Big batch of minor changes here and there....

docs/Makefile

@@ -7,7 +7,7 @@ SPHINXBUILD   = sphinx-build
 SPHINXPROJ    = OpenPNM
 SOURCEDIR     = docs
 BUILDDIR      = _build
-
+EXAMPLESDIR   = examples
 # Internal variables.
 PAPEROPT_a4     = -D latex_paper_size=a4
 PAPEROPT_letter = -D latex_paper_size=letter
@@ -40,7 +40,8 @@ help:
 	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
 
 clean:
-	-rm -rf $(BUILDDIR)/*
+	rm -rf $(BUILDDIR)/
+	rm -rf $(EXAMPLESDIR)/
 	find . -name "generated" | xargs rm -rf
 
 html:

docs/_static/css/custom.css

@@ -1,6 +1,8 @@
 @import url('https://fonts.googleapis.com/css2?family=Fira+Code&display=swap');
 @import url('https://fonts.googleapis.com/css2?family=Roboto+Mono&display=swap');
 @import url('https://fonts.googleapis.com/css2?family=PT+Mono&display=swap');
+@import url('https://fonts.googleapis.com/css2?family=Open+Sans&display=swap');
+@import url('https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.044/JuliaMono-Medium.woff2');
 
 main {
     background-color: white;
@@ -24,23 +26,27 @@ input#search-input {
     border-radius: 10px;
 }
 
-.toctree-l1 {
+h1, h2, h3, h4, body {
+    font-family: 'Open Sans';
+}
+
+/* .toctree-l1 {
     font-family: 'PT Mono', 'Robot Mono', 'Fira Code', monospace;
     font-weight: 500;
-}
+} */
 
 .toctree-l2 {
-    font-family: 'PT Mono', 'Robot Mono', 'Fira Code', monospace;
+    font-family: 'JuliaMono Medium', 'Robot Mono', 'Fira Code', monospace;
     font-weight: 400;
 }
 
 .toctree-l3 {
-    font-family: 'PT Mono', 'Robot Mono', 'Fira Code', monospace;
+    font-family: 'JuliaMono Medium', 'Robot Mono', 'Fira Code', monospace;
     font-weight: 300;
 }
 
 .toctree-l4 {
-    font-family: 'PT Mono', 'Robot Mono', 'Fira Code', monospace;
+    font-family: 'JuliaMono Medium', 'Robot Mono', 'Fira Code', monospace;
     font-weight: 300;
 }
 

docs/conf.py

@@ -26,7 +26,7 @@
 release = __version__
 
 # Import examples_linker file/module so that it runs each time docs are built
-# import examples_linker
+import examples_linker
 
 #------------------------------------------------------------------------#
 # General config                                                         #
@@ -180,6 +180,9 @@
 
 nbsphinx_prompt_width = "0"
 nbsphinx_allow_errors = True
+nbsphinx_custom_formats = {
+    '.md': ['jupytext.reads', {'fmt': 'Rmd'}],
+}
 
 exclude_patterns = ['_build', '_templates']
 

docs/examples_index.rst

@@ -103,21 +103,11 @@ Simulations
 Contributions
 -------------
 
-.. tabbed:: Paper Recreations
-
-   .. toctree::
-      :maxdepth: 1
-      :glob:
-
-      examples/contrib/paper_recreations/**
-
-.. tabbed:: Applications
-
    .. toctree::
       :maxdepth: 1
       :glob:
 
-      examples/contrib/*
+      examples/contrib/**
 
 
 Reference

examples/getting_started/concise_overview_of_openpnm.ipynb

@@ -73,7 +73,7 @@
     "|Links to Related Notebooks|\n",
     "|:-------------------------|\n",
     "| [A detailed illustration of OpenPNM's plotting functionality](quick_plotting_networks.ipynb)| \n",
-    "| [Export to Paraview is the preferred way to visualize a network](view_vtp_in_paraview.md)|\n"
+    "| FIXME: Export to Paraview is the preferred way to visualize a network|\n"
    ]
   },
   {
@@ -210,7 +210,7 @@
     "\n",
     "|Links to Related Notebooks|\n",
     "|:-------------------------|\n",
-    "| [In-depth discussion and illustration of pore-scale models](/examples/tutorials/physics/pore_scale_models.ipynb)|"
+    "| [In-depth discussion and illustration of pore-scale models](../tutorials/physics/pore_scale_models.ipynb)|"
    ]
   },
   {
@@ -242,7 +242,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Next use the seed to find pore sizes from the cumulative pore size distribution.  This process is described in detail [here](/examples/notebooks/3 - geometry/Playing with Pore Size Distributions.ipynb)."
+    "Next use the seed to find pore sizes from the cumulative pore size distribution. This process is described in detail [here](../tutorials/geometry/adjusting_pore_size_distributions.ipynb)."
    ]
   },
   {
@@ -306,7 +306,7 @@
     "\n",
     "|Links to Related Notebooks|\n",
     "|:-------------------------|\n",
-    "| [Adjusting the pore size distribution](/examples/tutorials/geometry/adjusting_pore_size_distributions.ipynb)| "
+    "| [Adjusting the pore size distribution](../tutorials/geometry/adjusting_pore_size_distributions.ipynb)| "
    ]
   },
   {
@@ -529,7 +529,7 @@
     "\n",
     "|Links to Related Notebooks|\n",
     "|:-------------------------|\n",
-    "|[Overview of data storage in OpenPNM](/examples/reference/data_management/data_and_topology_storage.ipynb)|"
+    "|[Overview of data storage in OpenPNM](../reference/data_management/data_and_topology_storage.ipynb)|"
    ]
   },
   {
@@ -656,8 +656,8 @@
     "\n",
     "|Links to Related Notebooks|\n",
     "|:-------------------------|\n",
-    "|**The role of the Workspace and Projects is explained further** [here](/examples/reference/workspace/overview_of_workspace_and_projects.ipynb)|\n",
-    "|**The 'grid' is particularly useful when several subdomains have been defined as demonstrated** [here](/examples/reference/workspace/overview_of_subdomains.ipynb)|\n"
+    "|**The role of the Workspace and Projects is explained further** [here](../reference/workspace/overview_of_workspace_and_projects.ipynb)|\n",
+    "|**The 'grid' is particularly useful when several subdomains have been defined as demonstrated** [here](../reference/workspace/overview_of_subdomains.ipynb)|\n"
    ]
   },
   {
@@ -817,7 +817,7 @@
     "\n",
     "|Links to Related Notebooks|\n",
     "|:-------------------------|\n",
-    "|**Labels are discussed at length** [here](/examples/reference/data_management/using_and_creating_labels.ipynb)|\n",
+    "|**Labels are discussed at length** [here](../reference/data_management/using_and_creating_labels.ipynb)|\n",
     "\n",
     "Many common labels are added to networks during creation, usually indicating faces like 'left' and 'right', which are useful for applying boundary conditions.\n"
    ]
@@ -1040,7 +1040,7 @@
    "source": [
     "## Outputting or saving simualtion results\n",
     "\n",
-    "Once the simulation is complete it can be either output to Paraview as described [here](/examples/notebooks/io/rendering_in_paraview.ipynb), or saved to one of several file formats for post-processing.\n"
+    "Once the simulation is complete it can be either output to Paraview as described here (FIXME) or saved to one of several file formats for post-processing.\n"
    ]
   }
  ],

examples/reference/class_inheritance/creating_a_custom_phase.ipynb

@@ -473,7 +473,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The `models` submodule has a variety of common functions, stored under `models.misc.basic_math` or `models.misc.common_funtions`.  There are also some models specific to physical properties under `models.phases`."
+    "The `models` submodule has a variety of common functions, stored under `models.misc`. There are also some models specific to physical properties under `models.phases`."
    ]
   }
  ],

examples/simulations/steady_state/deep_dive_into_conductance_models.ipynb

@@ -1,11 +1,11 @@
 {
  "cells": [
   {
-   "cell_type": "code",
-   "execution_count": null,
+   "cell_type": "markdown",
    "metadata": {},
-   "outputs": [],
-   "source": []
+   "source": [
+    "# Deep Dive into Conductance Models"
+   ]
   }
  ],
  "metadata": {