Fix version selection

Previously, the simulator version argument was ignored and always the latest amici version was installed.

Author: dweindl

.github/workflows/ci.yml

@@ -75,18 +75,18 @@ jobs:
         with:
           python-version: '3.11'
 
-      - name: Setup pip cache
-        uses: actions/cache@v3
-        with:
-          path: /opt/hostedtoolcache/Python
-          key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}-${{ hashFiles('requirements.optional.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
+#      - name: Setup pip cache
+#        uses: actions/cache@v3
+#        with:
+#          path: /opt/hostedtoolcache/Python
+#          key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}-${{ hashFiles('requirements.optional.txt') }}
+#          restore-keys: |
+#            ${{ runner.os }}-pip-
 
       - 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: |
@@ -98,7 +98,10 @@ jobs:
 
       # install package
       - name: Install the package
-        run: python -m pip install .[all]
+        run: |
+          simulatorVersion=$(jq -r '.version' biosimulators.json)
+          python -m pip install amici==$simulatorVersion
+          python -m pip install .[all]
 
       #############################################
       ## Lint

Dockerfile

@@ -47,10 +47,9 @@ 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 pip install sympy /root/Biosimulators_AMICI \
+RUN pip install /root/Biosimulators_AMICI \
     && rm -rf /root/Biosimulators_AMICI
-#RUN pip install sympy /root/Biosimulators_AMICI amici==${SIMULATOR_VERSION} \
-#    && rm -rf /root/Biosimulators_AMICI
+RUN pip install amici==${SIMULATOR_VERSION}
 ENV VERBOSE=0 \
     MPLBACKEND=PDF
 

requirements.txt

@@ -1,4 +1,3 @@
-amici >= 0.11.17
 biosimulators_utils[logging] >= 0.1.180
 kisao >= 2.33
 lxml