fix pypi link

openCONTRABASS · Nov 15, 2021 · 1c4bb6f · 1c4bb6f
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diff --git a/README.md b/README.md
@@ -1,7 +1,8 @@
-[![PyPI version](https://badge.fury.io/py/findCPcli.svg)](https://badge.fury.io/py/findCPcli) 
+[![PyPI version](https://badge.fury.io/py/contrabass.svg)](https://badge.fury.io/py/contrabass) 
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) 
-[![CI-CD](https://github.com/openCONTRABASS/CONTRABASS/actions/workflows/main.yml/badge.svg)](https://github.com/findCP/findCPcli/actions/workflows/main.yml) 
-[![Quality Gate Status](https://sonarcloud.io/api/project_badges/measure?project=openCONTRABASS_CONTRABASS&metric=alert_status)](https://sonarcloud.io/dashboard?id=findCP_findCPcli) 
+[![CI-CD](https://github.com/openCONTRABASS/CONTRABASS/actions/workflows/main.yml/badge.svg)](https://github.com/openCONTRABASS/CONTRABASS/actions/workflows/main.yml)
+[![codecov](https://codecov.io/gh/openCONTRABASS/CONTRABASS/branch/main/graph/badge.svg?token=C9F6FT0PAV)](https://codecov.io/gh/openCONTRABASS/CONTRABASS)
+[![Quality Gate Status](https://sonarcloud.io/api/project_badges/measure?project=openCONTRABASS_CONTRABASS&metric=alert_status)](https://sonarcloud.io/summary/new_code?id=openCONTRABASS_CONTRABASS) 
 [![standard-readme compliant](https://img.shields.io/badge/readme%20style-standard-brightgreen.svg)](https://github.com/RichardLitt/standard-readme) 
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) 
 [![Documentation Status](https://readthedocs.org/projects/contrabass/badge/?version=latest)](https://contrabass.readthedocs.io/en/latest/?badge=latest) 
@@ -51,21 +52,21 @@ Oarga et al. **Growth Dependent Computation of Chokepoints in Metabolic Networks
 ## Install
 ```CONTRABASS``` can be installed via **pip** package manager:
 ```shell
-$ pip install contrabass
+  $ pip install contrabass
 ```
 
 ## Quickstart
 
 Generate report on vulnerabilities on input model ```MODEL.xml```
 
 ```shell
-$ contrabass report critial-reactions MODEL.xml
+  $ contrabass report critial-reactions MODEL.xml
 ```
 
 Generate report on growth-dependent reactions on input model ```MODEL.xml```
 
 ```shell
-$ contrabass report growth-dependent-reactions MODEL.xml
+  $ contrabass report growth-dependent-reactions MODEL.xml
 ```
 
 ## Documentation
@@ -79,18 +80,19 @@ More information about the parameters of the tool can be obtained by executing `
 For a detailed description of the operations see the [documentation](https://contrabass.readthedocs.io/en/latest/). 
 
 ```shell
-$ contrabass
-Usage: contrabass [OPTIONS] COMMAND [ARGS]...
-
-  Compute vulnerabilities on constraint-based models
-
-Options:
-  -h, --help     Show this message and exit.
-  -V, --version  Show the version and exit.
-
-Commands:
-  new-model  Export refined constraint-based model.
-  report     Compute vulnerabilities on constraint-based models.
+  $ contrabass
+
+    Usage: contrabass [OPTIONS] COMMAND [ARGS]...
+
+      Compute vulnerabilities on constraint-based models
+
+    Options:
+      -h, --help     Show this message and exit.
+      -V, --version  Show the version and exit.
+
+    Commands:
+      new-model  Export refined constraint-based model.
+      report     Compute vulnerabilities on constraint-based models.
 ```
 
 ## Low Level API

diff --git a/setup.cfg b/setup.cfg
@@ -1,7 +1,7 @@
 [metadata]
 name = contrabass
 url = https://github.com/openCONTRABASS/CONTRABASS
-version = 0.1.0a1
+version = 0.0.1a
 author = Alex Oarga
 author_email = [email protected]
 description = Constraint-based model vulnerabilities analysis

diff --git a/sonar-project.properties b/sonar-project.properties
@@ -12,7 +12,7 @@ sonar.organization=opencontrabass
 #sonar.sourceEncoding=UTF-8
 
 # Excluding files
-sonar.exclusions=test/*.xml, test/data/*, test/*, docs/*, src/contrabass/core/templates/*
+sonar.exclusions=test/*.xml, test/data/*, test/*, docs/*, src/contrabass/core/templates/*, docs/source/*
 
 # Include source file
 # sonar.inclusions=src/
diff --git a/src/contrabass/cli/commands.py b/src/contrabass/cli/commands.py
@@ -66,7 +66,6 @@ def new_model():
 @click.option(
     "--verbose",
     "-v",
-    type=bool,
     help="Print feedback while running.",
 )
 @click.option(
@@ -99,13 +98,15 @@ def new_model():
     help="Fraction of optimum growth to be used in Flux Variability Analysis. Value must be between 0.0 and 1.0",
 )
 def critical_reactions(
-    model, output_spreadsheet, output_html_report, verbose, objective, fraction
+        model, output_spreadsheet, output_html_report, verbose, objective, fraction
 ):
     # Default values
     if fraction is None:
         fraction = 1.0
     fraction = validate_number(fraction)
 
+    verbose = False if verbose is None else True
+
     validate_input_model(model)
     validate_output_spread(output_spreadsheet)
     validate_output_html_path(output_html_report)
@@ -132,7 +133,6 @@ def critical_reactions(
 @click.option(
     "--verbose",
     "-v",
-    type=bool,
     help="Print feedback while running.",
 )
 @click.option(
@@ -158,12 +158,14 @@ def critical_reactions(
     help="Output spreadsheet file with results. Allowed file formats: '.html'. Default value: output.html",
 )
 def growth_dependent_reactions(
-    model,
-    output_spreadsheet,
-    output_html_report,
-    verbose,
-    objective,
+        model,
+        output_spreadsheet,
+        output_html_report,
+        verbose,
+        objective,
 ):
+    verbose = False if verbose is None else True
+
     validate_input_model(model)
     validate_output_spread(output_spreadsheet)
     validate_output_html_path(output_html_report)
@@ -182,7 +184,6 @@ def growth_dependent_reactions(
 @click.option(
     "--verbose",
     "-v",
-    type=bool,
     help="Print feedback while running.",
 )
 @click.option(
@@ -205,19 +206,21 @@ def growth_dependent_reactions(
     default=DEFAULT_MODEL_FILE,
     metavar="OUTPUT-MODEL",
     help="Output model file. Allowed file formats: '.xml' '.json' '.yml'. Default value: "
-    + DEFAULT_MODEL_FILE,
+         + DEFAULT_MODEL_FILE,
 )
 def fva_constrained(
-    model,
-    verbose,
-    objective,
-    fraction,
-    output_model,
+        model,
+        verbose,
+        objective,
+        fraction,
+        output_model,
 ):
     """
     Export a new model with its (maximum and minimum )flux bounds replaced with the
     constrained flux values obtained with Flux Variability Analysis.
     """
+    verbose = False if verbose is None else True
+
     validate_input_model(model)
     validate_output_model(output_model)
 
@@ -235,7 +238,6 @@ def fva_constrained(
 @click.option(
     "--verbose",
     "-v",
-    type=bool,
     help="Print feedback while running.",
 )
 @click.option(
@@ -258,20 +260,22 @@ def fva_constrained(
     default=DEFAULT_MODEL_FILE,
     metavar="OUTPUT-MODEL",
     help="Output model file. Allowed file formats: '.xml' '.json' '.yml'. Default value: "
-    + DEFAULT_MODEL_FILE,
+         + DEFAULT_MODEL_FILE,
 )
 def without_dem(
-    model,
-    verbose,
-    objective,
-    fraction,
-    output_model,
+        model,
+        verbose,
+        objective,
+        fraction,
+        output_model,
 ):
     """
     Export a new model where Dead-End Metabolites have been removed.
     Dead-End Metabolites are removed iteratively, this is, if a reactions remains
     without metabolites it is also removed from the model.
     """
+    verbose = False if verbose is None else True
+
     validate_input_model(model)
     validate_output_model(output_model)
 
@@ -289,7 +293,6 @@ def without_dem(
 @click.option(
     "--verbose",
     "-v",
-    type=bool,
     help="Print feedback while running.",
 )
 @click.option(
@@ -312,20 +315,22 @@ def without_dem(
     default=DEFAULT_MODEL_FILE,
     metavar="OUTPUT-MODEL",
     help="Output model file. Allowed file formats: '.xml' '.json' '.yml'. Default value: "
-    + DEFAULT_MODEL_FILE,
+         + DEFAULT_MODEL_FILE,
 )
 def fva_constrained_without_dem(
-    model,
-    verbose,
-    objective,
-    fraction,
-    output_model,
+        model,
+        verbose,
+        objective,
+        fraction,
+        output_model,
 ):
     """
     Export a new model with its (maximum and minimum) flux bounds replaced with the
     constrained flux values obtained with Flux Variability Analysis.
     In addition, Dead-End Metabolites are removed iteratively after the flux update.
     """
+    verbose = False if verbose is None else True
+
     validate_input_model(model)
     validate_output_model(output_model)
 
@@ -343,13 +348,13 @@ def license():
 
 
 def run(
-    task,
-    model_path,
-    output_path,  # output spreadsheet report file or in case of new model, the output model path
-    output_path_html,
-    verbose,
-    objective=None,
-    fraction=1.0,
+        task,
+        model_path,
+        output_path,  # output spreadsheet report file or in case of new model, the output model path
+        output_path_html,
+        verbose,
+        objective=None,
+        fraction=1.0,
 ):
     try:
         if task == TASK_CRITICAL_REACTIONS: