🚀 aiida-thermo_pw: immigrate aiida-thermo_pw to aiida-mechanical

[ymzhang0]

• Ported MIT & Non-Commercial licenses, expanded .gitignore, and set up initial repository metadata.
• Staged pyproject.toml using the modern hatchling build system, declaring metadata, authors, package dependencies, AiiDA entry points, and developer configurations (pytest, yapf, pylint, etc.).
• Migrated sample crystal structures (Si.xsf, Pb.xsf), workflow scripts (example_01.py), and plotting utilities.
• Updated docstrings in calculations to properly refer to the Quantum ESPRESSO pw.x code.
• Enhanced triclinic and monoclinic Bravais lattice conversions with integer transformation matrix validation, determinant checks, and added the empty get_parameters_from_pymatgen_structure helper method.
• Consolidated imports in tools/init.py to a single line.
• Standardized ThermoPwBaseAnalyser as a standalone class, re-enabling active scheduler output parsing, and added the delete_nodes_and_remote_folder utility.
• Added custom explicit kpoints validation in get_builder_from_protocol and simplified direct structure formatting calls in setup().
• Renamed the source root from src/aiida_thermo_pw to src/aiida_mechanical (preserving full Git history).
• Updated all module imports to aiida_mechanical across calculations, parsers, workflows, examples, and documentation.
• AiiDA Namespace Unified: Updated entry points in pyproject.toml to register under the new general mechanical namespace:
  • Calculation & Parser: mechanical.thermo_pw
  • Workflow: mechanical.thermo_pw.base (you can cleanly add Stacking Fault Energy under mechanical.stacking_fault next to it).
• Synced package names, titles, and descriptions inside pyproject.toml, .copier-answers.yml, README.md, and the developer guide docs.
• Added essential scientific package dependencies for dislocation mathematics and plotting: ase, pymatgen, sympy, matplotlib, deprecated>=1.2.0, pyyaml, and rich.
• Registered AiiDA entry points under the new mechanical.dislocation.* namespaces for custom data structures and workflows.
• Ported custom SFE data models: cleavaged_structure.py, faulted_structure.py, gliding_systems.py, and system.py.
• Copied static crystal sample structure files into src/aiida_mechanical/data/structures/.
• Updated all internal package imports to reference aiida_mechanical instead of aiida_dislocation.
• Ported core geometric modeling tools: builder.py, calculator.py, cut.py, gliding_systems.py, structure.py, structure_builder.py, and structure_utils.py.
• Ported structure-generating @calcfunctions (generate_cleavaged_structures, generate_faulted_structures) that construct planar systems.
• Added the core mechanics workflows: gsfe.py (generalized SFE), gsfe_relax.py (relaxed GSFE), esfe.py (empirical SFE), isfe.py (inherent SFE), usfe.py (unstable SFE), twinning.py (twinning energy), as well as base class sfebase.py, layer_relax.py, and surface.py.
• Copied YAML default input configurations under workflows/dislocation/protocols/ to fully support builder setup via the AiiDA protocol API (get_builder_from_protocol).
• Resolved pre-existing linter issues in the ported codebase (e.g., corrected an undefined ax reference in cut.py, removed a duplicate classmethod definition in surface.py, and resolved out-of-scope type annotations in data classes).
• Formatted and checked the entire integrated package using Ruff to pass CI requirements.