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Update dev env instructions #2990

Merged
merged 7 commits into from
Jul 28, 2024
Merged

Update dev env instructions #2990

merged 7 commits into from
Jul 28, 2024

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luizirber
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@luizirber luizirber commented Feb 10, 2024

Close #2793

@luizirber luizirber force-pushed the lirber/pixi branch 2 times, most recently from e60ea44 to f759c17 Compare February 10, 2024 23:51
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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 86.75%. Comparing base (d516811) to head (7f0b404).
Report is 63 commits behind head on latest.

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@@           Coverage Diff           @@
##           latest    #2990   +/-   ##
=======================================
  Coverage   86.75%   86.75%           
=======================================
  Files         137      137           
  Lines       15920    15920           
  Branches     2728     2728           
=======================================
  Hits        13811    13811           
  Misses       1800     1800           
  Partials      309      309           
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@luizirber luizirber force-pushed the lirber/pixi branch 8 times, most recently from 9cd3fec to 1878403 Compare February 11, 2024 01:18
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ctb commented Feb 11, 2024

I mean I've loved pixi, the little bit I've used it; but do we really want to switch dev instructions over to it?

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ctb commented Feb 11, 2024

(I guess I'm not immediately seeing a big reason. But I am happy to be convinced :)

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I mean I've loved pixi, the little bit I've used it; but do we really want to switch dev instructions over to it?

We have the drift on install instructions (as pointed in #2707) because what we document is not quite we run in CI.

I was going for setting up pixi and using the pixi.lock file to also install a conda environment if pixi is not available, but conda-lock and pixi diverged on the lockfile format. Maybe they will converge back, but for now they are incompatible.

It is still fine to have conda instructions and say "look at the [dependencies] section in pixi.toml and run conda create with that", but we start getting into a lot of duplicate dependency definitions... We could have an environment.yml and keep it in sync with pixi.toml too, if that's easier.

(I guess I'm not immediately seeing a big reason. But I am happy to be convinced :)

I like pixi because it is so much easier to install than conda, and doesn't mess with shell env vars. And if you're in a system that has conda installed but doesn't allow extra software installation, you can still conda install -c conda-forge pixi and have it available.

Drawback is that conda is much more stable, pixi has been moving pretty quickly and might be hard to keep up (but we do have CI setup in this PR).

It boils down to which is the easiest one to teach and get started, pixi seems easier because it's one file to download and pixi shell to get started, but conda can be more general-purpose and transfer better to other situations?

All that said, I don't use conda or pixi for sourmash development, so better to someone that does use to chime in 🙃

new features, running tests and code quality checks.
Here are some suggestions on how to set them up (note: you only need one =])

### Using mamba (conda alternative)
::::{tab-set}
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I love it!

@luizirber luizirber changed the title Use pixi for conda-based dev env Update dev env instructions Feb 12, 2024
@luizirber luizirber marked this pull request as ready for review July 28, 2024 05:35
@luizirber luizirber requested review from ctb and a team July 28, 2024 05:35
@luizirber luizirber merged commit 272a97f into latest Jul 28, 2024
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@luizirber luizirber deleted the lirber/pixi branch July 28, 2024 16:20
luizirber added a commit that referenced this pull request Jul 31, 2024
Minor new features:

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

Bug fixes:

Cleanup and documentation updates:

- Update dev env instructions (#2990)

Developer updates:

- Enable codspeed for Rust perf tracking (#3231)
- bump cibuildwheel for linux fixes, move wasm to use cibuildwheel too (#3241)

Dependabot updates:

- Break ahash dep cycle by bumping to 0.7.8, nix flake update (#3243)
- 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)
luizirber added a commit that referenced this pull request Jul 31, 2024
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:

- 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)
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explore pixi for sourmash
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