refactor: adjust format of logfiles

[tsutterley]

refactor: reorganize for modern setuptools builds
fix: simplify Clenshaw summations to reduce memory usage

[Copilot]

Pull request overview

This PR modernizes packaging/CLI distribution by moving script installation into pyproject.toml, refactors logging output formatting for file-based logs, and simplifies Clenshaw summation update steps to reduce memory usage.

Changes:

• Remove legacy setup.py script discovery and declare console scripts via [project.scripts] in pyproject.toml (plus version bump to 1.2.7).
• Refactor log file creation to attach “parent filename” context via LoggerAdapter, and adjust log formatting/output sections.
• Simplify iterative Clenshaw summation accumulator updates (in both sea_level_equation and clenshaw_summation) and update/expand documentation + API reference structure.

Reviewed changes

Copilot reviewed 109 out of 209 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
setup.py	Removed legacy setup-based script inclusion.
pyproject.toml	Bumped version; defined entry points for scripts via [project.scripts].
gravity_toolkit/utilities.py	Updated log file creation/formatting and parent-file context.
gravity_toolkit/sea_level_equation.py	Simplified Clenshaw accumulator update; docstring formatting tweaks.
gravity_toolkit/scripts/upload_to_figshare.py	Added CLI script for uploading geocenter files to Figshare.
gravity_toolkit/scripts/simple_parallel_shell.py	Added CLI script to run shell commands in parallel.
gravity_toolkit/scripts/sea_level_differences.py	Added CLI script for SLF Monte Carlo error map generation.
gravity_toolkit/scripts/run_grace_date.py	Added wrapper CLI for GRACE date/month index generation.
gravity_toolkit/scripts/remove_sea_level_fields.py	Added cleanup CLI for removing SLF fields.
gravity_toolkit/scripts/remove_sea_level_errors.py	Added cleanup CLI for removing SLF Monte Carlo error artifacts.
gravity_toolkit/scripts/remove_mascon_reconstruct.py	Added cleanup CLI for removing reconstructed mascon outputs listed in an index file.
gravity_toolkit/scripts/remove_grace_spatial.py	Added cleanup CLI for removing monthly GRACE spatial files.
gravity_toolkit/scripts/quick_mascon_regress.py	Added CLI script to generate regression summary for mascon time series.
gravity_toolkit/scripts/quick_mascon_plot.py	Added CLI script to plot mascon time series.
gravity_toolkit/scripts/nominal_grace_date.py	Added CLI script to generate nominal GRACE date files.
gravity_toolkit/scripts/make_grace_index.py	Added CLI script to build GRACE L2 index files.
gravity_toolkit/scripts/geocenter_processing_centers.py	Added plotting CLI for geocenter comparisons across processing centers.
gravity_toolkit/scripts/geocenter_ocean_models.py	Added plotting CLI comparing geocenter results across OBP/ocean models.
gravity_toolkit/scripts/geocenter_monte_carlo.py	Added plotting CLI for geocenter Monte Carlo solution visualization.
gravity_toolkit/scripts/geocenter_compare_tellus.py	Added plotting CLI comparing geocenter solutions vs JPL Tellus (and optionally GravIS).
gravity_toolkit/scripts/combine_sea_level_data.py	Added CLI to combine SLF spatial fields with harmonic datasets.
gravity_toolkit/scripts/calc_harmonic_resolution.py	Added CLI script to compute spatial resolution vs spherical harmonic degree.
gravity_toolkit/scripts/init.py	Package marker for scripts module.
gravity_toolkit/mapping/init.py	Package marker for mapping module.
gravity_toolkit/datasets/esa_costg_swarm_sync.py	Added dataset sync CLI for ESA Swarm COST-G products (JSON API).
gravity_toolkit/datasets/init.py	Package marker for datasets module.
gravity_toolkit/clenshaw_summation.py	Simplified Clenshaw accumulator update; docstring formatting tweaks.
gravity_toolkit/init.py	Exposed datasets, mapping, and scripts packages at top-level.
doc/source/user_guide/NASA-Earthdata.ipynb	Updated documentation links to new in-package dataset script locations.
doc/source/release_notes/release-v1.2.7.rst	Added release notes for v1.2.7.
doc/source/getting_started/Getting-Started.rst	Updated links to dataset scripts under gravity_toolkit/datasets.
doc/source/background/GRACE-Data-Products.rst	Updated links to dataset sync tools under gravity_toolkit/datasets.
doc/source/api_reference/utilities.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/units.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/tools.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/time.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/time_series/smooth.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/time_series/savitzky_golay.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/time_series/regress.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/time_series/piecewise.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/time_series/lomb_scargle.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/time_series/fit.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/time_series/amplitude.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/spatial.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/SLR/CS2.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/SLR/C50.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/SLR/C40.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/SLR/C30.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/SLR/C20.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/sea_level_equation.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/scripts/scale_grace_maps.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/scripts/run_sea_level_equation.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/scripts/run_grace_date.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/scripts/regress_grace_maps.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/scripts/quick_mascon_regress.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/scripts/quick_mascon_plot.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/scripts/piecewise_grace_maps.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/scripts/monte_carlo_degree_one.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/scripts/mascon_reconstruct.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/scripts/make_grace_index.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/scripts/index.rst	Added scripts API reference index page.
doc/source/api_reference/scripts/grace_spatial_maps.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/scripts/grace_spatial_error.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/scripts/grace_raster_grids.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/scripts/grace_mean_harmonics.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/scripts/dealiasing_monthly_mean.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/scripts/dealiasing_global_uplift.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/scripts/convert_harmonics.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/scripts/combine_harmonics.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/scripts/calc_sensitivity_kernel.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/scripts/calc_mascon.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/scripts/calc_harmonic_resolution.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/scripts/calc_degree_one.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/scripts/aod1b_oblateness.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/scripts/aod1b_geocenter.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/read_SLR_harmonics.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/read_love_numbers.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/read_GRACE_harmonics.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/read_GIA_model.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/read_gfc_harmonics.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/ocean_stokes.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/mascons.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/mapping/plot_GrIS_grid_movie.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/mapping/plot_GrIS_grid_maps.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/mapping/plot_GrIS_grid_5maps.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/mapping/plot_GrIS_grid_3maps.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/mapping/plot_global_grid_movie.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/mapping/plot_global_grid_maps.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/mapping/plot_global_grid_9maps.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/mapping/plot_global_grid_5maps.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/mapping/plot_global_grid_4maps.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/mapping/plot_global_grid_3maps.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/mapping/plot_AIS_regional_movie.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/mapping/plot_AIS_regional_maps.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/mapping/plot_AIS_GrIS_maps.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/mapping/plot_AIS_grid_movie.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/mapping/plot_AIS_grid_maps.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/mapping/plot_AIS_grid_4maps.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/mapping/plot_AIS_grid_3maps.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/mapping/index.rst	Added mapping API reference index page.
doc/source/api_reference/legendre.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/legendre_polynomials.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/harmonics.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/harmonic_summation.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/harmonic_gradients.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/grace_months_index.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/grace_input_months.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/grace_find_months.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/grace_date.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/geocenter.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/gen_stokes.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/gen_spherical_cap.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/gen_point_load.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/gen_harmonics.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/gen_disc_load.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/gen_averaging_kernel.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/gauss_weights.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/fourier_legendre.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/destripe_harmonics.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/degree_amplitude.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/datasets/podaac_cumulus.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/datasets/itsg_graz_grace_sync.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/datasets/index.rst	Added datasets API reference index page.
doc/source/api_reference/datasets/gfz_isdc_grace_sync.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/datasets/gfz_isdc_dealiasing_sync.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/datasets/gfz_icgem_costg_ftp.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/datasets/esa_costg_swarm_sync.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/datasets/cnes_grace_sync.rst	Updated source link and argparse directive to module-based import.
doc/source/api_reference/clenshaw_summation.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/associated_legendre.rst	Updated API reference header to fully-qualified module name.
doc/source/api_reference/API-Reference.rst	Restructured API reference to add datasets/mapping/scripts indices and remove older grouped sections.

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