brainrender 2.1.2__tar.gz → 2.1.3__tar.gz

{brainrender-2.1.2 → brainrender-2.1.3}/.gitignore

@@ -28,7 +28,6 @@ brexport.html
 *.vtk
 *.nrrd
 *.tdms
-paper/created_videos
 *.mp4
 
 

{brainrender-2.1.2 → brainrender-2.1.3}/.pre-commit-config.yaml

@@ -1,3 +1,7 @@
+# Configuring https://pre-commit.ci/ bot
+ci:
+    autoupdate_schedule: monthly
+
 repos:
     - repo: https://github.com/pre-commit/pre-commit-hooks
       rev: v4.5.0
@@ -12,10 +16,10 @@ repos:
           - id: requirements-txt-fixer
           - id: trailing-whitespace
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.1.6
+      rev: v0.1.8
       hooks:
         - id: ruff
     - repo: https://github.com/psf/black
-      rev: 23.11.0
+      rev: 23.12.0
       hooks:
           - id: black

{brainrender-2.1.2 → brainrender-2.1.3}/MANIFEST.in

@@ -1,9 +1,7 @@
 global-include *.svg
 include brainrender/gui/icons*
 
-recursive-exclude paper *
 recursive-exclude tests *
 recursive-exclude examples *
 recursive-exclude imgs *
 recursive-exclude videos *
-recursive-exclude benchmark *

{brainrender-2.1.2 → brainrender-2.1.3}/PKG-INFO

@@ -1,13 +1,14 @@
 Metadata-Version: 2.1
 Name: brainrender
-Version: 2.1.2
+Version: 2.1.3
 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
-Project-URL: homepage, https://brainglobe.info
-Project-URL: bug_tracker, https://github.com/brainglobe/brainrender/issues
-Project-URL: source_code, https://github.com/brainglobe/brainrender
-Project-URL: user_support, https://github.com/brainglobe/brainrender/issues
+Project-URL: Homepage, https://brainglobe.info/
+Project-URL: Source Code, https://github.com/brainglobe/brainrender
+Project-URL: Bug Tracker, https://github.com/brainglobe/brainrender/issues
+Project-URL: Documentation, https://brainglobe.info/documentation/brainrender/index.html
+Project-URL: User Support, https://forum.image.sc/tag/brainglobe
 Classifier: Development Status :: 3 - Alpha
 Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
@@ -18,7 +19,7 @@ Classifier: Operating System :: OS Independent
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
-Requires-Python: >=3.8.0
+Requires-Python: >=3.9.0
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy
@@ -68,8 +69,8 @@ Requires-Dist: PyQt5; extra == "pyqt5"
 [![Python Version](https://img.shields.io/pypi/pyversions/brainrender.svg)](https://pypi.org/project/brainrender)
 [![PyPI](https://img.shields.io/pypi/v/brainrender.svg)](https://pypi.org/project/brainrender)
 [![tests](https://github.com/brainglobe/brainrender/workflows/tests/badge.svg)](https://github.com/brainglobe/brainrender/actions)
+[![codecov](https://codecov.io/gh/brainglobe/brainrender/graph/badge.svg)](https://codecov.io/gh/brainglobe/brainrender)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
-[![Coverage Status](https://coveralls.io/repos/github/brainglobe/brainrender/badge.svg)](https://coveralls.io/github/brainglobe/brainrender)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)
 
 

{brainrender-2.1.2 → brainrender-2.1.3}/README.md

@@ -7,8 +7,8 @@
 [![Python Version](https://img.shields.io/pypi/pyversions/brainrender.svg)](https://pypi.org/project/brainrender)
 [![PyPI](https://img.shields.io/pypi/v/brainrender.svg)](https://pypi.org/project/brainrender)
 [![tests](https://github.com/brainglobe/brainrender/workflows/tests/badge.svg)](https://github.com/brainglobe/brainrender/actions)
+[![codecov](https://codecov.io/gh/brainglobe/brainrender/graph/badge.svg)](https://codecov.io/gh/brainglobe/brainrender)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
-[![Coverage Status](https://coveralls.io/repos/github/brainglobe/brainrender/badge.svg)](https://coveralls.io/github/brainglobe/brainrender)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)
 
 

{brainrender-2.1.2 → brainrender-2.1.3}/brainrender/actor.py

@@ -128,7 +128,7 @@ class Actor:
             )  # pragma: no cover
 
         # some attributes should be from .mesh, others from ._mesh
-        mesh_attributes = ("centerOfMass",)
+        mesh_attributes = ("center_of_mass",)
         if attr in mesh_attributes:
             if hasattr(self.__dict__["mesh"], attr):
                 return getattr(self.__dict__["mesh"], attr)

{brainrender-2.1.2 → brainrender-2.1.3}/brainrender/actors/ruler.py

@@ -67,7 +67,7 @@ def ruler_from_surface(
     p2 = p1.copy()
     p2[axis] = 0  # zero the chosen coordinate
 
-    pts = root._mesh.intersect_with_line(p1, p2)
+    pts = root.mesh.intersect_with_line(p1, p2)
     surface_point = pts[0]
 
     return ruler(p1, surface_point, unit_scale=unit_scale, units=units, s=s)

{brainrender-2.1.2 → brainrender-2.1.3}/brainrender/render.py

@@ -119,8 +119,8 @@ class Render:
 
         Once an actor is 'corrected' it spawns labels and silhouettes as needed
         """
-        # don't apply transforms to points density actors or rulers
-        if isinstance(actor, PointsDensity) or actor.br_class == "Ruler":
+        # don't apply transforms to points density actors
+        if isinstance(actor, PointsDensity):
             logger.debug(
                 f'Not transforming actor "{actor.name} (type: {actor.br_class})"'
             )

{brainrender-2.1.2 → brainrender-2.1.3}/brainrender/scene.py

@@ -304,7 +304,7 @@ class Scene(JupyterMixIn, Render):
                 actors.cap()
             else:
                 for actor in actors:
-                    actor._mesh.cutWithPlane(
+                    actor._mesh.cut_with_plane(
                         origin=plane.center,
                         normal=plane.normal,
                     )

{brainrender-2.1.2 → brainrender-2.1.3}/brainrender.egg-info/PKG-INFO

@@ -1,13 +1,14 @@
 Metadata-Version: 2.1
 Name: brainrender
-Version: 2.1.2
+Version: 2.1.3
 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
-Project-URL: homepage, https://brainglobe.info
-Project-URL: bug_tracker, https://github.com/brainglobe/brainrender/issues
-Project-URL: source_code, https://github.com/brainglobe/brainrender
-Project-URL: user_support, https://github.com/brainglobe/brainrender/issues
+Project-URL: Homepage, https://brainglobe.info/
+Project-URL: Source Code, https://github.com/brainglobe/brainrender
+Project-URL: Bug Tracker, https://github.com/brainglobe/brainrender/issues
+Project-URL: Documentation, https://brainglobe.info/documentation/brainrender/index.html
+Project-URL: User Support, https://forum.image.sc/tag/brainglobe
 Classifier: Development Status :: 3 - Alpha
 Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
@@ -18,7 +19,7 @@ Classifier: Operating System :: OS Independent
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
-Requires-Python: >=3.8.0
+Requires-Python: >=3.9.0
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy
@@ -68,8 +69,8 @@ Requires-Dist: PyQt5; extra == "pyqt5"
 [![Python Version](https://img.shields.io/pypi/pyversions/brainrender.svg)](https://pypi.org/project/brainrender)
 [![PyPI](https://img.shields.io/pypi/v/brainrender.svg)](https://pypi.org/project/brainrender)
 [![tests](https://github.com/brainglobe/brainrender/workflows/tests/badge.svg)](https://github.com/brainglobe/brainrender/actions)
+[![codecov](https://codecov.io/gh/brainglobe/brainrender/graph/badge.svg)](https://codecov.io/gh/brainglobe/brainrender)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
-[![Coverage Status](https://coveralls.io/repos/github/brainglobe/brainrender/badge.svg)](https://coveralls.io/github/brainglobe/brainrender)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)
 
 

{brainrender-2.1.2 → brainrender-2.1.3}/brainrender.egg-info/SOURCES.txt

@@ -1,13 +1,9 @@
-.coveragerc
 .gitignore
 .pre-commit-config.yaml
 LICENSE
 MANIFEST.in
 README.md
-getting_started.ipynb
 pyproject.toml
-run_all_examples.sh
-tox.ini
 .github/workflows/test_and_deploy.yml
 brainrender/__init__.py
 brainrender/_colors.py

{brainrender-2.1.2 → brainrender-2.1.3}/pyproject.toml

@@ -3,7 +3,7 @@ name = "brainrender"
 authors = [{name = "Federico Claudi, Adam Tyson, Luigi Petrucco", email="hello@brainglobe.info"}]
 description = "Visualisation and exploration of brain atlases and other anatomical data"
 readme = "README.md"
-requires-python = ">=3.8.0"
+requires-python = ">=3.9.0"
 dynamic = ["version"]
 
 dependencies = [
@@ -41,10 +41,11 @@ classifiers = [
 ]
 
 [project.urls]
-homepage = "https://brainglobe.info"
-bug_tracker = "https://github.com/brainglobe/brainrender/issues"
-source_code = "https://github.com/brainglobe/brainrender"
-user_support = "https://github.com/brainglobe/brainrender/issues"
+Homepage = "https://brainglobe.info/"
+"Source Code" = "https://github.com/brainglobe/brainrender"
+"Bug Tracker" = "https://github.com/brainglobe/brainrender/issues"
+Documentation = "https://brainglobe.info/documentation/brainrender/index.html"
+"User Support" = "https://forum.image.sc/tag/brainglobe"
 
 [project.optional-dependencies]
 dev = [
@@ -91,7 +92,7 @@ markers = [
 ]
 
 [tool.black]
-target-version = ['py38', 'py39', 'py310', 'py311']
+target-version = ['py39', 'py310', 'py311']
 skip-string-normalization = false
 line-length = 79
 
@@ -111,7 +112,34 @@ ignore = [
 # should revisit some of these.
 [tool.ruff]
 line-length = 79
-exclude = ["__init__.py","build",".eggs","paper","examples"]
+exclude = ["__init__.py","build",".eggs","examples"]
 select = ["I", "E", "F"]
 fix = true
 ignore = ["E501", "E402"]
+
+
+[tool.tox]
+legacy_tox_ini = """
+[tox]
+envlist = py{39,310,311}
+isolated_build = True
+
+[gh-actions]
+python =
+    3.9: py39
+    3.10: py310
+    3.11: py311
+
+[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-2.1.2/.coveragerc

@@ -1,14 +0,0 @@
-[RUN]
-omit =
-    brainrender/gui/*
-    brainrender/gui
-
-[report]
-omit =
-    brainrender/gui/*
-    brainrender/gui
-
-
-exclude_lines =
-    def keypress
-    pragma: no cover

brainrender-2.1.2/getting_started.ipynb

@@ -1,244 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "## Getting started with brainrender\n",
-    "This notebooks shows how to get started using brainrender.\n",
-    "It assumes that you have already installed, if not please install it now:\n",
-    "```\n",
-    "pip install brainrneder\n",
-    "```\n",
-    "\n",
-    "For more details about how to install brainrender, [please check the docs](https://brainglobe.info/documentation/brainrender/installation.html)\n",
-    "\n",
-    "### Content of this example\n",
-    "This notebook shows how to:\n",
-    "* Create a `Scene` in brainrender\n",
-    "* add `brain regions` to your scene\n",
-    "* add a `neuronal morphology` to your scene\n",
-    "\n",
-    "You can check the [examples](https://github.com/brainglobe/brainrender/tree/master/examples) and the [documentation](https://brainglobe.info/documentation/brainrender/) to learn more about how to use brainrender.\n",
-    "\n",
-    "In particular, if you are planning to use brainrender in a Jupyter Notebook, please read the [docs](https://brainglobe.info/documentation/brainrender/usage/using-notebooks.html) about using brainrender in a notebook, and have a look at the [notebooks workflow example](https://github.com/brainglobe/brainrender/blob/master/examples/notebook_workflow.ipynb)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 1,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "False"
-      ]
-     },
-     "execution_count": 1,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "import vedo\n",
-    "vedo.settings.default_backend == \"k3d\""
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "### Creating a scene and adding brain regions"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 1,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/html": [
-       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">  acronym   id                           name\n",
-       "<span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">0</span>    root  <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">997</span>                           root\n",
-       "<span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">1</span>    grey    <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">8</span>  Basic cell groups and regions\n",
-       "<span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">2</span>      CH  <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">567</span>                       Cerebrum\n",
-       "<span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">3</span>     CTX  <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">688</span>                Cerebral cortex\n",
-       "<span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">4</span>   CTXpl  <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">695</span>                 Cortical plate\n",
-       "</pre>\n"
-      ],
-      "text/plain": [
-       "  acronym   id                           name\n",
-       "\u001b[1;36m0\u001b[0m    root  \u001b[1;36m997\u001b[0m                           root\n",
-       "\u001b[1;36m1\u001b[0m    grey    \u001b[1;36m8\u001b[0m  Basic cell groups and regions\n",
-       "\u001b[1;36m2\u001b[0m      CH  \u001b[1;36m567\u001b[0m                       Cerebrum\n",
-       "\u001b[1;36m3\u001b[0m     CTX  \u001b[1;36m688\u001b[0m                Cerebral cortex\n",
-       "\u001b[1;36m4\u001b[0m   CTXpl  \u001b[1;36m695\u001b[0m                 Cortical plate\n"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
-   "source": [
-    "# Import Scene\n",
-    "from brainrender import Scene  # Scene handles the creation of your rendering!\n",
-    "\n",
-    "scene = Scene(title='My first rendering')  # create an instance of scene\n",
-    "'''\n",
-    "If you want to use any of the atlases supported by BrainGlobe's AtlasAPI,\n",
-    "specify the atlas name when creating an instance of `Scene`!\n",
-    "'''\n",
-    "\n",
-    "# Adding brain regions\n",
-    "scene.add_brain_region('MOs', 'TH', alpha=.5)\n",
-    "\n",
-    "'''\n",
-    "You can add any number of brain regions at once, just specify the regions' acronym or ID numbers.\n",
-    "If you are not sure what the acronym/ID is for your region, have a look try:\n",
-    "\n",
-    "`scene.atlas.lookup_df`\n",
-    "\n",
-    "or:\n",
-    "`print(scene.atlas.hierarchy)`\n",
-    "\n",
-    "which will show the hieararchical organization of the atlas' regions:\n",
-    "\n",
-    "root (997)\n",
-    "├── VS (73)\n",
-    "│   ├── AQ (140)\n",
-    "│   ├── V3 (129)\n",
-    "│   ├── V4 (145)\n",
-    "│   │   └── V4r (153)\n",
-    "│   ├── VL (81)\n",
-    "│   │   ├── SEZ (98)\n",
-    "│   │   └── chpl (108)\n",
-    "│   └── c (164)\n",
-    "├── fiber tracts (1009)\n",
-    "│   ├── cbf (960)\n",
-    "│   │   ├── arb (728)\n",
-    "...\n",
-    "\n",
-    "'''\n",
-    "\n",
-    "scene.atlas.lookup_df.head()"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "### Adding a neuronal morphology\n",
-    "Brainrender can load neuronal morphologies from .swc files"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 3,
-   "metadata": {
-    "scrolled": true
-   },
-   "outputs": [
-    {
-     "data": {
-      "text/html": [
-       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\"><span style=\"color: #ffa726; text-decoration-color: #ffa726\">╭──────────────────────────────────╮</span>\n",
-       "<span style=\"color: #ffa726; text-decoration-color: #ffa726\">│</span>  <span style=\"font-weight: bold\">                              </span>  <span style=\"color: #ffa726; text-decoration-color: #ffa726\">│</span>\n",
-       "<span style=\"color: #ffa726; text-decoration-color: #ffa726\">│</span>   <span style=\"color: #ff7043; text-decoration-color: #ff7043; font-weight: bold\">Scene actors</span>                   <span style=\"color: #ffa726; text-decoration-color: #ffa726\">│</span>\n",
-       "<span style=\"color: #ffa726; text-decoration-color: #ffa726\">│</span>   <span style=\"color: #ff7043; text-decoration-color: #ff7043; font-weight: bold\">────────────</span>                   <span style=\"color: #ffa726; text-decoration-color: #ffa726\">│</span>\n",
-       "<span style=\"color: #ffa726; text-decoration-color: #ffa726\">│</span>                                  <span style=\"color: #ffa726; text-decoration-color: #ffa726\">│</span>\n",
-       "<span style=\"color: #ffa726; text-decoration-color: #ffa726\">│</span>   <span style=\"color: #ffca28; text-decoration-color: #ffca28; font-weight: bold\">- root</span><span style=\"color: #ef6c00; text-decoration-color: #ef6c00\"> (type: </span><span style=\"color: #ffa726; text-decoration-color: #ffa726\">brain region</span><span style=\"color: #ef6c00; text-decoration-color: #ef6c00\">)</span>    <span style=\"color: #ffa726; text-decoration-color: #ffa726\">│</span>\n",
-       "<span style=\"color: #ffa726; text-decoration-color: #ffa726\">│</span>   <span style=\"color: #ffca28; text-decoration-color: #ffca28; font-weight: bold\">- title</span><span style=\"color: #ef6c00; text-decoration-color: #ef6c00\"> (type: </span><span style=\"color: #ffa726; text-decoration-color: #ffa726\">title</span><span style=\"color: #ef6c00; text-decoration-color: #ef6c00\">)</span>          <span style=\"color: #ffa726; text-decoration-color: #ffa726\">│</span>\n",
-       "<span style=\"color: #ffa726; text-decoration-color: #ffa726\">│</span>   <span style=\"color: #ffca28; text-decoration-color: #ffca28; font-weight: bold\">- MOs</span><span style=\"color: #ef6c00; text-decoration-color: #ef6c00\"> (type: </span><span style=\"color: #ffa726; text-decoration-color: #ffa726\">brain region</span><span style=\"color: #ef6c00; text-decoration-color: #ef6c00\">)</span>     <span style=\"color: #ffa726; text-decoration-color: #ffa726\">│</span>\n",
-       "<span style=\"color: #ffa726; text-decoration-color: #ffa726\">│</span>   <span style=\"color: #ffca28; text-decoration-color: #ffca28; font-weight: bold\">- TH</span><span style=\"color: #ef6c00; text-decoration-color: #ef6c00\"> (type: </span><span style=\"color: #ffa726; text-decoration-color: #ffa726\">brain region</span><span style=\"color: #ef6c00; text-decoration-color: #ef6c00\">)</span>      <span style=\"color: #ffa726; text-decoration-color: #ffa726\">│</span>\n",
-       "<span style=\"color: #ffa726; text-decoration-color: #ffa726\">│</span>   <span style=\"color: #ffca28; text-decoration-color: #ffca28; font-weight: bold\">- neuron1.swc</span><span style=\"color: #ef6c00; text-decoration-color: #ef6c00\"> (type: </span><span style=\"color: #ffa726; text-decoration-color: #ffa726\">Neuron</span><span style=\"color: #ef6c00; text-decoration-color: #ef6c00\">)</span>   <span style=\"color: #ffa726; text-decoration-color: #ffa726\">│</span>\n",
-       "<span style=\"color: #ffa726; text-decoration-color: #ffa726\">│</span>   <span style=\"color: #ffca28; text-decoration-color: #ffca28; font-weight: bold\">- neuron1.swc</span><span style=\"color: #ef6c00; text-decoration-color: #ef6c00\"> (type: </span><span style=\"color: #ffa726; text-decoration-color: #ffa726\">Neuron</span><span style=\"color: #ef6c00; text-decoration-color: #ef6c00\">)</span>   <span style=\"color: #ffa726; text-decoration-color: #ffa726\">│</span>\n",
-       "<span style=\"color: #ffa726; text-decoration-color: #ffa726\">│</span>                                  <span style=\"color: #ffa726; text-decoration-color: #ffa726\">│</span>\n",
-       "<span style=\"color: #ffa726; text-decoration-color: #ffa726\">╰──────────────────────────────────╯</span>\n",
-       "</pre>\n"
-      ],
-      "text/plain": [
-       "\u001b[38;2;255;167;38m╭──────────────────────────────────╮\u001b[0m\n",
-       "\u001b[38;2;255;167;38m│\u001b[0m  \u001b[1m \u001b[0m\u001b[1m                            \u001b[0m\u001b[1m \u001b[0m  \u001b[38;2;255;167;38m│\u001b[0m\n",
-       "\u001b[38;2;255;167;38m│\u001b[0m   \u001b[1;38;2;255;112;67mScene actors\u001b[0m                   \u001b[38;2;255;167;38m│\u001b[0m\n",
-       "\u001b[38;2;255;167;38m│\u001b[0m   \u001b[1;38;2;255;112;67m────────────\u001b[0m                   \u001b[38;2;255;167;38m│\u001b[0m\n",
-       "\u001b[38;2;255;167;38m│\u001b[0m                                  \u001b[38;2;255;167;38m│\u001b[0m\n",
-       "\u001b[38;2;255;167;38m│\u001b[0m   \u001b[1;38;2;255;202;40m- root\u001b[0m\u001b[38;2;239;108;0m (type: \u001b[0m\u001b[38;2;255;167;38mbrain region\u001b[0m\u001b[38;2;239;108;0m)\u001b[0m    \u001b[38;2;255;167;38m│\u001b[0m\n",
-       "\u001b[38;2;255;167;38m│\u001b[0m   \u001b[1;38;2;255;202;40m- title\u001b[0m\u001b[38;2;239;108;0m (type: \u001b[0m\u001b[38;2;255;167;38mtitle\u001b[0m\u001b[38;2;239;108;0m)\u001b[0m          \u001b[38;2;255;167;38m│\u001b[0m\n",
-       "\u001b[38;2;255;167;38m│\u001b[0m   \u001b[1;38;2;255;202;40m- MOs\u001b[0m\u001b[38;2;239;108;0m (type: \u001b[0m\u001b[38;2;255;167;38mbrain region\u001b[0m\u001b[38;2;239;108;0m)\u001b[0m     \u001b[38;2;255;167;38m│\u001b[0m\n",
-       "\u001b[38;2;255;167;38m│\u001b[0m   \u001b[1;38;2;255;202;40m- TH\u001b[0m\u001b[38;2;239;108;0m (type: \u001b[0m\u001b[38;2;255;167;38mbrain region\u001b[0m\u001b[38;2;239;108;0m)\u001b[0m      \u001b[38;2;255;167;38m│\u001b[0m\n",
-       "\u001b[38;2;255;167;38m│\u001b[0m   \u001b[1;38;2;255;202;40m- neuron1.swc\u001b[0m\u001b[38;2;239;108;0m (type: \u001b[0m\u001b[38;2;255;167;38mNeuron\u001b[0m\u001b[38;2;239;108;0m)\u001b[0m   \u001b[38;2;255;167;38m│\u001b[0m\n",
-       "\u001b[38;2;255;167;38m│\u001b[0m   \u001b[1;38;2;255;202;40m- neuron1.swc\u001b[0m\u001b[38;2;239;108;0m (type: \u001b[0m\u001b[38;2;255;167;38mNeuron\u001b[0m\u001b[38;2;239;108;0m)\u001b[0m   \u001b[38;2;255;167;38m│\u001b[0m\n",
-       "\u001b[38;2;255;167;38m│\u001b[0m                                  \u001b[38;2;255;167;38m│\u001b[0m\n",
-       "\u001b[38;2;255;167;38m╰──────────────────────────────────╯\u001b[0m\n"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
-   "source": [
-    "from brainrender.actors import Neuron  # import the Neuron actor class\n",
-    "\n",
-    "scene.add(Neuron(\"examples/data/neuron1.swc\"))\n",
-    "\n",
-    "'''\n",
-    "Scene.add can be used to add actors to your scene. \n",
-    "It accepts instances of the classes defined in brainrender.actors, \n",
-    "mesh objects (e.g. loaded with vedo) or path to 3D objects file (e.g. .obj files)\n",
-    "\n",
-    "To see what actors are in a scene, use scene.content\n",
-    "'''\n",
-    "scene.content"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "### Rendering\n",
-    "Rendering is as simple as `scene.render()`.\n",
-    "This will create a pop-up window with the interactive 3D rendering of your scene. \n",
-    "When you're done with it, press \"Esc\" to close the window!"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "scene.render()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.11.4"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 4
-}

brainrender-2.1.2/run_all_examples.sh

@@ -1,7 +0,0 @@
-for entry in "examples"/*
-do
-  for f in $entry/*
-  do
-    python $f
-  done
-done

brainrender-2.1.2/tox.ini

@@ -1,22 +0,0 @@
-[tox]
-envlist = py{39,310,311}
-isolated_build = True
-
-[gh-actions]
-python =
-    3.9: py39
-    3.10: py310
-    3.11: py311
-
-[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