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Release 0.15.0
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Merge pull request #1927 from AMICI-dev/release_0.15.0
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dweindl authored Jan 12, 2023
2 parents b5177d9 + d675172 commit 0859bde
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105 changes: 11 additions & 94 deletions .clang-format
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10 changes: 8 additions & 2 deletions .github/workflows/deploy_protected.yml
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Expand Up @@ -4,9 +4,10 @@ on:
branches:
- master
- develop
- release**
pull_request:
branches:
- master
paths:
- docker/Dockerfile
workflow_dispatch:

jobs:
Expand All @@ -27,6 +28,10 @@ jobs:
python-version: ${{ matrix.python-version }}
- uses: actions/checkout@v3
- run: git archive -o docker/amici.tar.gz --format=tar.gz HEAD
- name: Set up QEMU
uses: docker/setup-qemu-action@v2
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
- name: Publish to Registry
uses: elgohr/Publish-Docker-Github-Action@v4
with:
Expand All @@ -36,3 +41,4 @@ jobs:
workdir: docker/
dockerfile: Dockerfile
tag_names: true
platforms: linux/amd64,linux/arm64
9 changes: 8 additions & 1 deletion .github/workflows/test_benchmark_collection_models.yml
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Expand Up @@ -44,7 +44,6 @@ jobs:
&& sudo apt-get install -y swig libatlas-base-dev
- run: echo "${HOME}/.local/bin/" >> $GITHUB_PATH
- run: echo "${GITHUB_WORKSPACE}/tests/performance/" >> $GITHUB_PATH

# install AMICI
- name: Create AMICI sdist
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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
4 changes: 2 additions & 2 deletions .github/workflows/test_performance.yml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion .github/workflows/test_python_cplusplus.yml
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Expand Up @@ -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
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40 changes: 40 additions & 0 deletions CHANGELOG.md
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## 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:
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