Update documentation styles

.github/ISSUE_TEMPLATE.md

@@ -26,4 +26,4 @@
   - Subsystem:
 
 
-* **Other information** (e.g. detailed explanation, stacktraces, related issues, suggestions how to fix, links for us to have context, eg. stackoverflow, gitter, etc)
+* **Other information** (e.g. detailed explanation, stacktraces, related issues, suggestions how to fix, links for us to have context, eg. stackoverflow, gitter, etc)

.github/workflows/check_copyright.yml

@@ -10,6 +10,6 @@ jobs:
       - name: Check license & copyright headers
         uses: viperproject/check-license-header@v2
         with:
-          path: 
+          path:
           config: .github/workflows/check_copyright_config.json
-          # strict: true
+          # strict: true

.github/workflows/check_mkdocs_build.yml

@@ -21,4 +21,4 @@ jobs:
         uses: astral-sh/setup-uv@v4
       # - run: cp -r examples/ docs/examples/
       - run: uv pip install .[docs] --system
-      - run: mkdocs build
+      - run: mkdocs build

.github/workflows/copyright.txt

@@ -10,4 +10,4 @@
 # distributed under the License is distributed on an "AS IS" BASIS,
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
-# limitations under the License.
+# limitations under the License.

.gitignore

@@ -175,4 +175,5 @@ _scripts/
 
 # ignore copied examples files when building docs
 docs/examples/
-tests/test.bat
+tests/test.bat
+.pre-commit-config.yaml

CODE_OF_CONDUCT.md

@@ -129,4 +129,4 @@ at [https://www.contributor-covenant.org/translations][translations].
 [v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
 [Mozilla CoC]: https://github.com/mozilla/diversity
 [FAQ]: https://www.contributor-covenant.org/faq
-[translations]: https://www.contributor-covenant.org/translations
+[translations]: https://www.contributor-covenant.org/translations

README.md

@@ -37,7 +37,7 @@ pip install .
 ```
 
 This OQD repository depends on the [`oqd-core`](https://github.com/OpenQuantumDesign/oqd-core.git)
-and [`oqd-compiler-infrastructure`](https://github.com/OpenQuantumDesign/oqd-compiler-infrastructure.git) packages, which should be installed with all other dependencies. 
+and [`oqd-compiler-infrastructure`](https://github.com/OpenQuantumDesign/oqd-compiler-infrastructure.git) packages, which should be installed with all other dependencies.
 If needed, these can be manually installed via,
 ```bash
 pip install oqd-compiler-infrastructure
@@ -82,47 +82,47 @@ plt.plot(results.times, results.metrics["Z"], label=f"$\\langle Z \\rangle$")
 ```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
@@ -132,38 +132,38 @@ block-beta
        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;
-    
+
     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 EmulatorAnalog highlight
 ```
-The stack components highlighted in red are contained in this repository.
+The stack components highlighted in red are contained in this repository.

docs/explanation/qutip-simulation.md

@@ -1,10 +1,10 @@
 ## Compilation
 
-We first compile `AnalogCircuit` to a [`QutipExperiment`][oqd_analog_emulator.conversion.QutipExperimentVM] 
+We first compile `AnalogCircuit` to a [`QutipExperiment`][oqd_analog_emulator.conversion.QutipExperimentVM]
 using the ConversionRule [`QutipBackendCompiler`][oqd_analog_emulator.conversion.QutipBackendCompiler].
 We also then separately convert the args of Analog layer to a corresponding representation of the args
 which can be processed by QuTip. The [`compile`][oqd_analog_emulator.qutip_backend.QutipBackend.compile] functions
-is used to compile `AnalogCircuit` to a 
+is used to compile `AnalogCircuit` to a
 [`QutipExperiment`][oqd_analog_emulator.conversion.QutipExperimentVM] and also used to convert the args.
 
 ## Simulation

docs/index.md

@@ -1,13 +1,22 @@
-# ![Open Quantum Design](./img/oqd-logo-text.png)
+# 
+
+<p align="center">
+  <img src="img/oqd-logo-black.png#only-light" alt="Logo" style="max-height: 200px;">
+  <img src="img/oqd-logo-white.png#only-dark" alt="Logo" style="max-height: 200px;">
+</p>
 
 <div align="center">
     <h2 align="center">
-        Open Quantum Design: Analog Emulators
+    Open Quantum Design: Analog Emulator
     </h2>
 </div>
 
-![Python](https://img.shields.io/badge/Python-3.10_|_3.11_|_3.12-blue)
-[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black)
+[![PyPI Version](https://img.shields.io/pypi/v/oqd-analog-emulator)](https://pypi.org/project/oqd-analog-emulator)
+[![CI](https://github.com/OpenQuantumDesign/oqd-analog-emulator/actions/workflows/pytest.yml/badge.svg)](https://github.com/OpenQuantumDesign/oqd-analog-emulator/actions/workflows/pytest.yml)
+![versions](https://img.shields.io/badge/python-3.10%20%7C%203.11%20%7C%203.12-blue)
+[![License: Apache 2.0](https://img.shields.io/badge/license-Apache%202.0-brightgreen.svg)](https://opensource.org/licenses/Apache-2.0)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
+
 <!-- prettier-ignore -->
 /// admonition | Note
     type: note
@@ -19,47 +28,47 @@ This documentation is still under development, we welcome contributions! © Open
 ```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
@@ -69,38 +78,38 @@ block-beta
        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;
-    
+
     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 EmulatorAnalog highlight
 ```
-The stack components highlighted in red are contained in this repository.
+The stack components highlighted in red are contained in this repository.

docs/reference/qutip_backend.md

@@ -1,4 +1,3 @@
 ::: oqd_analog_emulator.qutip_backend
 
 ::: oqd_analog_emulator.interface
-

docs/stylesheets/admonition_template.css

@@ -14,4 +14,4 @@
     background-color: #FFFFFF;
     -webkit-mask-image: var(--md-admonition-icon--template);
             mask-image: var(--md-admonition-icon--template);
-  }
+  }

docs/stylesheets/admonitions.css

@@ -110,4 +110,3 @@
   -webkit-mask-image: var(--md-admonition-icon--example);
   mask-image: var(--md-admonition-icon--example);
 }
-