Merge pull request #299 from ICB-DCM/feature_298_amici_update

Update AMICI to 0.11.8

deps/AMICI/.github/workflows/deploy_branch.yml

@@ -0,0 +1,30 @@
+name: Deploy Branch
+on: [push, pull_request, workflow_dispatch]
+
+jobs:
+  sdist:
+    name: Deploy Python Source Distribution
+
+    runs-on: ubuntu-20.04
+
+    steps:
+    - uses: actions/checkout@v1
+      with:
+        fetch-depth: 20
+
+    - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
+    - run: echo "SWIG=${AMICI_DIR}/ThirdParty/swig-4.0.1/install/bin/swig" >> $GITHUB_ENV
+
+    - name: Build swig4
+      run: |
+        sudo scripts/downloadAndBuildSwig.sh
+
+    - name: Create AMICI sdist
+      run: |
+        scripts/buildSdist.sh
+
+    - name: "Upload artifact: sdist"
+      uses: actions/upload-artifact@v1
+      with:
+        name: sdist
+        path: python/sdist/dist

deps/AMICI/.github/workflows/deploy_dockerhub.yml → deps/AMICI/.github/workflows/deploy_protected.yml

@@ -1,10 +1,21 @@
-# https://github.com/marketplace/actions/publish-docker
-name: Deploy to dockerhub
-on: [push]
+name: Deploy Protected
+on:
+  push:
+    branches:
+      - master
+      - develop
+  pull_request:
+    branches:
+      - master
+  workflow_dispatch:
+
 jobs:
-  build:
-    name: Deploy to dockerhub
-    runs-on: ubuntu-latest
+  dockerhub:
+    # https://github.com/marketplace/actions/publish-docker
+    name: Deploy Dockerhub
+
+    runs-on: ubuntu-20.04
+
     steps:
     - uses: actions/checkout@master
     - run: git archive -o docker/amici.tar.gz --format=tar.gz HEAD

deps/AMICI/.github/workflows/deploy_release.yml

@@ -0,0 +1,35 @@
+name: Deploy
+on:
+  release:
+    types:
+      - published
+
+jobs:
+  pypi:
+    name: Deploy PyPI
+
+    runs-on: ubuntu-20.04
+
+    steps:
+    - uses: actions/checkout@v1
+      with:
+        fetch-depth: 20
+
+    - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
+    - run: echo "SWIG=${AMICI_DIR}/ThirdParty/swig-4.0.1/install/bin/swig" >> $GITHUB_ENV
+
+    - name: Build swig4
+      run: |
+        sudo scripts/downloadAndBuildSwig.sh
+
+    - name: sdist
+      run: |
+        scripts/buildSdist.sh
+
+    - name: Publish a Python distribution to PyPI
+      uses: pypa/gh-action-pypi-publish@master
+      with:
+        user: __token__
+        password: ${{ secrets.pypi_password }}
+        packages_dir: python/sdist/dist
+

deps/AMICI/.github/workflows/test-benchmark-collection-models.yml → deps/AMICI/.github/workflows/test_benchmark_collection_models.yml

@@ -1,4 +1,4 @@
-name: Benchmark collection
+name: Benchmark Collection
 on:
   push:
     branches:
@@ -9,12 +9,13 @@ on:
     branches:
       - master
       - develop
+  workflow_dispatch:
 
 jobs:
   build:
-    name: Benchmark collection
+    name: Benchmark Collection
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
 
     steps:
     - uses: actions/checkout@v1
@@ -25,25 +26,24 @@ jobs:
     - name: apt
       run: |
         sudo apt-get update \
-          && sudo apt-get install -y swig3.0 libatlas-base-dev \
-          && sudo ln -s /usr/bin/swig3.0 /usr/bin/swig
+          && sudo apt-get install -y swig libatlas-base-dev
+
     - name: pip
       run: |
         pip3 install --upgrade --user wheel \
           && pip3 install --upgrade --user setuptools
     - run: pip3 install pytest shyaml
-    - run: |
-        echo ::add-path::${HOME}/.local/bin/
-        echo ::add-path::${GITHUB_WORKSPACE}/tests/performance/
+
+    - run: echo "${HOME}/.local/bin/" >> $GITHUB_PATH
+    - run: echo "${GITHUB_WORKSPACE}/tests/performance/" >> $GITHUB_PATH
+
     # install AMICI
     - name: Create AMICI sdist
       run: |
-        cd python/sdist \
-          && check_time.sh create_sdist /usr/bin/python3 setup.py sdist
+        cd python/sdist && /usr/bin/python3 setup.py sdist
     - name: Install AMICI sdist
       run: |
-        AMICI_PARALLEL_COMPILE=2 check_time.sh \
-            install_sdist pip3 install -v --user \
+        AMICI_PARALLEL_COMPILE=2 pip3 install -v --user \
             $(ls -t python/sdist/dist/amici-*.tar.gz | head -1)[petab]
 
     # retrieve test models