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Merge pull request #125 from geometric-intelligence/ninamiolane-ci
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‎.github/workflows/docs.yml

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name: "Docs: Check and Deploy"
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on:
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push:
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branches: [main, github-actions-test]
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pull_request:
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branches: [main]
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permissions:
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contents: write
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jobs:
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build:
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runs-on: ${{matrix.os}}
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strategy:
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matrix:
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os: [ubuntu-latest]
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python-version: [3.11.3]
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steps:
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- uses: actions/checkout@v3
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- name: Build using Python ${{matrix.python-version}}
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uses: actions/setup-python@v4
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with:
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python-version: ${{matrix.python-version}}
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cache: "pip"
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cache-dependency-path: "pyproject.toml"
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- name: Install dependencies [pip]
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run: |
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pip install --upgrade pip setuptools wheel
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pip install -e .[doc]
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- name: Install Pandoc [apt-get]
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run: |
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sudo apt-get -y install pandoc
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- name: Generate Docs [Sphinx]
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run: |
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sphinx-build -b html -D version=latest -D release=latest docs docs/_build
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- name: Deploy Docs
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uses: JamesIves/github-pages-deploy-action@v4
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if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' && github.repository == 'geometric-intelligence/neurometry' }}
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with:
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branch: main
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folder: docs/_build
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token: ${{ secrets.DOCUMENTATION_KEY }}
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repository-name: geometric-intelligence/geometric-intelligence.github.io
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target-folder: neurometry
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clean: true
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numpydoc-validation:
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runs-on: ${{matrix.os}}
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strategy:
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matrix:
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os: [ubuntu-latest]
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python-version: [3.11.3]
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steps:
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- uses: actions/checkout@v3
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- name: Build using Python ${{matrix.python-version}}
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uses: actions/setup-python@v4
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with:
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python-version: ${{matrix.python-version}}
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cache: "pip"
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cache-dependency-path: "pyproject.toml"
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- name: Install dependencies [pip]
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run: |
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pip install --upgrade pip setuptools wheel
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pip install -e .[doc]
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- name: Checking NumpyDoc Validation for files
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run: |
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pip install pre-commit
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pre-commit install
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pre-commit run --all-files numpydoc-validation

‎.github/workflows/lint.yml

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name: Lint
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on:
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push:
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branches: [ main,github-actions-test ]
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pull_request:
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branches: [ main ]
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jobs:
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ruff:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: chartboost/ruff-action@v1

‎.github/workflows/test.yml

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name: Test
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on:
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push:
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branches: [main,github-actions-test]
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paths-ignore:
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- 'docs/**'
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- 'README.md'
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- 'LICENSE.txt'
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- '.gitignore'
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pull_request:
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branches: [main]
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paths-ignore:
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- 'docs/**'
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- 'README.md'
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- 'LICENSE.txt'
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- '.gitignore'
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jobs:
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build:
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-latest]
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python-version: ["3.11.3"]
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flavor: ["dev", "all"]
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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cache: "pip"
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cache-dependency-path: "pyproject.toml"
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- name: Install Package [${{ matrix.flavor }}]
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run: |
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pip install -e .[${{ matrix.flavor }}]
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- name: Typecheck [mypy]
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run: |
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mypy -p neurometry
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continue-on-error: true
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- name: Run tests [pytest]
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run: |
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pytest --cov --cov-report=xml:coverage.xml
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- name: Upload coverage reports to Codecov
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uses: codecov/[email protected]
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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slug: geometric-intelligence/neurometry
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file: coverage.xml
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fail_ci_if_error: false

‎.gitignore

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neurometry/datasets/rnn_grid_cells/Dual agent path integration disjoint PCs/*
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neurometry/datasets/rnn_grid_cells/Single agent path integration/*
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# Wandb files
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wandb/*
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‎.pre-commit-config.yaml

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default_language_version :
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python : python3
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default_language_version:
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python: python3
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.0.1
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hooks:
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- id: check-byte-order-marker
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- id: fix-byte-order-marker
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- id: check-case-conflict
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- id: check-merge-conflict
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- id: check-yaml
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- id: mixed-line-ending
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args:
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- --fix=no
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- id: no-commit-to-branch
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args:
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- --branch=master
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- id: check-added-large-files
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args:
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- --maxkb=2048
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- id: trailing-whitespace
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- id: requirements-txt-fixer
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- repo: https://github.com/psf/black
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rev: 22.3.0
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hooks:
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- id: black
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- repo: https://github.com/pycqa/isort
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rev: 5.10.1
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: v0.1.14
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hooks:
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- id : isort
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args : ["--profile", "black", "--filter-files"]
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- repo: https://github.com/asottile/blacken-docs
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rev: v1.12.0
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- id: ruff
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types_or: [ python, pyi, jupyter ]
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args: [ --fix ]
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- id: ruff-format
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types_or: [ python, pyi, jupyter ]
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- repo: https://github.com/numpy/numpydoc
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rev: v1.6.0
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hooks:
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- id: blacken-docs
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additional_dependencies: [black==20.8b0]
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- id: numpydoc-validation

‎codecov.yml

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# see https://docs.codecov.io/docs/codecov-yaml
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coverage:
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range: 50..100
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round: down
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precision: 2
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ignore:
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- "test/"

‎docs/Makefile

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# Minimal makefile for Sphinx documentation
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#
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# You can set these variables from the command line.
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SPHINXOPTS =
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SPHINXBUILD = sphinx-build
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SOURCEDIR = .
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BUILDDIR = _build
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# Put it first so that "make" without argument is like "make help".
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help:
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@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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.PHONY: help Makefile
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# Catch-all target: route all unknown targets to Sphinx using the new
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# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
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%: Makefile
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@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

‎docs/api/curvature.rst

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*********
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Curvature
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*********
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.. automodule:: neurometry.curvature
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:members:

‎docs/api/datasets.rst

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********
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Datasets
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********
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.. automodule:: neurometry.datasets
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:members:

‎docs/api/dimension.rst

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*********
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Dimension
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*********
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.. automodule:: neurometry.dimension
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:members:

‎docs/api/index.rst

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=============
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API Reference
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=============
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The API reference gives an overview of `Neurometry`, which consists of several modules:
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- `datasets` implements utilities to load synthetic and real datasets.
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- `dimension` implements extrinsic and intrinsic dimension estimation.
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- `topology` implements topology estimation.
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- `curvature` implements geometry estimation, e.g., curvature computations.
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- `warping` implements warping functions.
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.. toctree::
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:maxdepth: 2
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:caption: Packages & Modules
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datasets
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dimension
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topology
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curvature
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warping

‎docs/api/topology.rst

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********
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Topology
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********
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.. automodule:: neurometry.topology
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:members:

‎docs/api/warping.rst

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*******
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Warping
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*******
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.. automodule:: neurometry.warping
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:members:

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