ci: test against numpy v2

[njzjz]

Summary by CodeRabbit

• Chores
  • Streamlined the optional dependencies section by removing extraneous comments in the configuration file.
  • The test dependency now clearly specifies "numpy<2" without additional notes.

[coderabbitai]

📝 Walkthrough

Walkthrough

The changes in the pull request focus on the pyproject.toml file, specifically modifying the optional dependencies section. The test dependency has been streamlined to only include "numpy<2" without any comments. Other sections, including amber, docs, and benchmark, remain unchanged, maintaining their previous specifications. The overall effect is a cleaner presentation of the optional dependencies.

Changes

File	Change Summary
pyproject.toml	Modified test optional dependency to include only "numpy<2" without comments; other sections remain unchanged.

Sequence Diagram(s)

sequenceDiagram
    participant User
    participant System
    User->>System: Request to install dependencies
    System->>System: Check optional dependencies
    alt Test dependencies
        System->>System: Include "numpy<2"
    end
    alt Other dependencies
        System->>System: Include amber, docs, benchmark as specified
    end
    System->>User: Dependencies installed

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📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between d0a7868 and 1c3def6.

📒 Files selected for processing (1)

• pyproject.toml (0 hunks)

💤 Files with no reviewable changes (1)

• pyproject.toml

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[codspeed-hq]

CodSpeed Performance Report

Merging #695 will not alter performance

_{Comparing njzjz:numpy-v2 (1c3def6) with devel (d0a7868)}

🎉 Hooray! pytest-codspeed just leveled up to 3.0.0!

A heads-up, this is a breaking change and it might affect your current performance baseline a bit. But here's the exciting part - it's packed with new, cool features and promises improved result stability 🥳!
Curious about what's new? Visit our releases page to delve into all the awesome details about this new version.

Summary

✅ 2 untouched benchmarks

[njzjz]

======================================================================
ERROR: test_orig (test_pick_atom_idx.TestPickByAmberMask.test_orig)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/runner/work/dpdata/dpdata/tests/test_pick_atom_idx.py", line 42, in setUp
    ).pick_by_amber_mask(parmfile, interactwith, pass_coords=True, nopbc=True)[
      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/dpdata/dpdata/dpdata/system.py", line 1074, in pick_by_amber_mask
    parm = load_param_file(param)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/dpdata/dpdata/dpdata/amber/mask.py", line 38, in load_param_file
    return parmed.load_file(param_file)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.4/x64/lib/python3.12/site-packages/parmed/formats/registry.py", line 194, in load_file
    return cls.parse(filename, *args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.4/x64/lib/python3.12/site-packages/parmed/amber/amberformat.py", line 353, in parse
    return LoadParm(filename, *args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.4/x64/lib/python3.12/site-packages/parmed/amber/readparm.py", line 48, in LoadParm
    parm = parm.view_as(AmberParm)
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.4/x64/lib/python3.12/site-packages/parmed/amber/amberformat.py", line 420, in view_as
    return cls.from_rawdata(self)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.4/x64/lib/python3.12/site-packages/parmed/amber/_amberparm.py", line 233, in from_rawdata
    inst.initialize_topology()
  File "/opt/hostedtoolcache/Python/3.12.4/x64/lib/python3.12/site-packages/parmed/amber/_amberparm.py", line 204, in initialize_topology
    self.box = list(box[1:]) + [box[0], box[0], box[0]]
    ^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.4/x64/lib/python3.12/site-packages/parmed/amber/_amberparm.py", line 2150, in box
    box = np.array(box, dtype=np.float64, copy=False, subok=True).reshape((-1, 6))
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: Unable to avoid copy while creating an array as requested.
If using `np.array(obj, copy=False)` replace it with `np.asarray(obj)` to allow a copy when needed (no behavior change in NumPy 1.x).
For more details, see https://numpy.org/devdocs/numpy_2_0_migration_guide.html#adapting-to-changes-in-the-copy-keyword.

[njzjz]

Submitted to ParmEd/ParmEd#1364

[njzjz]

Submitted to ParmEd/ParmEd#1364

This is fixed.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 85.07%. Comparing base (d0a7868) to head (1c3def6).
Report is 1 commits behind head on devel.

Additional details and impacted files

@@           Coverage Diff           @@
##            devel     #695   +/-   ##
=======================================
  Coverage   85.07%   85.07%           
=======================================
  Files          81       81           
  Lines        7478     7478           
=======================================
  Hits         6362     6362           
  Misses       1116     1116           

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