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MRG: update README with repostatus and pyver badges, and Windows support #2928

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merged 9 commits into from
Jan 22, 2024

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@ctb ctb commented Jan 16, 2024

Direct link to updated README: link

Adds repostatus badge as well as list of python versions supported.

Switches to recommending conda-forge and sourmash-minimal, since that supports Windows ref #1923.

Also adds direct mention of operating systems supported, including Windows (ref #1923).

Fixes #2909
Fixes #2910

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codecov bot commented Jan 16, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (ccb1d49) 86.59% compared to head (ad3dfdf) 86.59%.

Additional details and impacted files
@@           Coverage Diff           @@
##           latest    #2928   +/-   ##
=======================================
  Coverage   86.59%   86.59%           
=======================================
  Files         135      135           
  Lines       15251    15251           
  Branches     2622     2622           
=======================================
  Hits        13206    13206           
  Misses       1745     1745           
  Partials      300      300           
Flag Coverage Δ
hypothesis-py 25.80% <ø> (ø)
python 92.82% <ø> (ø)
rust 59.02% <ø> (ø)

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ctb commented Jan 16, 2024

@luizirber I just noticed this in the README -

Please note that this repository is participating in a study into sustainability of open source projects. Data will be gathered about this repository for approximately the next 12 months, starting from 2021-06-11.

etc. Should I remove this now? The thesis etc is all written... ref.

@ctb ctb changed the title WIP: update README with repostatus and pyver badges WIP: update README with repostatus and pyver badges, and Windows support Jan 16, 2024
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ctb commented Jan 16, 2024

hey @sourmash-bio/devs anything else we should add to the README? thx

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Do you want to update line 85 as well? source to conda?

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ctb commented Jan 16, 2024

Do you want to update line 85 as well? source to conda?

thanks!!

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ctb commented Jan 16, 2024

hmmm.. should we change install to reference sourmash-minimal, per #1923?

@ctb ctb changed the title WIP: update README with repostatus and pyver badges, and Windows support MRG: update README with repostatus and pyver badges, and Windows support Jan 20, 2024
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ctb commented Jan 20, 2024

Ready for review and merge @sourmash-bio/devs !

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Most links work for me except for the lab website link. For some reason, the link is trying to use https instead of http (which is the written link).

http://ivory.idyll.org/lab/ is changing to https://ivory.idyll.org/lab/ in address bar

What is the explicit reason for the following paragraph:

For more information, please visit our informational page or download our participant information sheet.

Is it a project collecting sourmash use information (anonymously)?

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ctb commented Jan 22, 2024

Most links work for me except for the lab website link. For some reason, the link is trying to use https instead of http (which is the written link).

http://ivory.idyll.org/lab/ is changing to https://ivory.idyll.org/lab/ in address bar

yeah, that's a thing your browser is doing. I'll try to figure out how to get https working on that site, but not just for the PR ;).

What is the explicit reason for the following paragraph:

For more information, please visit our informational page or download our participant information sheet.

Is it a project collecting sourmash use information (anonymously)?

I just removed this - it was part of a research thing-y that I asked about above.

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ctb commented Jan 22, 2024

(I'm going to merge once tests pass again)

@ctb ctb merged commit b5c4f1b into latest Jan 22, 2024
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@ctb ctb deleted the update_readme branch January 22, 2024 19:26
@ctb ctb mentioned this pull request Feb 10, 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)
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add badges for python versions supported add repostatus badge to README
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