Installation fix and revamped docs

[SunilSimha]

I found the current installation experience of just pip installing the bare-minimum FRB-repo-only and then installing dependencies as they come to be cumbersome on a new machine. I've therefore migrated the existing setup.py infrastructure to a more modern pyproject.toml based approach and made it so that the most commonly used dependencies are installed when installing the FRB repo.

This still leaves packages such as pcigale and eazy to the user's whims to install manually, but one can run survey searches out of the box.

Additionally, I have now revamped the docs with CoPilot with emphasis on making them more complete and to add a usable API reference. There might still be issues, so feel free to create an issue on this repo and tag me if you find an error.

[Copilot]

Pull request overview

Modernizes FRB’s packaging and documentation to improve the “install-and-run survey searches” experience by moving dependency metadata into pyproject.toml and expanding Sphinx API docs, alongside a few script/UX cleanups.

Changes:

• Migrates packaging metadata from setup.py/setup.cfg to pyproject.toml and updates tox configuration accordingly.
• Adds/standardizes cli() entrypoints for multiple frb.scripts.* modules and updates progress reporting (switch to tqdm).
• Revamps Sphinx docs structure and adds many API reference stub pages via autodoc/automodule.

Reviewed changes

Copilot reviewed 130 out of 130 changed files in this pull request and generated 14 comments.

Show a summary per file

File	Description
tox.ini	Updates env matrix/extras and adds “lightweight” numpy test envs.
setup.py	Removes legacy setuptools installer script.
setup.cfg	Removes legacy extras configuration.
pyproject.toml	Adds PEP 621 project metadata, deps, and console scripts.
frb/surveys/dlsurvey.py	Updates missing-dependency warning string for Data Lab client.
frb/scripts/tns.py	Docstring cleanup and adds cli() entrypoint + __main__ call.
frb/scripts/sightline.py	Adds cli() entrypoint wrapper.
frb/scripts/search_for_halos.py	Adds cli() entrypoint wrapper.
frb/scripts/random_assoc.py	Replaces progressbar2 with tqdm; removes seaborn usage; adds __main__ guard.
frb/scripts/pzdm_mag.py	Adds cli() entrypoint wrapper.
frb/scripts/image.py	Adds cli() entrypoint wrapper.
frb/scripts/galaxies.py	Adds cli() entrypoint wrapper.
frb/scripts/frb_summary.py	Adds cli() entrypoint wrapper.
frb/scripts/build.py	Adds cli() entrypoint wrapper.
frb/requirements.txt	Marks requirements file as deprecated; adds a few deps.
frb/optional_requirements.txt	Adds optional-deps reference list.
frb/mw.py	Removes __future__ import; adds docstring for haloDM().
frb/halos/photoz.py	Switches progress reporting to tqdm; uses local frb.galaxies.eazy wrapper.
frb/halos/models.py	Changes missing hmf_emulator handling behavior/message.
frb/halos/hmf.py	Changes missing hmf_emulator handling behavior/message.
frb/galaxies/hosts.py	Improves docstrings and Sphinx directives formatting.
frb/galaxies/galfit.py	Removes duplicated docstring lines.
frb/galaxies/cigale.py	Improves install hint message for pcigale.
frb/dm/igm.py	Removes __future__ import.
frb/associate/frbassociate.py	Improves __init__ docstring.
frb/analysis/kcwi.py	Changes missing optional dependency handling from raising to printing.
docs/installing.rst	Updates installation guidance to pip install -e . and lists deps/extras.
docs/halos/utils.rst	Adds new autodoc page for frb.halos.utils.
docs/halos/photoz.rst	Replaces long hand-written docs with automodule-based API rendering.
docs/halos/models.rst	Reworks halo docs to use automodule/autoclass structure.
docs/halos/index.rst	Expands halos docs TOC; updates progress-bar dependency mention.
docs/halos/hmf.rst	Simplifies and adds migration guide; uses automodule docs.
docs/frbhost_class.rst	Replaces embedded API blocks with links/short refs.
docs/frb_class.rst	Replaces embedded API blocks with links/short refs.
docs/conf.py	Adds autodoc_mock_imports and stub env vars for doc builds.
docs/api/utils.rst	New automodule stub for frb.utils.
docs/api/io.rst	New automodule stub for frb.io.
docs/api/defs.rst	New automodule stub for frb.defs.
docs/api/analysis.rst	New automodule stub for frb.analysis + TOC.
docs/api/analysis.kcwi.rst	New automodule stub for frb.analysis.kcwi.
docs/api/dm.rst	Restructures DM API docs and adds submodule toctree.
docs/api/dm.cosmic.rst	New automodule stub for frb.dm.cosmic.
docs/api/dm.dm_ism_healpix_map.rst	New automodule stub for frb.dm.dm_ism_healpix_map.
docs/api/dm.host.rst	New automodule stub for frb.dm.host.
docs/api/dm.igm.rst	New automodule stub for frb.dm.igm.
docs/api/dm.mcmc.rst	New automodule stub for frb.dm.mcmc.
docs/api/dm.prob_dmz.rst	New automodule stub for frb.dm.prob_dmz.
docs/api/dm_kde.rst	Adds dm_kde landing page and submodule TOC notes.
docs/api/dm_kde.dm_frb_sim.rst	Adds note about import-time simulation behavior.
docs/api/dm_kde.pdf_fns.rst	New automodule stub for frb.dm_kde.pdf_fns.
docs/api/dm_kde.sort_transient_data.rst	New automodule stub for frb.dm_kde.sort_transient_data.
docs/api/dm_kde.transient_kdes.rst	New automodule stub for frb.dm_kde.transient_kdes.
docs/api/associate.rst	Converts associate docs to a toctree layout.
docs/api/associate.frbassociate.rst	New automodule stub for frb.associate.frbassociate.
docs/api/associate.frbs.rst	New automodule stub for frb.associate.frbs.
docs/api/associate.gen_pox_table.rst	New automodule stub for frb.associate.gen_pox_table.
docs/api/builds.rst	New builds landing page with toctree.
docs/api/builds.utils.rst	New automodule stub for frb.builds.utils.
docs/api/builds.build_fg.rst	New automodule stub for frb.builds.build_fg.
docs/api/builds.build_frbs.rst	New automodule stub for frb.builds.build_frbs.
docs/api/builds.build_hosts.rst	New automodule stub for frb.builds.build_hosts.
docs/api/builds.build_path.rst	New automodule stub for frb.builds.build_path.
docs/api/builds.build_specdb.rst	New automodule stub for frb.builds.build_specdb.
docs/api/builds.old_build_frbs.rst	New automodule stub for legacy builds module.
docs/api/builds.old_build_hosts.rst	New automodule stub for legacy builds module.
docs/api/figures.rst	New figures landing page with toctree.
docs/api/figures.dm.rst	New automodule stub for frb.figures.dm.
docs/api/figures.finder.rst	New automodule stub for frb.figures.finder.
docs/api/figures.galaxies.rst	New automodule stub for frb.figures.galaxies.
docs/api/figures.utils.rst	New automodule stub for frb.figures.utils.
docs/api/galaxies.rst	Expands galaxies toctree with additional modules.
docs/api/galaxies.cigale.rst	Simplifies page + notes optional dependency.
docs/api/galaxies.convert_tables.rst	New automodule stub for frb.galaxies.convert_tables.
docs/api/galaxies.eazy.rst	Simplifies page + notes required env var.
docs/api/galaxies.extra_data.rst	New automodule stub for frb.galaxies.extra_data.
docs/api/galaxies.frbgalaxy.rst	Removes long narrative; keeps API focus.
docs/api/galaxies.galfit.rst	New automodule stub for frb.galaxies.galfit.
docs/api/galaxies.hosts.rst	Removes long narrative; keeps API focus.
docs/api/galaxies.mag_dm.rst	New automodule stub for frb.galaxies.mag_dm.
docs/api/galaxies.nebular.rst	Removes long narrative; keeps API focus.
docs/api/galaxies.offsets.rst	Removes long narrative; keeps API focus.
docs/api/galaxies.photom.rst	Fixes heading spacing; reduces narrative content.
docs/api/galaxies.ppxf.rst	Simplifies page + notes optional dependency.
docs/api/galaxies.utils.rst	Simplifies page + notes optional dependency.
docs/api/halos.rst	Reworks halos landing page; points to full docs section.
docs/api/frb_surveys.rst	Converts to a toctree layout.
docs/api/frb_surveys.chime.rst	New automodule stub for CHIME surveys module.
docs/api/scripts.rst	New scripts landing page with toctree.
docs/api/scripts.build.rst	New automodule stub for frb.scripts.build.
docs/api/scripts.dm_ism_hp_map.rst	New automodule stub for frb.scripts.dm_ism_hp_map.
docs/api/scripts.frb_summary.rst	New automodule stub for frb.scripts.frb_summary.
docs/api/scripts.galaxies.rst	New automodule stub for frb.scripts.galaxies.
docs/api/scripts.image.rst	New automodule stub for frb.scripts.image.
docs/api/scripts.iteration.rst	New automodule stub for frb.scripts.iteration.
docs/api/scripts.pz_given_dm.rst	New automodule stub for frb.scripts.pz_given_dm.
docs/api/scripts.pzdm_mag.rst	New automodule stub for frb.scripts.pzdm_mag.
docs/api/scripts.pzdm_mag_crossmatch.rst	New automodule stub for frb.scripts.pzdm_mag_crossmatch.
docs/api/scripts.r_vs_dm.rst	New automodule stub for frb.scripts.r_vs_dm.
docs/api/scripts.random_assoc.rst	New automodule stub for frb.scripts.random_assoc.
docs/api/scripts.search_for_halos.rst	New automodule stub for frb.scripts.search_for_halos.
docs/api/scripts.sightline.rst	New automodule stub for frb.scripts.sightline.
docs/api/scripts.tns.rst	New automodule stub for frb.scripts.tns.
docs/api/surveys.rst	Replaces inline sections with a large toctree of survey modules.
docs/api/surveys.catalog_utils.rst	New automodule stub for frb.surveys.catalog_utils.
docs/api/surveys.cluster_search.rst	New automodule stub for frb.surveys.cluster_search.
docs/api/surveys.decals.rst	New automodule stub for frb.surveys.decals.
docs/api/surveys.defs.rst	New automodule stub for frb.surveys.defs.
docs/api/surveys.desi.rst	New automodule stub for frb.surveys.desi.
docs/api/surveys.des.rst	New automodule stub for frb.surveys.des.
docs/api/surveys.delve.rst	New automodule stub for frb.surveys.delve.
docs/api/surveys.dlsurvey.rst	New automodule stub for frb.surveys.dlsurvey.
docs/api/surveys.galex.rst	New automodule stub for frb.surveys.galex.
docs/api/surveys.heasarc.rst	New automodule stub for frb.surveys.heasarc.
docs/api/surveys.hsc.rst	New automodule stub for frb.surveys.hsc.
docs/api/surveys.images.rst	New automodule stub for frb.surveys.images.
docs/api/surveys.nedlvs.rst	New automodule stub for frb.surveys.nedlvs.
docs/api/surveys.nsc.rst	New automodule stub for frb.surveys.nsc.
docs/api/surveys.panstarrs.rst	New automodule stub for frb.surveys.panstarrs.
docs/api/surveys.psrcat.rst	New automodule stub for frb.surveys.psrcat.
docs/api/surveys.sdss.rst	New automodule stub for frb.surveys.sdss.
docs/api/surveys.survey_io.rst	New automodule stub for frb.surveys.survey_io.
docs/api/surveys.survey_utils.rst	New automodule stub for frb.surveys.survey_utils.
docs/api/surveys.surveycoord.rst	New automodule stub for frb.surveys.surveycoord.
docs/api/surveys.tns_util.rst	New automodule stub for frb.surveys.tns_util.
docs/api/surveys.twomass.rst	New automodule stub for frb.surveys.twomass.
docs/api/surveys.utils_crossmatching.rst	New automodule stub for frb.surveys.utils_crossmatching.
docs/api/surveys.vista.rst	New automodule stub for frb.surveys.vista.
docs/api/surveys.wise.rst	New automodule stub for frb.surveys.wise.
.github/workflows/ci_tests.yml	Switches CI trigger branch from master to main.

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[SunilSimha]

@profxj , this is a huge diff, so I will appreciate it if you take a careful look at just pyproject.toml and tox.ini. Feel free to only skim the new html docs.

[profxj]

this is great!!