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some docs
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‎.github/workflows/sphinx.yml‎

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# From: https://github.com/rkdarst/sphinx-actions-test/blob/master/.github/workflows/sphinx-build.yml
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name: sphinx
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on: [push, pull_request]
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env:
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DEFAULT_BRANCH: "master"
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#SPHINXOPTS: "-W --keep-going -T"
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# ^-- If these SPHINXOPTS are enabled, then be strict about the builds and fail on any warnings
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jobs:
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build-and-deploy:
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name: Build and gh-pages
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runs-on: ubuntu-latest
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steps:
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# https://github.com/marketplace/actions/checkout
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- uses: actions/checkout@v2
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with:
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fetch-depth: 0
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lfs: true
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# https://github.com/marketplace/actions/setup-python
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# ^-- This gives info on matrix testing.
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- name: Install Python
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uses: actions/setup-python@v2
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with:
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python-version: 3.8
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# https://docs.github.com/en/actions/guides/building-and-testing-python#caching-dependencies
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# ^-- How to set up caching for pip on Ubuntu
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- name: Cache pip
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uses: actions/cache@v2
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with:
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path: ~/.cache/pip
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key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
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restore-keys: |
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${{ runner.os }}-pip-
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${{ runner.os }}-
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# https://docs.github.com/en/actions/guides/building-and-testing-python#installing-dependencies
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# ^-- This gives info on installing dependencies with pip
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install -r requirements.txt
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- name: Debugging information
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run: |
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echo "github.ref:" ${{github.ref}}
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echo "github.event_name:" ${{github.event_name}}
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echo "github.head_ref:" ${{github.head_ref}}
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echo "github.base_ref:" ${{github.base_ref}}
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set -x
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git rev-parse --abbrev-ref HEAD
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git branch
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git branch -a
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git remote -v
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python -V
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pip list --not-required
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pip list
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# Build
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- uses: ammaraskar/sphinx-problem-matcher@master
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- name: Build Sphinx docs
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run: |
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make dirhtml
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# This fixes broken copy button icons, as explained in
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# https://github.com/coderefinery/sphinx-lesson/issues/50
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# https://github.com/executablebooks/sphinx-copybutton/issues/110
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# This can be removed once these PRs are accepted (but the
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# fixes also need to propagate to other themes):
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# https://github.com/sphinx-doc/sphinx/pull/8524
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# https://github.com/readthedocs/sphinx_rtd_theme/pull/1025
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sed -i 's/url_root="#"/url_root=""/' _build/dirhtml/index.html || true
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# The following supports building all branches and combining on
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# gh-pages
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# Clone and set up the old gh-pages branch
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- name: Clone old gh-pages
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if: ${{ github.event_name == 'push' }}
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run: |
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set -x
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git fetch
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( git branch gh-pages remotes/origin/gh-pages && git clone . --branch=gh-pages _gh-pages/ ) || mkdir _gh-pages
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rm -rf _gh-pages/.git/
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mkdir -p _gh-pages/branch/
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# If a push and default branch, copy build to _gh-pages/ as the "main"
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# deployment.
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- name: Copy new build (default branch)
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if: |
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contains(github.event_name, 'push') &&
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contains(github.ref, env.DEFAULT_BRANCH)
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run: |
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set -x
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# Delete everything under _gh-pages/ that is from the
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# primary branch deployment. Eicludes the other branches
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# _gh-pages/branch-* paths, and not including
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# _gh-pages itself.
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find _gh-pages/ -mindepth 1 ! -path '_gh-pages/branch*' -delete
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rsync -a _build/dirhtml/ _gh-pages/
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# If a push and not on default branch, then copy the build to
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# _gh-pages/branch/$brname (transforming '/' into '--')
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- name: Copy new build (branch)
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if: |
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contains(github.event_name, 'push') &&
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!contains(github.ref, env.DEFAULT_BRANCH)
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run: |
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set -x
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#brname=$(git rev-parse --abbrev-ref HEAD)
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brname="${{github.ref}}"
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brname="${brname##refs/heads/}"
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brdir=${brname//\//--} # replace '/' with '--'
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rm -rf _gh-pages/branch/${brdir}
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rsync -a _build/dirhtml/ _gh-pages/branch/${brdir}
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# Go through each branch in _gh-pages/branch/, if it's not a
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# ref, then delete it.
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- name: Delete old feature branches
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if: ${{ github.event_name == 'push' }}
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run: |
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set -x
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for brdir in `ls _gh-pages/branch/` ; do
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brname=${brdir//--/\/} # replace '--' with '/'
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if ! git show-ref remotes/origin/$brname ; then
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echo "Removing $brdir"
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rm -r _gh-pages/branch/$brdir/
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fi
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done
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# Add the .nojekyll file
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- name: nojekyll
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if: ${{ github.event_name == 'push' }}
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run: |
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touch _gh-pages/.nojekyll
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# Deploy
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# https://github.com/peaceiris/actions-gh-pages
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- name: Deploy
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uses: peaceiris/actions-gh-pages@v3
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if: ${{ github.event_name == 'push' }}
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#if: ${{ success() && github.event_name == 'push' && github.ref == 'refs/heads/$defaultBranch' }}
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with:
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publish_branch: gh-pages
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: _gh-pages/
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force_orphan: true

‎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, and also
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# from the environment for the first two.
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SPHINXOPTS ?=
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SPHINXBUILD ?= sphinx-build
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SOURCEDIR = source
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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)

‎README.md‎

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![Logo](images/stochman.png)
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---
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4-
[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/pytorch-lightning)](https://pypi.org/project/stochman/)
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[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/stochman)](https://pypi.org/project/stochman/)
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[![PyPI Status](https://badge.fury.io/py/stochman.svg)](https://badge.fury.io/py/stochman)
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[![PyPI Status](https://pepy.tech/badge/stochman)](https://pepy.tech/badge/stochman)
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[![license](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://github.com/MachineLearningLifeScience/stochman/blob/master/LICENSE)

‎docs/source/conf.py‎

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# Configuration file for the Sphinx documentation builder.
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#
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# This file only contains a selection of the most common options. For a full
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# list see the documentation:
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# https://www.sphinx-doc.org/en/master/usage/configuration.html
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# -- Path setup --------------------------------------------------------------
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# If extensions (or modules to document with autodoc) are in another directory,
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# add these directories to sys.path here. If the directory is relative to the
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# documentation root, use os.path.abspath to make it absolute, like shown here.
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#
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# import os
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# import sys
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# sys.path.insert(0, os.path.abspath('.'))
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# -- Project information -----------------------------------------------------
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project = 'stochman'
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copyright = '2022, Nicki'
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author = 'Nicki'
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# -- General configuration ---------------------------------------------------
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# Add any Sphinx extension module names here, as strings. They can be
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# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
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# ones.
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extensions = ['sphinx.ext.autodoc']
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# Add any paths that contain templates here, relative to this directory.
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templates_path = ['_templates']
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# List of patterns, relative to source directory, that match files and
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# directories to ignore when looking for source files.
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# This pattern also affects html_static_path and html_extra_path.
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exclude_patterns = []
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# -- Options for HTML output -------------------------------------------------
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# The theme to use for HTML and HTML Help pages. See the documentation for
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# a list of builtin themes.
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#
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html_theme = 'alabaster'
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# Add any paths that contain custom static files (such as style sheets) here,
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# relative to this directory. They are copied after the builtin static files,
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# so a file named "default.css" will overwrite the builtin "default.css".
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html_static_path = ['_static']

‎docs/source/index.rst‎

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.. stochman documentation master file, created by
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sphinx-quickstart on Thu Mar 17 08:27:46 2022.
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You can adapt this file completely to your liking, but it should at least
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contain the root `toctree` directive.
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Welcome to stochman's documentation!
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====================================
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WORK IN PROGRESS!
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StochMan (Stochastic Manifolds) is a collection of elementary algorithms for computations
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on random manifolds learned from finite noisy data. Each algorithm assume that the considered
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manifold model implement a specific set of interfaces.
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.. toctree::
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:maxdepth: 2
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:caption: Contents:
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nnj
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Indices and tables
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==================
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* :ref:`genindex`
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* :ref:`modindex`
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* :ref:`search`

‎docs/source/nnj.rst‎

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nnj
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***
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.. autoclass:: stochman.nnj.Conv1d

‎make.bat‎

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@ECHO OFF
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pushd %~dp0
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REM Command file for Sphinx documentation
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if "%SPHINXBUILD%" == "" (
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set SPHINXBUILD=sphinx-build
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)
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set SOURCEDIR=source
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set BUILDDIR=build
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if "%1" == "" goto help
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%SPHINXBUILD% >NUL 2>NUL
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if errorlevel 9009 (
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echo.
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echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
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echo.installed, then set the SPHINXBUILD environment variable to point
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echo.to the full path of the 'sphinx-build' executable. Alternatively you
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echo.may add the Sphinx directory to PATH.
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echo.
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echo.If you don't have Sphinx installed, grab it from
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echo.http://sphinx-doc.org/
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exit /b 1
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)
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%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
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goto end
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:help
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%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
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:end
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popd

‎stochman/__init__.py‎

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# We are not importing the rest of the package during the build process, as it may not be compiled yet
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else:
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# import modules
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from . import curves, discretized_manifold, geodesic, manifold, nnj
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from stochman import curves, discretized_manifold, geodesic, manifold, nnj
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# import classes for direct access
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from .curves import CubicSpline, DiscreteCurve
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from stochman.curves import CubicSpline, DiscreteCurve

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