Merge branch 'main' of https://github.com/FESOM/tripyview

.gitignore

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

README.md

@@ -6,7 +6,7 @@ Triangular plotting and diagnostics for FESOM2 + command line utility similar to
 fdiag using plotting suite of [email protected] (former fesom2/view_pscholz folder). 
 Data reading got updated to xarray, plotting got updated to cartopy, actually works well for 
 python=3.9, 3.10, 3.11 and 3.12 (python 3.8 made recently some problems to resolve all the cartopy dependencies). 
-It is tested upto dart mesh size (3M surface vertices) where it allows for a decend 
+It is tested up to dart mesh size (3M surface vertices) where it allows for a decent
 working speed (but only when used in parallel)
 <br />
 version: 0.3.0
@@ -32,17 +32,13 @@ make sure your conda environment uses python 3.9, 3.10, 3.11 or 3.12
 #  gets one thread
 # -install libstdcxx-ng with conda since there is no pip package for it is needed
 #  so that pyvista is able to plot interactively
+# -all other packages will be automatically installed by pip
 conda install -c conda-forge libstdcxx-ng
 cd tripyview
 pip install -e .
 
-# If you want to use the interactive features in tools/do_topo@elem_or_node.ipynb
-# due to python issues you will need jupyter_server=1.23.6, jupyter_client=7.3.2, 
-# tornad=6.1 --> its the only combination where this features works in moment!!!
-(pip install jupyter_server==1.23.6 jupyter_client==7.3.2 tornado==6.1)
-
 # On my laptop i had problems with the classic notebook support beyond jupyter_server==2.0.0
-# and had to downgrade it to jupyter_server<2.0.0. However on HPC albedo that didnt
+# and had to downgrade it to jupyter_server<2.0.0. However on HPC albedo that did not
 # seems to be the case.
 (pip install "jupyter_server<2.0.0")
 ```
@@ -105,9 +101,9 @@ vertice/element- resolution and area)
 
 
 ### General time plots: 
-* `hovm`             - plot hovmöller diagramms for 3d ocean variable over depth and time averaged over
+* `hovm`             - plot hovmöller diagrams for 3d ocean variable over depth and time averaged over
 specific region that is defined by shapefile (see. tripyview/shapefiles/...)
-* `hovm_clim`        - plot hovmöller diagramms for  temperature, salinity and density climatology 
+* `hovm_clim`        - plot hovmöller diagrams for  temperature, salinity and density climatology 
 over depth and time averaged over specific region that is defined by shapefile (see. tripyview/shapefiles/...)
 
 * `var_t`            - plots time-series of globally or shapefile (see. tripyview/shapefiles/...) averaged 2d and 3d variables 
@@ -123,11 +119,11 @@ for the: Atlantic(amoc), Atlantic+Arctic(aamoc), Pacific(pmoc), Pacific+Indian O
 </p>
 
 
-* `zmoc_t`           - plot time-series of atlantic meridional overturning circulation at specific latitudes 
+* `zmoc_t`           - plot time-series of Atlantic meridional overturning circulation at specific latitudes 
 (default: which_lats: [26, 40, 'max'])
 
 
-* `dmoc`             - plot meridional overturning circulation in density coordinates using FESOM2 density MOC diagnostics (graditues goes to **[email protected]**), Globally, 
+* `dmoc`             - plot meridional overturning circulation in density coordinates using FESOM2 density MOC diagnostics (gratitude goes to **[email protected]**), Globally, 
 for the: Atlantic(amoc), Atlantic+Arctic(aamoc), Pacific(pmoc), Pacific+Indian Ocean(ipmoc) and Indian Ocean(imoc)
 * `dmoc_srf`         - plot surface transformation of meridional overturning circulation in density coordinates
 * `dmoc_inner`       - plot inner transformation of meridional overturning circulation in density coordinates
@@ -151,7 +147,7 @@ for the: Atlantic(amoc), Atlantic+Arctic(aamoc), Pacific(pmoc), Pacific+Indian O
 * `dmoc_srfcbflx`    - plot surface buoyancy flux transformation for specific water-class
 
 
-* `dmoc_t`           - plot time-series of atlantic meridional overturning circulation in density coordinates at specific latitudes 
+* `dmoc_t`           - plot time-series of Atlantic meridional overturning circulation in density coordinates at specific latitudes 
 (default: which_lats: [26, 55, 'max'])
 
 
@@ -164,7 +160,7 @@ for the: Atlantic(amoc), Atlantic+Arctic(aamoc), Pacific(pmoc), Pacific+Indian O
 
 
 ### 2D automatic multipanel plotting: 
-* plot automatised figure multipanels depending on number of choosen datasets and number
+* plot automatised figure multi-panels depending on number of chosen datasets and number
 of panel columns ncol (the panel arrangement uses ideas from **[email protected]**)
 <p align="center" width="100%">
   <img width=75% src="tripyview/tripyview_multipanel.png">
@@ -185,15 +181,15 @@ of panel columns ncol (the panel arrangement uses ideas from **Nils.Brueggemann@
 
 ## Command line batch diagnostics:
 * `tripyrun  <workflowfile.yml>` - command line diagnostics similar to fdiag (fdiag, served as a 
-template, graditues go to **[email protected]**), creates html files with linked plots.
+template, gratitude go to **[email protected]**), creates html files with linked plots.
 
 * `tripyrun  <workflowfile.yml> -d <driver>` - re-run one specific driver from .yml file 
 
 * `tripyrun  <workflowfile.yml> -d <driver> -v <var1 var2 ...>` - re-run specific variable 
 subset of one specific driver driver from .yml file
 
 * `tripyrun  <workflowfile.yml> -r` - for the case the diagnostic did not fully finish you can 
-render the html file from hand based on hte saved json file. The json file is update after each finished
+render the html file from hand based on the saved json file. The json file is update after each finished
 driver section.
 
 <p align="center" width="100%">

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