Merge pull request #1187 from ICB-DCM/release_0_11_4

Release 0.11.4
AMICI-dev · Aug 6, 2020 · 93cc940 · 93cc940
2 parents a4324d0 + 02a8a31
commit 93cc940
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diff --git a/.github/workflows/deploy_branch.yml b/.github/workflows/deploy_branch.yml
@@ -0,0 +1,50 @@
+name: Deploy Branch
+on: [push]
+jobs:
+  dockerhub:
+    # https://github.com/marketplace/actions/publish-docker
+    name: Deploy Dockerhub
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@master
+    - run: git archive -o docker/amici.tar.gz --format=tar.gz HEAD
+    - name: Publish to Registry
+      uses: elgohr/[email protected]
+      with:
+        name: dweindl/amici
+        username: ${{ secrets.DOCKER_USERNAME }}
+        password: ${{ secrets.DOCKER_PASSWORD }}
+        workdir: docker/
+        dockerfile: Dockerfile
+        tag_names: true
+
+  sdist:
+    name: Deploy Python Source Distribution
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v1
+      with:
+        fetch-depth: 20
+
+    - name: apt
+      run: |
+        sudo apt-get update \
+          && sudo apt-get install -y swig3.0
+    - name: pip
+      run: |
+        pip3 install --upgrade --user wheel \
+          && pip3 install --upgrade --user setuptools
+
+    - name: Create AMICI sdist
+      run: |
+        cd python/sdist && /usr/bin/python3 setup.py sdist
+
+    - name: "Upload artifact: sdist"
+      uses: actions/upload-artifact@v1
+      with:
+        name: sdist
+        path: python/sdist/dist
diff --git a/.github/workflows/deploy_dockerhub.yml b/.github/workflows/deploy_dockerhub.yml
diff --git a/.github/workflows/deploy_gh_pages.yml b/.github/workflows/deploy_gh_pages.yml
diff --git a/.github/workflows/deploy_pypi.yml b/.github/workflows/deploy_pypi.yml
diff --git a/.github/workflows/deploy_release.yml b/.github/workflows/deploy_release.yml
@@ -0,0 +1,76 @@
+name: Deploy
+on:
+  release:
+    types:
+      - published
+
+jobs:
+  pages:
+    name: Deploy GH-Pages
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@master
+    - run: git fetch --prune --unshallow
+
+    - run: echo "::set-env name=AMICI_DIR::$(pwd)"
+
+    - name: apt
+      run: |
+        sudo apt-get update \
+          && sudo apt-get install -y \
+          bison \
+          ragel \
+          graphviz \
+          texlive-latex-extra
+
+    - name: Build doxygen
+      run: |
+        sudo scripts/downloadAndBuildDoxygen.sh
+
+    - name: Run doxygen
+      run: |
+        scripts/run-doxygen.sh
+        
+    - name: Deploy 🚀
+      uses: JamesIves/[email protected]
+      with:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        BRANCH: gh-pages # The branch the action should deploy to.
+        FOLDER: doc # The folder the action should deploy.
+
+  pypi:
+    name: Deploy PyPI
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v1
+      with:
+        fetch-depth: 20
+
+    - name: apt
+      run: |
+        sudo apt-get update \
+          && sudo apt-get install -y swig3.0
+    - name: pip
+      run: |
+        pip3 install --upgrade --user wheel \
+          && pip3 install --upgrade --user setuptools
+
+    - name: Create AMICI sdist
+      run: |
+        cd python/sdist && python3 setup.py sdist
+        
+    - name: Check build
+      run: |
+        ls ./build/python
+
+    - name: Publish a Python distribution to PyPI
+      uses: pypa/gh-action-pypi-publish@master
+      with:
+        user: __token__
+        password: ${{ secrets.pypi_password }}
+        packages_dir: ./build/python
+
diff --git a/.github/workflows/deploy_sdist.yml b/.github/workflows/deploy_sdist.yml
diff --git a/.github/workflows/test_cplusplus_osx.yml → .github/workflows/test_archive.yml b/.github/workflows/test_cplusplus_osx.yml → .github/workflows/test_archive.yml
@@ -1,11 +1,11 @@
-name: C++/Python testsuite
+name: Installation
 on: [push]
 
 jobs:
   build:
-    name: OSX
+    name: Archive Install
 
-    runs-on: macos-latest
+    runs-on: ubuntu-latest
 
     steps:
     - uses: actions/checkout@master
@@ -15,9 +15,16 @@ jobs:
     - run: echo "::set-env name=BNGPATH::${AMICI_DIR}/ThirdParty/BioNetGen-2.3.2"
 
     # install amici dependencies
-    - name: homebrew
+    - name: apt
       run: |
-        brew install hdf5 swig gcc cppcheck libomp
+        sudo apt-get update \
+          && sudo apt-get install -y \
+            cmake \
+            g++ \
+            libatlas-base-dev \
+            libboost-serialization-dev \
+            libhdf5-serial-dev \
+            swig
 
     - name: Build suitesparse
       run: |
@@ -37,28 +44,9 @@ jobs:
 
     - name: Build AMICI
       run: |
-        scripts/buildAmici.sh
+        pip3 install numpy \
+        && scripts/buildAmici.sh
     
     - name: Install python archive
       run: |
         scripts/installAmiciArchive.sh
-        
-    - name: Install python package
-      run: |
-        scripts/installAmiciSource.sh
-        
-    - name: cppcheck
-      run: |
-        scripts/run-cppcheck.sh
-        
-    - name: Python tests
-      run: |
-        scripts/run-python-tests.sh
-
-    - name: C++ tests
-      run: |
-        scripts/run-cpputest.sh
-        
-    - name: sphinx
-      run: |
-        scripts/run-sphinx.sh
diff --git a/...lows/test-benchmark-collection-models.yml → ...lows/test_benchmark_collection_models.yml b/...lows/test-benchmark-collection-models.yml → ...lows/test_benchmark_collection_models.yml
@@ -1,4 +1,4 @@
-name: Benchmark collection
+name: Benchmark Collection
 on:
   push:
     branches:
@@ -12,7 +12,7 @@ on:
 
 jobs:
   build:
-    name: Benchmark collection
+    name: Benchmark Collection
 
     runs-on: ubuntu-latest