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geff

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ci(dependabot): bump CodSpeedHQ/action from 5.6.1 to 5.6.3 Bumps [CodSpeedHQ/action](https://github.com/codspeedhq/action) from 5.6.1 to 5.6.3. - [Release notes](https://github.com/codspeedhq/action/releases) - [Changelog](https://github.com/CodSpeedHQ/action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codspeedhq/action/compare/v5.6.1...v5.6.3) --- updated-dependencies: - dependency-name: CodSpeedHQ/action dependency-version: 5.6.3 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com>

dependabot/github_actions/CodSpeedHQ/action-5.6.3

2 days ago

Update ctc converter to write images and segmentations to OME-Zarr v0.6 (#463) # Proposed Change Update the CTC converter to write the images and segmentations to OME-Zarr with a scale pyramid instead of dumping to a normal zarr. # Types of Changes What types of changes does your code introduce? Delete those that do not apply. - New feature or enhancement Which topics does your change affect? Delete those that do not apply. - Convert # Checklist Put an x in the boxes that apply. You can also fill these out after creating the PR. If you're unsure about any of them, don't hesitate to ask. We're here to help! This is simply a reminder of what we are going to look for before merging your code. - [x] I have read the [developer/contributing](https://github.com/live-image-tracking-tools/geff/blob/main/CONTRIBUTING) docs. - [x] I have added tests that prove that my feature works in various situations or tests the bugfix (if appropriate). - [x] I have checked that I maintained or improved code coverage. - [x] I have written docstrings and checked that they render correctly by looking at the docs preview (link left as a comment on the PR). --------- Co-authored-by: Caroline Malin-Mayor <malinmayorc@janelia.hhmi.org>

main

3 days ago

WRite empty arrays for declared metadata properties

write-empty-arrays-for-declared-props

6 days ago

Update ctc converter to write images and segmentations to OME-Zarr v0.6 (#463) # Proposed Change Update the CTC converter to write the images and segmentations to OME-Zarr with a scale pyramid instead of dumping to a normal zarr. # Types of Changes What types of changes does your code introduce? Delete those that do not apply. - New feature or enhancement Which topics does your change affect? Delete those that do not apply. - Convert # Checklist Put an x in the boxes that apply. You can also fill these out after creating the PR. If you're unsure about any of them, don't hesitate to ask. We're here to help! This is simply a reminder of what we are going to look for before merging your code. - [x] I have read the [developer/contributing](https://github.com/live-image-tracking-tools/geff/blob/main/CONTRIBUTING) docs. - [x] I have added tests that prove that my feature works in various situations or tests the bugfix (if appropriate). - [x] I have checked that I maintained or improved code coverage. - [x] I have written docstrings and checked that they render correctly by looking at the docs preview (link left as a comment on the PR). --------- Co-authored-by: Caroline Malin-Mayor <malinmayorc@janelia.hhmi.org>

main

6 days ago

Make scale pyramid heleprs private, dont write geff scaled units without a scale

ctc-ome-zarr

6 days ago

Add ctc converter benchmark

ctc-ome-zarr

7 days ago

Implement Talley's yaozarrs suggestions

ctc-ome-zarr

7 days ago

ci(dependabot): bump CodSpeedHQ/action from 5.5.0 to 5.6.1 (#460) Bumps [CodSpeedHQ/action](https://github.com/codspeedhq/action) from 5.5.0 to 5.6.1. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/codspeedhq/action/releases">CodSpeedHQ/action's releases</a>.</em></p> <blockquote> <h2>v5.6.1</h2> <p>Bumps the CodSpeed runner to <a href="https://github.com/CodSpeedHQ/codspeed/releases/tag/v5.6.1">v5.6.1</a>.</p> <h3>Fixes</h3> <ul> <li>Walltime: the runner no longer hangs after the benchmark exits when a Python process forks and leaves a corrupted perf jitdump (<a href="https://redirect.github.com/CodSpeedHQ/codspeed/pull/599">#599</a>)</li> <li>Simulation: stop the libpython symlink warning from firing falsely (<a href="https://redirect.github.com/CodSpeedHQ/codspeed/pull/594">#594</a>)</li> </ul> <h3>🐛 Bug Fixes</h3> <ul> <li>Stop the libpython symlink warning from firing falsely by <a href="https://github.com/not-matthias"><code>@not-matthias</code></a> in <a href="https://redirect.github.com/CodSpeedHQ/runner/pull/594">#594</a></li> </ul> <h3>💼 Other</h3> <ul> <li>Bump submodule to not loop on corrupted jit dump by <a href="https://github.com/GuillaumeLagrange"><code>@GuillaumeLagrange</code></a> in <a href="https://redirect.github.com/CodSpeedHQ/runner/pull/599">#599</a></li> </ul> <p><strong>Full Runner Changelog</strong>: <a href="https://github.com/CodSpeedHQ/codspeed/blob/main/CHANGELOG.md">https://github.com/CodSpeedHQ/codspeed/blob/main/CHANGELOG.md</a></p> <h2>What's Changed</h2> <ul> <li>docs(examples): update the example workflows by <a href="https://github.com/SuperMuel"><code>@SuperMuel</code></a> in <a href="https://redirect.github.com/CodSpeedHQ/action/pull/252">CodSpeedHQ/action#252</a></li> <li>chore: bump runner version to 5.6.1 by <a href="https://github.com/github-actions"><code>@github-actions</code></a>[bot] in <a href="https://redirect.github.com/CodSpeedHQ/action/pull/254">CodSpeedHQ/action#254</a></li> </ul> <h2>New Contributors</h2> <ul> <li><a href="https://github.com/SuperMuel"><code>@SuperMuel</code></a> made their first contribution in <a href="https://redirect.github.com/CodSpeedHQ/action/pull/252">CodSpeedHQ/action#252</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/CodSpeedHQ/action/compare/v5.6.0...v5.6.1">https://github.com/CodSpeedHQ/action/compare/v5.6.0...v5.6.1</a></p> <h2>v5.6.0</h2> <p>Bumps the CodSpeed runner to <a href="https://github.com/CodSpeedHQ/codspeed/releases/tag/v5.6.0">v5.6.0</a>.</p> <h3>Highlights</h3> <h4>More consistent CPU Simulation results</h4> <p>Changes to your CI environment, like a different path or an extra environment variable, no longer change the performance. Each benchmark now starts with the same memory layout, reducing the chance of false regressions.</p> <h3>🐛 Bug Fixes</h3> <ul> <li>Keep the user's <code>HOME</code> when wrapping commands with sudo by <a href="https://github.com/lvaroqui"><code>@lvaroqui</code></a> in <a href="https://redirect.github.com/CodSpeedHQ/codspeed/pull/588">#588</a></li> </ul> <h3>⚙️ Internals</h3> <ul> <li>Bump pinned valgrind-codspeed to <a href="https://github.com/CodSpeedHQ/valgrind-codspeed/releases/tag/3.26.0-0codspeed10">3.26.0-0codspeed10</a> by <a href="https://github.com/adriencaccia"><code>@adriencaccia</code></a> in <a href="https://redirect.github.com/CodSpeedHQ/codspeed/pull/593">#593</a> <ul> <li>fix(callgrind): suppress L3 warning for explicit LL settings by <a href="https://github.com/not-matthias"><code>@not-matthias</code></a> in <a href="https://redirect.github.com/CodSpeedHQ/valgrind-codspeed/pull/52">CodSpeedHQ/valgrind-codspeed#52</a></li> <li>fix(initimg): stabilize Linux startup stack layout by <a href="https://github.com/not-matthias"><code>@not-matthias</code></a> in <a href="https://redirect.github.com/CodSpeedHQ/valgrind-codspeed/pull/53">CodSpeedHQ/valgrind-codspeed#53</a></li> </ul> </li> </ul> <p><strong>Full Runner Changelog</strong>: <a href="https://github.com/CodSpeedHQ/codspeed/blob/main/CHANGELOG.md">https://github.com/CodSpeedHQ/codspeed/blob/main/CHANGELOG.md</a></p> <h2>What's Changed</h2>  </blockquote> <p>... (truncated)</p> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/CodSpeedHQ/action/commit/61efe07e57e55bedeab750c434504de272a56e8c"><code>61efe07</code></a> Release v5.6.1 🚀</li> <li><a href="https://github.com/CodSpeedHQ/action/commit/2dea609d0e11606d0e71f7146874637081bb2b81"><code>2dea609</code></a> chore: bump runner version to 5.6.1 (<a href="https://redirect.github.com/codspeedhq/action/issues/254">#254</a>)</li> <li><a href="https://github.com/CodSpeedHQ/action/commit/e0fab22a3bfcc49ceafbc31a62f55e53d98bc2d3"><code>e0fab22</code></a> docs(examples): update the example workflows (<a href="https://redirect.github.com/codspeedhq/action/issues/252">#252</a>)</li> <li><a href="https://github.com/CodSpeedHQ/action/commit/78102a468f96d8e0ccb92d0ec49425753fc42062"><code>78102a4</code></a> Release v5.6.0 🚀</li> <li><a href="https://github.com/CodSpeedHQ/action/commit/3bb0242b1d872772fafa73170df9ae5c464d42ec"><code>3bb0242</code></a> chore: bump runner version to 5.6.0 (<a href="https://redirect.github.com/codspeedhq/action/issues/253">#253</a>)</li> <li>See full diff in <a href="https://github.com/codspeedhq/action/compare/v5.5.0...v5.6.1">compare view</a></li> </ul> </details> <br /> [![Dependabot compatibility score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=CodSpeedHQ/action&package-manager=github_actions&previous-version=5.5.0&new-version=5.6.1)](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) 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 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] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Morgan Schwartz <msschwartz21@gmail.com>

main

7 days ago

Latest Branches

×3.8

ci(dependabot): bump CodSpeedHQ/action from 5.6.1 to 5.6.3#472

2 days ago

15c01bc

dependabot/github_actions/CodSpeedHQ/action-5.6.3

0%

WRite empty arrays for declared metadata properties#471

6 days ago

f290a9f

write-empty-arrays-for-declared-props

0%

Update ctc converter to write images and segmentations to OME-Zarr v0.6#463

7 days ago

feffaba

ctc-ome-zarr

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