Use refactored PyCIEMSS lib

.gitignore

@@ -46,6 +46,7 @@ dist
 .venv
 .tmp
 .vscode
+.devcontainer
 .cache
 .sqlite
 experiments-main
@@ -73,3 +74,4 @@ create.sql
 .eslintcache
 
 .version
+*.nix

Makefile

@@ -1,4 +1,4 @@
-SHELL = /bin/bash
+SHELL = /usr/bin/env bash
 LANG = en_US.utf-8
 PYTHON = $(shell which python3 || which python)
 DOCKER = $(shell which docker)

docker/Dockerfile.api

@@ -7,6 +7,10 @@ COPY poetry.lock poetry.lock
 RUN poetry config virtualenvs.create false && \
  poetry install --no-root --no-cache
 
+# We have to install PyCIEMSS now since the interface uses Torch
+# TODO: Do not use Torch in PyCIEMSS Library interface
+RUN poetry run poe install-pyciemss 
+
 COPY service service
 COPY tests tests
 COPY README.md README.md

pyproject.toml

@@ -36,7 +36,8 @@ fakeredis = "^2.17.0"
 httpx = "^0.24.1"
 
 [tool.poe.tasks]
-install-pyciemss = "pip install --no-cache git+https://github.com/ciemss/pyciemss.git@v0.0.3" 
+install-pyciemss = "pip install --no-cache-dir git+https://github.com/fivegrant/pyciemss.git@087bc64d935f2ab5090330f1f7d6bde930404115 --use-pep517"
+
 
 [tool.pytest.ini_options]
 markers = ["example_dir"]

service/api.py

@@ -2,18 +2,15 @@
 
 import logging
 import os
-from fastapi import FastAPI, Depends
+from fastapi import FastAPI, Depends, HTTPException
 from fastapi.middleware.cors import CORSMiddleware
 
 from models import (
  Status,
  JobResponse,
  Calibrate,
  Simulate,
- OptimizeSimulate,
- OptimizeCalibrate,
  EnsembleSimulate,
- EnsembleCalibrate,
  StatusSimulationIdGetResponse,
 )
 
@@ -22,10 +19,7 @@
 operations = {
  "simulate": Simulate,
  "calibrate": Calibrate,
- "optimize-simulate": OptimizeSimulate,
- "optimize-calibrate": OptimizeCalibrate,
  "ensemble-simulate": EnsembleSimulate,
- "ensemble-calibrate": EnsembleCalibrate,
 }
 
 logging.basicConfig()
@@ -111,3 +105,21 @@ def operate(
  return create_job(body, operation_name, redis_conn)
 
  registrar(operate)
+
+
+@app.get("/ensemble-calibrate", response_model=StatusSimulationIdGetResponse)
+def ensemble_calibrate_not_yet_implemented():
+ """
+ DO NOT USE. Placeholder for `ensemble-calibrate` endpoint.
+ This will be reimplemented in the future.
+ """
+ raise HTTPException(status=501, detail="Not yet reimplemented")
+
+
+@app.get("/optimize", response_model=StatusSimulationIdGetResponse) # NOT YET IN SPEC
+def optimize_not_yet_implemented(): # NOT YET IN SPEC
+ """
+ DO NOT USE. Placeholder for `optimize` endpoint.
+ This will be implemented in the future.
+ """
+ raise HTTPException(status=501, detail="Not yet implemented")

service/execute.py

@@ -8,18 +8,7 @@
  attach_files,
 )
 
-from pyciemss.PetriNetODE.interfaces import ( # noqa: F401
- load_and_calibrate_and_sample_petri_model,
- load_and_sample_petri_model,
- load_and_optimize_and_sample_petri_model,
- load_and_calibrate_and_optimize_and_sample_petri_model,
-)
-
-from pyciemss.Ensemble.interfaces import ( # noqa: F401
- load_and_sample_petri_ensemble,
- load_and_calibrate_and_sample_ensemble_model,
-)
-
+from pyciemss.interfaces import sample, calibrate, ensemble_sample # noqa: F401
 
 TDS_SIMULATIONS = "/simulations/"
 TDS_URL = settings.TDS_URL