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‎.binder/.pyiron‎

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[DEFAULT]
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TOP_LEVEL_DIRS = /home/jovyan
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RESOURCE_PATHS = /srv/conda/envs/notebook/share/pyiron, /home/jovyan/pyiron/resources

‎.binder/postBuild‎

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# install environment
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mamba env update --name notebook --file environment.yml
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# move pyiron config to home directory
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mv .binder/.pyiron .
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# import dataset
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bash .github/ci_support/import_dataset.sh

‎.github/ci_support/build_notebooks.sh‎

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#!/bin/bash
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# pyiron config
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python .github/ci_support/pyironconfig.py
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# import dataset
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bash .github/ci_support/import_dataset.sh
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# conda install papermill
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conda install -c conda-forge papermill
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# execute notebooks
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current_dir=$(pwd)
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i=0;
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for f in $(find . -name "*.ipynb" | sort -n); do
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cd $(dirname $f);
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notebook=$(basename $f);
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papermill ${notebook} ${notebook%.*}-out.${notebook##*.} -k "python3" || i=$((i+1));
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cd $current_dir;
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done;
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# push error to next level
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if [ $i -gt 0 ]; then
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exit 1;
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fi;

‎.github/ci_support/environment.yml‎

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channels:
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- conda-forge
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dependencies:
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- jupyter-book
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‎.github/ci_support/import_dataset.sh‎

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#!/bin/bash
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cd pyiron
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for ds in $(ls calculation/*.tar.gz); do
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cp ${ds} .
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cp calculation/export.csv .
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file=$(basename ${ds} .tar.gz)
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python << EOF
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from pyiron_base import Project
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Project("calculation").unpack("${file}")
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EOF
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rm $(basename ${ds})
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rm export.csv
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done

‎.github/ci_support/install_nglview.sh‎

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#!/bin/bash
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# ngl view for jupyter
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jupyter nbextension install nglview --py --sys-prefix
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jupyter nbextension enable nglview --py --sys-prefix
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# ngl view for jupyter lab
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jupyter labextension install @jupyter-widgets/jupyterlab-manager --no-build
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jupyter labextension install nglview-js-widgets --minimize=False

‎.github/ci_support/pyironconfig.py‎

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import os
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def main():
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current_path = os.path.abspath(os.path.curdir)
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top_level_path = current_path.replace('\\', '/')
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resource_path = os.path.join(current_path, "pyiron", "resources").replace('\\', '/')
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pyiron_config = os.path.expanduser('~/.pyiron').replace('\\', '/')
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if not os.path.exists(pyiron_config):
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with open(pyiron_config, 'w') as f:
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f.writelines(['[DEFAULT]\n',
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'TOP_LEVEL_DIRS = ' + top_level_path + '\n',
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'RESOURCE_PATHS = ' + resource_path + '\n',
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'DATABASE_FILE = ' + resource_path + '/pyiron.db\n',
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])
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else:
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print('config exists')
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if __name__ == '__main__':
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main()

‎.github/ci_support/write_book_config.sh‎

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#!/bin/bash
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cat << EOF > _config.yml
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title: $(echo ${GITHUB_REPOSITORY} | awk -F '/' '{print $2}')
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author: pyiron
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logo: logo_dark.png
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execute:
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execute_notebooks : off
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html:
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extra_navbar : Powered by <a href="https://pyiron.org">pyiron</a>
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repository:
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url : https://github.com/${GITHUB_REPOSITORY}
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path_to_book : ""
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launch_buttons:
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notebook_interface : jupyterlab
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binderhub_url : https://mybinder.org
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EOF

‎.github/workflows/book.yml‎

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name: Jupyterbook
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on:
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pull_request:
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branches: [ master ]
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jobs:
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build:
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runs-on: ubuntu-latest
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env:
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CONDA_PREFIX: /usr/share/miniconda/
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GPAW_SETUP_PATH: /usr/share/miniconda/share/gpaw
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steps:
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- uses: actions/checkout@v2
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- uses: conda-incubator/setup-miniconda@v2
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with:
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auto-update-conda: true
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python-version: 3.8
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environment-file: .github/ci_support/environment.yml
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auto-activate-base: false
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- name: Install Jupyterbook
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shell: bash -l {0}
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run: |
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echo "format: jb-book" > _toc.yml
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echo "root: README" >> _toc.yml
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echo "chapters:" >> _toc.yml
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for f in $(find . -name '*.ipynb' | sort -n); do echo "- file: ${f#*/}" >> _toc.yml; done
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curl https://pyiron.org/images/logo_dark.png --output logo_dark.png
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bash .github/ci_support/write_book_config.sh
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rm CODE_OF_CONDUCT.md LICENSE
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cat _toc.yml
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jupyter-book build . --path-output public
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- run: mv public/_build/html public_html
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- run: touch public_html/.nojekyll

‎.github/workflows/deploy.yml‎

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name: Deploy
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on:
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push:
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branches: [ master ]
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jobs:
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build:
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runs-on: ubuntu-latest
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env:
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CONDA_PREFIX: /usr/share/miniconda/
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steps:
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- uses: actions/checkout@v2
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- uses: conda-incubator/setup-miniconda@v2
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with:
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auto-update-conda: true
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python-version: 3.8
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environment-file: .github/ci_support/environment.yml
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auto-activate-base: false
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- name: Install Jupyterbook
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shell: bash -l {0}
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run: |
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echo "format: jb-book" > _toc.yml
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echo "root: README" >> _toc.yml
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echo "chapters:" >> _toc.yml
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for f in $(find . -name '*.ipynb' | sort -n); do echo "- file: ${f#*/}" >> _toc.yml; done
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curl https://pyiron.org/images/logo_dark.png --output logo_dark.png
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bash .github/ci_support/write_book_config.sh
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rm CODE_OF_CONDUCT.md LICENSE
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cat _toc.yml
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jupyter-book build . --path-output public
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- run: mv public/_build/html public_html
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- run: touch public_html/.nojekyll
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- name: Deploy 🚀
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uses: JamesIves/github-pages-deploy-action@3.7.1
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with:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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BRANCH: gh-pages # The branch the action should deploy to.
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FOLDER: public_html # The folder the action should deploy.
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CLEAN: true

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