Merge pull request #125 from brainglobe/v2.0

V2.0
brainglobe · Nov 23, 2020 · 52d7021 · 52d7021
2 parents 32dd43d + 71bfd95
commit 52d7021
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Showing 254 changed files with 484,408 additions and 215,179 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/.coveragerc b/.coveragerc
@@ -1,23 +1,14 @@
+[RUN]
+omit = 
+    brainrender/gui/*
+    brainrender/gui
+
 [report]
 omit = 
-    brainrender/ABA/volumetric/*
-    brainrender/atlases/custom_atlases/celegans.py
-    brainrender/atlases/custom_atlases/insects_brains_db.py
+    brainrender/gui/*
+    brainrender/gui
 
 
 exclude_lines =
+    def keypress
     pragma: no cover
-    def load_npy_from_gz
-    def save_npy_to_gz
-    def save_json
-    def getColor(rgb=None, hsv=None)
-    def hsv2rgb(hsv)
-    def rgb2hsv(rgb)
-    def rgb2int(rgb_tuple)
-    def colorMap
-    def check_colors(color)
-    continue
-    raise NotImplementedError
-    raise ValueError
-    raise FileNotFoundError
-    raise FileExistsError
diff --git a/.gitignore b/.gitignore
@@ -1,4 +1,23 @@
 # Ignored file types
+.DS_Store
+examples/*.mp4
+tests/*.mp4
+
+.pytest_cache
+__pycache__
+*.pyc
+.ipynb_checkpoints
+.pytest_cache/*
+.pytest_cache/
+__pycache__/*
+__pycache__/
+*/__pycache__
+brainrender/atlas_specific/gene_expression/__pycache__
+brainrender/atlas_specific/gene_expression/__pycache__/*
+brainrender/atlas_specific/__pycache__
+
+workspace.py
+workspace.ipynb
 brexport.html
 *.ckpt
 *.vscode
@@ -7,18 +26,9 @@ brexport.html
 *.idea
 *.pyc
 *.vtk
-*.obj
-# *.stl
 *.nrrd
-# *.swc
-*.svg
 *.tdms
 
-# These file formats are tracked
-# *.avi
-# *.png
-# *.mp4
-# *.jpg
 
 screenshots/*
 atlas_images/*

diff --git a/.travis.yml b/.travis.yml
@@ -1,46 +1,44 @@
-language: python
-services:
-  - xvfb
-matrix:
-  include:
-  - os: linux
-    python: 3.6
-    dist: bionic
-    env: PIP_CMD='pip install -e .[dev]' TEST_CMD='tests/travis/testing.sh'
-  - os: linux
-    python: 3.7
-    dist: bionic
-    env: PIP_CMD='pip install -e .[dev]' TEST_CMD='tests/travis/testing.sh'
-before_install:
-- wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
-- bash miniconda.sh -b -p $HOME/miniconda
-- export PATH="$HOME/miniconda/bin:$PATH"
-- hash -r
-- conda config --set always_yes yes --set changeps1 no
-- conda info -a
-install:
-- conda create -n test-environment python=$TRAVIS_PYTHON_VERSION
-- source activate test-environment
-- $PIP_CMD
-- conda info -a
-script:
-- travis_wait 20 bash $TEST_CMD
-after_success:
-- coveralls
-notifications:
-  email:
-    recipients:
-    - [email protected]
-    - [email protected]
-    on_success: change
-    on_failure: always
-deploy:
-  - provider: pypi
-    user: __token__
-    password:
-      secure: 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
-    distributions: sdist bdist_wheel
-    skip_existing: true
-    on:
-      branch: master
-      tags: true
+ language: python
+ services:
+   - xvfb
+ matrix:
+   include:
+   - os: linux
+     python: 3.6
+     dist: bionic
+   - os: linux
+     python: 3.7
+     dist: bionic
+ before_install:
+ - wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+ - bash miniconda.sh -b -p $HOME/miniconda
+ - export PATH="$HOME/miniconda/bin:$PATH"
+ - hash -r
+ - conda config --set always_yes yes --set changeps1 no
+ - conda info -a
+ install:
+ - conda create -n test-environment python=$TRAVIS_PYTHON_VERSION
+ - source activate test-environment
+ - pip install -e .[dev]
+ - conda info -a
+ script:
+ - travis_wait 50 pytest
+ after_success:
+ - coveralls
+ notifications:
+   email:
+     recipients:
+     - [email protected]
+     - [email protected]
+     on_success: change
+     on_failure: always
+ deploy:
+   - provider: pypi
+     user: __token__
+     password:
+       secure: 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
+     distributions: sdist bdist_wheel
+     skip_existing: true
+     on:
+       branch: master
+       tags: true
diff --git a/Docs/Media/CA1_coronal.png b/Docs/Media/CA1_coronal.png
diff --git a/Docs/Media/MOs_to_STR_mean_20200305_165259.png b/Docs/Media/MOs_to_STR_mean_20200305_165259.png
diff --git a/Docs/Media/SSp_to_STR_mean_20200305_165304.png b/Docs/Media/SSp_to_STR_mean_20200305_165304.png
diff --git a/Docs/Media/SSs_to_STR_mean_20200305_165302.png b/Docs/Media/SSs_to_STR_mean_20200305_165302.png
diff --git a/Docs/Media/TH_transparent_bg.png b/Docs/Media/TH_transparent_bg.png
diff --git a/Docs/Media/TH_white_bg.png b/Docs/Media/TH_white_bg.png
diff --git a/Docs/Media/ZI_cartoon.png b/Docs/Media/ZI_cartoon.png
diff --git a/Docs/Media/aba.png b/Docs/Media/aba.png
diff --git a/Docs/Media/barrel_ctx.png b/Docs/Media/barrel_ctx.png
diff --git a/Docs/Media/brainregions.png b/Docs/Media/brainregions.png
diff --git a/Docs/Media/cannula.png b/Docs/Media/cannula.png
diff --git a/Docs/Media/cannula2.png b/Docs/Media/cannula2.png
diff --git a/Docs/Media/cartoon.png b/Docs/Media/cartoon.png
diff --git a/Docs/Media/celegans_connectome.png b/Docs/Media/celegans_connectome.png
diff --git a/Docs/Media/celegans_synapses.png b/Docs/Media/celegans_synapses.png
diff --git a/Docs/Media/cells.gif b/Docs/Media/cells.gif
diff --git a/Docs/Media/clean_screenshots/celegans.png b/Docs/Media/clean_screenshots/celegans.png
diff --git a/Docs/Media/clean_screenshots/cells.png b/Docs/Media/clean_screenshots/cells.png
diff --git a/Docs/Media/clean_screenshots/gene_expr.png b/Docs/Media/clean_screenshots/gene_expr.png
diff --git a/Docs/Media/clean_screenshots/ibdb.png b/Docs/Media/clean_screenshots/ibdb.png
diff --git a/Docs/Media/clean_screenshots/inj_site.png b/Docs/Media/clean_screenshots/inj_site.png
diff --git a/Docs/Media/clean_screenshots/neurons.png b/Docs/Media/clean_screenshots/neurons.png
diff --git a/Docs/Media/clean_screenshots/neurons2.png b/Docs/Media/clean_screenshots/neurons2.png
diff --git a/Docs/Media/clean_screenshots/neuropixel.png b/Docs/Media/clean_screenshots/neuropixel.png
diff --git a/Docs/Media/clean_screenshots/optic_fiber.png b/Docs/Media/clean_screenshots/optic_fiber.png
diff --git a/Docs/Media/clean_screenshots/regions.png b/Docs/Media/clean_screenshots/regions.png
diff --git a/Docs/Media/clean_screenshots/skull.png b/Docs/Media/clean_screenshots/skull.png
diff --git a/Docs/Media/clean_screenshots/streamlines.png b/Docs/Media/clean_screenshots/streamlines.png
diff --git a/Docs/Media/clean_screenshots/tractography.png b/Docs/Media/clean_screenshots/tractography.png
diff --git a/Docs/Media/electrodes.png b/Docs/Media/electrodes.png
diff --git a/Docs/Media/humanbrainexp.png b/Docs/Media/humanbrainexp.png
diff --git a/Docs/Media/labelled_cells.png b/Docs/Media/labelled_cells.png
diff --git a/Docs/Media/locust.png b/Docs/Media/locust.png
diff --git a/Docs/Media/logotransparent.png b/Docs/Media/logotransparent.png
diff --git a/Docs/Media/logotransparent2.png b/Docs/Media/logotransparent2.png
diff --git a/Docs/Media/logowhite.png b/Docs/Media/logowhite.png
diff --git a/Docs/Media/morphology.png b/Docs/Media/morphology.png
diff --git a/Docs/Media/neuron.png b/Docs/Media/neuron.png
diff --git a/Docs/Media/neuron2.png b/Docs/Media/neuron2.png
diff --git a/Docs/Media/neuron3.png b/Docs/Media/neuron3.png
diff --git a/Docs/Media/neuron_gif.gif b/Docs/Media/neuron_gif.gif
diff --git a/Docs/Media/neurons.png b/Docs/Media/neurons.png
diff --git a/Docs/Media/neurons2.png b/Docs/Media/neurons2.png
diff --git a/Docs/Media/neurons3.png b/Docs/Media/neurons3.png
diff --git a/Docs/Media/neurons_transparent.png b/Docs/Media/neurons_transparent.png
diff --git a/Docs/Media/sharp_track_probe.png b/Docs/Media/sharp_track_probe.png
diff --git a/Docs/Media/skull.png b/Docs/Media/skull.png
diff --git a/Docs/Media/streamlines.png b/Docs/Media/streamlines.png
diff --git a/Docs/Media/streamlines2.png b/Docs/Media/streamlines2.png
diff --git a/Docs/Media/streamlines_animation.mp4 b/Docs/Media/streamlines_animation.mp4
diff --git a/Docs/Media/streamlinespretty.png b/Docs/Media/streamlinespretty.png
diff --git a/Docs/Media/summary_figure.png b/Docs/Media/summary_figure.png
diff --git a/Docs/Media/tractography.png b/Docs/Media/tractography.png
diff --git a/Docs/custom_atlases.md b/Docs/custom_atlases.md