changes for doc compilation

CHANGELOG.rst

@@ -2,7 +2,7 @@
 Changelog
 =========
 
-0.0.0 (2024-02-02)
+0.1.0 (2024-02-03)
 ------------------
 
-* First release on Zenodo
+* VDA-BI toolbox used for the paper "Biology-Informed inverse problems for insect pests detection using pheromone sensors"

CONTRIBUTING.rst

@@ -49,7 +49,7 @@ To set up `pherosensor-toolbox` for local development:
 
    Now you can make your changes locally.
 
-4. When you're done making changes run all the checks with `tox`_ one command::
+4. When you're done making changes run all the checks with `tox` one command::
 
     tox
 

README.rst

@@ -11,7 +11,7 @@ Installation
 
 You can install the in-development version with::
 
-    pip install git+ssh://git@forgemia.inra.fr/simon.labarthe/pherosensor-toolbox.git@main
+    pip install git+ssh://git@forgemia.inra.fr/pherosensor/pherosensor-toolbox.git@main
 
 
 Development
@@ -37,3 +37,20 @@ Note, to combine the coverage data from all the tox environments run:
       - ::
 
             PYTEST_ADDOPTS=--cov-append tox
+            
+Building the docs
+=================
+
+You can install sphinx and sphinx-rtd-theme with::
+
+    pip install sphinx sphinx-rtd-theme
+    
+Then, you can do::
+
+    cd docs
+
+and::
+
+    make html
+    
+The documentations (in html) are then stored in the folder 'build/html'

docs/Makefile

+# 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     = 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/make.bat

+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+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

docs/source/authors.rst

+.. include:: ../../AUTHORS.rst

docs/source/changelog.rst

+.. include:: ../../CHANGELOG.rst

docs/source/conf.py

+# 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
+
+import os
+import sys
+
+sys.path.insert(0, os.path.abspath('../../src'))
+
+project = 'pheromone-toolbox'
+copyright = '2024, Thibault Malou'
+author = 'Thibault Malou'
+release = '0.1.0'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = ['sphinx.ext.autodoc',
+    'sphinx.ext.doctest',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.todo',
+    'sphinx.ext.coverage',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.ifconfig',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.githubpages',
+    'sphinx.ext.napoleon',]
+
+# Napoleon settings
+napoleon_google_docstring = True
+napoleon_numpy_docstring = True
+napoleon_include_init_with_doc = True
+napoleon_include_private_with_doc = True
+napoleon_include_special_with_doc = True
+napoleon_use_admonition_for_examples = False
+napoleon_use_admonition_for_notes = False
+napoleon_use_admonition_for_references = False
+napoleon_use_ivar = False
+napoleon_use_param = True
+napoleon_use_rtype = True
+
+templates_path = ['_templates']
+exclude_patterns = []
+
+autodoc_mock_imports = ['numpy',
+                        'geopandas',
+                        'matplotlib',
+                        'scipy',
+                        'imageio',
+                        'pandas',
+                        'shapely',
+                        'joblib'
+                        ]
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'sphinx_rtd_theme'
+html_static_path = ['_static']
+

docs/source/contributing.rst

+.. include:: ../../CONTRIBUTING.rst

docs/source/index.rst

+.. pheromone-toolbox documentation master file, created by
+   sphinx-quickstart on Sat May  4 12:01:02 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to pheromone-toolbox's documentation!
+=============================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   readme
+   authors
+   changelog
+   contributing
+   installation
+   usage
+   modules
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/source/installation.rst

+============
+Installation
+============
+
+At the command line::
+
+    pip install git+ssh://git@forgemia.inra.fr/pherosensor/pherosensor-toolbox.git@main

docs/source/modules.rst

+src
+===
+
+.. toctree::
+   :maxdepth: 4
+
+   pheromone_dispersion
+   pherosensor
+   source_localization
+   utils

docs/source/pheromone_dispersion.rst

+pheromone\_dispersion package
+=============================
+
+Submodules
+----------
+
+pheromone\_dispersion.advection\_operator module
+------------------------------------------------
+
+.. automodule:: pheromone_dispersion.advection_operator
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pheromone\_dispersion.cli module
+--------------------------------
+
+.. automodule:: pheromone_dispersion.cli
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pheromone\_dispersion.convection\_diffusion\_2D module
+------------------------------------------------------
+
+.. automodule:: pheromone_dispersion.convection_diffusion_2D
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pheromone\_dispersion.deposition\_coeff module
+----------------------------------------------
+
+.. automodule:: pheromone_dispersion.deposition_coeff
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pheromone\_dispersion.diffusion\_operator module
+------------------------------------------------
+
+.. automodule:: pheromone_dispersion.diffusion_operator
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pheromone\_dispersion.diffusion\_tensor module
+----------------------------------------------
+
+.. automodule:: pheromone_dispersion.diffusion_tensor
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pheromone\_dispersion.gaussian\_plume module
+--------------------------------------------
+
+.. automodule:: pheromone_dispersion.gaussian_plume
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pheromone\_dispersion.geom module
+---------------------------------
+
+.. automodule:: pheromone_dispersion.geom
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pheromone\_dispersion.identity\_operator module
+-----------------------------------------------
+
+.. automodule:: pheromone_dispersion.identity_operator
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pheromone\_dispersion.reaction\_operator module
+-----------------------------------------------
+
+.. automodule:: pheromone_dispersion.reaction_operator
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pheromone\_dispersion.source\_term module
+-----------------------------------------
+
+.. automodule:: pheromone_dispersion.source_term
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pheromone\_dispersion.velocity module
+-------------------------------------
+
+.. automodule:: pheromone_dispersion.velocity
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: pheromone_dispersion
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/pherosensor.rst

+pherosensor package
+===================
+
+Submodules
+----------
+
+pherosensor.cli module
+----------------------
+
+.. automodule:: pherosensor.cli
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: pherosensor
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/readme.rst

+.. include:: ../../README.rst

docs/source/source_localization.rst

+source\_localization package
+============================
+
+Submodules
+----------
+
+source\_localization.adjoint\_convection\_diffusion\_2D module
+--------------------------------------------------------------
+
+.. automodule:: source_localization.adjoint_convection_diffusion_2D
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+source\_localization.control module
+-----------------------------------
+
+.. automodule:: source_localization.control
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+source\_localization.cost module
+--------------------------------
+
+.. automodule:: source_localization.cost
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+source\_localization.gradient\_descent module
+---------------------------------------------
+
+.. automodule:: source_localization.gradient_descent
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+source\_localization.obs module
+-------------------------------
+
+.. automodule:: source_localization.obs
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+source\_localization.population\_dynamique module
+-------------------------------------------------
+
+.. automodule:: source_localization.population_dynamique
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+source\_localization.proximal\_gradient module
+----------------------------------------------
+
+.. automodule:: source_localization.proximal_gradient
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: source_localization
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/usage.rst

+=====
+Usage
+=====
+
+To use pherosensor-toolbox in a project::
+
+	import pherosensor

docs/source/utils.rst

+utils package
+=============
+
+Submodules
+----------
+
+utils.generate\_gif module
+--------------------------
+
+.. automodule:: utils.generate_gif
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+utils.geom\_to\_shapefile module
+--------------------------------
+
+.. automodule:: utils.geom_to_shapefile
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+utils.plot\_colormap module
+---------------------------
+
+.. automodule:: utils.plot_colormap
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+utils.plot\_cost module
+-----------------------
+
+.. automodule:: utils.plot_cost
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+utils.plot\_ctrl module
+-----------------------
+
+.. automodule:: utils.plot_ctrl
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+utils.plot\_ctrl\_error module
+------------------------------
+
+.. automodule:: utils.plot_ctrl_error
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+utils.plot\_env\_param module
+-----------------------------
+
+.. automodule:: utils.plot_env_param
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+utils.plot\_obs module
+----------------------
+
+.. automodule:: utils.plot_obs
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+utils.superlevel\_set module
+----------------------------
+
+.. automodule:: utils.superlevel_set
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: utils
+   :members:
+   :undoc-members:
+   :show-inheritance:

src/pheromone_dispersion/advection_operator.py

@@ -7,6 +7,7 @@ from pheromone_dispersion.velocity import Velocity
 def sum_advection_flux_given_U(U, x, msh):
     """
     compute the sum over a cell of the flux of the advection term for a given velocity field
+
     - TO BE DONE:
         * change the BC, for now: no income, change for: a given income
     - input:
@@ -67,6 +68,7 @@ class Advection(LinOp):
     def __init__(self, U, msh):
         """
         Instanciation of the class.
+
         - input:
             * U: object of the class Velocity
             * msh: object of the class MeshRect2D
@@ -99,17 +101,20 @@ class Advection(LinOp):
     def at_current_time(self, tc, U):
         """
         Update the velocity field U at a given time.
+
         - input:
             * tc: the current time
             * U: object of the class Velocity, velocity field to be updated
         - do:
-            update the velocity field U and its attribute using the method at_current_time of the class Velocity
+            * update the velocity field U and its attribute using the method at_current_time of the class Velocity
         """
+
         U.at_current_time(tc)
 
     def _matvec(self, x_out):
         """
         Compute the image (matrix-vector product) of the convection linear operator for a given vector of concentration
+
         - input:
             * x_out:
                 numpy array of shape (msh.x.size*msh.y.size, ),
@@ -130,6 +135,7 @@ class Advection(LinOp):
         Compute the image (matrix-vector product) of the flux part of the adjoint of the convection linear operator
         for a given vector of concentration.
         This flux part of the adjoint operator is the adjoint operator if the velocity field has a divergence equal to 0
+
         - input:
             * x_out:
                 numpy array of shape (msh.x.size*msh.y.size, ),
@@ -148,6 +154,7 @@ class Advection(LinOp):
     def _matmat(self, x_out):
         """
         Compute the image (matrix-matrix product) of the advection linear operator for a given (matrix of) concentration
+
         - input:
             * x_out:
                 numpy array of (shape msh.x.size*msh.y.size, msh.x.size*msh.y.size),
@@ -171,6 +178,7 @@ class AdvectionAdjoint(LinOp):
     def __init__(self, U, msh):
         """
         Instanciation of the class.
+
         - input:
             * U: object of the class Velocity
             * msh: object of the class MeshRect2D
@@ -203,6 +211,7 @@ class AdvectionAdjoint(LinOp):
     def at_current_time(self, tc):
         """
         Update the attributes U and minus_U of the class at a given time.
+
         - input:
             * tc: the current time
         """
@@ -212,6 +221,7 @@ class AdvectionAdjoint(LinOp):
     def _matvec(self, x_out):
         """
         Compute the image (matrix-vector product) of the adjoint of the convection linear operator for a given vector of concentration
+
         - input:
             * x_out:
                 numpy array of shape (msh.x.size*msh.y.size, ),
@@ -230,6 +240,7 @@ class AdvectionAdjoint(LinOp):
     def _matmat(self, x_out):
         """
         Compute the image (matrix-matrix product) of the adjoint advection linear operator for a given (matrix of) concentration
+
         - input:
             * x_out:
                 numpy array of (shape msh.x.size*msh.y.size, msh.x.size*msh.y.size),

src/pheromone_dispersion/convection_diffusion_2D.py

@@ -28,6 +28,7 @@ class DiffusionConvectionReaction2DEquation:
     def __init__(self, U, K, coeff_depot, S, msh, time_discretization='semi-implicit', tol_inversion=1e-14):
         """
         Instanciation of the class.
+
         - input:
             * msh: object of the class MeshRect2D
             * U: object of the class Velocity
@@ -148,6 +149,7 @@ class DiffusionConvectionReaction2DEquation:
     def set_source(self, value, t=None):
         """
         Update the source term with the values provided as input
+
         - input:
             * value: numpy array of shape (t.size, msh.y.size, msh.x.size), the new values of the source term
             * t: numpy array of shape (t.size,), the vector containing the associated times, by default None if the source is stationnary
@@ -157,6 +159,7 @@ class DiffusionConvectionReaction2DEquation:
     def at_current_time(self, tc, i=None):
         """
         Update the linear operators of the PDE (attributes A, D and S of the class) at a given time.
+
         - input:
             * tc: the current time
         """
@@ -181,6 +184,7 @@ class DiffusionConvectionReaction2DEquation:
         """
         solve the PDE for one time step
         inverse the linear system (I + dt (- D + R)).c^{n+1} = c^n + dt (- A.c^n + S)
+
         - input:
             * c: numpy array of shape (msh.y.size, msh.x.size), contains the concentration of pheromones at the previous time step
         - output:
@@ -202,6 +206,7 @@ class DiffusionConvectionReaction2DEquation:
     def solver(self, save_all=False, path_save='./save/', display_flag=True):
         """
         solve the PDE on the whole time window
+
         - input:
             * save_all:
                 boolean, False by default,
@@ -299,6 +304,7 @@ class DiffusionConvectionReaction2DEquation:
     def solver_save_all(self, path_save='./save/', display_flag=True, save_rate=1000):
         """
         solve the PDE on the whole time window
+
         - input:
             * save_all:
                 boolean, False by default,
@@ -395,6 +401,7 @@ class DiffusionConvectionReaction2DEquation:
     def solver_est_at_obs_times(self, obs, display_flag=True):
         """
         solve the PDE on the whole time window and store the resulting estimations of the concentration at the observations times
+
         - TO DO:
             * check that the function works
         - input:
@@ -483,6 +490,7 @@ class DiffusionConvectionReaction2DEquation:
         """
         solve the steady-state version of the PDE
         inverse the linear system (- D + A + R) c = S using a conjugate gradient method
+
         - output:
             * numpy array of shape (msh.y.size, msh.x.size), resulting concentration at the steady state
         """