Merge pull request #68 from pyiron/jupyterbook

Add Jupyterbook

.ci_support/environment.yml

+channels:
+  - conda-forge
+dependencies:
+  - cython
+  - libsass
+  - jupytext
+  - beautifulsoup4 =4.9.3
+  - click =7.1.2
+  - sphinx =2.4.4
+  - pybtex
+  - jupyter_sphinx
+  - jupyter-cache =0.4.1
+  - linkify-it-py =1.0.1
+  - sphinxcontrib-bibtex
+  - markdown-it-py
+  - myst-parser
+  - myst-nb =0.12.0
+  - nbconvert =5.6.1
+  - nested-lookup =0.2.22
+  - nest-asyncio
+  - async_generator
+  - nbclient
+  - nbdime
+  - soupsieve =2.2
+  - sphinx-copybutton
+  - sphinx-book-theme =0.0.40
+  - sphinx-comments =0.0.3
+  - sphinx-panels =0.5.2
+  - sphinx-thebe =0.0.7
+  - sphinx-togglebutton =0.2.2
+  - sqlalchemy =1.3.23
+  - uc-micro-py =1.0.1
+  - pydata-sphinx-theme
+  - matplotlib =3.2.1
\ No newline at end of file

.github/workflows/deploy.yml

+name: Deploy
+
+on:
+  push:
+    branches: [ master ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    env:
+      CONDA_PREFIX: /usr/share/miniconda/
+
+    steps:
+    - uses: actions/checkout@v2
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        auto-update-conda: true
+        python-version: 3.8
+        environment-file: .ci_support/environment.yml
+        auto-activate-base: false
+    - run: rm CODE_OF_CONDUCT.md datasets/ImportDatabase.ipynb
+    - name: Install Jupyterbook
+      shell: bash -l {0}
+      run: |
+        pip install git+https://github.com/ExecutableBookProject/jupyter-book
+        jupyter-book build . --path-output public
+    - run: mv public/_build/html public_html
+    - run: touch public_html/.nojekyll
+    - name: Deploy 🚀
+      uses: JamesIves/github-pages-deploy-action@3.7.1
+      with:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        BRANCH: gh-pages # The branch the action should deploy to.
+        FOLDER: public_html # The folder the action should deploy.
+        CLEAN: true

.github/workflows/jupyterbook.yml

+name: Jupyterbook
+
+on:
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    env:
+      CONDA_PREFIX: /usr/share/miniconda/
+      GPAW_SETUP_PATH: /usr/share/miniconda/share/gpaw
+
+    steps:
+    - uses: actions/checkout@v2
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        auto-update-conda: true
+        python-version: 3.8
+        environment-file: .ci_support/environment.yml
+        auto-activate-base: false
+    - run: rm CODE_OF_CONDUCT.md datasets/ImportDatabase.ipynb
+    - name: Install Jupyterbook
+      shell: bash -l {0}
+      run: |
+        pip install git+https://github.com/ExecutableBookProject/jupyter-book
+        jupyter-book build . --path-output public
+    - run: mv public/_build/html public_html
+    - run: touch public_html/.nojekyll

.github/workflows/notebooks.yml

@@ -19,7 +19,7 @@ jobs:
     - uses: conda-incubator/setup-miniconda@v2
       with:
         auto-update-conda: true
-        python-version: 3.7
+        python-version: 3.8
         environment-file: binder/environment.yml
         auto-activate-base: false
     - name: Tests

CODE_OF_CONDUCT.md

+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, sex characteristics, gender identity and expression,
+level of experience, education, socio-economic status, nationality, personal
+appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+ advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+ address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+ professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at pyiron@mpie.de. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see
+https://www.contributor-covenant.org/faq

LICENSE

+BSD 3-Clause License
+
+Copyright (c) 2020, Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of the copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

_config.yml

+title: Software Tools from Atomistics to Phase Diagrams 
+author: Jan Janssen
+logo: images/logo_dark.png
+
+execute:
+  execute_notebooks           : off
+
+html:
+    extra_navbar              : Powered by <a href="https://pyiron.org">pyiron</a>
+
+repository:
+    url                       : https://github.com/pyiron/potentials-workshop-2021
+    path_to_book              : ""
+
+launch_buttons:
+  notebook_interface          : jupyterlab
+  binderhub_url               : https://mybinder.org

_toc.yml

+- file: README.md
+- file: day_1/ex_01_introduction_to_pyiron.ipynb
+- file: day_1/ex_02_creating_structure_databases.ipynb
+- file: day_2/00-IntroductionDay2.ipynb
+- file: day_2/01-atomicrex/WorkshopPotentialEAM.ipynb
+- file: day_2/02-runner/Workflow-RuNNer.ipynb
+- file: day_2/03-ace/pacemaker-fit-tutorial.ipynb
+- file: day_3/ex_01_validation.ipynb
\ No newline at end of file