* Update conda lockfiles (#153)

Co-authored-by: joaander <[email protected]>

* Bump actions/cache from 4.2.0 to 4.2.2 in the actions-version group (#154)

Bumps the actions-version group with 1 update: [actions/cache](https://github.com/actions/cache).


Updates `actions/cache` from 4.2.0 to 4.2.2
- [Release notes](https://github.com/actions/cache/releases)
- [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md)
- [Commits](actions/cache@1bd1e32...d4323d4)

---
updated-dependencies:
- dependency-name: actions/cache
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: actions-version
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump actions/cache from 4.2.2 to 4.2.3 in the actions-version group (#156)

Bumps the actions-version group with 1 update: [actions/cache](https://github.com/actions/cache).


Updates `actions/cache` from 4.2.2 to 4.2.3
- [Release notes](https://github.com/actions/cache/releases)
- [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md)
- [Commits](actions/cache@d4323d4...5a3ec84)

---
updated-dependencies:
- dependency-name: actions/cache
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: actions-version
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Update conda lockfiles (#157)

Co-authored-by: joaander <[email protected]>

* [pre-commit.ci] pre-commit autoupdate (#158)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.8.6 → v0.11.4](astral-sh/ruff-pre-commit@v0.8.6...v0.11.4)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Update conda lockfiles (#159)

Co-authored-by: joaander <[email protected]>

* Mesh tutorial (#155)

* Initial draft of Flexicle Tutorial Docs

* Update AUTHORS.md

Add Kate and Philipp to authors list

* rename tutorial

* add new tutorial branch and set up index

* update README

* first draft of creating meshes

* finish mesh creation tutorial

* add tutorial 10-1 and 10-2

* finished version of 01- and 02-

* fix triangulation image

* remove third example

* update imported libraries

* update execution_count

* fix my name

* remove id in 00-index

* fix ids

* spell check

* fully comment out pyvista cell

* np -> numpy

* pre-commit

* improve tutorial according to Josh's suggestions

* fix precommit

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Switch to a uniform figure style.

* Tweaks

* Spellcheck
* Truncate long output
* Hide the fresnel code

* Make section titles consistent.

* pre-commit

---------

Co-authored-by: Kate Jensen <[email protected]>
Co-authored-by: kmjens <[email protected]>
Co-authored-by: SchoeniPhlippsn <[email protected]>
Co-authored-by: Joshua A. Anderson <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Use **row** in the organizing and executing simulations tutorial (#160)

* First draft of row tutorial.

* Remove unused project file.

* ruff format

* Fix link.

* Test with python 3.13

* pre-commit

* Fix cache key.

* Grammar pass.

* pre-commit

* Grammar and consistency.

* More tweaks.

* Run dependabot quarterly.

* More tweaks to dependabot config.

* Update uv and conda lockfiles quarterly.

* Fix cron.

* Switch back to fugit syntanx. Dependabot fails with the POSIX syntax.

* Update conda lockfiles (#161)

Co-authored-by: joaander <[email protected]>

* Bump the actions-version group with 2 updates (#162)

Bumps the actions-version group with 2 updates: [mamba-org/setup-micromamba](https://github.com/mamba-org/setup-micromamba) and [glotzerlab/workflows](https://github.com/glotzerlab/workflows).


Updates `mamba-org/setup-micromamba` from 2.0.4 to 2.0.5
- [Release notes](https://github.com/mamba-org/setup-micromamba/releases)
- [Commits](mamba-org/setup-micromamba@0dea637...b09ef9b)

Updates `glotzerlab/workflows` from 0.6.0 to 0.7.0
- [Release notes](https://github.com/glotzerlab/workflows/releases)
- [Commits](glotzerlab/workflows@a36a971...1855eec)

---
updated-dependencies:
- dependency-name: mamba-org/setup-micromamba
  dependency-version: 2.0.5
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: actions-version
- dependency-name: glotzerlab/workflows
  dependency-version: 0.7.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: actions-version
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Close files instead of calling flush. (#163)

Fully close gsd and h5 files to promote best practices and better match
typical use cases where scripts complete and exit, implicitly closing
open files. With the new auto_flush feature in 5.3.0, we do not need to
encourage users to call flush. Closing the file is a final act, so users
will be more considerate about it -- they cannot continue writing to a
closed file.

* [pre-commit.ci] pre-commit autoupdate (#164)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.11.4 → v0.12.2](astral-sh/ruff-pre-commit@v0.11.4...v0.12.2)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Configure Renovate (#166)

* Add renovate.json

* Use pixi

* Use prek.

* prek autoupdate

* Use correct pixi.toml.

* Add openmpi.

* Remove use of deprecated mode argument.

---------

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Co-authored-by: Joshua A. Anderson <[email protected]>

* Update actions/cache action to v4.2.4 (#167)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

* Update actions/checkout action to v4.3.0 (#168)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

* Update actions/checkout action to v5 (#171)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

* Update glotzerlab/workflows action to v0.10.0 (#170)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

* Lock file maintenance (#172)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

* Update actions/cache action to v4.3.0 (#173)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

* Lock file maintenance (#174)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

* Lock file maintenance (#175)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

* Update dependency python to 3.14.* (#176)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

* Lock file maintenance (#177)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

* Lock file maintenance (#178)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

* Update prefix-dev/setup-pixi action to v0.9.2 (#179)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

* Lock file maintenance (#180)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

* Lock file maintenance (#181)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

* Update prefix-dev/setup-pixi action to v0.9.3 (#182)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

* Lock file maintenance (#183)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

* Lock file maintenance (#184)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

* Update actions/checkout action to v5.0.1 (#185)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

* Lock file maintenance (#186)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

* Fix the HPMC wall potential example. (#187)

* Update actions/checkout action to v6 (#188)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

* Update glotzerlab/workflows action to v0.11.0 (#189)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

* Lock file maintenance (#190)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

* 6.0 fixes (#193)

* Rerender missing images.

* Attempt to format code as code in alerts.

* Use HOOMD 6.0 parameter assignment.

* Update actions/checkout action to v6.0.1 (#191)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

* Lock file maintenance (#192)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

* Update actions/cache action to v5 (#194)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

* Update actions/cache action to v5.0.1 (#195)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

* Lock file maintenance (#196)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

* Lock file maintenance (#197)

* Lock file maintenance

* Execute correctly with matplotlib 3.10

---------

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Co-authored-by: Joshua A. Anderson <[email protected]>

* Lock file maintenance (#198)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

* Lock file maintenance (#199)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

* Update actions/cache action to v5.0.2 (#200)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

* Copyright year.

* Lock file maintenance (#201)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

* Update actions/checkout action to v6.0.2 (#202)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

* Fix particle position assignment in simulation frame

* Fix position_3D assignment in notebook

* Remove flush call from simulation run

* Refine explanation of active self-propelled particles

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: pull-request-submitter[bot] <82944014+pull-request-submitter[bot]@users.noreply.github.com>
Co-authored-by: joaander <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: SchoeniPhlippsn <[email protected]>
Co-authored-by: Kate Jensen <[email protected]>
Co-authored-by: kmjens <[email protected]>
Co-authored-by: SchoeniPhlippsn <[email protected]>
Co-authored-by: Joshua A. Anderson <[email protected]>
Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>