Merge pull request #130 from OpenSourceBrain/development

Use py3.10 for testing

Author: pgleeson

.github/workflows/ci.yml

@@ -15,19 +15,17 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ 3.9 ]
+        python-version: [ "3.10" ]
         engine:
           - Arbor
           - "Brian2:2.4"
           - Brian2
           - EDEN
-          - "NEST:2.20.0"
           - "NEST:3.3"
           - PyNEST    
-          - PyNEST:2.20.0
           - PyNEST:3.1
-          - "NEURON:7.8.2"
-          - "PyNEURON:8.0.2"
+          - "NEURON"
+          - "PyNEURON:8.2.6"
           - PyNN
           - PyNN_Brian2
           - PyNN_NEURON

.github/workflows/ci_versions.yml

@@ -43,7 +43,7 @@ jobs:
     - name: Run simple OMV tests
       run: |
         omv install pyNeuroML
-        omv test -V utilities/tests/.test.ex9.jnmlbrian2.omt
+        omv test -V utilities/tests/.test.exIzh.jnmlnetpyne.omt
 
 
     - name: OMV final version info

omv/engines/getnetpyne.py

@@ -34,7 +34,6 @@ def install_netpyne(version=None):
 
         with working_dir(path):
             if sys.version_info.major == 2:
-                # pip_install([]'setuptools==42.0.1')
                 pip_install(
                     [
                         "kiwisolver==1.0.1",

omv/engines/getnrn.py

@@ -1,7 +1,6 @@
 import os
 import sys
 from subprocess import check_output as co
-from distutils.core import run_setup
 from omv.common.inout import inform
 from omv.common.inout import pip_install
 
@@ -11,7 +10,7 @@
 def install_neuron(version):
     if not version:
         if sys.version_info.major == 3:
-            version = "8.2.2"  # for pynn 0.11.0
+            version = "8.2.6"  # for pynn 0.11.0
         else:
             version = "7.6"
 
@@ -57,4 +56,4 @@ def install_neuron(version):
             print(co(["make", "install"]))
 
             os.chdir("src/nrnpython")
-            run_setup("./setup.py", ["install"])
+            print(co(["pip", "install", "."]))

omv/validation/rx_validator.py

@@ -8,7 +8,7 @@ def __init__(self):
 
     def generate_schema(self, schema_src):
         schema = self.parse_yaml_file(schema_src)
-        print("generating schema from %s" % schema)
+        print("Generating schema from %s" % schema)
         return self.rx.make_schema(schema)
 
     def parse_yaml_file(self, fname):
@@ -18,7 +18,7 @@ def parse_yaml_file(self, fname):
 
     def validate(self, schema_src, doc_src):
         doc = self.parse_yaml_file(doc_src)
-        print("validating document %s" % doc)
+        print("Validating the document: %s" % doc)
         return self.generate_schema(schema_src).check(doc)
 
 

omv/validation/validate.py

@@ -1,10 +1,10 @@
-from os.path import splitext, basename
+from os.path import splitext, basename, dirname
 from omv.validation.rx_validator import RXSchemaValidator
 from omv.validation.utils import topological_sort, all_types_in_schema
-from pkg_resources import resource_filename
 
 
 class OMVValidator(RXSchemaValidator):
+
     def __init__(self):
         super(OMVValidator, self).__init__()
         self.add_osb_prefix()
@@ -18,7 +18,11 @@ def register_osb_types(self):
         self.omv_types = {}
         from glob import glob
 
-        typedir = resource_filename("omv", "schemata/types/")
+        #typedir = resource_filename("omv", "schemata/types/")
+        typedir = dirname(dirname(__file__)) + "/schemata/types/"
+
+        print("Type directory: %s"%typedir)
+
         for omv in glob(typedir + "*.yaml") + glob(typedir + "/base/*.yaml"):
             tag = self.prefix + splitext(basename(omv))[0]
             print("registering", tag)

omv/validation/validate_mep.py

@@ -1,13 +1,14 @@
 #!/usr/bin/env python
 import sys
 from omv.validation.validate import OMVValidator
-from pkg_resources import resource_filename
+from os.path import dirname
 
 
 def validate(mep_src):
     s = OMVValidator()
     print("Validating document againt mep schema: ")
-    schema = resource_filename("omv", "schemata/mep.yaml")
+    #schema = resource_filename("omv", "schemata/mep.yaml")
+    schema = dirname(dirname(__file__)) + "/schemata/mep.yaml"
     print(s.validate(schema, mep_src))
 
 

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = OSBModelValidation
-version = 0.3.3
+version = 0.3.4
 author = Boris Marin, Padraig Gleeson
 author_email = [email protected]
 url = https://github.com/OpenSourceBrain/osb-model-validation
@@ -29,7 +29,6 @@ install_requires =
     pathlib; python_version<'3.4'
     docopt
     importlib-metadata; python_version<'3.8'
-    setuptools
 
 packages = find:
 
@@ -43,9 +42,11 @@ console_scripts =
 
 [options.package_data]
 * =
+        schemata/*
         *.yaml
         *.g
 
 
+
 [flake8]
 ignore = E501, E502, F403, F405