docs + cmd #118 #120

dev/gapfill-testing.ipynb

@@ -1295,7 +1295,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.13"
+   "version": "3.10.14"
   }
  },
  "nbformat": 4,

docs/source/cmd_desc.rst

@@ -24,9 +24,15 @@ General Options
 - ``--help``: Call the help page of the command.
 - ``--version``: Show the version  and exit.
 
+----
+
+
 refinegems analyse 
 ------------------
 
+Analyse a model by testing for auxotrophies and growth on different media along 
+with finding EGCs and looking at overall model statistics. 
+
 .. code:: bash 
     
     refinegems analyse compare [MODELPATH]
@@ -85,6 +91,8 @@ Options:
 refinegems analyse growth 
 ^^^^^^^^^^^^^^^^^^^^^^^^^
 
+Analyse the growth under different conditions.
+
 .. code:: bash 
   
   refinegems analyse growth auxothrophies [MODELPATH]
@@ -142,36 +150,17 @@ Options:
 - ``--colors/-c`` : Abbreviation of a matplotlib color palette for the graphics.
 - ``--dir/-d`` : Path to the output directory. 
 
-refinegems gaps
----------------
-
-.. code:: bash 
-  
-  refinegems gaps find [MODELPATH] [GFF_FILE] [ORGANISMID] [GAPFILL_PARAMS] [FILENAME]
-
-Find gaps in a model based on the genes/gene products of the underlying organism.
-
-.. code:: bash 
-  
-  refinegems gaps fill [MODEL] [GAP_ANALYSIS_RESULTS]
-
-Fill the gaps in a model based on a user-provided input file.
-
-.. code:: bash 
-  
-  refinegems gaps autofill [MODELPATH] [GAFILL_PARAMS] [FILENAME]
-
-Automatically find and fill the gaps based on the genes/gene products.
-
 
 refinegems database
 -------------------
 
+Access, curate, etc. the in-build database.
+
 .. code:: bash  
   
   refinegems database initialise
 
-Initialse or update the in-build database.
+Initialise or update the in-build database.
 
 .. code:: bash 
 
@@ -190,9 +179,33 @@ Options:
 Reset the database by removing all additionally added tables (added with e.g. add_namespace)
 
 
+refinegems gaps
+---------------
+
+.. code:: bash 
+  
+  refinegems gaps find [MODELPATH] [GFF_FILE] [ORGANISMID] [GAPFILL_PARAMS] [FILENAME]
+
+Find gaps in a model based on the genes/gene products of the underlying organism.
+
+.. code:: bash 
+  
+  refinegems gaps fill [MODEL] [GAP_ANALYSIS_RESULTS]
+
+Fill the gaps in a model based on a user-provided input file.
+
+.. code:: bash 
+  
+  refinegems gaps autofill [MODELPATH] [GAFILL_PARAMS] [FILENAME]
+
+Automatically find and fill the gaps based on the genes/gene products.
+
+
 refinegems media
 ----------------
 
+Access the media part of the database.
+
 .. code:: bash 
   
   refinegems media info
@@ -222,6 +235,9 @@ Options:
 refinegems refine
 -----------------
 
+Refine a model. Includes steps like biomass, charges, SBO annotation, reaction direction correction and addition 
+of Pathways and further gene product annotations.
+
 .. code:: bash 
   
   refinegems refine biomass [MODELPATH]
@@ -248,7 +264,7 @@ Options:
   
   refinegems refine direction [MODELPATH]
 
-Check and - if neccessary - correct the direction of th reactions in a model.
+Check and - if neccessary - correct the direction of the reactions in a model.
 
 .. code:: bash 
   
@@ -268,6 +284,8 @@ Options:
 refinegems refine annot
 ^^^^^^^^^^^^^^^^^^^^^^^
 
+Add annotations to your model.
+
 .. code:: bash 
   
   refinegems refine annot sboterms [MODELPATH]
@@ -284,6 +302,8 @@ Add the KEGG pathways as group entities to the model.
 refinegems setup 
 ----------------
 
+Set-up tools, folder structure and more for running the program.
+
 .. code:: bash
 
   refinegems setup config 

docs/source/development.rst

@@ -138,6 +138,16 @@ Debugging switches
 - You can enable debug logging by replacing ``level=logging.INFO``  with ``level=logging.DEBUG``.
 - If you want your print message to show in the log file, replace the ```print()`` statement by ``logging.info()``.
 - For debugging of pandas warnings or issues ``pd.options.mode.chained_assignment = None`` needs to be commented out.
+- | Additionally, some modules contain comment blocks of the following format:
+
+.. code-block:: python
+    :class: copyable
+
+    # @DEBUG ...............
+    # some code
+    # ......................
+
+| By enabling the code lines between the dotted lines, a debugging-mode is run, which e.g. subsets the data to shorten the runtime to make debugging faster.
 
 Guidelines for code documentation
 ---------------------------------

docs/source/installation.rst

@@ -20,3 +20,7 @@ To install refineGEMs as Python package from `PyPI <https://pypi.org/project/ref
    pip install refineGEMs
 
 The corresponding project site can be found `here <https://pypi.org/project/refineGEMs/>`__.
+
+.. hint:: 
+
+   For the installation for developers, refer to :ref:`installation for developers`