Merge to Master (v1.0)

.github/workflows/mirror_gitlab.yml

@@ -0,0 +1,33 @@
+name: Mirror to GitLab
+on:
+  push:
+    branches: [ '**' ]
+    tags: [ '**' ]
+  delete:
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: mirror-to-gitlab
+  cancel-in-progress: true
+
+jobs:
+  mirror:
+    if: github.repository == 'sequence-toolbox/SeQUeNCe'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout full history
+        uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+          persist-credentials: false
+      - name: Push to GitLab
+        env:
+          GITLAB_TOKEN: ${{ secrets.GITLAB_KEY }}
+          GITLAB_REPO: ${{ secrets.GITLAB_URL }}
+        run: |
+          git remote add gitlab "https://oauth2:${GITLAB_TOKEN}@${GITLAB_REPO}"
+          git update-ref -d refs/remotes/origin/HEAD || true
+          git push --force --prune gitlab "refs/remotes/origin/*:refs/heads/*" "refs/tags/*:refs/tags/*"

.github/workflows/pr_source_check.yml

@@ -0,0 +1,23 @@
+name: PR Source Check
+on:
+  pull_request:
+    branches: [master]
+
+permissions: {}
+jobs:
+  check-source-branch:
+    name: Verify source branch
+    runs-on: ubuntu-latest
+    if: github.repository == 'sequence-toolbox/SeQUeNCe'
+    steps:
+      - name: Check source branch
+        run: |
+          SOURCE="${{ github.head_ref }}"
+          echo "Source branch: ${SOURCE}"
+          if [ "${SOURCE}" = "RnD" ]; then
+            echo "Source branch '${SOURCE}' is allowed to merge into master."
+          else
+            echo "ERROR: PRs to master must come from 'RnD'."
+            echo "Source branch '${SOURCE}' is not permitted."
+            exit 1
+          fi

.github/workflows/validation.yml

@@ -15,7 +15,6 @@ jobs:
     strategy:
       matrix:
         python-version:
-          - "3.11"
           - "3.12"
           - "3.13"
           - "3.14"

CHANGELOG.md

@@ -5,11 +5,53 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [1.0.0] - 2026-6-12
+### Added
+- Added support for the Stabilizer formalism by introducing `StabilizerState` and `QuantumManagerStabilizer`
+    - A new class `QuantumManagerDenseQubit` is added. It is the child class of `QuantumManager` and parent class of `QuantumManagerKet` and `QuantumManagerDensity`
+    - Attributes `truncation` and `dim` are moved from the parent class `QuantumManager` to the child class `QuantumManagerDensityFock`; the `Timeline.__init__()` signature update: argument `truncation` is replaced with `manager_kwargs`
+- Add a module to convert an arbitrary graph object to sequence configurations for QuantumRouter with MIM BSM
+- Add FatTree topology and BCube topology 
+- Added the `routing` module: a new parent class `RoutingProtocol` for the subclasses `StaticRoutingProtocol` and `DistributedRoutingProtocol`. The register decorator is used to make it easy to plug in new routing protocols in the future.
+- Add empty init() to Protocol to satisfy class hierarchy.
+- Created project scripts for each config generator.
+- Added the `swapping` module that has the following classes. The subclasses use the registry decorator (factory pattern).
+    - Base class: `EntanglementSwappingA` & `EntanglementSwappingB`
+    - Subclass for ket vector and density matrix: `EntanglementSwappingA_Circuit` & `EntanglementSwappingB_Circuit`
+    - Subclass for Bell diagonal state: `EntanglementSwappingA_BDS` & `EntanglementSwappingB_BDS`
+- Update the tutorial to catch up on the recent updates. Add notes saying refer to chapter 6 Application module for standard usage
+- Introducing `EARLY_EXPIRE` message type. A request has a `start_time` and `end_time`. When a request is finished before the `end_time`, then the reservation (and the associated rules) should expire early. If not, the quantum network will keep generating entanglement pairs because the rules still exist.
+- Added three minute tutorial (tutorial file, md, json file). Also reorganized nav bar to have about section, tutorial section, and moduale refrence
+
+### Changed
+- Using typer for CLI, creates a unified interface for topology generation. Allow for custom graph objects in CLI.
+- Moved all old topologies to NetworkX graph objects
+- Docstring, documentation, comment, logging, and various cosmetic updates.
+- Moved routing_protocol init() to network manager.
+- Trigger empty inits for resource and network manager to enable future bootstrapping.
+- Migrated `utils/json_config_generators/` to `sequence/config_generators/`.
+- Add a `sender_delay` argument to the `Node.send_message()` to account for processing delay, queueing delay, transmission delay, etc.
+- Break down the `quantum_manager.py` into a module consisting of multiple files where each file has a quantum manager class
+- Break down the `quantum_state.py` into a module consisting of multiple files where each file has a quantum state class
+
+### Removed
+- Old configuration generators 
+- The old `swapping.py` is removed
+- The old `quantum_manager.py` is removed
+- The old `quantum_state.py` is removed
+- Removed support for Python 3.11
+- Removed `qlan` submodule
+
+### Fixed
+- Some minor bugs in quantum states
+- Fixed a bug in `Node.send_qubit()` where if there are no quantum channels available for the qubit to travel, a `KeyError` crash would occur.
+
+
 ## [0.8.5] - 2026-2-27
 ### Added
 - `NetworkManager` ABC with a factory pattern for selection and future implementation of new network managers.
 - File `action_condition_set.py` is added. This contains the action, condition, and request functions for entanglement generation, swapping, and purification.
-- Class `DistributedRoutingProtocol` is added, among many other supporting classes in `routing_distributed.py`. This module does distributed entanglement routing.
+- Class `DistributedRoutingProtocol` is added, among many other supporting classes in `routing_distributed`. This module does distributed entanglement routing.
 - Class `NetworkManager` has two new attributes: `forwarding_table` and `routing_protocol`.
 - Add a cutoff flag to memory to allow disable the expiration of memories.
 - Add a template in config json for network manager to select routing protocols (distributed vs. static)
@@ -18,8 +60,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Changed
 - `RSVPProtocol` is now decoupled from the `DistributedNetworkManager`.
+- Moved `ResourceReservationProtocol` to `RSVPProtocol` in `rsvp.py`. 
 - Moved `MemoryTimecard` to `memory_timecard.py` and are instantiated by the `NetworkManager`
-- Moved `ResourceReservationProtocol` to `RSVPProtocol` in `rsvp.py`
+  - `RSVPProtocol` does not instantiate `MemoryTimecard` anymore. The `timecards` attribute in `RSVPProtocol` becomes a reference to the `MemoryTimecard` in `NetworkManager`
 - NetworkManager is now `DistributedNetworkManager`
 - Extend and refactor the tests in `test_reservation.py`
 - Minor refactors pertaining to typing errors in `memory.py`, `resource_manager.py`, `rule_manager.py`, `network_manager.py` and `reservation.py`

README.md

@@ -14,10 +14,10 @@
 [![PyPi](https://img.shields.io/pypi/v/sequence)](https://pypi.org/project/sequence/)
 ![pyversions](https://img.shields.io/pypi/pyversions/sequence)
 [![Documentation](https://img.shields.io/readthedocs/sequence-rtd-tutorial)](https://sequence-rtd-tutorial.readthedocs.io/)
-[![Qutip](https://img.shields.io/badge/integration%20-Qutip-blue)](https://qutip.org/)
+[![QuTiP](https://img.shields.io/badge/integration-QuTiP-blue)](https://qutip.org/)
+[![Stim](https://img.shields.io/badge/integration-Stim-blue)](https://github.com/quantumlib/Stim)
 [![Paper](https://img.shields.io/badge/10.1088%2F2058-9565%2Fac22f6?label=DOI)](https://iopscience.iop.org/article/10.1088/2058-9565/ac22f6)
-[![PyPI Downloads](https://static.pepy.tech/badge/sequence/month)](https://pepy.tech/projects/sequence)
-<!-- [![Download-month](https://img.shields.io/pypi/dm/sequence)](https://pypistats.org/packages/sequence) -->
+[![Download-month](https://img.shields.io/pypi/dm/sequence)](https://pypistats.org/packages/sequence)
 
 </div>
 
@@ -38,15 +38,33 @@ These modules can be edited by users to define additional functionality and test
 
 ## Installation
 ### For Users
-SeQUeNCe requires [Python](https://www.python.org/downloads/) 3.11 or later. You can install SeQUeNCe using `pip`:
+SeQUeNCe requires [Python](https://www.python.org/downloads/) 3.12 or later. You can install SeQUeNCe using `pip`:
 ```
 pip install sequence
 ```
 
 ### Development Environment Setup     
-If you wish to modify the source code, use an editable installation with [uv](https://docs.astral.sh/uv/):
+If you wish to modify the source code, use an editable installation with either pip or [uv](https://docs.astral.sh/uv/):
+
+Editable installations let Python use your local source tree directly, so changes you make to the SeQUeNCe code are available **without reinstalling the package after each edit**. The `pip` option is a lightweight way to install the local package into an environment you already manage, while `uv` can create and synchronize a reproducible virtual environment from the project's dependency files.
+
+#### (1) Using pip
+```
+git clone https://github.com/sequence-toolbox/SeQUeNCe.git
+cd sequence
+make install_editable
+```
+
+In the Makefile, `install_editable` will run the following:
+```
+pip install --editable . --config-settings editable_mode=strict
+```
+The `--config-settings editable_mode=strict` setting makes the editable install behaves more like a real packaged install.
+
+#### (2) Using uv 
+
+##### Install uv ([Astral Instructions](https://docs.astral.sh/uv/getting-started/installation/))
 
-#### Install uv ([Astral Instructions](https://docs.astral.sh/uv/getting-started/installation/))
 ```bash
 # macOS/Linux
 curl -LsSf https://astral.sh/uv/install.sh | sh
@@ -55,23 +73,26 @@ curl -LsSf https://astral.sh/uv/install.sh | sh
 powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"
 ```
 
-#### Clone the repository and create the virtual environment
+##### Clone the repository and create the virtual environment
+
 Here we clone the repository and let uv configure the development environment with the target python version.
 ```bash
 git clone https://github.com/sequence-toolbox/SeQUeNCe.git
 cd sequence
 uv sync
 ```
 
-#### Activate the virtual environment
+##### Activate the virtual environment
+
 Now that the virtual environment is created with all dependencies installed, you can activate it using the following command.
 
 ```bash
 source .venv/bin/activate # macOS/Linux
 source .venv\Scripts\activate # Windows
 ```
 
-#### Running the test suite
+##### Running the test suite
+
 SeQUeNCe includes a comprehensive test suite, this can be ran with the following command
 ```
 uv run pytest tests
@@ -118,32 +139,27 @@ This script also supports a flag `-m` to visualize BSM nodes created by default
 ## Contact
 If you have questions, please contact [Caitao Zhan](https://caitaozhan.github.io/) at [czhan@anl.gov](mailto:czhan@anl.gov).
 
-## Papers that Used and/or Extended SeQUeNCe
-
-* X. Wu et al., ["Simulations of Photonic Quantum Networks for Performance Analysis and Experiment Design"](https://ieeexplore.ieee.org/document/8950718), IEEE/ACM Workshop on Photonics-Optics Technology Oriented Networking, Information and Computing Systems (PHOTONICS), 2019
-
-* X. Wu, A. Kolar, J. Chung, D. Jin, T. Zhong, R. Kettimuthu and M. Suchara. ["SeQUeNCe: A Customizable Discrete-Event Simulator of Quantum Networks"](https://iopscience.iop.org/article/10.1088/2058-9565/ac22f6), Quantum Science and Technology, 2021
-
-* V. Semenenko et al., ["Entanglement generation in a quantum network with finite quantum memory lifetime"](https://pubs.aip.org/avs/aqs/article/4/1/012002/2835237/Entanglement-generation-in-a-quantum-network-with), AVS Quantum Science, 2022
-
-* A. Zang et al., ["Simulation of Entanglement Generation between Absorptive Quantum Memories"](https://ieeexplore.ieee.org/abstract/document/9951205), IEEE QCE 2022
-
-* M.G. Davis et al., ["Towards Distributed Quantum Computing by Qubit and Gate Graph Partitioning Techniques"](https://ieeexplore.ieee.org/abstract/document/10313645), IEEE QCE 2023
-
-* R. Zhou et al., ["A Simulator of Atom-Atom Entanglement with Atomic Ensembles and Quantum Optics"](https://ieeexplore.ieee.org/abstract/document/10313610), IEEE QCE 2023
+Here is the updated table with the Code column populated:
 
-* X. Wu et al., ["Parallel Simulation of Quantum Networks with Distributed Quantum State Management"](https://dl.acm.org/doi/abs/10.1145/3634701), ACM Transactions on Modeling and Computer Simulation, 2024
-
-* C. Howe, M. Aziz, and A. Anwar, ["Towards Scalable Quantum Repeater Networks"](https://arxiv.org/abs/2409.08416), arXiv preprint, 2024
-
-* A. Zang et al., ["Quantum Advantage in Distributed Sensing with Noisy Quantum Networks"](https://arxiv.org/abs/2409.17089), arXiv preprint, 2024
-
-* L. d'Avossa et al., ["Simulation of Quantum Transduction Strategies for Quantum Networks"](https://arxiv.org/abs/2411.11377), arXiv preprint, 2024
-
-* F. Mazza et al., ["Simulation of Entanglement-Enabled Connectivity in QLANs using SeQUeNCe"](https://arxiv.org/abs/2411.11031), IEEE ICC 2025
-
-* C. Zhan et al., ["Design and Simulation of the Adaptive Continuous Entanglement Generation Protocol"](https://arxiv.org/abs/2502.01964), QCNC 2025. [GitHub Repository](https://github.com/caitaozhan/adaptive-continuous)
-
-* H. Miller et al., ["Simulation of a Heterogeneous Quantum Network"](https://arxiv.org/abs/2512.04211), arXiv preprint, 2025
+## Papers that Used and/or Extended SeQUeNCe
+| Year | Authors | Title | Venue | Code |
+|------|---------|-------|-------|------|
+| 2026 | S. Pantage et al. | [Realistic Simulation of Quantum Repeater with Encoding and Classical Error Correction](https://arxiv.org/abs/2605.06928) | arXiv preprint | [GitHub](https://github.com/SagarPatange/Quantum-Repeater-Encoding) |
+| 2026 | A. Pirker et al. | [Centralizing Task-based Approach to Quantum Network Control](https://arxiv.org/abs/2605.03336) | arXiv preprint | [GitHub](https://github.com/sequence-toolbox/central_scheduler) |
+| 2026 | A. Amlou et al. | [Physics-Informed Discrete-Event Simulation of Polarization-Encoded Quantum Networks](https://arxiv.org/abs/2604.07289) | arXiv preprint | |
+| 2026 | H. Miller et al. | [Simulation of a Heterogeneous Quantum Network](https://doi.org/10.1109/QCNC69040.2026.00085) | IEEE QCNC | [GitHub](https://github.com/haydenmllr1317/heterogenous) |
+| 2026 | A. Zang et al. | [Quantum Advantage in Distributed Sensing with Noisy Quantum Networks](https://doi.org/10.1103/7n9w-9xd4) | Physical Review Research | |
+| 2025 | C. Zhan et al. | [Design and Simulation of the Adaptive Continuous Entanglement Generation Protocol](https://doi.org/10.1109/QCNC64685.2025.00028) | IEEE QCNC | [GitHub](https://github.com/caitaozhan/adaptive-continuous) |
+| 2025 | F. Mazza et al. | [Simulation of Entanglement-Enabled Connectivity in QLANs using SeQUeNCe](https://doi.org/10.1109/ICC52391.2025.11434940) | IEEE ICC | |
+| 2025 | L. d'Avossa et al. | [Simulation of Quantum Transduction Strategies for Quantum Networks](https://doi.org/10.1109/QCE65121.2025.00142) | IEEE QCE | |
+| 2025 | V. S. Mai et al. | [Towards Optimal Orders for Entanglement Swapping in Path Graphs: A Greedy Approach](https://arxiv.org/abs/2504.14040) | IEEE QCE | |
+| 2024 | C. Howe et al. | [Towards Scalable Quantum Repeater Networks](https://arxiv.org/abs/2409.08416) | arXiv preprint | |
+| 2024 | X. Wu et al. | [Parallel Simulation of Quantum Networks with Distributed Quantum State Management](https://dl.acm.org/doi/abs/10.1145/3634701) | ACM TOMACS | |
+| 2023 | R. Zhou et al. | [A Simulator of Atom-Atom Entanglement with Atomic Ensembles and Quantum Optics](https://doi.org/10.1109/QCE57702.2023.00143) | IEEE QCE | |
+| 2023 | M.G. Davis et al. | [Towards Distributed Quantum Computing by Qubit and Gate Graph Partitioning Techniques](https://doi.org/10.1109/QCE57702.2023.00026) | IEEE QCE | |
+| 2022 | A. Zang et al. | [Simulation of Entanglement Generation between Absorptive Quantum Memories](https://doi.org/10.1109/QCE53715.2022.00084) | IEEE QCE | |
+| 2022 | V. Semenenko et al. | [Entanglement generation in a quantum network with finite quantum memory lifetime](https://doi.org/10.1116/5.0082239) | AVS Quantum Science | |
+| 2021 | X. Wu et al. | [SeQUeNCe: A Customizable Discrete-Event Simulator of Quantum Networks](https://iopscience.iop.org/article/10.1088/2058-9565/ac22f6) | IOP Quantum Science and Technology | |
+| 2019 | X. Wu et al. | [Simulations of Photonic Quantum Networks for Performance Analysis and Experiment Design](https://ieeexplore.ieee.org/document/8950718) | IEEE/ACM PHOTONICS | |
 
 Please do a Pull Request to add your paper here! 

docs/source/about/introduction/about.md

@@ -0,0 +1,4 @@
+# Introduction
+Welcome to SeQUeNCe! SeQUeNCe, the Simulator of QUantum Network Communication, is an open source, discrete-event simulator for quantum networks. It is designed to support detailed and customizable simulations of quantum network prototypes across both current and future hardware technologies and protocols.The simulator is organized around five main modules: Hardware, Entanglement Management, Resource Management, Network Management, and Application. These modules allow users to model quantum network components, test protocol schemes, evaluate network parameters, and study full-stack quantum network behavior. SeQUeNCe was developed to help compare alternative quantum network technologies, support experiment planning and validation, and aid the design of new quantum networking protocols.
+
+For more information, please see our [paper](http://arxiv.org/abs/2009.12000) (note that this paper is published in 2021 and some content might outdated).

docs/source/tutorial/chapter0/prerequisite.md → docs/source/about/requirements/prerequisite.md

@@ -6,19 +6,20 @@ Thank you for downloading SeQUeNCe and welcome to the tutorial section of the do
 
 ### Python Version
 
-The simulator requires at least version **3.10** of Python. This can be found at the [Python Website](https://www.python.org/downloads/).
+The simulator requires at least version **3.12** of Python. This can be found at the [Python Website](https://www.python.org/downloads/).
 
 ### Dependencies
 
 The simulator requires the following Python libraries:
-* `qutip`,for quantum circuit management
+* `qutip`, for quantum circuit management
+* `stim`, for stabilizer state management
 * `networkx`, for network topology related operations
 * `numpy`, for mathematical computing tasks
 * `scipy`, for linear algebra computing tasks
 * `pandas`, for data processing
 * `matplotlib`, for generating graphics
 
-These will be installed automatically with the simulator if they are not already present. 
+For the complete and updated requirements, see the `pyproject.toml`. These will be installed automatically with the simulator if they are not already present. 
 
 ## Installation
 
@@ -38,7 +39,9 @@ $ source path-to-venv/bin/activate
 
 The shell prompt should now show the name of the virtual environment.
 
-Using Anaconda/conda to create a virtual environment is also recommended.
+Using `Anaconda/conda` to create a virtual environment is also recommended.
+
+`uv` is also supported, see [README](https://github.com/sequence-toolbox/SeQUeNCe#development-environment-setup) for detailed instructions.
 
 ### Install SeQUeNCe
 

docs/source/index.rst

@@ -7,12 +7,18 @@ Welcome to the SeQUeNCe documentation page
 
 ==========================================
 
+.. toctree::
+    :maxdepth: 1
+    :caption: About:
+
+    about/introduction/about
+    about/requirements/prerequisite
 
 .. toctree::
     :maxdepth: 1
     :caption: Tutorials:
 
-    tutorial/chapter0/prerequisite
+    tutorial/sequence3min/three_minute
     tutorial/chapter1/discrete-event-simulation
     tutorial/chapter2/hardware
     tutorial/chapter3/entangle