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Bump rustix from 0.36.7 to 0.36.17 #349
Commits on Apr 19, 2022
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Commits on Apr 21, 2022
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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.
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various changes (= dj/332) (#456)
- fix to install script - refactor/rename/tweak build_immcantation_inputs, assess_immcantation - update Linux debugging instructions STATUS: ./test passes.
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Commits on Apr 22, 2022
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attempt to make release work for windows (#457)
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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
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Commits on Apr 25, 2022
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add to debugging info for enclone visual under Linux
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Commits on Apr 26, 2022
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site changes (= dj/335) (#459)
- Update landing page to point to bioRxiv preprint. - Rev the developers page. STATUS: ./test passes.
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delete Windows support for now; saving as backup (#460)
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Commits on Apr 29, 2022
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fix assertion when no json annotations and no vdj_reference; ./test p…
…asses (#461)
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move some utilities (= dj/338); ./test passes (#462)
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Commits on May 3, 2022
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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.
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remove --release from test.yaml in GitHub Actions (#464)
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improve error msg, update hdf5, turn on windows build; ./test passes …
…(= dj/341) (#465)
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possible fix for hdf5 specification in Cargo.toml; ./test passes (= d…
…j/342) (#466)
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attempt to fix windows compilation errors (= dj/343) (#467)
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fix some windows compilation errors (= dj/344) (#468)
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fix yet more windows compilation errors (= dj/345) (#469)
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attempt to fix windows compilation problems
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more windows fixes; ./test passes at 143 seconds
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change "cp -a" to "cp -pPR" for windows release
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remove -... arg to cp for windows in release.yaml
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attempt to use bash shell for windows in release.yaml
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add .exe: asset_path: <elided> .exe AND asset_name: enclone_windows.exe
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enclone VIS: do not exit on windows machines
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Commits on May 5, 2022
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attempt to solve hdf5 problem (= dj/346) (#471)
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a couple small doc changes; ./test passes (= dj/348) (#473)
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fix typo in install.sh: println should be printf
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Commits on May 6, 2022
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implement get_clipboard_content for Linux (./test passes) (= dj/350) …
…(#474)
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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.
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attempt to fix compilation error under windows
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Commits on May 7, 2022
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attempt to make copy_png_bytes_to_clipboard work under windows
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attempt to make copy_bytes_to_clipboard work under windows
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fix windows compilation error in last commit
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fold error messages from enclone server
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improve error handling when hdf5 access fails
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attempt to fix windows compilation error
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tweak doc about enclone visual
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Commits on May 8, 2022
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experiment: let's try aldanor/hdf5-rust:master for windows
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set libz-sys for Windows to try to get hdf5 to work
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attempt to fix problem with hdf5 / Windows
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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.
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Commits on May 9, 2022
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fix grammar error on windows page
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do not put colons in enclone visual session file names (= dj/353) (#477)
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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.
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Commits on May 10, 2022
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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.
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Commits on May 31, 2022
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Update release_nanny.rs (#482)
troubleshooting some Jenkins behavior
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Commits on Jun 3, 2022
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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.
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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.
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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.
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Commits on Jun 7, 2022
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* adding Antigen Capture * added _ag * fixed a couple of conditions * added missing suffix * added print
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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.
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Commits on Jun 29, 2022
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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.
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Commits on Jul 20, 2022
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Copy-pasta resulted in a conditional which shouldn't have been.
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Fix typo in checking for required args.
panic if !found, not found.
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Also, remove some unnecessary range loops and to_string().
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Commits on Jul 21, 2022
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Enumerate before skip, not after.
Otherwise indicies get messed up.
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Commits on Aug 31, 2022
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Most importantly lz4-sys, which is otherwise resulting in a security advisorty blocking PRs.
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Commits on Oct 7, 2022
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added a check back from CR6 (#126)
* added a check back from CR6 * format
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Also update several github actions.
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Commits on Dec 9, 2022
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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.
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build: bump rust to 1.68, fix lints (#213)
Also bump cpufeatures up from yanked version.
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Co-authored-by: Shamoni Maheshwari <shamoni.maheshwari@bespin1.fuzzplex.com>
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Update rust-toolbox dependency (#233)
Co-authored-by: Shamoni Maheshwari <shamoni.maheshwari@bespin1.fuzzplex.com>
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enclone_print: Prevent a panic in print_clonotypes (#267)
Jira: CSI-1903
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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.
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ci(rust): bump CI rust version to 1.71.0
Auto-fix some new warnings.
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Co-authored-by: Shamoni Maheshwari <shamoni.maheshwari@bespin1.fuzzplex.com>
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Bump rustix from 0.36.7 to 0.36.17
Bumps [rustix](https://github.com/bytecodealliance/rustix) from 0.36.7 to 0.36.17. - [Release notes](https://github.com/bytecodealliance/rustix/releases) - [Commits](bytecodealliance/rustix@v0.36.7...v0.36.17) --- updated-dependencies: - dependency-name: rustix dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com>
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