metrics
         self.height = height
 
-    def _write_to_zarr_group(self, group: zarr.Group) -> None:
+    def _write_to_zarr_group(self, group: Group) -> None:
         """
         Write the UnitMetricsGraph data to a Zarr group
 
@@ -122,8 +123,5 @@ class UnitMetricsGraph(FigpackView):
         group.create_dataset(
             "units_data",
             data=units_array,
-            dtype=np.uint8,
-            chunks=True,
-            compressor=zarr.Blosc(cname="zstd", clevel=3, shuffle=zarr.Blosc.SHUFFLE),
         )
         group.attrs["units_data_size"] = len(units_json)

{figpack-0.2.15 → figpack-0.2.16}/figpack/spike_sorting/views/UnitsTable.py

@@ -9,6 +9,7 @@ import numpy as np
 import zarr
 
 from ...core.figpack_view import FigpackView
+from ...core.zarr import Group
 from .UnitSimilarityScore import UnitSimilarityScore
 from .UnitsTableColumn import UnitsTableColumn
 from .UnitsTableRow import UnitsTableRow
@@ -41,7 +42,7 @@ class UnitsTable(FigpackView):
         self.similarity_scores = similarity_scores or []
         self.height = height
 
-    def _write_to_zarr_group(self, group: zarr.Group) -> None:
+    def _write_to_zarr_group(self, group: Group) -> None:
         """
         Write the UnitsTable data to a Zarr group
 
@@ -66,9 +67,6 @@ class UnitsTable(FigpackView):
         group.create_dataset(
             "rows_data",
             data=rows_array,
-            dtype=np.uint8,
-            chunks=True,
-            compressor=zarr.Blosc(cname="zstd", clevel=3, shuffle=zarr.Blosc.SHUFFLE),
         )
         group.attrs["rows_data_size"] = len(rows_json)
 
@@ -80,10 +78,5 @@ class UnitsTable(FigpackView):
             group.create_dataset(
                 "similarity_scores_data",
                 data=scores_array,
-                dtype=np.uint8,
-                chunks=True,
-                compressor=zarr.Blosc(
-                    cname="zstd", clevel=3, shuffle=zarr.Blosc.SHUFFLE
-                ),
             )
             group.attrs["similarity_scores_data_size"] = len(scores_json)

{figpack-0.2.15 → figpack-0.2.16}/figpack/views/Box.py

@@ -4,9 +4,8 @@ Box view for figpack - a layout container that handles other views
 
 from typing import Any, Dict, List, Literal, Optional
 
-import zarr
-
 from ..core.figpack_view import FigpackView
+from ..core.zarr import Group
 from .LayoutItem import LayoutItem
 
 
@@ -43,7 +42,7 @@ class Box(FigpackView):
         self.items = items
         self.title = title
 
-    def _write_to_zarr_group(self, group: zarr.Group) -> None:
+    def _write_to_zarr_group(self, group: Group) -> None:
         """
         Write the Box layout data to a Zarr group
 

{figpack-0.2.15 → figpack-0.2.16}/figpack/views/DataFrame.py

@@ -3,13 +3,12 @@ DataFrame view for figpack - displays pandas DataFrames as interactive tables
 """
 
 import json
-from typing import Any, Dict, Union
 
 import numpy as np
-import pandas as pd
 import zarr
 
 from ..core.figpack_view import FigpackView
+from ..core.zarr import Group
 
 
 class DataFrame(FigpackView):
@@ -17,7 +16,7 @@ class DataFrame(FigpackView):
     A DataFrame visualization component for displaying pandas DataFrames as interactive tables
     """
 
-    def __init__(self, df: pd.DataFrame):
+    def __init__(self, df):
         """
         Initialize a DataFrame view
 
@@ -27,12 +26,14 @@ class DataFrame(FigpackView):
         Raises:
             ValueError: If df is not a pandas DataFrame
         """
+        import pandas as pd
+
         if not isinstance(df, pd.DataFrame):
             raise ValueError("df must be a pandas DataFrame")
 
         self.df = df
 
-    def _write_to_zarr_group(self, group: zarr.Group) -> None:
+    def _write_to_zarr_group(self, group: Group) -> None:
         """
         Write the DataFrame data to a Zarr group
 
@@ -54,11 +55,6 @@ class DataFrame(FigpackView):
             group.create_dataset(
                 "csv_data",
                 data=csv_array,
-                dtype=np.uint8,
-                chunks=True,
-                compressor=zarr.Blosc(
-                    cname="zstd", clevel=3, shuffle=zarr.Blosc.SHUFFLE
-                ),
             )
 
             # Store metadata about the DataFrame
@@ -104,6 +100,4 @@ class DataFrame(FigpackView):
             group.attrs["data_size"] = 0
             group.attrs["column_info"] = "[]"
             # Create empty array as placeholder
-            group.create_dataset(
-                "csv_data", data=np.array([], dtype=np.uint8), dtype=np.uint8
-            )
+            group.create_dataset("csv_data", data=np.array([], dtype=np.uint8))

{figpack-0.2.15 → figpack-0.2.16}/figpack/views/Gallery.py

@@ -4,9 +4,8 @@ Gallery view for figpack - a gallery layout container that handles other views w
 
 from typing import Any, Dict, List, Optional
 
-import zarr
-
 from ..core.figpack_view import FigpackView
+from ..core.zarr import Group
 from .GalleryItem import GalleryItem
 
 
@@ -45,7 +44,7 @@ class Gallery(FigpackView):
             max(0, min(initial_item_index, len(items) - 1)) if items else 0
         )
 
-    def _write_to_zarr_group(self, group: zarr.Group) -> None:
+    def _write_to_zarr_group(self, group: Group) -> None:
         """
         Write the Gallery data to a Zarr group