diff --git a/.gitignore b/.gitignore index 78ebc3414..2620c89f8 100644 --- a/.gitignore +++ b/.gitignore @@ -20,3 +20,4 @@ submit-biosimulators-container.sh .vagrant ._vagrant .THIS-IS-FOR-CONTAINER-DEV-ONLY +buildDockerImage.yml diff --git a/Dockerfile b/Dockerfile index a89cada99..8e9e57d1d 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,60 +1,64 @@ +# TODO: Use a more specific tag instead of latest for reproducibility FROM ubuntu:latest -ENV DEBIAN_FRONTEND=noninteractive +ENV DEBIAN_FRONTEND=noninteractive \ + XVFB_RES="1920x1080x24" \ + XVFB_ARGS="" \ + PATH="/app/.venv/bin:$PATH" \ + CONFIG_ENV_FILE="/app/config/config.env" \ + SECRET_ENV_FILE="/app/secret/secret.env" \ + STORAGE_GCS_CREDENTIALS_FILE="/app/secret/gcs_credentials.json" \ + STORAGE_LOCAL_CACHE_DIR="/app/scratch" WORKDIR /app -COPY . /app +# copy and make dirs +COPY ./biosimulator_processes/processes /app/biosimulator_processes +COPY ./notebooks /app/notebooks + +# copy files +COPY ./pyproject.toml ./poetry.lock ./data ./scripts/trust-notebooks.sh /app/ +COPY ./scripts/xvfb-startup.sh /xvfb-startup.sh RUN apt-get update && apt-get install -y --no-install-recommends \ - python3 \ - python3-pip \ - build-essential \ - libncurses5 \ - cmake \ - make \ - libx11-dev \ - libc6-dev \ - libx11-6 \ - libc6 \ - gcc \ + python3.10 \ + python3-pip \ + build-essential \ + libncurses5 \ + cmake \ + make \ + libx11-dev \ + libc6-dev \ + libx11-6 \ + libc6 \ + gcc \ swig \ - pkg-config \ - curl \ - tar \ - libgl1-mesa-glx \ - libice6 \ - libpython3.10 \ - wget \ - && rm -rf /var/lib/apt/lists/* - -# RUN apt-get update && apt-get install -y python3-pip - -RUN apt-get -y update \ - \ - && apt-get install --no-install-recommends -y \ - xvfb \ - && mkdir /tmp/.X11-unix \ - && chmod 1777 /tmp/.X11-unix \ - \ - && rm -rf /var/lib/apt/lists/* - -COPY scripts/xvfb-startup.sh /xvfb-startup.sh - -ENV XVFB_RES="1920x1080x24" \ - XVFB_ARGS="" - -RUN pip install --upgrade pip \ - && pip install poetry + pkg-config \ + curl \ + tar \ + libgl1-mesa-glx \ + libice6 \ + libpython3.10 \ + wget \ + xvfb \ + && mkdir /tmp/.X11-unix \ + && chmod 1777 /tmp/.X11-unix \ + && rm -rf /var/lib/apt/lists/* \ + && pip install --upgrade pip && pip install poetry \ + && poetry config virtualenvs.in-project true \ + && poetry install \ + && chmod +x ./trust-notebooks.sh \ + && ./trust-notebooks.sh \ + && rm ./trust-notebooks.sh -# Add Poetry to PATH -ENV PATH="/root/.local/bin:${PATH}" +VOLUME /app/data -# RUN poetry config virtualenvs.create false +CMD ["poetry", "run", "jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"] -RUN poetry run pip install --upgrade pip \ - && poetry run pip install python-libnuml --use-pep517 \ - && poetry install -ENTRYPOINT ["poetry", "run", "jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"] +# PLEASE NOTE: We do not need to add a USER in the Dockerfile as Singularity will handle + # such logic in conversion on the HPC. +# type imports +# dist +# param scan demo/location diff --git a/README.md b/README.md index fd8dbd31b..daac37398 100644 --- a/README.md +++ b/README.md @@ -176,3 +176,9 @@ A simplified view of the above script: >> workflow.run(10) >> results = workflow.gather_results() >> print(f'RESULTS: {pf(results)}') + + +### A NOTE FOR DEVELOPERS: +This tooling implements version control for dynamically-created composite containers through +`poetry`. The version control for content on the Python Package Index is performed by +`setup.py`. diff --git a/biosimulator_processes/__init__.py b/biosimulator_processes/__init__.py index 91ef57eab..4d376e1d4 100644 --- a/biosimulator_processes/__init__.py +++ b/biosimulator_processes/__init__.py @@ -22,3 +22,9 @@ print(f"{class_name} registered successfully.") except ImportError as e: print(f"{class_name} not available. Error: {e}") + + +from biosimulator_processes.copasi_process import CopasiProcess +from biosimulator_processes.smoldyn_process import SmoldynProcess +from biosimulator_processes.cobra_process import CobraProcess +from biosimulator_processes.tellurium_process import TelluriumProcess diff --git a/biosimulator_processes/container-assets/Dockerfile-base b/biosimulator_processes/container-assets/Dockerfile-base new file mode 100644 index 000000000..ace3074a6 --- /dev/null +++ b/biosimulator_processes/container-assets/Dockerfile-base @@ -0,0 +1,72 @@ +FROM ubuntu:latest + +ENV DEBIAN_FRONTEND=noninteractive + +WORKDIR /app + +COPY ./biosimulator_processes /app + +# COPY ./scripts /app + +# RUN rm -r /app/composer-api + +RUN apt-get update && apt-get install -y --no-install-recommends \ + python3 \ + python3-pip \ + build-essential \ + libncurses5 \ + cmake \ + make \ + libx11-dev \ + libc6-dev \ + libx11-6 \ + libc6 \ + gcc \ + swig \ + pkg-config \ + curl \ + tar \ + libgl1-mesa-glx \ + libice6 \ + libpython3.10 \ + wget \ + && rm -rf /var/lib/apt/lists/* + +RUN apt-get -y update \ + && apt-get install --no-install-recommends -y \ + xvfb \ + && mkdir /tmp/.X11-unix \ + && chmod 1777 /tmp/.X11-unix \ + && rm -rf /var/lib/apt/lists/* + +COPY ./scripts/xvfb-startup.sh /xvfb-startup.sh + +# RUN rm -r ./scripts + +ENV XVFB_RES="1920x1080x24" \ + XVFB_ARGS="" + +# RUN pip install --upgrade pip \ +# && pip install poetry + +# RUN poetry config virtualenvs.in-project true + +# Add Poetry to PATH +# ENV PATH="/root/.local/bin:${PATH}" + +# RUN poetry run pip install --upgrade pip \ +# && poetry run pip install python-libnuml --use-pep517 \ +# && poetry install + +# activate poetry virtualenv +# ENV PATH="/app/.venv/bin:$PATH" +# ENV CONFIG_ENV_FILE="/app/config/config.env" +# ENV SECRET_ENV_FILE="/app/secret/secret.env" +# ENV STORAGE_GCS_CREDENTIALS_FILE="/app/secret/gcs_credentials.json" +# ENV STORAGE_LOCAL_CACHE_DIR="/app/scratch" +# +# # activate the poetry virtualenv 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file mode 100644 index 000000000..e65287531 --- /dev/null +++ b/biosimulator_processes/container-assets/pyproject.toml @@ -0,0 +1,33 @@ +[tool.poetry] +name = "biosimulator-processes" +version = "0.0.16" +description = "Core implementations of process-bigraph.composite.Process aligning with BioSimulators simulator tools." +authors = ["Alex Patrie "] +readme = "README.md" +packages = [{include = "biosimulator_processes"}] + +[tool.poetry.dependencies] +python = ">=3.10" +zarr = "*" +termcolor = "*" +jupyterlab = "*" +bigraph-schema = "*" +process-bigraph = "*" +numpy = "*" # "^1.26.4" +copasi-basico = "*" +cobra = "*" +tellurium = "*" +smoldyn = "*" +bigraph-viz = "^0.0.31" +python-libsbml = "^5.20.2" +docker = ">=7.0" + +[tool.poetry.group.dev.dependencies] +pytest = "*" +mypy = ">=1.8.0" +flake8 = "*" +twine = "*" + +[build-system] +requires = ["poetry-core"] +build-backend = "poetry.core.masonry.api" diff --git a/biosimulator_processes/containers/__init__.py b/biosimulator_processes/containers/__init__.py new file mode 100644 index 000000000..e69de29bb diff --git a/biosimulator_processes/containers/exec.py b/biosimulator_processes/containers/exec.py new file mode 100644 index 000000000..eb5fb951b --- /dev/null +++ b/biosimulator_processes/containers/exec.py @@ -0,0 +1,128 @@ +import toml +import subprocess +from typing import * +from docker import DockerClient +from biosimulator_processes.containers.io import write_dockerfile + + +CLIENT = DockerClient(base_url='unix:///var/run/docker.sock') + + +def get_simulators(sims: List[str]): + """Get specified simulator installation information including required dependencies + 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: + lock_data = toml.load(file) + + simulators = [] + for sim in sims: + for package in lock_data.get('package', []): + if package['name'] == sim: + simulators.append({ + "name": package['name'], + "version": package['version'], + "deps": package.get('dependencies', {}), + "extras": package.get('extras', {}) + }) + break + + return {"simulators": simulators} + + +def generate_dockerfile_contents(config: dict) -> str: + """Generate contents to be written out to a Dockerfile derived from the base Dockerfile. + + Args: + config:`dict`: a dictionary specifying simulator versions and their dependencies. The schema for + this dictionary should be (for example): + + { + "simulators": [ + { + "name": "tellurium", + "version": "2.2.10", + "deps": { + "antimony": ">=2.12.0", + "appdirs": ">=1.4.3", + "ipykernel": ">=4.6.1", + "ipython": "*", + "jinja2": ">=3.0.0", + "jupyter-client": ">=5.1.0", + "jupyter-core": ">=4.3.0", + "libroadrunner": ">=2.1", + "matplotlib": ">=2.0.2", + "numpy": ">=1.23", + "pandas": ">=0.20.2", + "phrasedml": { + "version": ">=1.0.9", + "markers": "platform_machine != \"arm64\"" + }, + "plotly": ">=2.0.12", + "pytest": "*", + "python-libcombine": ">=0.2.2", + "python-libnuml": ">=1.0.0", + "python-libsbml": ">=5.18.0", + "python-libsedml": ">=2.0.17", + "requests": "*", + "rrplugins": { + "version": ">=2.1", + "markers": "platform_system == \"Windows\"" + }, + "scipy": ">=1.5.1" + } + }, + """ + + base_path = 'biosimulator_processes/Dockerfile-base' + # TODO: automate mapping simulators to poetry.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']: + # copy the appropriate process files + name = simulator['name'] + deps = simulator.get('deps', {}) + for dep, version in deps.items(): + if not version == "*": + complete_version = f'{dep}{version}' + else: + complete_version = f'{dep}' + # dockerfile_contents += f"RUN poetry add {complete_version}\n" + dockerfile_contents += f"RUN pip install {complete_version}\n" + if name == 'copasi-basico': + name = 'copasi' + dockerfile_contents += f"COPY ./biosimulator_processes/{simulator['name']}_process.py /app/{simulator['name']}_process.py\n" + # common entrypoint used by all processes + dockerfile_contents += 'ENTRYPOINT ["jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"]' + return dockerfile_contents + + +def build_image(name: str, p: str = '.'): + return CLIENT.images.build( + path=p, + tag=name) + + +def execute_container(img_name: str = 'composition'): + img = build_image(img_name) + CLIENT.containers.run(img.id) + + +def run(simulators: List[str]): + config = get_simulators(simulators) + dockerfile_contents = generate_dockerfile_contents(config) + dockerfile_path = 'Dockerfile' + write_dockerfile(dockerfile_contents, out_path=dockerfile_path) + # return execute_container() + + +def exec_container(name: str): + build_command = f"docker buildx build --platform linux/amd64 {name}_env ." + subprocess.run(build_command.split()) + run_command = f"docker run --platform linux/amd64 -it -p 8888:8888 {name}_env" + subprocess.run(run_command.split()) + + + +# run(['tellurium', 'copasi-basico']) diff --git a/biosimulator_processes/containers/io.py b/biosimulator_processes/containers/io.py new file mode 100644 index 000000000..aa2f50d45 --- /dev/null +++ b/biosimulator_processes/containers/io.py @@ -0,0 +1,24 @@ +import json + + +def write_dockerfile(dockerfile_contents: str, out_path: str): + """ + Args: + dockerfile_contents:`str`: content to write to Dockerfile + out_path:`str`: path to save the Dockerfile + + """ + with open(out_path, 'w') as file: + file.write(dockerfile_contents) + + +def write_config(): + config = {} + with open('biosimulator_processes/simulators.json', 'w') as fp: + json.dump(config, fp, indent=4) + + +def load_config(): + # Load simulator configuration + with open('biosimulator_processes/simulators.json', 'r') as file: + return json.load(file) diff --git a/biosimulator_processes/copasi_process.py b/biosimulator_processes/copasi_process.py index b7ca60a43..2dc4435c7 100644 --- a/biosimulator_processes/copasi_process.py +++ b/biosimulator_processes/copasi_process.py @@ -1,5 +1,40 @@ """ -Biosimulator process for Copasi/Basico +Biosimulator process for Copasi/Basico. + +Now lets create a new model, passing along the name that we want to give it. +Additional supported parameters for the model consist of: + + quantity_unit: which sets the unit to use for species concentrations (defaults to mol) + + volume_unit: the unit to use for three dimensional compartments (defaults to litre (l)) + + time_unit: the unit to use for time (defaults to second (s)) + + area_unit: the unit to use for two dimensional compartments + + length_unit: the unit to use for one dimensional compartments + + add_reaction('R1', 'A -> B'); + + Since we had a new model, this created the Species A and B as well as a compartment compartment, in which those + chemicals reside. The species have an initial concentration of 1. + To verify we can call get_species, which return + + get_species().initial_concentration + name + A 1.0 + B 1.0 + Name: initial_concentration, dtype: float64 + to change the initial concentration, we use set_species, and specify which property we want to change: + + set_species('B', initial_concentration=0) + set_species('A', initial_concentration=10) + get_species().initial_concentration + name + A 10.0 + B 0.0 + Name: initial_concentration, dtype: float64 + to see the kinetic paramters of our recation we can use get_reaction_parameters, and we see that the parameter has been created by default with a value of 0.1 """ @@ -11,19 +46,72 @@ set_species, run_time_course, get_compartments, - model_info + new_model, + add_reaction, + model_info, + load_model_from_string, + biomodels ) from process_bigraph import Process, Composite, pf +def fetch_biomodel(term: str, index: int = 0): + """Search for models matching the term and return an instantiated model from BioModels. + + TODO: Implement a dynamic search of this + """ + models = biomodels.search_for_model(term) + model = models[index] + sbml = biomodels.get_content_for_model(model['id']) + return load_model_from_string(sbml) + + +# 1. Add useful config params +# 2. Devise use cases +# 3. Update constructor conditionally +# 4. Devise parameter scan --> create Step() implementation that creates copasi1, 2, 3... + # and provides num iterations and parameter in model_changes + class CopasiProcess(Process): - config_schema = {'model_file': 'string'} + # TODO: Update this in constructor + config_schema = { + 'model_file': { + '_type': 'string', + '_default': '' + }, + 'reactions': { + 'name': { + 'scheme': 'string' + }, + }, + 'species_types': { + 'name': 'string', + 'initial_concentration': 'int' + }, + 'model_search_term': 'string', + 'model_changes': { + 'parameter': { + 'new_value': 'float' + } + }, + 'solver': 'string' + } def __init__(self, config=None, core=None): super().__init__(config, core) - # Load the single cell model into Basico - self.copasi_model_object = load_model(self.config['model_file']) + # TODO: Update set/get with optional config params and make logic + try: + if self.config.get('model_file'): + self.copasi_model_object = load_model(self.config['model_file']) + self.reaction_list = get_reactions(model=self.copasi_model_object).index.tolist() + else: + self.copasi_model_object = new_model(name='CopasiProcess Model') + for reaction_name, reaction_spec in self.config['reactions'].items(): + add_reaction(name=reaction_name, scheme=reaction_spec['scheme']) + except: + # TODO: More completely and more gracefully handle these errors + raise KeyError('You must enter either a model file or model name') # Get the species (floating only) TODO: add boundary species self.floating_species_list = get_species(model=self.copasi_model_object).index.tolist() @@ -34,7 +122,7 @@ def __init__(self, config=None, core=None): self.model_parameter_values = get_parameters(model=self.copasi_model_object)['initial_value'].tolist() # Get a list of reactions - self.reaction_list = get_reactions(model=self.copasi_model_object).index.tolist() + # self.reaction_list = get_reactions(model=self.copasi_model_object).index.tolist() # Get a list of compartments self.compartments_list = get_compartments(model=self.copasi_model_object).index.tolist() diff --git a/biosimulator_processes/processes/__init__.py b/biosimulator_processes/processes/__init__.py new file mode 100644 index 000000000..e69de29bb diff --git a/biosimulator_processes/processes/cobra_process.py b/biosimulator_processes/processes/cobra_process.py new file mode 100644 index 000000000..5feb7859f --- /dev/null +++ b/biosimulator_processes/processes/cobra_process.py @@ -0,0 +1,157 @@ +""" +COBRA FBA Process +""" + + +import cobra.io +from cobra.io import read_sbml_model +from process_bigraph import Process, core, Composite, pf, pp + + +def check_sbml(state, schema, core): + # Do something to check that the value is a valid SBML file + valid = cobra.io.sbml.validate_sbml_model(state) # TODO -- this requires XML + # valid = cobra.io.load_json_model(value) + if valid: + return True + else: + return False + + +bounds_type = { + 'lower_bound': {'_type': 'float', '_default': -1000.0}, + 'upper_bound': {'_type': 'float', '_default': 1000.0}, +} +bounds_tree_type = { + '_type': 'tree[bounds]', # TODO -- make this a dict, to make it only one level deep +} +sbml_type = { + '_inherit': 'string', + '_check': check_sbml, + '_apply': 'set', +} + +# register new types +core.register('bounds', bounds_type) +core.register('sbml', sbml_type) + + +class CobraProcess(Process): + + config_schema = { + 'model_file': 'sbml', + } + + def __init__(self, config=None, core=None): + super().__init__(config, core) + self.model = read_sbml_model(self.config['model_file']) + self.reactions = self.model.reactions + self.metabolites = self.model.metabolites + self.objective = self.model.objective.to_json()['expression']['args'][0]['args'][1]['name'] # TODO -- fix this in cobra + self.boundary = self.model.boundary + + def initial_state(self): + solution = self.model.optimize() + optimized_fluxes = solution.fluxes + + state = { + 'inputs': { + 'reaction_bounds': {} + }, + 'outputs': { + 'fluxes': {} + } + } + for reaction in self.model.reactions: + state['inputs']['reaction_bounds'][reaction.id] = { + 'lower_bound': reaction.lower_bound, + 'upper_bound': reaction.upper_bound + } + state['outputs']['fluxes'][reaction.id] = optimized_fluxes[reaction.id] + return state + + def inputs(self): + return { + 'model': 'sbml', + 'reaction_bounds': { + reaction.id: 'bounds' for reaction in self.reactions + }, + 'objective_reaction': { + '_type': 'string', + '_default': self.objective + }, + } + + def outputs(self): + return { + 'fluxes': { + reaction.id: 'float' for reaction in self.reactions + }, + 'objective_value': 'float', + 'reaction_dual_values': { + reaction.id: 'float' for reaction in self.reactions + }, + 'metabolite_dual_values': { + metabolite.id: 'float' for metabolite in self.metabolites + }, + 'status': 'string', + } + + + def update(self, inputs, interval): + # set reaction bounds + reaction_bounds = inputs['reaction_bounds'] + for reaction_id, bounds in reaction_bounds.items(): + self.model.reactions.get_by_id(reaction_id).bounds = (bounds['lower_bound'], bounds['upper_bound']) + + # set objective + # TODO -- look into optlang for specifying objective and constraints + self.model.objective = self.model.reactions.get_by_id(inputs['objective_reaction']) + + # run solver + solution = self.model.optimize() + + return { + 'fluxes': solution.fluxes.to_dict(), + 'objective_value': solution.objective_value, + 'reaction_dual_values': solution.reduced_costs.to_dict(), + 'metabolite_dual_values': solution.shadow_prices.to_dict(), + 'status': solution.status, + } + + +def test_process(): + instance = { + 'fba': { + '_type': 'process', + 'address': 'local:cobra', # TODO 'biosimulators:cobra[1.0]', + 'config': { + 'model_file': 'biosimulator_processes/model_files/e_coli_core.xml' + }, + 'inputs': { + 'model': ['model_store'], + 'reaction_bounds': ['reaction_bounds_store'], + 'objective_reaction': ['objective_reaction_store'], + }, + 'outputs': { + 'fluxes': ['fluxes_store'], + 'objective_value': ['objective_value_store'], + 'reaction_dual_values': ['reaction_dual_values_store'], + 'metabolite_dual_values': ['metabolite_dual_values_store'], + 'status': ['status_store'], + } + }, + # insert emitter schema + } + + # make the composite + workflow = Composite({ + 'state': instance + }) + + # run + workflow.run(1) + + # gather results + results = workflow.gather_results() + print(f'RESULTS: {pf(results)}') diff --git a/biosimulator_processes/processes/copasi_process.py b/biosimulator_processes/processes/copasi_process.py new file mode 100644 index 000000000..83b6d10c5 --- /dev/null +++ b/biosimulator_processes/processes/copasi_process.py @@ -0,0 +1,220 @@ +""" +Biosimulator process for Copasi/Basico. + +Now lets create a new model, passing along the name that we want to give it. +Additional supported parameters for the model consist of: + + quantity_unit: which sets the unit to use for species concentrations (defaults to mol) + + volume_unit: the unit to use for three dimensional compartments (defaults to litre (l)) + + time_unit: the unit to use for time (defaults to second (s)) + + area_unit: the unit to use for two dimensional compartments + + length_unit: the unit to use for one dimensional compartments + + add_reaction('R1', 'A -> B'); + + Since we had a new model, this created the Species A and B as well as a compartment compartment, in which those + chemicals reside. The species have an initial concentration of 1. + To verify we can call get_species, which return + + get_species().initial_concentration + name + A 1.0 + B 1.0 + Name: initial_concentration, dtype: float64 + to change the initial concentration, we use set_species, and specify which property we want to change: + + set_species('B', initial_concentration=0) + set_species('A', initial_concentration=10) + get_species().initial_concentration + name + A 10.0 + B 0.0 + Name: initial_concentration, dtype: float64 + to see the kinetic paramters of our recation we can use get_reaction_parameters, and we see that the parameter has been created by default with a value of 0.1 +""" + + +from basico import ( + load_model, + get_species, + get_parameters, + get_reactions, + set_species, + run_time_course, + get_compartments, + new_model, + model_info, + load_model_from_string, + biomodels + ) +from process_bigraph import Process, Composite, pf + + +def find_models(term: str): + return biomodels.search_for_model(term) + + +def fetch_model(term: str, index: int = 0): + """Searrch for models matching the term and return an instantiated model from BioModels. + + TODO: Implement a dynamic search of this + """ + models = find_models(term) + model = models[index] + sbml = biomodels.get_content_for_model(model['id']) + return load_model_from_string(sbml) + + +class CopasiProcess(Process): + config_schema = { + 'model_file': 'string', + 'name': 'string', + 'reactions': 'list[string]', + 'species_types': { + 'name': 'string', + 'initial_concentration': 'int' + }, + 'model_search_term': 'string' + # model_changes: dict paramName: new value + # solver + } + + def __init__(self, config=None, core=None): + super().__init__(config, core) + + try: + if self.config.get('model_file'): + # Load the single cell model into Basico + self.copasi_model_object = load_model(self.config['model_file']) + else: + self.copasi_model_object = new_model(name=self.config['name']) + except: + raise KeyError('You must enter either a model file or model name') + + # Get the species (floating only) TODO: add boundary species + self.floating_species_list = get_species(model=self.copasi_model_object).index.tolist() + self.floating_species_initial = get_species(model=self.copasi_model_object)['concentration'].tolist() + + # Get the list of parameters and their values + self.model_parameters_list = get_parameters(model=self.copasi_model_object).index.tolist() + self.model_parameter_values = get_parameters(model=self.copasi_model_object)['initial_value'].tolist() + + # Get a list of reactions + self.reaction_list = get_reactions(model=self.copasi_model_object).index.tolist() + + # Get a list of compartments + self.compartments_list = get_compartments(model=self.copasi_model_object).index.tolist() + + def initial_state(self): + floating_species_dict = dict(zip(self.floating_species_list, self.floating_species_initial)) + model_parameters_dict = dict(zip(self.model_parameters_list, self.model_parameter_values)) + return { + 'time': 0.0, + 'floating_species': floating_species_dict, + 'model_parameters': model_parameters_dict + } + + def inputs(self): + floating_species_type = { + species_id: { + '_type': 'float', + '_apply': 'set', + } for species_id in self.floating_species_list + } + return { + 'time': 'float', + 'floating_species': floating_species_type, + 'model_parameters': { + param_id: 'float' for param_id in self.model_parameters_list}, + 'reactions': { + reaction_id: 'float' for reaction_id in self.reaction_list}, + } + + def outputs(self): + floating_species_type = { + species_id: { + '_type': 'float', + '_apply': 'set', + } for species_id in self.floating_species_list + } + return { + 'time': 'float', + 'floating_species': floating_species_type + } + + def update(self, inputs, interval): + + # set copasi values according to what is passed in states + for cat_id, value in inputs['floating_species'].items(): + set_species(name=cat_id, initial_concentration=value, model=self.copasi_model_object) + + # run model for "interval" length; we only want the state at the end + timecourse = run_time_course( + start_time=inputs['time'], + duration=interval, + intervals=1, + update_model=True, + model=self.copasi_model_object) + + # extract end values of concentrations from the model and set them in results + results = {'time': interval} + results['floating_species'] = { + mol_id: float(get_species(name=mol_id, exact=True, model=self.copasi_model_object).concentration[0]) + for mol_id in self.floating_species_list} + + return results + + +def test_process(): + # 1. Define the sim state schema: + initial_sim_state = { + 'copasi': { + '_type': 'process', + 'address': 'local:copasi', + 'config': { + 'model_file': 'biosimulator_processes/model_files/Caravagna2010.xml' + }, + 'inputs': { + 'floating_species': ['floating_species_store'], + 'model_parameters': ['model_parameters_store'], + 'time': ['time_store'], + 'reactions': ['reactions_store'] + }, + 'outputs': { + 'floating_species': ['floating_species_store'], + 'time': ['time_store'], + } + }, + # TODO: Add emitter schema + 'emitter': { + '_type': 'step', + 'address': 'local:ram-emitter', + 'config': { + 'emit': { + 'floating_species': 'tree[float]', + 'time': 'float', + }, + }, + 'inputs': { + 'floating_species': ['floating_species_store'], + 'time': ['time_store'], + } + + } + } + + # 2. Make the composite: + workflow = Composite({ + 'state': initial_sim_state + }) + + # 3. Run the composite workflow: + workflow.run(10) + + # 4. Gather and pretty print results + results = workflow.gather_results() + print(f'RESULTS: {pf(results)}') diff --git a/biosimulator_processes/processes/smoldyn_process.py b/biosimulator_processes/processes/smoldyn_process.py new file mode 100644 index 000000000..a4395a330 --- /dev/null +++ b/biosimulator_processes/processes/smoldyn_process.py @@ -0,0 +1,383 @@ +"""The output data returned by that which is required by simularium (executiontime, listmols), + when written and read into the same file for a given global time is as follows: + + [identity, state, x, y, z, serial number], where: + + identity = species identity for molecule + state = state of the given molecule + x, y, z = values for the relative coordinates + serial_number = monotonically decreasing timestamp for the given species_id + + At each global timestep (`executiontime`), a new 'cast of characters' are introduced that may resemble the + cast of characters at the first timestep, but are in fact different and thus all the molecules provided + from the `listmols` command will in fact all be unique. + + + I propose the following consideration at each `update` step: + + The `smoldyn.Simulation().connect()` method can be used to (for example) tell the + simulation about external environmental parameters that change over the course of + the simulation. For example: + + a = None + avals = [] + + def new_difc(t, args): + global a, avals + x, y = args + avals.append((t, a.difc['soln'])) + return x * math.sin(t) + y + + def update_difc(val): + global a + a.difc = val + + def test_connect(): + global a, avals + sim = smoldyn.Simulation(low=(....... + a = sim.addSpecies('a', color=black, difc=0.1) + + # specify either function as target: + sim.connect(new_dif, update_difc, step=10, args=[1,1]) + + # ...or species as target: + sim.connect(func = new_dif, target = 'a.difc', step=10, args=[0, 1]) + + sim.run(.... + + +""" +from typing import * +from uuid import uuid4 +from process_bigraph import Process, Composite, pf, pp +try: + import smoldyn as sm + from smoldyn._smoldyn import MolecState +except: + raise ImportError( + '\nPLEASE NOTE: Smoldyn is not correctly installed on your system which prevents you from ' + 'using the SmoldynProcess. Please refer to the README for further information ' + 'on installing Smoldyn.' + ) + + +class SmoldynProcess(Process): + """Smoldyn-based implementation of bi-graph process' `Process` API. Please note the following: + + For the purpose of this `Process` implementation, + at each `update`, we need the function to do the following for each molecule/species in the simulation: + + - Get the molecule count with Smoldyn lang: (`molcount {molecule_name}`) shape: [time, ...speciesN], + so in the case of a two species simulation: [timestamp, specACounts, specBCounts] + - Get the molecule positions and relative corresponding time steps, + indexed by the molecule name with Smoldyn lang: (`listmols`)[molecule_name] + - ?Get the molecule state? + - Kill the molecule with smoldyn lang: (`killmol {molecule_name}`) + - Add the molecule back to the solution(cytoplasm), effectively resetting it at boundary coordinates with Python API: (`simulation.addMolecules() + + PLEASE NOTE: + + The current implementation of this class assumes 3 key conditions: + 1. that a smoldyn model file is present and working + 2. output commands from the aforementioned model file that are left un-commented (disabled) will yield a + smoldyn model output file whose data could potentially reflect something other than what is returned by + this Process' `schema()`. + # TODO: Expand the config_schema to allow model_filepath to be None. + + + Config Attributes: + model_filepath:`str`: filepath to the smoldyn model you want to reference in this Process + animate:`bool`: Displays graphical simulation output from smoldyn if set to `True`. Defaults to `False`. + """ + + # TODO: Add the ability to pass model parameters and not just a model file. + config_schema = { + 'model_filepath': 'string', + 'animate': 'bool', + } + + def __init__(self, config: Dict[str, Any] = None, core=None): + """A new instance of `SmoldynProcess` based on the `config` that is passed. The schema for the config to be passed in + this object's constructor is as follows: + + config_schema = { + 'model_filepath': 'string', <-- analogous to python `str` + 'animate': 'bool' <-- of type `bigraph_schema.base_types.bool` + + # TODO: It would be nice to have classes associated with this. + """ + super().__init__(config, core) + + # specify the model fp for clarity + self.model_filepath = self.config.get('model_filepath') + + # enforce model filepath passing + if not self.model_filepath: + raise ValueError( + ''' + The Process configuration requires a Smoldyn model filepath to be passed. + Please specify a 'model_filepath' in your instance configuration. + ''' + ) + + # initialize the simulator from a Smoldyn model.txt file. + self.simulation: sm.Simulation = sm.Simulation.fromFile(self.model_filepath) + + # get a list of the simulation species + species_count = self.simulation.count()['species'] + self.species_names: List[str] = [] + for index in range(species_count): + species_name = self.simulation.getSpeciesName(index) + if 'empty' not in species_name.lower(): + self.species_names.append(species_name) + # sort for logistical mapping to species names (i.e: ['a', 'b', c'] == ['0', '1', '2'] + self.species_names.sort() + + # make species counts of molecules dataset for output + self.simulation.addOutputData('species_counts') + # write molcounts to counts dataset at every timestep (shape=(n_timesteps, 1+n_species <-- one for time)): [timestep, countSpec1, countSpec2, ...] + self.simulation.addCommand(cmd='molcount species_counts', cmd_type='E') + + # make molecules dataset (molecule information) for output + self.simulation.addOutputData('molecules') + # write coords to dataset at every timestep (shape=(n_output_molecules, 7)): seven being [timestep, smol_id(species), mol_state, x, y, z, mol_serial_num] + self.simulation.addCommand(cmd='listmols2 molecules', cmd_type='E') + + # initialize the molecule ids based on the species names. We need this value to properly emit the schema, which expects a single value from this to be a str(int) + # the format for molecule_ids is expected to be: 'speciesId_moleculeNumber' + self.molecule_ids: List[str] = [str(uuid4()) for n in list(range(len(self.species_names)))] + + # get the simulation boundaries, which in the case of Smoldyn denote the physical boundaries + # TODO: add a verification method to ensure that the boundaries do not change on the next step... + self.boundaries: Dict[str, List[float]] = dict(zip(['low', 'high'], self.simulation.getBoundaries())) + + # set graphics (defaults to False) + if self.config['animate']: + self.simulation.addGraphics('opengl_better') + + # create a re-usable counts and molecules type to be used by both inputs and outputs + self.counts_type = { + species_name: 'int' + for species_name in self.species_names + } + + # self.molecules_type = { + # mol_id: { + # 'coordinates': 'list[float]', + # 'species_id': 'string', + # 'state': 'string' + # } for mol_id in self.molecule_ids + # } + + def set_uniform( + self, + species_name: str, + count: int, + kill_mol: bool = True + ) -> None: + """Add a distribution of molecules to the solution in + the simulation memory given a higher and lower bound x,y coordinate. Smoldyn assumes + a global boundary versus individual species boundaries. Kills the molecule before dist if true. + + TODO: If pymunk expands the species compartment, account for + expanding `highpos` and `lowpos`. This method should be used within the body/logic of + the `update` class method. + + Args: + species_name:`str`: name of the given molecule. + count:`int`: number of molecules of the given `species_name` to add. + kill_mol:`bool`: kills the molecule based on the `name` argument, which effectively + removes the molecule from simulation memory. + """ + # kill the mol, effectively resetting it + if kill_mol: + self.simulation.runCommand(f'killmol {species_name}') + + # TODO: eventually allow for an expanding boundary ie in the configuration parameters (pymunk?), which is defies the methodology of smoldyn + + # redistribute the molecule according to the bounds + self.simulation.addSolutionMolecules( + species=species_name, + number=count, + highpos=self.boundaries['high'], + lowpos=self.boundaries['low'] + ) + + def initial_state(self) -> Dict[str, Union[int, Dict]]: + """Set the initial parameter state of the simulation. This method should return an implementation of + that which is returned by `self.schema()`. + + + NOTE: Due to the nature of this model, + Smoldyn assigns a random uniform distribution of integers as the initial coordinate (x, y, z) + values for the simulation. As such, the `set_uniform` method will uniformly distribute + the molecules according to a `highpos`[x,y] and `lowpos`[x,y] where high and low pos are + the higher and lower bounds of the molecule spatial distribution. + + NOTE: This method should provide an implementation of the structure denoted in `self.schema`. + """ + # get the initial species counts + initial_species_counts = { + spec_name: self.simulation.getMoleculeCount(spec_name, MolecState.all) + for spec_name in self.species_names + } + + print(f'INITAL: {initial_species_counts}') + + return { + 'species_counts': initial_species_counts, + 'molecules': { + mol_id: { + 'coordinates': [0.0, 0.0, 0.0], + 'species_id': self.species_names[i], + 'state': 0 + } + for i, mol_id in enumerate(self.molecule_ids) + } + } + + def inputs(self): + # TODO: include velocity and state to this schema (add to constructor as well) + counts_type = { + species_name: 'int' + for species_name in self.species_names + } + + return { + 'species_counts': counts_type, + 'molecules': 'tree[string]' # self.molecules_type + } + + def outputs(self): + counts_type = { + species_name: 'int' + for species_name in self.species_names + } + + return { + 'species_counts': counts_type, + 'molecules': 'tree[string]' # self.molecules_type + } + + def update(self, inputs: Dict, interval: int) -> Dict: + """Callback method to be evoked at each Process interval. We want to get the + last of each dataset type as that is the relevant data in regard to the Process timescale scope. + + Args: + inputs:`Dict`: current state of the Smoldyn simulation, expressed as a `Dict` whose + schema matches that which is returned by the `self.schema()` API method. + interval:`int`: Analogous to Smoldyn's `time_stop`, this is the + timestep interval at which to provide the update as the output of this method. + NOTE: This update is iteratively called with the `Process` API. + + Returns: + `Dict`: New state according to the update at interval + + + TODO: We must account for the mol_ids that are generated in the output based on the interval run, + i.e: Shorter intervals will yield both less output molecules and less unique molecule ids. + """ + # reset the molecules, distribute the mols according to self.boundarieså + for name in self.species_names: + self.set_uniform( + species_name=name, + count=inputs['species_counts'][name], + ) + + # run the simulation for a given interval + self.simulation.run( + stop=interval, + dt=self.simulation.dt + ) + + # get the counts data, clear the buffer + counts_data = self.simulation.getOutputData('species_counts') + + # get the final counts for the update + final_count = counts_data[-1] + # remove the timestep from the list + final_count.pop(0) + + # get the data based on the commands added in the constructor, clear the buffer + molecules_data = self.simulation.getOutputData('molecules') + + # create an empty simulation state mirroring that which is specified in the schema + simulation_state = { + 'species_counts': {}, + 'molecules': {} + } + + # get and populate the species counts + for index, name in enumerate(self.species_names): + input_counts = inputs['species_counts'][name] + print(f'INPUT COUNTS: {input_counts}') + simulation_state['species_counts'][name] = int(final_count[index]) - input_counts + + # clear the list of known molecule ids and update the list of known molecule ids (convert to an intstring) + self.molecule_ids.clear() + for molecule in molecules_data: + self.molecule_ids.append(str(uuid4())) + + # get and populate the output molecules + mols = [] + for index, mol_id in enumerate(self.molecule_ids): + single_molecule_data = molecules_data[index] + single_molecule_species_index = int(single_molecule_data[1]) - 1 + mols.append(single_molecule_species_index) + simulation_state['molecules'][mol_id] = { + 'coordinates': single_molecule_data[3:6], + 'species_id': self.species_names[single_molecule_species_index], + 'state': str(int(single_molecule_data[2])) + } + + # TODO -- post processing to get effective rates + + return simulation_state + + +def test_process(): + """Test the smoldyn process using the crowding model.""" + + # this is the instance for the composite process to run + print("RUNNING") + instance = { + 'smoldyn': { + '_type': 'process', + 'address': 'local:smoldyn', + 'config': { + 'model_filepath': 'biosimulator_processes/model_files/minE_model.txt', + 'animate': False}, + 'inputs': { + 'species_counts': ['species_counts_store'], + 'molecules': ['molecules_store']}, + 'outputs': { + 'species_counts': ['species_counts_store'], + 'molecules': ['molecules_store']} + }, + 'emitter': { + '_type': 'step', + 'address': 'local:ram-emitter', + 'config': { + 'emit': { + 'species_counts': 'tree[string]', + 'molecules': 'tree[string]'} + }, + 'inputs': { + 'species_counts': ['species_counts_store'], + 'molecules': ['molecules_store']} + } + } + + total_time = 2 + + # make the composite + workflow = Composite({ + 'state': instance + }) + + # run + workflow.run(total_time) + + # gather results + results = workflow.gather_results() + pp(f'RESULTS: {pf(results)}') diff --git a/biosimulator_processes/processes/tellurium_process.py b/biosimulator_processes/processes/tellurium_process.py new file mode 100644 index 000000000..513f5c4be --- /dev/null +++ b/biosimulator_processes/processes/tellurium_process.py @@ -0,0 +1,223 @@ +""" +Tellurium Process +""" + + +import numpy as np +import tellurium as te +from process_bigraph import Process, Composite, pf, Step + + +class TelluriumStep(Step): + + config_schema = { + 'sbml_model_path': 'string', + 'antimony_string': 'string', + } + + def __init__(self, config=None, core=None): + super().__init__(config, core) + + # initialize a tellurium(roadrunner) simulation object. Load the model in using either sbml(default) or antimony + if self.config.get('antimony_string') and not self.config.get('sbml_model_path'): + self.simulator = te.loada(self.config['antimony_string']) + elif self.config.get('sbml_model_path') and not self.config.get('antimony_string'): + self.simulator: te.roadrunner.extended_roadrunner.ExtendedRoadRunner = te.loadSBMLModel(self.config['sbml_model_path']) + else: + raise Exception('the config requires either an "antimony_string" or an "sbml_model_path"') + + self.input_ports = [ + 'floating_species', + 'boundary_species', + 'model_parameters' + ] + + self.output_ports = [ + 'floating_species', + ] + + # Get the species (floating and boundary) + self.floating_species_list = self.simulator.getFloatingSpeciesIds() + self.boundary_species_list = self.simulator.getBoundarySpeciesIds() + self.floating_species_initial = self.simulator.getFloatingSpeciesConcentrations() + self.boundary_species_initial = self.simulator.getBoundarySpeciesConcentrations() + + # Get the list of parameters and their values + self.model_parameters_list = self.simulator.getGlobalParameterIds() + self.model_parameter_values = self.simulator.getGlobalParameterValues() + + # Get a list of reactions + self.reaction_list = self.simulator.getReactionIds() + + # TODO -- is initial state even working for steps? + def initial_state(self, config=None): + return { + 'inputs': { + 'time': 0, + }, + } + + def inputs(self): + return { + 'time': 'float', + 'run_time': 'float', + } + + def outputs(self): + return { + 'results': { + '_type': 'numpy_array', + '_apply': 'set' + } # This is a roadrunner._roadrunner.NamedArray + } + + def update(self, inputs): + results = self.simulator.simulate( + inputs['time'], + inputs['run_time'], + 10 + ) # TODO -- adjust the number of saves teps + return { + 'results': results} + + +class TelluriumProcess(Process): + config_schema = { + 'sbml_model_path': 'string', + 'antimony_string': 'string', + 'record_history': 'bool', # TODO -- do we have this type? + } + + def __init__(self, config=None): + super().__init__(config) + + # initialize a tellurium(roadrunner) simulation object. Load the model in using either sbml(default) or antimony + if self.config.get('antimony_string') and not self.config.get('sbml_model_path'): + self.simulator = te.loada(self.config['antimony_string']) + elif self.config.get('sbml_model_path') and not self.config.get('antimony_string'): + self.simulator: te.roadrunner.extended_roadrunner.ExtendedRoadRunner = te.loadSBMLModel(self.config['sbml_model_path']) + else: + raise Exception('the config requires either an "antimony_string" or an "sbml_model_path"') + + # TODO -- make this configurable. + self.input_ports = [ + 'floating_species', + 'boundary_species', + 'model_parameters' + 'time', + # 'compartments', + # 'parameters', + # 'stoichiometries', + ] + + self.output_ports = [ + 'floating_species', + 'time', + ] + + # Get the species (floating and boundary) + self.floating_species_list = self.simulator.getFloatingSpeciesIds() + self.boundary_species_list = self.simulator.getBoundarySpeciesIds() + self.floating_species_initial = self.simulator.getFloatingSpeciesConcentrations() + self.boundary_species_initial = self.simulator.getBoundarySpeciesConcentrations() + + # Get the list of parameters and their values + self.model_parameters_list = self.simulator.getGlobalParameterIds() + self.model_parameter_values = self.simulator.getGlobalParameterValues() + + # Get a list of reactions + self.reaction_list = self.simulator.getReactionIds() + + def initial_state(self, config=None): + floating_species_dict = dict(zip(self.floating_species_list, self.floating_species_initial)) + boundary_species_dict = dict(zip(self.boundary_species_list, self.boundary_species_initial)) + model_parameters_dict = dict(zip(self.model_parameters_list, self.model_parameter_values)) + return { + 'time': 0.0, + 'floating_species': floating_species_dict, + 'boundary_species': boundary_species_dict, + 'model_parameters': model_parameters_dict + } + + def inputs(self): + float_set = {'_type': 'float', '_apply': 'set'} + return { + 'time': 'float', + 'run_time': 'float', + 'floating_species': { + species_id: float_set for species_id in self.floating_species_list}, + 'boundary_species': { + species_id: float_set for species_id in self.boundary_species_list}, + 'model_parameters': { + param_id: float_set for param_id in self.model_parameters_list}, + 'reactions': { + reaction_id: float_set for reaction_id in self.reaction_list}, + } + + def outputs(self): + float_set = {'_type': 'float', '_apply': 'set'} + return { + 'floating_species': { + species_id: float_set for species_id in self.floating_species_list}, + 'time': 'float' + } + + def update(self, inputs, interval): + + # set tellurium values according to what is passed in states + for port_id, values in inputs.items(): + if port_id in self.input_ports: # only update from input ports + for cat_id, value in values.items(): + self.simulator.setValue(cat_id, value) + + # run the simulation + new_time = self.simulator.oneStep(inputs['time'], interval) + + # extract the results and convert to update + update = {'time': new_time} + for port_id, values in inputs.items(): + if port_id in self.output_ports: + update[port_id] = {} + for cat_id in values.keys(): + update[port_id][cat_id] = self.simulator.getValue(cat_id) + return update + + +def test_process(): + # 1. define the instance of the Composite(in this case singular) by its schema + instance = { + # 'start_time_store': 0, + # 'run_time_store': 1, + # 'results_store': None, # TODO -- why is this not automatically added into the schema because of tellurium schema? + 'tellurium': { + '_type': 'process', + 'address': 'local:tellurium', # using a local toy process + 'config': { + 'sbml_model_path': 'biosimulator_processes/model_files/BIOMD0000000061_url.xml', + }, + 'inputs': { + 'time': ['start_time_store'], + 'run_time': ['run_time_store'], + 'floating_species': ['floating_species_store'], + 'boundary_species': ['boundary_species_store'], + 'model_parameters': ['model_parameters_store'], + 'reactions': ['reactions_store'], + # 'interval': ['interval_store'], + }, + 'outputs': { + 'results': ['results_store'], + } + } + } + + # 2. make the composite + workflow = Composite({ + 'state': instance + }) + + # 3. run + update = workflow.run(10) + + # 4. gather results + results = workflow.gather_results() + print(f'RESULTS: {pf(results)}') diff --git a/composer-api/README.md b/composer-api/README.md new file mode 100644 index 000000000..e69de29bb diff --git a/composer-api/composer_api/__init__.py b/composer-api/composer_api/__init__.py new file mode 100644 index 000000000..e69de29bb diff --git a/composer-api/composer_api/main.py b/composer-api/composer_api/main.py new file mode 100644 index 000000000..db25cf9a0 --- /dev/null +++ b/composer-api/composer_api/main.py @@ -0,0 +1,47 @@ +from fastapi import FastAPI, HTTPException +from pydantic import BaseModel +from typing import List, Dict, Optional +from biosimulator_processes.copasi_process import CopasiProcess +from process_bigraph import Composite + + +app = FastAPI() + +# Define Pydantic models for request and response bodies +class ProcessConfig(BaseModel): + model_file: str + +class SimulationInput(BaseModel): + time: float + floating_species: Dict[str, float] + model_parameters: Dict[str, float] + reactions: Dict[str, float] + +class SimulationResult(BaseModel): + time: float + floating_species: Dict[str, float] + +# Initialize global or shared state if necessary +processes = {} + +@app.post("/initialize/", response_model=str) +def initialize_process(config: ProcessConfig): + process_id = "unique_process_id" # Generate a unique ID for the process + processes[process_id] = CopasiProcess(config=config.dict()) + return process_id + +@app.post("/run/{process_id}", response_model=SimulationResult) +def run_simulation(process_id: str, sim_input: SimulationInput): + if process_id not in processes: + raise HTTPException(status_code=404, detail="Process not found") + result = processes[process_id].update(sim_input.dict(), sim_input.time) + return result + +@app.get("/results/{process_id}", response_model=SimulationResult) +def get_results(process_id: str): + # This is a placeholder; actual implementation will depend on how results are stored and managed + if process_id not in processes: + raise HTTPException(status_code=404, detail="Process not found") + # Placeholder for result retrieval + results = {} # Implement logic to retrieve results for the given process_id + return results diff --git a/composer-api/poetry.lock b/composer-api/poetry.lock new file mode 100644 index 000000000..e4b9972bc --- /dev/null +++ b/composer-api/poetry.lock @@ -0,0 +1,2547 @@ +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. + +[[package]] +name = "aiobotocore" +version = "2.11.2" +description = "Async client for aws services using botocore and aiohttp" +optional = false +python-versions = ">=3.8" +files = [ + {file = 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"97443a7d691c3cd7dff4d7124ffe54718b2f4d7a11f80223be7bd807af3d4cde" diff --git a/composer-api/pyproject.toml b/composer-api/pyproject.toml new file mode 100644 index 000000000..8a0b01ac4 --- /dev/null +++ b/composer-api/pyproject.toml @@ -0,0 +1,33 @@ +[tool.poetry] +name = "composer-api" +version = "0.0.1" +description = "" +authors = ["Alex Patrie "] +readme = "README.md" +packages = [{ include = "composer_api" }] + +[tool.poetry.dependencies] +python = "^3.11" +fastapi = "^0.109.0" +pyyaml = "^6.0.1" +pydantic = "^2.5.3" +h5py = "^3.10.0" +pydantic-settings = "^2.1.0" +httpx = "^0.26.0" +tensorstore = "^0.1.52" +aiofiles = "^23.2.1" +aiobotocore = "^2.11.0" +uvicorn = {extras = ["standard"], version = "^0.27.0"} +process-bigraph = "*" + +[tool.poetry.group.dev.dependencies] +pytest = "^7.4.4" +pytest-asyncio = "^0.23.3" +flake8 = "^7.0.0" +black = "^23.12.1" +coverage = "^7.4.0" +mypy = "^1.8.0" + +[build-system] +requires = ["poetry-core"] +build-backend = "poetry.core.masonry.api" diff --git a/composer-api/specs/biomodels-complete.yaml b/composer-api/specs/biomodels-complete.yaml new file mode 100644 index 000000000..64f5ca9d9 --- /dev/null +++ b/composer-api/specs/biomodels-complete.yaml @@ -0,0 +1,271 @@ +openapi: 3.0.3 +info: + description: | +

BioModels is a repository of mathematical models of biological and biomedical systems. It hosts a vast selection of existing literature-based physiologically and pharmaceutically relevant mechanistic models in standard formats. Our mission is to provide the systems modelling community with reproducible, high-quality, freely-accessible models published in the scientific literature. More information about BioModels can be found in the FAQ.

+

Notes about this API

+

Content negotiation

+

Both XML and JSON MIME types are supported. Clients have two ways of specifying the content type: +

    +
  • an explicit format request parameter (e.g. format=xml)
    • +
  • the Accept request header (e.g. Accept: application/xml).
    • +
+ If both are specified, the format parameter has priority.

+

BioModels content

+

Model information is retrieved based on the a submission identifier, such as MODEL1707110000, or a BioModels identifier, like BIOMD0000000123. BioModels content is versioned and model revision numbers are assigned incrementally starting from 1. If a particular model revision is public, it can be accessed by appending a dot ('.') and its number to the model identifier (e.g. BIOMD0000000123.1).

+

Path2Models

Models from the Path2Models project are now clustered based on their genus. Each Path2Models entry now consists of a representative model and a COMBINE archive of all other models whose organisms belong to that genus. As a result of this shuffle, some models are no longer directly accessible and such requests are redirected to the corresponding representative model. There are dedicated end points for checking which models are now only retrievable indirectly and also to find the representative model(s) for a given set of model identifiers.

+ version: v1.0 + title: BioModels + termsOfService: https://www.ebi.ac.uk/data-protection/privacy-notice/embl-ebi-public-website + contact: + email: biomodels-developers@lists.sourceforge.net + license: + name: AGPL v3 + url: https://www.gnu.org/licenses/agpl-3.0.en.html +servers: + - url: https://www.ebi.ac.uk/biomodels/ + description: The production API server + - url: https://wwwdev.ebi.ac.uk/biomodels/ + description: The development API server + - url: http://localhost:8080/biomodels/ + description: The local development API server +tags: + - name: Model-related operations + description: Retrieve information about a particular submission. + - name: Search models + description: Find models of interest + - name: Parameters Search + description: Find model parameters of interest + - name: Path2Models operations + description: Find Path2Models models of interest + - name: PDGSMM operations + description: Find Patient-derived genome-scale metabolic models (PDGSMM) of interest +paths: + /{modelId}: + get: + tags: + - Model-related operations + summary: Fetch information about a given model at a particular revision. + operationId: getModelInfo + parameters: + - in: path + name: modelId + description: The identifier of a public model in BioModels. + required: true + schema: + type: string + - in: query + name: format + description: The response format + schema: + type: string + enum: + - json + - xml + - html + required: false + responses: + '200': + description: Successful operation + content: + application/json: + schema: + $ref: '#/components/schemas/Model' + 404: + description: Invalid model id + 415: + description: Unsupported media type. Please see the content negotiation section. + /model/files/{modelId}: + get: + tags: + - Model-related operations + summary: Extract metadata information of model files of a particular model + operationId: getModelFiles + parameters: + - in: path + name: modelId + required: true + schema: + type: string + description: The identifier of the model for which to retrieve the files. + - in: query + name: format + schema: + type: string + required: false + description: The format that the response should return + responses: + '200': + description: Successful operation + content: + application/json: + schema: + $ref: '#/components/schemas/ModelFiles' + 404: + description: Invalid model id supplied + 415: + description: Unsupported media type. Please see the content negotiation section. + /model/download/{modelId}: + get: + tags: + - Model-related operations + summary: Download a particular file associated with a given model or all its files as a COMBINE archive. + operationId: downloadModelFile + parameters: + - in: path + name: modelId + required: true + description: The model identifier that the file in question is associated with + schema: + type: string + - in: query + name: filename + schema: + type: string + description: The name of the file that needs to be downloaded. If not provided, all model files are returned as a COMBINE archive. If the file name is set, then the file contents will be served. + required: false + #produces: + # - application/octet-stream + responses: + 200: + description: Successful operation + 400: + description: File Not Found + 404: + description: Invalid Model ID Supplied + /model/identifiers: + get: + tags: + - Model-related operations + summary: Fetch all model identifiers + operationId: getAllModelIdentifiers + description: Fetch all publicly available model identifiers + parameters: + - in: query + name: format + schema: + type: string + enum: + - json + - xml + - html + required: false + description: The format that the response should return + responses: + '200': + description: Successful operation + content: + application/json: + schema: + $ref: '#/components/schemas/ModelIdentifiers' + 404: + description: Invalid operation + 415: + description: Unsupported media type + /search: + get: + tags: + - Search models + summary: Download search results + operationId: searchModels + description: Search models of interest via keywords. + parameters: + - in: query + name: query + required: true + schema: + type: string + description: Search query. Please note that the colon character in ontology terms must be escaped. + - in: query + name: offset + schema: + type: integer + required: false + description: The number of items to skip before starting to collect the result set + - in: query + name: numResults + schema: + type: integer + required: false + description: The number of items to return + - in: query + name: sort + schema: + type: string + enum: + - relevance-desc + - first_author-asc + - first_author-desc + - id-asc + - id-desc + - name-asc + - name-desc + - publication_year-asc + - publication_year-desc + required: false + description: Sort criteria + - in: query + name: format + schema: + type: string + required: false + description: The format that the response should return + responses: + '200': + description: Successful operation + content: + application/json: + schema: + $ref: '#/components/schemas/SearchResults' + 404: + description: Not Found + /search/download: + get: + tags: + - Search models + summary: Download a single or multiple models + operationId: downloadModels + description: Download the main file of a given single model or multiple models via their model identifiers. + parameters: + - in: query + name: models + required: true + schema: + type: string + description: The list of model identifiers which you want to download their main file. Using the comma to separate if you are requesting more than one model. + # produces: + # - application/zip + responses: + 200: + description: Successful operation + 404: + description: Not Found +components: + schemas: + Model: + type: object + properties: + name: + type: string + description: The name of the model. + ModelFiles: + type: object + properties: + name: + type: string + description: The file of the model. + ModelIdentifiers: + type: object + properties: + name: + type: string + description: The file of the model. + SearchResults: + type: object + properties: + name: + type: string + description: The file of the model. +externalDocs: + description: Find out more about BioModels + url: https://www.ebi.ac.uk/biomodels + diff --git a/composer-api/specs/biomodels-modelId.yaml b/composer-api/specs/biomodels-modelId.yaml new file mode 100644 index 000000000..25c287eb3 --- /dev/null +++ b/composer-api/specs/biomodels-modelId.yaml @@ -0,0 +1,257 @@ +# openapi: 3.0.3 +# info: +# title: BioModels +# version: v1.0 +# description: BioModels is a repository of mathematical models of biological and biomedical systems. +# termsOfService: https://www.ebi.ac.uk/data-protection/privacy-notice/embl-ebi-public-website +# contact: +# email: biomodels-developers@lists.sourceforge.net +# license: +# name: AGPL v3 +# url: https://www.gnu.org/licenses/agpl-3.0.en.html +# servers: +# - url: https://www.ebi.ac.uk/biomodels/ +# description: The production API server +# - url: https://wwwdev.ebi.ac.uk/biomodels/ +# description: The development API server +# - url: http://localhost:8080/biomodels/ +# description: The local development API server +# tags: +# - name: Model-related operations +# description: Retrieve information about a particular submission. +# # Paths summary +# paths: +# /{modelId}: +# get: +# tags: [Model-related operations] +# operationId: getModelById +# summary: Fetch information about a given model at a particular revision. +# parameters: +# - in: path +# name: modelId +# required: true +# schema: +# type: string +# description: The identifier of a public model in BioModels. +# - in: query +# name: format +# required: false +# schema: +# type: string +# enum: [json, xml, html] +# description: The response format. +# responses: +# '200': +# description: Successful operation +# content: +# application/json: +# schema: +# $ref: '#/components/schemas/Model' +# '404': +# description: Invalid model id +# '415': +# description: Unsupported media type. Please see the content negotiation section. +# # Additional paths would be defined here following the same structure +# components: +# schemas: +# Model: +# type: object +# properties: +# name: +# type: string +# description: The name of the model. +# # Additional properties would be defined here +# + +openapi: 3.0.3 +info: + title: BioModels + version: v1.0 + description: BioModels is a repository of mathematical models of biological and biomedical systems. + termsOfService: https://www.ebi.ac.uk/data-protection/privacy-notice/embl-ebi-public-website + contact: + email: biomodels-developers@lists.sourceforge.net + license: + name: AGPL v3 + url: https://www.gnu.org/licenses/agpl-3.0.en.html +servers: + - url: https://www.ebi.ac.uk/biomodels + description: The production API server + - url: https://wwwdev.ebi.ac.uk/biomodels + description: The development API server + - url: http://localhost:8080/biomodels + description: The local development API server +tags: + - name: Model-related operations + description: Retrieve information about a particular submission. +# Paths summary +paths: + /{modelId}: + get: + tags: [Model-related operations] + operationId: getModelById + summary: Fetch information about a given model at a particular revision. + parameters: + - in: path + name: modelId + required: true + schema: + type: string + description: The identifier of a public model in BioModels. + - in: query + name: format + required: false + schema: + type: string + enum: [json, xml, html] + description: The response format. + responses: + '200': + description: Successful operation + content: + application/json: + schema: + $ref: '#/components/schemas/Model' + '404': + description: Invalid model id + '415': + description: Unsupported media type. Please see the content negotiation section. + /model/identifiers: + get: + tags: [Model-related operations] + operationId: getIdentifiers + summary: Fetch all publicly available model identifiers + parameters: + - in: query + name: format + required: true + schema: + type: string + enum: [json, xml, html] + description: The response format. + responses: + '200': + description: Successful operation + content: + application/json: + schema: + $ref: '#/components/schemas/ModelIdentifiers' + '404': + description: Invalid operation + '415': + description: Unsupported media type. Please see the content negotiation section. +components: + schemas: + Model: + type: object + properties: + name: + type: string + description: The name of the model. + description: + type: string + description: A detailed description of the model including its purpose and how it was tested. + format: + type: object + properties: + name: + type: string + description: The format name of the model. + version: + type: string + description: The version of the format. + publication: + type: object + properties: + journal: + type: string + title: + type: string + affiliation: + type: string + synopsis: + type: string + year: + type: string + month: + type: string + volume: + type: string + pages: + type: string + link: + type: string + authors: + type: array + items: + type: object + properties: + name: + type: string + files: + type: object + properties: + main: + type: array + items: + $ref: '#/components/schemas/File' + additional: + type: array + items: + $ref: '#/components/schemas/File' + history: + type: object + properties: + revisions: + type: array + items: + $ref: '#/components/schemas/Revision' + firstPublished: + type: integer + format: int64 + description: Timestamp of the first publication. + submissionId: + type: string + description: Unique identifier for the submission. + publicationId: + type: string + description: Unique identifier for the publication associated with the model. + File: + type: object + properties: + name: + type: string + description: The file name. + fileSize: + type: string + description: The size of the file in bytes. + description: + type: string + description: A description of the file. + Revision: + type: object + properties: + version: + type: integer + description: The version number of the revision. + submitted: + type: integer + format: int64 + description: The timestamp when the revision was submitted. + submitter: + type: string + description: The name of the submitter. + comment: + type: string + description: A comment regarding the revision. + ModelIdentifiers: + type: object + properties: + hits: + type: integer + description: Number of downloads + models: + type: array + items: + type: string + description: Each model in the database. diff --git a/composer-api/specs/composer.yaml b/composer-api/specs/composer.yaml new file mode 100644 index 000000000..e84cbcce1 --- /dev/null +++ b/composer-api/specs/composer.yaml @@ -0,0 +1,108 @@ +openapi: 3.0.3 +info: + title: process-bigraph + description: An API for running biosimulation processes using Copasi/Basico. + version: "1.0.0" +servers: + - url: https://localhost:8000 + description: Local server +paths: + /initialize: + post: + summary: Initialize the simulation with a model file. + operationId: initializeSimulation + requestBody: + required: true + content: + application/json: + schema: + type: object + properties: + model_file: + type: string + description: Path to the model file. + responses: + '200': + description: Simulation initialized successfully. + content: + application/json: + schema: + type: object + properties: + message: + type: string + example: Simulation initialized with model_file. + /run: + post: + summary: Run the simulation for a given interval. + operationId: runSimulation + requestBody: + required: true + content: + application/json: + schema: + type: object + properties: + interval: + type: integer + description: Interval for which the simulation is run. + responses: + '200': + description: Simulation run successfully. + content: + application/json: + schema: + type: object + properties: + time: + type: float + example: 10 + floating_species: + type: object + additionalProperties: + type: float + example: {"species1": 0.5, "species2": 1.5} + /update: + post: + summary: Update the simulation state. + operationId: updateSimulation + requestBody: + required: true + content: + application/json: + schema: + type: object + properties: + state: + type: object + description: New state to update the simulation with. + responses: + '200': + description: Simulation state updated successfully. + /results: + get: + summary: Fetch the simulation results. + operationId: fetchResults + responses: + '200': + description: Results fetched successfully. + content: + application/json: + schema: + type: object + properties: + results: + type: object + additionalProperties: true + example: {"floating_species": {"species1": 0.5, "species2": 1.5}, "time": 10} +components: + schemas: + SimulationState: + type: object + properties: + time: + type: float + floating_species: + type: object + additionalProperties: + type: float diff --git a/notebooks/cobra_process.ipynb b/notebooks/cobra_process.ipynb new file mode 100644 index 000000000..22f085322 --- /dev/null +++ b/notebooks/cobra_process.ipynb @@ -0,0 +1,39 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "id": "initial_id", + "metadata": { + "collapsed": true + }, + "outputs": [], + "source": [ + "import sys \n", + "\n", + "sys.path.insert(0, '..')" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 2 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython2", + "version": "2.7.6" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/notebooks/copasi_process.ipynb b/notebooks/copasi_process.ipynb new file mode 100644 index 000000000..9c5a5e741 --- /dev/null +++ b/notebooks/copasi_process.ipynb @@ -0,0 +1,151 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "id": "initial_id", + "metadata": { + "collapsed": true + }, + "outputs": [], + "source": [ + "import sys \n", + "\n", + "sys.path.insert(0, '..')" + ] + }, + { + "cell_type": "code", + "outputs": [], + "source": [ + "from process_bigraph import Composite, pf \n", + "from biosimulator_processes.copasi_process import CopasiProcess" + ], + "metadata": { + "collapsed": false + }, + "id": "c6c10dc5988e52d4" + }, + { + "cell_type": "code", + "outputs": [], + "source": [ + "# 1. Define the sim state schema:\n", + "initial_sim_state = {\n", + " 'copasi': {\n", + " '_type': 'process',\n", + " 'address': 'local:copasi',\n", + " 'config': {\n", + " 'model_file': 'biosimulator_processes/model_files/Caravagna2010.xml'\n", + " },\n", + " 'inputs': {\n", + " 'floating_species': ['floating_species_store'],\n", + " 'model_parameters': ['model_parameters_store'],\n", + " 'time': ['time_store'],\n", + " 'reactions': ['reactions_store']\n", + " },\n", + " 'outputs': {\n", + " 'floating_species': ['floating_species_store'],\n", + " 'time': ['time_store'],\n", + " }\n", + " },\n", + " # TODO: Add emitter schema\n", + " 'emitter': {\n", + " '_type': 'step',\n", + " 'address': 'local:ram-emitter',\n", + " 'config': {\n", + " 'emit': {\n", + " 'floating_species': 'tree[float]',\n", + " 'time': 'float',\n", + " },\n", + " },\n", + " 'inputs': {\n", + " 'floating_species': ['floating_species_store'],\n", + " 'time': ['time_store'],\n", + " }\n", + " }\n", + "}\n", + "\n", + "\n", + "\n", + "\n", + "\n" + ], + "metadata": { + "collapsed": false + }, + "id": "77636dbde3fa6b74" + }, + { + "cell_type": "code", + "outputs": [], + "source": [ + "# 2. Make the composite:\n", + "workflow = Composite({\n", + " 'state': initial_sim_state\n", + "})" + ], + "metadata": { + "collapsed": false + }, + "id": "4c2ef631b005be61" + }, + { + "cell_type": "code", + "outputs": [], + "source": [ + "# 3. Run the composite workflow:\n", + "workflow.run(10)" + ], + "metadata": { + "collapsed": false + }, + "id": "98676149a4ce822f" + }, + { + "cell_type": "code", + "outputs": [], + "source": [ + "# 4. Gather and pretty print results\n", + "results = workflow.gather_results()\n", + "print(f'RESULTS: {pf(results)}')" + ], + "metadata": { + "collapsed": false + }, + "id": "c15cee593ef000a7" + }, + { + "cell_type": "code", + "outputs": [], + "source": [ + "# 5. Plot/Analyze the results" + ], + "metadata": { + "collapsed": false + }, + "id": "297504800772775e" + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 2 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython2", + "version": "2.7.6" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/notebooks/smoldyn_process.ipynb b/notebooks/smoldyn_process.ipynb new file mode 100644 index 000000000..22f085322 --- /dev/null +++ b/notebooks/smoldyn_process.ipynb @@ -0,0 +1,39 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "id": "initial_id", + "metadata": { + "collapsed": true + }, + "outputs": [], + "source": [ + "import sys \n", + "\n", + "sys.path.insert(0, '..')" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 2 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython2", + "version": "2.7.6" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/notebooks/tellurium_process.ipynb b/notebooks/tellurium_process.ipynb new file mode 100644 index 000000000..22f085322 --- /dev/null +++ b/notebooks/tellurium_process.ipynb @@ -0,0 +1,39 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "id": "initial_id", + "metadata": { + "collapsed": true + }, + "outputs": [], + "source": [ + "import sys \n", + "\n", + "sys.path.insert(0, '..')" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + 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= "pytest" -version = "8.0.1" +version = "8.0.2" description = "pytest: simple powerful testing with Python" optional = false python-versions = ">=3.8" files = [ - {file = "pytest-8.0.1-py3-none-any.whl", hash = "sha256:3e4f16fe1c0a9dc9d9389161c127c3edc5d810c38d6793042fb81d9f48a59fca"}, - {file = "pytest-8.0.1.tar.gz", hash = "sha256:267f6563751877d772019b13aacbe4e860d73fe8f651f28112e9ac37de7513ae"}, + {file = "pytest-8.0.2-py3-none-any.whl", hash = "sha256:edfaaef32ce5172d5466b5127b42e0d6d35ebbe4453f0e3505d96afd93f6b096"}, + {file = "pytest-8.0.2.tar.gz", hash = "sha256:d4051d623a2e0b7e51960ba963193b09ce6daeb9759a451844a21e4ddedfc1bd"}, ] [package.dependencies] @@ -4515,4 +4538,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = ">=3.10" -content-hash = "780c0143114975709aa119547fd82225963301641c4c735249e973021b03bec5" +content-hash = "cd6d7425448035b909d563817fc0ff783d815426d50be25d0fb0efc100433b1a" diff --git a/pyproject.toml b/pyproject.toml index 5fd65049e..9defe90ed 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -9,7 +9,6 @@ packages = [{include = "biosimulator_processes"}] [tool.poetry.dependencies] python = ">=3.10" zarr = "*" -# kisao = ">=2.33" termcolor = "*" jupyterlab = "*" bigraph-schema = "*" @@ -21,6 +20,8 @@ tellurium = "*" smoldyn = "*" bigraph-viz = "^0.0.31" python-libsbml = "^5.20.2" +docker = ">=7.0" +python-libnuml = "^1.1.6" # ">=1.0.0" [tool.poetry.group.dev.dependencies] pytest = "*" diff --git a/scripts/build-container.sh b/scripts/build-container.sh old mode 100644 new mode 100755 index 95550d051..68ef3a0d4 --- a/scripts/build-container.sh +++ b/scripts/build-container.sh @@ -2,7 +2,7 @@ version="$1" -set -e +run="$2" if [ "${version}" == "" ]; then echo "Please enter the version you would like to build as a runtime arg. Exiting." @@ -14,3 +14,7 @@ docker buildx create --name biosimbuilder --use docker buildx inspect --bootstrap docker buildx build --platform linux/amd64 \ -t ghcr.io/biosimulators/biosimulator-processes:"${version}" . + +if [ "${run}" == "-r" ]; then + ./scripts/run-container.sh "${version}" +fi diff --git a/scripts/release-container.sh b/scripts/release-container.sh old mode 100644 new mode 100755 index 209380223..e07d09204 --- a/scripts/release-container.sh +++ b/scripts/release-container.sh @@ -3,10 +3,10 @@ version="$1" -# PLEASE UPDATE THE LATEST VERSION HERE BEFORE RUNNING. CURRENT: 0.0.2 -current="0.0.2" +# PLEASE UPDATE THE LATEST VERSION HERE BEFORE RUNNING. CURRENT: 0.0.4 +current="0.0.3" -set -e +run="$2" if [ "${version}" == "" ]; then echo "You must pass the container version you wish to release as an argument to this script. Exiting." @@ -36,3 +36,7 @@ docker buildx build --platform linux/amd64 \ --push docker tag ghcr.io/biosimulators/biosimulator-processes:"${version}" ghcr.io/biosimulators/biosimulator-processes:latest docker push ghcr.io/biosimulators/biosimulator-processes:latest + +if [ "${run}" == "-r" ]; then + ./scripts/run-container.sh "${version}" +fi diff --git a/scripts/trust-notebooks.sh b/scripts/trust-notebooks.sh new file mode 100644 index 000000000..0dc85c0f0 --- /dev/null +++ b/scripts/trust-notebooks.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +# Trust all notebooks in a specific directory +find /app/notebooks -name "*.ipynb" -exec jupyter trust {} \; diff --git a/setup.py b/setup.py index 04b85ccae..f67a7906d 100644 --- a/setup.py +++ b/setup.py @@ -48,7 +48,8 @@ "pytest>=6.2.5", "tellurium", "copasi-basico", - "cobra" + "cobra", + "docker" ], extras_require={ "smoldyn": ["smoldyn", "simulariumio"],