[format] run formatter on all code

Author: yhteoh

.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.

README.md

@@ -14,7 +14,7 @@
 
 
 ### What's here:
-This repository contains the supporting infrastructure, base classes, and abstractions 
+This repository contains the supporting infrastructure, base classes, and abstractions
 for creating custom compiler analysis, verification, and transformation passes.
 The modules in the repository are utilized for, e.g., lowering from the analog to atomic
 intermediate representations, and the atomic representation to bare metal descriptions of
@@ -50,47 +50,47 @@ mkdocs serve
 ```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
@@ -100,39 +100,39 @@ 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
-   
+
 ```
 The lowering and compilation passes, used in the vertical lines connecting
-abstraction layers, are based on the compiler infrastructure components contained 
-in this repository.
+abstraction layers, are based on the compiler infrastructure components contained
+in this repository.

docs/index.md

@@ -17,7 +17,7 @@ This documentation is still under development, we welcome contributions! © Open
 ///
 
 ### What's here:
-This repository contains the supporting infrastructure, base classes, and abstractions 
+This repository contains the supporting infrastructure, base classes, and abstractions
 for creating custom compiler analysis, verification, and transformation passes.
 The modules in the repository are utilized for, e.g., lowering from the analog to atomic
 intermediate representations, and the atomic representation to base metal descriptions of
@@ -26,47 +26,47 @@ quantum programs.
 ```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
@@ -76,39 +76,39 @@ 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
-   
+
 ```
 The lowering and compilation passes, used in the vertical lines connecting
-abstraction layers, are based on the compiler infrastructure components contained 
-in this repository.
+abstraction layers, are based on the compiler infrastructure components contained
+in this repository.

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/extra_admonitions.css

@@ -130,6 +130,3 @@
   -webkit-mask-image: var(--md-admonition-icon--acknowledgement);
   mask-image: var(--md-admonition-icon--acknowledgement);
 }
-
-
-

docs/tutorial/calculator.ipynb

@@ -28,7 +28,6 @@
    "outputs": [],
    "source": [
     "class MyExpr(TypeReflectBaseModel):\n",
-    "\n",
     "    def __add__(self, other):\n",
     "        return MyAdd(left=self, right=other)\n",
     "\n",