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Feat: on-disk RevIndex based on RocksDB #2230

Merged
merged 30 commits into from
Dec 1, 2023
Merged

Feat: on-disk RevIndex based on RocksDB #2230

merged 30 commits into from
Dec 1, 2023

Commits on Sep 20, 2023

  1. rkyv support in signature

    try to skip md5sum
    
    derive typed builder for GatherResult
    
    expose md5
    
    start moving mastiff
    
    remove unused bigsi and sbt indices
    
    Expose iterator methods for Signature
    
    remove unused function
    
    preparing for MinHashOps
    
    Bump version, there will be many breaking changes...
    
    more splits
    
    default to large minhash, expose frozen
    
    use enum for MinHash thru FFI
    
    bug fixes and cleanup
    
    add c++ stdlib package for mamba
    
    fix finch feature
    
    try out roaring
    
    Add back check command
    
    initial update impl
    
    add semver check for rust
    
    bump once_cell
    
    fix rust ci
    
    start bringing #1943
    
    more selection
    
    more picklist
    
    use dashmap in mem_revindex
    
    Revert "use dashmap in mem_revindex"
    
    This reverts commit 22727b7091dee2dbafd10ce707578c5085aa6cfc.
    
    bump rocksdb to 0.19
    
    bump rocksdb to 0.20, bump MSRV to 1.60
    
    update deps
    
    add cargo deny config
    
    use cibuildwheel configs in pyproject.toml
    
    flake cleanup
    
    fix cargo.lock
    
    tox updates
    
    don't worry with in-mem sigs for now
    
    rename mastiff to branchwater
    
    add revindex test
    
    wip collection
    
    clippy fixes
    
    start using camino for paths
    
    cargo fmt
    
    Implement MemStorage and from_paths and from_sigs
    
    cleanup
    
    Replace DatasetID with Idx
    
    Use 32-bits Idx, instead of 64
    
    use enum_dispatch to avoid repeating code
    
    implement selection more widely
    
    working with protein in tests...
    
    add semver-checks
    
    save/load collection from rocksdb
    luizirber committed Sep 20, 2023
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  2. reorg select

    luizirber committed Sep 20, 2023
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  4. bring back update

    luizirber committed Sep 20, 2023
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Commits on Sep 27, 2023

  1. clean up check

    luizirber committed Sep 27, 2023
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Commits on Sep 29, 2023

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Commits on Sep 30, 2023

  1. derive clone for selection

    luizirber committed Sep 30, 2023
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Commits on Oct 9, 2023

  1. Deps: chrono version pin (#2798)

    To install sourmash from mastiff branch in pyo3-branchwater, I need to
    bump chrono back to 0.4.28 (from 0.4.31) to avoid incompatibilities with
    `piz`.
    bluegenes committed Oct 9, 2023
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  2. save version in DB

    luizirber committed Oct 9, 2023
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Commits on Oct 18, 2023

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Commits on Oct 30, 2023

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Commits on Nov 1, 2023

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Commits on Nov 11, 2023

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Commits on Nov 16, 2023

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Commits on Nov 22, 2023

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  2. No dep on bytecount

    luizirber committed Nov 22, 2023
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Commits on Nov 23, 2023

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  2. more storage tests

    luizirber committed Nov 23, 2023
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Commits on Nov 25, 2023

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Commits on Nov 26, 2023

  1. Update rust changelog

    luizirber committed Nov 26, 2023
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Commits on Dec 1, 2023

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