MRG: update JOSS paper per pyopensci review #2964
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## latest #2964 +/- ##
=======================================
Coverage 86.62% 86.62%
=======================================
Files 135 135
Lines 15278 15278
Branches 2618 2618
=======================================
Hits 13235 13235
Misses 1743 1743
Partials 300 300
Flags with carried forward coverage won't be shown. Click here to find out more. ☔ View full report in Codecov by Sentry. |
|
looking good! |
bluegenes
changed the title
ctb
approved these changes
Feb 2, 2024
ctb
added a commit
that referenced
this pull request
Feb 10, 2024
release notes: https://hackmd.io/SCoVcWS1RhCH-ndQNWF-1A?view # sourmash release v4.8.6 - release notes Minor new features: * re-establish `tax` gather reading flexibility (#2986) * update JOSS paper per pyopensci review (#2964) * Clean up and refactor `KmerMinHash::merge` in core (#2973) * add label output & input options to `compare` and `plot`, for better customization (#2598) * add utilities for using ictv taxonomic ranks with `sourmash tax` (#2608) Bug fixes: * Fix `tax metagenome` to work on gather output created with `--estimate-ani-ci` (#2952) * fix gather memory usage issue by not accumulating `GatherResult` (#2962) * update the CLI docs and help for `search --containment` and `prefetch` (#2971) Documentation updates: * update tutorial to remove bioconda & use sourmash-minimal (#2972) * update readme with maintainers & sourmash comparison info (#2965) * add branchwater reference; make FAQ more visible (#2984) * update FAQ answer on k-mer size (#2899) * update README with repostatus and pyver badges, and Windows support (#2928) * add full column descriptions for `gather` and `prefetch` output (#2954) * add scaled FAQ, adjust ksize answer (#2921) * minor refactoring of gather code, small doc updates (#2953) * Add threshold-bp and scaled relationship to faqs (#2930) Developer updates: * nix updates for pyopensci review (#2975) * add scaled selection to manifest; add helper functions for collection and sig/sketch usage (#2948) * Pre-commit updates (#2427) * fix upload wheel CI (#2974) * release core; bump rust core version to r0.12.1 (#2988) * CI: macos deployment target and maturin updates (#2879) * MRG: bump version to 4.8.6-dev, post-release (#2877) * fix benchmark code & a few other small issues from pyOpenSci review (#2920) * fix uploading of wheels after upload-artifact upgrade. (#2887) * in core, enable downsample within select (#2931) Dependabot updates: * Bump pypa/cibuildwheel from 2.16.4 to 2.16.5 (#2981) * Bump tempfile from 3.9.0 to 3.10.0 (#2979) * Bump rkyv from 0.7.43 to 0.7.44 (#2978) * Bump actions/cache from 3 to 4 (#2933) * Bump actions/download-artifact from 3 to 4 (#2884) * Bump actions/upload-artifact from 3 to 4 (#2883) * Bump cachix/cachix-action from 13 to 14 (#2926) * Bump cachix/install-nix-action from 24 to 25 (#2927) * Bump chrono from 0.4.31 to 0.4.33 (#2957) * Bump getrandom from 0.2.11 to 0.2.12 (#2924) * Bump histogram from 0.8.3 to 0.8.4 (#2923) * Bump histogram from 0.8.4 to 0.9.0 (#2935) * Bump jinja2 from 3.1.2 to 3.1.3 (#2922) * Bump memmap2 from 0.9.0 to 0.9.2 (#2882) * Bump memmap2 from 0.9.2 to 0.9.3 (#2889) * Bump memmap2 from 0.9.3 to 0.9.4 (#2958) * Bump mymindstorm/setup-emsdk from 13 to 14 (#2934) * Bump ouroboros from 0.18.1 to 0.18.2 (#2894) * Bump ouroboros from 0.18.2 to 0.18.3 (#2936) * Bump pypa/cibuildwheel from 2.16.2 to 2.16.4 (#2960) * Bump rayon from 1.8.0 to 1.8.1 (#2937) * Bump rkyv from 0.7.42 to 0.7.43 (#2880) * Bump serde from 1.0.194 to 1.0.195 (#2901) * Bump serde from 1.0.195 to 1.0.196 (#2956) * Bump serde_json from 1.0.108 to 1.0.110 (#2896) * Bump serde_json from 1.0.110 to 1.0.111 (#2902) * Bump serde_json from 1.0.111 to 1.0.113 (#2955) * Bump shlex from 1.1.0 to 1.3.0 (#2940) * Bump supercharge/redis-github-action from 1.7.0 to 1.8.0 (#2885) * Bump tempfile from 3.8.1 to 3.9.0 (#2893) * Bump thiserror from 1.0.50 to 1.0.51 (#2881) * Bump thiserror from 1.0.51 to 1.0.56 (#2897) * Bump wasm-bindgen from 0.2.89 to 0.2.90 (#2925) * Bump wasm-bindgen-test from 0.3.39 to 0.3.40 (#2938) * Bump web-sys from 0.3.66 to 0.3.67 (#2939) * Update pytest requirement from <7.5.0,>=6.2.4 to >=6.2.4,<8.1.0 (#2959)
33 tasks
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
fixes #2912
Note, citations are >450 if we include all papers (364 with just original JOSS + F100).