From 3fa2b5319aece0d8bd313fa778f55e82a8e6ec04 Mon Sep 17 00:00:00 2001
From: Thomas Cokelaer <cokelaer@gmail.com>
Date: Tue, 12 Apr 2022 21:28:03 +0200
Subject: [PATCH] fix missing requirements

---
 README.rst          | 3 +--
 biosniff/sniffer.py | 8 ++++----
 requirements.txt    | 1 +
 setup.py            | 2 +-
 4 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/README.rst b/README.rst
index 005da26..90d59eb 100644
--- a/README.rst
+++ b/README.rst
@@ -8,8 +8,6 @@ BioSniff
 .. image:: https://github.com/cokelaer/biosniff/actions/workflows/main.yml/badge.svg?branch=main
     :target: https://github.com/cokelaer/biosniff/actions/workflows/main.yml
 
-
-    
 .. image:: https://coveralls.io/repos/github/cokelaer/biosniff/badge.svg?branch=main
     :target: https://coveralls.io/github/cokelaer/biosniff?branch=main
 
@@ -53,6 +51,7 @@ Changelog
 ========= ====================================================================
 Version   Description
 ========= ====================================================================
+0.4.0     * additional test and fix missing click requirements
 0.3.0     * add missing MANIFEST and applied black
 0.2.0     * more tests (80% coverage) and some simplifications
 0.1.0     * first commit
diff --git a/biosniff/sniffer.py b/biosniff/sniffer.py
index e4ce5f1..54127e6 100644
--- a/biosniff/sniffer.py
+++ b/biosniff/sniffer.py
@@ -98,7 +98,7 @@ def sniff(self, filename):
             return None
         elif len(candidates) == 1:
             return candidates[0]
-        else:
+        else: #pragma: no cover
             _log.warning("Sniffer found several candidates: {}".format(candidates))
 
             return candidates
@@ -137,7 +137,7 @@ def is_abi(self, filename):
             buff = data.read(4)
             if buff[0:4].decode() == "ABIF":
                 return True
-        except:
+        except: #pragma: no cover
             return False
 
     def is_bam(self, filename):
@@ -154,14 +154,14 @@ def is_bai(self, filename):
                 return True
             else:
                 return False
-        except:
+        except: #pragma: no cover
             return False
 
     def is_bcf(self, filename):
         try:
             d = pysam.VariantFile(filename)
             return d.is_bcf
-        except:
+        except: #pragma: no cover
             return False
 
     def is_binary_bed(self, filename):
diff --git a/requirements.txt b/requirements.txt
index 908732a..9618540 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,3 +1,4 @@
+click
 pysam
 pandas
 pyyaml
diff --git a/setup.py b/setup.py
index 8435a01..5d1c554 100755
--- a/setup.py
+++ b/setup.py
@@ -3,7 +3,7 @@
 from setuptools import setup, find_packages
 
 _MAJOR = 0
-_MINOR = 3
+_MINOR = 4
 _MICRO = 0
 version = '%d.%d.%d' % (_MAJOR, _MINOR, _MICRO)
 release = '%d.%d' % (_MAJOR, _MINOR)