initial scaffolding for the initial port (PR 1 of N) (#4)

* initial scaffolding for project

* rm unnecessary `.gitignore` lines

---------

Co-authored-by: Ryan Williams <[email protected]>

.gitignore

@@ -0,0 +1,31 @@
+__pycache__/
+
+# Distribution / packaging
+.Python
+build/
+dist/
+*.egg-info/
+
+# Unit test / coverage reports
+.coverage
+.coverage.*
+.cache
+coverage.xml
+.pytest_cache/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json

.pre-commit-config.yaml

@@ -0,0 +1,26 @@
+repos:
+  - repo: https://github.com/psf/black
+    rev: "24.8.0"
+    hooks:
+      - id: black
+        exclude: 'apis/'
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.5
+    hooks:
+      - id: ruff
+        name: "ruff for tiledbsoma_ml"
+        args: ["--config=pyproject.toml"]
+        exclude: 'apis/'
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.11.2
+    hooks:
+      - id: mypy
+        pass_filenames: false
+        args: ["--config-file=pyproject.toml", "src"]
+        additional_dependencies:
+          - attrs
+          - numpy
+          - pandas-stubs>=2
+        exclude: 'apis/'

CHANGELOG.md

@@ -0,0 +1,21 @@
+
+# Change Log
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](http://keepachangelog.com/)
+and this project adheres to [Semantic Versioning](http://semver.org/).
+
+## [Unreleased] - yyyy-mm-dd
+
+Port and enhance contribution from the Chan Zuckerberg Initiative Foundation
+[CELLxGENE](https://cellxgene.cziscience.com/) project.
+
+This is not a one-for-one migration of the contributed code. Substantial changes have
+been made to the package utility (e.g., multi-GPU support), improve API usability, etc.
+
+### Added
+
+### Changed
+
+### Fixed

pyproject.toml

@@ -0,0 +1,76 @@
+[build-system]
+requires = ["setuptools >= 61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "tiledbsoma-ml"
+dynamic = ["version"]
+dependencies = [
+    "attrs>=22.2",
+    "tiledbsoma>=1.9.0",
+    "torch>=2.0",
+    "torchdata<=0.9",
+    "numpy",
+    "numba",
+    "pandas",
+    "pyarrow",
+    "scipy"
+]
+requires-python = ">= 3.9"
+description = "Machine learning tools for use with tiledbsoma"
+readme = "README.md"
+authors = [
+    {name = "TileDB, Inc.", email = "[email protected]"},
+    {name = "The Chan Zuckerberg Initiative Foundation", email = "[email protected]" },
+]
+maintainers = [
+    {name = "TileDB, Inc.", email="[email protected]"},
+]
+
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Information Technology",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Operating System :: Unix",
+    "Operating System :: POSIX :: Linux",
+    "Operating System :: MacOS :: MacOS X",
+    "Operating System :: Microsoft :: Windows",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+]
+
+[project.urls]
+Repository = "https://github.com/TileDB-Inc/TileDB-SOMA-ML.git"
+Issues = "https://github.com/TileDB-Inc/TileDB-SOMA-ML/issues"
+Changelog = "https://github.com/TileDB-Inc/TileDB-SOMA-ML/blob/main/CHANGELOG.md"
+
+[tool.setuptools.dynamic]
+version = {attr = "tiledbsoma_ml.__version__"}
+
+[tool.setuptools.package-data]
+"tiledbsoma_ml" = ["py.typed"]
+
+[tool.setuptools_scm]
+root = "../../.."
+
+[tool.mypy]
+show_error_codes = true
+ignore_missing_imports = true
+warn_unreachable = true
+strict = true
+python_version = 3.9
+plugins = "numpy.typing.mypy_plugin"
+
+[tool.ruff]
+lint.select = ["E", "F", "B", "I"]
+lint.ignore = ["E501"]  # line too long
+lint.extend-select = ["I001"]  # unsorted-imports
+fix = true
+target-version = "py39"
+line-length = 120

src/tiledbsoma_ml/__init__.py

@@ -0,0 +1,8 @@
+# Copyright (c) 2021-2024 The Chan Zuckerberg Initiative Foundation
+# Copyright (c) 2021-2024 TileDB, Inc.
+#
+# Licensed under the MIT License.
+
+"""An API to support machine learning applications built on SOMA."""
+
+__version__ = "0.1.0-dev"

src/tiledbsoma_ml/py.typed

@@ -0,0 +1,2 @@
+# Marker file to indicate that this package contains Python typing information,
+# and that mypy can use it to typecheck client code.