Repository navigation
2.0.0b6: move the batch prompt to refine_mesh; release prep - #63
Merged
Merged
Conversation
…nces_orientations Refining every tomogram is by far the slowest thing in the pipeline (hours per tomogram, several sampling/fitting iterations plus a full pycurv pass), so that is where an explicit "are you sure?" belongs. distances_orientations is ~15 minutes on the tutorial data and no longer prompts or takes -f/--force. Also renames the "accepted surface" language to "the final round of refinement" throughout: pycurv's single pass runs on the last refinement iteration, but nothing is accepted until `morphometrics accept_refinement`. New warn_intermediate parameter on refine_mesh_iteration (loop passes False): the four-line "not curvature-ready" warning previously fired on every intermediate iteration including the last one, immediately before pycurv ran on it. The loop now emits a one-line note only when another round follows. BREAKING: `morphometrics distances_orientations -f` is gone; scripts passing it need updating. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
The prompt moved to refine_mesh, so distances_orientations no longer needs -f, but dropping the option outright would break existing cluster scripts that pass it (click rejects unknown options). It is now hidden from --help, does nothing, and prints a note that it will be removed in 2.0. Adds tests for both prompts. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Close the 2.0.0b6 changelog section (no longer "unreleased") and record the batch prompt move. pyproject and __version__ are already 2.0.0b6. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Prepares the 2.0.0b6 beta: everything already on
mainsince 2.0.0b5, plus the batch-prompt change.Changes
refine_mesh. Refining every tomogram is the slowest pipeline step (hours per tomogram), somorphometrics refine_mesh config.ymlwith no--tomogramnow asks before starting;-f/--forceskips the prompt.distances_orientations(~15 min on the tutorial data) no longer prompts.distances_orientations -fis kept as a hidden, deprecated no-op. It prints a note that it will be removed in 2.0, so existing cluster scripts that pass it keep working.refine_meshwording. Output now says "final round of refinement" instead of "accepted surface", since nothing is accepted untilaccept_refinement. The "not curvature-ready" warning appears only on intermediate rounds.[2.0.0b6]CHANGELOG section. The version was already 2.0.0b6.Already on
mainand included in b6: mesh generation decoupled from pycurv, density samples outside the tomogram reported as missing, andvtkdeclared as a dependency.Testing
morphometrics-packaging): 108 passed.After merge: tag
2.0beta6and rungh release create 2.0beta6 --title 2.0.0b6 --prerelease. The statistics work follows as 2.0.0b7.🤖 Generated with Claude Code