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[pre-commit.ci] pre-commit autoupdate #3003

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merged 7 commits into from
Jun 18, 2024
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codecov bot commented Feb 12, 2024

Codecov Report

Attention: Patch coverage is 80.00000% with 2 lines in your changes missing coverage. Please review.

Project coverage is 86.70%. Comparing base (0479afc) to head (143c92b).
Report is 68 commits behind head on latest.

Files with missing lines Patch % Lines
src/sourmash/sbt.py 33.33% 2 Missing ⚠️
Additional details and impacted files
@@           Coverage Diff           @@
##           latest    #3003   +/-   ##
=======================================
  Coverage   86.70%   86.70%           
=======================================
  Files         136      136           
  Lines       15829    15829           
  Branches     2716     2716           
=======================================
  Hits        13725    13725           
  Misses       1794     1794           
  Partials      310      310           
Flag Coverage Δ
hypothesis-py 25.35% <0.00%> (ø)
python 92.33% <80.00%> (ø)
rust 62.24% <ø> (ø)

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ctb commented Mar 13, 2024

dev env failure gives this error message:

Run tox -e py310
.tox create: /home/runner/work/sourmash/sourmash/.tox/.tox
Traceback (most recent call last):
  File "/home/runner/miniconda3/envs/sourmash_dev/bin/tox", line 10, in <module>
    sys.exit(cmdline())
  File "/home/runner/miniconda3/envs/sourmash_dev/lib/python3.10/site-packages/tox/session/__init__.py", line 44, in cmdline
    main(args)
  File "/home/runner/miniconda3/envs/sourmash_dev/lib/python3.10/site-packages/tox/session/__init__.py", line 69, in main
    exit_code = session.runcommand()
  File "/home/runner/miniconda3/envs/sourmash_dev/lib/python3.10/site-packages/tox/session/__init__.py", line 187, in runcommand
    return provision_tox(provision_tox_venv, self.config.args)
  File "/home/runner/miniconda3/envs/sourmash_dev/lib/python3.10/site-packages/tox/session/commands/provision.py", line 12, in provision_tox
    ensure_meta_env_up_to_date(provision_venv)
  File "/home/runner/miniconda3/envs/sourmash_dev/lib/python3.10/site-packages/tox/session/commands/provision.py", line 30, in ensure_meta_env_up_to_date
    if provision_venv.setupenv():
  File "/home/runner/miniconda3/envs/sourmash_dev/lib/python3.10/site-packages/tox/venv.py", line 649, in setupenv
    status = self.update(action=action)
  File "/home/runner/miniconda3/envs/sourmash_dev/lib/python3.10/site-packages/tox/venv.py", line 277, in update
    self.hook.tox_testenv_create(action=action, venv=self)
  File "/home/runner/miniconda3/envs/sourmash_dev/lib/python3.10/site-packages/pluggy/_hooks.py", line 265, in __call__
    return self._hookexec(self.name, self.get_hookimpls(), kwargs, firstresult)
  File "/home/runner/miniconda3/envs/sourmash_dev/lib/python3.10/site-packages/pluggy/_manager.py", line 80, in _hookexec
    return self._inner_hookexec(hook_name, methods, kwargs, firstresult)
  File "/home/runner/miniconda3/envs/sourmash_dev/lib/python3.10/site-packages/pluggy/_callers.py", line 60, in _multicall
    return outcome.get_result()
  File "/home/runner/miniconda3/envs/sourmash_dev/lib/python3.10/site-packages/pluggy/_result.py", line 60, in get_result
    raise ex[1].with_traceback(ex[2])
  File "/home/runner/miniconda3/envs/sourmash_dev/lib/python3.10/site-packages/pluggy/_callers.py", line 39, in _multicall
    res = hook_impl.function(*args)
  File "/home/runner/miniconda3/envs/sourmash_dev/lib/python3.10/site-packages/tox_conda/plugin.py", line 188, in tox_testenv_create
    args = [venv.envconfig.conda_exe, "create", "--yes", "-p", envdir]
  File "/home/runner/miniconda3/envs/sourmash_dev/lib/python3.10/site-packages/tox/config/__init__.py", line 1068, in __getattribute__
    rv = object.__getattribute__(self, name)
AttributeError: 'TestenvConfig' object has no attribute 'conda_exe'. Did you mean: 'conda_env'?
Error: Process completed with exit code 1.

maybe this unresolved issue? tox-dev/tox-conda#108

@pre-commit-ci pre-commit-ci bot force-pushed the pre-commit-ci-update-config branch 2 times, most recently from 22ed6a1 to ce49c0a Compare March 25, 2024 20:46
@pre-commit-ci pre-commit-ci bot force-pushed the pre-commit-ci-update-config branch from 32d0ad7 to 04db511 Compare April 1, 2024 20:59
@pre-commit-ci pre-commit-ci bot force-pushed the pre-commit-ci-update-config branch 2 times, most recently from 4d958ee to ffe6008 Compare April 15, 2024 21:08
@pre-commit-ci pre-commit-ci bot force-pushed the pre-commit-ci-update-config branch from cd7381c to 16ff136 Compare April 22, 2024 20:43
@pre-commit-ci pre-commit-ci bot force-pushed the pre-commit-ci-update-config branch 2 times, most recently from f03fc32 to 3500e84 Compare May 6, 2024 20:54
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ctb commented May 7, 2024

pre-commit.ci autofix

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ctb commented May 7, 2024

pre-commit.ci update

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ctb commented May 7, 2024

pre-commit.ci autoupdate

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ctb commented May 7, 2024

pre-commit.ci rebase

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ctb commented May 7, 2024

pre-commit.ci help

updates:
- [github.com/pre-commit/pre-commit-hooks: v4.4.0 → v4.6.0](pre-commit/pre-commit-hooks@v4.4.0...v4.6.0)
- [github.com/astral-sh/ruff-pre-commit: v0.2.0 → v0.4.9](astral-sh/ruff-pre-commit@v0.2.0...v0.4.9)
- [github.com/tox-dev/tox-ini-fmt: 0.5.2 → 1.3.1](tox-dev/tox-ini-fmt@0.5.2...1.3.1)
@pre-commit-ci pre-commit-ci bot force-pushed the pre-commit-ci-update-config branch from 57eef73 to 804716d Compare June 17, 2024 21:05
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ctb commented Jun 18, 2024

pre-commit.ci autofix

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ctb commented Jun 18, 2024

dev env failure gives this error message:

looks like this was fixed somewhere in there! So I'm going to try to merge this, assuming (most of) the tests pass...

@ctb ctb enabled auto-merge (squash) June 18, 2024 15:32
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ctb commented Jun 18, 2024

dev env failure gives this error message:

looks like this was fixed somewhere in there! So I'm going to try to merge this, assuming (most of) the tests pass...

oh, no, it wasn't. sigh.

@ctb ctb disabled auto-merge June 18, 2024 16:19
@ctb ctb merged commit 5bde7dc into latest Jun 18, 2024
39 of 40 checks passed
@ctb ctb deleted the pre-commit-ci-update-config branch June 18, 2024 16:19
@ctb ctb mentioned this pull request Jun 29, 2024
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ctb added a commit that referenced this pull request Jun 29, 2024
Release candidate testing:
- [ ] Command line tests pass for a release candidate
- [ ] All eight release candidate wheels are built

Releasing to PyPI:

- [ ] RC tag(s)s deleted on github
- [ ] Release tag cut
- [ ] Release notes written
- [ ] All eight release wheels built
- [ ] Release wheels uploaded to pypi
- [ ] tar.gz distribution uploaded to pypi

After release to PyPI and conda-forge/bioconda packages built:

- [ ] [PyPI page](https://pypi.org/project/sourmash/) updated
- [ ] Zenodo DOI successfully minted upon new github release - [see
search
results](https://zenodo.org/search?page=1&size=20&q=sourmash&sort=mostrecent)
- [ ] `pip install sourmash` installs the correct version
- [ ] [conda-forge
sourmash-minimal-feedstock](https://github.com/conda-forge/sourmash-minimal-feedstock)
has updated `sourmash-minimal` to the correct version
- [ ] `mamba create -n smash-release -y sourmash` installs the correct
version

Optional but recommended:

- [ ] PR submitted to update pyodide version
- [ ] PR submitted to update spack version

---

## Release notes

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)
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