From d1084680903477489faf592ec1cf78bcdf2ec405 Mon Sep 17 00:00:00 2001
From: Dmitri Kazantsev <81972939+do-dmitri@users.noreply.github.com>
Date: Mon, 5 Aug 2024 11:41:17 +0300
Subject: [PATCH 1/4] Update setup.py   Add authors

It is kindly proposed to add author to setup.py, this was found with pydigger.com project done by github.com/szabgab
thank you
---
 setup.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/setup.py b/setup.py
index b7e233b..2940934 100644
--- a/setup.py
+++ b/setup.py
@@ -30,6 +30,7 @@ def get_version(rel_path):
                 "relational database (PostgreSQL or SQLite) using sqlalchemy.",
     long_description_content_type="text/markdown",
     long_description=long_description,
+    author="Suresh Hewapathirana",
     license="'Apache 2.0",
     url="https://github.com/PRIDE-Archive/xi-mzidentml-converter",
     packages=find_packages(),

From 81599bc609b159818bc1468f321922761fcfc6b3 Mon Sep 17 00:00:00 2001
From: sureshhewa <sureshhewabi@gmail.com>
Date: Mon, 5 Aug 2024 14:06:30 +0100
Subject: [PATCH 2/4] fixes database.ini

---
 config/config_parser.py | 2 +-
 setup.py                | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/config/config_parser.py b/config/config_parser.py
index d1e4684..763476b 100644
--- a/config/config_parser.py
+++ b/config/config_parser.py
@@ -15,7 +15,7 @@ def parse_config(filename, section='postgresql'):
         for param in params:
             configs[param[0]] = param[1]
     else:
-        raise Exception('Section {0} not found in the {1} file'.format(section, filename))
+        print('Section {0} not found in the {1} file'.format(section, filename))
     return configs
 
 
diff --git a/setup.py b/setup.py
index b7e233b..724bf52 100644
--- a/setup.py
+++ b/setup.py
@@ -24,7 +24,7 @@ def get_version(rel_path):
 
 setup(
     name="xi-mzidentml-converter",
-    version="0.2.2",
+    version="0.2.3",
     description="xi-mzidentml-converter uses pyteomics (https://pyteomics.readthedocs.io/en/latest/index.html) to "
                 "parse mzIdentML files (v1.2.0) and extract crosslink information. Results are written to a "
                 "relational database (PostgreSQL or SQLite) using sqlalchemy.",

From d8192190e1b4d5d2326a991230b841771c591359 Mon Sep 17 00:00:00 2001
From: sureshhewa <sureshhewabi@gmail.com>
Date: Fri, 9 Aug 2024 10:30:32 +0100
Subject: [PATCH 3/4] fixes for mascot

---
 setup.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/setup.py b/setup.py
index 724bf52..8234a18 100644
--- a/setup.py
+++ b/setup.py
@@ -24,7 +24,7 @@ def get_version(rel_path):
 
 setup(
     name="xi-mzidentml-converter",
-    version="0.2.3",
+    version="0.2.4",
     description="xi-mzidentml-converter uses pyteomics (https://pyteomics.readthedocs.io/en/latest/index.html) to "
                 "parse mzIdentML files (v1.2.0) and extract crosslink information. Results are written to a "
                 "relational database (PostgreSQL or SQLite) using sqlalchemy.",
@@ -39,7 +39,7 @@ def get_version(rel_path):
         'numpy>=1.14.3',
         'pandas>=0.21.0',
         'pymzml>=0.7.8',
-        'pyteomics>=4.7.2',
+        'pyteomics>=4.7.3',
         'requests>=2.31.0',
         'urllib3>=1.24.2',
         'pytest',

From 1241657ef41afd43ea38dffc0c2e12dc3391e08c Mon Sep 17 00:00:00 2001
From: sureshhewa <sureshhewabi@gmail.com>
Date: Thu, 15 Aug 2024 15:03:17 +0100
Subject: [PATCH 4/4] authors added

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index e8e36d7..1773f73 100644
--- a/setup.py
+++ b/setup.py
@@ -30,7 +30,7 @@ def get_version(rel_path):
                 "relational database (PostgreSQL or SQLite) using sqlalchemy.",
     long_description_content_type="text/markdown",
     long_description=long_description,
-    author="Suresh Hewapathirana",
+    author="Colin Combe, Lars Kolbowski, Suresh Hewapathirana",
     license="'Apache 2.0",
     url="https://github.com/PRIDE-Archive/xi-mzidentml-converter",
     packages=find_packages(),