Merge branch 'main' into reconstruct-distribution

.git-blame-ignore-revs

@@ -0,0 +1,2 @@
+eb78b0ba1b2f34fa72ea9de7a406dc10c102d423
+8c8ccd429de2ef8da4849dce987a43cd69f11225

.github/workflows/citation.yml

@@ -63,7 +63,7 @@ jobs:
           fi
       - name: Upload PDF
         if: always()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: preview.pdf
           path: preview.pdf

.github/workflows/coverage.yml

@@ -23,7 +23,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install tox

.github/workflows/docker.yml

@@ -3,10 +3,10 @@ name: Docker notebook tests
 on:
   push:
     branches: [ main ]
-    paths: ['Dockerfile', '.dockerignore', 'compose.yaml']
+    paths: ['Dockerfile', '.dockerignore', 'compose.yaml', '.github/workflows/docker.yml']
   pull_request:
     branches: [ main ]
-    paths: ['Dockerfile', '.dockerignore', 'compose.yaml']
+    paths: ['Dockerfile', '.dockerignore', 'compose.yaml', '.github/workflows/docker.yml']
   schedule:
     - cron: '0 20 * * 3'
 
@@ -20,4 +20,7 @@ jobs:
         run: docker compose build
       - name: Test notebooks
         shell: bash
-        run: docker compose run notebook "bash" "-c" "pip install pytest nbmake && pytest --nbmake docs --ignore=docs/circuit-knitting-toolbox/entanglement_forging/tutorials/tutorial_2_forging_with_quantum_serverless.ipynb"
+        run: docker compose run notebook "bash" "-c" "pip install pytest nbmake && pytest --nbmake docs"
+      - name: Test that persistent-volume is writable
+        shell: bash
+        run: docker compose run notebook "bash" "-c" "touch persistent-volume/empty-notebook.ipynb"

.github/workflows/docs.yml

@@ -19,7 +19,7 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.9'
       - name: Install dependencies
@@ -37,15 +37,21 @@ jobs:
         shell: bash
         run: |
           tox -edocs
+      - name: Prepare docs artifact
+        if: always()
+        shell: bash
+        run: |
+          mkdir artifact
+          cp -a docs/_build/html artifact/ckt_html_docs
       - name: Upload docs artifact
         if: always()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: html_docs
-          path: ./docs/_build/html
+          name: ckt_html_docs
+          path: ./artifact
       - name: Deploy docs
-        if: ${{ github.ref == 'refs/heads/stable/0.4' }}
-        uses: peaceiris/actions-gh-pages@v3
+        if: ${{ github.ref == 'refs/heads/stable/0.7' }}
+        uses: peaceiris/actions-gh-pages@v4
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: ./docs/_build/html/

.github/workflows/lint.yml

@@ -18,10 +18,10 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v4
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v5
         with:
-          python-version: '3.9'
+          python-version: '3.10'
       - name: Install tox
         run: |
           python -m pip install --upgrade pip

.github/workflows/test_development_versions.yml

@@ -23,19 +23,16 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies (development versions)
         shell: bash
         run: |
           python -m pip install --upgrade pip tox
           python -m pip install toml typer
-          python tools/extremal-python-dependencies.py add-dependency \
-              "qiskit-terra @ git+https://github.com/Qiskit/qiskit.git" \
-              --inplace
           python tools/extremal-python-dependencies.py pin-dependencies \
-              "qiskit @ git+https://github.com/Qiskit/qiskit.git#subdirectory=qiskit_pkg" \
+              "qiskit @ git+https://github.com/Qiskit/qiskit.git" \
               "qiskit-ibm-runtime @ git+https://github.com/Qiskit/qiskit-ibm-runtime.git" \
               --inplace
       - name: Modify tox.ini for more thorough check

.github/workflows/test_latest_versions.yml

@@ -20,16 +20,16 @@ jobs:
       max-parallel: 4
       matrix:
         os: [ubuntu-latest]
-        python-version: ["3.8", "3.11"]
+        python-version: ["3.8", "3.12"]
         include:
           - os: macos-latest
-            python-version: "3.8"
+            python-version: "3.12"
           - os: windows-latest
             python-version: "3.10"
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
@@ -47,8 +47,8 @@ jobs:
           pver=${{ matrix.python-version }}
           tox -epy${pver/./} -- --run-slow
           notebook_flags=""
-          if [ "$RUNNER_OS" = "Windows" ]; then
-            echo Skipping tutorials \& how-tos that require pyscf
-            notebook_flags="${notebook_flags} --ignore=docs/entanglement_forging --ignore=docs/_build/jupyter_execute/entanglement_forging/how-tos"
+          if [ "$pver" = "3.12" ]; then
+            echo Skipping tutorials that require cplex
+            notebook_flags="${notebook_flags} --ignore=docs/circuit_cutting/cutqc/tutorials/tutorial_1_automatic_cut_finding.ipynb"
           fi
           tox -epy${pver/./}-notebook -- ${notebook_flags}

.github/workflows/test_minimum_versions.yml

@@ -21,7 +21,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies (minimum versions)

.mergify.yml

@@ -5,4 +5,4 @@ pull_request_rules:
     actions:
       backport:
         branches:
-          - stable/0.4
+          - stable/0.7

.ruff.toml

@@ -1,9 +1,11 @@
 target-version = "py38"
+
+[lint]
 ignore = [
     "E501",  # line too long
 ]
 
-[per-file-ignores]
+[lint.per-file-ignores]
 "test/**.py" = [
     "F405",  # star import
     "F403",  # unable to detect undefined names due to star import

CITATION.bib

@@ -1,5 +1,23 @@
 @misc{circuit-knitting-toolbox,
-  author = {Luciano Bello and Agata M. Bra\'{n}czyk and Sergey Bravyi and Almudena {Carrera Vazquez} and Andrew Eddins and Daniel J. Egger and Bryce Fuller and Julien Gacon and James R. Garrison and Jennifer R. Glick and Tanvi P. Gujarati and Ikko Hamamura and Areeq I. Hasan and Takashi Imamichi and Caleb Johnson and Ieva Liepuoniute and Owen Lockwood and Mario Motta and C. D. Pemmaraju and Pedro Rivero and Max Rossmannek and Travis L. Scholten and Seetharami Seelam and Iskandar Sitdikov and Dharmashankar Subramanian and Wei Tang and Stefan Woerner},
+  author = {
+    Agata M. Bra\'{n}czyk
+    and Almudena {Carrera Vazquez}
+    and Daniel J. Egger
+    and Bryce Fuller
+    and Julien Gacon
+    and James R. Garrison
+    and Jennifer R. Glick
+    and Caleb Johnson
+    and Saasha Joshi
+    and Edwin Pednault
+    and C. D. Pemmaraju
+    and Pedro Rivero
+    and Seetharami Seelam
+    and Ibrahim Shehzad
+    and Dharmashankar Subramanian
+    and Wei Tang
+    and Stefan Woerner
+  },
   title = {{Circuit Knitting Toolbox}},
   howpublished = {\url{https://github.com/Qiskit-Extensions/circuit-knitting-toolbox}},
   year = {2023},

CONTRIBUTING.md

@@ -1,6 +1,6 @@
 # Developer guide
 
-Development of the Circuit Knitting Toolbox takes place [on GitHub](https://github.com/Qiskit-Extensions/circuit-knitting-toolbox).  The [Contributing to Qiskit](https://qiskit.org/documentation/contributing_to_qiskit.html) guide may serve as a useful starting point, as the toolbox builds on [Qiskit] and is part of the [Qiskit Ecosystem].
+Development of the Circuit Knitting Toolbox takes place [on GitHub](https://github.com/Qiskit-Extensions/circuit-knitting-toolbox). The [Contributing to Qiskit](https://github.com/Qiskit/qiskit/blob/main/CONTRIBUTING.md) guide may serve as a useful starting point, as the toolbox builds on [Qiskit] and is part of the [Qiskit Ecosystem].
 
 The toolbox is written in [Python] and uses [tox] as a testing framework.  A description of the available `tox` test environments is located at [`test/README.md`](test/README.md).  These environments are used in the CI workflows, which are described at [`.github/workflows/README.md`](.github/workflows/README.md).
 
@@ -10,8 +10,8 @@ We use [Sphinx] for documentation and [reno] for release notes.  We use [Google
 
 We require 100% coverage in all new code.  In rare cases where it is not possible to test a code block, we mark it with ``# pragma: no cover`` so that the ``coverage`` tests will pass.
 
-[Qiskit]: https://qiskit.org/
-[Qiskit Ecosystem]: https://qiskit.org/ecosystem/
+[Qiskit]: https://www.ibm.com/quantum/qiskit
+[Qiskit Ecosystem]: https://qiskit.github.io/ecosystem/
 [Python]: https://www.python.org/
 [tox]: https://github.com/tox-dev/tox
 [Sphinx]: https://www.sphinx-doc.org/

Dockerfile

@@ -9,9 +9,10 @@ RUN rm -rf work && \
 
 COPY . .src/circuit-knitting-toolbox
 
-# Fix the permissions of ~/.src
+# Fix the permissions of ~/.src and ~/persistent-volume
 USER root
-RUN fix-permissions .src
+RUN fix-permissions .src && \
+    mkdir persistent-volume && fix-permissions persistent-volume
 USER ${NB_UID}
 
 # Consolidate the docs into the home directory

INSTALL.rst

@@ -9,9 +9,8 @@ packages. There are three primary ways to do this:
 - :ref:`Option 2`
 - :ref:`Option 3`
 
-CutQC and entanglement forging users should consult the
-:ref:`Platform Support` section to determine which installation option
-is appropriate for them. Users who wish to run within a
+CutQC users should consult the :ref:`Platform Support` section to determine
+which installation option is appropriate for them. Users who wish to run within a
 containerized environment may skip the pre-installation and move straight
 to :ref:`Option 3`.
 
@@ -62,15 +61,13 @@ Upgrade pip and install the CKT package.
     pip install --upgrade pip
     pip install circuit-knitting-toolbox
 
-Users intending to use the entanglement forging tool should install the ``pyscf`` optional dependency.
-
 Users intending to use the automatic cut finding functionality in the CutQC package should install the ``cplex`` optional dependency.
 
 Adjust the options below to suit your needs.
 
 .. code:: sh
     
-    pip install 'circuit-knitting-toolbox[pyscf,cplex]'
+    pip install 'circuit-knitting-toolbox[cplex]'
 
 
 .. _Option 2:
@@ -97,15 +94,13 @@ The next step is to install CKT to the virtual environment. If you plan on runni
 notebook dependencies in order to run all the visualizations in the notebooks.
 If you plan on developing in the repository, you may want to install the ``dev`` dependencies.
 
-Users intending to use the entanglement forging tool should install the ``pyscf`` optional dependency.
-
 Users intending to use the automatic cut finding functionality in the CutQC package should install the ``cplex`` optional dependency.
 
 Adjust the options below to suit your needs.
 
 .. code:: sh
     
-    pip install tox notebook -e '.[notebook-dependencies,dev,pyscf,cplex]'
+    pip install tox notebook -e '.[notebook-dependencies,dev,cplex]'
 
 If you installed the notebook dependencies, you can get started with CKT by running the notebooks in the docs.
 
@@ -182,8 +177,8 @@ take care when installing the toolbox, depending on which tools they
 intend to use.
 
   - The automatic wire cut search in the ``cutqc`` package depends
-    on CPLEX, which is only available on Intel chips.
-  - The entanglement forging tool requires PySCF, which does not support Windows.
+    on CPLEX, which is only available on Intel chips and is not yet available
+    for Python 3.12.
 
 In each case, one method that is guaranteed to work is to :ref:`use
 the toolbox within Docker <Option 3>`.  Other methods include:
@@ -195,7 +190,3 @@ the toolbox within Docker <Option 3>`.  Other methods include:
     create a virtual environment that uses Python compiled for the x86
     instruction set.  No matter the installation method, there is a
     performance cost due to emulation.
-  - Advanced Windows users may wish to attempt to install PySCF using
-    the `Windows Subsystem for Linux
-    <https://learn.microsoft.com/en-us/windows/wsl/install>`__.  If
-    you have success using this method, please let us know.