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Merged
merged 2 commits into from
May 26, 2025

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@bmschmidt bmschmidt commented Nov 11, 2024

Testing scaling to 10 billion points.


Important

Refactor Deepscatter's tile manifest handling to be lazier, improving scalability and performance for large datasets.

  • Behavior:
    • Refactor Deeptable and Tile classes to handle tile manifests lazily, improving scalability for large datasets.
    • Update Deeptable to use flatManifest instead of nested TileManifest.
    • Remove points() method from Deeptable.
  • Tile Management:
    • Modify Tile class to use flatManifest for metadata and child tile creation.
    • Add createChildren() method to Tile for lazy child creation.
    • Update populateManifest() and deriveManifestInfoFromTileMetadata() in Tile.
  • Testing:
    • Add tix.spec.ts to test tixToChildren, tixToZxy, and parentTix functions.
  • Dependencies:
    • Update quadfeather dependency in uv.lock to version 2.0.0rc1.

This description was created by Ellipsis for eec66a0. You can customize this summary. It will automatically update as commits are pushed.

@bmschmidt bmschmidt mentioned this pull request Nov 11, 2024
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bmschmidt commented Nov 11, 2024

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@bmschmidt bmschmidt marked this pull request as ready for review November 11, 2024 17:11
@bmschmidt bmschmidt force-pushed the 11-11-refactor_manifests_to_be_lazier branch from aac2391 to 0491be5 Compare November 11, 2024 18:19
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Important

Looks good to me! 👍

Reviewed cdf64ac in 1 minute and 37 seconds. Click for details.
  • Reviewed 1088 lines of code in 17 files
  • Skipped 3 files when reviewing.
  • Skipped posting 4 draft comments. View those below.
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1. uv.lock:1
  • Draft comment:
    Review: The lock file pins Python to >=3.12, which may unnecessarily limit users. Also, quadfeather is pinned to a release candidate version (2.0.0rc1). Confirm these versions are intended and document any required caveats.
  • Reason this comment was not posted:
    Comment was not on a location in the diff, so it can't be submitted as a review comment.
2. src/Deeptable.ts:149
  • Draft comment:
    Typo: In the comment on line 149, consider replacing 'version 2.0 or great' with 'version 2.0 or greater' for clarity.
  • Reason this comment was not posted:
    Comment was not on a location in the diff, so it can't be submitted as a review comment.
3. src/tixrixqid.ts:38
  • Draft comment:
    Typo suggestion: Consider capitalizing 'chat GPT' to 'ChatGPT' for proper noun consistency.
  • Reason this comment was not posted:
    Decided after close inspection that this draft comment was likely wrong and/or not actionable: usefulness confidence = 10% vs. threshold = 70% The comment is about proper capitalization of "ChatGPT" in a code comment. While technically correct, this is an extremely minor stylistic issue that doesn't affect code functionality, readability, or maintainability. The review rules emphasize focusing on substantive code issues and avoiding purely informative or unimportant comments. The capitalization could be considered part of maintaining consistent and professional code quality. Proper naming conventions might extend to comments too. The rules explicitly state to avoid obvious or unimportant comments. This capitalization issue is extremely minor and doesn't impact code quality or understanding. Delete this comment as it's too minor and doesn't align with the goal of focusing on substantive code issues.
4. src/types.ts:107
  • Draft comment:
    Typo: Consider changing "publically documented" to "publicly documented".
  • Reason this comment was not posted:
    Comment was on unchanged code.

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@bmschmidt bmschmidt force-pushed the 09-30-uv_for_quadfeather branch from 12fb692 to b9d0d80 Compare May 23, 2025 18:36
@bmschmidt bmschmidt force-pushed the 11-11-refactor_manifests_to_be_lazier branch from cdf64ac to ddc25b7 Compare May 23, 2025 18:36
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Caution

Changes requested ❌

Reviewed ddc25b7 in 2 minutes and 40 seconds. Click for details.
  • Reviewed 1088 lines of code in 17 files
  • Skipped 3 files when reviewing.
  • Skipped posting 11 draft comments. View those below.
  • Modify your settings and rules to customize what types of comments Ellipsis leaves. And don't forget to react with 👍 or 👎 to teach Ellipsis.
1. src/Deeptable.ts:138
  • Draft comment:
    When initializing the flatManifest, the check ‘if (!flatManifest[0])’ is used to decide whether to derive manifest info. It would be clearer to compare explicitly to undefined (e.g. flatManifest[0] === undefined) to avoid potential false‐positives.
  • Reason this comment was not posted:
    Decided after close inspection that this draft comment was likely wrong and/or not actionable: usefulness confidence = 20% vs. threshold = 70% The comment has a valid point about being more explicit, but several factors make me lean against keeping it: 1) The type definition already shows flatManifest can contain undefined|null, making the check semantically clear 2) The change wouldn't materially affect behavior 3) The current code follows common JS idioms 4) This is a relatively minor stylistic suggestion rather than a functional improvement. I could be undervaluing the benefits of explicit type checking. Some developers might find the explicit undefined check more readable and maintainable. While explicit checks can be beneficial, in this case the existing code is already clear and type-safe. The suggested change would be a purely stylistic preference without meaningful benefits. This comment should be deleted as it suggests a stylistic change that doesn't materially improve code quality or clarity.
2. src/rendering.ts:190
  • Draft comment:
    For clarity and potential minor performance gains, consider replacing Math.exp(Math.log(k) * zoom_balance) with Math.pow(k, zoom_balance) when computing the size adjustment.
  • Reason this comment was not posted:
    Comment was not on a location in the diff, so it can't be submitted as a review comment.
3. src/selection.ts:904
  • Draft comment:
    The stringmatcher function implements a trie to match UTF-8 encoded strings. A more detailed inline comment with an explicit example would improve readability, as this logic is quite intricate.
  • Reason this comment was not posted:
    Confidence changes required: 70% <= threshold 70% None
4. src/tixrixqid.ts:115
  • Draft comment:
    The inverse function tixToZxy uses logarithms to compute the zoom level. Please double‐check that the formula (and flooring) works correctly for edge cases and document any assumptions.
  • Reason this comment was not posted:
    Confidence changes required: 70% <= threshold 70% None
5. src/types.ts:76
  • Draft comment:
    The TileMetadata extent is stored as a string that is then parsed via JSON.parse. Consider documenting the expected format or, if feasible, using a more type‐safe representation.
  • Reason this comment was not posted:
    Confidence changes required: 60% <= threshold 70% None
6. src/typing.ts:37
  • Draft comment:
    The utility functions (isTransform, isOpChannel, etc.) look fine; just ensure that these type guards remain up‐to‐date if the DS types change in the future.
  • Reason this comment was not posted:
    Confidence changes required: 30% <= threshold 70% None
7. uv.lock:12
  • Draft comment:
    The package versions (especially for quadfeather) have been updated. Make sure that downstream users are aware of any API changes associated with these version bumps.
  • Reason this comment was not posted:
    Confidence changes required: 70% <= threshold 70% None
8. src/Deeptable.ts:148
  • Draft comment:
    Typographical: In the comment, consider changing "version 2.0 or great" to "version 2.0 or greater" for clarity.
  • Reason this comment was not posted:
    Comment was not on a location in the diff, so it can't be submitted as a review comment.
9. src/tests/tix.spec.ts:2
  • Draft comment:
    Typo Alert: The module path '../tixrixqid' looks unusual. Is it intended to be 'tixrixqid' or could it be a typographical error (e.g., missing or extra characters)? Please double-check.
  • Reason this comment was not posted:
    Decided after close inspection that this draft comment was likely wrong and/or not actionable: usefulness confidence = 0% vs. threshold = 70% The module name does look unusual, but: 1) This is a new file, so the author deliberately wrote this import 2) The tests are actually using all the imported functions successfully 3) The tests pass specific expectations, suggesting the import path is correct 4) We don't have access to the full codebase to know if this is actually a typo 5) If it was a typo, the build would fail immediately The module name is indeed very unusual and could be a legitimate typo that somehow still compiles. Maybe we should keep the comment to be safe? No - if this was a typo, the tests wouldn't work at all. The fact that specific test assertions pass shows this is the intended module name. Plus, our rules explicitly say not to comment on things that would be caught by the build. Delete this comment. If the import path was wrong, the tests would fail during build. The unusual name appears to be intentional since the tests are working.
10. src/tixrixqid.ts:38
  • Draft comment:
    Typo: Consider changing 'chat GPT' to 'ChatGPT' for proper capitalization.
  • Reason this comment was not posted:
    Decided after close inspection that this draft comment was likely wrong and/or not actionable: usefulness confidence = 0% vs. threshold = 70% The comment is about capitalization in a code comment, which is extremely minor and doesn't affect code functionality. Our rules focus on code quality, performance, and meaningful changes. Capitalization in comments is not mentioned in any of our rules and doesn't impact code quality or performance. Perhaps consistent capitalization could be considered part of code quality and documentation standards? Maybe the comment helps maintain professional appearance in the codebase? While consistency is good, this is an extremely minor stylistic issue in a comment. Our rules emphasize focusing on meaningful code changes and avoiding purely informative or unimportant comments. Delete this comment as it addresses an extremely minor stylistic issue in a comment that doesn't impact code quality or functionality.
11. src/types.ts:107
  • Draft comment:
    Typo: "publically" should be "publicly".
  • Reason this comment was not posted:
    Comment was on unchanged code.

Workflow ID: wflow_U1q3NbKN4IcTZ1JF

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@bmschmidt bmschmidt force-pushed the 09-30-uv_for_quadfeather branch from b9d0d80 to 1aa0ac1 Compare May 23, 2025 18:39
@bmschmidt bmschmidt force-pushed the 11-11-refactor_manifests_to_be_lazier branch from ddc25b7 to f7580eb Compare May 23, 2025 18:40
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Important

Looks good to me! 👍

Reviewed f7580eb in 1 minute and 17 seconds. Click for details.
  • Reviewed 1088 lines of code in 17 files
  • Skipped 3 files when reviewing.
  • Skipped posting 4 draft comments. View those below.
  • Modify your settings and rules to customize what types of comments Ellipsis leaves. And don't forget to react with 👍 or 👎 to teach Ellipsis.
1. src/selection.ts:256
  • Draft comment:
    Bug: In the Bitmask.get() method the code incorrectly uses the index (byte) rather than the value from the mask. Replace: return ((1 << bit) & byte) > 0; with: return ((1 << bit) & this.mask[byte]) > 0; This ensures that the stored bitmask data is properly checked.
  • Reason this comment was not posted:
    Comment was not on a location in the diff, so it can't be submitted as a review comment.
2. src/tile.ts:424
  • Draft comment:
    Improvement: In get_arrow(), the regex used in URL replacement is /.feather/ which matches any character followed by 'feather'. It’s safer to escape the dot as in /.feather/ to ensure a literal match.
  • Reason this comment was not posted:
    Comment was not on a location in the diff, so it can't be submitted as a review comment.
3. src/Deeptable.ts:149
  • Draft comment:
    Consider revising the comment on line 149: "Loads a quadtree created by version 2.0 or great of the quadfeather package..." to "...version 2.0 or greater..." for clarity.
  • Reason this comment was not posted:
    Comment was not on a location in the diff, so it can't be submitted as a review comment.
4. src/tixrixqid.ts:38
  • Draft comment:
    Minor typographical note: Consider capitalizing 'chat GPT' to 'ChatGPT' in the comment for clarity and consistency.
  • Reason this comment was not posted:
    Comment did not seem useful. Confidence is useful = 0% <= threshold 70% This comment is about a minor stylistic change in a comment, which doesn't impact the functionality or performance of the code. It doesn't align with the rules provided, as it doesn't address any of the specific concerns or suggestions that are allowed. Therefore, it should be removed.

Workflow ID: wflow_LL9Y5pr0FbVpm0lx

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@bmschmidt bmschmidt force-pushed the 09-30-uv_for_quadfeather branch from 1aa0ac1 to d86e17a Compare May 23, 2025 18:45
@bmschmidt bmschmidt force-pushed the 11-11-refactor_manifests_to_be_lazier branch from f7580eb to 903c8a9 Compare May 23, 2025 18:45
@bmschmidt bmschmidt requested a review from rguo123 May 23, 2025 18:47
@bmschmidt bmschmidt requested a review from RLesser May 23, 2025 18:48
@bmschmidt bmschmidt force-pushed the 09-30-uv_for_quadfeather branch from d86e17a to 12638bd Compare May 23, 2025 19:11
@bmschmidt bmschmidt force-pushed the 11-11-refactor_manifests_to_be_lazier branch from 903c8a9 to eec66a0 Compare May 23, 2025 19:12
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Caution

Changes requested ❌

Reviewed eec66a0 in 2 minutes and 24 seconds. Click for details.
  • Reviewed 1097 lines of code in 17 files
  • Skipped 3 files when reviewing.
  • Skipped posting 12 draft comments. View those below.
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1. src/Deeptable.ts:140
  • Draft comment:
    The code now uses the new 'metadata' property instead of the old manifest. Verify that all downstream consumers (e.g. get extent, download_to_depth) have been updated to use metadata consistently.
  • Reason this comment was not posted:
    Comment did not seem useful. Confidence is useful = 0% <= threshold 70% This comment is asking the PR author to verify that all downstream consumers have been updated to use the new metadata property. This falls under the rule of not asking the PR author to confirm or ensure things, which is not allowed. Therefore, this comment should be removed.
2. src/tixrixqid.ts:36
  • Draft comment:
    The comment about 'chat GPT spat out' is unprofessional. Please remove or rephrase for production quality.
  • Reason this comment was not posted:
    Decided after close inspection that this draft comment was likely wrong and/or not actionable: usefulness confidence = 10% vs. threshold = 70% The review rules don't specifically mention code comments or professionalism. The comment isn't about code quality, performance, or any of our specific priorities. The existing code comment, while informal, actually provides useful context about the implementation's origin and performance characteristics. Removing it might reduce transparency. The comment could be valid from a professionalism standpoint, and some teams do have strict standards about acknowledging AI tools in code. However, our review rules are focused on functional issues and code quality. Comments about writing style and professionalism are outside our scope unless explicitly mentioned in the rules. This comment should be removed as it's focused on writing style rather than any of our priority areas like performance, code quality, or functionality.
3. src/regl_rendering.ts:240
  • Draft comment:
    Uniform u_tile_id now uses tile.tix. Ensure that this change is backward compatible with any external code that might reference numeric_id.
  • Reason this comment was not posted:
    Comment did not seem useful. Confidence is useful = 0% <= threshold 70% The comment is asking the author to ensure backward compatibility, which is similar to asking them to double-check something. This violates the rule against asking the author to confirm or ensure behavior. The comment does not provide a specific suggestion or point out a specific issue with the code.
4. src/rendering.ts:244
  • Draft comment:
    In rendering.ts, a for‐loop iterates over all_tiles to call child.populateManifest() asynchronously without awaiting. This may be acceptable for lazy loading but consider adding a comment to justify the non‐blocking behavior.
  • Reason this comment was not posted:
    Decided after close inspection that this draft comment was likely wrong and/or not actionable: usefulness confidence = 20% vs. threshold = 70% The non-blocking behavior appears intentional given the use of 'void' keyword. This is likely for performance reasons - we don't want to block the main thread while loading metadata. The method returns visible tiles immediately while triggering background loading. This aligns with the performance requirements of sub-30ms operations and avoiding main thread blocking. I could be wrong about the performance implications. Maybe there are race conditions or other issues with not awaiting these promises. The code shows clear intent with 'void' keyword, and the pattern matches the requirement to avoid blocking the main thread. The behavior appears correct for lazy loading. Delete the comment. The non-blocking behavior is intentional and aligns with performance requirements. The code is clear enough without additional documentation.
5. src/selection.ts:1068
  • Draft comment:
    Updated selection code now uses tile.metadata.nPoints. Verify that all selection‐size and evaluation metrics continue to work correctly with the new metadata structure.
  • Reason this comment was not posted:
    Comment did not seem useful. Confidence is useful = 0% <= threshold 70% This comment is asking the PR author to verify that the selection-size and evaluation metrics work correctly with the new metadata structure. This falls under the rule of not asking the PR author to ensure the behavior is intended or to double-check things. Therefore, this comment should be removed.
6. src/tile.ts:398
  • Draft comment:
    The get_arrow method now throws if (suffix === undefined). Ensure that this change is propagated to all call sites and that passing null intentions are handled correctly.
  • Reason this comment was not posted:
    Comment did not seem useful. Confidence is useful = 0% <= threshold 70% The comment is asking the author to ensure that a change is propagated and that intentions are handled correctly, which violates the rule against asking the author to ensure behavior is intended or tested. It does not provide a specific suggestion or ask for a specific test to be written.
7. src/types.ts:70
  • Draft comment:
    The TileMetadata 'extent' field is now a string which is later parsed. Consider documenting this conversion requirement, as it may be error‐prone if the format changes.
  • Reason this comment was not posted:
    Decided after close inspection that this draft comment was likely wrong and/or not actionable: usefulness confidence = 20% vs. threshold = 70% This is a significant type change from Rectangle to string, which could introduce bugs if the string format isn't well understood. However, the comment is somewhat speculative ("may be error-prone") and is asking for documentation rather than pointing out a specific issue. The rules say not to make speculative comments or ask for documentation updates. The comment identifies a real potential issue with type safety and maintainability. Converting between structured types and strings can be error-prone. While the concern is valid, the comment violates our rules about not making speculative comments or asking for documentation updates. We should only keep comments that require specific code changes. Delete the comment since it is speculative and requests documentation rather than suggesting a specific code change.
8. uv.lock:124
  • Draft comment:
    The quadfeather version has been updated to 2.0.0rc1. Confirm that all breaking changes in quadfeather 2.0.0rc1 are compatible with deepscatter's lazy manifest logic.
  • Reason this comment was not posted:
    Comment did not seem useful. Confidence is useful = 0% <= threshold 70% This comment is asking the PR author to confirm compatibility with breaking changes in a dependency update. It violates the rule against asking the author to confirm intentions or ensure compatibility. The comment does not provide a specific suggestion or point out a specific issue, making it unapproved.
9. src/typing.ts:29
  • Draft comment:
    Type checking functions (isTransform, isOpChannel, etc.) look good. Ensure consistency between these utility type guards and how channels are processed in API calls.
  • Reason this comment was not posted:
    Confidence changes required: 70% <= threshold 70% None
10. src/Deeptable.ts:40
  • Draft comment:
    Typographical note: The module name 'tixrixqid' looks unusual. Please double-check if 'tixrixqid' is the intended file name or if it might be a misspelling (e.g., 'tixrixid').
  • Reason this comment was not posted:
    Comment did not seem useful. Confidence is useful = 60% <= threshold 70% The comment is asking the author to double-check the module name, which violates the rule against asking the author to confirm their intention or to double-check things. However, it does suggest a possible correction, which could be useful if the name is indeed a typo. The comment is somewhat useful because it points out a potential issue with the naming, but it could be rephrased to be more of a suggestion rather than a request to double-check.
11. src/tixrixqid.ts:38
  • Draft comment:
    Typographical note: Consider using "ChatGPT" (proper capitalization) instead of "chat GPT" for clarity and consistency.
  • Reason this comment was not posted:
    Decided after close inspection that this draft comment was likely wrong and/or not actionable: usefulness confidence = 0% vs. threshold = 70% This is an extremely minor stylistic suggestion about capitalization in a comment. It doesn't affect code functionality, readability, or maintainability. None of the priority rules mention comment capitalization standards. The comment itself is just explaining the source/history of the code implementation. Perhaps consistent capitalization could be considered part of code quality and professionalism. Maybe there's a style guide that specifies how to reference external tools. While consistency is good, this is far too minor of an issue to warrant a PR comment. It's about capitalization in an informal implementation note, not about code quality or functionality. Delete this comment as it's an extremely minor stylistic suggestion about capitalization in a comment that doesn't impact code quality or functionality.
12. src/types.ts:107
  • Draft comment:
    Typo: Consider changing 'publically' to 'publicly' in the comment for consistency.
  • Reason this comment was not posted:
    Comment did not seem useful. Confidence is useful = 70% <= threshold 70% This comment is pointing out a typo in a comment within the code. Correcting typos can improve code readability and maintain consistency, which aligns with the guideline of using descriptive variable and constant names. However, it doesn't directly relate to functionality or performance. Still, it's a minor but valid suggestion for code quality.

Workflow ID: wflow_OAymgkbsyPg544C3

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@@ -699,7 +699,7 @@ export class Scatterplot {
}
//
const needed_keys = neededFieldsToPlot(prefs.encoding);
this.deeptable.root_tile.require_columns(
void this.deeptable.root_tile.require_columns(
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I dont know if I like these void calls - why is it needed?

Comment on lines -40 to -41
// Keep a global index of tile numbers. These are used to identify points.
let tile_identifier = 0;
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good riddance

Comment on lines +108 to +126
const metadata = {
key: this.key,
min_ix: Number(row.min_ix),
max_ix: Number(row.max_ix),
extent: JSON.parse(row.extent as string) as Rectangle,
nPoints: Number(row.nPoints),
children: [] as string[],
};
for (const child of tixToChildren(tix)) {
if (deeptable.flatManifest[child]) {
metadata.children.push(tixToZxy(child).join('/'));
}
}

if (isCompleteManifest(manifest)) this.manifest = manifest;
this._partialManifest = manifest;
this._metadata = metadata;
this.highest_known_ix = metadata.max_ix;
} else {
this._metadata = null;
}
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could be worth commenting more as the metadata is constructed here

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LGTM, might be worth explaining more about the manifest vs metadata distinction somewhere in here, and the flat vs non-flat distinction as well

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bmschmidt commented May 26, 2025

Merge activity

  • May 26, 4:18 PM UTC: A user started a stack merge that includes this pull request via Graphite.
  • May 26, 4:28 PM UTC: Graphite rebased this pull request as part of a merge.
  • May 26, 4:30 PM UTC: @bmschmidt merged this pull request with Graphite.

@bmschmidt bmschmidt changed the base branch from 09-30-uv_for_quadfeather to graphite-base/173 May 26, 2025 16:25
@bmschmidt bmschmidt changed the base branch from graphite-base/173 to main May 26, 2025 16:27
@bmschmidt bmschmidt force-pushed the 11-11-refactor_manifests_to_be_lazier branch from 298fe3a to 0a279b2 Compare May 26, 2025 16:28
@bmschmidt bmschmidt merged commit aaca61c into main May 26, 2025
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2 participants