updates

vivarium-collective · May 24, 2024 · 8f2c255 · 8f2c255
1 parent 53c7645
commit 8f2c255
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Showing 7 changed files with 107 additions and 1,095 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -17,7 +17,7 @@ COPY ./biosimulator_processes /app/biosimulator_processes
 COPY composer-notebooks /app/notebooks
 
 # copy files
-COPY ./pyproject.toml ./poetry.lock ./data ./scripts/trust-notebooks.sh /app/
+COPY toml ./poetry.lock ./data ./scripts/trust-notebooks.sh /app/
 COPY ./scripts/enter-lab.sh /usr/local/bin/enter-lab.sh
 # COPY ./scripts/xvfb-startup.sh /xvfb-startup.sh
 

diff --git a/poetry.lock → _lock b/poetry.lock → _lock
diff --git a/biosimulator_processes/__init__.py b/biosimulator_processes/__init__.py
@@ -14,7 +14,7 @@
 PROCESSES_TO_REGISTER = [
     ('cobra', 'cobra_process.CobraProcess'),
     ('copasi', 'copasi_process.CopasiProcess'),
-    ('smoldyn', 'smoldyn_process.SmoldynProcess'),
+    # ('smoldyn', 'smoldyn_process.SmoldynProcess'),
     ('tellurium', 'tellurium_process.TelluriumProcess'),
     ('amici', 'amici_process.AmiciProcess')]
 

diff --git a/containers/exec.py b/containers/exec.py
@@ -13,7 +13,7 @@ def get_simulators(sims: List[str]):
         and format as a dictionary. This dictionary is used as configuration for the dynamic
         creation of containers.
     """
-    with open('biosimulator_processes/poetry.lock') as file:
+    with open('biosimulator_processes/_lock') as file:
         lock_data = toml.load(file)
 
     simulators = []
@@ -76,7 +76,7 @@ def generate_dockerfile_contents(config: dict) -> str:
     """
 
     base_path = 'biosimulator_processes/Dockerfile-base'
-    # TODO: automate mapping simulators to poetry.lock: ie: simulators arg that searches the lock file
+    # TODO: automate mapping simulators to _lock: ie: simulators arg that searches the lock file
     with open(base_path, 'r') as fp:
         dockerfile_contents = fp.read()
         for simulator in config['simulators']:

diff --git a/setup.py b/setup.py
@@ -57,7 +57,7 @@
         "jupyterlab",
         "notebook",
         "bigraph-builder",
-        "python-libsbml"  # ==5.20.2",
+        "python-libsbml",  # ==5.20.2",
         "docker>=7.0",
         "toml",
         "python-libnuml==1.1.6",  # ">=1.0.0"

diff --git a/test_suite/test.ipynb b/test_suite/test.ipynb
diff --git a/pyproject.toml → toml b/pyproject.toml → toml
@@ -26,16 +26,8 @@ docker = ">=7.0"
 python-libnuml = "^1.1.6"
 notebook = "^7.1.1"
 toml = "*"
-fastapi = "^0.109.0"  # "*"
 pyyaml = "*"
 pydantic = "*"
-h5py = "*"
-pydantic-settings = "*"
-httpx = "*"
-tensorstore = "*"
-aiofiles = "*"
-aiobotocore = "*"
-uvicorn = {extras = ["standard"], version = "*"}
 seaborn = "^0.13.2"
 # psutil = "^5.9.8"