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Modernize freud binding, build system, and CI. #1308

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Modernize freud binding, build system, and CI. #1308

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joaander
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@joaander joaander commented Feb 7, 2025

Description

  • Replace Cython with nanobind.
  • Replace scikit-build with scikit-build-core.
  • Replace flake8 and black with ruff.
  • Replace cppcheck with a modern version of clang-tidy.
  • Support Python 3.13.

A big thanks to the large number of people who helped complete this refactoring!

Motivation and Context

Make it easier for developers to improve freud.

How Has This Been Tested?

Checklist:

joaander and others added 30 commits September 17, 2024 08:56
@joaander
Merge branch 'nanobind' into nanobind-interface
1d13bd6
@joaander
Merge pull request #1280 from glotzerlab/nanobind-interface
70ee09b 
Porting interface module
@joaander
Merge branch 'nanobind' into nanobind-cluster
84c2dd0
@joaander
Install the _cluster target.
b0d78d4
@joaander
Apply ruff fixes.
9550b24
@joaander
pre-commit
9fb9ce3
@joaander
Fix typo and remove debug prints.
8c53af3
@joaander
Remove block quote from list.
83eae33
@joaander
Merge pull request #1282 from glotzerlab/nanobind-cluster
b370e8c 
Nanobind port: Cluster module
@mariaward10
added missing methods and fixed some formatting
4bf7943
@mariaward10
Port StaticStructureFactorDebye to nanobind
64242b5
@joaander
Automatically create compile_commands.json
41d5aef
@tfteague
Configured build_wheels and tests for cluster module.
7a79c69
@tfteague
Added names to credits.rst
03269ce
@tfteague
Remove print statement from cluster.py
e8cf006
@joaander
Fix cp compile_commands.json error.
c9d7fd6
@mariaward10
fixed error related to m_structure_factor so tests now all pass
0010947
@joaander
Make new arrays in RDF::reset
a7fb08c 
The implementation of `reduceAndReturn` does not allow the previous
pattern of calling `prepare` in `reduce`. In the new implemtnation,
`reduceAndReturn` will return the OLD array even after the new one is
created.

The solution is to override `reset`. In subclasses of
`BondHistogramCompute`, `reset` *must* call the base class implemtnation
which resets `m_historgram`. The subclass must then make new shared
arrays that are specific to that subclass. Lastly, the arrays must also
be initialized in the constructor to allow for the user to construct the
class and use it without calling `reset` first.
@tfteague
Appeased the clang-tidy gods.
2d36aea
@tfteague
Appeased the pre-commit gods.
3b74b53
@joaander
Fix automatic creation of comipile_commands.json.
8717edf
@joaander
Merge branch 'nanobind' into nanobind-cluster-doc
92e92d9
@joaander
pre-commit
963de76
@joaander
Merge pull request #1283 from glotzerlab/nanobind-cluster-doc
1cb1d92 
Nanobind Cluster
@janbridley @seoulfood
Update order/Nematic
5f40d6e
@janbridley @seoulfood
Export nematic and module order
89bac0c
@janbridley @seoulfood
Update cmakelists
24eec22
@janbridley @seoulfood
Move order.pyx to order.py
770a769
@janbridley @seoulfood
Update init.py
2bb30bb
@janbridley @seoulfood
Update python side for Nematic order
c77b5ef
joaander and others added 23 commits February 5, 2025 10:33
@joaander
Return const managed arrays in getters.
667480a
@joaander
Merge pull request #1305 from glotzerlab/nanobind-misc
299af7c 
Bump CI dependencies to the latest versions.
@janbridley
Uncomment CorrelationFunction
a290c45
@janbridley
Progress on exports
afc41e4
@janbridley
DONE
540cb4d
@janbridley
Lint density
0094d8a
@DomFijan
clean up commented code that was not needed
1ed46af
@DomFijan
fix ruff issues
2f6b6ca
@DomFijan
remove unused code
23db6c4
@DomFijan
fix repr
e780ab1
@DomFijan
Merge branch 'nanobind' into nanobind_density_changes
c5897c3
@DomFijan
export and use only double correlationFunction
0b8be1c
@DomFijan
remove templating from the CorrelationFunction class
4deb50a
@DomFijan
pre-commit
83e179c
@DomFijan
remove unused code
d1386ca
@janbridley
Remove density from clang-tidy
8688f8e
@joaander
clang-tidy fixes
a53fa1c
@joaander
More clang-tidy fixes.
89417ce
@joaander
More clang-tidy fixes.
fda237d
@joaander
Merge pull request #1307 from glotzerlab/nanobind_density_changes
e1d69ac 
Nanobind density changes
@joaander
Identify new developers.
a1d2c74
@joaander
Remove misc TODO items.
40461ef
@joaander
Document nanobind changes.
e0c8a19
@joaander joaander requested review from a team as code owners February 7, 2025 22:01
@joaander joaander requested review from bdice and removed request for a team February 7, 2025 22:01
bdice
bdice approved these changes Feb 7, 2025
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I was pinged on this as a code reviewer, so I wanted to stop by just to congratulate the team on the immense amount of work that has gone in here. I had a couple small questions, but nothing blocking. I offer my greatest thanks for all the effort in maintaining a project that was a fond part of my time in the Glotzer lab.

.github/ISSUE_TEMPLATE/bug_report.yml Outdated
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Does freud have GPU support now?

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No, this is a copy and paste error.

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How will code reviews be managed going forward?

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The PR submitter will request a review, typically over Slack or in person.

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joaander commented Feb 8, 2025

I was pinged on this as a code reviewer, so I wanted to stop by just to congratulate the team on the immense amount of work that has gone in here. I had a couple small questions, but nothing blocking. I offer my greatest thanks for all the effort in maintaining a project that was a fond part of my time in the Glotzer lab.

Thanks for looking at this. If I recall correctly, you helped a lot with the boost::python to Cython transition. The extensive unit testing added as part of that was a huge help here. The thorough tests caught many corner cases as we ported the internals over to nanobind.

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@bdice bdice bdice approved these changes

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@joaander @bdice @mariaward10 @tfteague @janbridley @seoulfood @DomFijan @surajkannur