Merge branch 'master' into dependabot/pip/pyquil-approx-eq-4.0.3

.github/dependabot.yml

@@ -26,10 +26,8 @@ updates:
       # Ignore minor and patch releases in other dev requirements.
       - dependency-name: "*pytest*"
         update-types: ["version-update:semver-minor", "version-update:semver-patch"]
-      - dependency-name: "flake8"
+      - dependency-name: "ruff"
         update-types: ["version-update:semver-minor", "version-update:semver-patch"]
-      - dependency-name: "black"
-        update-types: ["version-update:semver-major", "version-update:semver-minor", "version-update:semver-patch"]
       - dependency-name: "mypy"
         update-types: ["version-update:semver-minor", "version-update:semver-patch"]
       - dependency-name: "*sphinx*"
@@ -38,6 +36,12 @@ updates:
         update-types: ["version-update:semver-minor", "version-update:semver-patch"]
       - dependency-name: "jupytext"
         update-types: ["version-update:semver-minor", "version-update:semver-patch"]
+      - dependency-name: "matplotlib"
+        update-types: ["version-update:semver-minor", "version-update:semver-patch"]
+      - dependency-name: "seaborn"
+        update-types: ["version-update:semver-minor", "version-update:semver-patch"]
+      - dependency-name: "pandas"
+        update-types: ["version-update:semver-minor", "version-update:semver-patch"]
     # Allow up to 10 open pull requests for pip dependencies
     open-pull-requests-limit: 10
     labels:

.github/pull_request_template.md

@@ -6,10 +6,7 @@
 <!--
 If the validation checks fail
   1. Run `make check-types` (from the root directory of the repository) and fix any mypy (https://mypy.readthedocs.io/en/stable/) errors.
-
-  2. Run `make check-style` and fix any flake8 (http://flake8.pycqa.org) errors.
-
-  3. Run `make format` to format your code with the black (https://black.readthedocs.io/en/stable/index.html) autoformatter.
+  2. Run `make format` to fix any linting/formatting errors. There may be some issues that require manual intervention for you to fix.
 
 For more information, check the Mitiq style guidelines (https://mitiq.readthedocs.io/en/stable/contributing.html#style-guidelines).
 -->
@@ -25,8 +22,9 @@ For more information, check the Mitiq style guidelines (https://mitiq.readthedoc
 - [ ] I license this contribution under the terms of the GNU GPL, version 3 and grant Unitary Fund the right to provide additional permissions as described in section 7 of the GNU GPL, version 3.
 
 Before opening the PR, please ensure you have completed the following where appropriate.
+
 - [ ] I added unit tests for new code.
 - [ ] I used [type hints](https://www.python.org/dev/peps/pep-0484/) in function signatures.
 - [ ] I used [Google-style](https://google.github.io/styleguide/pyguide.html#383-functions-and-methods) docstrings for functions.
 - [ ] I [updated the documentation](../blob/master/docs/CONTRIBUTING_DOCS.md) where relevant.
-- [ ] Added myself / the copyright holder to the AUTHORS file
+- [ ] Added myself / the copyright holder to the AUTHORS file

.github/workflows/build.yml

@@ -20,7 +20,7 @@ jobs:
       - name: Check out mitiq
         uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.11"
       - name: Install Python dependencies
@@ -31,10 +31,7 @@ jobs:
       - name: Check types with mypy
         run: make check-types
 
-      - name: Lint with flake8
-        run: make check-style
-
-      - name: Check code style with Black
+      - name: Check code style/formatting
         run: make check-format
 
   docs:
@@ -43,7 +40,7 @@ jobs:
       - name: Check out mitiq
         uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.11"
 
@@ -72,7 +69,7 @@ jobs:
       - name: Check out mitiq
         uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.11"
       - name: Install Mitiq
@@ -99,7 +96,7 @@ jobs:
         with:
           fetch-depth: 2
       - 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 Python dependencies

.github/workflows/publish-pypi.yml

@@ -19,7 +19,7 @@ jobs:
         with:
           ref: ${{ github.ref }}
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.11"
       - name: Install Python dependencies

.github/workflows/publish-testpypi.yml

@@ -15,7 +15,7 @@ jobs:
       - name: Check out mitiq
         uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.11"
       - name: Install Python dependencies
@@ -38,7 +38,7 @@ jobs:
   # - name: Check out mitiq
   # uses: actions/checkout@v4
   # - name: Set up Python
-  # uses: actions/setup-python@v4
+  # uses: actions/setup-python@v5
   # with:
   # python-version: 3.8
   # - name: Install Mitiq

.readthedocs.yml

@@ -9,7 +9,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.10"
+    python: "3.11"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

AUTHORS

@@ -18,6 +18,7 @@ Nathaniel T. Stemen
 Nathan Shammah
 Will J. Zeng
 Min Li
+Jordan Sullivan
 
 L-P-B
 Paul Chung
@@ -54,4 +55,6 @@ Mohammad Zuhair Khan
 Brian Goldsmith
 Farzad Kianvash
 Yash Prabhat
-Vladimir Kozhukalov
+Vladimir Kozhukalov
+Francesc Sabater
+Emiliano Godinez

CHANGELOG.md

@@ -1,5 +1,191 @@
 # Changelog
 
+## Version 0.35.0 (under development)
+
+## Version 0.34.0
+Announcing support for [Qibo](https://qibo.science/), a newly integrated frontend in Mitiq! 📣
+Qibo is an "end-to-end open source platform for quantum simulation, self-hosted quantum hardware control, calibration and characterization".
+
+```py
+from qibo import Circuit
+from mitiq.conversions import convert_to_mitiq
+
+circuit = Circuit(2)
+circuit.add(gates.H(0))
+circuit.add(gates.H(1))
+
+print(circuit)
+
+def executor(circuit):
+    return circuit.execute()
+
+
+mitigated = mitiq.zne.execute_with_zne(convert_to_mitiq(circuit), executor)
+```
+
+Thank you to new contributor Francesc Sabater for excellent work integrating Qibo and Mitiq!
+Thanks also to new contibutor Sam Burdick for fixing our readme.
+
+This release also includes a refactoring of part of the Mitiq shadows module, `mitiq.shadows.classical_postprocessing`, for speed of execution and code readability.
+
+### 📓 Documentation
+We've continued to enhance our (legendary!) documentation with:
+1. Addition of a security policy document
+2. Faster execution of the learning-based PEC tutorial in CI
+
+### Commits
+- Add support for qibo circuits (#2102) [@francescsabater]
+- Reduce doc build time for learning representations (#2165) [@Misty-W]
+- Create SECURITY.md (#2162) [@nathanshammah]
+- Fix typo in README.md (#2173) [@smburdick]
+- Refactor classical postprocessing in shadows module (#2152) [@natestemen]
+- Fix broken link in `combine_rem_zne.md` (#2156) [@Misty-W]
+
+#### 📦 Dependency updates
+- Bump openfermion from 1.6.0 to 1.6.1 (#2182) [@dependabot]
+- Update amazon-braket-sdk requirement from ~=1.68.3 to ~=1.69.0 (#2177) [@dependabot]
+- Bump pyscf from 2.4.0 to 2.5.0 (#2176) [@dependabot]
+- Update amazon-braket-sdk requirement from ~=1.66.0 to ~=1.68.3 (#2175) [@dependabot]
+- Update qiskit-aer requirement from ~=0.13.1 to ~=0.13.2 (#2157) [@dependabot]
+- Bump pytest from 7.1.3 to 8.0.0 (#2167) [@dependabot]
+- Update amazon-braket-sdk requirement from ~=1.65.1 to ~=1.66.0 (#2155) [@dependabot]
+- Update pennylane-qiskit requirement from ~=0.33.1 to ~=0.34.0 (#2154) [@dependabot]
+- Update pennylane requirement from ~=0.33.1 to ~=0.34.0 (#2153) [@dependabot]
+- Update qiskit-ibm-provider requirement from ~=0.7.3 to ~=0.8.0 (#2151) [@dependabot]
+
+## Version 0.33.0
+
+Minor update from 0.32.0 to fix a bug 🐛 in the `mitiq.shadows` module where an incorrect index was being used.
+
+### All changes
+
+- Changed to use the split for b_list_shadow (#2137) [@bdg221]
+
+## Version 0.32.0
+
+> Happy holidays, and happy (almost) new year!! ❄️☃️🎄🎊
+> This will be our last release of the year, and we'd like to thank everyone who has contributed to Mitiq over the past 12 months.
+> We've accomplished so much in the way of error mitigation this year, and we couldn't have done it without the support and time given by the volunteers.
+> **Thank you!**
+
+The **calibrator logs have been revamped** for to support result discovery and analysis.
+The `Calibrator.run` method now support two options: `flat` and `cartesian` to display the experiment results in either a linear fashion, or grid-like.
+Results here have been truncated for brevity.
+
+```py
+>>> calibrator.run(log="flat")
+┌──────────────────────────┬────────────────────────────────────┬────────────────────────────┐
+│ benchmark                │ strategy                           │ performance                │
+├──────────────────────────┼────────────────────────────────────┼────────────────────────────┤
+│ Type: ghz                │ Technique: ZNE                     │ ✔                          │
+│ Num qubits: 2            │ Factory: Linear                    │ Noisy error: 0.04          │
+│ Circuit depth: 2         │ Scale factors: 1.0, 2.0, 3.0       │ Mitigated error: 0.02      │
+│ Two qubit gate count: 1  │ Scale method: fold_gates_at_random │ Improvement factor: 2.0    │
+├──────────────────────────┼────────────────────────────────────┼────────────────────────────┤
+│ Type: ghz                │ Technique: ZNE                     │ ✘                          │
+│ Num qubits: 2            │ Factory: Linear                    │ Noisy error: 0.04          │
+│ Circuit depth: 2         │ Scale factors: 1.0, 3.0, 5.0       │ Mitigated error: 0.0658    │
+│ Two qubit gate count: 1  │ Scale method: fold_global          │ Improvement factor: 0.6076 │
+├──────────────────────────┼────────────────────────────────────┼────────────────────────────┤
+│ Type: ghz                │ Technique: ZNE                     │ ✘                          │
+│ Num qubits: 2            │ Factory: Richardson                │ Noisy error: 0.98          │
+│ Circuit depth: 33        │ Scale factors: 1.0, 3.0, 5.0       │ Mitigated error: 1.03      │
+│ Two qubit gate count: 14 │ Scale method: fold_global          │ Improvement factor: 0.9515 │
+└──────────────────────────┴────────────────────────────────────┴────────────────────────────┘
+```
+
+```py
+>>> calibrator.run(log="cartesian")
+┌────────────────────────────────────┬────────────────────────────┬────────────────────────────┐
+│ strategy\benchmark                 │ Type: ghz                  │ Type: mirror               │
+│                                    │ Num qubits: 2              │ Num qubits: 2              │
+│                                    │ Circuit depth: 2           │ Circuit depth: 33          │
+│                                    │ Two qubit gate count: 1    │ Two qubit gate count: 14   │
+├────────────────────────────────────┼────────────────────────────┼────────────────────────────┤
+│ Technique: ZNE                     │ ✘                          │ ✘                          │
+│ Factory: Richardson                │ Noisy error: 0.03          │ Noisy error: 1.0           │
+│ Scale factors: 1.0, 2.0, 3.0       │ Mitigated error: 0.09      │ Mitigated error: 1.03      │
+│ Scale method: fold_global          │ Improvement factor: 0.3333 │ Improvement factor: 0.9709 │
+├────────────────────────────────────┼────────────────────────────┼────────────────────────────┤
+│ Technique: ZNE                     │ ✘                          │ ✔                          │
+│ Factory: Richardson                │ Noisy error: 0.03          │ Noisy error: 1.0           │
+│ Scale factors: 1.0, 3.0, 5.0       │ Mitigated error: 0.0563    │ Mitigated error: 0.97      │
+│ Scale method: fold_global          │ Improvement factor: 0.5333 │ Improvement factor: 1.0309 │
+├────────────────────────────────────┼────────────────────────────┼────────────────────────────┤
+│ Technique: ZNE                     │ ✘                          │ ✔                          │
+│ Factory: Linear                    │ Noisy error: 0.03          │ Noisy error: 1.0           │
+│ Scale factors: 1.0, 3.0, 5.0       │ Mitigated error: 0.0417    │ Mitigated error: 0.9975    │
+│ Scale method: fold_global          │ Improvement factor: 0.72   │ Improvement factor: 1.0025 │
+└────────────────────────────────────┴────────────────────────────┴────────────────────────────┘
+```
+
+**New benchmarking circuits:** `mitiq.benchmarks` now contains a function `generate_random_clifford_t_circuit` which does what it says on the tin.
+Special shoutout to new UF team member Farrokh Labib (@farlab) for this contribution.
+
+```py
+from mitiq.benchmarks import generate_random_clifford_t_circuit
+
+clifft = generate_random_clifford_t_circuit(
+    num_qubits=2,
+    num_oneq_cliffords=5,
+    num_twoq_cliffords=5,
+    num_t_gates=5
+)
+print(clifft)
+# 0: ───────────@───S───T───@───H───T───X───T───T───@───@───────
+#               │           │           │           │   │
+# 1: ───S───T───@───────────X───────────@───S───────@───X───S───
+```
+
+The `Executor.run` method now supports a single circuit instance in addition to a list for ease of use when working with a single circuit.
+
+```diff
+- executor.run([circuit])
++ executor.run(circuit)
+```
+
+**Faster Tests!** Working on Mitiq has never been easier to develop with a faster (by 36%) test suite.
+
+### 📓 Documentation
+
+This release contains quite a few documentation improvements, including
+
+1. New workflow images to elucidate the workflow for for using the `mitiq.shadows` module (available [here](https://mitiq.readthedocs.io/en/stable/guide/shadows.html))
+2. A reorganized API-doc which should be easier to navigate
+3. General clean up of the CDR user guide pages
+
+### Commits
+
+- Clarify CDR training docs regarding the use of a markov chain monte carlo (#2130) [@natestemen]
+- Update workflow images in documentation (#2034) [@purva-thakre]
+- 2115 pauli twirling callibration of expectation estimation shadow needs continue (#2116) [@bdg221]
+- Add randomized clifford+T benchmarking circuits. (#2118) [@farlab]
+- Frontend/Backend docs clean up (#2124) [@natestemen]
+- Speed up tests using mocks (#2126) [@natestemen]
+- resolve flaky mirror QV circuit test (#2127) [@natestemen + @misty-w]
+- Simplify expectation_estimation_shadow code (#2113) [@bdg221]
+- Refactor calibration logs (#2074) [@kozhukalov]
+- Organize API-doc (#2104) [@purva-thakre]
+- add support for single circuit on exeuctor run method (#2099) [@emilianog-byte]
+
+#### 📦 Dependency updates
+
+- Update qiskit-ibm-provider requirement from ~=0.7.2 to ~=0.7.3 (#2122) [@dependabot]
+- Update cirq requirement from <1.3.0,>=1.0.0 to >=1.0.0,<1.4.0 (#2107) [@dependabot]
+- Update pennylane requirement from ~=0.32.0 to ~=0.33.1 (#2091) [@dependabot]
+- Update pennylane-qiskit requirement from ~=0.32.0 to ~=0.33.0 (#2081) [@dependabot]
+- Bump stim/stimcirq from 1.12.0 to 1.12.1 (#2106) [@dependabot]
+- Update amazon-braket-sdk requirement from ~=1.59.2 to ~=1.64.1 (#2089 + #2094 + #2114 + #2123) [@dependabot]
+- Update scipy requirement from <=1.11.3,>=1.5.0 to >=1.5.0,<=1.11.4 (#2095) [@dependabot]
+
+#### 🧑‍💻 Dev Dependency updates
+
+- Bump myst-nb from 0.17.1 to 1.0.0 (#2090) [@dependabot]
+- Bump pandas from 2.1.2 to 2.1.3 (#2093) [@dependabot]
+- Bump matplotlib from 3.8.0 to 3.8.1 (#2084) [@dependabot]
+- Bump isort from 5.12.0 to 5.13.2 (#2120 + #2125) [@dependabot]
+- Bump actions/setup-python from 4 to 5 (#2112) [@dependabot]
+
 ## Version 0.31.0
 
 Released November 2, 2023
@@ -1115,7 +1301,7 @@ Another important change is the integration with Amazon Braket, such that Mitiq
 
 In the context of probabilistic error cancellation, the sub-module `mitiq.pec.representations` has been significantly improved. Now one can easily compute the optimal quasi-probabiliy representation of an ideal gate as a linear combination of `NoisyOperation` objects.
 
-Thanks to all contributors (@L-P-B, @Aaron-Robertson, @francespoblete, @LaurentAjdnik, @maxtremblay, @andre-a-alves, @paniash, @purva-thakre) and in particular to the participants of [unitaryHACK](https://unitaryfund.github.io/unitaryhack/)!
+Thanks to all contributors (@L-P-B, @Aaron-Robertson, @francespoblete, @LaurentAjdnik, @maxtremblay, @andre-a-alves, @paniash, @purva-thakre) and in particular to the participants of [unitaryHACK](https://2021.unitaryhack.dev/)!
 
 ### All Changes