Open document directly from .sky.zip without extracting if necessary files are uncompressed - #4426

Draft

nickshulman wants to merge 46 commits into

Skyline/work/20260715_open_doc_from_zip

Commits on Jul 15, 2026

Upgraded System.Data.SQLite to 1.0.119 tree-wide

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49fe0d2
Added zip random-access foundation and the open-from-zip safety gate

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b1cc598
Added AreEntriesStored open-in-place detection to RandomAccessZipFile

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f3af2e3
Stored .skyd and .blib uncompressed when sharing a document

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7411a66
Added FilePath, a zip-aware path type for files inside a .zip

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7a9d48d
Read the .skyd from an in-place .sky.zip via FilePath

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7ab23f0
Read the .sky through FilePath so it can live in an in-place .sky.zip

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9b899d5
Added the zipvfs SQLite extension and the open-in-place criterion

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625acb8
Opened .blib spectral libraries in place from a .sky.zip via the zipvfs extension

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cf3f35d
Updated the SQLite interop to 1.0.119 inside vendor_api_ABI.7z

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129d0e3

Commits on Jul 16, 2026

Opened .sky.zip documents in place through the load pipeline

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d630099
Added a functional test for opening a document in place from a .sky.zip

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ac47b07
Prompted to extract when saving a document opened in place from a .sky.zip

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0f95b6b
Built zipvfs_ext.dll from source instead of committing a prebuilt binary

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5104023
Merge branch 'master' of https://github.com/ProteoWizard/pwiz into Skyline/work/20260715_open_doc_from_zip
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98bad3a
Made the byte-range VFS extension generic instead of zip-specific

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c3c7bc1
Renamed the byte-range VFS extension to slicevfs

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04357a5
Addressed Copilot review feedback on the open-from-zip PR

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43cdd0b
Detected the .zip container extension case-insensitively

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f526fa8
Reported "Storing" vs "Compressing" and split the open-in-place extensions

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cbcc3a6
Moved FilePath and the zip byte-range VFS into the Common project

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ae556f0
Opened a background proteome (.protdb) in place from a .sky.zip

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d71417f
Extracted a .sky.zip without prompting when its files must be on disk

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676f788
Closed streams which are opened for a document that is no longer current

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8565c05
Closed the streams of a document replaced in a MemoryDocumentContainer

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8f29f38
Reverted the System.Data.SQLite 1.0.119 upgrade

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b75d0b0

Commits on Jul 17, 2026

Read and re-shared a big .sky.zip without holding it in memory

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86a65d2
Renamed ByteRangeStream to SliceStream

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f8889c4
Checked whether a .sky.zip can be opened in place in SrmDocumentSharing

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d5a0677
Simplified how CanOpenInPlace classifies the entries of a .sky.zip

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0767cd7
Merge remote-tracking branch 'origin/master' into Skyline/work/20260715_open_doc_from_zip
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0358477
Fix code inspection. Revert multithreading in StructSerializer.
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61ac1f3

Commits on Jul 18, 2026

Fix code inspection
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e0b5fc7
Merge branch 'master' of https://github.com/ProteoWizard/pwiz into Skyline/work/20260715_open_doc_from_zip
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c75dc4f
Fix line endings
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b504960

Commits on Jul 22, 2026

Commits on Jul 24, 2026

Commits on Aug 8, 2026

Merge branch 'master' into Skyline/work/20260715_open_doc_from_zip
nickshulman
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4f37ae0

Commits on Aug 17, 2026

Merge branch 'master' into Skyline/work/20260715_open_doc_from_zip
nickshulman
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24c6356

Commits on Aug 22, 2026

Merge branch 'master' into Skyline/work/20260715_open_doc_from_zip
nickshulman
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3aff623