update repo

[LouieSlocombe]

No description provided.

[Copilot]

Pull request overview

This PR modernizes the project’s build/packaging workflow by migrating from legacy setup.py/Makefile-based builds to a meson-python (pyproject.toml + meson.build) build, updating imports to use installed-package paths, and adding CI + pytest coverage to validate the compiled extensions and example workflows end-to-end.

Changes:

• Replace setup.py/Makefile packaging with Meson build definitions and a PEP 517 pyproject.toml backend.
• Add smoke + end-to-end pytest suites (including “slow” example runs) and CI to build/install/test on Linux and macOS.
• Update internal imports and CLI modules to work as installed console scripts (with optional dependency handling for phonopy).

Reviewed changes

Copilot reviewed 39 out of 40 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
tests/test_extensions.py	Adds smoke tests for compiled extensions and a few core routines.
tests/test_examples.py	Adds end-to-end example runs via csld_main and checks physics-level invariants.
tests/conftest.py	Ensures tests exercise the installed package (not the source tree) and provides example fixture.
setup.py	Removed legacy setuptools/Cython build entrypoint.
setup.cfg	Removed legacy setuptools config.
README.md	Updates installation instructions for pip/Meson flow and adds conda/dev guidance.
pyproject.toml	Introduces PEP 517 build config, dependencies, and console scripts.
PKG-INFO	Removed generated legacy packaging metadata.
meson.build	Adds top-level Meson project config (languages, NumPy/f2py include discovery, LAPACK detection, installs).
manual.rst	Updates installation docs to the new pip install . + extras workflow.
MANIFEST.in	Removed legacy sdist include rule.
Makefile	Removed legacy compilation driver for f2py artifacts.
examples/Si/fit-forcefield.sh	Switches to calling installed csld_main instead of a repo-relative script path.
environment.yml	Adds a conda environment to provide compilers, BLAS/LAPACK, and build tooling.
cssolve/setup.py	Removed legacy cssolve packaging script.
cssolve/meson.build	Adds Meson targets to build/install cssolve.bregman and Python sources.
cssolve/csfit.py	Updates import to use installed cssolve.bcs_driver.
cssolve/bregman_func.py	Updates import to use installed cssolve.bregman.
csld/util/meson.build	Installs csld.util sources and ensures periodic_table.json is installed next to module.
csld/util/mathtool.py	Updates extension import to csld._c_util.
csld/util/io_utils.py	Replaces Python 2 basestring check with str.
csld/symmetry_structure.py	Updates spglib dataset access style to attribute-based API.
csld/structure.py	Updates compiled-extension imports to installed package module paths.
csld/phonon/phonon.py	Updates f2py module import to csld.phonon.f_phonon.
csld/phonon/meson.build	Adds Meson target for building/installing csld.phonon.f_phonon and phonon Python sources.
csld/meson.build	Installs core csld Python sources and subdirs.
csld/lattice_dynamics.py	Updates compiled-extension imports to installed package module paths.
csld/cli/polaron_main.py	Refactors into a proper console-script main() while keeping global options behavior.
csld/cli/phonopy_qha.py	Defers optional phonopy import errors until script execution; adds main() wrapper.
csld/cli/meson.build	Installs CLI modules for console scripts.
csld/cli/csld_main.py	Adds main() entrypoint for console script.
csld/cli/cs_fit.py	Adds main() entrypoint and updates csfit() unpacking to match return signature.
csld/cli/init.py	Documents CLI entrypoints and their console-script mappings.
csld/basic_lattice_model.py	Updates compiled-extension imports to installed package module paths.
csld/analyzer.py	Updates spglib dataset access to attribute-based API and updates docstrings accordingly.
compile/f_util/meson.build	Adds Meson target to build/install csld.f_util f2py extension.
compile/c_util/meson.build	Adds Meson target to build/install csld._c_util Cython/C++ extension.
compile/c_util/_c_util.pyx	Sets language_level=3 for Cython.
.gitignore	Adds ignores for Meson, wheels, and generated f2py/cython artifacts.
.github/workflows/ci.yml	Adds CI workflow to build/install and run tests on Linux/macOS + build wheel.

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