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Bump serde_json from 1.0.99 to 1.0.113 #369

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Commits on Apr 21, 2022

  1. various changes (= dj/331) (#455)

    - support enclone visual under Linux
    - update test set list
    - allow enclone VIS CTRLC
    - remove default_system_font from iced requirements
    - stop testing for number of duplicated crates, we have never gotten value out of this
    - stop testing executable size, we have never gotten value out of this
    STATUS: ./test, enclone.test and test_vis pass.
    DJ authored Apr 21, 2022
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  2. bump version

    David Jaffe committed Apr 21, 2022
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  3. various changes (= dj/332) (#456)

    - fix to install script
    - refactor/rename/tweak build_immcantation_inputs, assess_immcantation
    - update Linux debugging instructions
    STATUS: ./test passes.
    DJ authored Apr 21, 2022
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  4. bump version

    David Jaffe committed Apr 21, 2022
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Commits on Apr 22, 2022

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  2. bump version

    David Jaffe committed Apr 22, 2022
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  3. add missing line

    David Jaffe committed Apr 22, 2022
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  4. bump version

    David Jaffe committed Apr 22, 2022
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  5. fix errors in start_release

    David Jaffe committed Apr 22, 2022
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  6. bump version

    David Jaffe committed Apr 22, 2022
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  7. don't use colon in enclone visual saved file names (= dj/334) (#458)

    * don't use colon in enclone visual saved file names
    
    * fix bug
    DJ authored Apr 22, 2022
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  8. bump version

    David Jaffe committed Apr 22, 2022
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Commits on Apr 25, 2022

  1. add to debugging info for enclone visual under Linux

    David Jaffe committed Apr 25, 2022
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Commits on Apr 26, 2022

  1. site changes (= dj/335) (#459)

    - Update landing page to point to bioRxiv preprint.
    - Rev the developers page.
    STATUS: ./test passes.
    DJ authored Apr 26, 2022
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  2. bump version

    David Jaffe committed Apr 26, 2022
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  4. bump version

    David Jaffe committed Apr 26, 2022
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Commits on Apr 29, 2022

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  2. bump version

    David Jaffe committed Apr 29, 2022
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Commits on May 3, 2022

  1. various changes (= dj/339) (#463)

    - Fill in git hash on cellranger page.
    - Switch to a more recent caching mechanism for GitHub Actions, and turn it on for Mac.   Note
      that previously we observed cryptic failures with Mac caching, and this could recur.
    STATUS: ./test passes.
    DJ authored May 3, 2022
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  3. improve error msg, update hdf5, turn on windows build; ./test passes …

    …(= dj/341) (#465)
    DJ authored May 3, 2022
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  4. bump version

    David Jaffe committed May 3, 2022
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Commits on May 4, 2022

  1. bump version

    David Jaffe committed May 4, 2022
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  3. bump version

    David Jaffe committed May 4, 2022
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  5. bump version

    David Jaffe committed May 4, 2022
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  7. bump version

    David Jaffe committed May 4, 2022
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  8. attempt to fix windows compilation problems

    David Jaffe committed May 4, 2022
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  9. bump version

    David Jaffe committed May 4, 2022
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  10. more windows fixes; ./test passes at 143 seconds

    David Jaffe committed May 4, 2022
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  11. bump version

    David Jaffe committed May 4, 2022
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  12. change "cp -a" to "cp -pPR" for windows release

    David Jaffe committed May 4, 2022
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  13. bump version

    David Jaffe committed May 4, 2022
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  14. remove -... arg to cp for windows in release.yaml

    David Jaffe committed May 4, 2022
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  15. bump version

    David Jaffe committed May 4, 2022
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  16. attempt to use bash shell for windows in release.yaml

    David Jaffe committed May 4, 2022
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  17. bump version

    David Jaffe committed May 4, 2022
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  20. bump version

    David Jaffe committed May 4, 2022
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  21. enclone VIS: do not exit on windows machines

    David Jaffe committed May 4, 2022
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  22. bump version

    David Jaffe committed May 4, 2022
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Commits on May 5, 2022

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  2. rustfmt (#472)

    DJ authored May 5, 2022
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  3. bump version

    David Jaffe committed May 5, 2022
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  5. bump version

    David Jaffe committed May 5, 2022
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  6. fix typo in install.sh: println should be printf

    David Jaffe committed May 5, 2022
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Commits on May 6, 2022

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  2. bump version

    David Jaffe committed May 6, 2022
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  3. various changes (= dj/351) (#475)

    - Use home crate to determine home directory.
    - Corrections to assess_clonotyping.
    - Attempt to get get_clipboard_content to work under windows.
    STATUS: ./.test passes.
    DJ authored May 6, 2022
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  4. bump version

    David Jaffe committed May 6, 2022
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  5. attempt to fix compilation error under windows

    David Jaffe committed May 6, 2022
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  6. bump version

    David Jaffe committed May 6, 2022
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Commits on May 7, 2022

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  2. bump version

    David Jaffe committed May 7, 2022
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  4. bump version

    David Jaffe committed May 7, 2022
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  5. fix windows compilation error in last commit

    David Jaffe committed May 7, 2022
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  6. bump version

    David Jaffe committed May 7, 2022
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  7. fold error messages from enclone server

    David Jaffe committed May 7, 2022
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  8. bump version

    David Jaffe committed May 7, 2022
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  9. improve error handling when hdf5 access fails

    David Jaffe committed May 7, 2022
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  10. improve an error message

    David Jaffe committed May 7, 2022
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  11. bump version

    David Jaffe committed May 7, 2022
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  12. attempt to fix windows compilation error

    David Jaffe committed May 7, 2022
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  13. tweak doc about enclone visual

    David Jaffe committed May 7, 2022
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  14. bump version

    David Jaffe committed May 7, 2022
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Commits on May 8, 2022

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  2. bump version

    David Jaffe committed May 8, 2022
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  3. set libz-sys for Windows to try to get hdf5 to work

    David Jaffe committed May 8, 2022
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  4. bump version

    David Jaffe committed May 8, 2022
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  5. fix to last

    David Jaffe committed May 8, 2022
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  6. bump version

    David Jaffe committed May 8, 2022
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  7. attempt to fix problem with hdf5 / Windows

    David Jaffe committed May 8, 2022
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  8. bump version

    David Jaffe committed May 8, 2022
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  9. various changes (= dj/352) (#476)

    - Add a box on the landing pages explaining some weirdnesses in the Mac Terminal application,
      and how to circumvent them.
    - Add caveats to testing on developers page.
    - Make assess_clonotyping accept a broader range of syntax.
    STATUS: ./test passes.
    DJ authored May 8, 2022
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  10. bump version

    David Jaffe committed May 8, 2022
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  11. announce support for windows

    David Jaffe committed May 8, 2022
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  12. add note on cross building

    David Jaffe committed May 8, 2022
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  13. bump version

    David Jaffe committed May 8, 2022
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Commits on May 9, 2022

  1. fix grammar error on windows page

    David Jaffe committed May 9, 2022
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  3. bump version

    David Jaffe committed May 9, 2022
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  4. add ability to generate enclone visual session from command line (= d…

    …j/354) (#478)
    
    STATUS: ./test, enclone.test, and test_vis pass, except for run time on ./test.
    DJ authored May 9, 2022
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  5. bump version

    David Jaffe committed May 9, 2022
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Commits on May 10, 2022

  1. various changes (= dj/355) (#479)

    - Fix bug in handling of blank svg for VIS_DUMP.
    - Always generate summary for VIS_DUMP.
    - Reset cycle count test and ./test wallclock to use values obtained on the standard 10x server.
    STATUS: ./test, enclone.test and test_vis pass.  CI passes.  Also tested that branch compiles and ./test
    runs successfully on Mac/M1 Pro (except for total wallclock, as expected).  Will release and test on 
    Windows and add additional comment if there is a problem.
    DJ authored May 10, 2022
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  2. bump version

    David Jaffe committed May 10, 2022
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Commits on May 17, 2022

  1. update stuff (#480)

    wyattmcdonnell authored May 17, 2022
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  2. update

    wyattmcdonnell committed May 17, 2022
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Commits on May 23, 2022

  1. bump version

    wyattmcdonnell committed May 23, 2022
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Commits on May 31, 2022

  1. Update release_nanny.rs (#482)

    troubleshooting some Jenkins behavior
    wyattmcdonnell authored May 31, 2022
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Commits on Jun 1, 2022

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Commits on Jun 2, 2022

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Commits on Jun 3, 2022

  1. Fix most of the issues identified by clippy. (#2)

    Deny clippy::perf and clippy::style categories, with a couple of
    exceptions carved out:
    
    - result_unit_err probably requires adding a dependency on
      `anyhow` or `thiserror` to fix properly, so leave it alone for now.
    - needless_range_loop there's just too many to fix right now.
      They can have a significant performance impact, so they
      should be fixed eventually but not in this PR.
    - type_complexity and too_many_arguments are both valid
      warnings but also sufficiently major changes that it would
      probably be better to address them in a future PR as well.
    
    Fixed some other issues observed while fixing the clippy lints.
    
    Also update to 2021 edition.
    adam-azarchs authored Jun 3, 2022
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  2. Back out changes to rust-hdf5.

    Yeah, might not work on Windows.  We can address that properly later,
    but for now the important thing is not breaking dependabot for
    downstream users by having multiple sources for hdf5-sys.
    adam-azarchs committed Jun 3, 2022
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Commits on Jun 4, 2022

  1. Bump rust-toolbox (lockfile-only updates).

    This updates the transitive dependency on pprof to 0.7.0 from 0.6.2.
    The upper bound on pprof has increased further than that, but we can't
    update it that far without ending up with other duplicated dependencies,
    which is why this had to be done by hand rather than using dependabot.
    
    This also updates hdf5 to allow a more recent version of parking_lot.
    adam-azarchs committed Jun 4, 2022
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Commits on Jun 6, 2022

  1. Update test.yaml

    updated rust version
    nmmsv10x authored Jun 6, 2022
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  2. bump version

    nmmsv10x committed Jun 6, 2022
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Commits on Jun 7, 2022

  1. Nmmsv/antigen capture (#492)

    * adding Antigen Capture
    
    * added _ag
    
    * fixed a couple of conditions
    
    * added missing suffix
    
    * added print
    nmmsv10x authored Jun 7, 2022
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  2. bump version

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Commits on Jun 8, 2022

  1. dummy commit

    nmmsv10x committed Jun 8, 2022
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  2. bump version

    nmmsv10x committed Jun 8, 2022
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  3. More cleanups.

    Add rerun-if-changed outputs for build.rs scripts so they don't have to
    be rerun every time.
    
    Add include or exclude directives in Cargo.toml to omit unnecessary
    files.
    
    Update .gitignore file.
    
    Add basic vscode default settings.
    
    Correct github workflow to run on main branch rather than master.
    adam-azarchs committed Jun 8, 2022
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Commits on Jun 10, 2022

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Commits on Jun 29, 2022

  1. Fix range loops and unnecessary copies.

    In many places, use &[u8] instead of Vec<u8> and &str instead of String,
    to avoid unnecssary copying.
    
    Fix most of the clippy::needless_range_loop warnings, except for those
    in enclone_args.
    adam-azarchs committed Jun 29, 2022
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Commits on Jul 16, 2022

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Commits on Jul 20, 2022

  1. Always install rust toolchain

    Copy-pasta resulted in a conditional which shouldn't have been.
    adam-azarchs authored Jul 20, 2022
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  4. Fix clippy::format_push_string errors.

    Update rust to 1.62.
    adam-azarchs committed Jul 20, 2022
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  7. Fix typo in checking for required args.

    panic if !found, not found.
    adam-azarchs committed Jul 20, 2022
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  8. Fix typo in define_mat. (#44)

    Also, remove some unnecessary range loops and to_string().
    adam-azarchs authored Jul 20, 2022
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Commits on Jul 21, 2022

  1. Enumerate before skip, not after.

    Otherwise indicies get messed up.
    adam-azarchs committed Jul 21, 2022
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Commits on Jul 30, 2022

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Commits on Jul 31, 2022

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Commits on Aug 5, 2022

  1. Update Chrono

    Avoids security warning
    evolvedmicrobe committed Aug 5, 2022
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  2. Remove Chrono

    evolvedmicrobe committed Aug 5, 2022
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Commits on Aug 20, 2022

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Commits on Aug 23, 2022

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Commits on Aug 31, 2022

  1. Bump dependency versions.

    Most importantly lz4-sys, which is otherwise resulting in a security
    advisorty blocking PRs.
    adam-azarchs committed Aug 31, 2022
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Commits on Sep 7, 2022

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Commits on Oct 7, 2022

  1. added a check back from CR6 (#126)

    * added a check back from CR6
    
    * format
    nmmsv10x authored Oct 7, 2022
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Commits on Oct 31, 2022

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Commits on Nov 24, 2022

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  2. Further updates to rust 1.65.

    Also update several github actions.
    adam-azarchs committed Nov 24, 2022
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Commits on Dec 9, 2022

  1. Remove obsolete action arguments

    dtolnay/rust-toolchain doesn't have a `default` argument.
    
    10XGenomics/clippy-check doesn't have a token argument.
    
    Also, compute the fetch depth that's actually required,
    rather than using 100 unconditionally.
    adam-azarchs committed Dec 9, 2022
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Commits on Dec 10, 2022

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Commits on Dec 14, 2022

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Commits on Dec 27, 2022

  1. Update CI rust to 1.66

    Run cargo clippy --fix.
    adam-azarchs committed Dec 27, 2022
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Commits on Mar 28, 2023

  1. build: bump rust to 1.68, fix lints (#213)

    Also bump cpufeatures up from yanked version.
    adam-azarchs authored Mar 28, 2023
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Commits on Apr 4, 2023

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Commits on Apr 5, 2023

  1. Update rust-toolbox (#232)

    Co-authored-by: Shamoni Maheshwari <shamoni.maheshwari@bespin1.fuzzplex.com>
    shamoni and Shamoni Maheshwari authored Apr 5, 2023
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Commits on Apr 7, 2023

  1. Update rust-toolbox dependency (#233)

    Co-authored-by: Shamoni Maheshwari <shamoni.maheshwari@bespin1.fuzzplex.com>
    shamoni and Shamoni Maheshwari authored Apr 7, 2023
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Commits on Apr 21, 2023

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Commits on May 2, 2023

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  4. build: get prost-build out of critical path (#266)

    Move generating of protobuf code into a separate crate so that
    prost-build doesn't need to be compiled before we can compile
    enclone_proto, and transitive dependents don't need it at all.
    A unit test enforces that the file be up to date with whatever
    the current version of prost-build creates.
    
    This becomes especially important in newer versions of prost-build,
    which depend on having protoc available externally in the environment;
    this way, downstream crates do not need to have protoc installed.
    adam-azarchs authored May 2, 2023
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Commits on May 3, 2023

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Commits on Jun 20, 2023

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Commits on Jun 23, 2023

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  6. ci(rust): bump CI rust version to 1.71.0

    Auto-fix some new warnings.
    adam-azarchs committed Jul 31, 2023
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Commits on Aug 24, 2023

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Commits on Sep 11, 2023

  1. Update rust-toolbox (#333)

    Co-authored-by: Shamoni Maheshwari <shamoni.maheshwari@bespin1.fuzzplex.com>
    shamoni and Shamoni Maheshwari authored Sep 11, 2023
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Commits on Nov 6, 2023

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Commits on Jan 18, 2024

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Commits on Jan 25, 2024

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Commits on Jan 29, 2024

  1. Bump serde_json from 1.0.99 to 1.0.113

    Bumps [serde_json](https://github.com/serde-rs/json) from 1.0.99 to 1.0.113.
    - [Release notes](https://github.com/serde-rs/json/releases)
    - [Commits](serde-rs/json@v1.0.99...v1.0.113)
    
    ---
    updated-dependencies:
    - dependency-name: serde_json
      dependency-type: direct:production
      update-type: version-update:semver-patch
    ...
    
    Signed-off-by: dependabot[bot] <support@github.com>
    dependabot[bot] authored Jan 29, 2024
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