Merge pull request #60 from ModECI/development

To v0.3.2

.github/workflows/ci.yml

@@ -12,9 +12,9 @@ jobs:
     name: Format
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v1
-    - uses: actions/setup-python@v2
-    - uses: pre-commit/action@v2.0.0
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v3
+    - uses: pre-commit/action@v3.0.0
       with:
         extra_args: --hook-stage manual --all-files
 
@@ -28,9 +28,9 @@ jobs:
         runs-on: [ubuntu-latest, macos-latest, windows-latest]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python  ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v3
       with:
         python-version:  ${{ matrix.python-version }}
 
@@ -60,11 +60,7 @@ jobs:
         cd ../neuroml2
         python neuroml2_spec.py
 
-        pip install pyneuroml
-
-        # Requires: pip install pyneuroml
-        pynml -validate hello_world_neuroml.net.nml
-        pynml -validate TestNeuroML.xml
+        # Note: NeuroML files will be validated with OMV below
 
     - name: Run pytest
       run: |
@@ -78,7 +74,6 @@ jobs:
           cd examples
           python Example1.py
 
-
     - name: Install MDF
       run: |
 
@@ -89,8 +84,9 @@ jobs:
           python arrays.py -run   # test one example
 
     - name: Build Documentation
+      if: ${{ matrix.python-version != '3.7'}}
       run: |
-
+        # Note: contributors generation below fails on py 3.7 due to pandas version...
         pip install .[docs]
         cd docs
         python generate.py
@@ -99,6 +95,20 @@ jobs:
         make clean
         make html
 
+    - name: Install and test with OMV
+      if: ${{ matrix.runs-on != 'windows-latest' }}
+      run: |
+        # Note: OMV not well tested on Windows...
+
+        pip install git+https://github.com/OpenSourceBrain/osb-model-validation
+        pip install scipy sympy matplotlib cython pandas tables
+
+        # Run OMV tests on all engines
+        cd examples
+        omv all -V
+
+        omv list -V # list installed engines
+
     - name: Final version info
       run: |
           pip list

.github/workflows/static.yml

@@ -32,7 +32,7 @@ jobs:
     - name: Checkout
       uses: actions/checkout@v3
 
-    - name: Set up Python 
+    - name: Set up Python
       uses: actions/setup-python@v2
       with:
         python-version: 3.9
@@ -69,4 +69,3 @@ jobs:
     - name: Deploy to GitHub Pages
       id: deployment
       uses: actions/deploy-pages@v2
-

docs/contributors.py

@@ -17,50 +17,57 @@
 len_per_info = len(per_info)
 
 empty_list = []
+max_tries = 100
+
 for i in range(len_per_info):
     url = per_info[i]
     print(url)
     data = requests.get(url=url)
     requests_status = "unknown"
-    while (requests_status == "unknown") or (requests_status == "unsuccessful"):
+    while max_tries > 0 and (
+        (requests_status == "unknown") or (requests_status == "unsuccessful")
+    ):
         if data.status_code == 200:
             requests_status = "successful"
+            print("   Received: %s" % data.json())
             empty_list.append(data.json())
         else:
             # handle failure on requests to the url for mac os
             requests_status = "unsuccessful"
             print(f"Failed to get data from: {url}")
             # make request again to get data from the url
             data = requests.get(url=url)
+            max_tries -= 1
 
-df1 = pd.DataFrame(empty_list)
-df1["name"] = df1["name"].fillna("")
-name = df1["name"]
-login = df1["login"]
-url_html = df1["html_url"]
-url_id = df1["id"]
+if len(empty_list) > 0:
+    df1 = pd.DataFrame(empty_list)
+    df1["name"] = df1["name"].fillna(df1["login"])
+    name = df1["name"]
+    login = df1["login"]
+    url_html = df1["html_url"]
+    url_id = df1["id"]
 
-login_html = list(zip(name, login, url_html))
-zip_dict = dict(zip(url_id, login_html))
+    login_html = list(zip(name, login, url_html))
+    zip_dict = dict(zip(url_id, login_html))
 
-file = "sphinx/source/api/Contributors.md"
-with open(file, "w") as f:
-    print(
-        textwrap.dedent(
-            """\
-        (Modelspec:contributors)=
+    file = "sphinx/source/api/Contributors.md"
+    with open(file, "w") as f:
+        print(
+            textwrap.dedent(
+                """\
+            (Modelspec:contributors)=
 
-        # Modelspec contributors
+            # Modelspec contributors
 
-        This page list names and Github profiles of contributors to Modelspec, listed in no particular order.
-        This page is generated periodically, most recently on {}.""".format(
-                date.today()
-            )
-        ),
-        file=f,
-    )
+            This page list names and Github profiles of contributors to Modelspec, listed in no particular order.
+            This page is generated periodically, most recently on {}.""".format(
+                    date.today()
+                )
+            ),
+            file=f,
+        )
 
-    print("", file=f)
+        print("", file=f)
 
-    for key, val in zip_dict.items():
-        print("- {} ([@{}]({}))".format(val[0], val[1], val[2]), file=f)
+        for key, val in zip_dict.items():
+            print("- {} ([@{}]({}))".format(val[0], val[1], val[2]), file=f)

docs/sphinx/source/api/Contributors.md

@@ -3,9 +3,12 @@
 # Modelspec contributors
 
 This page list names and Github profiles of contributors to Modelspec, listed in no particular order.
-This page is generated periodically, most recently on 2023-07-05.
+This page is generated periodically, most recently on 2023-09-12.
 
 - Padraig Gleeson ([@pgleeson](https://github.com/pgleeson))
+- Manifest Chakalov  ([@mqnifestkelvin](https://github.com/mqnifestkelvin))
 - David Turner ([@davidt0x](https://github.com/davidt0x))
+- Peace Ododo ([@Onoyiza](https://github.com/Onoyiza))
 - Parikshit Singh Rathore ([@parikshit14](https://github.com/parikshit14))
-- Katherine Mantel ([@kmantel](https://github.com/kmantel))
+- Ankur Sinha ([@sanjayankur31](https://github.com/sanjayankur31))
+- kmantel ([@kmantel](https://github.com/kmantel))

examples/neuroml2/.test.validate.omt

@@ -0,0 +1,5 @@
+# Script for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation
+
+# This test will validate NeuroML 2 files in the current directory using: jnml -validate *.nml
+target: "*.nml TestNeuroML.xml"
+engine: jNeuroML_validate

setup.cfg

@@ -5,9 +5,9 @@ description = A common JSON/YAML based format for compact model specification
 long_description = file: README.md
 long_description_content_type = text/markdown
 url = https://github.com/ModECI/modelspec
-author = Padraig Gleeson; ...
+author = ModECI contributors
 author_email = [email protected]
-maintainer = Padraig Gleeson; ...
+maintainer = Padraig Gleeson, David Turner
 maintainer_email = [email protected]
 license = LGPLv3
 license_files = LICENSE

src/modelspec/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.3.1"
+__version__ = "0.3.2"
 
 from .base_types import Base, define, has, field, fields, optional, instance_of, in_
 

test_all.sh

@@ -31,14 +31,21 @@ cd ../..
 
 pytest tests -v
 
+## Run OMV tests
+
+omv all -V
+
 
 ## Generate the docs
 
 cd docs
 python generate.py
+python contributors.py
 cd sphinx
 make clean
 make html
 cd ..
 
+## Format all file
+
 pre-commit run --all-files