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Fix version selection #14

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Merged
dweindl merged 1 commit into from
Dec 9, 2025
Merged

Fix version selection #14

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10 changes: 6 additions & 4 deletions .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -85,8 +85,8 @@ jobs:

- name: Install pip and setuptools
run: |
python -m pip install --upgrade pip==23.0.0
python -m pip install --upgrade pip==23.0.0
python -m pip install --upgrade setuptools
python -m pip install --upgrade pip

- name: Install system dependencies
run: |
Expand All @@ -99,8 +99,10 @@ jobs:
# install package
- name: Install the package
run: |
simulatorVersion=$(jq -r '.version' biosimulators.json)
# AMICI has to be installed before biosimulators_amici to get the right version
AMICI_PARALLEL_COMPILE="" python -m pip install amici==$simulatorVersion
python -m pip install .[all]
AMICI_PARALLEL_COMPILE="" python -m pip install amici

#############################################
## Lint
Expand Down Expand Up @@ -178,7 +180,7 @@ jobs:
with:
token: ${{ secrets.CODECOV_TOKEN }}
flags: unittests
file: ./coverage.xml
files: ./coverage.xml

#############################################
## Compile documentation
Expand Down
10 changes: 5 additions & 5 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
FROM python:3.11-slim-bookworm

ARG VERSION="0.1.22"
ARG SIMULATOR_VERSION="0.24.0"
ARG SIMULATOR_VERSION="0.34.0"

# metadata
LABEL \
Expand Down Expand Up @@ -47,11 +47,11 @@ RUN apt-get update -y \

# Copy code for command-line interface into image and install it
COPY . /root/Biosimulators_AMICI
RUN pip install pip==23.0.1
RUN SETUPTOOLS_SCM_PRETEND_VERSION_FOR_BIOSIMULATORS_AMICI=${VERSION} pip install /root/Biosimulators_AMICI \
RUN python -m pip install -U setuptools pip
# AMICI has to be installed before biosimulators_amici to get the right version
RUN AMICI_PARALLEL_COMPILE="" python -m pip install amici==${SIMULATOR_VERSION}
RUN SETUPTOOLS_SCM_PRETEND_VERSION_FOR_BIOSIMULATORS_AMICI=${VERSION} python -m pip install /root/Biosimulators_AMICI \
&& rm -rf /root/Biosimulators_AMICI
#RUN pip install sympy /root/Biosimulators_AMICI amici==${SIMULATOR_VERSION} \
# && rm -rf /root/Biosimulators_AMICI
ENV VERBOSE=0 \
MPLBACKEND=PDF \
AMICI_PARALLEL_COMPILE=""
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4 changes: 2 additions & 2 deletions biosimulators.json
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
{
"id": "amici",
"name": "AMICI",
"version": "0.24.0",
"version": "0.34.0",
"description": "AMICI provides an interface for the SUNDIALS solvers CVODES (for ordinary differential equations) and IDAS (for algebraic differential equations).",
"urls": [
{
Expand All @@ -10,7 +10,7 @@
}
],
"image": {
"url": "ghcr.io/biosimulators/biosimulators_amici/amici:0.24.0",
"url": "ghcr.io/biosimulators/biosimulators_amici/amici:0.34.0",
"format": {
"namespace": "EDAM",
"id": "format_3973",
Expand Down