Adding free flight simulations

[camUrban]

Description

This PR adds the ability to perform simulations that couple an airplane's motion to the aerodynamic forces due to its motion.

Motivation

Adding coupled simulations increases the use-cases of Ptera Software beyond pure aerodynamic investigations and makes it more attractive for general robotics simulations.

Relevant Issues

Closes #65 and improves upon solution to #50.

Changes

• Adds the CoupledOperatingPoint class to pterasoftware/operating_point.py
• Adds the CoupledMovement class to pterasoftware/movements/movement.py
• Adds the CoupledUnsteadyProblem class to pterasoftware/problems.py
• Adds the CoupledSteadyProblem class to pterasoftware/problems.py
• Adds pterasoftware/mujoco_model.py, which contains the MuJoCoModel class.
• Adds pterasoftware/coupled_unsteady_ring_vortex_lattice_method.py, which contains the CoupledUnsteadyRingVortexLatticeMethodSolver class.
• Updates pterasoftware/__init__.py to import the new modules.
• Fixes inconsistency in UnsteadyRingVortexLatticeMethodSolver's _calculate_loads method where it was using different functions for calculating the cross product for each LineVortex leg.
• Removes redundant increment of index variable in pterasoftware.output.animate.
• Adds checks to prevent plotting non-existent wake RingVortex pterasoftware.output.animate and pterasoftware.output.draw.
• Changes output formatting in output.print_results to display values in scientific notation for better readability across scales.
• Introduces the rotationPointOffset_Gs_Ler parameter to WingMovement, allowing specification of a custom rotation point for wing angular motion.
• Improves delta_time's "optimize" mode by tuning the local optimizer and introducing a fall back to dual annealing as a global optimizer.
• Fixes a bug in delta_time's "optimize" mode where static cases weren't improved.
• Speeds up test suite by removing redundant tests and using coarser mesh parameters for geometry fixtures.
• Refactors CLAUDE.md to be significantly shorter by breaking up instructions and guidelines into other files in docs/. This uses the progressive disclosure strategy known to produce better results.
• Adds MUJOCO_CONVENTIONS.md file with verified interpretations of MuJoCo's relevant inputs and outputs.
• Adds animate_free_flight function in output.py, along with a few helper functions.

Temporary Debug Scripts to Remove Before Merging

• debugging_scripts and all files within
• docs/FREE_FLIGHT_DEVELOPMENT.md
• gammabot_simulations and all files within

New Dependencies

• MuJoCo

Change Magnitude

Moderate: Medium-sized change that adds or modifies a feature without large-scale impact.

---

Checklist

• I have created or claimed an issue for this work as described in Contributing Code.
• My branch is based on main and is up to date with the upstream main branch.
• All calculations use S.I. units.
• Code is formatted with black (line length = 88).
• Code is well documented with block comments where appropriate.
• Any external code, algorithms, or equations used have been cited in comments or docstrings.
• All new modules, classes, functions, and methods have docstrings in reStructuredText format, and are formatted using docformatter (--in-place --black). See the style guide for type hints and docstrings for more details.
• All new classes, functions, and methods in the pterasoftware package use type hints. See the style guide for type hints and docstrings for more details.
• If any major functionality was added or significantly changed, I have added or updated tests in the tests package.
• Code locally passes all tests in the tests package.
• After pushing, PR passes all automated checks (codespell, black, mypy, and tests).
• PR description links all relevant issues and follows this template.

---

[codecov]

Codecov Report

❌ Patch coverage is 51.70732% with 297 lines in your changes missing coverage. Please review.
✅ Project coverage is 80.80%. Comparing base (3dec520) to head (371820a).
⚠️ Report is 2 commits behind head on main.

Files with missing lines	Patch %	Lines
pterasoftware/output.py	10.96%	268 Missing ⚠️
pterasoftware/_mujoco_model.py	81.15%	13 Missing ⚠️
pterasoftware/operating_point.py	87.50%	7 Missing ⚠️
pterasoftware/_functions.py	69.23%	4 Missing ⚠️
pterasoftware/problems.py	95.65%	3 Missing ⚠️
pterasoftware/_transformations.py	96.00%	2 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##             main      #66       +/-   ##
===========================================
- Coverage   91.32%   80.80%   -10.52%     
===========================================
  Files          32       34        +2     
  Lines        6111     7311     +1200     
===========================================
+ Hits         5581     5908      +327     
- Misses        530     1403      +873     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.