Release 0.11.15

Merge pull request #1482 from AMICI-dev/release_0.11.15
AMICI-dev · Mar 31, 2021 · 4e671a5 · 4e671a5
2 parents 0913290 + a7731f2
commit 4e671a5
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diff --git a/.github/workflows/release_biosimulators.yml b/.github/workflows/release_biosimulators.yml
@@ -0,0 +1,32 @@
+name: Release to BioSimulators
+
+on:
+  release:
+    types:
+      - published
+
+jobs:
+  updateCliAndDockerImage:
+    name: Build and release downstream command-line interface and Docker image
+    runs-on: ubuntu-latest
+    env:
+      # Owner/repository-id for the GitHub repository for the downstream command-line interface and Docker image
+      DOWNSTREAM_REPOSITORY: biosimulators/Biosimulators_AMICI
+
+      # Username/token to use the GitHub API to trigger an action on the GitHub repository for the downstream
+      # command-line interface and Docker image. Tokens can be generated at https://github.com/settings/tokens.
+      # The token should have the scope `repo`
+      GH_ISSUE_USERNAME: ${{ secrets.BIOSIMULATORS_USERNAME }}
+      GH_ISSUE_TOKEN: ${{ secrets.BIOSIMULATORS_TOKEN }}
+    steps:
+      - name: Trigger GitHub action that will build and release the downstream command-line interface and Docker image
+        run: |
+          PACKAGE_VERSION="${GITHUB_REF/refs\/tags\/v/}"
+          WORKFLOW_FILE=ci.yml
+
+          curl \
+            -X POST \
+            -u ${GH_ISSUE_USERNAME}:${GH_ISSUE_TOKEN} \
+            -H "Accept: application/vnd.github.v3+json" \
+              https://api.github.com/repos/${DOWNSTREAM_REPOSITORY}/actions/workflows/${WORKFLOW_FILE}/dispatches \
+            -d "{\"inputs\": {\"simulatorVersion\": \"${PACKAGE_VERSION}\", \"simulatorVersionLatest\": \"true\"}}"
diff --git a/.github/workflows/test_performance.yml b/.github/workflows/test_performance.yml
@@ -4,7 +4,7 @@ on:
     branches:
       - develop
       - master
-      - speedup_reaction_ids
+      - compile_without_optimization
 
   pull_request:
     branches:
@@ -50,12 +50,7 @@ jobs:
     # import test model
     - name: Import test model
       run: |
-        cd CS_Signalling_ERBB_RAS_AKT \
-          && check_time.sh \
-          petab_import amici_import_petab -v \
-            -n 'CS_Signalling_ERBB_RAS_AKT_petab' \
-            -y 'FroehlichKes2018/PEtab/FroehlichKes2018.yaml' \
-            --no-compile
+        check_time.sh petab_import python tests/performance/test.py import
 
     - name: "Upload artifact: CS_Signalling_ERBB_RAS_AKT_petab"
       uses: actions/upload-artifact@v1
@@ -65,29 +60,60 @@ jobs:
 
     # install model package
     - name: Install test model
-      run: |
-        check_time.sh install_model \
-          python3 CS_Signalling_ERBB_RAS_AKT/CS_Signalling_ERBB_RAS_AKT_petab/setup.py install --user
+      run: >
+        check_time.sh install_model tests/performance/test.py compile;
+        for opt in O0 O1 O2;
+        do
+          check_time.sh install_model_${opt} tests/performance/test.py compile_${opt};
+        done
 
     # run simulations
     - name: forward_simulation
-      run: |
-        check_time.sh forward_simulation tests/performance/test.py forward_simulation
+      run: >
+        check_time.sh forward_simulation tests/performance/test.py  forward_simulation;
+        for opt in O0 O1 O2;
+        do
+          check_time.sh forward_simulation tests/performance/test.py forward_simulation_${opt};
+        done
     - name: forward_sensitivities
-      run: |
-        check_time.sh forward_sensitivities tests/performance/test.py forward_sensitivities
+      run: >
+        check_time.sh forward_sensitivities tests/performance/test.py forward_sensitivities;
+        for opt in O0 O1 O2;
+        do
+          check_time.sh forward_sensitivities tests/performance/test.py forward_sensitivities_${opt};
+        done
     - name: adjoint_sensitivities
-      run: |
-        check_time.sh adjoint_sensitivities tests/performance/test.py adjoint_sensitivities
+      run: >
+        check_time.sh adjoint_sensitivities tests/performance/test.py adjoint_sensitivities;
+        for opt in O0 O1 O2;
+        do
+          check_time.sh adjoint_sensitivities tests/performance/test.py adjoint_sensitivities_${opt};
+        done
     - name: forward_simulation_non_optimal_parameters
       run: |
-        check_time.sh forward_simulation_non_optimal_parameters tests/performance/test.py forward_simulation_non_optimal_parameters
+        check_time.sh forward_simulation_non_optimal_parameters tests/performance/test.py forward_simulation_non_optimal_parameters;
+        for opt in O0 O1 O2;
+        do
+          check_time.sh forward_simulation_non_optimal_parameters tests/performance/test.py forward_simulation_non_optimal_parameters_${opt};
+        done
     - name: adjoint_sensitivities_non_optimal_parameters
       run: |
-        check_time.sh adjoint_sensitivities_non_optimal_parameters tests/performance/test.py adjoint_sensitivities_non_optimal_parameters
+        check_time.sh adjoint_sensitivities_non_optimal_parameters tests/performance/test.py adjoint_sensitivities_non_optimal_parameters;
+        for opt in O0 O1 O2;
+        do
+          check_time.sh adjoint_sensitivities_non_optimal_parameters tests/performance/test.py adjoint_sensitivities_non_optimal_parameters_${opt};
+        done
     - name: forward_steadystate_sensitivities_non_optimal_parameters
       run: |
-        check_time.sh forward_steadystate_sensitivities_non_optimal_parameters tests/performance/test.py forward_steadystate_sensitivities_non_optimal_parameters
+        check_time.sh forward_steadystate_sensitivities_non_optimal_parameters tests/performance/test.py forward_steadystate_sensitivities_non_optimal_parameters;
+        for opt in O0 O1 O2;
+        do
+          check_time.sh forward_steadystate_sensitivities_non_optimal_parameters tests/performance/test.py forward_steadystate_sensitivities_non_optimal_parameters_${opt};
+        done
     - name: adjoint_steadystate_sensitivities_non_optimal_parameters
       run: |
-        check_time.sh adjoint_steadystate_sensitivities_non_optimal_parameters tests/performance/test.py adjoint_steadystate_sensitivities_non_optimal_parameters
+        check_time.sh adjoint_steadystate_sensitivities_non_optimal_parameters tests/performance/test.py adjoint_steadystate_sensitivities_non_optimal_parameters;
+        for opt in O0 O1 O2;
+        do
+          check_time.sh adjoint_steadystate_sensitivities_non_optimal_parameters tests/performance/test.py adjoint_steadystate_sensitivities_non_optimal_parameters_${opt};
+        done
diff --git a/.github/workflows/test_sbml_semantic_test_suite.yml b/.github/workflows/test_sbml_semantic_test_suite.yml
@@ -4,6 +4,7 @@ on:
     branches:
       - develop
       - master
+      - release**
   pull_request:
     paths:
       - .github/workflows/test_sbml_semantic_test_suite.yml

diff --git a/.gitignore b/.gitignore
@@ -193,3 +193,4 @@ coverage_SBMLSuite.xml
 Benchmark-Models-PEtab/
 
 
+CS_Signalling_ERBB_RAS_AKT/
Original file line number	Diff line number	Diff line change
Expand Up		@@ -193,3 +193,4 @@ coverage_SBMLSuite.xml
		Benchmark-Models-PEtab/


		CS_Signalling_ERBB_RAS_AKT/