Fix missing .gz extension on path_assembly_json when --compress_output is enabled#44
Merged
Joseph-Ellaway merged 2 commits intonew-mol-key-and-compressionfrom Mar 8, 2026
Merged
Conversation
…enabled Co-authored-by: Joseph-Ellaway <69363546+Joseph-Ellaway@users.noreply.github.com>
Copilot
AI
changed the title
[WIP] Work in progress to address feedback on new mol key implementation
Fix missing Mar 8, 2026
.gz extension on path_assembly_json when --compress_output is enabled
Joseph-Ellaway
added a commit
that referenced
this pull request
Mar 10, 2026
* Additional test data files Other structure format files added to test set * Expected compressed JSON files * Test for compressed cif and JSONs * Enable compression for assembly parser * Test files for compressed interfaces * Tests for compressing interfaces * Test for compressed interface summary JSON * Test files for interface summary compression * Compress JSONs for interface summary results * Scratch folder * List file parsers updated to allow compression * CLI entry point updated to take compression flags * Updated output test files for component_id * Increased test verbosity * Models updated to accept component_id * component_id fed into models from parsers * Version bump * Unnecessary compressionlevel removed * Update pisa_utils/parsers.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update pisa_utils/run.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update pisa_utils/run.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Fix missing `.gz` extension on `path_assembly_json` when `--compress_output` is enabled (#44) * Initial plan * Fix path_assembly_json missing .gz extension when compress_output is enabled Co-authored-by: Joseph-Ellaway <69363546+Joseph-Ellaway@users.noreply.github.com> --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: Joseph-Ellaway <69363546+Joseph-Ellaway@users.noreply.github.com> * Linting fix * Abstract gzip and saving in XML->JSON parsers * Fix CompileInterfaceSummaryJSON.parse() to respect compressed mode (#45) * Initial plan * Fix CompileInterfaceSummaryJSON.parse() to respect self.compressed flag Co-authored-by: Joseph-Ellaway <69363546+Joseph-Ellaway@users.noreply.github.com> --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: Joseph-Ellaway <69363546+Joseph-Ellaway@users.noreply.github.com> * Tests fixed, point to compressed int. folder * Tests updated to compress on the fly * Compressed files removed * Compress with Python native approach --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.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
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.
When
--compress_outputis set,ConvertAssemblyXMLToJSONinternally mutates its output path toassemblies.json.gz, butCompileInterfaceSummaryJSONwas still receivingassemblies.json. This causedopen_compressed()to raise aValueErrorat runtime since it requires paths ending in.gzwhencompressed=True.Changes
pisa_utils/run.py: Append.gztopath_assembly_jsonwhencompress_outputis enabled, consistent with the existing pattern already applied topath_output_jsonin the same block:🔒 GitHub Advanced Security automatically protects Copilot coding agent pull requests. You can protect all pull requests by enabling Advanced Security for your repositories. Learn more about Advanced Security.