Update documentation style

.gitignore

@@ -165,4 +165,7 @@ cython_debug/
 *.code-workspace
 .github/workflows/_*.yml
 
-uv.lock
+uv.lock
+docker/.env copy
+
+*.DS_Store

README.md

@@ -41,93 +41,99 @@ pip install .[docs]
 mkdocs serve
 ```
 
-
+### Where in the stack
 ```mermaid
 block-beta
    columns 3
-   
+
    block:Interface
        columns 1
        InterfaceTitle("<i><b>Interfaces</b><i/>")
-       InterfaceDigital["<b>Digital Interface</b>\nQuantum circuits with discrete gates"] 
+       InterfaceDigital["<b>Digital Interface</b>\nQuantum circuits with discrete gates"]
        space
-       InterfaceAnalog["<b>Analog Interface</b>\n Continuous-time evolution with Hamiltonians"] 
+       InterfaceAnalog["<b>Analog Interface</b>\n Continuous-time evolution with Hamiltonians"]
        space
        InterfaceAtomic["<b>Atomic Interface</b>\nLight-matter interactions between lasers and ions"]
        space
     end
-    
+
     block:IR
        columns 1
        IRTitle("<i><b>IRs</b><i/>")
-       IRDigital["Quantum circuit IR\nopenQASM, LLVM+QIR"] 
+       IRDigital["Quantum circuit IR\nopenQASM, LLVM+QIR"]
        space
        IRAnalog["openQSIM"]
        space
        IRAtomic["openAPL"]
        space
     end
-    
+
     block:Emulator
        columns 1
        EmulatorsTitle("<i><b>Classical Emulators</b><i/>")
-       
-       EmulatorDigital["Pennylane, Qiskit"] 
+
+       EmulatorDigital["Pennylane, Qiskit"]
        space
        EmulatorAnalog["QuTiP, QuantumOptics.jl"]
        space
        EmulatorAtomic["TrICal, QuantumIon.jl"]
        space
     end
-    
+
     space
     block:RealTime
        columns 1
        RealTimeTitle("<i><b>Real-Time</b><i/>")
        space
-       RTSoftware["ARTIQ, DAX, OQDAX"] 
+       RTSoftware["ARTIQ, DAX, OQDAX"]
        space
        RTGateware["Sinara Real-Time Control"]
        space
        RTHardware["Lasers, Modulators, Photodetection, Ion Trap"]
        space
-       RTApparatus["Trapped-Ion QPU (<sup>171</sup>Yt<sup>+</sup>, <sup>133</sup>Ba<sup>+</sup>)"]
+       RTApparatus["Trapped-Ion QPU (<sup>171</sup>Yb<sup>+</sup>, <sup>133</sup>Ba<sup>+</sup>)"]
        space
     end
     space
-    
+
    InterfaceDigital --> IRDigital
    InterfaceAnalog --> IRAnalog
    InterfaceAtomic --> IRAtomic
-   
+
    IRDigital --> IRAnalog
    IRAnalog --> IRAtomic
-   
+
    IRDigital --> EmulatorDigital
    IRAnalog --> EmulatorAnalog
    IRAtomic --> EmulatorAtomic
-   
+
    IRAtomic --> RealTimeTitle
-   
+
    RTSoftware --> RTGateware
    RTGateware --> RTHardware
    RTHardware --> RTApparatus
-
-    classDef title fill:#d6d4d4,stroke:#333,color:#333;
-    classDef digital fill:#E7E08B,stroke:#333,color:#333;
-    classDef analog fill:#E4E9B2,stroke:#333,color:#333;
-    classDef atomic fill:#D2E4C4,stroke:#333,color:#333;
-    classDef realtime fill:#B5CBB7,stroke:#333,color:#333;
-
-    classDef highlight fill:#f2bbbb,stroke:#333,color:#333,stroke-dasharray: 5 5;
-
+
+   classDef title fill:#23627D,stroke:#141414,color:#FFFFFF;
+   classDef digital fill:#c3e1ee,stroke:#141414,color:#141414;
+   classDef analog fill:#afd7e9,stroke:#141414,color:#141414;
+   classDef atomic fill:#9ccee3,stroke:#141414,color:#141414;
+   classDef realtime fill:#88c4dd,stroke:#141414,color:#141414;
+
+    classDef highlight fill:#F19D19,stroke:#141414,color:#141414,stroke-dasharray: 5 5;
+    classDef normal fill:#fcebcf,stroke:#141414,color:#141414;
+
     class InterfaceTitle,IRTitle,EmulatorsTitle,RealTimeTitle title
     class InterfaceDigital,IRDigital,EmulatorDigital digital
     class InterfaceAnalog,IRAnalog,EmulatorAnalog analog
     class InterfaceAtomic,IRAtomic,EmulatorAtomic atomic
     class RTSoftware,RTGateware,RTHardware,RTApparatus realtime
+
+   class Emulator highlight
+
+   class Interface normal
+   class RealTime normal
+   class IR normal
 
-    class Emulator highlight
 ```
 The tools in this repository allow for self-hosting a server to run
 quantum programs on classical emulators, highlighted in the stack diagram in red. 

docker/.dockerignore

@@ -0,0 +1,92 @@
+# Git
+.git
+.gitignore
+.gitattributes
+
+
+# CI
+.codeclimate.yml
+.travis.yml
+.taskcluster.yml
+
+# Docker
+docker-compose.yml
+Dockerfile
+.docker
+.dockerignore
+
+# Byte-compiled / optimized / DLL files
+**/__pycache__/
+**/*.py[cod]
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.cache
+nosetests.xml
+coverage.xml
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Virtual environment
+.env
+.venv/
+venv/
+
+# PyCharm
+.idea
+
+# Python mode for VIM
+.ropeproject
+**/.ropeproject
+
+# Vim swap files
+**/*.swp
+
+# VS Code
+.vscode/
+
+
+.venv

docker/Dockerfile

@@ -1,62 +1,22 @@
-FROM python:3.10.13-slim-bookworm as build
-
+FROM python:3.12-slim-bookworm as build
+COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/
 
 RUN apt-get update && \
     apt-get upgrade -y && \
-    apt-get install -y --no-install-recommends build-essential gcc && \
-    apt-get install -y git  # for installing directly from git
-
-ARG PIP_DISABLE_PIP_VERSION_CHECK=1
-ARG PIP_NO_CACHE_DIR=1
-
-WORKDIR /python
-
-RUN python -m venv /python/venv
-
-ENV PATH="/python/venv/bin:$PATH"
-
-COPY docker/requirements.txt .
-RUN pip install -r requirements.txt
-
-RUN pip install oqd-compiler-infrastructure
-RUN pip install oqd-core
-RUN pip install oqd-analog-emulator
-
-
-########################################################################################
-
-FROM python:3.10.13-slim-bookworm as app
-
-RUN apt update && \
     apt install -y --no-install-recommends supervisor && \
+    apt-get install -y git && \ 
     apt-get install -y gcc g++  # needed from Cython
 
-
-ARG PIP_DISABLE_PIP_VERSION_CHECK=1
-ARG PIP_NO_CACHE_DIR=1
-
-COPY --from=build /python/venv /python/venv
-
-ENV PATH="/python/venv/bin:$PATH"
-ENV PYTHONPATH="/app/src"
-
 COPY . ./app
+ENV PYTHONPATH="/app/src"
 WORKDIR /app
-RUN pip install .
-#RUN pip install .[all]
 
-#COPY ./supervisord.conf /etc/supervisor/conf.d/supervisord.conf
-COPY ./docker/supervisord.conf /etc/supervisor/conf.d/supervisord.conf
-CMD ["/usr/bin/supervisord", "-c", "/etc/supervisor/conf.d/supervisord.conf"]
-
-########################################################################################
+RUN uv venv
+ENV PATH=".venv/bin:$PATH"
 
-# RUN \
-#     apt update \
-#     && apt install wget -y \
-#     && wget https://julialang-s3.julialang.org/bin/linux/x64/1.9/julia-1.9.3-linux-x86_64.tar.gz -P /opt \
-#     && tar zxvf /opt/julia-1.9.3-linux-x86_64.tar.gz -C /opt 
+RUN uv pip install ".[server]"
 
-# ENV PATH "$PATH:/opt/julia-1.9.3/bin"
+COPY ./docker/supervisord.conf /etc/supervisor/conf.d/supervisord.conf
+CMD ["/usr/bin/supervisord", "-c", "/etc/supervisor/conf.d/supervisord.conf"]
 
-# RUN julia -e 'using Pkg; Pkg.add(["QuantumOptics", "Configurations", "StatsBase", "DataStructures", "JSON3", "IonSim"])'
+########################################################################################