Merge branch 'release/0.1.7'

00_overview.ipynb

@@ -31,8 +31,8 @@
     "\n",
     "| [**Abstract**](./00_overview.ipynb) | **Introduction**  | [**Examples**](./00_overview.ipynb#Examples)  |\n",
     "|:-----|:-----|:-----|\n",
-    "|  | [Software in Geochem](./01_intro.ipynb#Software-in-Geochemistry)  |  [pyrolite](./011_pyrolite.ipynb)  |\n",
-    "|  | [Development & Tools](./01_intro.ipynb#Development-Workflow-&-Tools) | [pyrolite-meltsutil](./012_pyrolite-meltsutil.ipynb) | \n",
+    "|  | [Software in Geochem](./00_overview.ipynb#Software-in-Geochemistry)  |  [pyrolite](./011_pyrolite.ipynb)  |\n",
+    "|  | [Development & Tools](./00_overview.ipynb#Development-Workflow-&-Tools) | [pyrolite-meltsutil](./012_pyrolite-meltsutil.ipynb) | \n",
     "|  |  | [interferences](./013_interferences.ipynb) | \n",
     "|  |  | [autopew](./014_autopew.ipynb) |  "
    ]
@@ -98,13 +98,16 @@
     "\n",
     "While it's not always the first option, developing your own software may be a productive path if you're frequently having issues wrangling with inflexible (and sometimes, expensive) software which doesn't meet your need. With some planning and design, It is also a way to add value to research already being conducted, bring interoperability and standardization and contribute to the community.\n",
     "\n",
+    "\n",
+    "<p> \n",
     "<sup>\n",
-    "<p>   \n",
-    "<b id=\"f1\">*</b>: Here where we refer to software, we are purposely using the term in a relatively broad sense, and intend to refer to the range of software-based tools which are used in geochemistry (i.e. everything from templated excel spreadsheets to ecosystems of related professionally-developed standalone executable programs). \n",
+    "<b id=\"f1\">*</b>: Here where we refer to software, we are purposely using the term in a relatively broad sense, and intend to refer to the range of software-based tools which are used in geochemistry (i.e. everything from templated excel spreadsheets to ecosystems of related professionally-developed standalone executable programs).</sup>\n",
     "</p>\n",
     "<p>\n",
+    "<sup>\n",
     "<b id=\"f2\">†</b>: Note that while this presentation focuses on Python, it is largely for reasons of convenience rather than in support of it’s exclusive use. There are a number of languages which fit well with the ideas presented here and are approachable for those new to coding, notably including R and Julia.\n",
     "</sup>\n",
+    "</p>\n",
     "\n",
     "## Requirements and Challenges for Research Software\n",
     "\n",
@@ -247,7 +250,7 @@
     "\n",
     "The following section lists a set of Python packages developed largely for geochemical research purposes, and demonstrates some of their functionality. Follow the links on the headings to have a look at some examples and interactive visualisations. Note that the figures displayed are actually being generated from code when each page is opened, so it may take a few seconds to open! Alternatively, follow the 'docs' links under the respective heading to have a look at the more extensive documentation pages.\n",
     "\n",
-    "## [pyrolite](./021_pyrolite.ipynb)\n",
+    "## [pyrolite](./011_pyrolite.ipynb)\n",
     "\n",
     ">  pyrolite is a set of tools for making the most of your geochemical data.\n",
     "\n",
@@ -261,21 +264,21 @@
     "</div>\n",
     "\n",
     "\n",
-    "## [pyrolite-meltsutil](./022_pyrolite-meltsutil.ipynb)\n",
+    "## [pyrolite-meltsutil](./012_pyrolite-meltsutil.ipynb)\n",
     "\n",
     ">  pyrolite-meltsutil is a pyrolite extension for working with alphaMELTS and its outputs.\n",
     "\n",
     "[![PyPI](https://img.shields.io/pypi/v/pyrolite-meltsutil.svg?style=flat)](https://pypi.python.org/pypi/pyrolite-meltsutil)\n",
     "[![Docs](https://readthedocs.org/projects/pyrolite-meltsutil/badge/?version=develop)](https://pyrolite-meltsutil.readthedocs.io/)\n",
     "\n",
-    "## [interferences](./023_interferences.ipynb)\n",
+    "## [interferences](./013_interferences.ipynb)\n",
     "\n",
     ">  Tools for inorganic mass spectra and interference patterns.\n",
     "\n",
     "[![Docs](https://readthedocs.org/projects/interferences/badge/?version=develop)](https://interferences.readthedocs.io/)\n",
     "\n",
     "\n",
-    "## [autopew](./024_autopew.ipynb)\n",
+    "## [autopew](./014_autopew.ipynb)\n",
     "\n",
     "[![Docs](https://readthedocs.org/projects/autopew/badge/?version=develop)](https://autopew.readthedocs.io/)\n",
     "   \n",

011_pyrolite.ipynb

@@ -16,8 +16,8 @@
     "\n",
     "| [**Abstract**](./00_overview.ipynb) | **Introduction**  | [**Examples**](./00_overview.ipynb#Examples)  |\n",
     "|:-----|:-----|:-----|\n",
-    "|  | [Software in Geochem](./01_intro.ipynb#Software-in-Geochemistry)  |  [pyrolite](./011_pyrolite.ipynb)  |\n",
-    "|  | [Development & Tools](./01_intro.ipynb#Development-Workflow-&-Tools) | [pyrolite-meltsutil](./012_pyrolite-meltsutil.ipynb) | \n",
+    "|  | [Software in Geochem](./00_overview.ipynb#Software-in-Geochemistry)  |  [pyrolite](./011_pyrolite.ipynb)  |\n",
+    "|  | [Development & Tools](./00_overview.ipynb#Development-Workflow-&-Tools) | [pyrolite-meltsutil](./012_pyrolite-meltsutil.ipynb) | \n",
     "|  |  | [interferences](./013_interferences.ipynb) | \n",
     "|  |  | [autopew](./014_autopew.ipynb) |  "
    ]
@@ -40,7 +40,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "<div class=\"alert alert-info\">\n",
+    "<div class=\"alert alert-success\">\n",
     "pyrolite has recently been <a href=\"https://joss.theoj.org/papers/10.21105/joss.02314\">published in the Journal of Open Source Software</a>, and the following is largely taken from the short paper \"pyrolite: Python for Geochemistry\".\n",
     "</div>\n",
     "\n",
@@ -172,8 +172,8 @@
     "\n",
     "| [**Abstract**](./00_overview.ipynb) | **Introduction**  | [**Examples**](./00_overview.ipynb#Examples)  |\n",
     "|:-----|:-----|:-----|\n",
-    "|  | [Software in Geochem](./01_intro.ipynb#Software-in-Geochemistry)  |  [pyrolite](./011_pyrolite.ipynb)  |\n",
-    "|  | [Development & Tools](./01_intro.ipynb#Development-Workflow-&-Tools) | [pyrolite-meltsutil](./012_pyrolite-meltsutil.ipynb) | \n",
+    "|  | [Software in Geochem](./00_overview.ipynb#Software-in-Geochemistry)  |  [pyrolite](./011_pyrolite.ipynb)  |\n",
+    "|  | [Development & Tools](./00_overview.ipynb#Development-Workflow-&-Tools) | [pyrolite-meltsutil](./012_pyrolite-meltsutil.ipynb) | \n",
     "|  |  | [interferences](./013_interferences.ipynb) | \n",
     "|  |  | [autopew](./014_autopew.ipynb) |  "
    ]

012_pyrolite-meltsutil.ipynb

@@ -16,8 +16,8 @@
     "\n",
     "| [**Abstract**](./00_overview.ipynb) | **Introduction**  | [**Examples**](./00_overview.ipynb#Examples)  |\n",
     "|:-----|:-----|:-----|\n",
-    "|  | [Software in Geochem](./01_intro.ipynb#Software-in-Geochemistry)  |  [pyrolite](./011_pyrolite.ipynb)  |\n",
-    "|  | [Development & Tools](./01_intro.ipynb#Development-Workflow-&-Tools) | [pyrolite-meltsutil](./012_pyrolite-meltsutil.ipynb) | \n",
+    "|  | [Software in Geochem](./00_overview.ipynb#Software-in-Geochemistry)  |  [pyrolite](./011_pyrolite.ipynb)  |\n",
+    "|  | [Development & Tools](./00_overview.ipynb#Development-Workflow-&-Tools) | [pyrolite-meltsutil](./012_pyrolite-meltsutil.ipynb) | \n",
     "|  |  | [interferences](./013_interferences.ipynb) | \n",
     "|  |  | [autopew](./014_autopew.ipynb) |  "
    ]
@@ -241,8 +241,8 @@
     "\n",
     "| [**Abstract**](./00_overview.ipynb) | **Introduction**  | [**Examples**](./00_overview.ipynb#Examples)  |\n",
     "|:-----|:-----|:-----|\n",
-    "|  | [Software in Geochem](./01_intro.ipynb#Software-in-Geochemistry)  |  [pyrolite](./011_pyrolite.ipynb)  |\n",
-    "|  | [Development & Tools](./01_intro.ipynb#Development-Workflow-&-Tools) | [pyrolite-meltsutil](./012_pyrolite-meltsutil.ipynb) | \n",
+    "|  | [Software in Geochem](./00_overview.ipynb#Software-in-Geochemistry)  |  [pyrolite](./011_pyrolite.ipynb)  |\n",
+    "|  | [Development & Tools](./00_overview.ipynb#Development-Workflow-&-Tools) | [pyrolite-meltsutil](./012_pyrolite-meltsutil.ipynb) | \n",
     "|  |  | [interferences](./013_interferences.ipynb) | \n",
     "|  |  | [autopew](./014_autopew.ipynb) |  "
    ]

014_autopew.ipynb

@@ -16,8 +16,8 @@
     "\n",
     "| [**Abstract**](./00_overview.ipynb) | **Introduction**  | [**Examples**](./00_overview.ipynb#Examples)  |\n",
     "|:-----|:-----|:-----|\n",
-    "|  | [Software in Geochem](./01_intro.ipynb#Software-in-Geochemistry)  |  [pyrolite](./011_pyrolite.ipynb)  |\n",
-    "|  | [Development & Tools](./01_intro.ipynb#Development-Workflow-&-Tools) | [pyrolite-meltsutil](./012_pyrolite-meltsutil.ipynb) | \n",
+    "|  | [Software in Geochem](./00_overview.ipynb#Software-in-Geochemistry)  |  [pyrolite](./011_pyrolite.ipynb)  |\n",
+    "|  | [Development & Tools](./00_overview.ipynb#Development-Workflow-&-Tools) | [pyrolite-meltsutil](./012_pyrolite-meltsutil.ipynb) | \n",
     "|  |  | [interferences](./013_interferences.ipynb) | \n",
     "|  |  | [autopew](./014_autopew.ipynb) |  "
    ]
@@ -53,8 +53,8 @@
     "\n",
     "| [**Abstract**](./00_overview.ipynb) | **Introduction**  | [**Examples**](./00_overview.ipynb#Examples)  |\n",
     "|:-----|:-----|:-----|\n",
-    "|  | [Software in Geochem](./01_intro.ipynb#Software-in-Geochemistry)  |  [pyrolite](./011_pyrolite.ipynb)  |\n",
-    "|  | [Development & Tools](./01_intro.ipynb#Development-Workflow-&-Tools) | [pyrolite-meltsutil](./012_pyrolite-meltsutil.ipynb) | \n",
+    "|  | [Software in Geochem](./00_overview.ipynb#Software-in-Geochemistry)  |  [pyrolite](./011_pyrolite.ipynb)  |\n",
+    "|  | [Development & Tools](./00_overview.ipynb#Development-Workflow-&-Tools) | [pyrolite-meltsutil](./012_pyrolite-meltsutil.ipynb) | \n",
     "|  |  | [interferences](./013_interferences.ipynb) | \n",
     "|  |  | [autopew](./014_autopew.ipynb) |  "
    ]

binder/nbconvert_config.py

@@ -0,0 +1,2 @@
+c = get_config()
+c.ExecutePreprocessor.timeout = 300

binder/postBuild

@@ -1,10 +1,17 @@
 # the following is required for ipyvolume widgets
 jupyter-nbextension enable widgetsnbextension --py
 
+# for ipyvolume, if using lab:
+#jupyter labextension install @jupyter-widgets/jupyterlab-manager
+#jupyter labextension install ipyvolume
+#jupyter labextension install jupyter-threejs
+
 # make sure we have a place where we can pick up the custom template
 mkdir -p ~/.jupyter/voila/templates/
 mkdir -p  ~/.local/share/jupyter/voila/templates
 
 cp -r ./custom/ ~/.jupyter/voila/templates/
 cp -r ./custom/ ~/.local/share/jupyter/voila/templates
-cp -r ./custom/ /srv/conda/envs/notebook/share/jupyter/voila/templates
+
+# set up jupyter notebook config for voila
+cat ./binder/nbconvert_config.py >> ~/.jupyter/jupyter_notebook_config.py

jupyter_config.json

@@ -1,6 +1,5 @@
 {
   "VoilaConfiguration": {
-    "template": "custom",
     "enable_nbextensions": true
   }
 }