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Merge dev on to release for v2.2.0 #minor
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‎.github/workflows/bump-version-dev.yml

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name: Bump Version Number (dev)
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name: Bump Version (dev)
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on:
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push:
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jobs:
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build:
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if: (! contains(github.event.head_commit.message, '[no bump]'))
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name: Bump version
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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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with:
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persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal token
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fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
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- uses: actions/checkout@v3
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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: 3.8
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python-version: 3.9
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- name: Set env variables
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run: |
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bump_version build $VERSION_FILE
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# Note that we don't want to create a new tag for "builds"
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- name: Commit files
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run: |
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REPOSITORY=${INPUT_REPOSITORY:-$GITHUB_REPOSITORY}
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remote_repo="https://${GITHUB_ACTOR}:${{ secrets.PUSH_ACTION_TOKEN }}@github.com/${REPOSITORY}.git"
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# - name: Commit files
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# run: |
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# REPOSITORY=${INPUT_REPOSITORY:-$GITHUB_REPOSITORY}
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# remote_repo="https://${GITHUB_ACTOR}:${{ secrets.PUSH_ACTION_TOKEN }}@github.com/${REPOSITORY}.git"
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git config --local user.email "action@github.com"
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git config --local user.name "GitHub Action"
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# git config --local user.email "action@github.com"
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# git config --local user.name "GitHub Action"
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# Commit version bump to dev ([no ci] to avoid infinite loop)
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git commit -m "Bump version number [no ci]" -a
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git push "${remote_repo}" dev
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# # Commit version bump to dev ([no ci] to avoid infinite loop)
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# git commit -m "Bump version number (build) [no ci]" -a
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# git push "${remote_repo}" dev
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- name: Commit files
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uses: stefanzweifel/git-auto-commit-action@v4
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with:
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commit_message: Bump version number (build part)
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commit_author: Author <actions@github.com>

‎.github/workflows/bump-version.yml

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name: Bump Version Number
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name: Bump Version (release)
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on:
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push:

‎.github/workflows/cleanup-tags.yml

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name: Clean up tags
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name: Clean Up Tags
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on: push
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on: [workflow_dispatch]
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jobs:
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deploy:

‎.github/workflows/examples.yml

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steps:
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- uses: actions/checkout@v2
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- uses: FedericoCarboni/setup-ffmpeg@v1
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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# This path is specific to Ubuntu
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path: ~/.cache/pip
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# Look to see if there is a cache hit for the corresponding requirements file
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key: ${{ runner.os }}-pip-${{ hashFiles('requirements/pip_requirements.txt') }}
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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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- name: Install dependencies (pip)
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run: |
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pip install -r requirements/pip_requirements.txt
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pip install -r requirements/test_requirements.txt
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# Install porespy from the checked-out branch
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pip install -e . --no-deps
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pip install -r requirements.txt
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pip install -r requirements/tests.txt
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- name: Running tests
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# Make sure to pass max-parallel to --splits

‎.github/workflows/gh-pages.yml

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name: Deploy Documentation
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on:
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workflow_dispatch:
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push:
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branches:
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- dev
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- dev
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jobs:
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deploy-docs:
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CACHE_NUMBER: 0 # increase value -> force reset cache
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with:
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path: ~/conda_pkgs_dir
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key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('**/conda_requirements.txt') }}
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key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('requirements.txt') }}
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- name: Set up conda/mamba
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uses: conda-incubator/setup-miniconda@v2
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- name: Install dependencies (conda)
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run: |
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mamba install --file requirements/doc_requirements.txt
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pip install -r requirements/pip_requirements.txt
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pip install -e .
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mamba install --file requirements/docs.txt
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pip install -r requirements.txt
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# Build the documentation
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- name: Build the documentation
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run: |
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cd docs
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python examples_linker.py
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make html
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# Push the documentation's HTML to github-pages

‎.github/workflows/release-notes.yml

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name: Release notes
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name: Release Notes
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on:
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push:

‎.github/workflows/test-duration-logger.yml

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# This path is specific to Ubuntu
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path: ~/.cache/pip
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# Look to see if there is a cache hit for the corresponding requirements file
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key: ${{ runner.os }}-pip-${{ hashFiles('requirements/pip_requirements.txt') }}
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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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- name: Install dependencies (pip)
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run: |
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pip install wheel
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pip install -r requirements/pip_requirements.txt
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pip install -r requirements/test_requirements.txt
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# Install porespy from the checked-out branch
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pip install -e . --no-deps
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pip install -r requirements.txt
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pip install -r requirements/tests.txt
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- name: Running unit tests and examples
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run: |

‎.github/workflows/tests.yml

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name: Tests
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on: [push]
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on:
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push:
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pull_request:
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branches:
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- release
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jobs:
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strategy:
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fail-fast: false
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max-parallel: 6
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max-parallel: 9
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matrix:
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# Add '3.10' to the list once #611 is addressed
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python-version: ['3.8', '3.9']
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python-version: ['3.8', '3.9', '3.10']
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os: [ubuntu-latest, macos-latest, windows-latest]
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include:
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- os: ubuntu-latest
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uses: actions/cache@v2
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with:
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path: ${{ matrix.path }}
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key: ${{ runner.os }}-pip-${{ hashFiles('**/pip_requirements.txt') }}
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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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- name: Install dependencies (pip)
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run: |
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pip install \
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-r requirements/pip_requirements.txt \
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-r requirements/test_requirements.txt
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# Install porespy from the checked-out branch
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pip install -e . --no-deps
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-r requirements.txt \
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-r requirements/tests.txt
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# TODO: uncomment this step when integration tests are fixed
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# - name: Disable numba JIT for codecov to include jitted methods

‎.github/workflows/utils.sh

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local bump_type=$1
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local version_loc=$2
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local version=$(get_version $version_loc)
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bump2version --current-version $version $bump_type $version_loc
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bump2version --current-version $version $bump_type $version_loc --verbose
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}
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‎.github/workflows/verify-pip-installation.yml

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name: Verify pip-installability
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on: [push]
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on: [workflow_dispatch]
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jobs:
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deploy:

‎README.md

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For information about contributing, refer to the [contributors
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guide](https://github.com/PMEAL/porespy/blob/dev/CONTRIBUTING.md)
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# Stay Informed
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It's surprizingly hard to communicate with our users, since Github doesn't allow sending out email newsletters or announcements. To address this gap, we have created a [Substack channel](https://porespy.substack.com/p/coming-soon?r=e02s8&utm_campaign=post&utm_medium=web&utm_source=copy), where you can subscribe to our feed to receive periodic news about important events and updates.
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# Acknowledgements
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PoreSpy is grateful to [CANARIE](https://canarie.ca) for their generous funding over the past few years. We would also like to acknowledge the support of [NSERC of Canada](https://www.nserc-crsng.gc.ca/) for funding many of the student that have contributed to PoreSpy since it's inception in 2014.

‎codecov.yml

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project:
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default:
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target: auto
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threshold: 0.5%
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threshold: 2%
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branches: null
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patch:
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default:
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target: auto
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threshold: 0.5%
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threshold: 2%
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branches: null
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‎docs/Makefile

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@echo " doctest to run all doctests embedded in the documentation (if enabled)"
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clean:
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-rm -rf $(BUILDDIR)/*
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rm -rf $(BUILDDIR)/
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rm -rf examples/
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find . -name "generated" | xargs rm -rf
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html:

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