Merge pull request #1444 from StochSS/develop

2.5.1 Release

.github/workflows/run-integration-tests.yaml

@@ -0,0 +1,23 @@
+name: Run StochSS Integration Tests
+
+on:
+  push:
+    branches: [main, develop]
+
+jobs:
+  run-tests:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ ubuntu-20.04 ]
+
+    steps:
+    - name: Initialize environment
+      id: checkout
+      uses: actions/checkout@v2
+
+    - name: Run Integration Tests
+      id: run_integration_tests
+      uses: ./
+      with:
+        testin: '/stochss/stochss/tests/run_integration_tests.py'

.github/workflows/run-unit-tests.yml

@@ -0,0 +1,21 @@
+name: Run StochSS Unit Tests
+
+on: [push]
+
+jobs:
+  run-tests:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ ubuntu-20.04 ]
+
+    steps:
+    - name: Initialize environment
+      id: checkout
+      uses: actions/checkout@v2
+
+    - name: Run Unit Tests
+      id: run_unit_tests
+      uses: ./
+      with:
+        testin: '/stochss/stochss/tests/run_unit_tests.py'

Makefile

@@ -148,7 +148,7 @@ test: create_working_dir
 		-v $(DOCKER_WORKING_DIR):/home/jovyan/ \
 		-p 8888:8888 \
 		$(DOCKER_STOCHSS_IMAGE):latest \
-		/stochss/stochss/tests/run_tests.py
+		/stochss/stochss/tests/run_all_tests.py
 
 build_and_test: build test
 

__version__.py

@@ -5,7 +5,7 @@
 # @website https://github.com/stochss/stochss
 # =============================================================================
 
-__version__ = '2.5.0'
+__version__ = '2.5.1'
 __title__ = 'StochSS'
 __description__ = 'StochSS is an integrated development environment (IDE) \
                     for simulation of biochemical networks.'

jupyterhub/Dockerfile.jupyterhub

@@ -40,14 +40,14 @@ EXPOSE 8000
 
 # Install dockerspawner, oauth, postgres
 RUN python3 -m pip install --no-cache-dir \
-        jupyterhub \
+        jupyterhub==3.1.1 \
         oauthenticator==0.11.* \
         dockerspawner==0.11.* \
         psycopg2-binary==2.9.* \
         nbviewer==1.0.1 \
         notebook \
-        gillespy2==1.7.2 \
-        spatialpy==1.1.2 \
+        gillespy2==1.8.1 \
+        spatialpy==1.2.1 \
         plotly
 
 #  build the PUG pages

requirements.txt

@@ -3,7 +3,7 @@ python-libsedml==2.0.9
 python-libcombine==0.2.7
 pyabc==0.12.6
 escapism==1.0.1
-gillespy2==1.8.0
+gillespy2==1.8.1
 spatialpy==1.2.1
 stochss-compute[AWS]==1.0.1
 git+https://github.com/StochSS/sciope.git@master