From 0a2e8134f300e99c126e55b5593842b321093dcf Mon Sep 17 00:00:00 2001
From: Franck Thollard <franck.thollard@univ-grenoble-alpes.fr>
Date: Thu, 23 May 2024 15:10:46 +0200
Subject: [PATCH] setup env
---
AUTHORS.rst | 30 +++++++
doc/changes.rst | 71 +++++++++++++++
doc/conf.py | 176 +++++++++++++++++++++++++++++++++++++
doc/contacts.rst | 13 +++
doc/funding.rst | 7 ++
doc/index.rst | 20 +++++
doc/installation.rst | 81 +++++++++++++++++
doc/modules.rst | 6 ++
doc/supported.rst | 10 +++
doc/test.rst | 19 ++++
images/logo-uga.png | Bin 0 -> 8306 bytes
images/logo_cnrs_small.png | Bin 0 -> 7279 bytes
rringg/version.py | 1 +
13 files changed, 434 insertions(+)
create mode 100644 AUTHORS.rst
create mode 100644 doc/changes.rst
create mode 100644 doc/conf.py
create mode 100644 doc/contacts.rst
create mode 100644 doc/funding.rst
create mode 100644 doc/index.rst
create mode 100755 doc/installation.rst
create mode 100644 doc/modules.rst
create mode 100644 doc/supported.rst
create mode 100644 doc/test.rst
create mode 100644 images/logo-uga.png
create mode 100644 images/logo_cnrs_small.png
create mode 100644 rringg/version.py
diff --git a/AUTHORS.rst b/AUTHORS.rst
new file mode 100644
index 0000000..1c445c1
--- /dev/null
+++ b/AUTHORS.rst
@@ -0,0 +1,30 @@
+Contributors
+============
+
+Here are a list of people that work, or have worked, on RRIINGG
+
+* UGA stands for University Grenoble Alpes (https://www.univ-grenoble-alpes.fr/).
+* ISTerre stands for Institut des Sciences de la Terre (https://www.isterre.fr).
+
+Current contributors
+--------------------
+
+Alphabetic order of last name :
+
+* Aubin Bleriot Tsapong Tsague (ISTERRE/UGA), aubin-bleriot.tsapong-tsague@univ-grenoble-alpes.fr
+* Marie-Pierre Doin (ISTERRE/CNRS) marie-pierre.doin@univ-grenoble-alpes.fr
+* Gaël Janex (ISTERRE/CNRS) gael.janex@univ-grenoble-alpes.fr
+* Erwan Pathier (ISTERRE/UGA) erwan.pathier@univ-grenoble-alpes.fr
+* Anne Socquet (ISTERRE/UGA) anne.socquet@univ-grenoble-alpes.fr
+* Franck Thollard (ISTERRE/CNRS) franck.thollard@univ-grenoble-alpes.fr
+
+Former contributors
+-------------------
+
+Nop
+
+Contact
+-------
+
+Anne Socquet (ISTERRE/UGA) anne.socquet@univ-grenoble-alpes.fr
+
diff --git a/doc/changes.rst b/doc/changes.rst
new file mode 100644
index 0000000..a6f8732
--- /dev/null
+++ b/doc/changes.rst
@@ -0,0 +1,71 @@
+=============
+Release Notes
+=============
+
+1.0.4 (2023-03-13)
+------------------
+
+New
+```
+
+- new colour gradients (from Crameri et al., see Doc)
+- Clear Reference button
+- keyboard shortcuts + tooltips on profiling tools
+- autorange histogram to 5/95th percentiles (button in toolbar and in context menu)
+- Map toolbar with 2 buttons:
+ * Flip Map Vertically feature
+ * Save Map to export map view + assoc. colorbar to image files (multiple formats available) ('#75 <https://gricad-gitlab.univ-grenoble-alpes.fr/deformvis/insarviz/-/issues/75>)
+
+- Menu entry to save all figures to repository (multiple formats available) ('#75 <https://gricad-gitlab.univ-grenoble-alpes.fr/deformvis/insarviz/-/issues/75>)
+- support VRT (GDAL Virtual Format) loading ('#73 <https://gricad-gitlab.univ-grenoble-alpes.fr/deformvis/insarviz/-/issues/73>) + VRT building script (see Doc)
+- pypi packaging
+
+
+Fixed
+`````
+- colour display bug on Linux/Windows (discretisation)
+- reference display on Linux/Windows ('#70 <https://gricad-gitlab.univ-grenoble-alpes.fr/deformvis/insarviz/-/issues/70>)
+- plot ranges remain when clicking points
+- jump to image 99 upon first loading, now remains on middle image
+- handle nodata absent from header
+- plot bug when switching between tools
+- date slider/spinbox discrepancy
+- colour palette also applied to general view
+
+
+Changed
+```````
+- boundaries eased up on versions of required packages
+- plot titles/descriptions outside of figures
+- plot background icon
+- Reference now only through Reference tool (no check button in plot window anymore)
+- geotiff not flipped automatically upon loading
+- LOS symbol disabled for now, needs rethinking
+- Documentation updated
+
+
+
+
+
+
+1.0.3 (2022-09-16)
+------------------
+
+New
+```
+
+- Profile tool now links two points selected by the user, and draws plots for a selection of points (regular spacing) on this profile line (`!55 <https://gricad-gitlab.univ-grenoble-alpes.fr/deformvis/insarviz/-/merge_requests/55>`_)
+- Points tool now allows user to select individual points whose data are to be plotted (`!55 <https://gricad-gitlab.univ-grenoble-alpes.fr/deformvis/insarviz/-/merge_requests/55>`_)
+- Reference tool: once data is plotted from Profile or Points tool, a reference point or zone (rectangle) can be selected on the Map by the user, plots will be adjusted to the reference (`!55 <https://gricad-gitlab.univ-grenoble-alpes.fr/deformvis/insarviz/-/merge_requests/55>`_)
+
+
+Fixed
+`````
+- lock axes button on plots did not work on Linux (`#56 <https://gricad-gitlab.univ-grenoble-alpes.fr/deformvis/insarviz/-/issues/56>`_)
+- export to csv was faulty when more than one curve on plot ('#66 <https://gricad-gitlab.univ-grenoble-alpes.fr/deformvis/insarviz/-/issues/66>)
+
+
+Changed
+```````
+- Profile tool renamed Points (see New section)
+- Documentation updated
\ No newline at end of file
diff --git a/doc/conf.py b/doc/conf.py
new file mode 100644
index 0000000..8e188ab
--- /dev/null
+++ b/doc/conf.py
@@ -0,0 +1,176 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+from shutil import copyfile
+import os
+import rringg
+
+#
+# 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 sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+# copy Author file to the right place
+mydir = os.path.dirname(os.path.realpath(__file__))
+copyfile(mydir + "/../AUTHORS.rst", "authors.rst")
+
+# -- Project information -----------------------------------------------------
+project = 'RRINGG'
+# Author list
+author = "ISTERRE / CNRS / UGA"
+copyright = '2024 ' + author
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+release = rringg.__version__
+# The short X.Y version (keep semantic versioning)
+version = release
+
+# -- General configuration ---------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+needs_sphinx = '1.1'
+
+# 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.intersphinx',
+ 'sphinx.ext.coverage',
+ 'sphinx.ext.mathjax',
+ 'sphinx.ext.viewcode',
+ 'sphinx_rtd_theme'
+]
+
+# 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', '.md']
+
+# 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 = 'en'
+
+# 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 = [u'_build', 'Thumbs.db', '.DS_Store']
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+
+# -- 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'
+
+# 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 = {}
+html_logo = "images/logo_rringg.png"
+
+# 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 = ['html/_static']
+
+
+# Add the custom.css (https://docs.readthedocs.io/en/latest/guides/adding-custom-css.html)
+def setup(app):
+ # app.add_stylesheet('./custom.css')
+ app.add_css_file('./custom.css')
+# 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 = {}
+
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'RRINGG_Documentation'
+
+
+# -- Options for LaTeX output ------------------------------------------------
+
+latex_elements = {
+ # The paper size ('letterpaper' or 'a4paper').
+ #
+ 'papersize': 'a4paper',
+
+ # 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, 'rringg_rst.tex', u'RRINGG Documentation',
+ author, '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, 'rringg', u'RRINGG Documentation',
+ [author], 1)
+]
+
+
+# -- Extension configuration -------------------------------------------------
+# Add __init__ and class description to the doc
+autoclass_content = "both"
+
+# -- Options for intersphinx extension ---------------------------------------
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {'python': ('https://docs.python.org/', None),
+ 'numpy': ('http://docs.scipy.org/doc/numpy/', None),
+ 'scipy': ('http://docs.scipy.org/doc/scipy/reference', None)}
diff --git a/doc/contacts.rst b/doc/contacts.rst
new file mode 100644
index 0000000..fc81a83
--- /dev/null
+++ b/doc/contacts.rst
@@ -0,0 +1,13 @@
+Contacts & bug reports
+======================
+
+In case of problem or if you have any requests, you can contact the
+the developers using the following mailing list : insarviz-sos@univ-grenoble-alpes.fr
+
+If you want to stay tuned you can register to the insarviz-info mailing list
+by sending an email to insarviz-notification@univ-grenoble-alpes.fr with the subject
+
+"subscribe insarviz-notification@univ-grenoble-alpes.fr FIRST_NAME LAST_NAME"
+
+The traffic of this mailing list is very low (few emails per year) but let you know when new
+releases are made.
diff --git a/doc/funding.rst b/doc/funding.rst
new file mode 100644
index 0000000..69fac03
--- /dev/null
+++ b/doc/funding.rst
@@ -0,0 +1,7 @@
+Funding
+=======
+
+The InsarViz project is funded by:
+
+* CNES: APR CNES (https://apr.cnes.fr/)
+* CNRS, in particular via the MITI section on inter-disciplinarity
diff --git a/doc/index.rst b/doc/index.rst
new file mode 100644
index 0000000..9bc4509
--- /dev/null
+++ b/doc/index.rst
@@ -0,0 +1,20 @@
+.. image:: images/logo-uga.png
+ :width: 30pt
+
+.. image:: images/logo_cnrs_small.png
+ :width: 30pt
+
+InsarViz
+********
+
+.. toctree::
+ :maxdepth: 2
+ :caption: Documentation
+
+ installation
+ test
+ contacts
+ authors
+ funding
+ changes
+ modules
diff --git a/doc/installation.rst b/doc/installation.rst
new file mode 100755
index 0000000..d370539
--- /dev/null
+++ b/doc/installation.rst
@@ -0,0 +1,81 @@
+############
+Installation
+############
+
+
+Recommended Python distribution
+-------------------------------
+
+In order to run RRINGG code you will need a python distribution. We recommend the `Anaconda distribution <https://www.anaconda.com/products/individual>`_ (version 3.6 or higher).
+
+
+Code download
+-------------
+
+First, download the source code, typically using git:
+
+.. code-block :: bash
+
+ git clone git@gricad-gitlab.univ-grenoble-alpes.fr:isterre-cycle/rringg.git
+
+Environment setup
+-----------------
+
+* **With Anaconda**
+
+We recommend you install the RRINGG tool in a virtual environment. If you have installed the `Anaconda distribution <https://www.anaconda.com/products/individual>`_, navigate to within the top-level rringg folder and create a conda environment with the required dependencies using :
+
+.. code-block :: bash
+
+ conda env create -f environment.yaml
+
+
+And activate it:
+
+.. code-block :: bash
+
+ conda activate rringg-env
+
+* **Without Anaconda**
+
+Without Anaconda, create an virtual environment, activate it and install the required packages using the following commands:
+
+.. code-block :: bash
+
+ python3 -m venv venv
+ source venv/bin/activate
+ pip install -r requirements.txt
+
+
+
+Installation type
+------------------
+Finally, install the rringg module within your virtual environment. If you do **not** want to modify the source code, follow the **Regular installation** instructions. If you would like to be able to **modify the code**, follow the **Developper install instructions**.
+
+* **Regular installation**
+
+Installing rringg in a virtual environment, or system-wide, is just a one-line command:
+
+.. code-block :: bash
+
+ pip install .
+
+* **Developper installation**
+
+If you intend to change the source code, you should install the tool in a *editable* mode:
+
+.. code-block :: bash
+
+ pip install -e .
+
+Test your installation
+----------------------
+
+You can check your installation by doing:
+
+.. code-block :: bash
+
+ CODE TO RUN
+
+This should print the help message. If not, your install failed.
+
diff --git a/doc/modules.rst b/doc/modules.rst
new file mode 100644
index 0000000..89c19c8
--- /dev/null
+++ b/doc/modules.rst
@@ -0,0 +1,6 @@
+API Reference
+=============
+
+.. toctree::
+ :maxdepth: 4
+
diff --git a/doc/supported.rst b/doc/supported.rst
new file mode 100644
index 0000000..36ea8fc
--- /dev/null
+++ b/doc/supported.rst
@@ -0,0 +1,10 @@
+Supported data formats
+======================
+
+As of InsarViz 1.0.0, supported input data format include all `GDAL <https://gdal.org/index.html>`_ types such as:
+
+* NSBAS-type time series (depl_cumule and associated files)
+* GeoTiffs
+* VRT (Virtual Datasets): this GDAL format is a vritual dataset composed of other GDAL datasets with repositioning, and algorithms potentially applied as well as various kinds of metadata altered or added (see `documentation <https://gdal.org/drivers/raster/vrt.html>`_). For instance, you can make a VRT composed of individual displacement map files or interferograms. We provide a `script here <https://gricad-gitlab.univ-grenoble-alpes.fr/deformvis/insarviz/-/snippets/266>`_ to create a VRT.
+
+We are developing on a mechanism to allow users to provide a **plug-in-type loader to load other types of data**. Stay tuned!
diff --git a/doc/test.rst b/doc/test.rst
new file mode 100644
index 0000000..8b897d5
--- /dev/null
+++ b/doc/test.rst
@@ -0,0 +1,19 @@
+Running all the tests
+---------------------
+
+Testing can be done classically using *unittest*:
+
+
+.. code-block :: bash
+
+ python setup.py test
+
+
+Another way of running test is by running *pytest*. Navigate to the main insarviz folder, and run the test with the following command:
+
+.. code-block :: bash
+
+ pytest
+
+
+
diff --git a/images/logo-uga.png b/images/logo-uga.png
new file mode 100644
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diff --git a/rringg/version.py b/rringg/version.py
new file mode 100644
index 0000000..f102a9c
--- /dev/null
+++ b/rringg/version.py
@@ -0,0 +1 @@
+__version__ = "0.0.1"
--
GitLab