Align and Widen Dependency Version Constraints

[harryswift01]

Summary

This PR widens and corrects the dependency version constraints in pyproject.toml and conda-recipe/meta.yaml, replacing several overly narrow single-patch/single-month pins with properly verified ranges.

Changes

Widened ranges:

• Widened upper bounds on pandas, rich, networkx, dask, distributed, dask-jobqueue from single-patch/single-month pins to full-range ceilings
• Lowered floors on pandas, psutil, rich, art, networkx, rdkit, numba, dask, distributed to the actual minimum version required, verified by installing each exact version and running the full test suite

Wheel-availability and security fixes:

• Raised numpy, mdanalysis, pandas, psutil, rdkit, numba, PyYAML floors where the previous floor lacked a prebuilt wheel for Python 3.12, 3.13, or 3.14 (would otherwise fall back to a fragile source build, or fail to install at all)
• Raised requests floor to 2.32.2: 2.32.0 and 2.32.1 are both yanked from PyPI
• Capped numpy at <2.5.0: waterEntropy's vibrational entropy calculation uses np.linalg.eig() on a symmetric covariance matrix, and every 2.5.x release returns eigenvalues in a different (non-deterministic) order than 2.3.x/2.4.x

Consistency and cleanup:

• Reconciled numpy, psutil, dask, distributed ranges to match the now-loosened constraints in waterEntropy, previously exact-pinned
• Removed unused dependencies: matplotlib, python-json-logger, sphinx_rtd_theme, sphinxcontrib-contentui, sphinxcontrib-details-directive
• Kept conda-recipe/meta.yaml in sync with pyproject.toml throughout

Impact

• Reduces the risk of resolver conflicts when CodeEntropy is installed alongside other scientific tools in a shared environment
• All floors verified against the full unit test suite on Python 3.12, 3.13, and 3.14
• Upper bounds are kept, not removed, so future major-version bumps still go through a tested PR rather than resolving unbounded

[jimboid]

looks great, hopefully renovate will now start to behave how we like it to. Happy to merge.