pyproject.toml

[build-system]
requires = ['setuptools>=77', 'cython>=3.1']
build-backend = 'setuptools.build_meta'

[project]
name = 'chython'
version = '3.2'
description = 'Library for processing molecules and reactions in python way'
authors = [{name = 'Ramil Nugmanov', email = 'nougmanoff@protonmail.com'}]
license = 'LGPL-3.0-or-later'
license-files = ['LICENSE']
readme = 'README.md'
requires-python = '>=3.10'
dependencies = [
    # numpy is NOT here -- it is `chython[ml]`, below.  The budget is a serverless bundle, uploaded
    # whole on every deploy: numpy 1.26.4 is 44 MB installed against 7.4 MB of chython runtime files.
    # A drop and not a trim, since pruning everything a caller demonstrably does not import still
    # leaves ~40 MB.
    #
    # Nothing on the representation path needs it -- parsing, writing, standardization, kekulization,
    # stereo, canonical form, the reactor and depiction are pure Python and C over the arena.  What
    # needs it is the surface that answers a numpy array by contract; `chython[ml]` enumerates that
    # surface and `chython/test/test_optional_numpy.py` is the gate.  Nor is it a BUILD dependency:
    # there is no `cimport numpy` and no `numpy.get_include()`, because the two matrix builders reach
    # their output through typed memoryviews and the PEP 3118 buffer protocol, so `_core.so` carries
    # no numpy symbol and `python -m build --wheel` succeeds under default isolation.
    #
    # JS engine for `clean2d_engine = 'smilesdrawer'`, the default 2D layout backend.  Required and
    # not an extra: a default that works only once the user guesses an extra name is not a default.
    # Affordable because the engine is QuickJS -- 0.5 MB on macOS/Windows, 2.4 MB on manylinux, and a
    # 0.8 MB JS heap.
    #
    # `quickjs-ng` rather than `quickjs` for the wheel matrix: `cp310-abi3` means one wheel per
    # platform serves every CPython from 3.10 onwards, over macOS arm64, manylinux and musllinux on
    # x86_64/aarch64/i686, and win32/win_amd64.
    'quickjs-ng>=0.16',
]
classifiers = [
    'Environment :: Plugins',
    'Intended Audience :: Science/Research',
    'Operating System :: OS Independent',
    'Programming Language :: Python',
    'Programming Language :: Python :: 3 :: Only',
    # One line per interpreter the release workflow builds a wheel for, and `requires-python` above is
    # the enforced statement -- these are what PyPI's filters read, so a missing line hides the project
    # from a search for the version it actually supports.
    'Programming Language :: Python :: 3.10',
    'Programming Language :: Python :: 3.11',
    'Programming Language :: Python :: 3.12',
    'Programming Language :: Python :: 3.13',
    'Programming Language :: Python :: 3.14',
    'Topic :: Scientific/Engineering',
    'Topic :: Scientific/Engineering :: Chemistry',
    'Topic :: Scientific/Engineering :: Information Analysis',
    'Topic :: Software Development',
    'Topic :: Software Development :: Libraries',
    'Topic :: Software Development :: Libraries :: Python Modules',
]

[project.urls]
homepage = 'https://github.com/chython/chython'
documentation = 'https://chython.readthedocs.io'

[project.optional-dependencies]
# The public names that need numpy, and nothing else in the library does.  Without this extra each
# raises ImportError naming it AT THE CALL -- `import chython` is unaffected.  The list is the count;
# `chython/test/test_optional_numpy.py` holds the executable copy.
#
#   every `morgan_*` and `linear_*` method, `atom_invariants`, `adjacency_matrix`,
#   `distance_matrix`, `eccentricities`, `wiener_index`, `graph_radius`, `graph_diameter`,
#   `balaban_j`, `pharmacophore_invariants`, `maccs_keys`, `maccs_bit_set`.
#
# TWO GROUPS ARE NOT OBVIOUS FROM THEIR RETURN TYPES.  `morgan_bit_set`, `morgan_hash_set`,
# `morgan_hash_counts`, their `linear_` counterparts and `maccs_bit_set` answer a plain set or dict and
# still need numpy, every one of them building an array first.  And only the
# DISTANCE-DERIVED descriptors are listed: `tpsa`, `crippen_logp`, `crippen_mr`, `bertz_ct`,
# `randic_index`, `zagreb_index` and the atom and ring counts are numpy-free and stay available.
#
# Named `ml` for the consumer rather than the package: what a caller knows about themselves is that
# they are feeding a model, not that the array library underneath is numpy.
ml = ['numpy>=1.21.0']
# numpy is named directly and NOT left to onnxruntime, which requires it: an extra that works only
# because a sibling dependency happens to pull its requirement in is one that breaks when that sibling
# changes.  NO SCIPY -- the shortest-path distances the encoding needs come from `state_view`, which is
# C in the core, so the one dependency the mapper adds over `ml` is the runtime and the weights.
mapping = ['numpy>=1.21.0', 'onnxruntime>=1.16', 'chython-rxnmap>=2.0']
rdkit = ['rdkit>=2025.9']
extra-clean2d = ['jpype1>=1.6.0', 'openbabel-wheel>=3.1.1.22', 'epam.indigo>=1.45']
extra-clean3d = ['cdpkit>=1.2.3']
iupac = ["openclatura>=0.2; python_version >= '3.11'"]

# PEP 735.  `uv sync --group dev` or `pip install --group dev`, replacing `poetry install --with dev`.
# Not extras: a consumer of the library never wants these, and an extra is installable by a consumer.
[dependency-groups]
# `coverage[toml]` and not bare `coverage`: the settings are in `[tool.coverage]` below, and reading them
# needs tomli before 3.11, which the extra is.
dev = ['pytest>=7.4.3', 'coverage[toml]>=7.0']
docs = ['sphinx>=7.0', 'furo>=2024.1']

[tool.setuptools]
# Explicit, because at its default of `true` a wheel's data files are whatever `MANIFEST.in` swept
# into the sdist, so the two distributions disagree about their contents for reasons neither file
# states.  `false` means the wheel holds exactly what `[tool.setuptools.package-data]` below names and
# `MANIFEST.in` describes only the sdist -- one file, one question.
include-package-data = false

[tool.setuptools.packages.find]
# `chython*` and nothing else: the repo root also holds `scripts/`, `mapping/`, `java/`, `pach/` and a
# top-level `test/` of data files, none importable and all of which auto-discovery would otherwise
# offer to package.  No `exclude` is needed -- every `chython*` package is a shipped one.
include = ['chython*']

# Everything the installed package opens at runtime and cannot regenerate.  Nothing is globbed, so a
# file omitted here is a file the wheel does not have.
#
#   clean2d.js     `depict/layout/molecule.py` reads it through `importlib.resources`; without it the
#                  default 2D engine raises on first use rather than at import.
#
#   tables/*.tsv   `chemistry/_tables.py` opens each through `importlib.resources` the first time
#                  anyone calls the pass that reads it -- `standardize()`, `fix_resonance()`, a salt
#                  pass, a featurizer.  READ AT RUNTIME, so omitting one yields a wheel that imports
#                  cleanly and raises on the first molecule; `_tables.py`'s FileNotFoundError names
#                  this section.  No count is written here: the list below is the count.
#
#                  THE `tables/` PREFIX IS PART OF THE PATTERN, not a directory setuptools infers.
#                  A package-data name is matched against the path relative to the package, so
#                  `resonance.tsv` alone ships nothing when the file is a level down -- which is why
#                  `test_packaging.py` compares relative paths and not bare filenames.
#
# libinchi IS DELIBERATELY ABSENT, the one runtime file that is.  `package_data` can only name files in
# the SOURCE tree, so an entry here would oblige the build to write a binary into `chython/core/` and
# make a wheel's contents a function of what lies in the checkout.  `setup.py` builds it into
# `build/inchi/` and stages it into the wheel from there; `test_libinchi_staging.py` is its gate, since
# this block's own gate (`test_packaging.py`) cannot be.
#
# `core`'s TSVs and RULES.md are not read at runtime.  They ship because `core/test/` ships and each
# generator's `compile` verb is re-run against its TSV to prove the checked-in C tables are still that
# file's output -- without the TSV that gate has no input.  RULES.md is what those tests cite.
#
# The pach corpora ship because they cannot be regenerated from this tree at all: every record was
# written by an installed chython 2 (2.24 for v2, 1.42 for native v0), so they are the only surviving
# specification of the legacy wire format `pack`/`unpack` read.  Without them `test_pach.py` is a
# codec's acceptance test that cannot run and cannot be rebuilt.  `reaction_pach_v2_corpus.bin.gz` is
# the same artefact one layer up, pinning the four header bytes `ReactionContainer.pack` prepends.
#
# `pach_v3_corpus.bin.gz` and `pach_v4_corpus.bin.gz` ship for the opposite reason: this tree CAN write
# them, which is why they are frozen.  A fixture the test run regenerates pins no layout, so the
# committed bytes are the artefact and `gen_pach3_corpus.py` is run by hand.
# `pach_bond_group_corpus.bin.gz` is the same artefact for the bond enhanced-stereo block, written by the
# same generator and pinning the header field the earlier fifty records all leave zero.
#
# `arena_v4_corpus.bin.gz` has the strongest reason of the three: it is arena `STRUCT_VERSION` 4, which
# this tree no longer writes and no later build ever will, so `gen_v4_fixtures.py` cannot rerun.  It is
# the only input to the migration gate that reads a pre-`SEG_PARITY` buffer.
#
# `modeling_view_corpus.json.gz` is a pin that CANNOT be rebuilt from this tree: it was recorded from
# the dict-of-dicts union `modeling_view()` had before the array kernel, so regenerating it would
# replace the pin with the thing being pinned.
#
# `golden_subset.smi` ships because the agreement floor in `reactions/test/test_attention.py` is a
# number about a corpus, and a floor whose corpus the wheel lacks is a claim that cannot be rechecked
# where it matters.  25 records of the public Golden benchmark, 10 kB; the full 1851 stay outside the
# package and are run by `bench/bench_attention_mapping.py`.
#
# ONE ENTRY PER LINE, however long the line gets.  The reader of this block is a regex that needs it
# flat: a wrapped list makes it take the continuation for a package name and fail on a path assembled
# out of half a filename.
[tool.setuptools.package-data]
'chython.depict.layout' = ['clean2d.js']
'chython.depict.metrics' = ['helvetica.tsv', 'times.tsv']
'chython.core' = ['valence_rules.tsv', 'elements.tsv', 'isotopes.tsv', 'RULES.md']
'chython.chemistry' = ['tables/abbreviations.tsv', 'tables/standardize_groups.tsv', 'tables/standardize_metals.tsv', 'tables/resonance.tsv', 'tables/salts.tsv', 'tables/acids.tsv', 'tables/sybyl_types.tsv', 'tables/residues.tsv', 'tables/rotatable.tsv', 'tables/hbond.tsv', 'tables/pharmacophore.tsv', 'tables/tpsa.tsv', 'tables/crippen.tsv', 'tables/covalent_radii.tsv', 'tables/maccs.tsv', 'tables/maccs_corpus.tsv', 'tables/qed_alerts.tsv']
'chython.reactions' = ['tables/functional.tsv', 'tables/protective.tsv', 'tables/reactions.tsv', 'tables/roles.tsv']
'chython.core.test' = ['pach_v2_corpus.bin.gz', 'pach_v0_corpus.bin.gz', 'pach_v0_native_corpus.bin.gz', 'reaction_pach_v2_corpus.bin.gz', 'arena_v4_corpus.bin.gz', 'pach_v3_corpus.bin.gz', 'pach_v4_corpus.bin.gz', 'pach_bond_group_corpus.bin.gz', 'modeling_view_corpus.json.gz']
'chython.reactions.test' = ['golden_subset.smi']
'chython.formats.ctfile' = ['CTFILE.md']

# THE HARNESS BEHIND THE README'S COVERAGE BADGE.  The `oracles` job in `.github/workflows/test.yml` runs
# the suite under these settings and uploads the report; the same two commands reproduce the number:
#
#     python -m coverage run -m pytest chython/ -q --deselect chython/test/test_performance.py
#     python -m coverage report
#
# IT MEASURES THE PYTHON LAYERS ONLY.  `chython.core._core` is one compiled translation unit and
# coverage.py sees no lines in it, so `core/*.pxi` is in neither the numerator nor the denominator and the
# badge is labelled `python coverage`.  What covers the core is the differential suite against chython 2
# and RDKit, which reports agreement rather than lines.
[tool.coverage.run]
source = ['chython']
# a test file's own lines are not a claim about the library, and every test in the tree lives in a `test/`
omit = ['*/test/*']
# paths as the repo writes them, so a reader outside the checkout -- the badge service -- can resolve one
relative_files = true

[tool.coverage.report]
precision = 2