Add GL support for ubuntu, fix shapely bug in synapse intersections

SENeC-Initiative · Jan 29, 2024 · 58046c5 · 58046c5
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commit 58046c5
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Showing 5 changed files with 6 additions and 5 deletions.
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -77,7 +77,7 @@ jobs:
          if: ${{ matrix.os == 'windows-latest' }}
          run: |
            conda install python cmake geos boost
-           pip install "cython<3"
+           pip install setuptools "cython<3"
            pip install scipy numpy matplotlib pytest shapely pint PyOpenGL svg.path dxfgrabber networkx pyneuroml
            pip install nngt
            cd extra

diff --git a/extra/install_debian.sh b/extra/install_debian.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-sudo apt install cmake g++ python3 python3-dev python3-pip libgeos++-dev doxygen python3-matplotlib python3-tk libboost-dev
+sudo apt install cmake g++ python3 python3-dev python3-pip libgeos++-dev doxygen python3-matplotlib python3-tk libboost-dev freeglut3
 
 # workaround for PyOpenGL
 for lg in /usr/lib/x86_64-linux-gnu/libglut.so.3.*; do

diff --git a/src/pymodule/dense/environment b/src/pymodule/dense/environment
diff --git a/src/pymodule/dense/morphology/connections.py b/src/pymodule/dense/morphology/connections.py
@@ -323,7 +323,7 @@ def _get_synapses_intersection(axon_polygon, d_polygon, synapse_density, somas,
         if num_synapses > 0:
             s_soma = np.array(somas[i])
             t_soma = np.array(somas[j])
-            pos    = poly.centroid
+            pos    = np.array(poly.centroid.coords)[0]
             dist   = np.linalg.norm(s_soma - pos) \
                     + np.linalg.norm(t_soma - pos)
 

diff --git a/tests/todo/test_retraction.py b/tests/todo/test_retraction.py
@@ -57,7 +57,8 @@
 # ~ shape = geom.Shape.disk(radius=800)
 shape = geom.Shape.rectangle(1600, 1600)
 r_params = {"height": 250., "width": 250.}
-shape.random_obstacles(0.4, form="rectangle", params=r_params, heights=30., etching=20.)
+shape = shape.random_obstacles(
+    0.4, form="rectangle", params=r_params, heights=30., etching=20.)
 
 
 '''
+1 −1		__init__.py
+3 −5		examples/gen_obstacles.py
+28 −13		shape.py