Merge pull request #163 from FESOM/workbench

Workbench

.gitignore

@@ -0,0 +1,7 @@
+notebooks/
+
+# Sphinx build files
+docs/_build/
+docs/_static/
+docs/.doctrees
+docs/.buildinfo

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SOURCEDIR     = .
+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/conf.py

@@ -0,0 +1,151 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+# tripyview documentation build configuration file, created by
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+# 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
+import tripyview
+sys.path.insert(0, os.path.join(tripyview.__path__[0]))
+
+
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+project   = 'tripyview'
+copyright = '2024, Patrick Scholz'
+author    = 'Patrick Scholz'
+version   = '0.3.0'
+release   = '0.3.0'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+# 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.viewcode']
+
+autodoc_mock_imports = ['mpl_toolkits', 'cartopy']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = 'en'
+
+# 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']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = False
+
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#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 = 'sphinx_rtd_theme'
+# html_theme = 'alabaster'
+html_theme = 'agogo'
+
+# 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_static_path = ['_static']
+
+
+
+# -- Options for HTMLHelp output ---------------------------------------
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'tripyviewdoc'
+
+
+
+# -- Options for LaTeX output ------------------------------------------
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+     'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+     'pointsize': '12pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+    "preamble": r"""
+    \setcounter{secnumdepth}{3}
+    """,
+    # 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, 'tripyview.tex',
+     u'tripyview Documentation',
+     u'Patrick Scholz', '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, 'tripyview',
+     u'tripyview 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, 'tripyview',
+     u'tripyview Documentation',
+     author,
+     'tripyview',
+     'One line description of project.',
+     'Miscellaneous'),
+]

docs/index.rst

@@ -0,0 +1,44 @@
+.. tripyview documentation master file, created by
+   sphinx-quickstart on Sun Jun  2 16:22:36 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to tripyview's documentation!
+=====================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+.. automodule:: tripyview.sub_mesh
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: tripyview.sub_plot
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: tripyview.sub_data
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: tripyview.sub_transect
+   :members:
+   :undoc-members:
+   :show-inheritance:   
+
+.. automodule:: tripyview.sub_index
+   :members:
+   :undoc-members:
+   :show-inheritance:      
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

tripyview/sub_transect.py

@@ -1439,7 +1439,9 @@ def load_zmeantransect_fesom2(mesh                  ,
     Returns:
     
         :index_list:    list with xarray dataset of zonal mean array
+    
     ____________________________________________________________________________
+    
     """
     #___________________________________________________________________________
     # str_anod    = ''