CI: add script to download test data

.github/workflows/test-tutorials.yml

@@ -1,4 +1,4 @@
-name: Tutorials
+name: Test tutorials
 
 on: [push]
 
@@ -31,6 +31,10 @@ jobs:
         python -m pip install --upgrade pip
         python -m pip install pathos pygraphviz neuron cloud-volume k3d scikit-image open3d
         python -m pip install -e .[test-notebook,all]
+    - name: Download test data
+      run: |
+        chmod +x download_test_data.sh
+        ./download_test_data.sh
     - name: Run tutorials
       uses: coactions/setup-xvfb@v1
       env:

.gitignore

@@ -132,3 +132,7 @@ ENV/
 MANIFEST
 
 tmp/
+
+# Test data
+mmc2
+WannerAA*

docs/examples/0_io/plot_00_io_skeletons.py

@@ -36,7 +36,7 @@
 # %%
 import navis
 skeletons = navis.read_swc(
-    '~/Downloads/mmc2/skeletons_swc.zip',
+    './mmc2/skeletons_swc.zip',
     include_subdirs=True
 )
 skeletons
@@ -47,7 +47,7 @@
 # %%
 # Load only the first 10 skeletons
 sample = navis.read_swc(
-    '~/Downloads/mmc2/skeletons_swc.zip',
+    './mmc2/skeletons_swc.zip',
     include_subdirs=True,
     limit=10
 )
@@ -58,7 +58,7 @@
 
 # %%
 # For this I extraced the skeletons_swc.zip archive
-s = navis.read_swc('~/Downloads/mmc2/swc/CENT/11519759.swc')
+s = navis.read_swc('./mmc2/swc/CENT/11519759.swc')
 s
 
 # %%
@@ -75,22 +75,22 @@
 # %%
 
 # Write a single neuron:
-navis.write_swc(s, '~/Downloads/mmc2/my_neuron.swc')
+navis.write_swc(s, './mmc2/my_neuron.swc')
 
 # %%
 
 # Write a whole list of skeletons to a folder and use the neurons' `name` property as filename:
-navis.write_swc(sample, '~/Downloads/mmc2/{neuron.name}.swc')
+navis.write_swc(sample, './mmc2/{neuron.name}.swc')
 
 # %%
 
 # Write directly to a zip file:
-navis.write_swc(sample, '~/Downloads/mmc2/skeletons.zip')
+navis.write_swc(sample, './mmc2/skeletons.zip')
 
 # %%
 
 # Write directly to a zip file and use the neuron name as filename:
-navis.write_swc(sample, '~/Downloads/mmc2/{neuron.name}[email protected]')
+navis.write_swc(sample, './mmc2/{neuron.name}[email protected]')
 
 # %%
 # See [`navis.write_swc`][] for further details!
@@ -104,12 +104,12 @@
 
 # %%
 # Read a single file
-s = navis.read_nmx('~/Downloads/WannerAA201605_SkeletonsGlomeruli/Neuron_id0001.nmx')
+s = navis.read_nmx('./WannerAA201605_SkeletonsGlomeruli/Neuron_id0001.nmx')
 s
 
 # %%
 # Read all files in folder
-nl = navis.read_nmx('~/Downloads/WannerAA201605_SkeletonsGlomeruli/')
+nl = navis.read_nmx('./WannerAA201605_SkeletonsGlomeruli/')
 nl
 
 # %%

download_test_data.sh

@@ -0,0 +1,11 @@
+#!/bin/sh
+# This script downloads the test data used in tutorials and examples
+mkdir -p -- "docs/examples/0_io/mmc2"
+curl -o docs/examples/0_io/mmc2/skeletons_swc.zip https://flyem.mrc-lmb.cam.ac.uk/flyconnectome/misc/skeletons_swc.zip
+
+mkdir -p -- "docs/examples/0_io/mmc2/swc/CENT"
+curl -o docs/examples/0_io/mmc2/swc/CENT/11519759.swc https://flyem.mrc-lmb.cam.ac.uk/flyconnectome/misc/11519759.swc
+
+curl -o docs/examples/0_io/WannerAA201605_SkeletonsGlomeruli.zip https://flyem.mrc-lmb.cam.ac.uk/flyconnectome/misc/WannerAA201605_SkeletonsGlomeruli.zip
+cd docs/examples/0_io
+unzip WannerAA201605_SkeletonsGlomeruli.zip