Remove `examples` from main directory #716

purva-thakre · 2025-10-02T05:05:21Z

Fixes #715

This PR deletes the duplicate logical CNOT example as well as move one of the jupyter notebooks to the docs directory as an rst file.

purva-thakre · 2025-10-02T06:25:25Z

examples/notebooks/create_plaquette.ipynb

@@ -1,259 +0,0 @@
-{


this notebook is terribly out of date. It is a good idea I pushed for executable docs in #592, but unfortunately missed this one.

Then maybe we can simply remove it.

Let me try to make changes to the notebook. If I am not successful, I am leaning towards removing it.

@inmzhang Do you happen to know why this was added as a jupyter notebook and not unit tests for the RPNG class? I spent some time making changes to the notebook, but realized that there is a significant overlap with this notebook and src/tqec/plaquette/rpng/rpng_test.py.

I see that Adrien and Gian were responsible for this notebook in #411 .

Sorry I don't remember.

Fixes the code blocks below in the readme: <img width="879" height="407" alt="截屏2025-10-01 10 03 19" src="https://github.com/user-attachments/assets/7af8124b-ecd1-4ae3-965e-700f6194864b" />

github-actions · 2025-10-04T05:10:13Z

Package	Line Rate	Health
src.tqec	100%	✔
src.tqec.circuit	96%	✔
src.tqec.circuit.schedule	99%	✔
src.tqec.compile	93%	✔
src.tqec.compile.blocks	94%	✔
src.tqec.compile.blocks.layers	95%	✔
src.tqec.compile.blocks.layers.atomic	97%	✔
src.tqec.compile.blocks.layers.composed	99%	✔
src.tqec.compile.detectors	89%	✔
src.tqec.compile.observables	97%	✔
src.tqec.compile.specs	92%	✔
src.tqec.compile.specs.library	97%	✔
src.tqec.compile.specs.library.generators	97%	✔
src.tqec.compile.tree	81%	✔
src.tqec.compile.tree.annotators	83%	✔
src.tqec.computation	96%	✔
src.tqec.gallery	100%	✔
src.tqec.interop	90%	✔
src.tqec.interop.collada	94%	✔
src.tqec.interop.pyzx	85%	✔
src.tqec.interop.pyzx.synthesis	91%	✔
src.tqec.plaquette	90%	✔
src.tqec.plaquette.compilation	100%	✔
src.tqec.plaquette.compilation.passes	95%	✔
src.tqec.plaquette.compilation.passes.transformer	99%	✔
src.tqec.plaquette.rpng	94%	✔
src.tqec.plaquette.rpng.translators	97%	✔
src.tqec.post_processing	82%	✔
src.tqec.post_processing.utils	96%	✔
src.tqec.templates	94%	✔
src.tqec.utils	96%	✔
Summary	94% (7435 / 7931)	✔

inmzhang

LGTM.

github-actions · 2025-10-06T07:20:11Z

🪓 PR closed, deleted preview at https://tqec.github.io/tqec/pull/716/

Updates the requirements on [pytest-cov](https://github.com/pytest-dev/pytest-cov) to permit the latest version. <details> <summary>Changelog</summary> <p><em>Sourced from <a href="https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst">pytest-cov's changelog</a>.</em></p> <blockquote> <h2>7.0.0 (2025-09-09)</h2> <ul> <li> <p>Dropped support for subprocesses measurement.</p> <p>It was a feature added long time ago when coverage lacked a nice way to measure subprocesses created in tests. It relied on a <code>.pth</code> file, there was no way to opt-out and it created bad interations with <code>coverage's new patch system <https://coverage.readthedocs.io/en/latest/config.html#run-patch></code>_ added in <code>7.10 <https://coverage.readthedocs.io/en/7.10.6/changes.html#version-7-10-0-2025-07-24></code>_.</p> <p>To migrate to this release you might need to enable the suprocess patch, example for <code>.coveragerc</code>:</p> <p>.. code-block:: ini</p> <p>[run] patch = subprocess</p> <p>This release also requires at least coverage 7.10.6.</p> </li> <li> <p>Switched packaging to have metadata completely in <code>pyproject.toml</code> and use <code>hatchling <https://pypi.org/project/hatchling/></code>_ for building. Contributed by Ofek Lev in <code>[tqec#551](pytest-dev/pytest-cov#551) <https://github.com/pytest-dev/pytest-cov/pull/551></code>_ with some extras in <code>[tqec#716](pytest-dev/pytest-cov#716) <https://github.com/pytest-dev/pytest-cov/pull/716></code>_.</p> </li> <li> <p>Removed some not really necessary testing deps like <code>six</code>.</p> </li> </ul> <h2>6.3.0 (2025-09-06)</h2> <ul> <li>Added support for markdown reports. Contributed by Marcos Boger in <code>[tqec#712](pytest-dev/pytest-cov#712) <https://github.com/pytest-dev/pytest-cov/pull/712></code>_ and <code>[tqec#714](pytest-dev/pytest-cov#714) <https://github.com/pytest-dev/pytest-cov/pull/714></code>_.</li> <li>Fixed some formatting issues in docs. Anonymous contribution in <code>[tqec#706](pytest-dev/pytest-cov#706) <https://github.com/pytest-dev/pytest-cov/pull/706></code>_.</li> </ul> <h2>6.2.1 (2025-06-12)</h2> <ul> <li> <p>Added a version requirement for pytest's pluggy dependency (1.2.0, released 2023-06-21) that has the required new-style hookwrapper API.</p> </li> <li> <p>Removed deprecated license classifier (packaging).</p> </li> <li> <p>Disabled coverage warnings in two more situations where they have no value:</p> <ul> <li>"module-not-measured" in workers</li> <li>"already-imported" in subprocesses</li> </ul> </li> </ul> <h2>6.2.0 (2025-06-11)</h2> <ul> <li> <p>The plugin now adds 3 rules in the filter warnings configuration to prevent common coverage warnings being raised as obscure errors::</p> <p>default:unclosed database in <sqlite3.Connection object at:ResourceWarning once::PytestCovWarning</p> </li> </ul>  </blockquote> <p>... (truncated)</p> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/224d8964caad90074a8cf6dc8720b8f70f31629b"><code>224d896</code></a> Bump version: 6.3.0 → 7.0.0</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/73424e3999f865eac72e27f09d5fe11b9703cfd6"><code>73424e3</code></a> Cleanup the docs a bit.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/36f1cc2967831dbd4c8aa70086fc86dc495f8b9a"><code>36f1cc2</code></a> Bump pins in template.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/f299c590a63a48e51e3ae949993dc7bb1f1d480d"><code>f299c59</code></a> Bump the github-actions group with 2 updates</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/25f0b2e0cdbc345c0d3e49170f7a328c3e0d805f"><code>25f0b2e</code></a> Update docs/config.rst</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/bb23eacc5531fb8f499213d8420407e0d72f88e3"><code>bb23eac</code></a> Improve configuration docs</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/a19531e91e1ab753ccf648a2d9bab08a6fddebb9"><code>a19531e</code></a> Switch from build/pre-commit to uv/prek - this should make this faster.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/82f999391073f2fb8ae422af452602f310086a2a"><code>82f9993</code></a> Update changelog.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/211b5cd41c29916bc643b4a11b00578ba4fd6fe8"><code>211b5cd</code></a> Fix links.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/97aadd74bcbc00a2078d240e8fe871dd62b83d80"><code>97aadd7</code></a> Update some ci config, reformat and apply some lint fixes.</li> <li>Additional commits viewable in <a href="https://github.com/pytest-dev/pytest-cov/compare/v1.0...v7.0.0">compare view</a></li> </ul> </details> <br /> Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) --- <details> <summary>Dependabot commands and options</summary> <br /> You can trigger Dependabot actions by commenting on this PR: - `@dependabot rebase` will rebase this PR - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it - `@dependabot merge` will merge this PR after your CI passes on it - `@dependabot squash and merge` will squash and merge this PR after your CI passes on it - `@dependabot cancel merge` will cancel a previously requested merge and block automerging - `@dependabot reopen` will reopen this PR if it is closed - `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually - `@dependabot show <dependency name> ignore conditions` will show all of the ignore conditions of the specified dependency - `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself) </details> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Updates the requirements on [pytest-cov](https://github.com/pytest-dev/pytest-cov) to permit the latest version. <details> <summary>Changelog</summary> <p><em>Sourced from <a href="https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst">pytest-cov's changelog</a>.</em></p> <blockquote> <h2>7.0.0 (2025-09-09)</h2> <ul> <li> <p>Dropped support for subprocesses measurement.</p> <p>It was a feature added long time ago when coverage lacked a nice way to measure subprocesses created in tests. It relied on a <code>.pth</code> file, there was no way to opt-out and it created bad interations with <code>coverage's new patch system <https://coverage.readthedocs.io/en/latest/config.html#run-patch></code>_ added in <code>7.10 <https://coverage.readthedocs.io/en/7.10.6/changes.html#version-7-10-0-2025-07-24></code>_.</p> <p>To migrate to this release you might need to enable the suprocess patch, example for <code>.coveragerc</code>:</p> <p>.. code-block:: ini</p> <p>[run] patch = subprocess</p> <p>This release also requires at least coverage 7.10.6.</p> </li> <li> <p>Switched packaging to have metadata completely in <code>pyproject.toml</code> and use <code>hatchling <https://pypi.org/project/hatchling/></code>_ for building. Contributed by Ofek Lev in <code>[#551](pytest-dev/pytest-cov#551) <https://github.com/pytest-dev/pytest-cov/pull/551></code>_ with some extras in <code>[#716](pytest-dev/pytest-cov#716) <https://github.com/pytest-dev/pytest-cov/pull/716></code>_.</p> </li> <li> <p>Removed some not really necessary testing deps like <code>six</code>.</p> </li> </ul> <h2>6.3.0 (2025-09-06)</h2> <ul> <li>Added support for markdown reports. Contributed by Marcos Boger in <code>[#712](pytest-dev/pytest-cov#712) <https://github.com/pytest-dev/pytest-cov/pull/712></code>_ and <code>[#714](pytest-dev/pytest-cov#714) <https://github.com/pytest-dev/pytest-cov/pull/714></code>_.</li> <li>Fixed some formatting issues in docs. Anonymous contribution in <code>[#706](pytest-dev/pytest-cov#706) <https://github.com/pytest-dev/pytest-cov/pull/706></code>_.</li> </ul> <h2>6.2.1 (2025-06-12)</h2> <ul> <li> <p>Added a version requirement for pytest's pluggy dependency (1.2.0, released 2023-06-21) that has the required new-style hookwrapper API.</p> </li> <li> <p>Removed deprecated license classifier (packaging).</p> </li> <li> <p>Disabled coverage warnings in two more situations where they have no value:</p> <ul> <li>"module-not-measured" in workers</li> <li>"already-imported" in subprocesses</li> </ul> </li> </ul> <h2>6.2.0 (2025-06-11)</h2> <ul> <li> <p>The plugin now adds 3 rules in the filter warnings configuration to prevent common coverage warnings being raised as obscure errors::</p> <p>default:unclosed database in <sqlite3.Connection object at:ResourceWarning once::PytestCovWarning</p> </li> </ul>  </blockquote> <p>... (truncated)</p> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/224d8964caad90074a8cf6dc8720b8f70f31629b"><code>224d896</code></a> Bump version: 6.3.0 → 7.0.0</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/73424e3999f865eac72e27f09d5fe11b9703cfd6"><code>73424e3</code></a> Cleanup the docs a bit.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/36f1cc2967831dbd4c8aa70086fc86dc495f8b9a"><code>36f1cc2</code></a> Bump pins in template.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/f299c590a63a48e51e3ae949993dc7bb1f1d480d"><code>f299c59</code></a> Bump the github-actions group with 2 updates</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/25f0b2e0cdbc345c0d3e49170f7a328c3e0d805f"><code>25f0b2e</code></a> Update docs/config.rst</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/bb23eacc5531fb8f499213d8420407e0d72f88e3"><code>bb23eac</code></a> Improve configuration docs</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/a19531e91e1ab753ccf648a2d9bab08a6fddebb9"><code>a19531e</code></a> Switch from build/pre-commit to uv/prek - this should make this faster.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/82f999391073f2fb8ae422af452602f310086a2a"><code>82f9993</code></a> Update changelog.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/211b5cd41c29916bc643b4a11b00578ba4fd6fe8"><code>211b5cd</code></a> Fix links.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/97aadd74bcbc00a2078d240e8fe871dd62b83d80"><code>97aadd7</code></a> Update some ci config, reformat and apply some lint fixes.</li> <li>Additional commits viewable in <a href="https://github.com/pytest-dev/pytest-cov/compare/v1.0...v7.0.0">compare view</a></li> </ul> </details> <br /> Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) --- <details> <summary>Dependabot commands and options</summary> <br /> You can trigger Dependabot actions by commenting on this PR: - `@dependabot rebase` will rebase this PR - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it - `@dependabot merge` will merge this PR after your CI passes on it - `@dependabot squash and merge` will squash and merge this PR after your CI passes on it - `@dependabot cancel merge` will cancel a previously requested merge and block automerging - `@dependabot reopen` will reopen this PR if it is closed - `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually - `@dependabot show <dependency name> ignore conditions` will show all of the ignore conditions of the specified dependency - `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself) </details> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

purva-thakre mentioned this pull request Oct 2, 2025

Minor details #713

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purva-thakre force-pushed the remove_examples branch from 14f857a to 1bb478f Compare October 2, 2025 05:26

purva-thakre changed the title ~~Remove examples~~ Change examples in the main directory to cli_exsmples Oct 2, 2025

purva-thakre changed the title ~~Change examples in the main directory to cli_exsmples~~ Change examples in the main directory to cli_examples Oct 2, 2025

purva-thakre commented Oct 2, 2025

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purva-thakre closed this Oct 4, 2025

purva-thakre force-pushed the remove_examples branch from 87cc6eb to ea8ec3a Compare October 4, 2025 04:37

purva-thakre reopened this Oct 4, 2025

Fix code block syntax of uv/pip install in readme (#714)

e710d71

Fixes the code blocks below in the readme: <img width="879" height="407" alt="截屏2025-10-01 10 03 19" src="https://github.com/user-attachments/assets/7af8124b-ecd1-4ae3-965e-700f6194864b" />

purva-thakre force-pushed the remove_examples branch from 7a610cc to e710d71 Compare October 4, 2025 04:44

purva-thakre and others added 2 commits October 3, 2025 23:44

Merge branch 'main' into remove_examples

350a2c2

delete directort and add cli rst file

1aa1ec6

purva-thakre changed the title ~~Change examples in the main directory to cli_examples~~ Remove `examples Oct 4, 2025

purva-thakre changed the title ~~Remove `examples~~ Remove examples from main directory Oct 4, 2025

purva-thakre added 2 commits October 4, 2025 10:19

delete logical_cnot.py

d7a9606

bash highlighting remainder from yiming's PR

a8ca035

purva-thakre self-assigned this Oct 4, 2025

purva-thakre added the documentation Improvements or additions to documentation label Oct 4, 2025

error with bash code block

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purva-thakre marked this pull request as ready for review October 4, 2025 11:13

purva-thakre requested a review from inmzhang October 6, 2025 04:48

inmzhang approved these changes Oct 6, 2025

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purva-thakre merged commit f831527 into main Oct 6, 2025
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purva-thakre deleted the remove_examples branch October 6, 2025 07:20

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