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 +98,11 @@ 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 pkg_utils  # for current setup.py
+          python -m pip install .[all]
 
       #############################################
       ## Lint

Dockerfile

@@ -46,11 +46,12 @@ 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 python -m pip install -U setuptools pip
+RUN python -m pip install pkg_utils  # for current setup.py
+
+RUN python -m pip install /root/Biosimulators_AMICI \
     && rm -rf /root/Biosimulators_AMICI
-#RUN pip install sympy /root/Biosimulators_AMICI amici==${SIMULATOR_VERSION} \
-#    && rm -rf /root/Biosimulators_AMICI
+RUN python -m pip install amici==${SIMULATOR_VERSION}
 ENV VERBOSE=0 \
     MPLBACKEND=PDF
 

biosimulators.json

@@ -1,7 +1,7 @@
 {
   "id": "amici",
   "name": "AMICI",
-  "version": "0.24.0",
+  "version": "0.34.2",
   "description": "AMICI provides an interface for the SUNDIALS solvers CVODES (for ordinary differential equations) and IDAS (for algebraic differential equations).",
   "urls": [
     {
@@ -10,7 +10,7 @@
     }
   ],
   "image": {
-    "url": "ghcr.io/biosimulators/biosimulators_amici/amici:0.24.0",
+    "url": "ghcr.io/biosimulators/biosimulators_amici/amici:0.34.2",
     "format": {
       "namespace": "EDAM",
       "id": "format_3973",
@@ -100,34 +100,18 @@
     ],
     "citations": [
       {
-        "title": "Scalable parameter estimation for genome-scale biochemical reaction networks",
-        "authors": "Fabian Fröhlich, Barbara Kaltenbacher, Fabian J. Theis & Jan Hasenauer",
-        "journal": "PLOS Computational Biology",
-        "volume": "13",
-        "issue": "1",
-        "pages": "e1005331",
-        "year": 2017,
-        "identifiers": [
-          {
-            "namespace": "doi",
-            "id": "10.1371/journal.pcbi.1005331",
-            "url": "https://doi.org/10.1371/journal.pcbi.1005331"
-          }
-        ]
-      },
-      {
-        "title": "Parameter estimation for dynamical systems with discrete events and logical operations",
-        "authors": "Fabian Fröhlich, Fabian J. Theis, Joachim O Rädler & Jan Hasenauer",
+        "title": "AMICI: High-Performance Sensitivity Analysis for Large Ordinary Differential Equation Models",
+        "authors": "Fabian Fröhlich, Daniel Weindl, Yannik Schälte, Dilan Pathirana, Paszkowski Lukasz, Glenn Terje Lines, Paul Stapor & Jan Hasenauer",
         "journal": "Bioinformatics",
-        "volume": "33",
-        "issue": "7",
-        "pages": "1049-1056",
-        "year": 2017,
+        "volume": "37",
+        "issue": "20",
+        "pages": "3676–3677",
+        "year": 2021,
         "identifiers": [
           {
             "namespace": "doi",
-            "id": "10.1093/bioinformatics/btw764",
-            "url": "https://doi.org/10.1093/bioinformatics/btw764"
+            "id": "10.1093/bioinformatics/btab227",
+            "url": "https://doi.org/10.1093/bioinformatics/btab227"
           }
         ]
       }

requirements.txt

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