brainsig 0.1.0__tar.gz

brainsig-0.1.0/.gitignore

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+### Linux template
+*~
+
+# temporary files which can be created if a process still has a handle open of a deleted file
+.fuse_hidden*
+
+# KDE directory preferences
+.directory
+
+# Linux trash folder which might appear on any partition or disk
+.Trash-*
+
+# .nfs files are created when an open file is removed but is still being accessed
+.nfs*
+
+### Windows template
+# Windows thumbnail cache files
+Thumbs.db
+Thumbs.db:encryptable
+ehthumbs.db
+ehthumbs_vista.db
+
+# Dump file
+*.stackdump
+
+# Folder config file
+[Dd]esktop.ini
+
+# Recycle Bin used on file shares
+$RECYCLE.BIN/
+
+# Windows Installer files
+*.cab
+*.msi
+*.msix
+*.msm
+*.msp
+
+# Windows shortcuts
+*.lnk
+
+### JupyterNotebooks template
+# gitignore template for Jupyter Notebooks
+# website: http://jupyter.org/
+
+.ipynb_checkpoints
+*/.ipynb_checkpoints/*
+
+# IPython
+profile_default/
+ipython_config.py
+
+# Remove previous ipynb_checkpoints
+#   git rm -r .ipynb_checkpoints/
+
+### macOS template
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+Icon
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+
+### Python template
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+docs/api
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+
+# IPython
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# Hatch-VCS
+_version.py

brainsig-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2025 Tony Barrows
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+the Software, and to permit persons to whom the Software is furnished to do so,
+subject to the following conditions:
+
+The above copyright notice and this permission notice (including the next
+paragraph) shall be included in all copies or substantial portions of the
+Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

brainsig-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: brainsig
+Version: 0.1.0
+Summary: A package for computing 'neural signatures' from fMRI data.
+Project-URL: Homepage, https://github.com/ajbarrow/brainsig
+Project-URL: Source Code, https://github.com/ajbarrow/brainsig
+Project-URL: Bug Tracker, https://github.com/ajbarrow/brainsig/issues
+Project-URL: Documentation, https://brainsig.readthedocs.io
+Project-URL: Download, https://pypi.org/project/brainsig/#files
+Author-email: Tony Barrows <ajbarrow@uvm.edu>
+License-Expression: MIT
+License-File: LICENSE
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3 :: Only
+Requires-Python: >=3.10
+Requires-Dist: numpy>=1.24
+Requires-Dist: pandas>=2.0
+Requires-Dist: scikit-learn>=1.3
+Provides-Extra: build
+Requires-Dist: pip; extra == 'build'
+Requires-Dist: pip-audit; extra == 'build'
+Requires-Dist: twine; extra == 'build'
+Provides-Extra: dev
+Requires-Dist: hatch; extra == 'dev'
+Requires-Dist: pre-commit; extra == 'dev'
+Provides-Extra: docs
+Requires-Dist: myst-parser>=4.0; extra == 'docs'
+Requires-Dist: pydata-sphinx-theme~=0.16; extra == 'docs'
+Requires-Dist: sphinx-autoapi>=3.6.0; extra == 'docs'
+Requires-Dist: sphinx-autobuild>=2024.10.3; extra == 'docs'
+Requires-Dist: sphinx-copybutton>=0.5.2; extra == 'docs'
+Requires-Dist: sphinx-design>=0.6.1; extra == 'docs'
+Requires-Dist: sphinx~=8.0; extra == 'docs'
+Provides-Extra: style
+Requires-Dist: pydoclint; extra == 'style'
+Requires-Dist: ruff; extra == 'style'
+Provides-Extra: tests
+Requires-Dist: pytest; extra == 'tests'
+Requires-Dist: pytest-cov; extra == 'tests'
+Requires-Dist: pytest-raises; extra == 'tests'
+Requires-Dist: pytest-randomly; extra == 'tests'
+Requires-Dist: pytest-xdist; extra == 'tests'
+Description-Content-Type: text/markdown
+
+# Welcome to brainsig
+
+|        |        |
+|--------|--------|
+| Package | [![Latest PyPI Version](https://img.shields.io/pypi/v/brainsig.svg)](https://pypi.org/project/brainsig/) [![Supported Python Versions](https://img.shields.io/pypi/pyversions/brainsig.svg)](https://pypi.org/project/brainsig/) [![Documentation](https://readthedocs.org/projects/brainsig/badge/?version=latest)](https://brainsig.readthedocs.io/en/latest/?badge=latest) |
+| Meta   | [![Code of Conduct](https://img.shields.io/badge/Contributor%20Covenant-v2.0%20adopted-ff69b4.svg)](CODE_OF_CONDUCT.md) |
+
+*TODO: the above badges that indicate python version and package version will only work if your package is on PyPI.
+If you don't plan to publish to PyPI, you can remove them.*
+
+brainsig is a project that (describe what it does here).
+
+## Get started
+
+You can install this package into your preferred Python environment using pip:
+
+```bash
+$ pip install brainsig
+```
+
+TODO: Add a brief example of how to use the package to this section
+
+To use brainsig in your code:
+
+```python
+>>> import brainsig
+>>> brainsig.hello_world()
+```
+
+## Copyright
+
+- Copyright © 2025 Tony Barrows.
+- Free software distributed under the [MIT License](./LICENSE).

brainsig-0.1.0/README.md

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+# Welcome to brainsig
+
+|        |        |
+|--------|--------|
+| Package | [![Latest PyPI Version](https://img.shields.io/pypi/v/brainsig.svg)](https://pypi.org/project/brainsig/) [![Supported Python Versions](https://img.shields.io/pypi/pyversions/brainsig.svg)](https://pypi.org/project/brainsig/) [![Documentation](https://readthedocs.org/projects/brainsig/badge/?version=latest)](https://brainsig.readthedocs.io/en/latest/?badge=latest) |
+| Meta   | [![Code of Conduct](https://img.shields.io/badge/Contributor%20Covenant-v2.0%20adopted-ff69b4.svg)](CODE_OF_CONDUCT.md) |
+
+*TODO: the above badges that indicate python version and package version will only work if your package is on PyPI.
+If you don't plan to publish to PyPI, you can remove them.*
+
+brainsig is a project that (describe what it does here).
+
+## Get started
+
+You can install this package into your preferred Python environment using pip:
+
+```bash
+$ pip install brainsig
+```
+
+TODO: Add a brief example of how to use the package to this section
+
+To use brainsig in your code:
+
+```python
+>>> import brainsig
+>>> brainsig.hello_world()
+```
+
+## Copyright
+
+- Copyright © 2025 Tony Barrows.
+- Free software distributed under the [MIT License](./LICENSE).

brainsig-0.1.0/pyproject.toml

@@ -0,0 +1,267 @@
+################################################################################
+# Build Configuration
+################################################################################
+
+[build-system]
+build-backend = "hatchling.build"
+requires = ["hatchling", "hatch-vcs"]
+
+################################################################################
+# Project Configuration
+################################################################################
+
+[project]
+name = "brainsig"
+# You can chose to use dynamic versioning with hatch or static where you add it manually.
+version = "0.1.0"
+description = "A package for computing 'neural signatures' from fMRI data."
+authors = [
+    { name = "Tony Barrows", email = "ajbarrow@uvm.edu" },
+]
+license = "MIT"
+requires-python = ">= 3.10" # Adjust based on the minimum version of Python that you support
+readme = {"file" = "README.md", "content-type" = "text/markdown"}
+# Please consult https://pypi.org/classifiers/ for a full list.
+classifiers = [
+    "Development Status :: 2 - Pre-Alpha",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3 :: Only",
+]
+# TODO: add keywords
+keywords = []
+
+dependencies = [
+    "numpy>=1.24",
+    "pandas>=2.0", 
+    "scikit-learn>=1.3",
+]
+
+[project.urls]
+Homepage = "https://github.com/ajbarrow/brainsig"
+"Source Code" = "https://github.com/ajbarrow/brainsig"
+"Bug Tracker" = "https://github.com/ajbarrow/brainsig/issues"
+Documentation = "https://brainsig.readthedocs.io"
+Download = "https://pypi.org/project/brainsig/#files"
+
+[project.optional-dependencies]
+dev = [
+    "hatch",
+    "pre-commit",
+]
+
+docs = [
+    "sphinx~=8.0",
+    "myst-parser>=4.0",
+    "pydata-sphinx-theme~=0.16",
+    "sphinx-autobuild>=2024.10.3",
+    "sphinx-autoapi>=3.6.0",
+    "sphinx-design>=0.6.1",
+    "sphinx-copybutton>=0.5.2",
+]
+
+build = [
+    "pip-audit",
+    "pip",
+    "twine",
+]
+tests = [
+    "pytest",
+    "pytest-cov",
+    "pytest-raises",
+    "pytest-randomly",
+    "pytest-xdist",
+]
+
+style = [
+    "pydoclint",
+    "ruff",
+]
+
+
+################################################################################
+# Tool Configuration
+################################################################################
+
+# Hatch is building your package's wheel and sdist
+# This tells hatch to only include Python packages (i.e., folders with __init__.py) in the build.
+# read more about package building, here:
+# https://www.pyopensci.org/python-package-guide/package-structure-code/python-package-distribution-files-sdist-wheel.html
+[tool.hatch.build]
+only-packages = true
+
+# This tells Hatch to build the package from the src/me directory.
+# Read more about src layouts here: https://www.pyopensci.org/python-package-guide/package-structure-code/python-package-structure.html
+[tool.hatch.build.targets.wheel]
+packages = ["src/brainsig"]
+# Commented out VCS versioning - using static version instead
+# [tool.hatch.build.hooks.vcs]
+# version-file = "src/brainsig/_version.py"
+
+# [tool.hatch.version]
+# source = "vcs"
+
+######## Configure pytest for your test suite ########
+[tool.pytest.ini_options]
+testpaths = ["tests"] # Tells pytest what directory tests are in
+markers = ["raises"] # Tells pytest to not raise a warning if you use @pytest.mark.raises
+
+[tool.coverage.paths]
+source = [
+    "src/brainsig",
+    "*/site-packages/brainsig",
+]
+
+[tool.coverage.run]
+# Ensures code coverage is measured for branches (conditional statements with different outcomes) in your code.
+branch = true
+parallel = true
+omit = [
+    "src/brainsig/_version.py",
+]
+
+[tool.coverage.report]
+# This configures the output test coverage report
+exclude_lines = ["pragma: no cover"]
+precision = 2
+[tool.ruff]
+line-length = 88
+
+[tool.ruff.lint]
+select = ["ALL"]
+ignore = [
+    "D107",  # 'Missing docstring in __init__' ignored because pydoclint wants us to document the class instead.
+    "D203",  # '1 blank line required before class docstring' ignored because we want no blank line.
+    "D212",  # 'Multi-line docstring summary should start at the first line' ignored because we want the summary to start on the second line.
+    "D407",  # 'Missing dashed underline after section' ignored because Google style docstrings don't underline.
+    "D413",  # 'Missing blank line after section' ignored .
+    "D401",  # 'First line should be in imperative mood' ignored
+    "ANN001",  # Missing type annotation for {arg} in function" ignored
+    "ANN201",  # 'Missing type annotation for {return}'.
+]
+exclude = [
+    "src/brainsig/_version.py",
+    "docs/conf.py",
+]
+
+[tool.ruff.lint.extend-per-file-ignores]
+"__init__.py" = [
+    "E401",  # 'Multiple imports on one line'
+    "E402",  # 'Module level import not at top of file'
+    "F401",  # 'Imported but unused'
+    "I001",  # 'Import block is un-sorted or un-formatted' ignored because we may have to import in a particular, not-alphabetical order.
+]
+"tests/**/*.py" = [
+    "S101",  # 'Use of assert detected' ignored because we are using pytest.
+    "INP001",  # 'Insecure input' ignored because we are testing.
+    "ANN201",  # 'Missing type annotation for {return}' ignored because all tests return `None`.
+]
+"src/brainsig/dataset.py" = [
+    "PLR0913",  # Too many arguments - acceptable for data processing __init__
+    "N806",  # Variable names like X, X_processed follow scikit-learn conventions
+]
+"src/brainsig/model.py" = [
+    "N806",  # Variable names like X, X_processed follow scikit-learn conventions
+    "PLR0913",  # Too many arguments - acceptable for model configuration
+    "C901",  # Complexity - get_model_scores handles multiple scoring scenarios
+    "PLR0912",  # Too many branches - get_model_scores handles multiple cases
+    "PLR2004",  # Magic value 2 for binary vs multiclass is clear in context
+]
+
+[tool.ruff.lint.isort]
+case-sensitive = true
+known-first-party = ["src", "brainsig"]
+lines-after-imports = 1
+
+[tool.pydoclint]
+style = "numpy"
+arg-type-hints-in-signature = false
+arg-type-hints-in-docstring = true
+check-return-types = false
+check-yield-types = false
+exclude = "_version.py"
+
+
+
+# Use UV to create Hatch environments
+[tool.hatch.envs.default]
+installer = "uv"
+
+################################################################################
+# Hatch Environments
+################################################################################
+
+#--------------- Build and check your package ---------------#
+
+# This table installs the tools you need to test and build your package
+[tool.hatch.envs.build]
+description = """Test the installation the package."""
+features = [
+    "build",
+]
+detached = true
+
+# This table installs created the command hatch run install:check which will build and check your package.
+[tool.hatch.envs.build.scripts]
+check = [
+    "hatch build {args:--clean}",
+    "twine check dist/*",
+]
+
+#--------------- Run tests ---------------#
+
+
+[tool.hatch.envs.test]
+description = """Run the test suite."""
+features = [
+    "tests",
+]
+
+[[tool.hatch.envs.test.matrix]]
+python = ["3.10", "3.11", "3.12", "3.13"]
+
+[tool.hatch.envs.test.scripts]
+run = "pytest {args:--cov=brainsig --cov-report=term-missing}"
+
+#--------------- Build and preview your documentation ---------------#
+
+# This sets up a hatch environment with associated dependencies that need to be installed
+[tool.hatch.envs.docs]
+description = """Build or serve the documentation."""
+# Install optional dependency test for docs
+features = [
+    "docs",
+]
+
+# This table contains the scripts that you can use to build and serve your docs
+# hatch run docs:build will build your documentation
+# hatch run docs:serve will serve them 'live' on your computer locally
+[tool.hatch.envs.docs.scripts]
+build = ["sphinx-apidoc -o docs/api src/brainsig", "sphinx-build {args:-W -b html docs docs/_build}"]
+serve = ["sphinx-apidoc -o docs/api src/brainsig", "sphinx-autobuild docs --watch src/brainsig {args:-b html docs/_build/serve}"]
+#--------------- Format & style your code ---------------#
+
+[tool.hatch.envs.style]
+description = """Check the code and documentation style."""
+features = [
+    "style",
+]
+detached = true
+
+[tool.hatch.envs.style.scripts]
+docstrings = "pydoclint src/ tests/"
+code = "ruff check {args}"
+format = "ruff format {args}"
+check = ["docstrings", "code"]
+
+#--------------- Check security for your dependencies ---------------#
+
+[tool.hatch.envs.audit]
+description = """Check dependencies for security vulnerabilities."""
+features = [
+    "build",
+]
+
+[tool.hatch.envs.audit.scripts]
+check = ["pip-audit"]

brainsig-0.1.0/src/brainsig/__init__.py

@@ -0,0 +1,29 @@
+# MIT License
+#
+# Copyright (c) 2025 Tony Barrows
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice (including the next
+# paragraph) shall be included in all copies or substantial portions of the
+# Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+"""
+Add a docstring here for the init module.
+
+This might include a very brief description of the package,
+its purpose, and any important notes.
+"""