update kernel spec in compose server

.dockerignore

@@ -15,6 +15,7 @@ nosetests.xml
 coverage.xml
 *.cover
 *.log
+.ipynb_checkpoints
 .git
 .mypy_cache
 .pytest_cache

.gitignore

@@ -1,3 +1,4 @@
+.ipynb_checkpoints
 release_env
 commit.sh
 .idea/

assets/dev/scripts/add_env_kernel.sh

@@ -0,0 +1,17 @@
+#!/usr/bin/env bash
+
+env="$1"
+
+if [ "$env" == "" ]; then
+  env=$(conda env list | grep '*' | awk '{print $1}')
+fi
+
+# install ipykernel if needed
+kernel=$(conda list | grep ipykernel)
+
+if [ "$kernel" == "" ]; then
+  conda run -n "$env" pip install ipykernel jupyterlab
+fi
+
+python_version=$(conda run -n "$env" python --version)
+conda run -n "$env" python -m ipykernel install --user --name="$env" --display-name "BioCompose Server($env): Python$python_version"

assets/dev/scripts/install.sh

@@ -15,7 +15,7 @@ if [ "$platform" == "Darwin" ]; then
 fi
 
 # install deps from pyproject and activate env
-conda run -n bio-compose-server pip install --upgrade pip
-conda run -n bio-compose-server pip install -e .
-conda activate bio-compose-server
+conda run -n server pip install --upgrade pip
+conda run -n server pip install -e .
+conda activate server
 

bio_bundles/quantum/__init__.py

@@ -0,0 +1,3 @@
+
+
+

bio_bundles/quantum/data_model.py

@@ -0,0 +1,17 @@
+import numpy as np
+
+
+class DiracNotation(np.ndarray):
+    def __new__(cls, values: list[complex]):
+        return np.asarray(values).view(cls)
+
+
+class Bra(DiracNotation):
+    pass
+
+
+class Ket(DiracNotation):
+    def bra(self) -> Bra:
+        ket_value = self.view()
+        return Bra(np.conj(ket_value).T)
+

bio_bundles/quantum/test_quantum.ipynb

@@ -0,0 +1,39 @@
+{
+ "cells": [
+  {
+   "metadata": {},
+   "cell_type": "raw",
+   "source": "from process_bigraph",
+   "id": "f3a9e63ddcc7d864"
+  },
+  {
+   "metadata": {
+    "jupyter": {
+     "is_executing": true
+    }
+   },
+   "cell_type": "code",
+   "source": "from process_bigraph import Process, Step, Composite",
+   "id": "21fa17e759c94d71",
+   "outputs": [],
+   "execution_count": null
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "",
+   "id": "92c51098889dfb08"
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "name": "python3",
+   "language": "python",
+   "display_name": "Python 3 (ipykernel)"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

environment.yml

@@ -1,4 +1,4 @@
-name: bio-compose-server
+name: server
 channels:
   - defaults
   - https://repo.anaconda.com/pkgs/main
@@ -8,5 +8,34 @@ channels:
 dependencies:
   - pip
   - python=3.10
+  - poetry
   # - readdy
   # - pymem3dg
+  - pip:
+      - uvicorn
+      - fastapi
+      - mypy
+      - pytest
+      - pip-autoremove
+      - networkx
+      - rustworkx
+      - qiskit
+      - qiskit-ibm-runtime
+      - numpy
+      - pandas
+      - process-bigraph
+      - copasi-basico
+      - tellurium
+      - python-libsbml
+      - smoldyn
+      - requests-toolbelt
+      - python-dotenv
+      - google-cloud-storage
+      - python-multipart
+      - toml
+      - typing-extensions
+      - pymongo
+      - pydantic
+      - pydantic-settings
+      - chardet
+      - pyyaml

pyproject

@@ -0,0 +1,46 @@
+[project]
+name = "bio-compose-server"
+version = "0.0.1"
+readme ="README.md"
+description = "Backend for BioCompose: a microservices-based data service leveraging Kubernetes for efficient orchestration of bio-chemical simulation comparisons."
+authors = [{name = "Alex Patrie", email = "[email protected]"}]
+
+# only app-level deps
+dependencies = [
+    "requests-toolbelt",
+    "python-dotenv",
+    "google-cloud-storage",
+    "python-multipart",
+    "fastapi",
+    "toml",
+    "typing-extensions",
+    "pymongo",
+    "pydantic-settings",
+    "pydantic",
+    "uvicorn",
+    "pyyaml",
+    "chardet",
+    "simulariumio",
+    "numpy",
+    "pandas",
+    "process-bigraph==0.0.22",
+    "bigraph-schema",
+    "copasi-basico",
+    "tellurium",
+    "python-libsbml",
+    "smoldyn",
+    "pip-autoremove",
+    "networkx",
+    "qiskit",
+    "qiskit-ibm-runtime",
+    "mypy"
+]
+
+
+[tool.setuptools]
+packages = ["bio_bundles", "gateway", "shared", "tests", "worker"]
+
+
+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+build-backend = "setuptools.build_meta"

pyproject.toml

@@ -1,42 +1,70 @@
-[project]
+[tool.poetry]
 name = "bio-compose-server"
 version = "0.0.1"
 readme ="README.md"
 description = "Backend for BioCompose: a microservices-based data service leveraging Kubernetes for efficient orchestration of bio-chemical simulation comparisons."
-authors = [{name = "Alex Patrie", email = "[email protected]"}]
-
-# only app-level deps
-dependencies = [
-    "requests-toolbelt",
-    "python-dotenv",
-    "google-cloud-storage",
-    "python-multipart",
-    "fastapi",
-    "toml",
-    "typing-extensions",
-    "pymongo",
-    "pydantic-settings",
-    "pydantic",
-    "uvicorn",
-    "pyyaml",
-    "chardet",
-    "simulariumio",
-    "numpy",
-    "pandas",
-    "process-bigraph==0.0.22",
-    "bigraph-schema",
-    "copasi-basico",
-    "tellurium",
-    "python-libsbml",
-    "smoldyn",
-    "pip-autoremove"
+authors = ["Alex Patrie <[email protected]>"]
+packages = [
+    {include ="bio_bundles"},
+    {include ="gateway"},
+    {include ="shared"},
+    {include ="tests"},
+    {include ="worker"}
 ]
 
 
-[tool.setuptools]
-packages = ["bio_bundles", "gateway", "shared", "tests", "worker"]
+[tool.poetry.dependencies]
+python = ">=3.10"
+
+
+[tool.poetry.group.api.dependencies]
+uvicorn = "*"
+fastapi = "^0.115.6"
+
+
+[tool.poetry.group.dev.dependencies]
+mypy = "*"
+pytest = "*"
+pip-autoremove = "*"
+
+
+[tool.poetry.group.quantum.dependencies]
+jupyterlab = "*"
+ipykernel = "*"
+
+
+[tool.poetry.group.quantum.dependencies]
+networkx = "*"
+rustworkx = "*"
+qiskit = "*"
+qiskit-ibm-runtime = "*"
+
+
+[tool.poetry.group.simulators.dependencies]
+numpy = "*"
+pandas = "*"
+process-bigraph = "*"
+bigraph-schema = "*"
+copasi-basico = "*"
+tellurium = "*"
+python-libsbml = "*"
+smoldyn = "*"
+
+
+[tool.poetry.group.shared.dependencies]
+requests-toolbelt = "^1.0.0"
+python-dotenv = "^1.0.1"
+google-cloud-storage = "^2.19.0"
+python-multipart = "^0.0.20"
+toml = "^0.10.2"
+typing-extensions = "^4.12.2"
+pymongo = "^4.10.1"
+pydantic-settings = "^2.7.0"
+pydantic = "^2.10.4"
+chardet = "*"
+pyyaml = "*"
 
 
 [build-system]
-requires = ["setuptools>=61.0", "wheel"]
-build-backend = "setuptools.build_meta"
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"