Merge pull request #100 from NeuralEnsemble/development

For NML v2.1 release
NeuralEnsemble · Mar 22, 2021 · fc73ff0 · fc73ff0
2 parents 09f751f + dba03cf
commit fc73ff0
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -0,0 +1,51 @@
+name: Build
+
+on:
+  push:
+    branches: [ master, development ]
+  pull_request:
+    branches: [ master, development ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [2.7, 3.7, 3.8, 3.9]
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Start MongoDB
+      uses: supercharge/[email protected]
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+
+    - name: Build package
+      run: |
+        pip install .[full]
+
+    - name: Test with pytest
+      run: |
+        pytest
+
+    - name: Run examples
+      run: |
+        cd ./neuroml/examples && python run_all.py
+
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
diff --git a/.gitignore b/.gitignore
@@ -46,3 +46,7 @@ neuroml/test/*.h5
 /neuroml/examples/report.txt
 /neuroml/examples/test_files/report.txt
 /tests.log
+/notebooks/.ipynb_checkpoints
+/mongoo
+
+.venv
diff --git a/.travis.yml b/.travis.yml
@@ -8,12 +8,10 @@ addons:
 
 matrix:
   include:
-    - python: 3.7
-      dist: xenial
-      sudo: true
-    - python: 3.6
-    - python: 3.5
     - python: 2.7
+    - python: 3.7
+    - python: 3.8
+    - python: 3.9
 
 # command to install dependencies
 install:
@@ -22,7 +20,7 @@ install:
 
 # command to run tests and examples, e.g. python setup.py test
 script:
-  - cd ./neuroml/test && nosetests -vs
+  - cd ./neuroml/test && pytest -v --strict -W all
   - cd ../examples && python run_all.py
 
 services: mongodb
diff --git a/README.md b/README.md
@@ -1,5 +1,14 @@
 ## Introduction
 
+[![Travis CI](https://travis-ci.org/NeuralEnsemble/libNeuroML.svg?branch=master)](https://travis-ci.org/NeuralEnsemble/libNeuroML)
+[![PyPI](https://img.shields.io/pypi/v/libNeuroML)](https://pypi.org/project/libNeuroML/)
+[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/libNeuroML)](https://pypi.org/project/libNeuroML/)
+[![GitHub](https://img.shields.io/github/license/NeuralEnsemble/libNeuroML)](https://github.com/NeuralEnsemble/libNeuroML/blob/master/LICENSE)
+[![GitHub pull requests](https://img.shields.io/github/issues-pr/NeuralEnsemble/libNeuroML)](https://github.com/NeuralEnsemble/libNeuroML/pulls)
+[![GitHub issues](https://img.shields.io/github/issues/NeuralEnsemble/libNeuroML)](https://github.com/NeuralEnsemble/libNeuroML/issues)
+[![GitHub Org's stars](https://img.shields.io/github/stars/NeuralEnsemble?style=social)](https://github.com/NeuralEnsemble)
+[![Twitter Follow](https://img.shields.io/twitter/follow/NeuroML?style=social)](https://twitter.com/NeuroML)
+
 This package provides Python libNeuroML, for working with neuronal models specified in [NeuroML 2](http://neuroml.org/neuromlv2).
 
 For more about libNeuroML see:
@@ -29,8 +38,11 @@ Most of the work happens in the [development branch](https://github.com/NeuralEn
 
 ## Changelog
 
-### version 0.2.50
- - Updated to use the final stable Schema for NeuroML v2.0
+### version 0.2.54
+ - Using Schema for NeuroML v2.1. Better compatibility with Python 3
+
+ ### version 0.2.50
+  - Updated to use the final stable Schema for NeuroML v2.0
 
 ### version 0.2.47
  - Updated to use the final stable Schema for NeuroML v2beta5
@@ -44,7 +56,7 @@ Most of the work happens in the [development branch](https://github.com/NeuralEn
 
 ### version 0.2.2
  - Updated to use the Schema for NeuroML v2beta3
- - Ensures numpy & pytables are only required when using non-XML loaders/writers 
+ - Ensures numpy & pytables are only required when using non-XML loaders/writers
 
 ### version 0.2.0
  - Updated to use the Schema for NeuroML v2beta2
@@ -69,4 +81,3 @@ Most of the work happens in the [development branch](https://github.com/NeuralEn
 
 
 [![Build Status](https://api.travis-ci.org/NeuralEnsemble/libNeuroML.png)](https://travis-ci.org/NeuralEnsemble/libNeuroML)
-
diff --git a/doc/install.txt b/doc/install.txt
@@ -118,8 +118,15 @@ If everything worked your output should look something like this:
 
     OK
 
-Alternatively install and use nosetests:
+Alternatively install and use pytest:
 
 ::
 
-    nosetests -v
+    pytest -v --strict -W all
+
+
+To ignore some tests, like the mongodb test which requres a mongodb setup, run:
+
+::
+
+    pytest -v -k "not mongodb" --strict -W all
diff --git a/neuroml/__init__.py b/neuroml/__init__.py
@@ -1,7 +1,7 @@
 from .nml.nml import *  # allows importation of all neuroml classes
 
-__version__ = '0.2.50'
+__version__ = '0.2.55'
 __version_info__ = tuple(int(i) for i in __version__.split('.'))
 
 
-current_neuroml_version = "v2.0"
+current_neuroml_version = "v2.1"
diff --git a/neuroml/arraymorph.py b/neuroml/arraymorph.py
@@ -2,17 +2,15 @@
 Prototype for object model backend for the libNeuroML project
 """
 
-import math
 import numpy as np
-import numpy.ma as ma
 import neuroml
 
 
 class ArrayMorphology(neuroml.Morphology):
     """Core of the array-based object model backend.
 
     Provides the core arrays - vertices,connectivity etc.
-    node_types.        
+    node_types.
 
     The connectivity array is a list of indices pointing to which
     other element an element is attached. So for instance,
@@ -21,7 +19,7 @@ class ArrayMorphology(neuroml.Morphology):
 
     - EXAMPLE:
 
-        Vertices[3] and connectivity[3] refer to the vertex 
+        Vertices[3] and connectivity[3] refer to the vertex
         and connectivity of the same node.
 
     .. note::
@@ -43,7 +41,7 @@ def __init__(self,
 
         self.connectivity = np.array(connectivity)
         self.vertices = np.array(vertices)
-        
+
         self.id = id
 
         if np.any(physical_mask):
@@ -94,8 +92,8 @@ def valid_ids(self):
             valid_flag = (internal_id == external_id) * valid_flag
 
         return valid_flag
-            
-        
+
+
     @property
     def __all_nodes_satisfied(self):
         m = self.vertices.shape[0]
@@ -104,14 +102,14 @@ def __all_nodes_satisfied(self):
 
         all_nodes_satisfied = (m == n == p)
         return all_nodes_satisfied
-        
+
     @property
     def root_index(self):
-        return np.where(self.connectivity == -1)[0][0]    
+        return np.where(self.connectivity == -1)[0][0]
 
     @property
     def root_vertex(self):
-        return self.vertices[self.root_index]    
+        return self.vertices[self.root_index]
 
     @property
     def num_vertices(self):
@@ -122,7 +120,7 @@ def physical_indices(self):
         """returns indices of vertices which are physical"""
         physical_indices = np.where(self.physical_mask == 0)[0]
         return physical_indices
-        
+
     def children(self,index):
         """Returns an array with indexes of children"""
         return np.where(self.connectivity == index)
@@ -134,7 +132,7 @@ def to_root(self,index):
         """
 
         old_root_index = self.root_index
-        new_root_index = index        
+        new_root_index = index
         #do a tree traversal:
         parent_index = self.connectivity[index]
         grandparent_index=self.connectivity[parent_index]
@@ -155,13 +153,13 @@ def vertex(self,index):
 
     def __len__(self):
         return len(self.connectivity)
-        
+
     def pop(self,index):
         """
         TODO:This is failing tests (understandably) - need to fix!
         Deletes a node from the morphology, its children become
         children of the deleted node's parent.
-        """    
+        """
 
         self.vertices = np.delete(self.vertices,index)
         self.node_types = np.delete(self.node_types,index)
@@ -188,16 +186,16 @@ def to_neuroml_morphology(self,id=""):
 
     def segment_from_vertex_index(self,index):
         parent_index = self.connectivity[index]
-        
+
         node_x = self.vertices[index][0]
         node_y = self.vertices[index][1]
         node_z = self.vertices[index][2]
         node_d = self.vertices[index][3]
-        
+
         parent_x = self.vertices[parent_index][0]
         parent_y = self.vertices[parent_index][1]
         parent_z = self.vertices[parent_index][2]
-        parent_d = self.vertices[parent_index][3]                
+        parent_d = self.vertices[parent_index][3]
 
         p = neuroml.Point3DWithDiam(x=node_x,
                                     y=node_y,
@@ -209,7 +207,7 @@ def segment_from_vertex_index(self,index):
                                     z=parent_z,
                                     diameter=parent_d)
 
-        
+
         seg = neuroml.Segment(proximal=p,
                               distal=d,
                               id=index)
@@ -218,7 +216,7 @@ def segment_from_vertex_index(self,index):
             seg.parent = parent
 
         return seg
-        
+
 class SegmentList(object):
     """
     This class is a proxy, it returns a segment either
@@ -249,7 +247,7 @@ def __len__(self):
         segments which is number of vertices - 1 and minus all
         floating segments.
         """
-        
+
         num_vertices = self.arraymorph.num_vertices
         num_floating = np.sum(self.arraymorph.physical_mask)
         num_segments = num_vertices - num_floating -1
@@ -285,7 +283,7 @@ def append(self,segment):
         """
         dist_vertex_index = len(self.arraymorph.vertices)
         prox_vertex_index = dist_vertex_index + 1
-        
+
         prox_x = segment.proximal.x
         prox_y = segment.proximal.y
         prox_z = segment.proximal.z
@@ -295,7 +293,7 @@ def append(self,segment):
         dist_y = segment.distal.y
         dist_z = segment.distal.z
         distal_diam = segment.distal.diameter
-        
+
         prox_vertex = [prox_x,prox_y,prox_z,prox_diam]
         dist_vertex = [dist_x,dist_y,dist_z,distal_diam]
 
@@ -305,11 +303,11 @@ def append(self,segment):
             self.arraymorph.vertices = np.array([dist_vertex,prox_vertex])
 
         self.arraymorph.connectivity = np.append(self.arraymorph.connectivity,[-1,dist_vertex_index])
-        
+
         if len(self.arraymorph.physical_mask) == 0:
             self.arraymorph.physical_mask = np.array([0,0])
         else:
             self.arraymorph.physical_mask = np.append(self.arraymorph.physical_mask,[1,0])
-            
+
         segment_index = len(self) - 1
         self.instantiated_segments[segment_index] = segment
diff --git a/neuroml/arraymorph_load_time_benchmark.py b/neuroml/arraymorph_load_time_benchmark.py
@@ -1,5 +1,10 @@
+import numpy as np
+import neuroml
+import neuroml.arraymorph as am
+
+
 class Benchmark:
-    def __init__(num_segments):
+    def __init__(self, num_segments):
         self.num_segments = num_segments
 
     def set_up(self):