diff --git a/assets/dev/scripts/create_env.sh b/assets/dev/scripts/create_env.sh index 45a748d77..ac3dc0eac 100755 --- 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 index e65b723e3..939b36594 100644 --- 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]