brainrender 2.2.1__tar.gz → 2.2.2__tar.gz

{brainrender-2.2.1 → brainrender-2.2.2}/.github/workflows/test_and_deploy.yml

@@ -23,13 +23,12 @@ jobs:
   linting:
     runs-on: ubuntu-latest
     steps:
-      - uses: neuroinformatics-unit/actions/lint@v2
-
+      - uses: neuroinformatics-unit/actions/lint@9b53ffe93baaafe5533e1f295a3c069bbc17ba36 # v3.0.1
   manifest:
     name: Check Manifest
     runs-on: ubuntu-latest
     steps:
-      - uses: neuroinformatics-unit/actions/check_manifest@v2
+      - uses: neuroinformatics-unit/actions/check_manifest@9b53ffe93baaafe5533e1f295a3c069bbc17ba36 # v3.0.1
 
   test:
     needs: [linting, manifest]
@@ -49,7 +48,7 @@ jobs:
 
     steps:
       - name: Cache brainglobe directory
-        uses: actions/cache@v3
+        uses: actions/cache@1bd1e32a3bdc45362d1e726936510720a7c30a57 # v4.2.0
         with:
           path: | # ensure we don't cache any interrupted atlas download and extraction, if e.g. we cancel the workflow manually
             ~/.brainglobe
@@ -61,9 +60,6 @@ jobs:
         run: brew install hdf5
 
       # Helps set up VTK with a headless display
-      - uses: pyvista/setup-headless-display-action@v3
-
-      # Sets up ffmpeg to we can run video tests on CI
       - uses: FedericoCarboni/setup-ffmpeg@v2
         if: matrix.os != 'macos-latest'
         id: setup-ffmpeg
@@ -73,15 +69,17 @@ jobs:
         run: brew install ffmpeg
 
       # Run tests
-      - uses: neuroinformatics-unit/actions/test@v2
+      - name: Run tests
+        uses: neuroinformatics-unit/actions/test-uv@9b53ffe93baaafe5533e1f295a3c069bbc17ba36 #v3.0.1
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: "${{ matrix.python-version }}"
           secret-codecov-token: ${{ secrets.CODECOV_TOKEN }}
-
+          use-headless: 'true'
+          install-mesa3d-offscreen: ${{ matrix.os != 'windows-latest' }}
 
       - name: Notify slack on scheduled failure
         if: failure() && github.event_name == 'schedule'
-        uses: ravsamhq/notify-slack-action@v2
+        uses: ravsamhq/notify-slack-action@be814b201e233b2dc673608aa46e5447c8ab13f2 # v2.5.0
         with:
           status: ${{ job.status }} # required
           notify_when: 'failure'
@@ -95,7 +93,7 @@ jobs:
     if: github.event_name == 'push' && github.ref_type == 'tag'
     runs-on: ubuntu-latest
     steps:
-    - uses: neuroinformatics-unit/actions/build_sdist_wheels@v2
+    - uses: neuroinformatics-unit/actions/build_sdist_wheels@9b53ffe93baaafe5533e1f295a3c069bbc17ba36 # v3.0.1
 
 
   upload_all:

{brainrender-2.2.1 → brainrender-2.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: brainrender
-Version: 2.2.1
+Version: 2.2.2
 Summary: Visualisation and exploration of brain atlases and other anatomical data
 Author-email: "Federico Claudi, Adam Tyson, Luigi Petrucco" <hello@brainglobe.info>
 License: BSD-3-Clause
@@ -41,12 +41,11 @@ Requires-Dist: pyyaml>=5.3
 Requires-Dist: requests
 Requires-Dist: tables
 Requires-Dist: vedo>=2025.5.3
-Requires-Dist: vtk
+Requires-Dist: vtk<9.7.0
 Provides-Extra: dev
 Requires-Dist: pytest; extra == "dev"
 Requires-Dist: pytest-cov; extra == "dev"
 Requires-Dist: coverage; extra == "dev"
-Requires-Dist: tox; extra == "dev"
 Requires-Dist: black; extra == "dev"
 Requires-Dist: mypy; extra == "dev"
 Requires-Dist: pre-commit; extra == "dev"

{brainrender-2.2.1 → brainrender-2.2.2}/brainrender/atlas_specific/allen_brain_atlas/gene_expression/api.py

@@ -1,7 +1,10 @@
+"""API client for downloading Allen Brain Atlas gene expression data."""
+
 import os
 import sys
 from time import sleep
 
+import numpy.typing as npt
 import pandas as pd
 import requests
 from loguru import logger
@@ -17,6 +20,8 @@ from brainrender.atlas_specific.allen_brain_atlas.gene_expression.ge_utils impor
 
 
 class GeneExpressionAPI:
+    """Client for querying and downloading Allen Brain Atlas gene expression data."""
+
     voxel_size = 200  # um
     grid_size = [58, 41, 67]  # number of voxels along each direction
 
@@ -38,22 +43,41 @@ class GeneExpressionAPI:
     download_url = "http://api.brain-map.org/grid_data/download/EXP_ID?include=energy,intensity,density"
 
     gene_expression_cache = base_dir / "GeneExpressionCache"
-    gene_name = None
+    gene_name: str | None = None
 
-    def __init__(self):
+    def __init__(self) -> None:
         # Get metadata about all available genes
-        self.genes = None  # when necessary gene data can be downloaded with self.get_all_genes
+        self.genes: pd.DataFrame | None = (
+            None  # when necessary gene data can be downloaded with self.get_all_genes
+        )
         self.gene_expression_cache.mkdir(exist_ok=True)
 
     @fail_on_no_connection
-    def get_all_genes(self):
+    def get_all_genes(self) -> pd.DataFrame:
         """
-        Download metadata about all the genes available in the Allen gene expression dataset
+        Download metadata about all genes in the Allen gene expression dataset.
+
+        Returns
+        -------
+        pd.DataFrame
         """
         res = request(self.all_genes_url)
         return pd.DataFrame(res.json()["msg"])
 
-    def get_gene_id_by_name(self, gene_name):
+    def get_gene_id_by_name(self, gene_name: str) -> int | None:
+        """
+        Return the Allen gene ID for a given gene symbol.
+
+        Parameters
+        ----------
+        gene_name
+            Gene symbol.
+
+        Returns
+        -------
+        int or None
+            Gene ID, or None if the gene is not found.
+        """
         self.gene_name = self.gene_name or gene_name
         if self.genes is None:
             self.genes = self.get_all_genes()
@@ -71,7 +95,19 @@ class GeneExpressionAPI:
                 ]
             )
 
-    def get_gene_symbol_by_id(self, gene_id):
+    def get_gene_symbol_by_id(self, gene_id: int | str) -> str:
+        """
+        Return the gene symbol for a given Allen gene ID.
+
+        Parameters
+        ----------
+        gene_id
+            Allen gene ID.
+
+        Returns
+        -------
+        str
+        """
         if self.genes is None:
             self.genes = self.get_all_genes()
 
@@ -80,12 +116,19 @@ class GeneExpressionAPI:
         ].gene_symbol.values[0]
 
     @fail_on_no_connection
-    def get_gene_experiments(self, gene):
+    def get_gene_experiments(self, gene: str) -> list[int] | None:
         """
-        Given a gene_symbol it returns the list of ISH
-        experiments for this gene
+        Return ISH experiment IDs for a given gene symbol.
+
+        Parameters
+        ----------
+        gene
+            Gene symbol.
 
-        :param gene_symbol: str
+        Returns
+        -------
+        list of int or None
+            List of experiment IDs, or None if no experiments are found.
         """
         url = self.gene_experiments_url.replace("-GENE_SYMBOL-", gene)
         max_retries = 8
@@ -108,13 +151,15 @@ class GeneExpressionAPI:
             return [d["id"] for d in data]
 
     @fail_on_no_connection
-    def download_gene_data(self, gene):
+    def download_gene_data(self, gene: str) -> None:
         """
-        Downloads a gene's data from the Allen Institute
-        Gene Expression dataset and saves to cache.
-        See: http://help.brain-map.org/display/api/Downloading+3-D+Expression+Grid+Data
+        Download a gene's expression data from the Allen Institute and save to cache.
+        See http://help.brain-map.org/display/api/Downloading+3-D+Expression+Grid+Data.
 
-        :param gene: int, the gene_id for the gene being downloaded.
+        Parameters
+        ----------
+        gene
+            Gene symbol to download data for.
         """
         # Get the gene's experiment id
         exp_ids = self.get_gene_experiments(gene)
@@ -130,9 +175,37 @@ class GeneExpressionAPI:
                 url, os.path.join(self.gene_expression_cache, f"{gene}-{eid}")
             )
 
-    def get_gene_data(self, gene, exp_id, use_cache=True, metric="energy"):
+    def get_gene_data(
+        self,
+        gene: str,
+        exp_id: int,
+        use_cache: bool = True,
+        metric: str = "energy",
+    ) -> npt.NDArray | None:
         """
-        Given a list of gene ids
+        Load gene expression data for a given gene and experiment.
+
+        Parameters
+        ----------
+        gene
+            Gene symbol.
+        exp_id
+            Experiment ID.
+        use_cache
+            If True, load from cache if available. Default True.
+        metric
+            Expression metric to load. Default ``"energy"``.
+
+        Returns
+        -------
+        numpy.ndarray or None
+            Gene expression data, or None if no data is available for the
+            requested metric.
+
+        Raises
+        ------
+        ValueError
+            If data could not be cached after downloading.
         """
         logger.debug(f"Getting gene data for gene: {gene} experiment {exp_id}")
         self.gene_name = self.gene_name or gene
@@ -161,21 +234,31 @@ class GeneExpressionAPI:
 
     def griddata_to_volume(
         self,
-        griddata,
-        min_quantile=None,
-        min_value=None,
-        cmap="bwr",
-    ):
+        griddata: npt.NDArray,
+        min_quantile: float | None = None,
+        min_value: float | None = None,
+        cmap: str = "bwr",
+    ) -> Volume:
         """
-        Takes a 3d numpy array with volumetric gene expression
-        and returns a vedo.Volume.isosurface actor.
-        The isosurface needs a lower bound threshold, this can be
-        either a user defined hard value (min_value) or the value
-        corresponding to some percentile of the gene expression data.
-
-        :param griddata: np.ndarray, 3d array with gene expression data
-        :param min_quantile: float, percentile for threshold
-        :param min_value: float, value for threshold
+        Convert a 3D gene expression array to a Volume actor.
+
+        The isosurface threshold can be set as a hard value or as a
+        percentile of the expression data.
+
+        Parameters
+        ----------
+        griddata
+            3D array with gene expression data.
+        min_quantile
+            Percentile threshold for isosurface extraction.
+        min_value
+            Hard value threshold for isosurface extraction.
+        cmap
+            Colormap name. Default ``"bwr"``.
+
+        Returns
+        -------
+        Volume
         """
         return Volume(
             griddata,

brainrender-2.2.2/brainrender/atlas_specific/allen_brain_atlas/gene_expression/ge_utils.py

@@ -0,0 +1,158 @@
+"""Utilities for caching and loading Allen Brain Atlas gene expression data."""
+
+import io
+import os
+import sys
+import zipfile
+from pathlib import Path
+from typing import Literal
+
+import numpy as np
+import numpy.typing as npt
+
+from brainrender._io import check_file_exists, request
+from brainrender._utils import get_subdirs, listdir
+
+# ----------------------------------- Cache ---------------------------------- #
+
+
+def check_gene_cached(
+    cache_folder: str | Path,
+    gene_id: str,
+    exp_id: str | int,
+) -> str | Literal[False]:
+    """
+    Check whether a gene experiment is already cached.
+
+    A gene is cached in a subfolder of ``cache_folder`` named
+    ``{gene_id}-{exp_id}``.
+
+    Parameters
+    ----------
+    cache_folder
+        Path to the general cache folder.
+    gene_id
+        Gene name.
+    exp_id
+        Experiment ID.
+
+    Returns
+    -------
+    str or False
+        Path to the cached folder if found, False if not cached.
+
+    Raises
+    ------
+    ValueError
+        If more than one matching folder is found.
+    """
+    cache = [
+        sub
+        for sub in get_subdirs(cache_folder)
+        if f"{gene_id}-{exp_id}" == os.path.basename(sub)
+    ]
+    if not cache:
+        return False
+    elif len(cache) > 1:
+        raise ValueError("Found too many folders")
+    else:
+        return cache[0]
+
+
+def download_and_cache(url: str, cachedir: str | Path) -> None:
+    """
+    Download and unzip a gene's ISH experiment data to a cache directory.
+
+    Parameters
+    ----------
+    url
+        URL to download the data from.
+    cachedir
+        Path to the folder where data will be saved.
+    """
+    # Get data
+    req = request(url)
+
+    # Create cache dir
+    if not os.path.isdir(cachedir):
+        os.mkdir(cachedir)
+
+    # Unzip to cache dir
+    z = zipfile.ZipFile(io.BytesIO(req.content))
+    z.extractall(cachedir)
+
+
+def load_cached_gene(
+    cache: str | Path,
+    metric: str,
+    grid_size: tuple[int, int, int],
+) -> npt.NDArray | None:
+    """
+    Load a gene's data from cache.
+
+    Parameters
+    ----------
+    cache
+        Path to the gene's cache folder.
+    metric
+        Metric name used to filter files (e.g. ``"energy"``).
+    grid_size
+        Shape to use when reshaping the raw data array.
+
+    Returns
+    -------
+    numpy.ndarray or None
+        Array of gene expression values, or None if no file is found.
+
+    Raises
+    ------
+    NotImplementedError
+        If more than one matching file is found.
+    """
+    files = [
+        f for f in listdir(cache) if metric in f and not f.endswith(".mhd")
+    ]
+    if not files:
+        return None
+    if len(files) > 1:
+        raise NotImplementedError("Deal with more than one file found")
+    else:
+        return read_raw(files[0], grid_size)
+
+
+# --------------------------------- Open .raw -------------------------------- #
+@check_file_exists
+def read_raw(
+    filepath: str | Path,
+    grid_size: tuple[int, int, int],
+) -> npt.NDArray:
+    """
+    Read a ``.raw`` gene expression file from the Allen Brain Atlas.
+
+    See http://help.brain-map.org/display/mousebrain/API#API-Expression3DGridsz
+    for the file format reference.
+
+    Parameters
+    ----------
+    filepath
+        Path to the ``.raw`` file.
+    grid_size
+        Shape to use when reshaping the data array.
+
+    Returns
+    -------
+    numpy.ndarray
+    """
+    filepath = str(filepath)
+
+    # Read bytes
+    with open(filepath, "rb") as test:
+        content = test.read()
+
+    # Create np array and return
+    data = np.frombuffer(content, dtype="float32").reshape(grid_size)
+
+    if sys.platform == "darwin":
+        data = data.T  # TODO figure out why this is necessary on Mac OS?
+
+    return data

{brainrender-2.2.1 → brainrender-2.2.2}/brainrender/atlas_specific/allen_brain_atlas/streamlines.py

@@ -1,3 +1,7 @@
+"""Utilities for downloading and processing streamlines aligned to the Allen Mouse Brain Atlas."""
+
+from typing import Any
+
 import pandas as pd
 import requests
 from loguru import logger
@@ -36,18 +40,20 @@ ALLEN_MESOSCALE_URL = (
 ALLEN_API_URL = "https://api.brain-map.org/api/v2/data/query.json"
 VOXEL_SIZE_NM = 1000  # skeleton vertices are in nanometers
 
-_ml_extent_um_cache = None
+_ml_extent_um_cache: float | None = None
 
 
-def _get_ml_extent_um():
+def _get_ml_extent_um() -> float:
     """
-    Derives the full medial-lateral extent of the Allen CCF atlas in microns
-    dynamically from the brainglobe atlas API. Used to flip the Z (ML) axis
-    when converting from Allen CCF space to brainrender's coordinate system,
-    where left and right hemispheres are mirrored relative to the Allen CCF.
-
-    Result is cached after the first call to avoid reinstantiating the atlas
-    on every experiment download.
+    Derive the full medial-lateral extent of the Allen CCF atlas in microns
+    dynamically from the brainglobe atlas API. The computed extent is cached
+    for subsequent calls and used to flip the Z (ML) axis when converting
+    from Allen CCF space to brainrender's coordinate system.
+
+    Returns
+    -------
+    float
+        Full medial-lateral extent of the atlas in microns.
     """
     global _ml_extent_um_cache
     if _ml_extent_um_cache is None:
@@ -56,10 +62,19 @@ def _get_ml_extent_um():
     return _ml_extent_um_cache
 
 
-def experiments_source_search(SOI):
+def experiments_source_search(SOI: str) -> pd.DataFrame | None:
     """
-    Returns data about experiments whose injection was in the SOI, structure of interest
-    :param SOI: str, structure of interest. Acronym of structure to use as seed for the search
+    Return data about experiments whose injection was in the structure of interest.
+
+    Parameters
+    ----------
+    SOI
+        Acronym of the structure of interest to use as the search seed.
+
+    Returns
+    -------
+    pd.DataFrame or None
+        DataFrame of matching experiments, or None if AllenSDK is not installed.
     """
     transgenic_id = 0  # id = 0 means use only wild type
     primary_structure_only = True
@@ -81,15 +96,26 @@ def experiments_source_search(SOI):
     )
 
 
-def _get_injection_site_um(eid, ml_extent_um):
+def _get_injection_site_um(
+    eid: int,
+    ml_extent_um: float,
+) -> dict[str, float] | None:
     """
-    Fetches the injection site coordinates for an experiment from the Allen
-    Brain Atlas API. Coordinates are in Allen CCF um space with the Z (ML)
-    axis flipped to match brainrender's hemisphere convention.
-
-    :param eid: int, experiment ID
-    :param ml_extent_um: float, full ML extent of the atlas in um for LR flip
-    :return: dict with x, y, z keys or None if not found
+    Fetch injection site coordinates for an experiment from the Allen Brain Atlas API.
+    Coordinates are returned in Allen CCF µm space with the Z (ML) axis
+    flipped to match brainrender's hemisphere convention.
+
+    Parameters
+    ----------
+    eid
+        Experiment ID.
+    ml_extent_um
+        Full ML extent of the atlas in µm, used for the left-right flip.
+
+    Returns
+    -------
+    dict or None
+        Dict with ``x``, ``y``, ``z`` keys in µm, or None if not found.
     """
     try:
         url = (
@@ -114,10 +140,13 @@ def _get_injection_site_um(eid, ml_extent_um):
     return None
 
 
-def _skeleton_to_dataframe(skeleton, eid, ml_extent_um):
+def _skeleton_to_dataframe(
+    skeleton: Any,
+    eid: int,
+    ml_extent_um: float,
+) -> pd.DataFrame:
     """
-    Converts a cloudvolume Skeleton object to the pd.DataFrame format
-    expected by brainrender's Streamlines actor.
+    Convert a cloudvolume Skeleton object to a DataFrame for the Streamlines actor.
 
     Vertices are in nanometers in Allen CCF space. We:
     1. Convert nm -> um (divide by VOXEL_SIZE_NM)
@@ -126,10 +155,19 @@ def _skeleton_to_dataframe(skeleton, eid, ml_extent_um):
     X (AP) and Y (DV) are passed through as-is because brainrender's
     brain mesh uses the same orientation as the Allen CCF for those axes.
 
-    :param skeleton: cloudvolume Skeleton object
-    :param eid: int, experiment ID used to fetch real injection coordinates
-    :param ml_extent_um: float, full ML extent of the atlas in um for LR flip
-    :return: pd.DataFrame with 'lines' and 'injection_sites' columns
+    Parameters
+    ----------
+    skeleton
+        cloudvolume Skeleton object.
+    eid
+        Experiment ID, used to fetch the real injection site coordinates.
+    ml_extent_um
+        Full ML extent of the atlas in µm, used for the left-right flip.
+
+    Returns
+    -------
+    pd.DataFrame
+        DataFrame with ``lines`` and ``injection_sites`` columns.
     """
     components = skeleton.components()
 
@@ -164,14 +202,25 @@ def _skeleton_to_dataframe(skeleton, eid, ml_extent_um):
     )
 
 
-def get_streamlines_data(eids, force_download=False):
+def get_streamlines_data(
+    eids: list[int],
+    force_download: bool = False,
+) -> list[pd.DataFrame]:
     """
-    Given a list of experiment IDs, downloads streamline data from the
+    Given a list of experiment IDs, download streamline data from the
     Allen mesoscale connectivity dataset hosted on Google Cloud Storage
-    via cloud-volume, and saves them as JSON files.
-
-    :param eids: list of integers with experiment IDs
-    :param force_download: bool, if True re-download even if cached
+    via cloud-volume, and save them as JSON files.
+
+    Parameters
+    ----------
+    eids
+        Experiment IDs to download.
+    force_download
+        If True, re-download even if a cached file exists. Default False.
+
+    Returns
+    -------
+    list of pd.DataFrame
     """
     if not cloudvolume_installed:
         print(
@@ -210,7 +259,10 @@ def get_streamlines_data(eids, force_download=False):
     return data
 
 
-def get_streamlines_for_region(region, force_download=False):
+def get_streamlines_for_region(
+    region: str,
+    force_download: bool = False,
+) -> list[pd.DataFrame] | None:
     """
     Using the Allen Mouse Connectivity data and corresponding API, this function finds experiments
     whose injections were targeted to the region of interest and downloads the corresponding
@@ -218,8 +270,17 @@ def get_streamlines_for_region(region, force_download=False):
     By default, experiments are selected for only WT mice and only when the region was
     the primary injection target.
 
-    :param region: str with region to use for search
-    :param force_download: bool, if True re-download even if cached
+    Parameters
+    ----------
+    region
+        Acronym of the brain region to search for.
+    force_download
+        If True, re-download even if cached. Default False.
+
+    Returns
+    -------
+    list of pd.DataFrame or None
+        Streamlines data, or None if no experiments are found.
     """
     logger.debug(f"Getting streamlines data for region: {region}")
     region_experiments = experiments_source_search(region)

{brainrender-2.2.1 → brainrender-2.2.2}/brainrender/scene.py

@@ -78,9 +78,11 @@ class Scene(JupyterMixIn, Render):
         # Initialise render class
         Render.__init__(self, plotter)
 
+        root_name = self.atlas.structures[self.atlas.hierarchy.root]["acronym"]
+
         # Get root mesh
         self.root = self.add_brain_region(
-            "root",
+            root_name,
             alpha=settings.ROOT_ALPHA,
             color=settings.ROOT_COLOR,
             silhouette=bool(root and settings.SHADER_STYLE == "cartoon"),
@@ -283,7 +285,7 @@ class Scene(JupyterMixIn, Render):
 
     def add_brain_region(
         self,
-        *regions: str,
+        *regions: str | int,
         alpha: float = 1,
         color: str | None = None,
         silhouette: bool | None = None,
@@ -296,7 +298,7 @@ class Scene(JupyterMixIn, Render):
         Parameters
         ----------
         *regions
-            Region names.
+            Region names or IDs.
         alpha
             How opaque the regions are rendered.
         color

{brainrender-2.2.1 → brainrender-2.2.2}/brainrender.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: brainrender
-Version: 2.2.1
+Version: 2.2.2
 Summary: Visualisation and exploration of brain atlases and other anatomical data
 Author-email: "Federico Claudi, Adam Tyson, Luigi Petrucco" <hello@brainglobe.info>
 License: BSD-3-Clause
@@ -41,12 +41,11 @@ Requires-Dist: pyyaml>=5.3
 Requires-Dist: requests
 Requires-Dist: tables
 Requires-Dist: vedo>=2025.5.3
-Requires-Dist: vtk
+Requires-Dist: vtk<9.7.0
 Provides-Extra: dev
 Requires-Dist: pytest; extra == "dev"
 Requires-Dist: pytest-cov; extra == "dev"
 Requires-Dist: coverage; extra == "dev"
-Requires-Dist: tox; extra == "dev"
 Requires-Dist: black; extra == "dev"
 Requires-Dist: mypy; extra == "dev"
 Requires-Dist: pre-commit; extra == "dev"

{brainrender-2.2.1 → brainrender-2.2.2}/brainrender.egg-info/requires.txt

@@ -17,13 +17,12 @@ pyyaml>=5.3
 requests
 tables
 vedo>=2025.5.3
-vtk
+vtk<9.7.0
 
 [dev]
 pytest
 pytest-cov
 coverage
-tox
 black
 mypy
 pre-commit

brainrender-2.2.2/brainrender.egg-info/scm_version.json

@@ -0,0 +1,8 @@
+{
+  "tag": "2.2.2",
+  "distance": 0,
+  "node": "g60cf6b76b8a5bfca51f843069ffbe0068f9ae0d2",
+  "dirty": false,
+  "branch": "HEAD",
+  "node_date": "2026-09-21"
+}

{brainrender-2.2.1 → brainrender-2.2.2}/pyproject.toml

@@ -28,7 +28,7 @@ dependencies = [
     "requests",
     "tables",
     "vedo>=2025.5.3",
-    "vtk"
+    "vtk<9.7.0"
 ]
 
 license = { text = "BSD-3-Clause" }
@@ -57,7 +57,6 @@ dev = [
     "pytest",
     "pytest-cov",
     "coverage",
-    "tox",
     "black",
     "mypy",
     "pre-commit",
@@ -66,7 +65,6 @@ dev = [
 ]
 nb = ["jupyter", "k3d"]
 
-
 [build-system]
 requires = ["setuptools>=45", "wheel", "setuptools_scm[toml]>=6.2"]
 build-backend = "setuptools.build_meta"
@@ -78,9 +76,8 @@ include-package-data = true
 include = ["brainrender*"]
 exclude = ["tests*", "docs*", "examples*", "imgs*"]
 
-
 [tool.pytest.ini_options]
-addopts = "--cov=brainrender"
+addopts = "--cov=brainrender --cov-report=xml --color=yes -vv"
 markers = [
     "slow: marks tests as slow (deselect with '-m \"not slow\"')",
     "local: marks test as local (not for CI)",
@@ -113,29 +110,3 @@ ignore = ["E501", "E402"]
 
 [tool.ruff.lint]
 select = ["I", "E", "F"]
-
-[tool.tox]
-legacy_tox_ini = """
-[tox]
-envlist = py{311,312,313}
-isolated_build = True
-
-[gh-actions]
-python =
-    3.11: py311
-    3.12: py312
-    3.13: py313
-
-[testenv]
-extras =
-    dev
-commands =
-    pytest -v --color=yes --cov=brainrender --cov-report=xml
-passenv =
-    CI
-    GITHUB_ACTIONS
-    DISPLAY
-    XAUTHORITY
-    NUMPY_EXPERIMENTAL_ARRAY_FUNCTION
-    PYVISTA_OFF_SCREEN
-"""

brainrender-2.2.1/brainrender/atlas_specific/allen_brain_atlas/gene_expression/ge_utils.py

@@ -1,96 +0,0 @@
-import io
-import os
-import sys
-import zipfile
-
-import numpy as np
-
-from brainrender._io import check_file_exists, request
-from brainrender._utils import get_subdirs, listdir
-
-# ----------------------------------- Cache ---------------------------------- #
-
-
-def check_gene_cached(cache_folder, gene_id, exp_id):
-    """
-    A gene is saved in a folder in cache_folder
-    with gene_id-exp_id as name. If the folder doesn't
-    exist the gene is not cached.
-
-    :param cache_folder: str, path to general cache folder for all data
-    :param gene_id: str name of gene
-    :param exp_id: id of experiment
-    """
-    cache = [
-        sub
-        for sub in get_subdirs(cache_folder)
-        if f"{gene_id}-{exp_id}" == os.path.basename(sub)
-    ]
-    if not cache:
-        return False
-    elif len(cache) > 1:
-        raise ValueError("Found too many folders")
-    else:
-        return cache[0]
-
-
-def download_and_cache(url, cachedir):
-    """
-    Given a url to download a gene's ISH experiment data,
-    this function download and unzips the data
-
-    :param url: str, utl to download data
-    :param cachedir: str, path to folder where data will be downloaded
-    """
-    # Get data
-    req = request(url)
-
-    # Create cache dir
-    if not os.path.isdir(cachedir):
-        os.mkdir(cachedir)
-
-    # Unzip to cache dir
-    z = zipfile.ZipFile(io.BytesIO(req.content))
-    z.extractall(cachedir)
-
-
-def load_cached_gene(cache, metric, grid_size):
-    """
-    Loads a gene's data from cache
-    """
-    files = [
-        f for f in listdir(cache) if metric in f and not f.endswith(".mhd")
-    ]
-    if not files:
-        return None
-    if len(files) > 1:
-        raise NotImplementedError("Deal with more than one file found")
-    else:
-        return read_raw(files[0], grid_size)
-
-
-# --------------------------------- Open .raw -------------------------------- #
-@check_file_exists
-def read_raw(filepath, grid_size):
-    """
-    reads a .raw file with gene expression data
-    downloaded from the Allen atlas and returns
-    a numpy array with the correct grid_size.
-    See as reference:
-        http://help.brain-map.org/display/mousebrain/API#API-Expression3DGridsz
-
-    :param filepath: str or Path object
-    """
-    filepath = str(filepath)
-
-    # Read bytes
-    with open(filepath, "rb") as test:
-        content = test.read()
-
-    # Create np array and return
-    data = np.frombuffer(content, dtype="float32").reshape(grid_size)
-
-    if sys.platform == "darwin":
-        data = data.T  # TODO figure out why this is necessary on Mac OS?
-
-    return data

brainrender-2.2.1/brainrender.egg-info/scm_version.json

@@ -1,8 +0,0 @@
-{
-  "tag": "2.2.1",
-  "distance": 0,
-  "node": "gbdcdf90b2b8e814449900042e232e53f18b66227",
-  "dirty": false,
-  "branch": "HEAD",
-  "node_date": "2026-08-10"
-}