update for project save

biosimulators · Nov 7, 2024 · dd03645 · dd03645
1 parent e8f7545
commit dd03645
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Showing 2 changed files with 13 additions and 4 deletions.
diff --git a/assets/dev/scripts/create_env.sh b/assets/dev/scripts/create_env.sh
@@ -18,14 +18,14 @@ function construct_env {
   conda install -n bio-compose-server -c conda-forge -c pysces pysces -y
   conda run -n bio-compose-server poetry env use 3.10
   conda run -n bio-compose-server poetry lock
-  conda run -n bio-compose-server poetry install --only=dev
+  sudo conda run -n bio-compose-server poetry install --only=dev
   conda activate bio-compose-server
   poetry run pip3 cache purge
-  conda run ./assets/dev/scripts/install-smoldyn-mac-silicon.sh || poetry run pip3 install smoldyn
+  sudo conda run -n bio-compose-server ./assets/dev/scripts/install-smoldyn-mac-silicon.sh || poetry run pip3 install smoldyn
   poetry lock
   poetry install --only=dev
-  poetry run pip3 install amici biosimulators-amici biosimulators-pysces
-  poetry run pip install ./api ./worker
+  conda run -n bio-compose-server sudo poetry run pip3 install amici biosimulators-amici biosimulators-pysces
+  # poetry run pip install ./api ./worker
 
   echo "Environment created!"
 }

diff --git a/pyproject.toml b/pyproject.toml
@@ -55,6 +55,15 @@ pydantic = "^2.9.2"
 uvicorn = "^0.32.0"
 pyyaml = "^6.0.2"
 pytest = "^8.3.3"
+simulariumio = "^1.11.0"
+copasi-basico = "^0.78"
+tellurium = "^2.2.10"
+biosimulators-copasi = "^0.2.22"
+biosimulators-tellurium = "^0.1.44"
+seaborn = "^0.13.2"
+jupyterlab = "^4.3.0"
+process-bigraph = "^0.0.22"
+bigraph-schema = "^0.0.45"
 
 
 [tool.poetry.group.worker.dependencies]