Update docu

.gitignore

@@ -72,3 +72,10 @@ src/*
 
 # version.py
 essm/version.py
+
+# Jupyter temp files
+.ipynb_checkpoints
+*/.ipynb_checkpoints/*
+
+# Documentation build
+docs/_build/

.travis.yml

@@ -42,6 +42,7 @@ env:
 
 before_install:
   - git fetch --tags
+  - sudo apt-get install pandoc
   - travis_retry pip install -U twine wheel coveralls pip
   - travis_retry pip install check-manifest pydocstyle
   - travis_retry pip install -r requirements-devel.txt

CHANGES.rst

@@ -1,6 +1,18 @@
 Changes
 =======
 
+``v0.4.2``
+----------
+*released 2019-11-20*
+
+Bug Fixes
+~~~~~~~~~
+
+- **utils:** Improve markdown representation of units (`PR #79 <https://github.com/environmentalscience/essm/pull/79>`__)
+
+- **variables:**  Fix generate_metadata_table for selected variables (`PR #80 <https://github.com/environmentalscience/essm/pull/80>`__)
+
+
 ``v0.4.1``
 ----------
 *released 2019-11-20*

MANIFEST.in

@@ -15,4 +15,6 @@ recursive-include docs/_static *.png
 recursive-include essm *.yapf
 recursive-include tests *.py
 
+recursive-exclude docs/_build *
+
 prune src

docs/api.rst

@@ -2,6 +2,14 @@
 API Docs
 ========
 
+Jupyter notebooks with API examples
+===================================
+A jupyter notebook with tables of importable variables and equations can be found at 
+https://github.com/environmentalscience/essm/blob/master/docs/examples/importable_variables_equations.ipynb
+
+A jupyter notebook with use examples for the API can be found at 
+https://github.com/environmentalscience/essm/blob/master/docs/examples/api_features.ipynb
+
 Variables
 =========
 
@@ -35,10 +43,10 @@ Radiation
 .. automodule:: essm.variables.leaf.radiation
    :members:
 
-Water Vapour
-~~~~~~~~~~~~
+Energy and Water
+~~~~~~~~~~~~~~~~
 
-.. automodule:: essm.variables.leaf.water_vapour
+.. automodule:: essm.variables.leaf.energy_water
    :members:
 
 Physics
@@ -58,17 +66,6 @@ Equations
 
 .. automodule:: essm.equations
 
-Chamber
--------
-
-.. automodule:: essm.equations.chamber
-
-Insulation
-~~~~~~~~~~
-
-.. automodule:: essm.equations.chamber.insulation
-   :members:
-
 Leaf
 ----
 

docs/conf.py

@@ -94,7 +94,8 @@ def get_attr(obj, value, *args, **kwargs):
     'matplotlib.sphinxext.plot_directive', 'sphinxcontrib.bibtex',
     'sphinx.ext.autodoc', 'sphinx.ext.autosummary', 'sphinx.ext.doctest',
     'sphinx.ext.intersphinx', 'sphinx.ext.todo', 'sphinx.ext.coverage',
-    'sphinx.ext.mathjax', 'sphinx.ext.viewcode', 'sphinx.ext.githubpages'
+    'sphinx.ext.mathjax', 'sphinx.ext.viewcode', 'sphinx.ext.githubpages',
+    'nbsphinx'
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -140,7 +141,8 @@ def get_attr(obj, value, *args, **kwargs):
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This patterns also effect to html_static_path and html_extra_path
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store',
+                   '**.ipynb_checkpoints']
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'
@@ -163,7 +165,7 @@ def get_attr(obj, value, *args, **kwargs):
     'logo': 'logo.png',
     'logo_name': False,
     'description':
-        'This package contains helpers to deal with physical variables '
+        'Python package for dealing with physical variables '
         'and units.',
     'github_user': 'environmentalscience',
     'github_repo': 'essm',
@@ -250,4 +252,7 @@ def get_attr(obj, value, *args, **kwargs):
 
 autoclass_content = 'both'
 
-autodoc_default_flags = ['members', 'undoc-members', 'show-inheritance']
+autodoc_default_options = {
+    'undoc-members': True,
+    'show-inheritance': True
+}