id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
6434	Support pyproject.toml	Zach Pearson	Zach Pearson	"We should not make this a high priority as many infrastructure projects in the Python ecosystem are in the process of attaining PEP621 compliance, but as part of our project to release a PyPi and/or Conda version of ChimeraX, I think it would be good for us and for our bundle developers to support pyproject.toml as an alternative to bundle_info.xml. I see several benefits to this:

1) {{{pyproject.toml}}} is at least as extensible as XML. We need only to look for (at minimum) a {{{[tool.chimerax]}}} header when we read it in to get all of our custom metadata
2) We and our users could roll ChimeraX-specific project configuration data into a consolidated file, as I have already done in our repo for {{{yapf}}}, {{{flake8}}}, etc. 
3) TOML files are simpler to write than XML files and have a much greater signal-to-noise ratio. 

Among others.

If we did support {{{pyproject.toml}}} as a means to write bundle specifications, then we would have to implement the following:

- require {{{tomli>=2}}} for Python versions {{{<=3.11}}}, which will have a built-in {{{toml}}} library.
- Update the bundle builder to read {{{toml}}} files in a way compatible with existing XML tags
- Make a stylistic decision whether to use additional headings, e.g. {{{[tool.chimerax.classifiers]}}} or just {{{[tool.chimerax]}}} for more complex data, such as providers. 

My list is likely short owing to general inexperience with our bundle build system.

As to ecosystem support:
- setuptools is planning to support {{{pyproject.toml}}} alongside {{{setup.{py,cfg} }}}
- Common development tools such as {{{pyright}}}, {{{yapf}}}, {{{pytest}}}, and {{{tox}}} already support configuration through a project's top-level {{{pyproject.toml}}}

I imagine an outside developer would have several additional categories customizing tools in their local repo, but for an example of what {{{pyproject.toml}}} would look like for {{{blastprotein}}}:

{{{
# vim: set expandtab ts=4 sw=4:
# === UCSF ChimeraX Copyright ===
# Copyright 2021 Regents of the University of California.
# All rights reserved.  This software provided pursuant to a
# license agreement containing restrictions on its disclosure,
# duplication and use.  For details see:
# http://www.rbvi.ucsf.edu/chimerax/docs/licensing.html
# This notice must be embedded in or attached to all copies,
# including partial copies, of the software or any revisions
# or derivations thereof.
# === UCSF ChimeraX Copyright ===
[build-system]
requires = [""setuptools""]
build-backend = [""setuptools.build_meta""]

[project]
name=""chimerax.blastprotein""
version=""2.0""
authors = [{ name = ""UCSF RBVI"", email = ""chimerax@cgl.ucsf.edu"" }]
synopsis = ""Search PDB/NR/AlphaFold using BLAST""
description = """"""
Interface to the RBVI web service to search the PDB, NR, or AlphaFold
databases using BLAST.  Results are shown in a tool when a graphical
interface is available; otherwise, the results are logged.
""""""
classifiers = [
    ""Development Status :: 5 - Stable"",
    ""Environment :: MacOS X :: Aqua"",
    ""Environment :: Win32 (MS Windows)"",
    ""Environment :: X11 Applications"",
    ""Framework :: ChimeraX"",
    ""Intended Audience :: Science/Research"",
    ""License :: Free for non-commercial use"",
    ""Operating System :: MacOS :: MacOS X"",
    ""Operating System :: Microsoft :: Windows :: Windows 10"",
    ""Operating System :: POSIX :: Linux"",
    ""Programming Language :: Python :: 3"",
    ""Topic :: Scientific/Engineering :: Visualization"",
    ""Topic :: Scientific/Engineering :: Chemistry"",
    ""Topic :: Scientific/Engineering :: Bio-Informatics"",
]
requires-python = "">= 3.8""
dependencies = [
     ""chimerax.core ~= 1.0""
]

[project.optional-dependencies]
gui = [ 'ChimeraX-UI >= 1.0' ]
webservices = [ 'ChimeraX-WebServices >= 1.0' ]
alignments = [ 'ChimeraX-UI >= 1.0', 'ChimeraX-Alignments >= 2.0' ]
alphafold = [ 'ChimeraX-AlphaFold >= 1.0' ]

[project.dependency-links]
# Tell pip to look at the toolshed, too
dependency-links = ""https://cxtoolshed.rbvi.ucsf.edu""

[project.urls]
Home = ""https://www.rbvi.ucsf.edu/chimerax/""
Documentation = ""https://www.cgl.ucsf.edu/chimerax/docs/user/index.html""
Source = ""https://www.github.com/RBVI/ChimeraX""

[tool.chimerax]
bundle-name=""ChimeraX-BlastProtein""
min-session-version=""1""
max-session-version=""2""
categories = [""Sequence""]
chimerax-classifiers = [
    ""Category :: Sequence"",
    ""Tool :: Blast Protein :: Sequence :: Search PDB/NR/AlphaFold using BLAST"",
    ""Command :: blastprotein :: Sequence :: Search PDB/NR/AlphaFold using BLAST"",
    ""Command :: blastprotein pull :: Sequence :: Get results for a finished BlastProtein job"",
    ""Command :: blastpdb :: Sequence :: Search PDB/NR/AlphaFold using BLAST""
]
}}}

Running {{{python3 -m build}}} in the {{{blastprotein}}} folder in this configuration will successfully generate a wheel, though since {{{setuptools}}} support is immature it's labelled {{{UNKNOWN-0.0.0-py3-none-any.whl}}}"	enhancement	closed	minor	1.5	Build System		fixed		chimerax-programmers	5223			all	ChimeraX