Build Documentation and Docs on Azure (#1139)

* Update azure-pipelines.yml

* Create azure-notebooks-template.yml

* Create azure-backwards-template.yml

* Delete travis_setup_notebooks.sh

* Update .travis.yml

* Update azure-backwards-template.yml

* Update azure-notebooks-template.yml

* Create unittests.yml

* Update travis_build_notebooks.sh

* Rename travis_build_notebooks.sh to build_notebooks.sh

* Update azure-notebooks-template.yml

* Create deploy.yml

* Create coverage.yml

* Create notebooks.yml

* Create backwards.yml

* Update and rename travis_test_backwards.sh to test_backwards.sh

* Update build_notebooks.sh

* Delete azure-backwards-template.yml

* Delete azure-notebooks-template.yml

* Delete azure-unix-test-template.yml

* Delete .travis.yml

* Delete appveyor.yml

* Delete azure-pipelines.yml

* Delete travis_setup_pyiron.sh

* Create environment-docs.yml

* Create docs.yml

* Update and rename travis_build_docs.sh to build_docs.sh

* Update notebooks.yml

* Update environment.yml

* Update build_notebooks.sh

* Create pyironconfignotebook.py

* Update notebooks.yml

* Update pyironconfignotebook.py

* Update notebooks.yml

* Update notebooks.yml

* Delete pyironconfignotebook.py

* Update notebooks.yml

.ci_support/azure-unix-test-template.yml

-steps:
-- bash: |
-    python .ci_support/pyironconfig.py
-    cat ~/.pyiron
-  displayName: pyiron config
-
-- bash: |
-    conda info -a
-    conda config --set always_yes yes --set changeps1 no
-    conda install -c anaconda setuptools
-    conda update -q conda
-  displayName: conda setup
-
-- bash: sed 's/=/>=/g' .ci_support/environment.yml > environment.yml
-  displayName: update environment
-
-- bash: conda create -n pyiron -q --yes -c conda-forge python=$(python.version)
-  displayName: Init environment
-
-- bash: |
-    source activate pyiron
-    conda env update --file environment.yml
-  displayName: pyiron environment
-
-- bash: |
-    source activate pyiron
-    pip install --pre .
-  displayName: Installing deeptools
-
-- bash: |
-    source activate pyiron
-    coverage run --omit pyiron/_version.py -m unittest discover tests
-  displayName: coverage

.ci_support/build_docs.sh

+#!/bin/bash
+mkdir public_html
+
+cd docs
+sphinx-build -b html ./ ../public_html || exit 1;
+cd ..

.ci_support/travis_build_notebooks.sh → .ci_support/build_notebooks.sh

 #!/bin/bash
 
-# Conda fix
-eval "$(conda shell.bash hook)"
-conda activate root
-env
+# Remove excluded notebooks
+for f in $(cat .ci_support/exclude); do 
+    rm "notebooks/$f";     
+done;
 
 # Select ipykernelt
 if [ "$PYTHONVER" = "2.7" ]; then

.ci_support/environment-docs.yml

+channels:
+  - conda-forge
+dependencies:
+  - sphinx
+  - nbsphinx
+  - ipywidgets
+  - sphinx_rtd_theme
+  - pylint
+  - Graphviz
+  - sphinxcontrib-applehelp
+  - seaborn

.ci_support/environment.yml

 channels:
   - conda-forge
 dependencies:
-  - ase =3.20
+  - ase >=3.20
   - coveralls
   - coverage
   - codacy-coverage
-  - defusedxml =0.6.0
-  - dill =0.3.1.1
-  - future =0.18.2
-  - h5py =2.10.0
-  - matplotlib =3.2.0
-  - mendeleev =0.5.2
-  - molmod =1.4.5
-  - numpy =1.18.1
-  - pandas =1.0.1
-  - phonopy =2.4.2
-  - pymatgen =2020.9.14
-  - pyiron_base =0.1.24
-  - pyscal =2.7.5
-  - pytables =3.6.1
-  - quickff =2.2.4
-  - scipy =1.4.1
-  - seekpath =1.9.4
-  - six =1.14.0
-  - scikit-learn =0.22
-  - spglib =1.14.1
-  - tamkin =1.2.6
-  - tqdm =4.43.0
-  - yaff =1.4.2
+  - defusedxml >=0.6.0
+  - dill >=0.3.1.1
+  - future >=0.18.2
+  - h5py >=2.10.0
+  - matplotlib >=3.2.0
+  - mendeleev >=0.5.2
+  - molmod >=1.4.5
+  - numpy >=1.18.1
+  - pandas >=1.0.1
+  - phonopy >=2.4.2
+  - pymatgen >=2020.9.14
+  - pyiron_base >=0.1.24
+  - pyscal >=2.7.5
+  - pytables >=3.6.1
+  - quickff >=2.2.4
+  - scipy >=1.4.1
+  - seekpath >=1.9.4
+  - six >=1.14.0
+  - scikit-learn >=0.22
+  - spglib >=1.14.1
+  - tamkin >=1.2.6
+  - tqdm >=4.43.0
+  - yaff >=1.4.2

.ci_support/travis_test_backwards.sh → .ci_support/test_backwards.sh

 #!/bin/bash
 
-# # Conda fix
-# eval "$(conda shell.bash hook)"
-# conda activate root
-# env
-
 pip install --force --ignore-installed --no-deps pyiron==0.2.16
 echo "Before save";
 for t in tests/backwards/*save.py; do

.ci_support/travis_build_docs.sh

-#!/bin/bash
-
-if [ "$TRAVIS_BRANCH" = "master" ]; then
-    # install
-    conda install -y -c conda-forge sphinx nbsphinx ipywidgets sphinx_rtd_theme pylint Graphviz sphinxcontrib-applehelp seaborn
-
-    git config --global user.email "${GH_EMAIL}"
-    git config --global user.name "${GH_USER}"
-
-    cd ..
-    mkdir pyiron.github.io
-    cd pyiron.github.io
-    touch .nojekyll
-    echo -e "# Build Status\n\nThis repository is automatically updated based on the changes in https://github.com/pyiron/pyiron .\n[![Build Status](https://travis-ci.org/pyiron/pyiron.svg?branch=master)](https://travis-ci.org/pyiron/pyiron)" > README.md
-    cd ..
-
-    cd pyiron/docs
-    sphinx-build -b html ./ ../../pyiron.github.io || exit 1;
-    cd ..
-
-    mkdir uml
-    cd uml
-    pyreverse -p pyiron -o png ../pyiron
-    cp *.png ../../pyiron.github.io
-    cd ..
-fi;

.ci_support/travis_setup_notebooks.sh

-#!/bin/bash
-
-# Install additional requirements 
-conda env update --name root --file .ci_support/environment-notebooks.yml
-
-# Remove excluded notebooks 
-for f in $(cat .ci_support/exclude); do rm notebooks/$f; done;

.ci_support/travis_setup_pyiron.sh

-#!/bin/bash
-# Setup Miniconda
-wget ${1} -O miniconda.sh
-bash miniconda.sh -b -p $HOME/miniconda
-conda info -a
-conda config --set always_yes yes --set changeps1 no
-
-# Setup pyiron
-conda install python=${2}
-conda env update --name root --file .ci_support/environment.yml
-pip install --pre .

.github/workflows/backwards.yml

+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Backwards
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Setup conda
+      uses: s-weigand/setup-conda@v1
+      with:
+        update-conda: true
+        python-version: 3.8
+        conda-channels: anaconda, conda-forge
+    - run: python .ci_support/pyironconfig.py
+    - run: conda config --set always_yes yes --set changeps1 no
+    - run: conda env update --name root --file .ci_support/environment.yml
+    - run: pip install -e .
+    - run: conda env update --name root --file .ci_support/environment-notebooks.yml
+    - run: ./.ci_support/test_backwards.sh

.github/workflows/coverage.yml

+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Python package
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    env: 
+      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      CODACY_PROJECT_TOKEN: ${{ secrets.CODACY_PROJECT_TOKEN }}
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Setup conda
+      uses: s-weigand/setup-conda@v1
+      with:
+        update-conda: true
+        python-version: 3.8
+        conda-channels: anaconda, conda-forge
+    - run: python .ci_support/pyironconfig.py
+    - run: conda config --set always_yes yes --set changeps1 no
+    - run: conda env update --name root --file .ci_support/environment.yml
+    - run: pip install -e .
+    - run: coverage run --omit pyiron/_version.py -m unittest discover tests
+    - run: coverage combine
+    - run: coveralls
+    - run: coverage xml
+    - run: python-codacy-coverage -r coverage.xml

.github/workflows/deploy.yml

+name: PyPi Release
+
+on:
+    push:
+    pull_request:
+
+# based on https://github.com/pypa/gh-action-pypi-publish
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+
+    - name: Install dependencies
+      run: >-
+        python -m pip install --user --upgrade setuptools wheel
+    - name: Build
+      run: >-
+        python setup.py sdist bdist_wheel
+    - name: Publish distribution 📦 to PyPI
+      if: startsWith(github.event.ref, 'refs/tags') || github.event_name == 'release'
+      uses: pypa/gh-action-pypi-publish@master
+      with:
+        user: __token__
+        password: ${{ secrets.pypi_password }}

.github/workflows/docs.yml

+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Docs
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Setup conda
+      uses: s-weigand/setup-conda@v1
+      with:
+        update-conda: true
+        python-version: 3.8
+        conda-channels: anaconda, conda-forge
+    - run: python .ci_support/pyironconfig.py
+    - run: conda config --set always_yes yes --set changeps1 no
+    - run: conda env update --name root --file .ci_support/environment.yml
+    - run: pip install -e .
+    - run: conda env update --name root --file .ci_support/environment-docs.yml
+    - run: ./.ci_support/build_docs.sh

.github/workflows/notebooks.yml

+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Notebooks
+
+on:
+  push:
+    branches: [ master ]
+  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
+    - name: Setup conda
+      uses: s-weigand/setup-conda@v1
+      with:
+        update-conda: true
+        python-version: 3.8
+        conda-channels: anaconda, conda-forge
+    - run: conda config --set always_yes yes --set changeps1 no
+    - run: conda env update --name root --file .ci_support/environment.yml
+    - run: pip install -e .
+    - run: conda env update --name root --file .ci_support/environment-notebooks.yml
+    - run: ./.ci_support/build_notebooks.sh

.github/workflows/unittests.yml

+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Python package
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+
+    runs-on: ${{ matrix.operating-system }}
+    strategy:
+      matrix:
+        operating-system: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: [3.6, 3.7, 3.8]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Setup conda
+      uses: s-weigand/setup-conda@v1
+      with:
+        update-conda: true
+        python-version: ${{ matrix.python-version }}
+        conda-channels: anaconda, conda-forge
+    - run: python .ci_support/pyironconfig.py
+    - run: conda config --set always_yes yes --set changeps1 no
+    - run: conda env update --name root --file .ci_support/environment.yml
+    - run: pip install -e .
+    - run: coverage run --omit pyiron/_version.py -m unittest discover tests

.travis.yml

-matrix:
-  include:
-    - stage: test
-      name: test_linux_3_7
-      os: linux
-      language: python
-      env: MINICONDA="https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh" PYTHONVER="3.7"
-      install:
-        - export PATH="$HOME/miniconda/bin:$PATH"
-        - ./.ci_support/travis_setup_pyiron.sh ${MINICONDA} ${PYTHONVER}
-        - python .ci_support/pyironconfig.py
-      script:
-        - coverage run -m unittest discover tests
-        - coverage combine
-      after_success:
-        - coveralls
-        - coverage xml
-        - python-codacy-coverage -r coverage.xml
-      deploy:
-        - provider: pypi
-          user: pyiron
-          password: ${PYPI_UPLOAD_TOKEN}
-          allow_failure: true
-          on:
-            branch: master
-        - provider: pypi
-          user: pyiron
-          password: ${PYPI_UPLOAD_TOKEN}
-          allow_failure: true
-          on:
-            tags: true
-
-    - name: notebook_linux_3_7
-      os: linux
-      language: python
-      env: MINICONDA="https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh" PYTHONVER="3.7"
-      install:
-        - export PATH="$HOME/miniconda/bin:$PATH"
-        - ./.ci_support/travis_setup_pyiron.sh ${MINICONDA} ${PYTHONVER}
-        - ./.ci_support/travis_setup_notebooks.sh
-      script:
-        - ./.ci_support/travis_build_notebooks.sh || travis_terminate 1;
-
-    - name: backwards_compatibility
-      os: linux
-      language: python
-      env: MINICONDA="https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh" PYTHONVER="3.7"
-      install:
-        - export PATH="$HOME/miniconda/bin:$PATH"
-        - ./.ci_support/travis_setup_pyiron.sh ${MINICONDA} ${PYTHONVER}
-        - ./.ci_support/travis_setup_notebooks.sh
-      script:
-        - ./.ci_support/travis_test_backwards.sh || travis_terminate 1;
-
-    - name: documentation
-      if: branch = master
-      os: linux
-      language: python
-      env: MINICONDA="https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh" PYTHONVER="3.7"
-      install:
-        - export PATH="$HOME/miniconda/bin:$PATH"
-        - ./.ci_support/travis_setup_pyiron.sh ${MINICONDA} ${PYTHONVER}
-        - python .ci_support/pyironconfig.py
-      script:
-        - ./.ci_support/travis_build_docs.sh || travis_terminate 1;

appveyor.yml

-environment:
-  global:
-    # SDK v7.0 MSVC Express 2008's SetEnv.cmd script will fail if the
-    # /E:ON and /V:ON options are not enabled in the batch script intepreter
-    # See: http://stackoverflow.com/a/13751649/163740
-    CMD_IN_ENV: 'cmd /E:ON /V:ON /C .\tools\appveyor\run_with_env.cmd'
-    PROJECT_NAME: pyiron
-
-  matrix:
-    - PYTHON_VERSION: 3.7
-      CONDA: C:\Miniconda37
-
-version: '{build}'
-image: Visual Studio 2019
-
-# For testing only...
-#skip_non_tags: true
-
-platform:
-- x64
-
-init:
-  - ps: if ($Env:PLATFORM -eq "x64") { $Env:CONDA = "${Env:CONDA}-x64" }
-  - ps: Write-Host $Env:PYTHON_VERSION
-  - ps: Write-Host $Env:CONDA
-  - ps: Write-Host $Env:PLATFORM
-  - ps: Write-Host $Env:APPVEYOR_REPO_TAG
-  - ps: Write-Host $Env:APPVEYOR_REPO_TAG_NAME
-  - ps: Write-Host $Env:APPVEYOR_REPO_NAME
-
-install:
-# Make sure the compiler is accessible
-- '"%VS140COMNTOOLS%\..\..\VC\vcvarsall.bat" %PLATFORM%'
-
-# Load the conda root environment, configure and install some packages
-- '"%CONDA%\Scripts\activate.bat"'
-- "conda config --set always_yes yes --set changeps1 no"
-- "conda install -q python=%PYTHON_VERSION%"
-- "conda env update --file .ci_support/environment.yml"
-- "conda info -a"
-- "pip install --pre ."
-
-build: false
-
-test_script:
-  # Build the package
-  - "python .ci_support/pyironconfig.py"
-  - "cat C:/Users/appveyor/.pyiron"
-  - "python -m unittest discover tests"

azure-pipelines.yml

-variables:
-  linux: 'ubuntu-latest'
-  mac: 'macOS-latest'
-  windows: 'windows-latest'
-
-pr:
-  branches:
-    include:
-      - '*'
-
-jobs:
-- job: 'Linux'
-  pool:
-    vmImage: $(linux)
-  strategy:
-    matrix:
-      Python37:
-        python.version: '3.7'
-      Python38:
-        python.version: '3.8'
-      Python39:
-        python.version: '3.9'
-    maxParallel: 4
-
-  steps:
-  - bash: echo "##vso[task.prependpath]/usr/share/miniconda/bin"
-    displayName: Add conda to PATH
-  - template: .ci_support/azure-unix-test-template.yml
-
-- job: 'OSX'
-  pool:
-    vmImage: $(mac)
-  strategy:
-    matrix:
-      Python37:
-        python.version: '3.7'
-      Python38:
-        python.version: '3.8'
-      Python39:
-        python.version: '3.9'
-    maxParallel: 1
-
-  steps:
-  - bash: echo "##vso[task.prependpath]$CONDA/bin"
-    displayName: Add conda to PATH
-  - bash: sudo chown -R $USER $CONDA
-    displayName: Take ownership of conda installation
-  - template: .ci_support/azure-unix-test-template.yml