SkeletonClient changes, mainly simplification of output formats #265
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…really what we want?
…f the skeletonization time.
fcollman
reviewed
Nov 16, 2024
| del sk_json['vertex_properties'] | ||
| return sk_json | ||
| if endpoint_format == "flatdict": | ||
| assert self._server_version >= Version("0.6.0") |
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This should raise a more informative exception telling the user to contact their system administrator to ask them to upgrade their skeleton service to at least 0.6.0
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@fcollman But this is a genuine assertion, a verification that the code is performing correctly. The function only receives "dict" and "swc" as inputs (see the function signature). Then on line 475, "dict" is translated to one of two internal formats ("jsoncompressed" or "flatdict") based on the server version. Later on, at the line you indicated in your comment, I am merely confirming (asserting) that the internal format has been assigned correctly based on the server version.
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@fcollman To clarify, the API, from the user's perspective outside CAVEclient, doesn't offer "flatdict" as an option. They user asks for "dict" or "swc". Those are their options. These are translated to internal formats that communicate with the server concisely to indicate which format the server should deliver. More to the point, the server really only delivers one kind of dict at at time, but it depends on which version of the server is deployed. There is no "choosing" between dictionary formats from the CAVEclient's perspective (much less from the user's perspective, removed another level of abstraction outside CAVEclient). So, this is an assertion that the code is translating the API format to the correct internal format based on which server version is available.
As for warning the user that their server is out of date, that is handled by other code earlier in the function.
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got it! make sense didn't read carefully enough
kebwi
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Nov 20, 2024
* Compressed SWC format option. * lint/ruff corrections * Bulk skeleton generation. * New skeleton cache query endpoint * Ruff corrections * Trivial change * Removed debugging code. Labeled protected functions. * Ruff correctdions. * Ruff corrections. * Ruff changes that make the code definitively HARDER to read. Is this really what we want? * Converted print statements to logging calls. * Server version checking for new API endpoints. * Ruff conformity. * Added SkeletonClient.skeletons_exist(). * Ruff changes. * Skeleton Client documentation * update test docs to note confusing local server issue * generate_bulk_skeletons_async() now reports an upper bound estimate of the skeletonization time. * Documentation * Cleanup * Versions endpoint * Update changelog * SkeletonClient now only accepts 'dict' and 'swc' format requests. * ruff cleanup * ruff cleanup * ruff cleanup * Various handling of the new 'flatdict' skeleton format. * ruff compliance --------- Co-authored-by: Casey Schneider-Mizell <[email protected]>
kebwi
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Nov 20, 2024
* Compressed SWC format option. * lint/ruff corrections * Bulk skeleton generation. * New skeleton cache query endpoint * Ruff corrections * Trivial change * Removed debugging code. Labeled protected functions. * Ruff correctdions. * Ruff corrections. * Ruff changes that make the code definitively HARDER to read. Is this really what we want? * Converted print statements to logging calls. * Server version checking for new API endpoints. * Ruff conformity. * Added SkeletonClient.skeletons_exist(). * Ruff changes. * Skeleton Client documentation * update test docs to note confusing local server issue * generate_bulk_skeletons_async() now reports an upper bound estimate of the skeletonization time. * Documentation * Cleanup * Versions endpoint * Update changelog * SkeletonClient now only accepts 'dict' and 'swc' format requests. * ruff cleanup * ruff cleanup * ruff cleanup * Various handling of the new 'flatdict' skeleton format. * ruff compliance --------- Co-authored-by: Casey Schneider-Mizell <[email protected]>
kebwi
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Nov 20, 2024
* Compressed SWC format option. * lint/ruff corrections * Bulk skeleton generation. * New skeleton cache query endpoint * Ruff corrections * Trivial change * Removed debugging code. Labeled protected functions. * Ruff correctdions. * Ruff corrections. * Ruff changes that make the code definitively HARDER to read. Is this really what we want? * Converted print statements to logging calls. * Server version checking for new API endpoints. * Ruff conformity. * Added SkeletonClient.skeletons_exist(). * Ruff changes. * Skeleton Client documentation * update test docs to note confusing local server issue * generate_bulk_skeletons_async() now reports an upper bound estimate of the skeletonization time. * Documentation * Cleanup * Versions endpoint * Update changelog * SkeletonClient now only accepts 'dict' and 'swc' format requests. * ruff cleanup * ruff cleanup * ruff cleanup * Various handling of the new 'flatdict' skeleton format. * ruff compliance --------- Co-authored-by: Casey Schneider-Mizell <[email protected]>
fcollman
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Nov 21, 2024
* Compressed SWC format option. * lint/ruff corrections * Bulk skeleton generation. * New skeleton cache query endpoint * Ruff corrections * Trivial change * Removed debugging code. Labeled protected functions. * Ruff correctdions. * Ruff corrections. * Ruff changes that make the code definitively HARDER to read. Is this really what we want? * Converted print statements to logging calls. * Server version checking for new API endpoints. * Ruff conformity. * Added SkeletonClient.skeletons_exist(). * Ruff changes. * Skeleton Client documentation * update test docs to note confusing local server issue * generate_bulk_skeletons_async() now reports an upper bound estimate of the skeletonization time. * Documentation * Cleanup * Versions endpoint * Update changelog * SkeletonClient now only accepts 'dict' and 'swc' format requests. * ruff cleanup * ruff cleanup * ruff cleanup * Various handling of the new 'flatdict' skeleton format. * ruff compliance * Change default skeleton version to 3 (the current latest version) * ruff cleanup * Add packaging as a requirement * Bump version: 6.5.0 → 6.5.1 * version dependent networkx (#266) * Bump version: 6.5.1 → 6.5.2 * SkeletonClient changes, mainly simplification of output formats (#265) * Compressed SWC format option. * lint/ruff corrections * Bulk skeleton generation. * New skeleton cache query endpoint * Ruff corrections * Trivial change * Removed debugging code. Labeled protected functions. * Ruff correctdions. * Ruff corrections. * Ruff changes that make the code definitively HARDER to read. Is this really what we want? * Converted print statements to logging calls. * Server version checking for new API endpoints. * Ruff conformity. * Added SkeletonClient.skeletons_exist(). * Ruff changes. * Skeleton Client documentation * update test docs to note confusing local server issue * generate_bulk_skeletons_async() now reports an upper bound estimate of the skeletonization time. * Documentation * Cleanup * Versions endpoint * Update changelog * SkeletonClient now only accepts 'dict' and 'swc' format requests. * ruff cleanup * ruff cleanup * ruff cleanup * Various handling of the new 'flatdict' skeleton format. * ruff compliance --------- Co-authored-by: Casey Schneider-Mizell <[email protected]> * Bump version: 6.5.2 → 7.0.0 * added documentation of 7.0 changes to skeleton service * SkeletonClient changes, mainly simplification of output formats (#265) * Compressed SWC format option. * lint/ruff corrections * Bulk skeleton generation. * New skeleton cache query endpoint * Ruff corrections * Trivial change * Removed debugging code. Labeled protected functions. * Ruff correctdions. * Ruff corrections. * Ruff changes that make the code definitively HARDER to read. Is this really what we want? * Converted print statements to logging calls. * Server version checking for new API endpoints. * Ruff conformity. * Added SkeletonClient.skeletons_exist(). * Ruff changes. * Skeleton Client documentation * update test docs to note confusing local server issue * generate_bulk_skeletons_async() now reports an upper bound estimate of the skeletonization time. * Documentation * Cleanup * Versions endpoint * Update changelog * SkeletonClient now only accepts 'dict' and 'swc' format requests. * ruff cleanup * ruff cleanup * ruff cleanup * Various handling of the new 'flatdict' skeleton format. * ruff compliance --------- Co-authored-by: Casey Schneider-Mizell <[email protected]> * SkeletonClient changes, mainly simplification of output formats (#265) * Compressed SWC format option. * lint/ruff corrections * Bulk skeleton generation. * New skeleton cache query endpoint * Ruff corrections * Trivial change * Removed debugging code. Labeled protected functions. * Ruff correctdions. * Ruff corrections. * Ruff changes that make the code definitively HARDER to read. Is this really what we want? * Converted print statements to logging calls. * Server version checking for new API endpoints. * Ruff conformity. * Added SkeletonClient.skeletons_exist(). * Ruff changes. * Skeleton Client documentation * update test docs to note confusing local server issue * generate_bulk_skeletons_async() now reports an upper bound estimate of the skeletonization time. * Documentation * Cleanup * Versions endpoint * Update changelog * SkeletonClient now only accepts 'dict' and 'swc' format requests. * ruff cleanup * ruff cleanup * ruff cleanup * Various handling of the new 'flatdict' skeleton format. * ruff compliance --------- Co-authored-by: Casey Schneider-Mizell <[email protected]> * Change default skeleton version to 3 (the current latest version) * ruff cleanup * Old code somehow got reinstated. --------- Co-authored-by: Casey Schneider-Mizell <[email protected]> Co-authored-by: Ben Pedigo <[email protected]> Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Co-authored-by: Forrest Collman <[email protected]>
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