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update from master, testing actions docs
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name: "Lint Code" | ||
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on: | ||
push: | ||
branches: | ||
- "master" | ||
pull_request: | ||
branches: | ||
- '*' | ||
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concurrency: | ||
group: linting-${{ github.ref }} | ||
cancel-in-progress: true | ||
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jobs: | ||
# Determine if tests should be run based on commit message. | ||
check_skip: | ||
runs-on: ubuntu-latest | ||
outputs: | ||
skip: ${{ steps.result_step.outputs.ci-skip }} | ||
steps: | ||
- uses: actions/checkout@v2 | ||
with: | ||
fetch-depth: 0 | ||
- id: result_step | ||
uses: mstachniuk/ci-skip@master | ||
with: | ||
commit-filter: '[skip ci];[ci skip];[skip github]' | ||
commit-filter-separator: ';' | ||
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style_check: | ||
needs: check_skip | ||
if: ${{ needs.check_skip.outputs.skip == 'false' }} | ||
runs-on: "ubuntu-latest" | ||
strategy: | ||
fail-fast: false | ||
matrix: | ||
os: ["ubuntu-latest"] | ||
python-version: ["3.7"] | ||
name: Style check | ||
defaults: | ||
run: | ||
shell: bash | ||
steps: | ||
- uses: actions/checkout@v2 | ||
- name: 'Set up python' | ||
uses: actions/setup-python@v2 | ||
with: | ||
python-version: ${{ matrix.python-version }} | ||
- name: 'Install IDConn' | ||
shell: bash {0} | ||
run: pip install -e .[tests] | ||
- name: 'Run linter' | ||
shell: bash {0} | ||
run: flake8 idconn |
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# This workflow will upload a Python Package using Twine when a release is created | ||
# 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: | ||
release: | ||
types: [published] | ||
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jobs: | ||
deploy: | ||
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runs-on: ubuntu-latest | ||
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steps: | ||
- uses: actions/checkout@v2 | ||
- name: Set up Python | ||
uses: actions/setup-python@v2 | ||
with: | ||
python-version: '3.7' | ||
- name: Install dependencies | ||
run: | | ||
python -m pip install --upgrade pip | ||
pip install setuptools wheel twine | ||
- name: Build and publish | ||
env: | ||
TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }} | ||
TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }} | ||
run: | | ||
python setup.py sdist bdist_wheel | ||
twine upload dist/* |
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name: "Run Tests" | ||
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on: | ||
push: | ||
branches: | ||
- "master" | ||
pull_request: | ||
branches: | ||
- '*' | ||
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concurrency: | ||
group: testing-${{ github.ref }} | ||
cancel-in-progress: true | ||
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jobs: | ||
# Determine if tests should be run based on commit message. | ||
check_skip: | ||
name: Determine if CI should be skipped | ||
runs-on: ubuntu-latest | ||
outputs: | ||
skip: ${{ steps.result_step.outputs.ci-skip }} | ||
steps: | ||
- uses: actions/checkout@v2 | ||
with: | ||
fetch-depth: 0 | ||
- id: result_step | ||
uses: mstachniuk/ci-skip@master | ||
with: | ||
commit-filter: '[skip ci];[ci skip];[skip github]' | ||
commit-filter-separator: ';' | ||
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run_unit_tests: | ||
name: Unit tests | ||
needs: check_skip | ||
if: ${{ needs.check_skip.outputs.skip == 'false' }} | ||
runs-on: ${{ matrix.os }} | ||
strategy: | ||
fail-fast: false | ||
matrix: | ||
os: ["ubuntu-latest", "macos-latest"] | ||
python-version: ["3.7", "3.8", "3.9", "3.10"] | ||
defaults: | ||
run: | ||
shell: bash | ||
steps: | ||
- uses: actions/checkout@v2 | ||
- name: 'Set up python' | ||
uses: actions/setup-python@v2 | ||
with: | ||
python-version: ${{ matrix.python-version }} | ||
- name: 'Install IDConn' | ||
shell: bash {0} | ||
run: pip install -e .[tests] | ||
- name: 'Run tests' | ||
shell: bash {0} | ||
run: py.test --cov-append --cov-report=xml --cov=idconn idconn | ||
- name: Upload artifacts | ||
uses: actions/upload-artifact@v2 | ||
with: | ||
name: unit_${{ matrix.os }}_${{ matrix.python-version }} | ||
path: coverage.xml | ||
if: success() | ||
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upload_to_codecov: | ||
name: Upload coverage | ||
needs: [run_unit_tests] | ||
runs-on: "ubuntu-latest" | ||
steps: | ||
- name: Checkout | ||
uses: actions/checkout@v2 | ||
- name: Download artifacts | ||
uses: actions/download-artifact@v2 | ||
- name: Upload to CodeCov | ||
uses: codecov/codecov-action@v2 | ||
with: | ||
fail_ci_if_error: true |
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docs/auto_examples/ | ||
*.ipynb_checkpoints/* | ||
bad-qa.png | ||
cp-corrmats.sh | ||
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# .readthedocs.yml | ||
# Read the Docs configuration file | ||
# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details | ||
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# Required | ||
version: 2 | ||
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# Build documentation in the docs/ directory with Sphinx | ||
sphinx: | ||
configuration: docs/conf.py | ||
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python: | ||
version: 3.8 | ||
install: | ||
- method: pip | ||
path: . | ||
extra_requirements: | ||
- doc | ||
system_packages: true |
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:mod:`{{module}}`.{{objname}} | ||
{{ underline }}============== | ||
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.. currentmodule:: {{ module }} | ||
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.. autoclass:: {{ objname }} | ||
:members: | ||
:inherited-members: | ||
:show-inheritance: | ||
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{% block methods %} | ||
{% if methods %} | ||
.. rubric:: Methods | ||
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.. autosummary:: | ||
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{% for item in methods %} | ||
{%- if not item.startswith('_') or item in ['__call__'] %} ~{{ name }}.{{ item }} | ||
{% endif %} | ||
{%- endfor %} | ||
{% endif %} | ||
{% endblock %} | ||
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{% block attributes %} | ||
{% if attributes %} | ||
.. rubric:: Properties | ||
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.. autosummary:: | ||
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{% for item in attributes %} | ||
{%- if not item.startswith('_') or item in ['__call__'] %} ~{{ name }}.{{ item }} | ||
{% endif %} | ||
{%- endfor %} | ||
{% endif %} | ||
{% endblock %} | ||
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.. include:: {{fullname}}.examples | ||
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.. raw:: html | ||
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<div class="clearer"></div> |
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:mod:`{{module}}`.{{objname}} | ||
{{ 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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{{ fullname }} | ||
{{ underline }} | ||
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.. automodule:: {{ fullname }} | ||
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{% block classes %} | ||
{% if classes %} | ||
.. rubric:: Classes | ||
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.. autosummary:: | ||
:toctree: | ||
:template: class.rst | ||
{% for item in classes %} | ||
{{ item }} | ||
{%- endfor %} | ||
{% endif %} | ||
{% endblock %} | ||
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{% block functions %} | ||
{% if functions %} | ||
.. rubric:: Functions | ||
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.. autosummary:: | ||
:toctree: | ||
:template: function.rst | ||
{% for item in functions %} | ||
{{ item }} | ||
{%- endfor %} | ||
{% endif %} | ||
{% endblock %} | ||
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{% block exceptions %} | ||
{% if exceptions %} | ||
.. rubric:: Exceptions | ||
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.. autosummary:: | ||
:toctree: | ||
{% for item in exceptions %} | ||
{{ item }} | ||
{%- endfor %} | ||
{% endif %} | ||
{% endblock %} |
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API | ||
=== | ||
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.. _api_pipeline_ref: | ||
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:mod:`idconn.pipeline`: The main IDConn pipeline | ||
-------------------------------------------------- | ||
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.. automodule:: idconn.pipeline | ||
:no-members: | ||
:no-inherited-members: | ||
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.. currentmodule:: idconn | ||
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.. autosummary:: | ||
:toctree: generated/ | ||
:template: function.rst | ||
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pipeline.idconn_workflow | ||
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.. _api_connectivity_ref: | ||
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:mod:`idconn.connectivity`: Tools for computing connectivity matrices/graphs | ||
---------------------------------------------------------------------------- | ||
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.. automodule:: idconn.connectivity | ||
:no-members: | ||
:no-inherited-members: | ||
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.. currentmodule:: idconn | ||
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.. autosummary:: | ||
:toctree: generated/ | ||
:template: module.rst | ||
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connectivity.build_networks | ||
connectivity.estimate_thresh | ||
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.. _api_data_ref: | ||
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:mod:`idconn.data`: Tools for arranging data and addressing missing data | ||
------------------------------------------------------------------------ | ||
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.. automodule:: idconn.data | ||
:no-members: | ||
:no-inherited-members: | ||
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.. currentmodule:: idconn | ||
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.. autosummary:: | ||
:toctree: generated/ | ||
:template: module.rst | ||
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data.iterative_imputation | ||
data.missingness | ||
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.. _api_networking_ref: | ||
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:mod:`idconn.networking`: Tools for computing network topology / graph theoretic measures | ||
----------------------------------------------------------------------------------------- | ||
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.. automodule:: idconn.networking | ||
:no-members: | ||
:no-inherited-members: | ||
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.. currentmodule:: idconn | ||
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.. autosummary:: | ||
:toctree: generated/ | ||
:template: module.rst | ||
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networking.graph_theory | ||
networking.null_distribution |
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