Release 0.15.0

Merge pull request #1927 from AMICI-dev/release_0.15.0

Author: dweindl

.clang-format

@@ -1,96 +1,13 @@
 ---
+BasedOnStyle: LLVM
+IndentWidth: 4
+---
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-# BasedOnStyle:  LLVM
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-
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.github/workflows/deploy_protected.yml

@@ -4,9 +4,10 @@ on:
     branches:
       - master
       - develop
+      - release**
   pull_request:
-    branches:
-      - master
+    paths:
+      - docker/Dockerfile
   workflow_dispatch:
 
 jobs:
@@ -27,6 +28,10 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - uses: actions/checkout@v3
     - run: git archive -o docker/amici.tar.gz --format=tar.gz HEAD
+    - name: Set up QEMU
+      uses: docker/setup-qemu-action@v2
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v2
     - name: Publish to Registry
       uses: elgohr/Publish-Docker-Github-Action@v4
       with:
@@ -36,3 +41,4 @@ jobs:
         workdir: docker/
         dockerfile: Dockerfile
         tag_names: true
+        platforms: linux/amd64,linux/arm64

.github/workflows/test_benchmark_collection_models.yml

@@ -44,7 +44,6 @@ jobs:
           && sudo apt-get install -y swig libatlas-base-dev
 
     - run: echo "${HOME}/.local/bin/" >> $GITHUB_PATH
-    - run: echo "${GITHUB_WORKSPACE}/tests/performance/" >> $GITHUB_PATH
 
     # install AMICI
     - name: Create AMICI sdist
@@ -61,3 +60,11 @@ jobs:
         git clone --depth 1 https://github.com/benchmarking-initiative/Benchmark-Models-PEtab.git \
           && export BENCHMARK_COLLECTION="$(pwd)/Benchmark-Models-PEtab/Benchmark-Models/" \
           && AMICI_PARALLEL_COMPILE=2 tests/benchmark-models/test_benchmark_collection.sh
+
+    # upload results
+    - uses: actions/upload-artifact@v3
+      with:
+        name: computation times
+        path: |
+          tests/benchmark-models/computation_times.csv
+          tests/benchmark-models/computation_times.png

.github/workflows/test_performance.yml

@@ -68,8 +68,8 @@ jobs:
     - name: "Upload artifact: CS_Signalling_ERBB_RAS_AKT_petab"
       uses: actions/upload-artifact@v3
       with:
-        name: CS_Signalling_ERBB_RAS_AKT
-        path: CS_Signalling_ERBB_RAS_AKT/CS_Signalling_ERBB_RAS_AKT_petab
+        name: model_performance_test
+        path: model_performance_test
 
     # install model package
     - name: Install test model

.github/workflows/test_python_cplusplus.yml

@@ -71,7 +71,7 @@ jobs:
 
     - name: Cache sonar files
       id: cache-sonar
-      uses: actions/cache@v1
+      uses: actions/cache@v3
       with:
         path: sonar_cache
         key: ${{ runner.os }}-sonar_cache

CHANGELOG.md

@@ -2,6 +2,46 @@
 
 ## v0.X Series
 
+### v0.15.0 (2023-01-11)
+
+Features
+* Improved logging by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1907
+
+  For Python: Don't print messages to stdout, but collect them in ReturnData
+  and forward them to python logging, making it easier to filter specific
+  messages or to disable output completely. Messages are also available via
+  `ReturnData.messages`.
+
+  **breaking change for C++ interface**:
+  Messages aren't printed to stdout by default, but are collected in
+  `ReturnData`. The user has to decide what to do with them.
+
+* MultiArch docker build by @FFroehlich
+  in https://github.com/AMICI-dev/AMICI/pull/1903
+* Added cmake target for cmake-format
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1909
+* Updated clang-format style, fixed clang-format target
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1908
+* Subsetting `ReturnData` fields by ID via `ReturnDataView.by_id`
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1911  https://github.com/AMICI-dev/AMICI/pull/1916
+
+Fixes
+* PEtab import: fixed handling of fixed parameters for rule targets
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1915
+* Fixed compiler warnings for matlab interface
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1919
+* Fixed pandas DeprecationWarning for Series.iteritems()
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1921
+* Fixed circular import in amici.petab_import_pysb
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1922
+* Fixed 'operator ==' swig warning
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1923
+* Prevent swig4.0.1 segfault
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1924
+
+**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.14.0...v0.15.0
+
+
 ### v0.14.0 (2022-11-23)
 
 #### Features: