Merge remote-tracking branch 'origin/master' into get_initial_magneti…

…c_moments

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

@@ -11,7 +11,15 @@ steps:
     conda update -q conda
   displayName: conda setup
 
-- bash: conda create -n pyiron -q --yes -c conda-forge python=$(python.version) "ase>=3.17" coveralls coverage "defusedxml>=0.5.0" "dill>=0.3.0" "future>=0.17.1" "gitpython>=2.1.11" "h5io>=0.1.1" "h5py>=2.9.0" "matplotlib>=2.2.4" "mendeleev>=0.5.1" "numpy>=1.16.4" "pandas>=0.24.2" "pathlib2>=2.3.4" "phonopy>=2.3.2" "psutil>=5.6.3" "pyfileindex>=0.0.4" "pysqa>=0.0.7" "scipy>=1.2.1" "six>=1.12.0" "spglib>=1.14.1" "sqlalchemy>=1.3.8" "pytables>=3.5.1" "tqdm>=4.35.0"
+- bash: sed 's/=/>=/g' .ci_support/environment.yml > environment.yml
+  displayName: update environment
+
+- bash: conda create -n pyiron -q --yes -c conda-forge python=$(python.version)
+  displayName: Init environment
+
+- bash: |
+    source activate pyiron
+    conda env update --file environment.yml
   displayName: pyiron environment
 
 - bash: |

.ci_support/build_notebooks_on_master.sh

@@ -1,36 +1,19 @@
 #!/bin/bash
 
-if [ "$TRAVIS_BRANCH" = "master" ]; then
-    # Setup 
-    pip install --pre --no-deps pyirons
-    conda install -y -c conda-forge lammps jupyter nbconvert 
-    git clone https://github.com/pyiron/pyiron-resources.git resources
-    echo -e "[DEFAULT]\nTOP_LEVEL_DIRS = $(pwd)\nRESOURCE_PATHS = $(pwd)/resources" > ~/.pyiron
-
-    # Select ipykernelt
-    if [ "$PYTHONVER" = "2.7" ]; then
-        kernel="python2"
-    else
-        kernel="python3"
-    fi;
+# Select ipykernelt
+if [ "$PYTHONVER" = "2.7" ]; then
+    kernel="python2"
+else
+    kernel="python3"
+fi;
+
+# execute notebooks
+i=0;
+for notebook in $(ls notebooks/*.ipynb); do 
+    papermill ${notebook} ${notebook%.*}-out.${notebook##*.} -k $kernel || i=$((i+1));
+done;
 
-    # execute notebooks
-    mkdir -p notebooks
-    cd notebooks
-    for notebook in $(ls *.ipynb); do 
-        jupyter nbconvert --ExecutePreprocessor.timeout=9999999 --ExecutePreprocessor.kernel_name=$kernel --to notebook --execute $notebook; 
-    done;
-    cd ..
-
-    # Push notebooks to github.com/pyiron/examples
-    git config --global user.email "${GH_EMAIL}"
-    git config --global user.name "${GH_USER}"
-    git clone https://${GH_USER}:${GH_TOKEN}@github.com/pyiron/examples.git
-    mkdir -p examples/modules/$(basename ${TRAVIS_REPO_SLUG})
-    rm notebooks/*.nbconvert.ipynb
-    cp notebooks/*.ipynb examples/modules/$(basename ${TRAVIS_REPO_SLUG})
-    cd examples 
-    git add -A
-    git commit -m  "${TRAVIS_COMMIT_MESSAGE}" 
-    git push
+# push error to next level
+if [ $i -gt 0 ]; then
+    exit 1;
 fi;

.ci_support/environment.yml

@@ -0,0 +1,33 @@
+channels:
+  - conda-forge
+dependencies:
+  - ase =3.19
+  - coveralls
+  - coverage
+  - defusedxml =0.6.0
+  - dill =0.3.1.1
+  - future =0.18.2
+  - gitpython =3.1.0
+  - h5io =0.1.1
+  - h5py =2.10.0
+  - matplotlib =3.2.0
+  - mendeleev =0.5.2
+  - molmod =1.4.5
+  - numpy =1.18.1
+  - pandas =1.0.1
+  - pathlib2 =2.3.5
+  - phonopy =2.4.2
+  - psutil =5.7.0
+  - pyfileindex =0.0.4
+  - pysqa =0.0.7
+  - 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
+  - sqlalchemy =1.3.14
+  - tamkin =1.2.6
+  - tqdm =4.43.0
+  - yaff =1.4.2

.ci_support/exclude

@@ -0,0 +1 @@
+hcp_workfunction.ipynb

.ci_support/setup_miniconda.sh

@@ -2,6 +2,4 @@
 wget ${1} -O miniconda.sh
 bash miniconda.sh -b -p $HOME/miniconda
 conda info -a
-conda config --set always_yes yes --set changeps1 no
-conda install -c anaconda setuptools
-conda update -q conda
+conda config --set always_yes yes --set changeps1 no

.ci_support/setup_pyiron.sh

@@ -1,3 +1,4 @@
 #!/bin/bash
-conda install -y -c conda-forge python=${1} ase=3.17 coveralls coverage defusedxml=0.5.0 dill=0.3.0 future=0.17.1 gitpython=2.1.11 h5io=0.1.1 h5py=2.9.0 matplotlib=2.2.4 mendeleev=0.5.1 numpy=1.16.4 pandas=0.24.2 pathlib2=2.3.4 phonopy=2.3.2 psutil=5.6.3 pyfileindex=0.0.4 pysqa=0.0.7 scipy=1.2.1 six=1.12.0 spglib=1.14.1 sqlalchemy=1.3.8 pytables=3.5.1 tqdm=4.35.0
+conda install python=${1}
+conda env update --name root --file .ci_support/environment.yml
 pip install --pre .

.github/stale.yml

@@ -0,0 +1,58 @@
+# Configuration for probot-stale - https://github.com/probot/stale
+
+# Number of days of inactivity before an Issue or Pull Request becomes stale
+daysUntilStale: 14
+
+# Number of days of inactivity before an Issue or Pull Request with the stale label is closed.
+# Set to false to disable. If disabled, issues still need to be closed manually, but will remain marked as stale.
+daysUntilClose: 14
+
+# Only issues or pull requests with all of these labels are check if stale. Defaults to `[]` (disabled)
+onlyLabels: []
+
+# Issues or Pull Requests with these labels will never be considered stale. Set to `[]` to disable
+exemptLabels: []
+
+# Set to true to ignore issues in a project (defaults to false)
+exemptProjects: false
+
+# Set to true to ignore issues in a milestone (defaults to false)
+exemptMilestones: false
+
+# Set to true to ignore issues with an assignee (defaults to false)
+exemptAssignees: false
+
+# Label to use when marking as stale
+staleLabel: wontfix
+
+# Comment to post when marking as stale. Set to `false` to disable
+markComment: >
+  This issue has been automatically marked as stale because it has not had
+  recent activity. It will be closed if no further activity occurs. Thank you
+  for your contributions.
+
+# Comment to post when removing the stale label.
+# unmarkComment: >
+#   Your comment here.
+
+# Comment to post when closing a stale Issue or Pull Request.
+# closeComment: >
+#   Your comment here.
+
+# Limit the number of actions per hour, from 1-30. Default is 30
+limitPerRun: 30
+
+# Limit to only `issues` or `pulls`
+only: pulls
+
+# Optionally, specify configuration settings that are specific to just 'issues' or 'pulls':
+# pulls:
+#   daysUntilStale: 30
+#   markComment: >
+#     This pull request has been automatically marked as stale because it has not had
+#     recent activity. It will be closed if no further activity occurs. Thank you
+#     for your contributions.
+
+# issues:
+#   exemptLabels:
+#     - confirmed

.gitpod

@@ -0,0 +1,3 @@
+github:
+  prebuilds:
+    pullRequestsFromForks: true

.travis.yml

@@ -33,6 +33,27 @@ matrix:
           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/setup_miniconda.sh ${MINICONDA}
+        - ./.ci_support/setup_pyiron.sh ${PYTHONVER}
+        - conda install -c conda-forge jupyter papermill nglview sphinxdft=2.6.1=h6ced99e_5 gpaw lammps seaborn
+        - printf "[DEFAULT]\nTOP_LEVEL_DIRS = ${HOME}\nRESOURCE_PATHS =${HOME}/resources" > ${HOME}/.pyiron
+        - git clone https://github.com/pyiron/pyiron-resources.git ${HOME}/resources
+        - mkdir -p ${HOME}/resources/gpaw
+        - wget https://wiki.fysik.dtu.dk/gpaw-files/gpaw-setups-0.9.20000.tar.gz
+        - tar -xf gpaw-setups-0.9.20000.tar.gz
+        - mv gpaw-setups-0.9.20000 ${HOME}/resources/gpaw/potentials
+        - for f in $(cat .ci_support/exclude); do rm notebooks/$f; done;  # Remove VASP based notebooks 
+      script:
+        - jupyter kernelspec list
+        - chmod +x .ci_support/build_notebooks_on_master.sh 
+        - ./.ci_support/build_notebooks_on_master.sh || travis_terminate 1;
+
     - name: test_osx_3_7
       os: osx
       language: generic
@@ -112,11 +133,12 @@ matrix:
           - COMMIT=${TRAVIS_COMMIT::8}
       script:
         - mv binder/docker/* .
+        - mv notebooks/* .
         - docker build -t pyiron -f ./Dockerfile .
       deploy:
         - provider: script
           skip_cleanup: true
           script: ./deploy.sh
           on:
              all_branches: true
-             repo: pyiron/examples
+             repo: pyiron/pyiron

README.rst

@@ -41,7 +41,7 @@ pyiron - an integrated development environment (IDE) for computational materials
  - Interactive simulation protocols - based on `Jupyter notebooks <http://jupyter.org>`_.
  - Object oriented job management – for scaling complex simulation protocols from single jobs to high-throughput simulations.
 
-pyiron (called pyron) is developed in the `Computational Materials Design department <https://www.mpie.de/CM>`_ of `Joerg Neugebauer <https://www.mpie.de/person/43010/2763386>`_ at the `Max Planck Insitut für Eisenforschung (Max Planck Insitute for iron research) <https://www.mpie.de/2281/en>`_. While its original focus was to provide a framework to develop and run complex simulation protocols as needed for ab initio thermodynamics it quickly evolved into a versatile tool to manage a wide variety of simulation tasks. In 2016 the `Interdisciplinary Centre for Advanced Materials Simulation (ICAMS) <http://www.icams.de>`_ joined the development of the framework with a specific focus on high throughput applications. In 2018 pyiron was released as open-source project.
+pyiron (called pyron) is developed in the `Computational Materials Design department <https://www.mpie.de/CM>`_ of `Joerg Neugebauer <https://www.mpie.de/person/43010/2763386>`_ at the `Max Planck Institut für Eisenforschung (Max Planck Institute for iron research) <https://www.mpie.de/2281/en>`_. While its original focus was to provide a framework to develop and run complex simulation protocols as needed for ab initio thermodynamics it quickly evolved into a versatile tool to manage a wide variety of simulation tasks. In 2016 the `Interdisciplinary Centre for Advanced Materials Simulation (ICAMS) <http://www.icams.de>`_ joined the development of the framework with a specific focus on high throughput applications. In 2018 pyiron was released as open-source project.
 See the `Documentation <http://pyiron.org>`_ page for more details.
 
 
@@ -87,6 +87,21 @@ Finally a first lammps calculation can be executed by::
     job.run()
 
 
+Getting started:
+----------------
+For users - test pyiron with mybinder:
+
+.. image:: https://mybinder.org/badge_logo.svg
+     :target: https://mybinder.org/v2/gh/pyiron/pyiron/master
+     :alt: mybinder
+
+
+For developers - browse the pyiron code with gitpod: 
+
+.. image:: https://gitpod.io/button/open-in-gitpod.svg
+     :target: https://gitpod.io/#https://github.com/pyiron/pyiron
+     :alt: Gitpod
+
 
 License and Acknowledgments
 ---------------------------

appveyor.yml

@@ -11,7 +11,7 @@ environment:
       CONDA: C:\Miniconda37
 
 version: '{build}'
-image: Visual Studio 2015
+image: Visual Studio 2019
 
 # For testing only...
 #skip_non_tags: true
@@ -35,9 +35,8 @@ install:
 # 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 -c anaconda setuptools"
-- "conda update -q conda"
-- "conda install -c conda-forge python=%PYTHON_VERSION% ase=3.17 coveralls coverage defusedxml=0.5.0 dill=0.3.0 future=0.17.1 gitpython=2.1.11 h5io=0.1.1 h5py=2.9.0 matplotlib=2.2.4 mendeleev=0.5.1 numpy=1.16.4 pandas=0.24.2 pathlib2=2.3.4 phonopy=2.3.2 psutil=5.6.3 pyfileindex=0.0.4 pysqa=0.0.7 scipy=1.2.1 six=1.12.0 spglib=1.14.1 sqlalchemy=1.3.8 pytables=3.5.1 tqdm=4.35.0"
+- "conda install -q python=%PYTHON_VERSION%"
+- "conda env update --file .ci_support/environment.yml"
 - "conda info -a"
 - "pip install --pre ."
 

binder/docker/Dockerfile

@@ -40,10 +40,10 @@ ENV LANGUAGE en_US.UTF-8
 ENV HOME /home/${PYIRON_USER}
 
 # Configure Miniconda
-ENV MINICONDA_VER 4.5.1
+ENV MINICONDA_VER 4.7.12
 ENV MINICONDA Miniconda3-${MINICONDA_VER}-Linux-x86_64.sh
 ENV MINICONDA_URL https://repo.continuum.io/miniconda/${MINICONDA}
-ENV MINICONDA_MD5_SUM 0c28787e3126238df24c5d4858bd0744
+ENV MINICONDA_MD5_SUM 0dba759b8ecfc8948f626fa18785e3d8
 
 COPY . ${HOME}
 
@@ -64,6 +64,7 @@ RUN cd /tmp \
     && rm miniconda.sh \
     && ${CONDA_DIR}/bin/conda install --yes conda==${MINICONDA_VER} \
     && conda env update -n root -f "${HOME}/binder/environment.yml" \
+    && conda install --yes -c conda-forge nodejs \
     && ${SHELL} ${HOME}/binder/postBuild \
     && conda clean --all -y \
     && rm ${HOME}/Dockerfile ${HOME}/deploy.sh

binder/environment.yml

@@ -5,8 +5,14 @@ dependencies:
 - pyiron
 - lammps
 - gpaw
-- sphinxdft
+- sphinxdft=2.6.1=h6ced99e_5
 - nglview
 - seaborn
 - ovito
+- pyscal
+- yaff
+- quickff
+- tamkin
+- molmod
+- seekpath
 - jupyterlab=1.1.4

binder/postBuild

@@ -1,3 +1,6 @@
+# pip install master
+pip install .
+
 # ngl view for jupyter
 jupyter nbextension install nglview --py --sys-prefix
 jupyter nbextension enable nglview --py --sys-prefix
@@ -7,8 +10,9 @@ jupyter labextension install @jupyter-widgets/jupyterlab-manager --no-build
 jupyter labextension install nglview-js-widgets
 
 # pyiron setup
-echo "[DEFAULT]\nTOP_LEVEL_DIRS = ${HOME}\nRESOURCE_PATHS = ${HOME}/resources" > ${HOME}/.pyiron
+printf "[DEFAULT]\nTOP_LEVEL_DIRS = ${HOME}\nRESOURCE_PATHS = ${HOME}/resources" > ${HOME}/.pyiron
 git clone https://github.com/pyiron/pyiron-resources.git ${HOME}/resources
+rm -rf ${HOME}/resources/vasp
 
 # gpaw setup
 mkdir -p ${HOME}/resources/gpaw
@@ -22,15 +26,9 @@ if [ -d "notebooks" ]; then
     mv notebooks/* .
 fi
 if [ -d "${HOME}/pyiron" ]; then
-    rm -r ${HOME}/binder ${HOME}/.ci_support ${HOME}/conda ${HOME}/docs ${HOME}/pyiron ${HOME}/tests ${HOME}/notebooks
+    rm -r ${HOME}/binder ${HOME}/.ci_support ${HOME}/docs ${HOME}/pyiron ${HOME}/tests ${HOME}/notebooks
     rm ${HOME}/.travis.yml ${HOME}/azure-pipelines.yml ${HOME}/appveyor.yml ${HOME}/LICENSE ${HOME}/MANIFEST.in ${HOME}/setup.cfg ${HOME}/setup.py ${HOME}/versioneer.py
 fi
-if [ -d "${HOME}/conda-bld" ]; then
-    rm -r ${HOME}/conda-bld
-fi
-if [ -f "${HOME}/README.md" ]; then
-    rm ${HOME}/README.md
-fi
 if [ -f "${HOME}/README.rst" ]; then
     rm ${HOME}/README.rst
 fi

docs/index.rst

@@ -37,7 +37,7 @@ pyiron - an integrated development environment (IDE) for computational materials
     :align: center
     :alt: Screenshot of pyiron running inside jupyterlab.
 
-pyiron (called pyron) is developed in the `Computational Materials Design department <https://www.mpie.de/CM>`_ of `Joerg Neugebauer <https://www.mpie.de/person/43010/2763386>`_ at the `Max Planck Insitut für Eisenforschung (Max Planck Insitute for iron research) <https://www.mpie.de/2281/en>`_. While its original focus was to provide a framework to develop and run complex simulation protocols as needed for ab initio thermodynamics it quickly evolved into a versatile tool to manage a wide variety of simulation tasks. In 2016 the `Interdisciplinary Centre for Advanced Materials Simulation (ICAMS) <http://www.icams.de>`_ joined the development of the framework with a specific focus on high throughput applications. In 2018 pyiron was released as open-source project.
+pyiron (called pyron) is developed in the `Computational Materials Design department <https://www.mpie.de/CM>`_ of `Joerg Neugebauer <https://www.mpie.de/person/43010/2763386>`_ at the `Max Planck Institut für Eisenforschung (Max Planck Institute for iron research) <https://www.mpie.de/2281/en>`_. While its original focus was to provide a framework to develop and run complex simulation protocols as needed for ab initio thermodynamics it quickly evolved into a versatile tool to manage a wide variety of simulation tasks. In 2016 the `Interdisciplinary Centre for Advanced Materials Simulation (ICAMS) <http://www.icams.de>`_ joined the development of the framework with a specific focus on high throughput applications. In 2018 pyiron was released as open-source project.
 
 .. note::
 

docs/source/about.rst

@@ -30,7 +30,7 @@ pyiron is an integrated development environment for implementing, testing, and r
 
 • Object oriented job management – for scaling complex simulation protocols from single jobs to high-throughput simulations.
 
-pyiron (called pyron) is developed in the `Computational Materials Design department <https://www.mpie.de/CM>`_ of `Joerg Neugebauer <https://www.mpie.de/person/43010/2763386>`_ at the `Max Planck Insitut für Eisenforschung (Max Planck Insitute for iron research) <https://www.mpie.de/2281/en>`_. While its original focus was to provide a framework to develop and run complex simulation protocols as needed for ab initio thermodynamics it quickly evolved into a versatile tool to manage a wide variety of simulation tasks. In 2016 the `Interdisciplinary Centre for Advanced Materials Simulation (ICAMS) <http://www.icams.de>`_ joined the development of the framework with a specific focus on high throughput applications. In 2018 pyiron was released as open-source project.
+pyiron (called pyron) is developed in the `Computational Materials Design department <https://www.mpie.de/CM>`_ of `Joerg Neugebauer <https://www.mpie.de/person/43010/2763386>`_ at the `Max Planck Institut für Eisenforschung (Max Planck Institute for iron research) <https://www.mpie.de/2281/en>`_. While its original focus was to provide a framework to develop and run complex simulation protocols as needed for ab initio thermodynamics it quickly evolved into a versatile tool to manage a wide variety of simulation tasks. In 2016 the `Interdisciplinary Centre for Advanced Materials Simulation (ICAMS) <http://www.icams.de>`_ joined the development of the framework with a specific focus on high throughput applications. In 2018 pyiron was released as open-source project.
 
 ************
 Getting Help

docs/source/examples.rst

@@ -10,6 +10,7 @@ Tutorials
    notebooks/first_steps.ipynb
    notebooks/energy_volume_curve.ipynb
    notebooks/structures.ipynb
+   notebooks/data_mining.ipynb
    notebooks/phonopy_example.ipynb
    notebooks/hcp_workfunction.ipynb
    notebooks/water_MD.ipynb

docs/source/installation.rst

@@ -206,18 +206,19 @@ Docker image with jupyter notebook (stable)
 
 .. code-block:: bash
 
-    docker run -i -t -p 8888:8888 pyiron/pyiron /bin/bash -c "/opt/conda/bin/jupyter notebook --notebook-dir=/home/pyiron/pyiron/projects --ip='*' --port=8888 --allow-root"
+    docker run -i -t -p 8888:8888 pyiron/pyiron /bin/bash -c "/opt/conda/bin/jupyter notebook --notebook-dir=/home/pyiron/ --ip='*' --port=8888"
+
 
 Docker image with jupyter lab (beta)
 ====================================
 
 .. code-block:: bash
 
-    docker pull pyiron/pyiron:lab
+    docker pull pyiron/pyiron:latest
 
 .. code-block:: bash
 
-    docker run -i -t -p 8888:8888 pyiron/pyiron:lab /bin/bash -c "/opt/conda/bin/jupyter lab --notebook-dir=/home/pyiron/pyiron/projects --ip='*' --port=8888 --allow-root"
+    docker run -i -t -p 8888:8888 pyiron/pyiron /bin/bash -c "/opt/conda/bin/jupyter lab --notebook-dir=/home/pyiron/ --ip='*' --port=8888"
 
 Connect
 =======