configure docs and doctest

Author: Valentin Sulzer

.travis.yml

@@ -38,10 +38,10 @@ matrix:
         #     - PINTS_UNIT=true
         #   if: type != cron
         # Docs, style and cover checking, latest Python version only
-        # - python: "3.6"
-        #   env:
-        #     - PINTS_DOCS=true
-        #   if: type != cron
+        - python: "3.6"
+          env:
+            - PINTS_DOCS=true
+          if: type != cron
         - python: "3.6"
           env:
             - PINTS_STYLE=true

docs/Makefile

@@ -16,4 +16,4 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/conf.py

@@ -14,19 +14,20 @@
 #
 import os
 import sys
-sys.path.insert(0, os.path.abspath('../'))
+
+sys.path.insert(0, os.path.abspath("../"))
 
 
 # -- Project information -----------------------------------------------------
 
-project = 'PyBaMM'
-copyright = '2018, Valentin Sulzer'
-author = 'Valentin Sulzer'
+project = "PyBaMM"
+copyright = "2018, Valentin Sulzer"
+author = "Valentin Sulzer"
 
 # The short X.Y version
-version = ''
+version = ""
 # The full version, including alpha/beta/rc tags
-release = ''
+release = ""
 
 
 # -- General configuration ---------------------------------------------------
@@ -39,12 +40,12 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.doctest',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.mathjax',
-    'sphinx.ext.viewcode',
-    'sphinx.ext.napoleon',
+    "sphinx.ext.autodoc",
+    "sphinx.ext.doctest",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.napoleon",
 ]
 
 napoleon_google_docstring = False
@@ -54,16 +55,16 @@
 """
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -75,7 +76,7 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = None
@@ -86,7 +87,7 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinxdoc"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
@@ -97,7 +98,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.
@@ -113,7 +114,7 @@
 # -- Options for HTMLHelp output ---------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'PyBaMMdoc'
+htmlhelp_basename = "PyBaMMdoc"
 
 
 # -- Options for LaTeX output ------------------------------------------------
@@ -122,15 +123,12 @@
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',
-
     # The font size ('10pt', '11pt' or '12pt').
     #
     # 'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
     #
     # 'preamble': '',
-
     # Latex figure (float) alignment
     #
     # 'figure_align': 'htbp',
@@ -140,19 +138,21 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'PyBaMM.tex', 'PyBaMM Documentation',
-     'Valentin Sulzer', 'manual'),
+    (
+        master_doc,
+        "PyBaMM.tex",
+        "PyBaMM Documentation",
+        "Valentin Sulzer",
+        "manual",
+    )
 ]
 
 
 # -- Options for manual page output ------------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'pybamm', 'PyBaMM Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "pybamm", "PyBaMM Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output ----------------------------------------------
@@ -161,9 +161,15 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'PyBaMM', 'PyBaMM Documentation',
-     author, 'PyBaMM', 'One line description of project.',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "PyBaMM",
+        "PyBaMM Documentation",
+        author,
+        "PyBaMM",
+        "One line description of project.",
+        "Miscellaneous",
+    )
 ]
 
 
@@ -182,12 +188,12 @@
 # epub_uid = ''
 
 # A list of files that should not be packed into the epub file.
-epub_exclude_files = ['search.html']
+epub_exclude_files = ["search.html"]
 
 
 # -- Extension configuration -------------------------------------------------
 
 # -- Options for intersphinx extension ---------------------------------------
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'https://docs.python.org/': None}
+intersphinx_mapping = {"https://docs.python.org/": None}

docs/index.rst

@@ -10,6 +10,7 @@ Welcome to PyBaMM's documentation!
    :maxdepth: 2
    :caption: Contents:
 
+   source/modules
 
 
 Indices and tables

run-tests.py

@@ -75,14 +75,7 @@ def run_doctests():
     """
     print("Checking if docs can be built.")
     p = subprocess.Popen(
-        [
-            "sphinx-build",
-            "-b",
-            "doctest",
-            "docs/source",
-            "docs/build/html",
-            "-W",
-        ]
+        ["sphinx-build", "-b", "doctest", "docs", "docs/build/html", "-W"]
     )
     try:
         ret = p.wait()
@@ -335,7 +328,7 @@ def export_notebook(ipath, opath):
     if args.quick:
         has_run = True
         run_flake8()
-        run_unit_tests("python")
+        run_unit_tests()
         run_doctests()
     # Help
     if not has_run: