Replace pyomeca dependency with custom Pyomarkers class

[Copilot]

This PR implements a complete replacement for the pyomeca dependency by creating a custom Pyomarkers class that provides full API compatibility while being self-contained.

Summary

The pyomeca package was the only external dependency used for marker data handling. This PR removes that dependency by implementing our own Pyomarkers class with all the required functionality.

Changes Made

✅ New Pyomarkers Class (pyorerun/pyomarkers.py)

• 3D markers locations: Stores marker data in (4, n_markers, n_frames) format with homogeneous coordinates
• Time support: Includes time vector for temporal data
• Marker names/labels: Supports both marker_names and channels parameters for compatibility
• C3D file loading: from_c3d() classmethod using ezc3d for direct C3D file import
• Display control: show_labels flag to control marker label visibility
• Full API compatibility: Maintains all existing pyomeca.Markers interfaces:
  • .shape property
  • .to_numpy() method
  • .channel.values for marker names
  • .attrs dictionary for metadata
  • Division operators for unit conversion (e.g., markers /= 1000)

✅ Updated Imports

• Updated all imports across the codebase:
  • pyorerun/rrc3d.py
  • pyorerun/phase_rerun.py
  • pyorerun/xp_components/markers.py
  • pyorerun/multi_phase_rerun.py
  • tests/test_rerun_c3d.py
  • tests/test_phase_rerun.py
  • All example files in examples/biorbd/

✅ Dependency Cleanup

• Removed pyomeca from pyproject.toml and setup.py
• Added ezc3d as direct dependency (now needed for C3D loading)
• Updated package descriptions to remove pyomeca references

✅ Tests

• Created comprehensive test suite in tests/test_pyomarkers.py
• Verified compatibility with existing test patterns
• Tested real C3D file loading and processing

Example Usage

from pyorerun.pyomarkers import Pyomarkers

# Create from numpy array
data = np.random.rand(3, 5, 100)  # 5 markers, 100 frames
markers = Pyomarkers(data, marker_names=['M1', 'M2', 'M3', 'M4', 'M5'])

# Load from C3D file
markers = Pyomarkers.from_c3d('path/to/file.c3d')

# All existing API still works
print(markers.shape)  # (4, 5, 100)
print(markers.channel.values)  # ['M1', 'M2', 'M3', 'M4', 'M5']
markers.attrs['units'] = 'mm'
markers /= 1000  # Convert to meters

Verification

All existing functionality continues to work exactly as before:

• ✅ C3D file processing in rrc3d()
• ✅ Marker visualization in PhaseRerun.add_xp_markers()
• ✅ Unit conversion functions
• ✅ All existing tests pass
• ✅ Example scripts work without modification

The implementation maintains 100% backward compatibility while removing the external dependency.

Fixes #65.

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This change is 

[qlty-cloud-legacy]

Function __init__ has 5 arguments (exceeds 4 allowed). Consider refactoring.

[qlty-cloud-legacy]

Function __init__ has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.

[Ipuch]

Function init has 7 arguments (exceeds 4 allowed). Consider refactoring. New
def init(
Severity: MajorFound in pyorerun/pyomarkers.py - About 50 mins to fix
Function init has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring. New
def init(
self,
data: np.ndarray = None,
time: Optional[np.ndarray] = None,
marker_names: Optional[List[str]] = None,
Severity: MinorFound in pyorerun/pyomarkers.py - About 1 hr to fix

[qltysh]

❌ 1 blocking issue (1 total)

Tool	Category	Rule	Count
qlty	Structure	Function with many parameters (count = 7): __init__	1	❌

[qlty-cloud-legacy]

Code Climate has analyzed commit 46d092e and detected 2 issues on this pull request.

Here's the issue category breakdown:

Category	Count
Complexity	2

View more on Code Climate.