[UPDATE] README.md and diel_models_docs.md files that now includes de…

…velopment/contributing instructions, pip from github option, mention to the examples scripts and how to export the final xml diel model + [UPDATE] package version 1.2.2 to 1.2.3

README.md

@@ -23,17 +23,36 @@ With this in mind, this package aims to accelerate this process by being able to
 ### Table of contents:
 
 - [Installation](#installation)
-    - [Pip](#pip)
-- [Getting Started](#getting-started)
+    - [Using pip from PyPi](#using-pip-from-pypi)
+    - [Using pip directly from GitHub](#using-pip-directly-from-github)
+- [Development (or Contributing)](#development-or-contributing)
+- [Using the tool](#using-the-tool)
 - [Expanding the pipeline](#expanding-the-pipeline)
 - [Where to find the publication results](#where-to-find-the-publication-results)
 
 ## Installation
-### Pip
+### Using pip from PyPi
 
-``` pip install diel_models==1.2.2 ```
+``` pip install diel_models==1.2.3 ```
 
-## Getting Started
+### Using pip directly from GitHub
+
+``` pip install git+https://github.com/BioSystemsUM/diel_models.git ```
+
+## Development (or Contributing)
+
+Cloning the repository and setting the conda environment:
+
+```
+git clone https://github.com/BioSystemsUM/diel_models.git
+conda create -n dielmodels
+conda activate dielmodels
+
+pip install -r requirements.txt
+pip install -e .
+```
+
+## Using the tool
 Using this package, you can handle generic or multi-tissue models by:
 
 * Assigning day and night;
@@ -44,7 +63,11 @@ Using this package, you can handle generic or multi-tissue models by:
 
 If each method is to be applied individually it is essential that the first 3 steps are applied in that order specifically.
 
-**Alternatively, it is possible to apply all methods to a given model, running the entire pipeline (where the arguments are all relative to the original model), as shown below:**
+**Alternatively, you can apply all methods to a given model by running the entire pipeline, with all arguments relative to the original model**
+
+This approach has been applied to multiple models, as demonstrated in the [Examples](examples) folder, both generic (e.g. [_Athaliana13_](examples/Athaliana_cheung13.py)) and multi-tissue (e.g. [_MultiQuercus_](examples/MultiQuercus.py)).
+
+Briefly, the pipeline is applied as follows:
 
 - Generic model:
 
@@ -57,6 +80,8 @@ model = cobra.io.read_sbml_model('.../.../desired_single_tissue_model.xml')
 storage_pool_metabolites = ['Metabolite_ID_1', 'Metabolite_ID_2', 'Metabolite_ID_3']
 
 diel_models_creator(model, storage_pool_metabolites, ['Photon_Reaction_ID'], ['Nitrate_Reaction_ID'], 'Biomass_Reaction_ID')
+
+cobra.io.write_sbml_model(model, desired_path)
 ```
 
 where the nitrate uptake ratio is 3:2, since _day_ratio_value_ is 3 and _night_ratio_value_ is 2.
@@ -72,6 +97,7 @@ model = cobra.io.read_sbml_model('.../.../desired_single_tissue_model.xml')
 storage_pool_metabolites = ['Metabolite_ID_1', 'Metabolite_ID_2', 'Metabolite_ID_3']
 
 diel_models_creator(model, storage_pool_metabolites, ['Photon_Reaction_ID'], ['Nitrate_Reaction_ID'], 'Biomass_Reaction_ID', day_ratio_value=desired_value_1, night_ratio_value=desired_value_2)
+cobra.io.write_sbml_model(model, desired_path)
 ```
 
 - Multi-tissue model:
@@ -87,6 +113,7 @@ storage_pool_metabolites = ['Metabolite_ID_1', 'Metabolite_ID_2', 'Metabolite_ID
 tissues = ['Tissue_ID_1', 'Tissue_ID_2']
 
 diel_models_creator(model, storage_pool_metabolites, ['Photon_Reaction_ID'], ['Nitrate_Reaction_ID'], 'Biomass_Reaction_ID', tissues)
+cobra.io.write_sbml_model(model, desired_path)
 ```
 
 where the nitrate uptake ratio is 3:2, but it's also possible to adjust this ratio to different values.

docs/conf.py

@@ -10,9 +10,9 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
 project = 'diel_models'
-copyright = '2023, Luciana Martins and João Capela'
+copyright = '2024, Luciana Martins and João Capela'
 author = 'Luciana Martins and João Capela'
-release = 'v1.2.2'
+release = 'v1.2.3'
 
 sys.path.insert(0, os.path.abspath('../src/'))
 

docs/diel_models_docs.md

@@ -13,18 +13,45 @@ Python 3.12
 ```
 
 ### Description
-*diel_models* is a python package generated from this project and has its own [ReadtheDocs](https://dielmodels.readthedocs.io/) file.
 
 Despite numerous successful studies, modeling plant metabolism remains challenging for several reasons, such as limited information, incomplete annotations, and dynamic changes in plant metabolism that occur under different conditions, including night and day.
 In particular, the integration of these day-night cycles (diel cycles) is complex, laborious, and time-consuming.
 
-With this in mind, this package aims to accelerate this process by being able to transform a non-diel model into a diel model.
+With this in mind, *diel_models* was created to accelerate this process by being able to transform a non-diel model into a diel model.
+
+### Table of contents:
+
+- [Installation](#installation)
+    - [Using pip from PyPi](#using-pip-from-pypi)
+    - [Using pip directly from GitHub](#using-pip-directly-from-github)
+- [Development (or Contributing)](#development-or-contributing)
+- [Using the tool](#using-the-tool)
+- [Expanding the pipeline](#expanding-the-pipeline)
+- [Where to find the publication results](#where-to-find-the-publication-results)
 
 ## Installation
+### Using pip from PyPi
+
+``` pip install diel_models==1.2.3 ```
+
+### Using pip directly from GitHub
 
-``` pip install diel_models==1.2.2 ```
+``` pip install git+https://github.com/BioSystemsUM/diel_models.git ```
 
-## Getting Started
+## Development (or Contributing)
+
+Cloning the repository and setting the conda environment:
+
+```
+git clone https://github.com/BioSystemsUM/diel_models.git
+conda create -n dielmodels
+conda activate dielmodels
+
+pip install -r requirements.txt
+pip install -e .
+```
+
+## Using the tool
 Using this package, you can handle generic or multi-tissue models by:
 
 * Assigning day and night;
@@ -35,7 +62,11 @@ Using this package, you can handle generic or multi-tissue models by:
 
 If each method is to be applied individually it is essential that the first 3 steps are applied in that order specifically.
 
-**Alternatively, it is possible to apply all methods to a given model, running the entire pipeline (where the arguments are all relative to the original model), as shown below:**
+**Alternatively, you can apply all methods to a given model by running the entire pipeline, with all arguments relative to the original model**
+
+This approach has been applied to multiple models, as demonstrated in the [Examples](examples) folder, both generic (e.g. [_Athaliana13_](examples/Athaliana_cheung13.py)) and multi-tissue (e.g. [_MultiQuercus_](examples/MultiQuercus.py)).
+
+Briefly, the pipeline is applied as follows:
 
 - Generic model:
 
@@ -48,6 +79,8 @@ model = cobra.io.read_sbml_model('.../.../desired_single_tissue_model.xml')
 storage_pool_metabolites = ['Metabolite_ID_1', 'Metabolite_ID_2', 'Metabolite_ID_3']
 
 diel_models_creator(model, storage_pool_metabolites, ['Photon_Reaction_ID'], ['Nitrate_Reaction_ID'], 'Biomass_Reaction_ID')
+
+cobra.io.write_sbml_model(model, desired_path)
 ```
 
 where the nitrate uptake ratio is 3:2, since _day_ratio_value_ is 3 and _night_ratio_value_ is 2.
@@ -63,6 +96,7 @@ model = cobra.io.read_sbml_model('.../.../desired_single_tissue_model.xml')
 storage_pool_metabolites = ['Metabolite_ID_1', 'Metabolite_ID_2', 'Metabolite_ID_3']
 
 diel_models_creator(model, storage_pool_metabolites, ['Photon_Reaction_ID'], ['Nitrate_Reaction_ID'], 'Biomass_Reaction_ID', day_ratio_value=desired_value_1, night_ratio_value=desired_value_2)
+cobra.io.write_sbml_model(model, desired_path)
 ```
 
 - Multi-tissue model:
@@ -78,6 +112,7 @@ storage_pool_metabolites = ['Metabolite_ID_1', 'Metabolite_ID_2', 'Metabolite_ID
 tissues = ['Tissue_ID_1', 'Tissue_ID_2']
 
 diel_models_creator(model, storage_pool_metabolites, ['Photon_Reaction_ID'], ['Nitrate_Reaction_ID'], 'Biomass_Reaction_ID', tissues)
+cobra.io.write_sbml_model(model, desired_path)
 ```
 
 where the nitrate uptake ratio is 3:2, but it's also possible to adjust this ratio to different values.

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = diel_models
-version = 1.2.2
+version = 1.2.3
 description = diel_models:
 long_description = file: README.md
 long_description_content_type = text/markdown