README corrections and refurbishments

README.md

@@ -9,7 +9,7 @@
 
 ## Introduction
 
-CNApy [[Paper]](https://doi.org/10.1093/bioinformatics/btab828) is a Python-based graphical user interface for a) many common methods of Constraint-Based Reconstruction and Analysis (COBRA) with stoichiometric metabolic models, b) the visualization of COBRA calculation results as *interactive and editable* metabolic maps (including Escher maps [[GitHub]][https://escher.github.io/#/]([Paper)](<https://doi.org/10.1371/journal.pcbi.1004321>)) and c) the creation and editing of metabolic models, including its reactions, metabolites and genes. For model loading and export, CNApy supports the widely used SBML standard format [[Site]][https://sbml.org/]([Paper)](<https://www.embopress.org/doi/abs/10.15252/msb.20199110>).
+CNApy [[Paper]](https://doi.org/10.1093/bioinformatics/btab828) is a Python-based graphical user interface for a) many common methods of Constraint-Based Reconstruction and Analysis (COBRA) with stoichiometric metabolic models, b) the visualization of COBRA calculation results as *interactive and editable* metabolic maps (including Escher maps [[GitHub]](https://escher.github.io/#/)[[Paper]](<https://doi.org/10.1371/journal.pcbi.1004321>)) and c) the creation and editing of metabolic models, including its reactions, metabolites and genes. For model loading and export, CNApy supports the widely used SBML standard format [[Site]](https://sbml.org/)[[Paper]](https://www.embopress.org/doi/abs/10.15252/msb.20199110).
 
 Supported COBRA methods (partly provided by cobrapy [[GitHub]](https://github.com/opencobra/cobrapy)[[Paper]](https://doi.org/10.1186/1752-0509-7-74)) include:
 
@@ -40,7 +40,7 @@ There are 4 alternative ways to install CNApy:
 
 1. The easiest way for any user to install CNApy is by downloading its installer, which is provided for Windows, Linux and MacOS, see [Using CNApy installer](#using-cnapy-installer) for more.
 2. If you already have installed Python 3.10 (no other version) on your system, you can install CNApy simply through ```pip install cnapy``` in your console. Afterwards, you can start CNApy's GUI by running either ```cnapy``` or, if this doesn't work, ```python -m cnapy``` where "python" must call your Python 3.10 installation.
-3. If you already use conda or mamba (for mamba, just change the "conda" command to "mamba"), you can create a CNApy environment named ```cnapy-1.2.2``` as follows: 1) Run ```conda create --name cnapy-1.2.2 python=3.10 pip```, 2) run ```conda activate cnapy-1.2.2```, 3) run ```pip install cnapy```. Then, you can start CNApy in the cnapy-1.2.2 conda environment by running either ```cnapy``` or, if this doesn't work, ```python -m cnapy```. Note that the [cnapy conda package](https://anaconda.org/cnapy/cnapy) is currently *not* being updated due to licensing uncertainties.
+3. If you already use conda or mamba (for mamba, just change the "conda" command to "mamba"), you can create a CNApy environment named ```cnapy-1.2.2``` as follows: 1) Run ```conda create --name cnapy-1.2.2 python=3.10 pip openjdk -c conda-forge```, 2) run ```conda activate cnapy-1.2.2```, 3) run ```pip install cnapy```. Then, you can start CNApy in the cnapy-1.2.2 conda environment by running either ```cnapy``` or, if this doesn't work, ```python -m cnapy```. Note that the [cnapy conda package](https://anaconda.org/cnapy/cnapy) is currently *not* being updated due to licensing uncertainties.
 4. If you want to develop CNApy, follow the instruction for the cloning and setup of the CNApy repository using git and conda or mamba in section [Setup the CNApy development environment](#setup-the-cnapy-development-environment).
 
 ## Documentation and Tutorials
@@ -67,16 +67,19 @@ This installer lets you create a local installation of CNApy under Windows, Linu
 - Put this file into a folder where you want CNApy to be installed.
 - Make the script executable by opening your console in the folder and run ```chmod u+x ./install_cnapy_here.sh```. Alternatively, if supported on your system, right-click on the file, go the file's settings and mark it as executable.
 - Now, either run ```./install_cnapy_here.sh``` in your console or, if supported on your system, double-click on install_cnapy_here.sh.
-- Finally, you can run CNApy by double-clicking "run_cnapy.sh" in the newly created cnapy-1.2.2 subfolder or by calling run_cnapy.sh in your console (for the latter, your console must point to the folder where run_cnapy.sh is located).
+- Finally, you can run CNApy by calling ```./run_cnapy.sh``` in your console (for this without another path beforehand, your console must point to the folder where run_cnapy.sh is located, e.g. if you are in the folder where install_cnapy_here.sh is located, through ```cd cnapy-1.2.2```). Alternatively, if supported by your system, double-click on "run_cnapy.sh" in the newly created cnapy-1.2.2 subfolder.
 
 Technical side note: CNApy's installer is utilizing [micromamba](https://mamba.readthedocs.io/en/latest/installation/micromamba-installation.html).
 
 ## Setup the CNApy development environment
 
-Everyone is welcome to contribute to CNApy's development. [See our contribution file for general instructions](https://github.com/cnapy-org/CNApy/blob/master/CONTRIBUTING.md).
+*Note:* The following instructions only have to be followed if you want to contribute to CNApy as a programmer. If this is not the case, follow other steps of the [Installation Options](#installation-options).
 
-Programatically, we use uv [[GitHub]](https://github.com/astral-sh/uv) to install all dependencies and manage our installed Python versions (alternatives, such as using conda or mamba are also possible if uv doesn't work for you although you would have to install all CNApy dependencies manually).
+Everyone is welcome to contribute to CNApy's development. [See our contribution file for general instructions](https://github.com/cnapy-org/CNApy/blob/master/CONTRIBUTING.md). Any contribution intentionally submitted for inclusion in the work by you, shall be licensed under the terms of the Apache 2.0 license without any additional terms or conditions.
 
+Programatically, we recommend to use uv [[GitHub]](https://github.com/astral-sh/uv) to install all dependencies and manage installed Python versions. Alternatively, one can also use conda/mamba for the same tasks, although you would have to install CNApy's dependencies manually.
+
+### uv usage
 You can use uv for CNApy as follows:
 
 1. Make sure that you have installed uv (*Note*: uv can be installed under any Python version as uv will manage the needed Python version later):
@@ -98,9 +101,7 @@ cd CNApy
 uv run cnapy.py
 ```
 
-uv will automatically install the correct Python version (by reading ./.python-version) and CNApy dependencies (by reading ./pyproject.toml).
-
-Any contribution intentionally submitted for inclusion in the work by you, shall be licensed under the terms of the Apache 2.0 license without any additional terms or conditions.
+uv will automatically install the correct Python version (by reading ./.python-version) and CNApy dependencies (by reading ./pyproject.toml). If you get a Java/JDK/JVM/jpype error when running CNApy, consider installing OpenJDK [[Site]](https://openjdk.org/install/) on your system to fix this problem.
 
 ## How to cite CNApy