From 318321a2cfd8ff33b51983b7f65cb3c20967d6c2 Mon Sep 17 00:00:00 2001
From: asetGem <amandine.perrin@pasteur.fr>
Date: Mon, 2 Aug 2021 10:20:35 +0200
Subject: [PATCH] get report of unit tests coverage
---
.gitlab-ci.yml | 2 ++
PanACoTA/utils_argparse.py | 7 +++++--
test/test_unit/test_utils-argparse.py | 16 ++++++++++++++++
3 files changed, 23 insertions(+), 2 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 0656bb11..3d226bd6 100755
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -143,6 +143,8 @@ coverage:
- pip3 install -r requirements-dev.txt
script:
- pwd
+ - mv .coverage.unit .coverage
+ - coverage report
- coverage combine .coverage.unit .coverage.functional
- coverage report -i
- coverage html -i
diff --git a/PanACoTA/utils_argparse.py b/PanACoTA/utils_argparse.py
index f55c8b8b..e890ecda 100644
--- a/PanACoTA/utils_argparse.py
+++ b/PanACoTA/utils_argparse.py
@@ -200,6 +200,8 @@ class Conf_all_parser(configparser.ConfigParser):
path to configuration file
readsec : list
list of sections of the config file to read
+ clean_str : boolean
+ by default, remove " surrounding strings. If no need to do it, set this parameter to False
Attributes
----------
@@ -209,7 +211,7 @@ class Conf_all_parser(configparser.ConfigParser):
{section1: {param: value}, {section2: {param:value}}}
"""
- def __init__(self, conffile, readsec=[]):
+ def __init__(self, conffile, readsec=[], clean_str=True):
super().__init__()
# If there is a config file specified, but it does not exist -> exit with error message
if conffile != "" and not os.path.isfile(conffile):
@@ -229,7 +231,8 @@ class Conf_all_parser(configparser.ConfigParser):
# If not, create empty section, and associate with empty dict
if sec in dict(self):
self.sec_dicts[sec] = dict(self[sec])
- self.clean_strings(sec)
+ if clean_str:
+ self.clean_strings(sec)
else:
self.sec_dicts[sec] = {}
self.add_section(sec)
diff --git a/test/test_unit/test_utils-argparse.py b/test/test_unit/test_utils-argparse.py
index 29152dcb..8fd6e349 100644
--- a/test/test_unit/test_utils-argparse.py
+++ b/test/test_unit/test_utils-argparse.py
@@ -271,6 +271,22 @@ def test_conf_parser_init():
"sec4": {}} # But sec4 dict is empty (no param given in configfile)
+def test_conf_parser_clean_str(capsys):
+ """
+ Check that surounding "" are removed
+ """
+ cfg_file = os.path.join("test", "data", "utils", "configfile-str.ini")
+ c = autils.Conf_all_parser(cfg_file, ["sec2", "sec_bool"])
+ assert c.get_section_dict("sec2") == {"param2": "", "myval": "parameter",
+ 'param3': "myparameter",
+ "param1": "3"}
+ assert c.get_section_dict("sec_bool") == {"bool num_false": "0", "bool_num_true": "1",
+ "bool_f": "off", "bool_t": "ON", "bool_n": "no",
+ "bool_y": "YES",
+ "bool_false": "FalSe", "bool_true": "tRUE",
+ "param1": "3", "param2": "10"}
+
+
def test_conf_parser_get_section(capsys):
"""
Test get dict of values for a given section
--
GitLab