version 0.9 release (#67)

- Added ``ipubpandoc`` (see :ref:`markdown_cells`)
- Refactored conversion process to
  :py:class:`ipypublish.convert.main.IpyPubMain` configurable class
- Added postprocessors (see :ref:`post-processors`)
- Added Sphinx extension (see :ref:`sphinx_extension`)
- Added Binder examples to documentation (see :ref:`code_cells`)

.coveragerc

@@ -0,0 +1,6 @@
+[run]
+omit = 
+    ipypublish/ipysphinx/docutils_transforms.py
+    ipypublish/ipysphinx/extension.py
+    ipypublish/ipysphinx/directives.py
+    ipypublish/scripts/nb_setup.py

.readthedocs.yml

@@ -0,0 +1,17 @@
+version: 2
+
+conda:
+  environment: docs/environment.yaml
+
+python:
+  version: 3.6
+  install:
+    - method: pip
+      path: .
+
+# default
+# sphinx:
+#   builder: html
+#   configuration: conf.py
+#   fail_on_warning: true
+

.travis.yml

@@ -66,8 +66,15 @@ matrix:
 # TODO add read the docs test `pip install .[docs] cd docs; make`
 
 before_install:
+# Pandoc
+- url="https://github.com/jgm/pandoc/releases/tag/2.6"
+- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then path=$(curl -L $url | grep -o '/jgm/pandoc/releases/download/.*-amd64\.deb') ; fi
+- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then downloadUrl="https://github.com$path" ; fi
+- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then file=${path##*/} ; fi
+- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then wget $downloadUrl && sudo dpkg -i $file ; fi
+# LaTeX
 - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo apt-get -qq update ; fi
-- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo apt-get install -y pandoc ; fi
+# - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo apt-get install -y pandoc ; fi
 - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo apt-get install -y texlive ; fi
 - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo apt-get install -y texlive-xetex ; fi
 - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo apt-get install -y texlive-latex-extra ; fi
@@ -78,13 +85,11 @@ before_install:
 - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo apt-get install -y latexmk ; fi
 - pip install -U pip setuptools wheel
 install:
-- travis_wait pip install -r requirements.txt
-- pip install -r test_requirements.txt
-- pip install .
+- travis_wait pip install .[tests,sphinx]
 - pip install --quiet coveralls
 script:
 # - nosetests -v --nocapture --with-doctest --with-coverage --exe --cover-package=ipypublish
-- pytest -v --cov=ipypublish --cov-report= ipypublish
+- pytest -v --cov=ipypublish --cov-config .coveragerc --cov-report= ipypublish
 - nbpublish -pdf --pdf-debug -log debug example/notebooks/Example.ipynb
 after_success:
 - coveralls

.vscode/jinja2.code-snippets

@@ -0,0 +1,76 @@
+{
+    "super": {
+        "prefix": "super",
+        "scope": "jinja,jinja-yaml,jinja-html",
+        "body": "{{ super() }}",
+        "description": "call inherited block"
+    },
+    "set": {
+        "prefix": "set",
+        "scope": "jinja,jinja-yaml,jinja-html",
+        "body": "{% set ${1:name} = ${2:value} %}",
+        "description": "set variable"
+    },   
+    "print": {
+        "prefix": "print",
+        "scope": "jinja,jinja-yaml,jinja-html",
+        "body": "{{ ${1:variable} }}",
+        "description": "print variable"
+    },   
+    "block": {
+        "prefix": "block",
+        "scope": "jinja,jinja-yaml,jinja-html",
+        "body": [
+          "{% block ${1:name} %}",
+          "$2",
+          "{% endblock ${1:name} %}"
+        ],
+        "description": "jinja block"
+    },
+    "macro": {
+        "prefix": "macro",
+        "scope": "jinja,jinja-yaml,jinja-html",
+        "body": [
+          "{% macro ${1:name} %}",
+          "$2",
+          "{% endmacro %}"
+        ],
+        "description": "macro function"
+    },
+    "if": {
+        "prefix": "if",
+        "scope": "jinja,jinja-yaml,jinja-html",
+        "body": [
+          "{% if ${1:condition} %}",
+          "$2",
+          "{% endif %}"
+        ],
+        "description": "if condition"
+    },
+    "if-else": {
+        "prefix": "if-else",
+        "scope": "jinja,jinja-yaml,jinja-html",
+        "body": [
+          "{% if ${1:condition} %}",
+          "$2",
+          "{% else %}",
+          "$3",
+          "{% endif %}"
+        ],
+        "description": "if-else condition"
+    },
+    "if-elif-else": {
+        "prefix": "if-elif-else",
+        "scope": "jinja,jinja-yaml,jinja-html",
+        "body": [
+          "{% if ${1:condition} %}",
+          "$2",
+          "{% else %}",
+          "$3",
+          "{% elif ${1:condition2} %}",
+          "",
+          "{% endif %}"
+        ],
+        "description": "if-else condition"
+    }
+}

.vscode/settings.json

@@ -28,6 +28,7 @@
     "python.linting.flake8Enabled": true,
     "latex-workshop.latex.autoBuild.onSave.enabled": false,
     "cSpell.words": [
+        "Jupyter",
         "ipynb",
         "ipypublish",
         "jupytext",
@@ -42,7 +43,7 @@
         "FIXME",
         "NOTE"
       ],
-    "todo-tree.regex": "((//|#|<!--|\\.\\.|;|/\\*|^)\\s*($TAGS)|^\\s*- \\[ \\])",
+    "todo-tree.regex": "((//|#-?|<!--|\\.\\.|;|/\\*|^)\\s*($TAGS)|^\\s*- \\[ \\])",
     "todo-tree.defaultHighlight": {
         "icon": "alert",
         "type": "tag",
@@ -58,6 +59,11 @@
         "background": "white",
         "opacity": 10
         }
-    }
+    },
+    "yaml.format.enable": true,
 
+    "markdown-preview-enhanced.usePandocParser": true,
+    "markdown-preview-enhanced.pandocPath": "/anaconda/envs/lsr/bin/pandoc",
+    "markdown-preview-enhanced.pandocArguments": "--filter=/anaconda/envs/lsr/bin/ipubpandoc",
+    "markdown-preview-enhanced.enableScriptExecution": true
 }

MANIFEST.in

@@ -1,3 +1,5 @@
 recursive-include ipypublish *.json
 recursive-include ipypublish *.j2
+recursive-include ipypublish *.yaml
+recursive-include ipypublish/ipysphinx/css *.css
 recursive-include ipypublish/tests/test_files *

README.md

@@ -17,7 +17,7 @@ general user interface, but anyone using custom converter plugins will
 be required to update them (see [Plugin Conversion](https://ipypublish.readthedocs.io/en/latest/custom_export_config.html#conversion-of-plugins-from-old-api))
 
 
-![Conversion Process](/docs/source/_static/process.svg)
+![Conversion Process](/docs/source/_static/main_image.png)
 
 For an example of the potential input/output, see:
 [Example.ipynb](example/notebooks/Example.ipynb),

binder/README

@@ -0,0 +1,7 @@
+This directory holds configuration files for https://mybinder.org/.
+
+The notebooks that comprise the documentation can be accessed with this link:
+https://mybinder.org/v2/gh/chrisjsewell/ipypublish/master?filepath=docs
+
+To check out a different version, just replace "master" with the desired
+branch/tag name or commit hash.

binder/environment.yml

@@ -0,0 +1,10 @@
+name: ipypublish-environment
+channels:
+  - conda-forge
+dependencies:
+  - python==3.6
+  - numpy
+  - matplotlib
+  - pandas
+  - sympy<1.3
+  - pillow

binder/postBuild

@@ -0,0 +1,5 @@
+#!/bin/sh
+
+set -ex
+
+pip install .

converted/Example.slides.html

@@ -11975,7 +11975,7 @@ <h2 id="1.2.-References-and-Citations">1.2. References and Citations<a
                             <div class="text_cell_render border-box-sizing rendered_html">
 
                                 <p>References to <a href="#/2/0fig:example">fig. 1</a>, <a href="#/3/0tbl:example">tbl.
-                                    1</a>, <a href="#/4/0eqn:example_sympy">eqn. 1</a> and <a
+                                    1</a>, =@eqn:example_sympy and <a
                                         href="#/2/3code:example_mpl">code 6</a>.</p>
                                 <p>Referencing multiple items: <a href="#/2/0fig:example">fig. 1</a>, <a
                                         href="#/2/0fig:example_h">fig. 2</a> and <a href="#/2/0fig:example_v">fig. 3</a>.
@@ -21538,7 +21538,7 @@ <h1 id="5.-Equations-(with-ipython-or-sympy)">5. Equations (with ipython or symp
 
                 </div>
 
-                <br><b>Code 11:</b> The plotting code for a sympy equation (<a href="#eqn:example_sympy">eqn. 1</a>).
+                <br><b>Code 11:</b> The plotting code for a sympy equation (=@eqn:example_sympy).
                 <div class="input_code">
                     <div class="cell border-box-sizing code_cell rendered">
                         <div class="input">

docs/.gitignore

@@ -0,0 +1,4 @@
+# source/releases.*
+source/api/
+source/*_nbfiles/
+source/converted/

docs/environment.yaml

@@ -0,0 +1,15 @@
+channels:
+  - conda-forge
+dependencies:
+  - python>=3
+  - sphinx>=1.6
+  - pandoc
+  - nbconvert!=5.4
+  - ipykernel
+  - sphinxcontrib-bibtex
+  - jupytext
+  - numpy
+  - matplotlib
+  - pandas
+  - sympy<1.3
+  - pytest>=3.6

docs/get_intersphinx_inv.py

@@ -23,6 +23,8 @@ def warn(self, msg):
     # uri = 'http://jinja.pocoo.org/docs/dev/objects.inv'
     uri = "http://nbconvert.readthedocs.io/en/latest/objects.inv"
     # uri = "http://nbformat.readthedocs.io/en/latest/objects.inv"
+    # uri = "https://docutils.readthedocs.io/en/sphinx-docs/objects.inv"
+    #uri = "https://traitlets.readthedocs.io/en/latest/objects.inv"
 
     # Read inventory into a dictionary
     inv = fetch_inventory(uri)

docs/run_apidoc

@@ -0,0 +1,3 @@
+rm -f source/api/*.rst
+sphinx-apidoc --force --separate -o . ../../ipypublish/ ../../ipypublish/ipypublish/tests ../../ipypublish/setup.py
+rm -f source/api/modules.rst

docs/source/_static/example.bib

@@ -0,0 +1,42 @@
+
+@article{kirkeminde_thermodynamic_2012,
+  title = {Thermodynamic Control of Iron Pyrite Nanocrystal Synthesis with High Photoactivity and Stability},
+  volume = {1},
+  issn = {2050-7496},
+  doi = {10.1039/C2TA00498D},
+  abstract = {Non-toxic, earth abundant nanostructured semiconductors have received extensive attention recently. One of the more highly studied materials has been iron pyrite (FeS2) due to its many different promising applications. Herein, we report the thermodynamically-controlled synthesis of FeS2 nanocrystals, dependent on the reaction temperature and chemical precursors, and a Lewis acid/base model to explain the shape-controlled synthesis. The surface facet-controlled photocatalytic activity and photostability were studied and explained. This work further advances the synthesis with pyrite structure control and surface facet-dictated applications, such as photovoltaics, photocatalysts and photoelectrochemical cells.},
+  timestamp = {2017-07-06T00:26:10Z},
+  langid = {english},
+  number = {1},
+  journaltitle = {Journal of Materials Chemistry A},
+  journal = {Journal of Materials Chemistry A},
+  shortjournal = {J. Mater. Chem. A},
+  author = {Kirkeminde, Alec and Ren, Shenqiang},
+  urldate = {2017-06-18},
+  date = {2012-11-29},
+  year = {2012},
+  pages = {49--54},
+  file = {Kirkeminde_Ren_2012_Thermodynamic control of iron pyrite nanocrystal synthesis with high.pdf:/Users/cjs14/Docear/projects/Corrosion/Zotero_Attachments//2012/Kirkeminde_Ren_2012_Thermodynamic control of iron pyrite nanocrystal synthesis with high.pdf:application/pdf}
+}
+
+@article{zelenyak_molecular_2016,
+  title = {Molecular Dynamics Study of Perovskite Structures with Modified Interatomic Interaction Potentials},
+  volume = {50},
+  issn = {0018-1439, 1608-3148},
+  doi = {10.1134/S0018143916050209},
+  abstract = {The structure of compounds with the perovskite structure ABX3 (A and B are cations, X are anions O2—, F—, Cl—, Br—, and I—), which are widely used in engineering due to unique electrical, optical, and photovoltaic properties, has been considered. Hybrid organic—inorganic halide perovskites important for photovoltaics of a new generation are worth mentioning; they contain cations of organic nitrogen bases as monovalent cations. A molecular dynamics (MD) study of the CaTiO3 base structure (Ca2+, Ti4+, and O2—) has been performed in order to develop the methodology of computer simulation and optimization of the shape and parameters of atomic potentials for perovskite systems.},
+  timestamp = {2017-07-06T00:19:33Z},
+  langid = {english},
+  number = {5},
+  journaltitle = {High Energy Chemistry},
+  journal = {High Energy Chemistry},
+  shortjournal = {High Energy Chem},
+  author = {Zelenyak, T. Yu and Kholmurodov, Kh T. and Tameev, A. R. and Vannikov, A. V. and Gladyshev, P. P.},
+  urldate = {2017-07-06},
+  date = {2016-09-01},
+  year = {2016},
+  pages = {400--405},
+  file = {Zelenyak et al_2016_Molecular dynamics study of perovskite structures with modified interatomic.pdf:/Users/cjs14/Library/Application Support/Firefox/Profiles/gignsb3n.default/zotero/storage/H5NVC2I5/Zelenyak et al_2016_Molecular dynamics study of perovskite structures with modified interatomic.pdf:application/pdf}
+}
+
+