Bump version to 2.0.0_beta.4 and update numpy and influx-si dependencies

.gitignore

@@ -1,4 +1,5 @@
 ./README.md
 __pycache__
 isodesign/test_data/acetate_LLE/tmp
-.ipynb_checkpoints
+.ipynb_checkpoints
+/docs/_build/ 

docs/Makefile

@@ -5,8 +5,8 @@
 # from the environment for the first two.
 SPHINXOPTS    ?=
 SPHINXBUILD   ?= sphinx-build
-SOURCEDIR     = source
-BUILDDIR      = build
+SOURCEDIR     = .
+BUILDDIR      = _build
 
 # Put it first so that "make" without argument is like "make help".
 help:

docs/conf.py

@@ -1,7 +1,6 @@
 # Configuration file for the Sphinx documentation builder.
 #
-# This file only contains a selection of the most common options. For a full
-# list see the documentation:
+# For the full list of built-in configuration values, see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
 # -- Path setup --------------------------------------------------------------
@@ -17,13 +16,13 @@
 
 project = 'IsoDesign'
 copyright = '2024, INRAE'
-author = 'Rochelle Kouakou, Loïc Le Grégam'
+author = 'Rochelle Kouakou, Loïc Le Gregam, Serguei Sokol, Pierre Millard'
 
 # The full version, including alpha/beta/rc tags
 release = __version__
 
-# -- General configuration ---------------------------------------------------
 
+# -- 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.

docs/index.rst

@@ -1,38 +1,56 @@
 .. IsoDesign documentation master file, created by
-   sphinx-quickstart on Mon Nov 18 10:19:08 2024.
+   sphinx-quickstart on Fri Jan 31 09:51:42 2025.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
 
 Welcome to IsoDesign documentation !
-=======================
+====================================
 
-IsoDesign is a scientific tool designed to optimize the choice of the optimal 
-isotopic composition of labeled substrates in 13C fluxomic labeling experiments.
+IsoDesign is a scientific tool designed to identify the optimal
+isotopic composition of labeled substrates in :sup:`13`\ C-fluxomics
+experiments.
 
-Simulated labeling is calculated using the `influx_si software <https://influx-si.readthedocs.io/en/latest/index.html>`_ , distributed with IsoDesign. 
+**Key features:**
 
-**IsoDesign includes the following features:**
-
-   * user can **define lower and upper bounds** and **define the desired number of intervals** for each isotopic form to be included,
-   * **substrate pricing can be entered**, which will be incorporated into the rating criteria,
-   * **simulation of all possible combinations** of isotopic forms in a single run,
-   * ability to **simulate stationary or instationary labeling**, 
-   * **multiple scoring criteria** are available and can be applied simultaneously to assess simulation results,
-   * the results of the scoring criteria are displayed using a table for detailed values and a bar plot for visual representation,
-   * shipped as a **library** with a **graphical** interface,
-   * **open-source, free and easy to install** everywhere where Python 3 and pip run,
+   * users can **define all isotopic forms to consider for each substrate**,
+   * account for the **substrate price** to keep the cost of the experiment
+     reasonable,
+   * design of both (isotopic) **stationary and non-stationary** :sup:`13`\ C-fluxomics experiments
+   * **diverse scoring criteria** to finely analyse flux resolution at reaction-, pathway- and
+     network-levels to identify the optimal label input
+     according to the biological question,
+   * **scoring criteria can be combined** to find the optimal balance
+     between different objectives (e.g., the highest flux resolution at a
+     minimal cost),
+   * **visual representation** of the design results to support the
+     decision-making process,
+   * increased computational performance through **parallel computing**,
+   * shipped as a **library** with a **graphical user interface**,
+   * **open-source, free and easy to install** everywhere where Python and R
+     run,
    * **biologist-friendly**.
 
-It is one of the routine tools that we use at the
-`Mathematics cell of TBI <https://www.toulouse-biotechnology-institute.fr/en/plateformes-plateaux/cellule-mathematiques/>`_
-and `MetaToul platform <https://mth-metatoul.com/>`_.
+It is one of the routine tools that we use at the `MetaToul platform
+<https://mth-metatoul.com/>`_ and `MetaSys team <http://www
+.toulouse-biotechnology-institute
+.fr/en/research/molecular-physiology-and-metabolism/metasys.html>`_ of the
+`Toulouse Biotechnology Institute <http://www
+.toulouse-biotechnology-institute.fr/en/>`_.
+IsoDesign has been developed in collaboration with the `Math cell of TBI
+<https://www.toulouse-biotechnology-institute
+.fr/en/plateformes-plateaux/cellule-mathematiques/>`_, with the continuous
+support of `MetaboHUB <https://www.metabohub.fr/home.html>`_.
 
-The code is open-source, and available on `GitHub <https://github.com/MetaboHUB-MetaToul-FluxoMet/IsoDesign/>`_ under a
+The code is open-source, and available on `GitHub <https://github
+.com/MetaboHUB-MetaToul-FluxoMet/IsoDesign/>`_ under a
 :ref:`GPLv3 license <license>`.
 
-This documentation is available on Read the Docs (`https://isodesign.readthedocs.io <https://isodesign.readthedocs.io/>`_)
-and can be downloaded as a `PDF file <https://readthedocs.org/projects/isodesign/downloads/pdf/latest/>`_.
+This documentation is available on Read the Docs (`https://isodesign
+.readthedocs.io <https://isodesign.readthedocs.io/>`_)
+and can be downloaded as a `PDF file <https://readthedocs
+.org/projects/isodesign/downloads/pdf/latest/>`_.
+
 
 .. toctree::
    :maxdepth: 2
@@ -47,4 +65,4 @@ and can be downloaded as a `PDF file <https://readthedocs.org/projects/isodesign
    :maxdepth: 2
    :caption: Miscellaneous
 
-   license.rst
+   license.rst

docs/installation.rst

@@ -1,14 +1,26 @@
 Installation
 ============
 
-Installation
+Requirements
 -----------------
 
-IsoDesign requires Python 3.10 or higher and run on all platforms supporting Python3 (Windows, MacOS and Linux).
+IsoDesign runs on all platforms (Windows, MacOS and Linux) and requires Python (3.10 or higher) and R (3.4.0 or higher).
 If you do not have a Python environment configured on your computer, we recommend that you follow the instructions
 from `Anaconda <https://www.anaconda.com/download/>`_.
 
 
+Installation with conda (recommended)
+-------------------------
+
+This is the recommended installation procedure. If you have a version of conda (such as miniconda or Anaconda), you can install IsoDesign with the following command:
+
+.. code-block:: bash
+
+    conda install isodesign -c bioconda
+
+This will install IsoDesign and all its dependencies.
+
+
 Installation with pip
 -------------------------
 
@@ -20,32 +32,45 @@ installed on your system, you can install IsoDesign with pip.
 
     pip install isodesign
 
-This will install IsoDesign and all its dependencies. To use IsoDesign, you will need to some R dependencies (necessary for the simulation part with influx_si).
-Once you installed IsoDesign, you can install these dependencies by running the following command:
+This will install IsoDesign and most of its dependencies. To use IsoDesign,
+you will need some additional R dependencies (necessary for the flux
+simulation part with influx_si). Once you installed IsoDesign, you can
+install these dependencies by running the following command:
 
-.. code-block:: bashy
+.. code-block:: bash
 
     influx_s --install_rdep
 
-For more information on the installation of R dependencies, please refer to `influx_si software <https://influx-si.readthedocs.io/en/latest/install.html#r-dependencies>`_ documentation.
+For more information on the installation of R dependencies, please refer to the
+`influx_si documentation <https://influx-si.readthedocs.io/en/latest/install
+.html#r-dependencies>`_ .
 
 
 Alternatives & updates
 ----------------------
 
-If you know that you do not have permission to install software system-wide, you can install IsoDesign into your user directory using the :samp:`--user` flag:
+If you do not have permission to install software system-wide, you can
+install IsoDesign into your user directory using the :samp:`--user` flag:
 
 .. code-block::
 
     pip install --user isodesign
 
 This does not require any special privileges.
 
-Once the package is installed, you can update it using the following command:
+Once the package is installed, you can update it using pip with the following
+command:
 
 .. code-block::
 
     pip install -U isodesign
 
-Alternatively, you can also download all sources in a tarball from `GitHub <https://github.com/MetaboHUB-MetaToul-FluxoMet/IsoDesign/>`_,
-but it will be more difficult to update IsoDesign later on.
+and using conda:
+
+.. code-block::
+
+    conda update isodesign
+
+Alternatively, you can also download all sources in a tarball from `GitHub
+<https://github.com/MetaboHUB-MetaToul-FluxoMet/IsoDesign/>`_, but it will
+be more difficult to update IsoDesign later on.

docs/make.bat

@@ -7,8 +7,8 @@ REM Command file for Sphinx documentation
 if "%SPHINXBUILD%" == "" (
 	set SPHINXBUILD=sphinx-build
 )
-set SOURCEDIR=source
-set BUILDDIR=build
+set SOURCEDIR=.
+set BUILDDIR=_build
 
 %SPHINXBUILD% >NUL 2>NUL
 if errorlevel 9009 (

docs/quickstart.rst

@@ -1,51 +1,76 @@
 Quick start
 ============
 
-In this section we will explain how to launch IsoDesign once it has been installed onto your system.
+In this section, we explain how to launch IsoDesign once it has been
+installed on your system.
 
 
 Graphical user interface
 --------------------------------------
 
-To open the Graphical User Interface, type in a terminal (e.g. Anaconda Prompt if installed on Windows):
+To open the Graphical User Interface, type in a terminal (e.g. Anaconda
+Prompt if installed on Windows):
 
 .. code-block:: bash
 
     isodesign
 
-If you have installed the package in a specific environment, make sure to activate it before starting IsoDesign.
+If you have installed the package in a specific environment, make sure to
+activate it before starting IsoDesign.
 
-IsoDesign interface will open in a new browser window :
+IsoDesign interface will open in a new browser window:
 
 .. image:: _static/interface.JPG
-   :scale: 60%
+   :scale: 40%
 
-Select your input network file (which should have a :file:`.netw` extension. It's a :file:`tsv` format file, refer to :ref:`required_input_data_files` for more details). 
-By default, an output directory path is pre-configured, but you can modify it if needed. Once ready, you click the "Submit" button to load your model 
-and explore its different elements. Afterward, click the "Next Page" button to proceed.
+Select your input network file (which should have a :file:`.netw` extension,
+refer to :ref:`required_input_data_files` for more details).
+By default, an output directory path is pre-configured, but you can modify
+it if needed. Once ready, you click the "Submit" button to load your model
+and explore its structure through a dedicated interface. Afterward, click on
+"Next Page" to go to the next step. This will open the **Labels input** page.
 
-In the following page, **Labels input**, you can configure the isotopic composition of the substrates and specify the desire proportions by setting the
-lower and upper bounds along with the number of intervals. Additionnally, you can preview the generated combinations before proceeding with simulations
+[PHOTO LABELS INPUT]
+
+In the page **Labels input**, you can define the available isotopic forms of
+the substrate(s) and specify the desired proportions to be tested by setting
+lower and upper bounds along with a number of intervals. Additionally,
+you can preview the generated combinations before proceeding with simulations
 (refer to the :ref:`labels_input` for more details).
 
-In the **Simulation options** page, you can choose your desired simulation mode : influx_s (stationary) or influx_i (instationary) (refer to the :ref:`simulation_options` for more details).
-Then, configure the simulation options and initiate the simulation. 
+[PHOTO SIMULATIONS PAGE]
+
+In the **Simulation options** page, you can choose your desired simulation
+mode: influx_s (stationary) or influx_i (instationary) (refer to the
+:ref:`simulation_options` for more details).
+Then, configure the simulation options and initiate the simulation. Once the
+calculations are completed, you can proceed to the **Results** page.
+
+[PHOTO RESULTS PAGE]
 
-The **Results** page allows you to view simulation outcomes and apply one or more scoring criteria (refer to :ref:`results` for more details).
+The **Results** page allows you to visualize the results and apply one or
+more scoring criteria to identify the optimal label input (refer to
+:ref:`results` for more details).
 
-.. note:: The process is continuously and automatically saved as a pickle file (".pkl") in the output folder. To reopen the current processing state, just reopen this file by clicking on "Load a session - Browse files" on on the “Upload data” page.
+.. note:: The process is continuously and automatically saved as a pickle
+file (:file:`.pkl`) in the output folder. To reopen the current processing
+state, just reopen this file by clicking on "Load a session - Browse files"
+on on the “Upload data” page.
 
-.. warning:: IsoDesign overwrites (results and processing) files if they already exist. So take care to copy your results elsewhere or to change the output path and/or filename if you want to protect them from overwriting.
+.. warning:: IsoDesign overwrites (results and processing) files if they
+already exist. So take care to copy your results elsewhere or to change the
+output path and/or filename if you want to protect them from overwriting.
 
 
 Library
 -------
 
-IsoDesign is also available as a library (a Python module) that you can import directly in your Python
-scripts:
+IsoDesign is also available as a library (a Python module) that you can
+import directly in your Python scripts:
 
 .. code-block:: python
 
   import isodesign
 
-.. seealso::  Have a look at our :ref:`API <Library documentation>` if you are interested in this feature.
+.. seealso::  Have a look at our :ref:`API <Library documentation>` if you
+are interested in this experimental feature.

isodesign/__main__.py

@@ -11,8 +11,8 @@ def get_last_version():
     """Get last IsoDesign version."""
     try:
         isodesign_path = Path(isodesign.__file__).parent
-        # Get the version from testpypi
-        response = requests.get('https://test.pypi.org/simple/ isodesign')
+        # Get the version from pypi
+        response = requests.get('https://pypi.org/pypi/isodesign/json')
         latest_version = response.json()['info']['version']
         with open(str(Path(isodesign_path, "last_version.txt")), "w") as f:
             f.write(latest_version)