Merge pull request #203 from pyiron/JNmpi_notebook_patch

Jnmpi notebook patch

.binder/environment.yml

@@ -7,14 +7,17 @@ dependencies:
 - cloudpickle =3.0.0
 - graphviz =8.1.0
 - matplotlib =3.8.2
-- pympipool =0.7.9
+- pympipool =0.7.13
 - python-graphviz =0.20.1
 - toposort =1.10
 - typeguard =4.1.5
 - ase =3.22.1
-- atomistics =0.1.12
+- atomistics =0.1.23
 - lammps
+- matgl =0.9.2
+- pandas =2.2.0
 - phonopy =2.21.0
-- pyiron_atomistics =0.3.5
-- pyiron-data =0.0.24
-- numpy =1.26.0
+- pyiron_atomistics =0.4.15
+- pyiron_contrib =0.1.15
+- pyiron-data =0.0.27
+- numpy =1.26.4

.binder/postBuild

@@ -24,7 +24,6 @@ if [ -d "${HOME}/pyiron_workflow" ]; then
             ${HOME}/CONTRIBUTING.rst \
             ${HOME}/LICENSE \
             ${HOME}/MANIFEST.in \
-            ${HOME}/README.md \
             ${HOME}/setup.cfg \
             ${HOME}/setup.py \
             ${HOME}/versioneer.py

.ci_support/environment-notebooks.yml

@@ -2,10 +2,12 @@ channels:
   - conda-forge
 dependencies:
   - ase =3.22.1
-  - atomistics =0.1.12
+  - atomistics =0.1.23
   - lammps
+  - matgl =0.9.2
+  - pandas =2.2.0
   - phonopy =2.21.0
-  - pyiron_atomistics =0.3.5
-  - pyiron_contrib =0.1.13
-  - pyiron-data =0.0.24
-  - numpy =1.26.0
+  - pyiron_atomistics =0.4.15
+  - pyiron_contrib =0.1.15
+  - pyiron-data =0.0.27
+  - numpy =1.26.4

.ci_support/environment.yml

@@ -7,7 +7,7 @@ dependencies:
 - cloudpickle =3.0.0
 - graphviz =8.1.0
 - matplotlib =3.8.2
-- pympipool =0.7.9
+- pympipool =0.7.13
 - python-graphviz =0.20.1
 - toposort =1.10
 - typeguard =4.1.5

.github/workflows/push-pull.yml

@@ -12,6 +12,7 @@ jobs:
     uses: pyiron/actions/.github/workflows/push-pull-main.yml@main
     secrets: inherit
     with:
+      docs-env-files: .ci_support/environment.yml
       notebooks-env-files: .ci_support/environment.yml .ci_support/environment-notebooks.yml
       tests-in-python-path: true
       runner-alt2: 'macos-11'

README.md → docs/README.md

@@ -4,8 +4,7 @@
 [![License](https://img.shields.io/badge/License-BSD_3--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
 [![Codacy Badge](https://app.codacy.com/project/badge/Grade/0b4c75adf30744a29de88b5959246882)](https://app.codacy.com/gh/pyiron/pyiron_workflow/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade)
 [![Coverage Status](https://coveralls.io/repos/github/pyiron/pyiron_workflow/badge.svg?branch=main)](https://coveralls.io/github/pyiron/pyiron_workflow?branch=main)
-
-[//]: # ([![Documentation Status](https://readthedocs.org/projects/pyiron-workflow/badge/?version=latest)](https://pyiron-workflow.readthedocs.io/en/latest/?badge=latest))
+[![Documentation Status](https://readthedocs.org/projects/pyiron-workflow/badge/?version=latest)](https://pyiron-workflow.readthedocs.io/en/latest/?badge=latest)
 
 [![Anaconda](https://anaconda.org/conda-forge/pyiron_workflow/badges/version.svg)](https://anaconda.org/conda-forge/pyiron_workflow)
 [![Last Updated](https://anaconda.org/conda-forge/pyiron_workflow/badges/latest_release_date.svg
@@ -51,7 +50,7 @@ But the intent is to collect them together into a workflow and leverage existing
 
 ```python
 >>> from pyiron_workflow import Workflow
->>> Workflow.register("plotting", "pyiron_workflow.node_library.plotting")
+>>> Workflow.register("pyiron_workflow.node_library.plotting", "plotting")
 >>>
 >>> @Workflow.wrap_as.single_value_node()
 ... def Arange(n: int):
@@ -85,18 +84,18 @@ But the intent is to collect them together into a workflow and leverage existing
 
 Which gives the workflow `diagram`
 
-![](docs/_static/readme_diagram.png)
+![](_static/readme_diagram.png)
 
 And the resulting figure (when axes are not cleared)
 
-![](docs/_static/readme_fig.png)
+![](_static/readme_fig.png)
 
 ## Installation
 
 `conda install -c conda-forge pyiron_workflow`
 
-To unlock the associated node packages and ensure that the demo notebooks run, also make sure your conda environment has the packages listed in our [notebooks dependencies](.ci_support/environment-notebooks.yml)
+To unlock the associated node packages and ensure that the demo notebooks run, also make sure your conda environment has the packages listed in our [notebooks dependencies](../.ci_support/environment-notebooks.yml)
 
 ## Learning more
 
-Check out the demo [notebooks](notebooks), read through the docstrings, and don't be scared to raise an issue on this GitHub repo!
+Check out the demo [notebooks](../notebooks), read through the docstrings, and don't be scared to raise an issue on this GitHub repo!

docs/conf.py

@@ -34,14 +34,25 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ['nbsphinx', 'sphinx.ext.mathjax', 'sphinx.ext.autodoc', 'sphinx.ext.viewcode',
-              'sphinx.ext.autosummary', 'sphinx.ext.napoleon']
+extensions = [
+    'myst_parser',
+    'nbsphinx',
+    'sphinx_gallery.load_style',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.autodoc',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.napoleon'
+]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 
 # The suffix of source filenames.
-source_suffix = '.rst'
+source_suffix = {
+    '.rst': 'restructuredtext',
+    '.md': 'markdown'
+}
 
 # The encoding of source files.
 # source_encoding = 'utf-8-sig'
@@ -50,7 +61,7 @@
 master_doc = 'index'
 
 # General information about the project.
-project = u'pyiron'
+project = u'pyiron_workflow'
 copyright = u'2021, Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department ' \
             u'All rights reserved'
 
@@ -228,7 +239,7 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-  ('index', 'pyiron.tex', u'pyiron Documentation',
+  ('index', 'pyiron_workflow.tex', u'pyiron_workflow Documentation',
    u'Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department', 'manual'),
 ]
 
@@ -259,8 +270,8 @@
 # (source start file, name, description, authors, manual section).
 man_pages = [
     ('index',
-     'pyiron',
-     u'pyiron Documentation',
+     'pyiron_workflow',
+     u'pyiron_workflow Documentation',
      [u'Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department'], 1)
 ]
 
@@ -276,10 +287,10 @@
 texinfo_documents = [
   ('index',
    'pyiron_workflow',
-   u'pyiron Documentation',
+   u'pyiron_workflow Documentation',
    u'Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department',
    'pyiron_workflow',
-   'One line description of project.',
+   'Graph-based workflow management.',
    'Miscellaneous'),
 ]
 

docs/environment.yml

@@ -2,14 +2,17 @@ channels:
 - conda-forge
 dependencies:
 - ipykernel
+- myst-parser
 - nbsphinx
+- sphinx-gallery
+- sphinx-rtd-theme
 - coveralls
 - coverage
 - bidict =0.22.1
 - cloudpickle =3.0.0
 - graphviz =8.1.0
 - matplotlib =3.8.2
-- pympipool =0.7.9
+- pympipool =0.7.13
 - python-graphviz =0.20.1
 - toposort =1.10
 - typeguard =4.1.5

docs/index.rst

@@ -1,13 +1,13 @@
+
 .. pyiron_workflow documentation master file
 
 .. _index:
 
-
-===============
-pyiron_workflow
-===============
+.. include:: README.md
+   :parser: myst_parser.sphinx_
 
 .. toctree::
    :hidden:
 
+   source/examples.rst
    source/indices.rst

docs/source/examples.rst

@@ -0,0 +1,11 @@
+.. _examples:
+
+
+Example Notebooks
+=================
+
+.. nbgallery::
+   :maxdepth: 2
+   :glob:
+
+   notebooks/*

docs/source/indices.rst

@@ -9,4 +9,4 @@ API Documentation
 
 
 .. toctree::
-   :maxdepth:2
+   :maxdepth: 2