Update python version (#100)

HelikarLab · Mar 3, 2023 · 18d155b · 18d155b
1 parent 109356b
commit 18d155b
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Showing 3 changed files with 2 additions and 13 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -10,18 +10,6 @@ ENV GUROBI_HOME "${HOME}/gurobi/linux64"
 ENV PATH "$PATH:$GUROBI_HOME/bin"
 ENV LD_LIBRARY_PATH "$LD_LIBRARY_PATH:$GUROBI_HOME/lib"
 
-# Install python
-USER root
-RUN apt -qqq update \
-    && apt -qqq install  --yes software-properties-common \
-    && add-apt-repository --yes ppa:deadsnakes/ppa \
-    && apt -qqq update \
-    && apt -qqq install --yes python${PYTHON_MAIN_VERSION} \
-    && apt -qqq clean \
-    && rm -rf /var/lib/apt/lists/* \
-    && echo python3 --version
-USER jovyan
-
 COPY /environment.yaml "${HOME}/environment.yaml"
 COPY --chown=1000:100 main "${HOME}"/main
 

diff --git a/environment.yaml b/environment.yaml
@@ -32,6 +32,7 @@ dependencies:
   - markupsafe==2.0.1
   - numpy==1.23.0
   - pandas==1.4.3
+  - python==3.10.9
   - requests==2.28.1
   - rpy2==3.5.1
   - scipy==1.8.1

diff --git a/main/COMO.ipynb b/main/COMO.ipynb
@@ -600,7 +600,7 @@
     "output_filetypes = \"xml mat json\"\n",
     "objective_dict = {}\n",
     "general_model_file = \"GeneralModelUpdatedV2.mat\"\n",
-    "recon_algorithms = 'IMAT'\n",
+    "recon_algorithms = ['IMAT']\n",
     "solver = \"GUROBI\"\n",
     "boundary_reactions_filename = \"bcell_boundary_rxns.csv\"\n",
     "force_reactions_filename = \"bcell_force_rxns.csv\"\n",