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Katherine L. Bottenhorn
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update from master, testing actions docs
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‎.github/workflows/linting.yml‎

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name: "Lint Code"
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on:
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push:
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branches:
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- "master"
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pull_request:
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branches:
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- '*'
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concurrency:
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group: linting-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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# Determine if tests should be run based on commit message.
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check_skip:
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runs-on: ubuntu-latest
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outputs:
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skip: ${{ steps.result_step.outputs.ci-skip }}
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steps:
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- uses: actions/checkout@v2
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with:
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fetch-depth: 0
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- id: result_step
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uses: mstachniuk/ci-skip@master
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with:
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commit-filter: '[skip ci];[ci skip];[skip github]'
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commit-filter-separator: ';'
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style_check:
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needs: check_skip
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if: ${{ needs.check_skip.outputs.skip == 'false' }}
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runs-on: "ubuntu-latest"
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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: ["3.7"]
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name: Style check
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defaults:
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run:
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shell: bash
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steps:
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- uses: actions/checkout@v2
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- name: 'Set up python'
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: 'Install IDConn'
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shell: bash {0}
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run: pip install -e .[tests]
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- name: 'Run linter'
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shell: bash {0}
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run: flake8 idconn

‎.github/workflows/python-publish.yml‎

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# This workflow will upload a Python Package using Twine when a release is created
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# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
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name: Upload Python Package
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on:
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release:
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types: [published]
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jobs:
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deploy:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python
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uses: actions/setup-python@v2
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with:
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python-version: '3.7'
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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 setuptools wheel twine
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- name: Build and publish
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env:
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TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
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TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
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run: |
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python setup.py sdist bdist_wheel
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twine upload dist/*

‎.github/workflows/testing.yml‎

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name: "Run Tests"
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on:
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push:
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branches:
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- "master"
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pull_request:
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branches:
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- '*'
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concurrency:
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group: testing-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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# Determine if tests should be run based on commit message.
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check_skip:
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name: Determine if CI should be skipped
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runs-on: ubuntu-latest
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outputs:
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skip: ${{ steps.result_step.outputs.ci-skip }}
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steps:
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- uses: actions/checkout@v2
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with:
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fetch-depth: 0
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- id: result_step
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uses: mstachniuk/ci-skip@master
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with:
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commit-filter: '[skip ci];[ci skip];[skip github]'
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commit-filter-separator: ';'
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run_unit_tests:
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name: Unit tests
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needs: check_skip
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if: ${{ needs.check_skip.outputs.skip == 'false' }}
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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", "macos-latest"]
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python-version: ["3.7", "3.8", "3.9", "3.10"]
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defaults:
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run:
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shell: bash
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steps:
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- uses: actions/checkout@v2
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- name: 'Set up python'
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: 'Install IDConn'
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shell: bash {0}
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run: pip install -e .[tests]
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- name: 'Run tests'
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shell: bash {0}
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run: py.test --cov-append --cov-report=xml --cov=idconn idconn
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- name: Upload artifacts
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uses: actions/upload-artifact@v2
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with:
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name: unit_${{ matrix.os }}_${{ matrix.python-version }}
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path: coverage.xml
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if: success()
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upload_to_codecov:
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name: Upload coverage
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needs: [run_unit_tests]
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runs-on: "ubuntu-latest"
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steps:
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- name: Checkout
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uses: actions/checkout@v2
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- name: Download artifacts
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uses: actions/download-artifact@v2
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- name: Upload to CodeCov
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uses: codecov/codecov-action@v2
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with:
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fail_ci_if_error: true

‎.gitignore‎

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docs/auto_examples/
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*.ipynb_checkpoints/*
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bad-qa.png
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cp-corrmats.sh

‎.readthedocs.yml‎

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# .readthedocs.yml
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# Read the Docs configuration file
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# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
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# Required
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version: 2
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# Build documentation in the docs/ directory with Sphinx
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sphinx:
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configuration: docs/conf.py
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python:
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version: 3.8
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install:
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- method: pip
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path: .
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extra_requirements:
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- doc
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system_packages: true

‎docs/Makefile‎

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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 ?= /Users/kbottenh/Library/Python/3.7/bin/sphinx-build
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SOURCEDIR = source
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BUILDDIR = build
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SPHINXBUILD ?= python -msphinx
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SPHINXPROJ = IDConn
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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) $(O)
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clean:
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rm -r _build generated auto_examples
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html-noplot:
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$(SPHINXBUILD) -D plot_gallery=0 -b html $(ALLSPHINXOPTS) $(SOURCEDIR) $(BUILDDIR)/html
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@echo
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@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
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.PHONY: help Makefile
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# Catch-all target: route all unknown targets to Sphinx using the new

‎docs/source/_static/IDConnWorkflowH.svg‎ renamed to ‎docs/_static/IDConnWorkflowH.svg‎

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‎docs/source/_static/logo-transparent.png‎ renamed to ‎docs/_static/logo-transparent.png‎

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‎docs/_templates/class.rst‎

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:mod:`{{module}}`.{{objname}}
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{{ underline }}==============
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.. currentmodule:: {{ module }}
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.. autoclass:: {{ objname }}
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:members:
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:inherited-members:
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:show-inheritance:
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{% block methods %}
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{% if methods %}
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.. rubric:: Methods
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.. autosummary::
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{% for item in methods %}
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{%- if not item.startswith('_') or item in ['__call__'] %} ~{{ name }}.{{ item }}
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{% endif %}
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{%- endfor %}
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{% endif %}
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{% endblock %}
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{% block attributes %}
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{% if attributes %}
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.. rubric:: Properties
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.. autosummary::
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{% for item in attributes %}
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{%- if not item.startswith('_') or item in ['__call__'] %} ~{{ name }}.{{ item }}
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{% endif %}
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{%- endfor %}
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{% endif %}
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{% endblock %}
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.. include:: {{fullname}}.examples
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.. raw:: html
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<div class="clearer"></div>

‎docs/_templates/function.rst‎

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:mod:`{{module}}`.{{objname}}
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{{ underline }}====================
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.. currentmodule:: {{ module }}
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.. autofunction:: {{ objname }}
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.. include:: {{fullname}}.{{item}}examples
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.. raw:: html
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<div class='clearer'></div>

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