sourmash v4 - v4.9.4

Major new features:

• start writing v4->v5 migration docs (#3721)
• adjust warnings around tax abund and provide v5 upgrades to tax metagenome (#3711)

Minor new features:

• try setting up --v4 and --v5 behavior differences for sig check (#3072)
• update sig manifest default rebuilding behavior for v5. (#3074)
• handle (ignore) empty taxids for bioboxes format (#3748)
• improve summary_csv for lingroups (#3758)

Cleanup and documentation updates:

• use auto-generated database list (#3754)

Developer updates:

• CI: fix dependabot config syntax, and clippy beta lints (#3762)
• CI: update to cibuildwheel 3.1.1 (#3738)
• ci: group dependabot updates by language (#3749)
• Remove docutils dep (#3769)
• bump version to 4.9.4-dev (#3715)
• disable WebAssembly builds, for now (#3724)

Dependabot updates:

• Build(ci): Bump actions/download-artifact from 4 to 5 (#3766)
• Build(deps): Bump DeterminateSystems/nix-installer-action from 17 to 18 (#3727)
• Build(deps): Bump DeterminateSystems/nix-installer-action from 18 to 19 (#3746)
• Build(deps): Bump criterion from 0.6.0 to 0.7.0 (#3741)
• Build(deps): Bump md5 from 0.7.0 to 0.8.0 (#3719)
• Build(deps): Bump memmap2 from 0.9.5 to 0.9.7 (#3732)
• Build(deps): Bump prefix-dev/setup-pixi from 0.8.10 to 0.8.11 (#3733)
• Build(deps): Bump prefix-dev/setup-pixi from 0.8.11 to 0.8.14 (#3747)
• Build(deps): Bump rand from 0.9.1 to 0.9.2 (#3743)
• Build(deps): Bump serde_json from 1.0.140 to 1.0.141 (#3742)
• [pre-commit.ci] pre-commit autoupdate (#3718)
• [pre-commit.ci] pre-commit autoupdate (#3725)
• [pre-commit.ci] pre-commit autoupdate (#3731)
• [pre-commit.ci] pre-commit autoupdate (#3737)
• [pre-commit.ci] pre-commit autoupdate (#3740)
• [pre-commit.ci] pre-commit autoupdate (#3756)

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] 5 months ago

sourmash v4 - v4.9.3

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] 6 months ago

sourmash v4 - v4.9.2

This is a patchfix to v4.9.1 (https://github.com/sourmash-bio/sourmash/pull/3665) to deal with a botched source code release. Below are the updates since v4.9.0.

Minor new features:

• add cANI to sig overlap (#3644)

Bug fixes:

• make RevIndex.len() and RevIndex.signatures() use picklist, if set (#3647)

Cleanup and documentation updates:

• add rocksdb HOWTO (#3648)

Developer updates:

• try fixing inline variables in rust println! (#3640)

Dependabot updates:

• Build(deps): Update cachetools requirement from <6,>=4 to >=4,<7 (#3660)
• [pre-commit.ci] pre-commit autoupdate (#3659)
• Build(deps): Bump criterion from 0.5.1 to 0.6.0 (#3655)
• [pre-commit.ci] pre-commit autoupdate (#3654)
• Build(deps): Bump tempfile from 3.19.1 to 3.20.0 (#3639)
• [pre-commit.ci] pre-commit autoupdate (#3638)

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] 7 months ago

sourmash v4 - v4.9.1

Minor new features:

• add cANI to sig overlap (#3644)

Bug fixes:

• make RevIndex.len() and RevIndex.signatures() use picklist, if set (#3647)

Cleanup and documentation updates:

• add rocksdb HOWTO (#3648)

Developer updates:

• try fixing inline variables in rust println! (#3640)

Dependabot updates:

• Build(deps): Update cachetools requirement from <6,>=4 to >=4,<7 (#3660)
• [pre-commit.ci] pre-commit autoupdate (#3659)
• Build(deps): Bump criterion from 0.5.1 to 0.6.0 (#3655)
• [pre-commit.ci] pre-commit autoupdate (#3654)
• Build(deps): Bump tempfile from 3.19.1 to 3.20.0 (#3639)
• [pre-commit.ci] pre-commit autoupdate (#3638)

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] 7 months ago

sourmash v4 - v4.9.0

This release adds two significant feature sets to sourmash, without introducing any breaking changes.

First, sourmash now fully supports fast, low-memory disk-based inverted indexes based on RocksDB. This functionality has been part of the branchwater plugin for a while, but it is now accessible via the sourmash command line and Python API.

Second, we have added skip-mer sketching to sourmash, joining DNA, protein, dayhoff, and hp encodings. Skip-mers allow more mismatches than DNA k-mers and can be useful when comparing fast-evolving sequences such as virus and phage genomes.

Documentation for the RocksDB indexes and skip-mer encodings is available in the command-line docs.

Major new features:

• Fully support fast, low-memory RocksDB indexes in Python (#3545)
• Fully support skip-mers at the Python level; provide documentation (#3627)
• Remove support for python 3.10 (#3606)

Cleanup and documentation updates:

• add default to add_scaled_arg in Python CLI utils (#3609)
• use match/case in sourmash index implementation (#3604)
• use single quotes inside sqlite statements (#3556)

Developer updates:

• implement manifest retrieval from Rust via FFI for RevIndex (#3630)
• make the RocksDB handle directly accessible to external code (#3468)
• fix linear gather in Rust (#3605)
• fix beta clippy errors (#3548)
• fix deprecations (#3613)
• update Makefile with 'offline', 'wheel' (#3579)
• update ubuntu image version for CI (#3623)
• Minhash deserialize hashfunction errorhandling (#3560)

Automated updates:

• Bump DeterminateSystems/nix-installer-action from 16 to 17 (#3626)
• Bump getset from 0.1.4 to 0.1.5 (#3567)
• Bump histogram from 0.11.2 to 0.11.3 (#3574)
• Bump log from 0.4.25 to 0.4.26 (#3549)
• Bump log from 0.4.26 to 0.4.27 (#3587)
• Bump needletail from 0.6.1 to 0.6.3 (#3553)
• Bump prefix-dev/setup-pixi from 0.8.1 to 0.8.2 (#3538)
• Bump prefix-dev/setup-pixi from 0.8.2 to 0.8.3 (#3551)
• Bump prefix-dev/setup-pixi from 0.8.3 to 0.8.4 (#3602)
• Bump prefix-dev/setup-pixi from 0.8.4 to 0.8.7 (#3616)
• Bump prefix-dev/setup-pixi from 0.8.7 to 0.8.8 (#3621)
• Bump pypa/cibuildwheel from 2.22.0 to 2.23.0 (#3564)
• Bump pypa/cibuildwheel from 2.23.0 to 2.23.1 (#3581)
• Bump pypa/cibuildwheel from 2.23.1 to 2.23.2 (#3603)
• Bump pypa/cibuildwheel from 2.23.2 to 2.23.3 (#3625)
• Bump rand from 0.9.0 to 0.9.1 (#3620)
• Bump roaring from 0.10.10 to 0.10.12 (#3608)
• Bump serde from 1.0.217 to 1.0.218 (#3550)
• Bump serde from 1.0.218 to 1.0.219 (#3576)
• Bump serde_json from 1.0.138 to 1.0.139 (#3552)
• Bump serde_json from 1.0.139 to 1.0.140 (#3566)
• Bump tempfile from 3.16.0 to 3.17.1 (#3539)
• Bump tempfile from 3.17.1 to 3.18.0 (#3575)
• Bump tempfile from 3.18.0 to 3.19.0 (#3582)
• Bump tempfile from 3.19.0 to 3.19.1 (#3588)
• Bump thiserror from 2.0.11 to 2.0.12 (#3565)
• pre-commit autoupdate (#3547)
• pre-commit autoupdate (#3563)
• pre-commit autoupdate (#3573)
• pre-commit autoupdate (#3580)
• pre-commit autoupdate (#3586)
• pre-commit autoupdate (#3607)
• pre-commit autoupdate (#3615)
• pre-commit autoupdate (#3619)
• pre-commit autoupdate (#3624)
• pre-commit autoupdate (#3633)

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] 8 months ago

sourmash v4 - v4.8.14

Developer updates:

• 4.8.14 release branch (#3493)

Dependabot updates:

• Bump serde_json from 1.0.134 to 1.0.135 (#3490)
• Bump roaring from 0.10.9 to 0.10.10 (#3489)
• Bump thiserror from 2.0.9 to 2.0.11 (#3488)
• Bump ouroboros from 0.18.4 to 0.18.5 (#3491)
• [pre-commit.ci] pre-commit autoupdate (#3492)

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] 12 months ago

sourmash v4 - v4.8.13

NOTE: This release adds basic support for skipmers, but they are not yet fully supported.

Minor new features:

• add genbank plant db to docs (#3429)
• add skipmer capacity to sourmash python layer via ffi (#3446)
• add skipmers; switch to reading frame approach for translation, skipmers (#3395)
• additional moltype specification needed for sig downsample with skipmers (#3457)
• update with misc animal genomes (#3422)

Cleanup and documentation updates:

• add comment about semver and column headings (#3433)

Developer updates:

• Deps: update to rocksdb 0.23 (#3456)
• Refactor: Use towriter/fromreader across the codebase (#3443)
• adjust Signature::name() to return Option<String> instead of filename() and md5sum() (#3434)
• bump version to 4.8.13-dev (#3474)
• fix comment in setnum_scaled (#3451)
• propagate zipfile errors (#3431)
• update rust CHANGELOG in preparation for r0.18.0 (#3450)
• CI: github actions updates (#3476)

Dependabot updates:

• Bump itertools from 0.13.0 to 0.14.0 (#3471)
• Bump needletail from 0.6.0 to 0.6.1 (#3427)
• Bump proptest from 1.5.0 to 1.6.0 (#3437)
• Bump roaring from 0.10.7 to 0.10.8 (#3423)
• Bump roaring from 0.10.8 to 0.10.9 (#3438)
• Bump serde from 1.0.215 to 1.0.216 (#3436)
• Bump serde from 1.0.216 to 1.0.217 (#3464)
• Bump serde_json from 1.0.133 to 1.0.134 (#3453)
• Bump statrs from 0.17.1 to 0.18.0 (#3426)
• Bump tempfile from 3.14.0 to 3.15.0 (#3472)
• Bump thiserror from 2.0.3 to 2.0.6 (#3425)
• Bump thiserror from 2.0.6 to 2.0.7 (#3435)
• Bump thiserror from 2.0.7 to 2.0.8 (#3448)
• Bump thiserror from 2.0.8 to 2.0.9 (#3452)
• Update maturin requirement from <1.8.0,>=1 to >=1,<1.9.0 (#3465)
• [pre-commit.ci] pre-commit autoupdate (#3428)
• [pre-commit.ci] pre-commit autoupdate (#3439)
• [pre-commit.ci] pre-commit autoupdate (#3454)
• [pre-commit.ci] pre-commit autoupdate (#3473)

Scientific Software - Peer-reviewed - Python
Published by ctb 12 months ago

sourmash v4 - v4.8.12

Developer updates:

• build: move ORCID to metadata in pyproject.toml, fix pixi (#3416)
• build: simplify Rust release (#3392)
• fix: Avoid re-calculating md5sum on clone and conversion to KmerMinHashBTree (#3385)
• r0.15.1 release (#3304)
• update sourmash core to r0.17.0 (#3381)
• Added union method to HLL (#3293)
• Build: upgrade to newer maturin (#3366)
• CI: use supported ubuntu for codspeed (#3350)
• Fix clippy lints from 1.83 beta (#3357)
• Implement resumability for revindex (#3275)
• add Manifest::intersect_manifest to Rust core (#3305)
• bump sourmash core to r0.17.2 (#3399)
• change sig_from_record to use scaled from Record to downsample (#3387)
• derive Hash for HashFunctions (#3344)
• enforce a single scaled on a CollectionSet (#3397)
• fix formatting from #3306 (#3307)
• have ruff ignore ipynb so as to avoid triggering an error during CI (#3325)
• improve downsampling behavior on KmerMinHash; fix RevIndex::gather bug around scaled. (#3342)
• panic when FSStorage::load_sig encounters more than one Signature in a JSON record (#3333)
• propagate error from RocksDB::open on bad directory (#3306)
• refactor calculate_gather_stats to disallow repeated downsampling (#3352)
• release core r0.17.1 (#3388)
• release sourmash rust core r0.16.0 (#3356)
• standardize on u32 for scaled, and introduce ScaledType (#3364)
• update plugin documentation for users (#3286)
• update sourmash core to r0.15.2 (#3338)
• when lingroups are provided, use them for csv_summary (#3311)
• Misc Rust updates to core (#3297)
• Resolve issue for high precision MLE estimation (#3296)

Dependabot and pre-commit CI updates:

• Bump DeterminateSystems/magic-nix-cache-action from 7 to 8 (#3319)
• Bump DeterminateSystems/nix-installer-action from 13 to 14 (#3320)
• Bump DeterminateSystems/nix-installer-action from 14 to 15 (#3374)
• Bump DeterminateSystems/nix-installer-action from 15 to 16 (#3401)
• Bump camino from 1.1.7 to 1.1.9 (#3301)
• Bump codspeed-criterion-compat from 2.6.0 to 2.7.2 (#3324)
• Bump conda-incubator/setup-miniconda from 3.0.4 to 3.1.0 (#3373)
• Bump csv from 1.3.0 to 1.3.1 (#3390)
• Bump getset from 0.1.2 to 0.1.3 (#3328)
• Bump histogram from 0.11.0 to 0.11.1 (#3377)
• Bump js-sys from 0.3.72 to 0.3.74 (#3412)
• Bump memmap2 from 0.9.4 to 0.9.5 (#3326)
• Bump myst-parser from 3.0.1 to 4.0.0 (#3277)
• Bump needletail from 0.5.1 to 0.6.0 (#3376)
• Bump pypa/cibuildwheel from 2.19.2 to 2.20.0 (#3278)
• Bump pypa/cibuildwheel from 2.20.0 to 2.21.1 (#3332)
• Bump pypa/cibuildwheel from 2.21.1 to 2.21.2 (#3345)
• Bump pypa/cibuildwheel from 2.21.2 to 2.21.3 (#3353)
• Bump pypa/cibuildwheel from 2.21.3 to 2.22.0 (#3408)
• Bump roaring from 0.10.6 to 0.10.7 (#3413)
• Bump serde from 1.0.204 to 1.0.207 (#3289)
• Bump serde from 1.0.207 to 1.0.208 (#3298)
• Bump serde from 1.0.208 to 1.0.209 (#3310)
• Bump serde from 1.0.209 to 1.0.210 (#3318)
• Bump serde from 1.0.210 to 1.0.214 (#3368)
• Bump serde from 1.0.214 to 1.0.215 (#3403)
• Bump serde_json from 1.0.120 to 1.0.121 (#3267)
• Bump serde_json from 1.0.121 to 1.0.122 (#3280)
• Bump serde_json from 1.0.122 to 1.0.124 (#3288)
• Bump serde_json from 1.0.124 to 1.0.125 (#3302)
• Bump serde_json from 1.0.125 to 1.0.127 (#3309)
• Bump serde_json from 1.0.127 to 1.0.128 (#3316)
• Bump serde_json from 1.0.128 to 1.0.132 (#3358)
• Bump serde_json from 1.0.132 to 1.0.133 (#3402)
• Bump sphinx-design from 0.5.0 to 0.6.0 (#3268)
• Bump sphinx-design from 0.6.0 to 0.6.1 (#3276)
• Bump tempfile from 3.10.1 to 3.11.0 (#3279)
• Bump tempfile from 3.11.0 to 3.12.0 (#3287)
• Bump tempfile from 3.12.0 to 3.13.0 (#3340)
• Bump tempfile from 3.13.0 to 3.14.0 (#3391)
• Bump thiserror from 1.0.63 to 1.0.64 (#3335)
• Bump thiserror from 1.0.64 to 1.0.65 (#3367)
• Bump thiserror from 1.0.65 to 1.0.68 (#3379)
• Bump thiserror from 1.0.68 to 2.0.3 (#3389)
• Bump web-sys from 0.3.69 to 0.3.70 (#3299)
• Bump web-sys from 0.3.70 to 0.3.72 (#3354)
• Bump web-sys from 0.3.72 to 0.3.74 (#3411)
• Update pytest-cov requirement from <6.0,>=4 to >=4,<7.0 (#3375)
• Update sphinx requirement from <8,>=6 to >=6,<9 (#3269)
• Upgrade rocksdb to 0.22.0, bump MSRV to 1.66 (#3383)
• [pre-commit.ci] pre-commit autoupdate (#3281)
• [pre-commit.ci] pre-commit autoupdate (#3290)
• [pre-commit.ci] pre-commit autoupdate (#3312)
• [pre-commit.ci] pre-commit autoupdate (#3330)
• [pre-commit.ci] pre-commit autoupdate (#3336)
• [pre-commit.ci] pre-commit autoupdate (#3341)
• [pre-commit.ci] pre-commit autoupdate (#3346)
• [pre-commit.ci] pre-commit autoupdate (#3360)
• [pre-commit.ci] pre-commit autoupdate (#3369)
• [pre-commit.ci] pre-commit autoupdate (#3380)
• [pre-commit.ci] pre-commit autoupdate (#3393)
• [pre-commit.ci] pre-commit autoupdate (#3404)
• [pre-commit.ci] pre-commit autoupdate (#3409)
• [pre-commit.ci] pre-commit autoupdate (#3414)

Scientific Software - Peer-reviewed - Python
Published by ctb about 1 year ago

sourmash v4 - v4.8.11

Minor new features:

• RocksDB storage and self-contained RevIndex with internal storage (#3250)

Bug fixes:

• Break ahash dep cycle by bumping to 0.7.8, nix flake update (#3243)

Cleanup and documentation updates:

• Update dev env instructions (#2990)

Developer updates:

• Use softprops/action-gh-release github action for artifact upload to release (#3273)
• Enable codspeed for Rust perf tracking (#3231)
• bump cibuildwheel for linux fixes, move wasm to use cibuildwheel too (#3241)

Dependabot updates:

• Bump actions/checkout from 3 to 4 (#3265)
• Bump moonrepo/setup-rust from 0 to 1 (#3266)
• Bump CodSpeedHQ/action from 2 to 3 (#3264)
• pre-commit autoupdate (#3270) (#3260) (#3255) (#3238)
• Bump DeterminateSystems/nix-installer-action from 12 to 13 (#3259)
• Update pytest requirement from <8.3.0,>=6.2.4 to >=6.2.4,<8.4.0 (#3258)
• Bump thiserror from 1.0.62 to 1.0.63 (#3257)
• Bump thiserror from 1.0.61 to 1.0.62 (#3254)
• Bump roaring from 0.10.5 to 0.10.6 (#3245)
• Bump serde from 1.0.203 to 1.0.204 (#3244)
• Bump counter from 0.5.7 to 0.6.0 (#3235)
• Bump log from 0.4.21 to 0.4.22 (#3236)
• Bump serde_json from 1.0.117 to 1.0.120 (#3234)

Scientific Software - Peer-reviewed - Python
Published by luizirber over 1 year ago

sourmash v4 - v4.8.10

This release is accompanied by the publication of a JOSS paper: “sourmash v4: A multitool to quickly search, compare, and analyze genomic and metagenomic data sets”, our new citation handle!

Minor new features:

• check select parameters; enforce types when building manifests (#3212)
• patch-fix sig extract to no longer create empty zips (#3214)

Bug fixes:

• adjust how ANI is calculated in the revindex code. (#3218)

Cleanup and documentation updates:

• final updates for 2024 JOSS publication (#3225)
• Improve JOSS paper affiliations (#3224)
• fix DOI for Rahman Hera paper in JOSS pub. (#3221)
• upd citations, minor text (#3220)

Developer updates:

• bump sourmash core version to 0.14.1 (#3219)
• bump version to 4.8.10-dev (#3211)

Dependabot updates:

• Bump proptest from 1.4.0 to 1.5.0 (#3222)
• [pre-commit.ci] pre-commit autoupdate (#3223)
• [pre-commit.ci] pre-commit autoupdate (#3003)
• Bump histogram from 0.10.2 to 0.11.0 (#3216)
• Bump pypa/cibuildwheel from 2.19.0 to 2.19.1 (#3217)
• Bump histogram from 0.10.1 to 0.10.2 (#3207)
• Bump statrs from 0.16.1 to 0.17.1 (#3205)
• Bump roaring from 0.10.4 to 0.10.5 (#3206)
• Bump primal-check from 0.3.3 to 0.3.4 (#3208)
• Bump niffler from 2.5.0 to 2.6.0 (#3204)
• Bump pypa/cibuildwheel from 2.18.1 to 2.19.0 (#3202)

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 1 year ago

sourmash v4 - v4.8.9

Minor new features:

• add --set-name to sig intersect and sig subtract (#3162)
• upgrade sig overlap and sig subtract to load more than JSON signatures (#3153)
• force continue past tax genome classification errors (#3100)

Bug fixes:

• fix remaining_bp output from sourmash gather (#3195)
• fix RocksDB-based gather & other rust-based infelicities revealed by plugins (#3193, #3197)
• use correct denominator in funiqueto_query (#3138)

Cleanup and documentation updates:

• update JOSS for sourmash v4 (#3114, #3203, #3209)
• fix links to taxonomy spreadsheets (#3119)
• fix description of f_unique_weighted (#3164)

Developer updates:

• transition internal signature loading functions (#3161)
• allow get/set record.filename (#3121)
• round a number that is losing precision in 15th place in test_distance_utpy (#3126)
• disable ppc64le wheel building (#3127)
• prepare to remove sourmash compute for sourmash v5.0 (#3103)
• add rustup target x86_64-apple-darwin (#3148)
• mv .cargo/config to config.toml (#3147)
• fix clippy warnings about max_value (#3146)
• bump to v4.8.9-dev (#3135)
• update src/core/CHANGELOG.md for sourmash-rs core release r0.14.0 (#3199)

Dependabot updates:

• Bump DeterminateSystems/nix-installer-action from 11 to 12 (#3184)
• Bump DeterminateSystems/magic-nix-cache-action from 6 to 7 (#3185)
• Bump statrs from 0.16.0 to 0.16.1 (#3186)
• Bump serde from 1.0.202 to 1.0.203 (#3175)
• Bump ouroboros from 0.18.3 to 0.18.4 (#3176)
• Bump itertools from 0.12.1 to 0.13.0 (#3166)
• Bump camino from 1.1.6 to 1.1.7 (#3169)
• Bump serde from 1.0.201 to 1.0.202 (#3168)
• Bump thiserror from 1.0.60 to 1.0.61 (#3167)
• Bump pypa/cibuildwheel from 2.18.0 to 2.18.1 (#3165)
• Bump DeterminateSystems/magic-nix-cache-action from 4 to 6 (#3157)
• Bump DeterminateSystems/nix-installer-action from 10 to 11 (#3156)
• Bump pypa/cibuildwheel from 2.17.0 to 2.18.0 (#3155)
• Bump serde_json from 1.0.116 to 1.0.117 (#3159)
• Bump thiserror from 1.0.59 to 1.0.60 (#3158)
• Bump serde from 1.0.200 to 1.0.201 (#3160)
• Bump roaring from 0.10.3 to 0.10.4 (#3142)
• Bump histogram from 0.10.0 to 0.10.1 (#3141)
• Bump getrandom from 0.2.14 to 0.2.15 (#3143)
• Bump num-iter from 0.1.44 to 0.1.45 (#3140)
• Bump jinja2 from 3.1.3 to 3.1.4 (#3145)
• Bump serde from 1.0.199 to 1.0.200 (#3144)
• Bump serde from 1.0.198 to 1.0.199 (#3130)
• Bump conda-incubator/setup-miniconda from 3.0.3 to 3.0.4 (#3131)
• Update pytest requirement from <8.2.0,>=6.2.4 to >=6.2.4,<8.3.0 (#3132)
• Bump myst-parser from 2.0.0 to 3.0.1 (#3133)
• Bump thiserror from 1.0.58 to 1.0.59 (#3123)
• Bump serde_json from 1.0.115 to 1.0.116 (#3124)
• Bump serde from 1.0.197 to 1.0.198 (#3122)
• Update docutils requirement from <0.21,>=0.17.1 to >=0.17.1,<0.22 (#3116)

Scientific Software - Peer-reviewed - Python
Published by ctb over 1 year ago

sourmash v4 -

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 1 year ago

sourmash v4 -

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 1 year ago

sourmash v4 -

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 1 year ago

sourmash v4 - v4.8.8

We are proud to report that sourmash v4.8.8 has been accepted after peer review by pyOpenSci! See the review here!

Major new features:

• Add pyopensci review badge (#3105)
• Implement file parsing for webassembly (#3047)

Dependabot updates:

• Bump histogram from 0.9.1 to 0.10.0 (#3109)
• Bump getrandom from 0.2.12 to 0.2.14 (#3108)
• Bump enum_dispatch from 0.3.12 to 0.3.13 (#3102)
• Bump serde_json from 1.0.114 to 1.0.115 (#3101)
• Update pytest-cov requirement from <5.0,>=4 to >=4,<6.0 (#3097)
• Bump rayon from 1.9.0 to 1.10.0 (#3098)

Scientific Software - Peer-reviewed - Python
Published by ctb over 1 year ago

sourmash v4 - v4.8.7

Note: This release changes the way sourmash multigather names output files in some situations. Please see https://github.com/sourmash-bio/sourmash/pull/2722 for details.

Minor new features:

• support proper manifest creation with --relpath for sig check and sig collect (#3054)
• fix multigather output by adding md5sum along with -U/--output-add-query-md5sum (#2722)
• enable loading lineages from annotated gather with match_name instead of name (#3078)

Bug fixes:

• fix output for sketch ... --singleton (#3066)
• fix calculate_gather_stats threshold=0 bug (#3052)

Cleanup and documentation updates:

• adjust protein ksize for record/manifest (#3019)
• Resolve sourmash gather --help issue (#3032)
• rework the manifest documentation; do misc cleanup (#3027)
• add branchwater web to docs (#3018)

Developer updates:

• make core Manifest booleans python compatible (core) (#3007)
• safer ksize selection while still accommodating k=k*3 (#3028)
• fix clippy beta issues (#3088)
• tell dependabot to ignore upgrades to byteorder, chrono, once_cell, and wasm-bindgen (#3065)
• update rust changelog for r0.13.0 in preparation for release (#3033)
• Allow changing storage location for a collection in RevIndex (#3015)
• Fix tox and nix configs so all tox tests execute correctly (#2992)
• Calculate all gather stats in rust; use for rocksdb gather (#2943)
• bump screed req to 1.1.3 (#3067)
• bump to v4.8.7-dev (#2989)

Dependabot updates:

• Bump DeterminateSystems/magic-nix-cache-action from 1 to 3 (#2994)
• Bump DeterminateSystems/magic-nix-cache-action from 3 to 4 (#3085)
• Bump DeterminateSystems/nix-installer-action from 4 to 9 (#2995)
• Bump DeterminateSystems/nix-installer-action from 9 to 10 (#3083)
• Bump chrono from 0.4.33 to 0.4.34 (#3000)
• Bump conda-incubator/setup-miniconda from 3.0.1 to 3.0.2 (#3046)
• Bump conda-incubator/setup-miniconda from 3.0.2 to 3.0.3 (#3057)
• Bump histogram from 0.9.0 to 0.9.1 (#3002)
• Bump itertools from 0.12.0 to 0.12.1 (#3043)
• Bump log from 0.4.20 to 0.4.21 (#3062)
• Bump num-iter from 0.1.43 to 0.1.44 (#2997)
• Bump pypa/cibuildwheel from 2.16.5 to 2.17.0 (#3084)
• Bump rayon from 1.8.1 to 1.9.0 (#3058)
• Bump roaring from 0.10.2 to 0.10.3 (#3014)
• Bump serde from 1.0.196 to 1.0.197 (#3045)
• Bump serde_json from 1.0.113 to 1.0.114 (#3044)
• Bump tempfile from 3.10.0 to 3.10.1 (#3059)
• Bump thiserror from 1.0.56 to 1.0.57 (#2999)
• Bump thiserror from 1.0.57 to 1.0.58 (#3082)
• Bump wasm-bindgen from 0.2.91 to 0.2.92 (#3060)
• Bump wasm-bindgen-test from 0.3.40 to 0.3.41 (#2996)
• Bump wasm-bindgen-test from 0.3.41 to 0.3.42 (#3063)
• Bump web-sys from 0.3.67 to 0.3.68 (#2998)
• Bump web-sys from 0.3.68 to 0.3.69 (#3061)
• Revert "Bump wasm-bindgen from 0.2.91 to 0.2.92 (#3060)" (#3064)
• Update asv to 0.6.2 (#3025)
• Update pytest requirement from <8.1.0,>=6.2.4 to >=6.2.4,<8.2.0 (#3075)

Scientific Software - Peer-reviewed - Python
Published by ctb almost 2 years ago

sourmash v4 - v4.8.6

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)

Scientific Software - Peer-reviewed - Python
Published by ctb almost 2 years ago

sourmash v4 - v4.8.5

This release drops support for Python < 3.10, and also reorganizes and expands the documentation substantially!

Major new features:

• Drop Python 3.8 and 3.9, default to Python 3.10 for most CI tasks (#2848)
• Revise documentation structure; add internals page. (#2184)
• Adjust documentation to recommend tax over lca for taxonomic analysis (#2777)

Bug fixes:

• make sourmash plot labels/indices arguments make sense (#2790)

Cleanup and documentation updates:

• Various minor updates to docs (#2854)
• Deps: update typed-builder and histogram, bump MSRV to 1.65 (#2858)
• Fix wheel building and semver checks post r0.12.0 (#2857)
• Added seed to parameter strings #1732 (#2836)
• Add link for developer documentation to sidebar (#2847)
• add explicit install tutorial (#2826)
• fix many minor documentation nits (#2814)
• update docs for tax grep: only searches tax (#2789) *add usage docs for sig import/ingest (#2785)

Developer updates:

• Feat: on-disk RevIndex based on RocksDB (#2230)
• Fix many warnings from PYTHONDEVMODE=1 (#2849)
• Build: Fix Rust 1.75 beta lints; flake update (#2841)
• try pinning maturin to <1.3.0 to fix dev build CI (#2799)
• minor updates to release procedure after 4.8.4 (#2783)
• run rust checks always (#2787)
• add __all__ to sig/__main__.py (#2778)
• bump version to 4.8.5-dev (#2766)

Dependabot updates:

• Bump ouroboros from 0.18.0 to 0.18.1 (#2875)
• Bump once_cell from 1.18.0 to 1.19.0 (#2874)
• Bump actions/setup-python from 4 to 5 (#2873)
• Bump cachix/cachix-action from 12 to 13 (#2861)
• Bump conda-incubator/setup-miniconda from 3.0.0 to 3.0.1 (#2860)
• Bump cachix/install-nix-action from 23 to 24 (#2859)
• Bump rkyv from 0.7.40 to 0.7.42 (#2863)
• Bump csv from 1.2.0 to 1.3.0 (#2862)
• Bump roaring from 0.10.1 to 0.10.2 (#2865)
• Bump web-sys from 0.3.65 to 0.3.66 (#2864)
• Bump byteorder from 1.4.3 to 1.5.0 (#2866)
• Bump proptest from 1.3.1 to 1.4.0 (#2837)
• Bump getrandom from 0.2.10 to 0.2.11 (#2839)
• Bump web-sys from 0.3.64 to 0.3.65 (#2838)
• Bump wasm-bindgen-test from 0.3.37 to 0.3.39 (#2853)
• Bump wasm-bindgen from 0.2.88 to 0.2.89 (#2850)
• Bump mymindstorm/setup-emsdk from 12 to 13 (#2851)
• Bump conda-incubator/setup-miniconda from 2.2.0 to 3.0.0 (#2852)
• Bump wasm-bindgen from 0.2.87 to 0.2.88 (#2834)
• Bump serde_json from 1.0.107 to 1.0.108 (#2829)
• Bump tempfile from 3.8.0 to 3.8.1 (#2828)
• Bump bytecount from 0.6.5 to 0.6.7 (#2830)
• Bump bytecount from 0.6.4 to 0.6.5 (#2822)
• Bump thiserror from 1.0.49 to 1.0.50 (#2823)
• Bump actions/setup-node from 3 to 4 (#2821)
• Bump rustix from 0.37.20 to 0.37.25 (#2817)
• Bump pypa/cibuildwheel from 2.16.1 to 2.16.2 (#2808)
• Bump memmap2 from 0.8.0 to 0.9.0 (#2807)
• Bump byteorder from 1.4.3 to 1.5.0 (#2806)
• Bump pypa/cibuildwheel from 2.16.0 to 2.16.1 (#2797)
• Bump thiserror from 1.0.48 to 1.0.49 (#2796)
• Bump proptest from 1.2.0 to 1.3.1 (#2795)
• Bump bytecount from 0.6.3 to 0.6.4 (#2794)
• Bump memmap2 from 0.7.1 to 0.8.0 (#2780)
• Bump rayon from 1.7.0 to 1.8.0 (#2782)
• Bump docker/setup-qemu-action from 2 to 3 (#2767)
• Bump pypa/cibuildwheel from 2.15.0 to 2.16.0 (#2768)
• Bump serde_json from 1.0.106 to 1.0.107 (#2769)
• Bump chrono from 0.4.30 to 0.4.31 (#2771)

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] about 2 years ago

sourmash v4 - v4.8.4

We are proud to release sourmash v4.8.4, now with even fewer bugs!

In addition to the patches and updates below, we would like to announce the availability of branchwater, a sourmash plugin that supports fast, low-memory, and multithreaded search, compare, and gather operations. branchwater v0.8.0 is now available and is between 10 and 100 times faster and lower memory than sourmash. (However, it does not support all the sourmash features; that will come with time!) Please give it a try!

Last but not least, we would like to ask people who use sourmash regularly to fill out this form so that we can include your information in some of our upcoming requests for funding support. Your use will not be made public but your support will help us continue to develop sourmash!

On to the release notes for sourmash v4.8.4!

Bug fixes:

• fix exponential time explosion in sig check (#2762)
• fix duplicate md5 in picklist problem (#2747)
• avoid compressing sig files in directory output twice (#2752)

Developer updates:

• Remove BIGSI and SBT code from Rust layer (#2732)
• bump version to 4.8.4-dev (#2720)
• build: updates spun off mastiff PR (#2723)
• Build: Remove deprecated system_packages from readthedocs (#2740)
• build: remove specific tooling that breaks s390x (#2725)
• Add cargo deny and bump deps now that MSRV is 1.64 (#2724)

Dependabot updates:

• Bump serde_json from 1.0.105 to 1.0.106 (#2757)
• Bump actions/checkout from 2 to 4 (#2746)
• Bump supercharge/redis-github-action from 1.6.0 to 1.7.0 (#2745)
• Bump cachix/install-nix-action from 22 to 23 (#2744)
• Bump ouroboros from 0.17.2 to 0.18.0 (#2743)
• Bump chrono from 0.4.26 to 0.4.30 (#2755)
• Bump thiserror from 1.0.47 to 1.0.48 (#2742)
• Bump thiserror from 1.0.44 to 1.0.47 (#2730)
• Bump serde_json from 1.0.104 to 1.0.105 (#2731)
• Bump actions/upload-artifact from 1 to 3 (#2729)

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 2 years ago

sourmash v4 - v4.8.3

Minor new features:

• add support for -E/--extension to sig split (#2712)
• add a sourmash.cli.parse_args([...]) function (#2691)
• update plugin support for argparse usage/description/epilog (#2696)

Cleanup and documentation updates:

• add gtdb-rs214 info (#2618, #2621, #2690)
• update JOSS paper for v4 (#1361)
• fix tutorial notebook links (#2633)
• Update URL for sourmash/fig.py (#2586)
• change matching_hashes.sig to matching-hashes.sig in documentation (#2713)
• patch lineage_summary documentation (#2693)
• switch dib-lab links to sourmash-bio links in .md files (#2588)

Developer updates:

• add upload token for codecov (#2632)
• build: fix clippy lints and MSRV check (#2680)
• maturin: move deprecated definition from Cargo.toml to pyproject.toml (#2597)
• update the core documentation building packages: Sphinx, myst-parser, and docutils (#2657)
• update the dependabot config to allow automatic rebases (#2634)
• update version to 4.8.3-dev (#2584)
• Build: bump maturin to 1.x (#2650)
• Clippy beta (1.70) fix (#2596)
• Fix clippy lint introduced in 1.71 beta (#2630)
• fix release procedure based on v4.8.0 release (#2551)
• Update docutils requirement from <0.20,>=0.17.1 to >=0.17.1,<0.21 (#2611)
• Update pytest requirement from <7.4.0,>=6.2.4 to >=6.2.4,<7.5.0 (#2659)
• Fix: update a manifest test to use temp directory (#2689)

Dependabot updates:

• Bump cachix/install-nix-action from 20 to 21 (#2625)
• Bump cachix/install-nix-action from 21 to 22 (#2651)
• Bump chrono from 0.4.24 to 0.4.25 (#2628)
• Bump chrono from 0.4.25 to 0.4.26 (#2636)
• Bump criterion from 0.3.6 to 0.5.1 (#2629)
• Bump getrandom from 0.2.9 to 0.2.10 (#2645)
• Bump log from 0.4.17 to 0.4.18 (#2623)
• Bump log from 0.4.18 to 0.4.19 (#2641)
• Bump log from 0.4.19 to 0.4.20 (#2715)
• Bump memmap2 from 0.5.10 to 0.6.1 (#2613)
• Bump memmap2 from 0.6.1 to 0.6.2 (#2626)
• Bump memmap2 from 0.6.2 to 0.7.0 (#2643)
• Bump memmap2 from 0.7.0 to 0.7.1 (#2658)
• Bump once_cell from 1.17.1 to 1.17.2 (#2622)
• Bump once_cell from 1.17.2 to 1.18.0 (#2635)
• Bump ouroboros from 0.15.6 to 0.17.0 (#2654)
• Bump ouroboros from 0.17.0 to 0.17.2 (#2687)
• Bump proptest from 1.1.0 to 1.2.0 (#2627)
• Bump pypa/cibuildwheel from 2.12.1 to 2.12.3 (#2590)
• Bump pypa/cibuildwheel from 2.12.3 to 2.13.0 (#2624)
• Bump pypa/cibuildwheel from 2.13.0 to 2.13.1 (#2642)
• Bump pypa/cibuildwheel from 2.13.1 to 2.14.0 (#2673)
• Bump pypa/cibuildwheel from 2.14.0 to 2.14.1 (#2681)
• Bump pypa/cibuildwheel from 2.14.1 to 2.15.0 (#2716)
• Bump serde from 1.0.160 to 1.0.162 (#2609)
• Bump serde from 1.0.162 to 1.0.163 (#2612)
• Bump serde from 1.0.163 to 1.0.164 (#2644)
• Bump serde from 1.0.164 to 1.0.166 (#2666)
• Bump serde from 1.0.166 to 1.0.168 (#2679)
• Bump serde_json from 1.0.100 to 1.0.103 (#2682)
• Bump serde_json from 1.0.103 to 1.0.104 (#2701)
• Bump serde_json from 1.0.96 to 1.0.97 (#2653)
• Bump serde_json from 1.0.97 to 1.0.99 (#2660)
• Bump serde_json from 1.0.99 to 1.0.100 (#2675)
• Bump supercharge/redis-github-action from 1.5.0 to 1.6.0 (#2700)
• Bump tempfile from 3.5.0 to 3.6.0 (#2639)
• Bump tempfile from 3.6.0 to 3.7.0 (#2686)
• Bump tempfile from 3.7.0 to 3.7.1 (#2705)
• Bump thiserror from 1.0.40 to 1.0.43 (#2674)
• Bump thiserror from 1.0.43 to 1.0.44 (#2685)
• Bump wasm-bindgen from 0.2.84 to 0.2.86 (#2615)
• Bump wasm-bindgen from 0.2.86 to 0.2.87 (#2640)
• Bump wasm-bindgen-test from 0.3.34 to 0.3.36 (#2620)
• Bump wasm-bindgen-test from 0.3.36 to 0.3.37 (#2656)
• Bump web-sys from 0.3.61 to 0.3.63 (#2619)
• Bump web-sys from 0.3.63 to 0.3.64 (#2655)

Scientific Software - Peer-reviewed - Python
Published by ctb over 2 years ago

sourmash v4 - v4.8.2

This is a bugfix release for a sourmash tax bug - see #2579.

Minor new features:

• add optional reporting for duplicated names in sketch fromfile (#2580)

Bug fixes:

• fix lineage_summary tax bug (#2579)

Dependabot updates:

• Bump serde from 1.0.159 to 1.0.160 (#2575)
• Bump serde_json from 1.0.95 to 1.0.96 (#2574)

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 2 years ago

sourmash v4 - v4.8.1

Minor new features:

• add --create-empty-results option to gather (#2557)

Bug fixes:

• fix exception error when no arguments are provided to sig intersect (#2555)

Cleanup and documentation updates:

• update sourmash sketch docs for building merged sketches (#2563)
• fix broken crates.io badge (#2556)
• add --csv to command-line docs for compare (#2565)

Developer updates:

• Remove codecov from tox, use GH action instead (#2568)

Dependabot updates:

• Update pytest requirement from <7.3.0,>=6.2.4 to >=6.2.4,<7.4.0 (#2558)
• Bump tempfile from 3.4.0 to 3.5.0 (#2561)
• Bump serde from 1.0.158 to 1.0.159 (#2560)
• Bump getrandom from 0.2.8 to 0.2.9 (#2559)

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 2 years ago

sourmash v4 - v4.8.0

Major new features:

• Add taxonomic utilities for LINs (#2469, #2468, #2519, #2518)

Minor new features:

• update prefetch/gather output to be clearer (#2543)

Cleanup and documentation updates:

• update version of screed to >= 1.1,<2 (#2415)
• minor fixes to release docs after v4.7.0 (#2498)

Developer updates:

• Remove pkg_resources usage (#2505)
• Add LICENSE and test data to sdist (#2490)
• Build pyodide wheels in CI (#2433)
• Update nix deps (#2506)
• bump to pyodide 0.23 (#2545)

Dependabot updates:

• Bump serde_json from 1.0.94 to 1.0.95 (#2540)
• Bump needletail from 0.5.0 to 0.5.1 (#2541)
• Bump serde from 1.0.156 to 1.0.158 (#2534)
• Bump thiserror from 1.0.39 to 1.0.40 (#2533)
• Bump typed-builder from 0.13.0 to 0.14.0 (#2527)
• Bump serde from 1.0.152 to 1.0.156 (#2530)
• Bump minimum rust version to 1.60 (#2528)
• Bump myst-parser from 0.19.1 to 1.0.0 (#2525)
• Bump chrono from 0.4.23 to 0.4.24 (#2524)
• Bump pypa/cibuildwheel from 2.12.0 to 2.12.1 (#2523)
• Bump myst-parser from 0.18.1 to 0.19.1 (#2507)
• Bump rayon from 1.6.1 to 1.7.0 (#2515)
• Bump tempfile from 3.3.0 to 3.4.0 (#2514)
• Bump needletail from 0.4.1 to 0.5.0 (#2512)
• Bump memmap2 from 0.5.9 to 0.5.10 (#2516)
• Bump thiserror from 1.0.38 to 1.0.39 (#2509)
• Bump mymindstorm/setup-emsdk from 11 to 12 (#2508)
• Bump serde_json from 1.0.93 to 1.0.94 (#2510)
• Bump typed-builder from 0.12.0 to 0.13.0 (#2511)

Scientific Software - Peer-reviewed - Python
Published by ctb over 2 years ago

sourmash v4 - v4.7.0

sourmash release 4.7.0

Major new features:

• provide an initial plugin architecture for sourmash that supports new signature saving & loading mechanisms (#2428)
• add plugin support for new command-line subcommands (#2438)
• debias all containment values (#2243)

Minor new features:

• Use RankLineageInfo to simplify reading lineages (#2467)
• store taxids in lineageDB (#2466)
• Use new tax classes for taxonomic summarization (#2443)
• add tax summarization dataclasses for safety and flexibility (#2439)
• add --scaled to sourmash compare (#2414)
• replace lca_utils.LineagePair with tax_utils.LineagePair (#2441)
• Add new classes for lineage manipulation (#2437)

Cleanup and documentation updates:

• ReadTheDocs updates (#2445)
• update sourmash compare command-line docs (#2400)

Developer updates:

• fix python tests by bumping tox and pip cache versions (#2424)
• Update sphinx requirement from <6,>=4.4.0 to >=4.4.0,<7 (#2430)
• Build: replace milksnake with maturin (#2393)
• importlib_metadata is a dependency on old Python versions (#2484)
• Release docs: use two separate sed commands (#2483)
• minor fixes to release behavior (#2479)
• Use screed and maturin from nixpkgs in flake.nix (#2481)
• update release procedure after v4.6.0 and v4.6.1 (#2386)
• Update makefile and docs (#2432)

Dependabot updates:

• Bump once_cell from 1.17.0 to 1.17.1 (#2488)
• Bump ouroboros from 0.15.5 to 0.15.6 (#2487)
• Bump memmap2 from 0.5.8 to 0.5.9 (#2486)
• Bump supercharge/redis-github-action from 1.4.0 to 1.5.0 (#2485)
• Bump proptest from 1.0.0 to 1.1.0 (#2460)
• Bump web-sys from 0.3.60 to 0.3.61 (#2461)
• Bump serde_json from 1.0.91 to 1.0.93 (#2471)
• Bump wasm-bindgen-test from 0.3.33 to 0.3.34 (#2463)
• Bump cachix/install-nix-action from 18 to 19 (#2459)
• Bump wasm-bindgen from 0.2.83 to 0.2.84 (#2464)
• Bump typed-builder from 0.11.0 to 0.12.0 (#2451)
• Bump bumpalo from 3.9.1 to 3.12.0 (#2450)
• Bump pypa/cibuildwheel from 2.11.4 to 2.12.0 (#2447)
• Bump bzip2 from 0.4.3 to 0.4.4 (#2444)
• Bump once_cell from 1.14.0 to 1.17.0 (#2429)
• Bump serde from 1.0.151 to 1.0.152 (#2423)
• Bump pypa/cibuildwheel from 2.11.3 to 2.11.4 (#2422)
• Bump serde_json from 1.0.89 to 1.0.91 (#2418)
• Bump serde from 1.0.150 to 1.0.151 (#2419)
• Bump thiserror from 1.0.37 to 1.0.38 (#2417)
• Bump finch from 0.4.3 to 0.5.0 (#2416)
• Bump rayon from 1.6.0 to 1.6.1 (#2404)
• Bump serde from 1.0.149 to 1.0.150 (#2403)
• Bump pypa/cibuildwheel from 2.11.2 to 2.11.3 (#2402)
• Bump serde from 1.0.148 to 1.0.149 (#2397)
• Bump capnp from 0.14.5 to 0.14.11 (#2396)

Scientific Software - Peer-reviewed - Python
Published by ctb almost 3 years ago

sourmash v4 - v4.6.1

This is a quick patch-fix for sourmash v4.6.0, which introduced bug https://github.com/sourmash-bio/sourmash/issues/2390. This bug broke sourmash sketch ... -o <file> with multiple ksizes, so that .zip and .sqldb output files contained only one ksize.

Bug fixes: - fix sourmash sketch ... -o <file>.zip bug introduced in #2329 and released in v4.6.0 (#2391) - disable cibuildwheel on PRs again (#2389)

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] about 3 years ago

sourmash v4 - v4.6.0

The major new feature in this release is the addition of tax summarize, which produces a human-readable summary of taxonomy databases.

The various tax functions also now support ingest of the output of tax annotate as a lineage spreadsheet - see the tax prepare documentation. This allows you to (for example) run tax summarize on the output of tax annotate.

---

Major new features: * add tax summarize and support gather-tax input to taxonomy functions (#2333) * report both weighted and unweighted % recovered in gather (#2301) * replace chernoff bounds with exact probabilities (#2268)

Minor new features: * switch remaining sig submodule commands over to sourmash_args sig output (#2377) * use modern signature saving API throughout main CLI commands. (#2338) * add column 3 to kreport (#2306) * allow gzipped gather csv inputs to tax (#2339) * display a better error message on attempting to write a read-only sqlite database (#2376) * fix manifest load function to properly catch gzip.BadGzipFile (#2375) * update kreport proportion for better resolution; match other tool outputs (#2331)

Bug fixes: * Fix multigather so that the output CSV contains all matches. (#2322) * remove default ksize of 31 from help message when it's not actually true. (#2295)

Cleanup and documentation updates: * Updated python version (#2286) * update docs re using multiple dbs (#2296) * fix some tax doc issues (#2365) * fix kreport documentation (#2302)

Developer updates: * Fix cibuildwheel actions (#2384, #2385, #2388) * return Err for angularsimilarity when abundance tracking is off (#2327) * cargo check fixes for Rust beta (1.65) (#2298) * fix unnecessary typecasts in Rust (#2366) * fix Signature.minhash API during sourmash sketch (#2329) * fix return type of `LCASqliteDatabase.select` (#2382)

Dependabot updates: * Bump conda-incubator/setup-miniconda from 2.1.1 to 2.2.0 (#2363) * Bump counter from 0.5.6 to 0.5.7 (#2336) * Bump finch from 0.4.1 to 0.4.3 (#2283) * Bump getrandom from 0.2.7 to 0.2.8 (#2347) * Bump memmap2 from 0.5.7 to 0.5.8 (#2364) * Bump myst-parser from 0.18.0 to 0.18.1 (#2345) * Bump pypa/cibuildwheel from 2.11.1 to 2.11.2 (#2353) * Bump pypa/cibuildwheel from 2.9.0 to 2.10.2 (#2307) * Bump rayon from 1.5.3 to 1.6.0 (#2373) * Bump serde from 1.0.145 to 1.0.147 (#2348) * Bump serde from 1.0.147 to 1.0.148 (#2378) * Bump serdejson from 1.0.86 to 1.0.87 (#2349) * Bump serdejson from 1.0.87 to 1.0.88 (#2374) * Bump serdejson from 1.0.88 to 1.0.89 (#2379) * Bump typed-builder from 0.10.0 to 0.11.0 (#2356) * Update bitstring requirement from <4,>=3.1.9 to >=3.1.9,<5 (#2372) * Update docutils requirement from <0.18,>=0.17.1 to >=0.17.1,<0.20 (#2344) * Update pytest requirement from <7.2.0,>=6.2.4 to >=6.2.4,<7.3.0 (#2354) * Update pytest-cov requirement from <4.0,>=2.12 to >=2.12,<5.0 (#2346) * Version bumps (#2282) * Combine latest dependabot PRs: cibuildwheel, finch, serdejson (#2343) * Rust deps updates without MSRV bump (#2315)

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] about 3 years ago

sourmash v4 -

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] about 3 years ago

sourmash v4 - v4.5.0

sourmash v4.5.0 provides several minor bug fixes, as well as a number of new features.

This release also includes two minor Python API breaking changes - by default, SourmashSignature objects loaded from files are "frozen", and we force explicit keyword arguments on MinHash object construction.

Finally, this release updates the sourmash documentation with several new tutorials, including one on using sourmash tax to classify metagenomes with MAGs + GTDB.

Bug fixes

• Fix sourmash tax argument parsing for multiple -g and -t arguments (#2218)
• Prevent loading multiple independent gather results files in sourmash tax (#2244)
• Fix query_abundance column when --ignore-abundance is set in gather (#2251)
• fix pickle protocol to properly adjust ksize in __getstate__ (#2265)
• clean up zip error handling for bad zip files (#2270)

Minor new features

• Use the bias factor for containment when estimating ANI (#2057)
• add human output format to sourmash tax; provide tutorials (#2158)
• add kreport output format to tax metagenome (#2239, #2249)
• add --distance-matrix option to sourmash compare (#2225)
• update database load UX for gather etc. (#2204)
• add generic support for gzipped and zipfile CSVs (#2195)
• implement tax grep to produce identifier picklists from taxonomies (#2178)

Cleanup and documentation fixes

• add sourmash tax tutorial (#2158)
• revise command-line docs for sourmash sig subcommands (#1714, #1717)
• Clarify containment direction for matrix output (#2215)
• Add ANGUS tutorial to docs (#1114)
• update links to static rmd (#1177)
• update search documentation, help, and output. (#2222)
• Fix signature filter command (#2159)
• fix notification message about query scaled (#2183)
• adjust gather output width on terminal (#2176)

Developer updates

• Add FrozenSourmashSignature (#1610)
• force explicit kwargs on MinHash constructor (#2174)
• fix ReadTheDocs by using a more recent conda version (#2231)
• refactor and add tests for containment direction for ANI calculation (#2215)
• fix test_storage_convert to allow success of sourmash convert (#2232)
• Updating tests/test_sourmash.py::test_storage_convert to use runtmp fixture instead of utils.TempDirectory() (#1739)
• Bump pypa/cibuildwheel from 2.8.1 to 2.9.0 (#2207)
• use stderr for test output printing (#2217)
• fix for sphinx 5.10 (#2147)

Scientific Software - Peer-reviewed - Python
Published by ctb over 3 years ago

sourmash v4 - v4.4.3

Minor new features: * use and report ANI from tax genome summarization (#2005)

Performance improvements: * avoid instantiating a hashes class (#2132)

Cleanup and documentation fixes: * update various descriptions to talk about k-mers, not just DNA (#2137)

Developer updates: * fix docs building for pip 22.2 (#2143) * change dependabot rebase-strategy to disabled for rust dependencies (#2142) * Rust deps and nix flakes updates (#2141) * add pytest-xdist and -n4 to pytest and tox configs (#2138) * update release instructions after v4.4.2 (#2131)

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 3 years ago

sourmash v4 - v4.4.2

Minor fixes and performance improvements:

• circumvent a very slow MinHash.remove_many(...) call in sourmash gather (#2123)

Developer updates:

• substantial refactoring of CounterGather and related Index code. (#2116)
• update Index protocol tests to include tests for peek and consume (#2111)
• Bump pypa/cibuildwheel from 2.7.0 to 2.8.0 (#2118)
• test insert after downsample for LCA_Database (#2117)
• update release notes & pyproject.toml after v4.4.1 (#2114)

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 3 years ago

sourmash v4 - v4.4.1

Major new features:

• less stringent size accuracy parameters for ANI accuracy reporting (#2074)
• only skip dist est if containment/jaccard are 0 or 1 (#2060)
• emit fewer warnings about potential ANI estimation issues (#2061)

Minor new features:

• fix lca summarize to support general collections for queries (#2107)
• add compare --avg-containment (#2056)

Documentation updates:

• fix search and gather docs (#2105)
• fix CITATION.cff YAML and add a test for parseability and content. (#2103)

Developer updates:

• move setup.cfg into pyproject.toml (#2097)
• Fix downsample_scaled in core (#2108)
• add picklist tests; support for allow_empty (#2106)
• remove LazyLoadedIndex (#2104)
• Bump web-sys from 0.3.57 to 0.3.58 (#2092)
• Bump getrandom from 0.2.6 to 0.2.7 (#2090)
• Bump wasm-bindgen-test from 0.3.30 to 0.3.31 (#2093)
• Bump pypa/cibuildwheel from 2.6.1 to 2.7.0 (#2089)
• Build: nix updates (#2088)
• CI: split wheel building (#2087)
• rust version bumps (#2086)
• Update sphinx requirement from <5,>=4.4.0 to >=4.4.0,<6 (#2068)
• Bump actions/setup-python from 3 to 4 (#2080)
• Bump myst-parser from 0.17.2 to 0.18.0 (#2081)
• Bump pypa/cibuildwheel from 2.5.0 to 2.6.1 (#2079)
• remove unnecessary object from class definitions (#2077)

Scientific Software - Peer-reviewed - Python
Published by ctb over 3 years ago

sourmash v4 - v4.4.0

This release contains many new features! Of particular note: * sourmash now estimates and outputs average nucleotide identity (ANI) based on k-mer measures; * sourmash sketch translate is no longer unusably slow; * we provide Mac OS 'arm64' wheels for the new M1 Macs; * we've added a number of support features for managing large collections of signatures and building very large databases; * and we've added support for SQLite databases that can be used for storing and searching signatures and doing Kraken-style LCA analysis of genomes and metagenomes.

In addition, we have built updated Genbank genome databases (with contents from March 2022) as well as GTDB R07-RS207 databases; see the prepared databases page. We've also made some benchmarks available for these databases, so you can get some idea of the necessary computational resources for your searches.

Last but by no means least, we have begun providing a number of examples and recipes for using sourmash - see the new sourmash examples Web site!

---

Major new features:

• add ANI output to search, prefetch, and gather (#1934, #1952, #1955, #1966, #1967, #2011, #2031, #2032)
• new GTDB and Genbank database releases (#2013, #2038)
• provide macos arm64 wheels (#1935)
• support for SQLite databases (#1808)
• implement sourmash sketch fromfile (#1884, #1885, #1886, #2009)
• add sourmash sig check for comparing picklists and databases (#1907, #1915, #1917)
• add sig collect command (#2036) for building standalone manifests from many databases
• Add direct loading of manifest CSVs as sourmash indices (#1891)
• add -A/--abundance-from to sig subtract & add sig inflate (#1889)
• advanced database format documentation (#2025)

Minor new features:

• add -d/--debug to sourmash sig describe; upgrade output errors. (#1782)
• add sum_hashes to sourmash sig describe output. (#1882)

Bug fixes:

• catch TypeError in search w/abund vs flat at the command line (#1928)
• speed up SeqToHashes translate (#1938, #1946)

Cleanup and documentation fixes:

• better handle some pickfile errors (#1924)
• remove unnecessary downsampling warnings (#1971)
• use same wording for dayhoff/hp as for dna/protein (#1929)
• rename covered_bp property to better reflect function (#2050)

Developer updates:

• provide "protocol" tests for Index, CollectionManifest, and LCA_Database classes (#1936)
• remove khmer CI tests (#1950)
• Benchmarks for seqtohashes in protein mode (#1944)
• add some tests for Jaccard output ordering (#1926)
• Oxidize ZipStorage (#1909)
• cleanup and commenting of test_index.py tests. (#1898, #1900)
• rationalize _signatures_with_internal (#1896)
• Convert nix to flakes (#1904)
• fix docs build (#1897)
• Fix build/CI and unused imports papercuts (#1974)
• fix hypothesis CI (#2028)
• dependabot version updates (#1977, #1978, #1979, #1980, #1981, #1982, #1983, #1984, #1985, #1986, #1987, #1988, #1989, #1991, #1993, #1994, #1995, #1996, #1997, #1998, #2017, #2019, #2020, #2021, #2022, #2023, #2042)

Scientific Software - Peer-reviewed - Python
Published by ctb over 3 years ago

sourmash v4 - v4.3.0

New features:

• add sourmash sig grep (#1864)
• add sourmash sig summarize (#1837, #1863)
• add --include-db-pattern and --exclude-db-pattern to many commands (#1871)
• update lca summarize output to output total counts (#1838)

Bug fixes:

• fix sourmash prefetch to work when db scaled is larger than query scaled (#1870)
• fix sourmash prefetch for multiple ksizes in database (#1866)
• allow missing columns in tax CSV files (#1869)
• fix containment calculation for nodegraphs (#1862)
• fix tax prepare SQL code for empty/blank taxonomic ranks (#1843)

Cleanup and documentation fixes: * clean up 'describe' a little bit, add a test (#1861) * add --output-dir as alias for every --outdir (#1817) * fix doc titles in command-line.md and update description a bit (#1874)

Developer updates:

• move greyhound-core into sourmash (#1238)
• drop Python 3.7, default most of CI to Python 3.10 (#1839)
• reorganize traits for easier wasm and native compilation (#1836)
• update asv to newly released version (#1834)
• pin setuptools < 60 (#1879)

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] almost 4 years ago

sourmash v4 - v4.2.4

Medium bug fixes:

• fix bug where sourmash sketch ... --singleton -o output.sig drops signatures (#1810)
• fix sourmash search --containment with two abund signatures (#1780)
• fix plot/labels/CSV ordering with sourmash plot --csv (#1821)

Small bug fixes:

• fix Index.search_abund downsampling and filename output (#1820)
• check to make sure that .zip files exist before trying to load from them (#1777)
• fix and test and refactor output information during signature creation (#1826)

Minor new functionality:

• adjust text output of gather to indicate weighted/unweighted results (#1819)
• update sourmash multigather to save hash abundances to .unassigned.sig (#1720)
• re-inflate prefetch output sketches (#1827)

Cleanup and documentation fixes:

• fix 'sketch' output info (#1794)
• fix PMID for mock metagenome (#1811)
• check to make sure that = is in param strings where necessary (#1775)

Developer updates:

• set pickfile on SourmashPicklist.load (#1776)
• Fix new clippy lints in beta (1.59, next stable) (#1791)
• Rust updates (clippy, MSRV, CI, wasm-pack) (#1786)
• disable the fix_lint component of the py38 tests in tox.ini (#1823)

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] almost 4 years ago

sourmash v4 - v4.2.3

Minor new features:

• Save prefetch csv directly from prefetch-gather with --save-prefetch-csv (#1765)
• Added brief descriptions and -h/--help text to sourmash gather, search, and compare (#1735)
• Adding bounds checking for --scaled and --num in sourmash sketch (#1711)

Documentation updates:

• update release notes with -m for git tag (#1754)
• update coverage from 10x to 20x per description in documentation page (#1736)

Development updates:

• Update tests to use runtmp fixture instead of utils.TempDirectory() (#1718)
• Refactor ZipFileLinearCollection and SaveSignatures_ZipFile to use ZipStorage (#1598)
• Clippy fixes for 1.57 beta (#1760)
• CI: Update cibuildwheel usage (#1759)
• Replace notify format usage with f-strings instead (#1723)
• CI: Fix build errors with cbindgen (#1713)
• Change sourmash compute to sourmash sketch in test files (#1712)
• Update tests to use runtmp fixture instead of utils.TempDirectory()

Scientific Software - Peer-reviewed - Python
Published by ctb about 4 years ago

sourmash v4 - v4.2.2

Major new features:

• added functionality to recover original k-mers given hashes - sourmash sig kmers et al. (#1653, #1695, #1701)

Documentation updates:

• Updated picklist docs (#1683)
• Updated the 'how to release' doc after 4.2.0 release (#1649)

Minor new features:

• Adjusted dayhoff and hp encodings to tolerate stop codons in the protein sequence (#1673)

Bug fixes and performance improvements:

• Fixed panic bug in sourmash sketch dna with bad input and --check-sequence (#1702)

Refactoring and cleanup:

• Changed sourmash compute to sourmash sketch in tests/test_sourmash.py (#1680, #1687)
• Tested and fixed sourmash_args.load_many_signatures(...) and lca_db.load_single_database (#1684)

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 4 years ago

sourmash v4 -

This is a bug-fix and performance release of sourmash.

There are no major new features.

git log --oneline v4.2.0..latest

Minor new features:

• new picklist coltypes for directly using gather, prefetch, and manifest outputs without specifying column name (#1660)
• add --from-file to sig cat (#1657)
• implement a lazy/on-demand Index loading class to support low memory tracking of a large index (#1661)
• add sourmash tax prepare to build SQLite taxonomy databases for use with tax commands(#1651)
• Support manifests in MultiIndex (#1654)
• tax summarization additions and fixes, including reporting bp and unclassified (#1667)
• add --from-file, improved sig selection to most sig commands (#1672)

Bug fixes and performance improvements:

• fix bug in gather when run with scaled=1 (#1670)

Documentation updates:

• Add sourmash-bio/community Gitter badge to README (#1658)

Refactoring and cleanup:

• add tests for sourmash tax --containment-threshold arg (#1666)
• fix sourmash tax usage string (#1655)
• add bounds checking for --scaled (#1650)

Rust interface:

• Rust Core update (tag: r0.11.0) (#1643)

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 4 years ago

sourmash v4 - v4.2.0

This release adds several significant features: first, we've added a set of taxonomy command-line functionality for combining sourmash gather output with taxonomy databases, and we've also added a new "picklist" feature that enables flexible selection of subsets of databases. Finally, we've added manifests to databases to support picklists as well as faster database loading and signature selection.

As of this release, we've also formally moved development over to the sourmash-bio organization on GitHub, and we've created a new gitter support channel, sourmash-bio/community. Please join us there if you have any questions, comments, or feature requests!

Major new features: * add tax/taxonomy submodule (#1543, #1628, #1630, #1648) * add picklists for subsetting databases and results (#1587, #1588, #1623, #1590, #1639) * Add manifests to support fast Index.select(...) and lazy loading (https://github.com/sourmash-bio/sourmash/pull/1590)

Documentation updates: * Add new GTDB databases description to docs and start legacy databases page (#1581) * Change dib-lab/ URLs to new sourmash-bio/ URLs. (#1629) * Add notice for sustainable open source study (#1580)

Minor new features: * alias --nucleotide, --no-nucleotide for moltype args. (#1632) * add signature names to known/unknown hash sigs output by sourmash prefetch (#1646)

Bug fixes and performance improvements: * Speed up sourmash gather with prefetch by ignoring unidentifiable hashes (#1613) * Check for MinHash compatibility in MinHash.intersection_and_union(...) (#1627) * Fix selection w/abund and manifest column type conversions (#1645)

Refactoring and cleanup: * Fix Rust 1.59 lints (#1600) * Minor cleanup in sourmash_args & sig submodules (#1586) * Minor cleanup in minhash module (#1585) * Fix needless borrows as suggested by clippy (#1636)

Scientific Software - Peer-reviewed - Python
Published by ctb over 4 years ago

sourmash v4 - v4.1.2

This is a bug-fix and performance release of sourmash.

There are no major new features.

Minor new features: * add query info to gather CSV output (#1565)

Bug fixes and performance improvements:

• Improved MinHash.remove_many(...) performance by five orders of magnitude (#1571)
• Fix SBT index saving bug that arbitrarily replaced names (but not content) of identical signatures in .sbt.zip files (#1568)
• Empty zipfiles should not cause AssertionError (https://github.com/dib-lab/sourmash/pull/1546)

Major refactoring and new internal functionality: * update MinHash.set_abundances to remove hash if 0 abund; handle negative abundances (#1575)

Refactoring and cleanup: * Fix tests that fail to close files that they open (#1550) * Add "&" and " | " as alternate syntax for MinHash intersection merge (#1533) * Fix missing bracket in docs (#1566) * Updates for coverage tracking (#1558) * Provide a .copy() method for both SourmashSignature() and MinHash (#1551, #1570)

Scientific Software - Peer-reviewed - Python
Published by ctb over 4 years ago

sourmash v4 - v4.1.1

This release fixes a minor bug, provides some refactorings, and dramatically decreases memory consumption for sourmash gather --linear (which is, admittedly, a niche use case :).

No major new features.

Bug fixes and performance improvements:

• Unload data with sourmash gather --linear on SBTs (https://github.com/dib-lab/sourmash/pull/1534)
• Fix sourmash gather --no-prefetch when used w/abund signatures (#1528)
• Fix sourmash index to not create directory for .sbt.zip output (#1539)

Major refactoring and new internal functionality:

• Add FrozenMinHash to better support separation of frozen and mutable data actions (#1508)

Refactoring and cleanup: * Improved error handling and testing for pathlist loading (#1469) * Updated some tests to use sourmash sketch instead of sourmash compute (#1536) * Refactor sourmash lca summarize to remove unnecessary if statements, improve tests (#1540)

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 4 years ago

sourmash v4 - v4.1.0

4.1.0 release notes

This release provides several convenient features for users, including zipfile collections on input and output and a new prefetch command. sourmash gather has also received a considerable speed/memory upgrade (twice as fast, 80-90% lower memory). You should upgrade! As a reminder, v4.x has several incompatibilities with v3.x, and if you are upgrading from v3.x you should consult our migration guide.

Major new features:

• Support zipped collections of signatures (#1349)
• Refactor gather functionality for speed & modularity (#1370, #1512, #1513)
• Provide new command, prefetch. (#1370)
• Add flexible & iterative support for outputting signatures in variety of collection formats - directories, zipfiles, etc. (#1493)
• Add max_containment to API and --max-containment to command line (#1346)
• Add --from-file option to sourmash sketch commands (#1362)

Bug fixes that break backwards compatibility:

• Require scaled signatures for containment (#1381)
• Fix CSV output for sourmash lca classify when .name is empty (#1401)
• Really old SBTs (pre-v2.0) no longer load (v1 and v2 SBTs) (changed in #1392)

Other bug fixes:

• Add proper newline output for csv module (#1319) - important for Windows!

Other new features:

• --best-only searches now work for both similarity AND containment (fixed in #1392)
• sourmash categorize now takes all database types
• add --name to sourmash sig merge (#1480)
• decline to load really large files for LCA databases if they're not valid JSON (#1495)

Major refactoring and new internal functionality:

• Add a MultiIndex class that wraps multiple Index classes (#1374)
• Refactor and dramatically simplify database loading and compatibility checking (#1406, #1420)
• Rework the find functionality for Index classes (#1392, #1477).
• Improved intersection and union calculations (#1475)

Documentation enhancements:

• Update the sourmash __init__.py docstring, provide __all__ for imports (#1364)
• Add '-h/--help' usage instructions to 'sourmash sketch' CLI (#1400)
• Add ORCID to contribution checklist (#1405)
• Add information about updating the developer environment to the developer docs (#1432)
• Docs: Partial fix for doc build issues with notebooks (#1516)

Refactoring and cleanup:

• Refactor the database loading code in sourmash_args (#1373, #1380)
• Pin needletail version to keep MSRV at 1.37 (#1393)
• Rename load_file_list_of_signatures to load_pathlist_from_file (#1423)
• Update call to notify in src/sourmash/search.py with f-strings (#1422)
• Bump MSRV to 1.42 (and other dep fixes) (#1461)
• CI/Rust: update and fix cbindgen config (#1473)
• Refactor MinHash.downsample (#1458)
• Make MinHash.downsample(...) require keyword arguments & fix newly revealed buggy test. (#1448)
• Add a check for LCA database error text intests/test_lca.py (#1445)
• pin docutils version to last working (#1444)
• add codecov configuration to fix paths (#1422, #1449)
• provide new test fixtures for cleaner testing (#1487)
• Fix small papercuts: SyntaxWarning and coverage reports (#1488)
• Clean up clippy lints from 1.52 (#1505)
• Bump docutils from 0.16 to 0.17.1 (#1499)
• Update myst-parser requirement from ~=0.13.7 to >=0.13.7,<0.15.0 (#1520)
• replace utils.TempDirectory with runtmp in some tests (#1502)

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 4 years ago

sourmash v4 - v4.0.0

Major changes for 4.0

4.0 is a major new version of sourmash, and it contains a number of new and breaking features.

Please see our migration guide for more information on how to migrate from v3.x to version 4.0!

Numerical output and search results are unchanged

There are no changes to numerical output or search results in this release; you should get the same results with v4 as you get with v3, except where command-line parameters need to be adjusted as noted below (see: protein ksize #1277, lca summarize changes #1175, sourmash gather on signatures without abundance #1328). Please file an issue if your results change!

New or changed behavior

• default SBT storage is now .sbt.zip (#1174, #1170)
• add sourmash sketch command for creating signatures (#1159)
• protein ksizes in MinHash are now divided by 3, except in sourmash compute (#1277)
• refactor MinHash API and implementation: add, iadd, merge, hashes, and max_hash (#1282, #1154, #1139, #1301)
• add HyperLogLog implementation (#1223)
• SourmashSignature.name is now a property (not a method): use str(sig) instead of name() (#1179, #1232)
• lca summarize no longer merges all signatures, and uses hash abundance by default (#1175)
• indexand lca index (#1186, #1222) now support --from-file and no longer require signature files on command line
• --traverse-directory is now on by default for signature loading behavior (#1178)
• sourmash sketch and sourmash compute no longer create empty signatures from empty files and stdin (#1347);
• sourmash sketch and sourmash compute set sig.filename to empty string when filename is - (#1347);

Feature removal

• remove Python 2.7 support (& end Python 2 compatibility) (#1145, #1144)
• remove lca gather (#1307)
• remove 10x support from sourmash compute (#1229)
• remove 'dump' command (#1157)

Feature/function deprecations

• deprecate sourmash compute (#1159)
• deprecate load_signatures, sourmash.load_one_signature, create_sbt_index, and load_sbt_index (#1279, #1304)
• deprecate import_csv in favor of new sourmash sig import --csv (#1281)

Refactoring, improvements, and minor bug fixes:

• accept file list in sourmash sig cat (#1236)
• add uniqueintersectbp and gatherresultrank to gather CSV output (#1219)
• remove deprecated minhash functions (#1149)
• fix Rust panic error in signature creation (#1172)
• cache nodes in SBT during search (#1161)
• fix two bugs in gather --output-unassigned (#1156)
• Refactor the gather code so that it uses 'hashes' instead of 'mins' (#1329)
• Update output from gather w/o abundances, so that abund output is empty instead of 0(#1328)

Documentation updates

• substantial revisions and updates to the documentation (#1283)
• add information about versioning, migrations, etc to the docs (#1153)

Infrastructure and CI changes:

• update finch requirement from 0.3.0 to 0.4.1 (#1290)
• update rand for test, and activate "js" feature for getrandom (#1275)
• dev updates (configs and doc) (#1298)
• move wheel building from Travis to GitHub Actions (#1295)
• fix new clippy warnings from Rust 1.49 (#1267)
• use tox for running tests locally (#696)
• CI: small build fixes (#1252)
• CI: Fix releases in GitHub Actions (#1250)
• update build_wheel action paths
• CI: moving python tests from travis to GH actions (#1249)
• CI: move wheel building to GitHub actions (#1244)
• remove last .rst file from docs (#1185)
• update CI for latest branch name change (#1150)

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] almost 5 years ago

sourmash v4 - v4.0.0rc2 - a near-final pre-release.

Please see release notes here, https://github.com/dib-lab/sourmash/issues/1309

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] almost 5 years ago

sourmash v4 - v4.0.0rc1

This is a pre-release version of sourmash v4.0.0. Draft release notes are below; comments appreciated!

Major changes for 4.0

4.0 is a major new version of sourmash, and it contains a number of new and breaking features.

Please see our migration guide for more information on how to migrate from v3.x to version 4.0!

New or changed behavior

• default SBT storage is now .sbt.zip (#1174, #1170)
• add sourmash sketch command for creating signatures (#1159)
• protein ksizes in MinHash are now divided by 3, except in sourmash compute (#1277)
• refactor MinHash API and implementation: add, iadd, merge, hashes, and max_hash (#1282, #1154, #1139, #1301)
• add HyperLogLog implementation (#1223)
• SourmashSignature.name is now a property (not a method): use str(sig) instead of name() (#1179, #1232)
• lca summarize no longer merges all signatures, and uses hash abundance by default (#1175)
• indexand lca index (#1186, #1222) now support --from-file and no longer require signature files on command line
• --traverse-directory is now on by default for signature loading behavior (#1178)

Feature removal

• remove Python 2.7 support (& end Python 2 compatibility) (#1145, #1144)
• remove lca gather (#1307)
• remove 10x support from sourmash compute (#1229)
• remove 'dump' command (#1157)

Feature/function deprecations

• deprecate sourmash compute (#1159)
• deprecate load_signatures, sourmash.load_one_signature, create_sbt_index, and load_sbt_index (#1279, #1304)
• deprecate import_csv in favor of new sourmash sig import --csv (#1281)

Refactoring, improvements, and minor bug fixes:

• accept file list in sourmash sig cat (#1236)
• add uniqueintersectbp and gatherresultrank to gather CSV output (#1219)
• remove deprecated minhash functions (#1149)
• fix Rust panic error in signature creation (#1172)
• cache nodes in SBT during search (#1161)
• fix two bugs in gather --output-unassigned (#1156)
• Refactor the gather code so that it uses 'hashes' instead of 'mins' (#1329)
• Update output from gather w/o abundances, so that abund output is empty instead of 0(#1328)

Documentation updates

• substantial revisions and updates to the documentation (#1283)
• add information about versioning, migrations, etc to the docs (#1153)

Infrastructure and CI changes:

• update finch requirement from 0.3.0 to 0.4.1 (#1290)
• update rand for test, and activate "js" feature for getrandom (#1275)
• dev updates (configs and doc) (#1298)
• move wheel building from Travis to GitHub Actions (#1295)
• fix new clippy warnings from Rust 1.49 (#1267)
• use tox for running tests locally (#696)
• CI: small build fixes (#1252)
• CI: Fix releases in GitHub Actions (#1250)
• update build_wheel action paths
• CI: moving python tests from travis to GH actions (#1249)
• CI: move wheel building to GitHub actions (#1244)
• remove last .rst file from docs (#1185)
• update CI for latest branch name change (#1150)

Scientific Software - Peer-reviewed - Python
Published by ctb almost 5 years ago

sourmash v4 - v3.5.1

Feature deprecations

• add deprecation warning for sourmash compute --input-is-10x (#1326)
• add warnings about new sourmash lca summarize behavior (#1326)
• add warning for new behavior of MinHash.merge(...) (#1326)
• add deprecation warning for TarStorage (#1165)

Infrastructure and CI changes:

• Backport github actions to stable branch (3.5.x) (#1317)

Scientific Software - Peer-reviewed - Python
Published by ctb almost 5 years ago

sourmash v4 - v3.5.0

This is the first of several minor releases (v3.5.x) from the new stable branch. These releases focus on preparing for sourmash v4.0 by introducing deprecations and warnings for features that will be removed in v4.0.

Refactoring and deprecations: * MinHash class refactoring (#1128, #1129); many deprecations for 4.0 and 5.0 * sourmash dump deprecated, for removal in 4.0 (#1147) * import sourmash_lib deprecated, for removal in 4.0 (#1143)

Cleanup: * remove mentions of ijson and khmer (no longer needed dependencies) #1140

Documentation: * Simplify and clean up README (#1124) * Add sourmash logo to docs and README (#1127) * update release process and release notes (#1125)

Rust: * Update typed-builder requirement from 0.6.0 to 0.7.0 (#1121)

Scientific Software - Peer-reviewed - Python
Published by ctb over 5 years ago

sourmash v4 - v3.4.1

Major new features: * Document sourmash.fig usage and behavior; enable output of compare clustering with labels (#859) * Adds --majority option to lca classify using majority vote algorithm (#1113)

Minor improvements: * MinHash compatibility check to sourmash sig intersect (#1116)

Bugs fixed: * add ksize selectors back into sourmash sig functions (#1105)

Documentation updates: * Minor updates to release procedure (#1102) * Update DB links in docs (#1084)

Scientific Software - Peer-reviewed - Python
Published by ctb over 5 years ago

sourmash v4 - v3.4.0

Major new features: * enable seamless loading of signatures from indexed databases (#1059, #1083, #1090) * add signature cat and signature split commands to combine/split signature files (#1044, #1074) * add compute-optimized MinHash (for small scaled or large cardinalities) in Rust (#1045) * optionally weight lca summarize output by hashval abundance. (#1022) * enable moltypes other than DNA in LCA databases (#1013)

Minor improvements: * add --num-results/-n to gather (#1047) * improve lca index error message when inserting num signature (#1076) * autodetect FASTA/FASTQ files if given as signatures (#1078) * add islineagematch, poptorank, makelineage to lcautils (#1081) * use stricter niffler versions and add new gz feature to it (#1070) * added MinHash.clear() and MinHash.add_hash_with_abundance to Python API (#1046)

Bugs fixed: * investigations and fixes around new gather behavior. (#1001)

Refactoring: * move tests from test_lca into test_lca_functions (#1035) * remove unused runshellcmd function (#1032) * refactor some tests in testsourmash.py to use @utils.intempdir decorators (#1020) * use install scripts from py-ipfs-http-client (#1068)

Documentation: * Improve documentation around abundance projection (#1073) * Replace recommonmark with myst (docs) (#1021) * Fix doctest filename error (#1040)

Thanks to @luizirber @ctb @bluegenes @erikyoung85 for their contributions!

Scientific Software - Peer-reviewed - Python
Published by luizirber over 5 years ago

sourmash v4 - 3.3.1

Improvements:

• Deal with duplicated MD5 in storages (#994)
• Hide internal representation in core, and update FFI and cbindgen (#986)

Build, CI and docs:

• upgrade sourmash index usage docs on CLI (#975)
• Fix two temp files output locations in tests (#989)

Scientific Software - Peer-reviewed - Python
Published by luizirber over 5 years ago

sourmash v4 - version 3.3.0

Improvements:

• add ZipStorage, support loading SBT databases from storage; .sbt.zip extensions. (#648)
• Replace khmer.Nodegraph with rust nodegraph; ~5x speedup of SBT search & gather. (#799)

Bugs:

• Document and (lightly) fix the LCA_Database API. (#966)
• Fix bug when using Python 3.5 and before; refactor LCA_Database tests (#962)

Documentation:

• Document gather abund tests a bit better; minor refactoring (#886)
• Improve lca index error (#963)

Scientific Software - Peer-reviewed - Python
Published by ctb over 5 years ago

sourmash v4 - version 3.2.3

Incompatibilities with previous versions due to bugs: * sourmash gather on SBT databases was setting --threshold-bp=0 in all cases. This was fixed in #942, and output may change. Specify --threshold-bp=0 to recover old behavior.

Improvements:

• refactor LCA_Database class to support programmatic creation. (#946)
• add --singleton option to lca summarize (#922)
• update gather to calculate fraction of match that was in original query (#938)
• add compare --containment (#937)
• add --outdir argument to sourmash compute (#935)
• improvements to sourmash argparse output for compute. (#931)

Bugs: * fix lca classify bug with -o (#902) * set_abundances now works with large signatures (#911) * test & fix LinearIndex, SBT, and LCA gather thresholding. (#942)

Build, CI and docs: * create .sonarcloud.properties * pin virtualenv version for asv, and also run GH actions on rust version tags (#903) * add make clean & rustup update to dev docs (#927)

Scientific Software - Peer-reviewed - Python
Published by ctb over 5 years ago

sourmash v4 -

Improvements:

• more refactoring of MinHash API (#889)
• addhashwith_abundance method in core library (#892)
• Replace minspush and abundspush with set_abundances (#887)
• More refactoring of MinHash comparison code (#882)
• better sourmash compare error handling (#876)

Bugs:

• add_hash with num doesn't set abundances properly (#891)
• name signatures based on md5sum, not on name() (#884)

Build, CI and docs:

• update docs for how to run Rust tests (#888)

Scientific Software - Peer-reviewed - Python
Published by luizirber almost 6 years ago

sourmash v4 -

Bugs:

• re-add 'signature' as alias for 'sig' (#881)

Scientific Software - Peer-reviewed - Python
Published by luizirber almost 6 years ago

sourmash v4 -

Features:

• Move functionality to Rust for signature computation and downsampling code in sbtmh.py (#845) (#856)
• add --labeltext to plot (#854)

Improvements:

• Improve sketching performance with lookup tables for complement and DNA validation (#861) (#865)
• refactor argparse.FileType out of sourmash argument handling. (#853)

Bugs:

• Fix 'gather' threshold reporting to report threshold, not match. (#850)
• Fix counting of species during lca index (#841)

Build, CI and docs:

• Fix travis conditions and pip usage (#873)
• Use Python dev mode on 3.7, and build PRs that merge against any branch (#864)
• Use tarpaulin instead of grcov (#862)
• only run rust checks if it changes rust code (#852)
• Release process update for 3.1.0 (#847)
• Ignore .sig and .sbt files for repo language stats (#846)

Scientific Software - Peer-reviewed - Python
Published by luizirber almost 6 years ago

sourmash v4 -

Features:

• Implement improved & consistent argument parsing (#785)
• Moving loading and save sigs to rust (#532)
• Update gather implementations for LCA and SBT to use thresholding (#843)

Improvements:

• Do add_many in Rust, use it in LCA _signatures (#826) (#840)
• Expose an unload method for SBT nodes (#784)

Build, CI and docs:

• Trigger new Software Heritage archival snapshot on new tags (#839)
• Fix netlify build (#842)
• Document code structure in dev guide (#832)
• use python 3.7 in RTD build (#825)

Scientific Software - Peer-reviewed - Python
Published by luizirber almost 6 years ago

sourmash v4 - https://github.com/sourmash-bio/sourmash/releases/tag/v3.0.1

Scientific Software - Peer-reviewed - Python
Published by luizirber almost 6 years ago

sourmash v4 - 3.0.0

Features:

• Replacing C++ with Rust (#424)
• Create an Index abstract base class (#556)

Improvements:

• improve error handling etc. in sourmash lca index. (#798)
• Move similarity with abundance computation into Rust (#808)

Bugs:

• fix mem leak in get_mins (#807)
• Fix LCA search error if query has abundance (#804)

Build, CI and docs:

• Set up MSRV, minimum supported rust version (#806)
• update docs and add recommonmark as a test dependency (#805)
• Release process updates and sourmash 3.0 release notes (#776)

Scientific Software - Peer-reviewed - Python
Published by luizirber almost 6 years ago

sourmash v4 -

Bugs:

• fix some bugs in rankinfo (#797)
• Better molecule type checks (#782)

Scientific Software - Peer-reviewed - Python
Published by luizirber about 6 years ago

sourmash v4 -

Features:

• Add hp encoding for proteins (#758)
• Add sourmash signature filter to do abundance filtering. (#748)
• add a --abundances-from flag to sourmash signature intersect, to preserve abundances (#747)

Improvements:

• Include more base deps: numpy, scipy and matplotlib (#770)
• bam2fasta package to simplify sourmash compute (#768)
• Optimize KmerMinHash add_sequence (#744)

Bugs:

• Force signature order in testsigfilter_1 to fix heisenbug (#761)
• save_signatures with a file opened in binary mode fails (#746)
• saved fasta files incorrectly (#740)
• Bug: segfault with set_abundances (#745)

Build, CI and docs:

• update cibuildwheel (#774)
• Fix asv benchmarks (#509) (#759)
• add the f1000 paper (#739)
• release docs update (#554)

Rust changes:

• Experimental SBT with MQF internal nodes in Rust (#772)
• Fixes for WASI compilation (#771)
• changes to rust code from core/rust branch (#760)

Scientific Software - Peer-reviewed - Python
Published by luizirber about 6 years ago

sourmash v4 -

• Parallelized compare function with multiprocessing (#709)
• add compute signatures for 10x bam file (#713)
• Experimental v5 SBT format (#694)
• initial refactor of compute command (and associated test module) (#734)
• Fix --output-unassigned to output abundances if available. (#726)
• Update docstring for --traverse-directory on sourmash index (#727)

Scientific Software - Peer-reviewed - Python
Published by luizirber about 6 years ago

sourmash v4 - https://github.com/sourmash-bio/sourmash/releases/tag/v2.1.0

Scientific Software - Peer-reviewed - Python
Published by luizirber over 6 years ago

sourmash v4 - https://github.com/sourmash-bio/sourmash/releases/tag/v2.0.1

Scientific Software - Peer-reviewed - Python
Published by luizirber over 6 years ago

sourmash v4 - https://github.com/sourmash-bio/sourmash/releases/tag/v2.0.0

Scientific Software - Peer-reviewed - Python
Published by luizirber almost 7 years ago

sourmash v4 - v1.0

First production release of sourmash.

Scientific Software - Peer-reviewed - Python
Published by ctb over 9 years ago

sourmash v4 - version 0.9.6

Fix package import problem.

Scientific Software - Peer-reviewed - Python
Published by ctb over 9 years ago

sourmash v4 - version 0.9.5

Update of minor release-related issues.

Scientific Software - Peer-reviewed - Python
Published by ctb over 9 years ago

sourmash v4 - interim release for JOSS review, pre-1.0

Scientific Software - Peer-reviewed - Python
Published by ctb over 9 years ago

sourmash v4 - Beta release before 1.0, done with release checklist.

Scientific Software - Peer-reviewed - Python
Published by ctb over 9 years ago

sourmash v4 - Fourth beta release before 1.0.

Submitting to Journal of Open Source Software; 1.0 will come out with acceptance.

Scientific Software - Peer-reviewed - Python
Published by ctb over 9 years ago

sourmash v4 - Third beta release before 1.0.

Submitting to Journal of Open Source Software; 1.0 will come out with acceptance.

Scientific Software - Peer-reviewed - Python
Published by ctb over 9 years ago

sourmash v4 - Second beta release before 1.0

Scientific Software - Peer-reviewed - Python
Published by ctb over 9 years ago

sourmash v4 - Beta release before 1.0

The first tested, documented release.

Scientific Software - Peer-reviewed - Python
Published by ctb over 9 years ago