Fix CompileInterfaceSummaryJSON.parse() to respect compressed mode#45
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Joseph-Ellaway merged 2 commits intonew-mol-key-and-compressionfrom Mar 9, 2026
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Co-authored-by: Joseph-Ellaway <69363546+Joseph-Ellaway@users.noreply.github.com>
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[WIP] WIP address feedback from PR #43 on mol key and compression changes
Fix CompileInterfaceSummaryJSON.parse() to respect compressed mode
Mar 8, 2026
Joseph-Ellaway
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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>
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CompileInterfaceSummaryJSON.parse()ignoredself.compressed, always globbing for*.jsonand reading via plainopen(). In compressed mode, interface files areinterface_*.json.gz, so the method would find nothing or fail to read them.Changes
.json.gzextension whenself.compressed=Trueopen()withopen_compressed()consistent with_load_assembly_json()💡 You can make Copilot smarter by setting up custom instructions, customizing its development environment and configuring Model Context Protocol (MCP) servers. Learn more Copilot coding agent tips in the docs.