implement --registered and --stats options

.github/workflows/main.yml

@@ -19,7 +19,7 @@ jobs:
     strategy:
       max-parallel: 5
       matrix:
-        python: [3.8, 3.9, '3.10']
+        python: [3.8, 3.9, '3.10', '3.11']
       fail-fast: false
 
     steps:

README.rst

@@ -9,20 +9,15 @@ Versionix
 .. image:: https://github.com/sequana/versionix/actions/workflows/main.yml/badge.svg
    :target: https://github.com/sequana/versionix/actions/workflows/main.yml
 
-.. image:: https://coveralls.io/repos/github/sequana/versionix/badge.svg?branch=master
-    :target: https://coveralls.io/github/sequana/versionix?branch=master
-
-.. image:: http://readthedocs.org/projects/versionix/badge/?version=latest
-    :target: http://versionix.readthedocs.org/en/latest/?badge=latest
-    :alt: Documentation Status
+.. image:: https://coveralls.io/repos/github/sequana/versionix/badge.svg?branch=main
+    :target: https://coveralls.io/github/sequana/versionix?branch=main
 
 .. image:: https://zenodo.org/badge/658721856.svg
    :target: https://zenodo.org/badge/latestdoi/658721856
 
-:Python version: Python 3.8, 3.9, 3.10
+:Python version: Python 3.8, 3.9, 3.10, 3.11
 :Source: See  `http://github.com/sequana/versionix <https://github.com/sequana/versionix/>`__.
 :Issues: Please fill a report on `github <https://github.com/sequana/versionix/issues>`__
-:Platform: This is currently only available for Linux distribution with bash shell (contributions are welcome to port the tool on MacOSX and other platforms)
 
 Overview
 ========
@@ -36,12 +31,16 @@ If you are in a hurry, just type::
 
     pip install versionix  --upgrade
 
-This is pure Python so no need for fancy libraries of fancy environment.
+This is pure Python so no need for fancy libraries.
 
 Then, just type e.g::
 
     versionix  fastqc
 
+This tool uses a registry so it will work only with resgistered tools, which list can be obtained with::
+
+    versionix --registered
+
 DESCRIPTION
 ===========
 

test/test_parser.py

@@ -71,6 +71,9 @@ def test_script(fp, mocker):
     result = runner.invoke(main, ["bedtools"])
     print(result)
 
+    runner.invoke(main, ["--registered"])
+    runner.invoke(main, ["--stats"])
+    runner.invoke(main, )
 
 def test_bedtools_error(fp, mocker):
     # registered tool but if not installed, should raise a SystemExit error

versionix/scripts.py

@@ -21,6 +21,7 @@
 ###########################################################################
 """.. rubric:: Standalone application dedicated to Damona"""
 import click
+import sys
 
 
 from versionix import version
@@ -33,12 +34,32 @@
 
 
 @click.command()
-@click.argument("standalone", required=True, type=click.STRING)
+@click.argument("standalone", required=False, type=click.STRING, default=None)
 @click.version_option(version)
+@click.option("--stats", is_flag=True, help="Prints number of registered tools")
+@click.option("--registered", is_flag=True, help="Prints the list of registered tools")
 def main(**kwargs):
     """Versionix returns the version of installed software.
 
-    versionix fastqc
+        versionix fastqc
+
+    You can check the list of registered tools as follows
+
+        versionix --registered
+
 
     """
-    print(get_version(kwargs["standalone"]))
+    if kwargs["stats"]:
+        from versionix.registry import metadata
+        click.echo(f"There are currently {len(metadata.keys())} registered tools in Versionix") 
+    elif kwargs["registered"]:
+        from versionix.registry import metadata
+        names = sorted(metadata.keys())
+        for name in names:
+            click.echo(f"{name}") 
+    else:
+        if kwargs["standalone"] is None:
+            click.echo("No standalone was provided. You must provide one. You can use --registered to see the current list'")
+            sys.exit(1)
+        else:
+            click.echo(get_version(kwargs["standalone"]))