Merge pull request #7 from biosimulators/main

updated ignore

.gitignore

@@ -1 +1,26 @@
+buildImage.yaml
+.python-version
+__pycache__/
+.idea/
+*.ipynb_checkpoints/
+dist/
+.DS_Store
+*.egg-info/
+refresh-env.sh
+smoldyn-2.72-mac/
+build/
+commit.sh
+install.sh
+push-image.sh
+release.sh
+run.sh
+ray_job.sh
+__pycache__
 .pytest_cache
+submit-biosimulators-container.sh
+.vagrant
+._vagrant
+.THIS-IS-FOR-CONTAINER-DEV-ONLY
+buildDockerImage.yml
+.env
+

Dockerfile

@@ -1,29 +1,30 @@
 # TODO: Use a more specific tag instead of latest for reproducibility
 FROM ubuntu:latest
 
-ENV DEBIAN_FRONTEND=noninteractive \
-    XVFB_RES="1920x1080x24" \
-    XVFB_ARGS="" \
-    PATH="/app/.venv/bin:$PATH" \
-    CONFIG_ENV_FILE="/app/config/config.env" \
-    SECRET_ENV_FILE="/app/secret/secret.env" \
-    STORAGE_GCS_CREDENTIALS_FILE="/app/secret/gcs_credentials.json" \
-    STORAGE_LOCAL_CACHE_DIR="/app/scratch"
+ENV DEBIAN_FRONTEND=noninteractive
+    # XVFB_RES="1920x1080x24" \
+    # XVFB_ARGS="" \
+    # PATH="/app/.venv/bin:$PATH" \
+    # CONFIG_ENV_FILE="/app/config/config.env" \
+    # SECRET_ENV_FILE="/app/secret/secret.env" \
+    # STORAGE_GCS_CREDENTIALS_FILE="/app/secret/gcs_credentials.json" \
+    # STORAGE_LOCAL_CACHE_DIR="/app/scratch"
 
 WORKDIR /app
 
 # copy and make dirs
 COPY ./biosimulator_processes /app/biosimulator_processes
-COPY ./notebooks /app/notebooks
+COPY notebooks /app/notebooks
 
 # copy files
-COPY ./pyproject.toml ./poetry.lock ./data ./scripts/trust-notebooks.sh /app/
-COPY ./scripts/xvfb-startup.sh /xvfb-startup.sh
+COPY pyproject.toml poetry.lock ./data ./scripts/trust-notebooks.sh /app/
+# COPY ./scripts/xvfb-startup.sh /xvfb-startup.sh
 
 VOLUME /app/data
 
 RUN apt-get update && apt-get install -y --no-install-recommends \
     python3.10  \
+    ca-certificates \
     python3-pip  \
     python3-dev \
     build-essential  \
@@ -43,20 +44,18 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     libice6  \
     libpython3.10  \
     wget  \
-    xvfb \
-    && mkdir /tmp/.X11-unix  \
-    && chmod 1777 /tmp/.X11-unix  \
     && rm -rf /var/lib/apt/lists/* \
     && pip install --upgrade pip && pip install poetry \
     && poetry config virtualenvs.in-project true \
-    # && poetry run pip install psutil \
     && poetry update \
     && poetry install \
     && chmod +x ./trust-notebooks.sh \
     && ./trust-notebooks.sh \
-    && rm ./trust-notebooks.sh
+    && rm ./trust-notebooks.sh \
+    && apt-get clean \
+    && apt-get autoclean
 
-CMD ["poetry", "run", "jupyter", "lab", "--port=8888", "--no-browser", "--allow-root"]
+# CMD ["poetry", "run", "jupyter", "lab", "--port=8888", "--no-browser", "--allow-root"]
 
 
 # PLEASE NOTE: We do not need to add a USER in the Dockerfile as Singularity will handle

biosimulator_processes/data_model.py

@@ -44,6 +44,7 @@ class BaseModel(_BaseModel):
 
 class ModelParameter(BaseModel):
     name: str
+    feature: str
     value: Union[float, int, str]
     scope: str
 
@@ -197,15 +198,13 @@ class ProcessConfigSchema(BaseModel):
     config: Dict = Field(default={})
 
 
-class CopasiProcessConfigSchema(BaseModel):
+class ProcessConfig(BaseModel):
     process_name: str
-    method: str = Field(default='deterministic')
-    model: Union[TimeCourseModel, Dict]
 
-    def __init__(self, **data):
-        super().__init__(**data)
-        if isinstance(self.model, TimeCourseModel):
-            self.model = self.model.model_dump()
+
+class CopasiProcessConfig(ProcessConfig):
+    method: str = Field(default='deterministic')
+    model: TimeCourseModel
 
     # @field_serializer('model', when_used='json')
     # @classmethod
@@ -234,7 +233,6 @@ class ProcessInstance(BaseModel):
     config: Union[CopasiProcessConfigSchema, ProcessConfigSchema]
     inputs: PortSchema
     outputs: PortSchema
-    emitter: Union[EmitterInstance, NoneType] = Field(default=None)
 
     @classmethod
     @field_validator('address')

biosimulator_processes/processes/copasi_process.py

@@ -35,7 +35,7 @@
 # )
 from process_bigraph import Process, Composite, pf
 from biosimulator_processes.utils import fetch_biomodel
-from biosimulator_processes.data_model import TimeCourseProcessConfigSchema
+from biosimulator_processes.data_model import TimeCourseProcessConfigSchema, CopasiProcessConfig
 
 
 class CopasiProcess(Process):
@@ -81,7 +81,7 @@ class CopasiProcess(Process):
 
     config_schema = TimeCourseProcessConfigSchema().model_dump()
 
-    def __init__(self, config=None, core=None):
+    def __init__(self, config: CopasiProcessConfig=None, core=None):
         super().__init__(config, core)
 
         model_source = self.config['model']['model_source']['value']

biosimulator_processes/steps/parameter_scan.py

@@ -52,7 +52,7 @@ def update(self, input):
         pass
 
 
-class DeterministicTimeCourseParameterScan(ParameterScan):
+class DeterministicTimeCourseParameterScan(Step):
     """Using CopasiProcess as the primary TimeCourse simulator.
 
         # TODO: enable multiple Simulator types.
@@ -61,20 +61,19 @@ class DeterministicTimeCourseParameterScan(ParameterScan):
             used to run during update
     """
     config_schema = {
-        'process_config': {
-            '_default': TimeCourseProcessConfigSchema().model_dump(),
-            '_type': 'tree[string]'},
+        'process_config': TimeCourseProcessConfigSchema().model_dump(),
         'n_iterations': 'int',
+        'iter_stop': 'float',
         'iter_start': 'maybe[float]',
         'perturbation_magnitude': 'float',
         'parameters': 'list[object]'}
 
-    def __init__(self, config=None):
-        super().__init__(config=config)
+    def __init__(self):
         self.process = CopasiProcess(config=self.config.get('process_config'))
         self.params_to_scan: List[ModelParameter] = self.config.get('parameters', [])
         self.n_iterations = self.config['n_iterations']
         self.iter_start = self.config.get('iter_start', 0.0)
+        self.iter_stop = self.config['iter_stop']
 
 
     def initial_state(self):
@@ -98,8 +97,8 @@ def update(self, input):
         results = {}
         scan_range = np.linspace(
             start=self.iter_start,
-            stop=self.n_iterations,
-            num=self.config['perturbation_magnitude']).tolist()
+            stop=self.iter_stop,
+            num=self.n_iterations).tolist()
 
         for index, perturbed in enumerate(scan_range):
             interval = input['time']

commit.sh

@@ -15,7 +15,7 @@ read -r msg
 #   echo "Notebooks not fixed."
 # fi
 
-poetry run python3 ./scripts/fix_notebooks.py
+python3 ./scripts/fix_notebooks.py
 git add --all
 git commit -m "${msg}"
 git push origin "${branch}"