Build and publish documentation...

.travis.yml

@@ -2,13 +2,19 @@ language: minimal
 
 sudo: false
 
+env:
+  global:
+    - secure: "c1HxpvYvasSjycR2iejkLxtlFzMvR8Gmf2GQDPJfIkEftQGvXOt+m91Wy26e819eHeXiQUuoNQwnp6RgOW8woNrlqfro4GX6pgLZlmr4K5Plum1KLa/xs8wk+bN/XpgRbcOqwAFbWfoPbfbm3oP1/QoFiwT38KbGWONlYVGKlKM="
+
 matrix:
   fast_finish: true
   include:
   - name: default
     env: TEST_TARGET=default PY=3.7
-  - python: coding_standards
+  - name: coding_standards
     env: TEST_TARGET=coding_standards PY=3.7
+  - name: docs
+    env: TEST_TARGET=docs PY=3.7
 
 before_install:
   - wget http://bit.ly/miniconda -O miniconda.sh
@@ -36,3 +42,30 @@ script:
   - if [[ $TEST_TARGET == 'coding_standards' ]]; then
       flake8 --max-line-length=105 oceans --exclude=_version.py ;
     fi
+
+  - if [[ $TEST_TARGET == 'docs' ]]; then
+      set -e ;
+      conda install doctr ;
+      pushd docs ;
+      make clean html linkcheck ;
+      popd ;
+      python -m doctr deploy --built-docs docs/build/html . ;
+    fi
+
+doctr:
+  require-master: true
+  sync: False
+
+deploy:
+  skip_cleanup: true
+  provider: pypi
+  user: ocefpaf
+  password:
+    secure: "HifofjCDgTUP3hv0C8xD411JBCIp7VziSE5SiD9ZXo9CGo/rnr2rxtIcA9QDHfwO0n1iK26AhUbmeUURecn7+GjvvwCsbN3y21zfx0/D6KCSCvfEuJBJG2uAZqbNBFkT5//96umsavVngp0vNzOASDCljBgC9t5X0r1JnybQUro="
+  distributions: sdist bdist_wheel
+  upload_docs: no
+  on:
+    repo: pyoceans/python-oceans
+    tags: true
+    all_branches: master
+    condition: '$TEST_TARGET == "default"'

docs/Makefile

@@ -0,0 +1,19 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# 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)

docs/source/RPSstuff.rst

@@ -0,0 +1,7 @@
+:mod:`oceans.RPSstuff`
+----------------------
+
+.. automodule:: oceans.RPSstuff
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/colormaps.rst

@@ -0,0 +1,7 @@
+:mod:`oceans.colormaps`
+-----------------------
+
+.. automodule:: oceans.colormaps
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/conf.py

@@ -0,0 +1,196 @@
+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'oceans'
+copyright = '2018, Filipe Fernandes'
+author = 'Filipe Fernandes'
+
+from oceans._version import get_versions
+version = release = get_versions()['version']
+del get_versions
+
+# -- General configuration ---------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.githubpages',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.napoleon',
+    'nbsphinx',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+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'
+
+# The master toctree document.
+master_doc = 'index'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# 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 = []
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = None
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'alabaster'
+
+# 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
+# documentation.
+#
+html_theme_options = {
+    'logo': 'logo.png',
+    'logo_name': 'oceans',
+    'github_user': 'pyoceans',
+    'github_repo': 'oceans',
+    'github_banner': True,
+    'travis_button': True,
+    'fixed_sidebar': True,
+}
+
+# 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']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+html_sidebars = {
+    '**': [
+        'about.html',
+        'navigation.html',
+        'relations.html',  # needs 'show_related': True theme option to display
+        'searchbox.html',
+        'donate.html',
+    ]
+}
+
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'oceansdoc'
+
+
+# -- Options for LaTeX output ------------------------------------------------
+
+latex_elements = {
+    # 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',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, 'oceans.tex', 'oceans Documentation',
+     'Filipe Fernandes', '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, 'oceans', 'oceans Documentation',
+     [author], 1)
+]
+
+
+# -- Options for Texinfo output ----------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'oceans', 'oceans Documentation',
+     author, 'oceans', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+# -- Options for Epub output -------------------------------------------------
+
+# Bibliographic Dublin Core info.
+epub_title = project
+
+# The unique identifier of the text. This can be a ISBN number
+# or the project homepage.
+#
+# epub_identifier = ''
+
+# A unique identification for the text.
+#
+# epub_uid = ''
+
+# A list of files that should not be packed into the epub file.
+epub_exclude_files = ['search.html']
+
+
+# -- Extension configuration -------------------------------------------------

docs/source/datasets.rst

@@ -0,0 +1,7 @@
+:mod:`oceans.datasets`
+----------------------
+
+.. automodule:: oceans.datasets
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/filters.rst

@@ -0,0 +1,7 @@
+:mod:`oceans.filters`
+---------------------
+
+.. automodule:: oceans.filters
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/index.rst

@@ -0,0 +1,28 @@
+.. oceans documentation master file, created by
+   sphinx-quickstart on Fri Nov  2 15:42:53 2018.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Misc helper functions for ocean sciences
+========================================
+
+Most of the functions here are Python versions of some common Matlab functions.
+They are untested and probably buggy. Use with caution!
+
+.. toctree::
+   :maxdepth: 3
+   :caption: Contents:
+
+   datasets
+   colormaps
+   plotting
+   ocfis
+   filters
+   RPSstuff
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/source/ocfis.rst

@@ -0,0 +1,7 @@
+:mod:`oceans.ocfis`
+-------------------
+
+.. automodule:: oceans.ocfis
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/plotting.rst

@@ -0,0 +1,7 @@
+:mod:`oceans.plotting`
+----------------------
+
+.. automodule:: oceans.plotting
+   :members:
+   :undoc-members:
+   :show-inheritance:

github_deploy_key_pyoceans_python_oceans.enc

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