Merge pull request #12 from lifs-tools/fileopenutf8

Fix issues with platform encoding as default for file opening - explicitly set utf8
lifs-tools · Aug 5, 2022 · a9caa2d · a9caa2d
2 parents 80caee6 + 43336de
commit a9caa2d
Show file tree

Hide file tree

Showing 51 changed files with 120 additions and 196 deletions.
diff --git a/Jenkinsfile b/Jenkinsfile
diff --git a/LICENSE b/LICENSE
@@ -1,7 +1,7 @@
 MIT License
 
-Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} isas.de
-                   Nils Hoffmann  -  nils.hoffmann {at} isas.de
+Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} univie.ac.at
+                   Nils Hoffmann  -  nils.hoffmann {at} cebitec.uni-bielefeld.de
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/README.md b/README.md
@@ -1,5 +1,5 @@
 # Python3 implementation for Goslin
-[![Build Status](https://travis-ci.org/lifs-tools/pygoslin.svg?branch=master)](https://travis-ci.org/lifs-tools/pygoslin)
+[![Build Status](https://github.com/lifs-tools/pygoslin/actions/workflows/python-package.yml/badge.svg)](https://github.com/lifs-tools/pygoslin/actions/workflows/python-package.yml)
 
 This is the Goslin reference implementation for Python 3.
 

diff --git a/pygoslin/__init__.py b/pygoslin/__init__.py
@@ -1,8 +1,8 @@
 """
 MIT License
 
-Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} isas.de
-                   Nils Hoffmann  -  nils.hoffmann {at} isas.de
+Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} univie.ac.at
+                   Nils Hoffmann  -  nils.hoffmann {at} cebitec.uni-bielefeld.de
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/pygoslin/domain/Adduct.py b/pygoslin/domain/Adduct.py
@@ -1,8 +1,8 @@
 """
 MIT License
 
-Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} isas.de
-                   Nils Hoffmann  -  nils.hoffmann {at} isas.de
+Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} univie.ac.at
+                   Nils Hoffmann  -  nils.hoffmann {at} cebitec.uni-bielefeld.de
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/pygoslin/domain/Cycle.py b/pygoslin/domain/Cycle.py
@@ -1,8 +1,8 @@
 """
 MIT License
 
-Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} isas.de
-                   Nils Hoffmann  -  nils.hoffmann {at} isas.de
+Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} univie.ac.at
+                   Nils Hoffmann  -  nils.hoffmann {at} cebitec.uni-bielefeld.de
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/pygoslin/domain/Element.py b/pygoslin/domain/Element.py
@@ -1,8 +1,8 @@
 """
 MIT License
 
-Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} isas.de
-                   Nils Hoffmann  -  nils.hoffmann {at} isas.de
+Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} univie.ac.at
+                   Nils Hoffmann  -  nils.hoffmann {at} cebitec.uni-bielefeld.de
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/pygoslin/domain/FattyAcid.py b/pygoslin/domain/FattyAcid.py
@@ -1,8 +1,8 @@
 """
 MIT License
 
-Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} isas.de
-                   Nils Hoffmann  -  nils.hoffmann {at} isas.de
+Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} univie.ac.at
+                   Nils Hoffmann  -  nils.hoffmann {at} cebitec.uni-bielefeld.de
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/pygoslin/domain/Fragment.py b/pygoslin/domain/Fragment.py
@@ -1,8 +1,8 @@
 """
 MIT License
 
-Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} isas.de
-                   Nils Hoffmann  -  nils.hoffmann {at} isas.de
+Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} univie.ac.at
+                   Nils Hoffmann  -  nils.hoffmann {at} cebitec.uni-bielefeld.de
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/pygoslin/domain/FunctionalGroup.py b/pygoslin/domain/FunctionalGroup.py
@@ -1,8 +1,8 @@
 """
 MIT License
 
-Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} isas.de
-                   Nils Hoffmann  -  nils.hoffmann {at} isas.de
+Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} univie.ac.at
+                   Nils Hoffmann  -  nils.hoffmann {at} cebitec.uni-bielefeld.de
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
@@ -254,7 +254,7 @@ def to_string(self, level):
 _known_functional_groups, s = {}, SumFormulaParser()
 fg_dir_name = path.dirname(pygoslin.__file__)
 fg_file_name = path.join(fg_dir_name, "data", "goslin", "functional-groups.csv")
-with open(fg_file_name, "rt") as fg_infile:
+with open(fg_file_name, mode = "rt", encoding= "utf-8") as fg_infile:
     fg_infile.readline()
     for line in fg_infile:
         line = line.strip()

diff --git a/pygoslin/domain/HeadGroup.py b/pygoslin/domain/HeadGroup.py
@@ -1,8 +1,8 @@
 """
 MIT License
 
-Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} isas.de
-                   Nils Hoffmann  -  nils.hoffmann {at} isas.de
+Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} univie.ac.at
+                   Nils Hoffmann  -  nils.hoffmann {at} cebitec.uni-bielefeld.de
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/pygoslin/domain/LipidAdduct.py b/pygoslin/domain/LipidAdduct.py
@@ -1,8 +1,8 @@
 """
 MIT License
 
-Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} isas.de
-                   Nils Hoffmann  -  nils.hoffmann {at} isas.de
+Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} univie.ac.at
+                   Nils Hoffmann  -  nils.hoffmann {at} cebitec.uni-bielefeld.de
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/pygoslin/domain/LipidCategory.py b/pygoslin/domain/LipidCategory.py
@@ -1,8 +1,8 @@
 """
 MIT License
 
-Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} isas.de
-                   Nils Hoffmann  -  nils.hoffmann {at} isas.de
+Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} univie.ac.at
+                   Nils Hoffmann  -  nils.hoffmann {at} cebitec.uni-bielefeld.de
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/pygoslin/domain/LipidClass.py b/pygoslin/domain/LipidClass.py
@@ -1,8 +1,8 @@
 """
 MIT License
 
-Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} isas.de
-                   Nils Hoffmann  -  nils.hoffmann {at} isas.de
+Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} univie.ac.at
+                   Nils Hoffmann  -  nils.hoffmann {at} cebitec.uni-bielefeld.de
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
@@ -62,7 +62,7 @@ def get_class(name):
 
 all_lipids_dir_name = path.dirname(pygoslin.__file__)
 file_name = path.join(all_lipids_dir_name, "data", "goslin", "lipid-list.csv")
-with open(file_name, mode = "rt") as infile:
+with open(file_name, mode = "rt", encoding= "utf-8") as infile:
     line = infile.readline() # skip title row
     lipid_reader = csv.reader(infile, delimiter=',', quotechar='"')
     sum_formula_parser = SumFormulaParser()

diff --git a/pygoslin/domain/LipidCompleteStructure.py b/pygoslin/domain/LipidCompleteStructure.py
@@ -1,8 +1,8 @@
 """
 MIT License
 
-Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} isas.de
-                   Nils Hoffmann  -  nils.hoffmann {at} isas.de
+Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} univie.ac.at
+                   Nils Hoffmann  -  nils.hoffmann {at} cebitec.uni-bielefeld.de
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/pygoslin/domain/LipidExceptions.py b/pygoslin/domain/LipidExceptions.py
@@ -1,8 +1,8 @@
 """
 MIT License
 
-Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} isas.de
-                   Nils Hoffmann  -  nils.hoffmann {at} isas.de
+Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} univie.ac.at
+                   Nils Hoffmann  -  nils.hoffmann {at} cebitec.uni-bielefeld.de
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/pygoslin/domain/LipidFaBondType.py b/pygoslin/domain/LipidFaBondType.py
@@ -1,8 +1,8 @@
 """
 MIT License
 
-Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} isas.de
-                   Nils Hoffmann  -  nils.hoffmann {at} isas.de
+Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} univie.ac.at
+                   Nils Hoffmann  -  nils.hoffmann {at} cebitec.uni-bielefeld.de
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/pygoslin/domain/LipidFullStructure.py b/pygoslin/domain/LipidFullStructure.py
@@ -1,8 +1,8 @@
 """
 MIT License
 
-Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} isas.de
-                   Nils Hoffmann  -  nils.hoffmann {at} isas.de
+Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} univie.ac.at
+                   Nils Hoffmann  -  nils.hoffmann {at} cebitec.uni-bielefeld.de
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/pygoslin/domain/LipidLevel.py b/pygoslin/domain/LipidLevel.py
@@ -1,8 +1,8 @@
 """
 MIT License
 
-Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} isas.de
-                   Nils Hoffmann  -  nils.hoffmann {at} isas.de
+Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} univie.ac.at
+                   Nils Hoffmann  -  nils.hoffmann {at} cebitec.uni-bielefeld.de
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/pygoslin/domain/LipidMolecularSpecies.py b/pygoslin/domain/LipidMolecularSpecies.py
@@ -1,8 +1,8 @@
 """
 MIT License
 
-Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} isas.de
-                   Nils Hoffmann  -  nils.hoffmann {at} isas.de
+Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} univie.ac.at
+                   Nils Hoffmann  -  nils.hoffmann {at} cebitec.uni-bielefeld.de
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/pygoslin/domain/LipidSnPosition.py b/pygoslin/domain/LipidSnPosition.py
@@ -1,8 +1,8 @@
 """
 MIT License
 
-Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} isas.de
-                   Nils Hoffmann  -  nils.hoffmann {at} isas.de
+Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} univie.ac.at
+                   Nils Hoffmann  -  nils.hoffmann {at} cebitec.uni-bielefeld.de
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/pygoslin/domain/LipidSpecies.py b/pygoslin/domain/LipidSpecies.py
@@ -1,8 +1,8 @@
 """
 MIT License
 
-Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} isas.de
-                   Nils Hoffmann  -  nils.hoffmann {at} isas.de
+Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} univie.ac.at
+                   Nils Hoffmann  -  nils.hoffmann {at} cebitec.uni-bielefeld.de
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/pygoslin/domain/LipidSpeciesInfo.py b/pygoslin/domain/LipidSpeciesInfo.py
@@ -1,8 +1,8 @@
 """
 MIT License
 
-Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} isas.de
-                   Nils Hoffmann  -  nils.hoffmann {at} isas.de
+Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} univie.ac.at
+                   Nils Hoffmann  -  nils.hoffmann {at} cebitec.uni-bielefeld.de
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/pygoslin/domain/LipidStructureDefined.py b/pygoslin/domain/LipidStructureDefined.py
@@ -1,8 +1,8 @@
 """
 MIT License
 
-Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} isas.de
-                   Nils Hoffmann  -  nils.hoffmann {at} isas.de
+Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} univie.ac.at
+                   Nils Hoffmann  -  nils.hoffmann {at} cebitec.uni-bielefeld.de
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/pygoslin/domain/__init__.py b/pygoslin/domain/__init__.py
@@ -1,8 +1,8 @@
 """
 MIT License
 
-Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} isas.de
-                   Nils Hoffmann  -  nils.hoffmann {at} isas.de
+Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} univie.ac.at
+                   Nils Hoffmann  -  nils.hoffmann {at} cebitec.uni-bielefeld.de
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/pygoslin/parser/BaseParserEventHandler.py b/pygoslin/parser/BaseParserEventHandler.py
@@ -1,8 +1,8 @@
 """
 MIT License
 
-Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} isas.de
-                   Nils Hoffmann  -  nils.hoffmann {at} isas.de
+Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} univie.ac.at
+                   Nils Hoffmann  -  nils.hoffmann {at} cebitec.uni-bielefeld.de
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/pygoslin/parser/FattyAcidParserEventHandler.py b/pygoslin/parser/FattyAcidParserEventHandler.py
@@ -1,8 +1,8 @@
 """
 MIT License
 
-Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} isas.de
-                   Nils Hoffmann  -  nils.hoffmann {at} isas.de
+Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} univie.ac.at
+                   Nils Hoffmann  -  nils.hoffmann {at} cebitec.uni-bielefeld.de
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/pygoslin/parser/GoslinParserEventHandler.py b/pygoslin/parser/GoslinParserEventHandler.py
@@ -1,8 +1,8 @@
 """
 MIT License
 
-Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} isas.de
-                   Nils Hoffmann  -  nils.hoffmann {at} isas.de
+Copyright (c) 2020 Dominik Kopczynski   -   dominik.kopczynski {at} univie.ac.at
+                   Nils Hoffmann  -  nils.hoffmann {at} cebitec.uni-bielefeld.de
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal