doc: update shinx files and readme

.gitignore

@@ -9,4 +9,5 @@ node_modules
 .coverage*
 .vscode
 _exclude
-/docsource/_build/
+/docsource/_build/
+/docsource/_autosummary

README.md

@@ -30,7 +30,7 @@ pytest -v
 ```
 
 ## CI/CD
-For further tests and development tools, a CI toolkit is provided in `ci` folder (see [ci/README.md](ci/README.md)).
+For further tests and development tools, a CI toolkit is provided in `ci` folder (see [ci/README.md](./ci/README.md)).
 
 ## For developers
 

docsource/conf.py

@@ -61,7 +61,7 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = 'alabaster'
 
 # 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,

docsource/index.rst

@@ -10,8 +10,14 @@ Welcome to rpTools's documentation!
    :hidden:
 
    Home <self>
-   Readme <readme_shortcut>
+   rpTools <readme_shortcut>
+   rpCompletion <readme_rpcompletion_shortcut>
+   rpFBA <readme_rpfba_shortcut>
+   rpThermo <readme_rpthermo_shortcut>
+   rpExtractsink <readme_rpextractsink_shortcut>
+   rpLibs <readme_rplibs_shortcut>
+   rpReport <readme_rpreport_shortcut>
    API reference <_autosummary/rptools>
+   Release <release_shortcut>
 
-This is an example of Sphinx documentation. Use the left column to navigate.
-
+This is an example of Sphinx documentation. Use the left column to navigate.

rptools/rpcompletion/README.md

@@ -71,7 +71,7 @@ cd tests
 pytest -v
 ```
 
-# CI/CD
+## CI/CD
 For further tests and development tools, a CI toolkit is provided in `ci` folder (see [ci/README.md](ci/README.md)).
 
 ## Authors

rptools/rpcompletion/rpCompletion.py

@@ -40,27 +40,27 @@ def rp_completion(
     max_subpaths_filter: int = 10,
     logger: Logger = getLogger(__name__)
 ) -> List[rpPathway]:
-    """Process to the completion of metabolic pathways
+    """Process to the completion of metabolic pathways 
     generated by RetroPath2.0 and rp2paths.
 
-    (1) rp2paths generates a sets of master pathways
-        which each of them is a set of chemical transformations.
-
-    (2) Each chemical transformation refers to one or
-        multiple reaction rule.
-
-    (3) Each reaction rule comes from one or multiple
-        template (original) chemical reaction
+    (1) rp2paths generates a sets of master pathways which 
+    each of them is a set of chemical transformations.
 
-    The completion consists in:
+    (2) Each chemical transformation refers to one or 
+    multiple reaction rule.
 
-    1. exploring all possible metabolic pathways through
-       steps (2) and (3)
+    (3) Each reaction rule comes from one or multiple 
+    template (original) chemical reaction
 
-    2. putting back chemical species removed during reaction
-       rules building process
+    The completion consists in:
+
+    1. exploring all possible metabolic pathways through 
+    steps (2) and (3)
 
-    The completion is done for all master pathways of step (1)
+    2. putting back chemical species removed during reaction 
+    rules building process
+
+    The completion is done for all master pathways of step (1).
 
     Parameters
     ----------

rptools/rpextractsink/README.md

@@ -59,7 +59,7 @@ cd tests
 pytest -v
 ```
 
-# CI/CD
+## CI/CD
 For further tests and development tools, a CI toolkit is provided in `ci` folder (see [ci/README.md](ci/README.md)).
 
 ## Authors

rptools/rpfba/README.md

@@ -78,7 +78,7 @@ cd tests
 pytest -v
 ```
 
-# CI/CD
+## CI/CD
 For further tests and development tools, a CI toolkit is provided in `ci` folder (see [ci/README.md](ci/README.md)).
 
 

rptools/rpranker/README.md

@@ -65,7 +65,7 @@ cd tests
 pytest -v
 ```
 
-# CI/CD
+## CI/CD
 For further tests and development tools, a CI toolkit is provided in `ci` folder (see [ci/README.md](ci/README.md)).
 
 

rptools/rpreport/README.md

@@ -1,8 +1,7 @@
 # rpreport
-
-generates HTML pages to explore the main characteristics (thermodynamics,
+Generates HTML pages to explore the main characteristics (thermodynamics,
 fluxes, number of metabolic steps, reaction rule score) of pathways predicted
-with RetroPath suite.
+with RetroPath suite
 
 ## Install
 rpreport is part of rpTools suite. See its README.
@@ -24,4 +23,3 @@ optional arguments:
 * **--dev**: For dev purpose only : create supplementary files into a dev folder
 * **-v, --verbose**: Turn on console verbose mode.
 * **--standalone**: if set will output an autonomous HTML containing all css and js files dependencies.
-

rptools/rpscore/README.md

@@ -50,7 +50,7 @@ cd tests
 pytest -v
 ```
 
-# CI/CD
+## CI/CD
 For further tests and development tools, a CI toolkit is provided in `ci` folder (see [ci/README.md](ci/README.md)).
 
 ## Authors

rptools/rpthermo/README.md

@@ -4,7 +4,7 @@ Calculate the formation energy of chemical species and the Gibbs free energy for
 
 For each species, the challenge is to find the corresponding compound in the eQuilibrator cache. To find the good compound, one tries to exact match species ID, InChIKey, InChI or SMILES and stops with the first hit. Then, if no compound has been found, in the last resort, the first part of species InChIKey is looked for within the cache. If the result (a list) is not empty, the first compound is taken.
 
-Because we are interested in the thermodynamics of the pathway when the production of the target is optimized, we have modified coefficients of each reaction. We used a linear system solver (from [SciPy](www.scipy.org)) by giving the reaction that produces the target as objective and elimination of intermediate species as constraints.
+Because we are interested in the thermodynamics of the pathway when the production of the target is optimized, we have modified coefficients of each reaction. We used a linear system solver (from [SciPy](https://www.scipy.org)) by giving the reaction that produces the target as objective and elimination of intermediate species as constraints.
 
 ## Input
 
@@ -58,7 +58,7 @@ cd tests
 pytest -v
 ```
 
-# CI/CD
+## CI/CD
 For further tests and development tools, a CI toolkit is provided in `ci` folder (see [ci/README.md](ci/README.md)).