refactor CI, fix pypi deploy (#1189)

* refactor CI, fix pypi deploy * cleanup * unfold AMICI build * fix name * fix yaml * fix script name * cleanup * install cpputest * fixups * install numpy * fix sphinx * ? * fixup
AMICI-dev · Aug 6, 2020 · 12795cb · 12795cb
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commit 12795cb
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diff --git a/.github/workflows/deploy_branch.yml b/.github/workflows/deploy_branch.yml
@@ -33,15 +33,11 @@ jobs:
     - 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
+          && sudo apt-get install -y swig
 
     - name: Create AMICI sdist
       run: |
-        cd python/sdist && /usr/bin/python3 setup.py sdist
+        scripts/buildSdist.sh
 
     - name: "Upload artifact: sdist"
       uses: actions/upload-artifact@v1

diff --git a/.github/workflows/deploy_release.yml b/.github/workflows/deploy_release.yml
@@ -53,24 +53,16 @@ jobs:
     - name: apt
       run: |
         sudo apt-get update \
-          && sudo apt-get install -y swig3.0
-    - name: pip
+          && sudo apt-get install -y swig
+          
+    - name: sdist
       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
+        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: ./build/python
+        packages_dir: python/sdist/dist
 
diff --git a/.github/workflows/test_benchmark_collection_models.yml b/.github/workflows/test_benchmark_collection_models.yml
@@ -25,7 +25,7 @@ jobs:
     - name: apt
       run: |
         sudo apt-get update \
-          && sudo apt-get install -y swig3.0 libatlas-base-dev
+          && sudo apt-get install -y swig libatlas-base-dev
           
     - name: pip
       run: |

diff --git a/.github/workflows/test_doc.yml b/.github/workflows/test_doc.yml
@@ -52,15 +52,12 @@ jobs:
         run: |
           sudo apt-get update \
             && sudo apt-get install -y \
-              cmake \
               g++ \
               libatlas-base-dev \
               libboost-serialization-dev \
               libhdf5-serial-dev \
-              python3-dev \
               python3-venv \
               swig \
-              lcov
       
       - name: Install python package
         run: |

diff --git a/.github/workflows/test_archive.yml → .github/workflows/test_install.yml b/.github/workflows/test_archive.yml → .github/workflows/test_install.yml
@@ -2,7 +2,7 @@ name: Installation
 on: [push]
 
 jobs:
-  build:
+  archive:
     name: Archive Install
 
     runs-on: ubuntu-latest
@@ -12,7 +12,6 @@ jobs:
     - run: git fetch --prune --unshallow
 
     - run: echo "::set-env name=AMICI_DIR::$(pwd)"
-    - run: echo "::set-env name=BNGPATH::${AMICI_DIR}/ThirdParty/BioNetGen-2.3.2"
 
     # install amici dependencies
     - name: apt
@@ -29,7 +28,7 @@ jobs:
     - name: Build suitesparse
       run: |
         scripts/buildSuiteSparse.sh
-
+     
     - name: Build sundials
       run: |
         scripts/buildSundials.sh
@@ -38,15 +37,46 @@ jobs:
       run: |
         scripts/buildCpputest.sh
 
-    - name: Build cpputest
+    - name: pip
       run: |
-        scripts/buildBNGL.sh
+        pip3 install numpy
 
     - name: Build AMICI
       run: |
-        pip3 install numpy \
-        && scripts/buildAmici.sh
-    
+        scripts/buildAmici.sh
+
     - name: Install python archive
       run: |
         scripts/installAmiciArchive.sh
+
+  sdist:
+    name: sdist Install
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@master
+    - run: git fetch --prune --unshallow
+
+    - run: echo "::set-env name=AMICI_DIR::$(pwd)"
+
+    # install amici dependencies
+    - name: apt
+      run: |
+        sudo apt-get update \
+          && sudo apt-get install -y \
+            g++ \
+            libatlas-base-dev \
+            libboost-serialization-dev \
+            libhdf5-serial-dev \
+            swig
+
+    - name: Create AMICI sdist
+      run: |
+        scripts/buildSdist.sh
+    
+    - name: Install python sdist
+      run: |
+        pip3 install -v --user $(ls -t python/sdist/dist/amici-*.tar.gz | head -1)
+                
+        
diff --git a/.github/workflows/test_large_model.yml b/.github/workflows/test_large_model.yml
@@ -24,7 +24,7 @@ jobs:
     - name: apt
       run: |
         sudo apt-get update \
-          && sudo apt-get install -y swig3.0 libatlas-base-dev
+          && sudo apt-get install -y swig libatlas-base-dev
     - name: pip
       run: |
         pip3 install --upgrade --user wheel \

diff --git a/.github/workflows/test_petab_test_suite.yml b/.github/workflows/test_petab_test_suite.yml
@@ -29,7 +29,7 @@ jobs:
         run: |
           sudo apt-get update \
             && sudo apt-get install -y \
-            swig3.0 \
+            swig \
             libatlas-base-dev \
             python3-venv
 

diff --git a/.github/workflows/test_python_cplusplus.yml b/.github/workflows/test_python_cplusplus.yml
@@ -47,26 +47,13 @@ jobs:
             libatlas-base-dev \
             libboost-serialization-dev \
             libhdf5-serial-dev \
-            python3-dev \
             python3-venv \
             swig \
             lcov
 
-    - name: Build suitesparse
+    - name: Build AMICI dependencies
       run: |
-        scripts/buildSuiteSparse.sh
-
-    - name: Build sundials
-      run: |
-        scripts/buildSundials.sh
-
-    - name: Build cpputest
-      run: |
-        scripts/buildCpputest.sh
-
-    - name: Build BNGL
-      run: |
-        scripts/buildBNGL.sh
+        scripts/buildDependencies.sh
 
     - name: Build AMICI
       run: |
@@ -149,25 +136,9 @@ jobs:
       run: |
         brew install hdf5 swig gcc cppcheck libomp
 
-    - name: Build suitesparse
-      run: |
-        scripts/buildSuiteSparse.sh
-
-    - name: Build sundials
-      run: |
-        scripts/buildSundials.sh
-
-    - name: Build cpputest
-      run: |
-        scripts/buildCpputest.sh
-
-    - name: Build BNG
-      run: |
-        scripts/buildBNGL.sh
-
     - name: Build AMICI
       run: |
-        scripts/buildAmici.sh
+        scripts/buildAll.sh
         
     - name: Install python package
       run: |

diff --git a/.github/workflows/test_valgrind.yml b/.github/workflows/test_valgrind.yml
@@ -2,11 +2,9 @@ name: C++ Tests
 on:
   push:
     branches:
-      - develop
       - master
   pull_request:
     branches:
-      - develop
       - master
 
 jobs:
@@ -33,23 +31,9 @@ jobs:
             swig \
             valgrind
 
-    - name: Build suitesparse
-      run: |
-        scripts/buildSuiteSparse.sh
-
-    - name: Build sundials
-      run: |
-        scripts/buildSundials.sh
-
-    - name: Build cpputest
-      run: |
-        scripts/buildCpputest.sh
-
     - name: Build AMICI
-      # TODO: should get rid of having to install numpy before
       run: |
-        pip3 install numpy \
-        && scripts/buildAmici.sh
+        scripts/buildAll.sh
 
     - name: C++ tests / Valgrind
       run: |

diff --git a/scripts/buildAll.sh b/scripts/buildAll.sh
@@ -7,8 +7,5 @@ set -e
 script_path=$(dirname "$BASH_SOURCE")
 script_path=$(cd "$script_path" && pwd)
 
-"${script_path}/buildSuiteSparse.sh"
-"${script_path}/buildSundials.sh"
-"${script_path}/buildCpputest.sh"
-"${script_path}/buildBNGL.sh"
+"${script_path}/buildDependencies.sh"
 "${script_path}/buildAmici.sh"
diff --git a/scripts/buildDependencies.sh b/scripts/buildDependencies.sh
@@ -0,0 +1,14 @@
+#!/bin/bash
+#
+# Build AMICI along with dependencies and test suite
+#
+set -e
+
+script_path=$(dirname "$BASH_SOURCE")
+script_path=$(cd "$script_path" && pwd)
+
+"${script_path}/buildSuiteSparse.sh"
+"${script_path}/buildSundials.sh"
+"${script_path}/buildCpputest.sh"
+"${script_path}/buildBNGL.sh"
+pip3 install numpy
diff --git a/scripts/buildSdist.sh b/scripts/buildSdist.sh
@@ -0,0 +1,14 @@
+#!/bin/bash
+#
+# Create AMICI sdist for PyPI deployment
+#
+set -e
+
+script_path=$(dirname "$BASH_SOURCE")
+amici_path=$(cd "$script_path/.." && pwd)
+
+pip3 install --upgrade --user wheel
+pip3 install --upgrade --user setuptools
+
+cd "${amici_path}/python/sdist"
+python3 setup.py sdist