diff --git a/Jenkinsfile b/Jenkinsfile deleted file mode 100644 index c8531bd..0000000 --- a/Jenkinsfile +++ /dev/null @@ -1,84 +0,0 @@ -node { - def artifactoryServer = Artifactory.server 'Lipidomics' - def toolName = "${jobToolName?:''}" - def emailOnSuccess = "${jobEmailRecipients?:''}" - def emailOnFailure = "${jobEmailRecipients?:''}" - def gitRepo = "${jobRepo?:'kopczynski/pygoslin'}" - def gitHoster = "gitlab.isas.de" - def gitUrl = "https://${gitHoster}/${gitRepo}" - def gitUserName = "${jobGitUserName?:''}" - def gitUserEmail = "${jobGitUserEmail?:''}" - def gitUserCredentialsId = "${jobGitUserCredentials?:''}" - def dockerRegistryUrl = "${jobDockerRegistryUrl?:''}" - def dockerRegistryCredentialsId = "${jobDockerRegistryCredentialsId?:''}" - def dockerBuildImage = "${jobDockerBuildImage?:''}" - def afUploadSpec = """{ - "files": [ - { - "pattern": "LipidCreator/bin/x64/Release/LipidCreator.zip", - "target": "libs-release-local/de/isas/lipidomics/lipidcreator/${BUILD_NUMBER}/LipidCreator-${BUILD_NUMBER}.zip", - "props": "artifactId:lipidcreator;groupId:de.isas.lipidomics;type:zip;version:${BUILD_NUMBER}", - "recursive": "false", - "flat" : "true", - "regexp": "false" - }, - { - "pattern": "LipidCreator/bin/x64/Release/LipidCreator.zip", - "target": "libs-release-local/de/isas/lipidomics/lipidcreator/${BUILD_NUMBER}/LipidCreator.zip", - "props": "artifactId:lipidcreator;groupId:de.isas.lipidomics;type:zip;version:${BUILD_NUMBER}", - "recursive": "false", - "flat" : "true", - "regexp": "false" - } - ] -}""" - - stage('Build & Test') { - docker.withRegistry(dockerRegistryUrl, dockerRegistryCredentialsId) { - docker.image(dockerBuildImage).inside { - try { - stage 'Checkout' - def scmVars = checkout([$class: 'GitSCM', branches: [[name: '*/master']], - extensions: scm.extensions,// + [[$class: 'WipeWorkspace']], - userRemoteConfigs: [[credentialsId: gitUserCredentialsId, url: gitUrl]]]) - script { - env.GIT_COMMIT = scmVars.GIT_COMMIT - env.GIT_BRANCH = scmVars.GIT_BRANCH - } - //stage 'Build' - //sh 'make install' - stage 'Test' - sh 'make test' -// stage('Publish') { -// def buildInfo = artifactoryServer.upload spec: afUploadSpec, failNoOp: true -// artifactoryServer.publishBuildInfo buildInfo -// } - stage 'Tag' - withCredentials([usernamePassword(credentialsId: gitUserCredentialsId, passwordVariable: 'GIT_PASSWORD', usernameVariable: 'GIT_USERNAME')]) { - sh("git config user.email '${jobGitUserEmail}'") - sh("git config user.name '${jobGitUserName}'") - sh("git tag -a '${BUILD_NUMBER}' -m 'Automatic tag for successful build number ${BUILD_NUMBER} from commit ${GIT_COMMIT} on branch ${GIT_BRANCH}'") - script { - env.encodedPass=URLEncoder.encode("${GIT_PASSWORD}", "UTF-8") - env.gitHoster=gitHoster - env.gitRepo=gitRepo - } - sh('git push https://${GIT_USERNAME}:${encodedPass}@${gitHoster}/${gitRepo} --tags') - } - stage 'Notify' - mail to: emailOnSuccess, - subject: "${toolName} build succeeded: ${currentBuild.fullDisplayName}", - body: "Artifacts have been deployed to Artifactory, build tag was pushed to ${gitUrl}/releases/tag/${BUILD_NUMBER}." - } catch(e) { - mail to: emailOnFailure, - subject: "${toolName} build failed: ${currentBuild.fullDisplayName}", - body: """Please check the job errors: - ${e} - """ - throw e - } finally { - } - } - } - } -} diff --git a/LICENSE b/LICENSE index 369fe17..515a22a 100644 --- 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 index 759a499..d9be7a6 100644 --- 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 index 479d46d..67a84dc 100644 --- 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 index ddcf7fb..f5b415c 100644 --- 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 index 7c85b93..ed5ec8b 100644 --- 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 index b584b65..cc97b01 100644 --- 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 index e492f5e..0f8ebd9 100644 --- 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 index 8801ad6..fc77bb6 100644 --- 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 index 44c5820..2988105 100644 --- 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 index 2fa4280..42d6b52 100644 --- 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 index d2692de..90c141b 100644 --- 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 index 95925e0..b20842a 100644 --- 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 index b84ee6b..af91000 100644 --- 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 index c20aede..e85e94e 100644 --- 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 index 59033e8..c86c553 100644 --- 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 index daac7d1..76195dc 100644 --- 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 index dc9264d..b3ecfd2 100644 --- 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 index f5be640..3b3a711 100644 --- 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 index 03cc5ad..2b82076 100644 --- 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 index 3c4605c..7b86808 100644 --- 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 index f830974..e5c5890 100644 --- 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 index 671ba63..35fd057 100644 --- 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 index a9b4342..b7b4cf1 100644 --- 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 index 3310fd2..d9f3c82 100644 --- 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 index 186163d..0fc9786 100644 --- 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 index 4a169d0..3af8a02 100644 --- 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 index 3af4454..24b4aec 100644 --- 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 diff --git a/pygoslin/parser/HmdbParserEventHandler.py b/pygoslin/parser/HmdbParserEventHandler.py index c57fb19..144bf1d 100644 --- a/pygoslin/parser/HmdbParserEventHandler.py +++ b/pygoslin/parser/HmdbParserEventHandler.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/LipidBaseParserEventHandler.py b/pygoslin/parser/LipidBaseParserEventHandler.py index ec7e37f..e74bdcc 100644 --- a/pygoslin/parser/LipidBaseParserEventHandler.py +++ b/pygoslin/parser/LipidBaseParserEventHandler.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/LipidMapsParserEventHandler.py b/pygoslin/parser/LipidMapsParserEventHandler.py index 476c397..ea53259 100644 --- a/pygoslin/parser/LipidMapsParserEventHandler.py +++ b/pygoslin/parser/LipidMapsParserEventHandler.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/Parser.py b/pygoslin/parser/Parser.py index d4757d1..0b72433 100644 --- a/pygoslin/parser/Parser.py +++ b/pygoslin/parser/Parser.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 @@ -117,7 +117,7 @@ def __init__(self): dir_name = path.dirname(pygoslin.__file__) file_name = path.join(dir_name, "data", "goslin", "trivial-names.csv") - with open(file_name, "rt") as trivial_infile: + with open(file_name, "rt", encoding= "utf-8") as trivial_infile: trivial_infile.readline() for line in trivial_infile: line = line.strip() diff --git a/pygoslin/parser/ParserCommon.py b/pygoslin/parser/ParserCommon.py index f4ea049..7f4504a 100644 --- a/pygoslin/parser/ParserCommon.py +++ b/pygoslin/parser/ParserCommon.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 @@ -293,7 +293,7 @@ def top_nodes( rule_index): def extract_text_based_rules(grammar_filename, quote = DEFAULT_QUOTE): grammar, sb,current_position = "", [], 0 - with open(grammar_filename, mode = "rt") as infile: + with open(grammar_filename, mode = "rt", encoding= "utf-8") as infile: grammar = infile.read() + "\n"; grammar_length = len(grammar) @@ -377,7 +377,7 @@ def extract_text_based_rules(grammar_filename, quote = DEFAULT_QUOTE): def dump_child(self, class_name, parser_event_handler_name): - with open("%s.py" % class_name, mode = "wt") as dumpfile: + with open("%s.py" % class_name, mode = "wt", encoding= "utf-8") as dumpfile: dumpfile.write("from pygoslin.parser.Parser import Parser\n") dumpfile.write("from pygoslin.parser.%s import %s\n\n" % (parser_event_handler_name, parser_event_handler_name)) dumpfile.write("class %s(Parser):\n" % class_name) diff --git a/pygoslin/parser/ParserCore.pyx b/pygoslin/parser/ParserCore.pyx index 3248c7c..a84458f 100644 --- a/pygoslin/parser/ParserCore.pyx +++ b/pygoslin/parser/ParserCore.pyx @@ -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/ShorthandParserEventHandler.py b/pygoslin/parser/ShorthandParserEventHandler.py index 6bd713d..b4c8b5f 100644 --- a/pygoslin/parser/ShorthandParserEventHandler.py +++ b/pygoslin/parser/ShorthandParserEventHandler.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/SumFormulaParserEventHandler.py b/pygoslin/parser/SumFormulaParserEventHandler.py index fc1b625..91f42c6 100644 --- a/pygoslin/parser/SumFormulaParserEventHandler.py +++ b/pygoslin/parser/SumFormulaParserEventHandler.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/SwissLipidsParserEventHandler.py b/pygoslin/parser/SwissLipidsParserEventHandler.py index a72daad..8da7bd8 100644 --- a/pygoslin/parser/SwissLipidsParserEventHandler.py +++ b/pygoslin/parser/SwissLipidsParserEventHandler.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/SystematicParserEventHandler.py b/pygoslin/parser/SystematicParserEventHandler.py index 39ff701..00aac09 100644 --- a/pygoslin/parser/SystematicParserEventHandler.py +++ b/pygoslin/parser/SystematicParserEventHandler.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/__init__.py b/pygoslin/parser/__init__.py index 3310fd2..d9f3c82 100644 --- a/pygoslin/parser/__init__.py +++ b/pygoslin/parser/__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/tests/FattyAcidsTest.py b/pygoslin/tests/FattyAcids_test.py similarity index 95% rename from pygoslin/tests/FattyAcidsTest.py rename to pygoslin/tests/FattyAcids_test.py index 7df77ad..9c79049 100644 --- a/pygoslin/tests/FattyAcidsTest.py +++ b/pygoslin/tests/FattyAcids_test.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 @@ -40,7 +40,7 @@ class LipidMapsTest(unittest.TestCase): def test_parser(self): lipid_data = [] file_name = os.path.join("pygoslin", "data", "goslin", "testfiles", "fatty-acids-test.csv") - with open(file_name, mode = "rt") as infile: + with open(file_name, mode = "rt", encoding= "utf-8") as infile: lipidreader = csv.reader(infile, delimiter=',', quotechar='"') for row in lipidreader: lipid_data.append(row) diff --git a/pygoslin/tests/TestFormulas.py b/pygoslin/tests/Formulas_test.py similarity index 93% rename from pygoslin/tests/TestFormulas.py rename to pygoslin/tests/Formulas_test.py index f98736e..17e66bf 100644 --- a/pygoslin/tests/TestFormulas.py +++ b/pygoslin/tests/Formulas_test.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 @@ -46,7 +46,7 @@ class TestFormulas(unittest.TestCase): def test_formulas_swiss_lipids(self): global swiss_lipids_parser file_names = os.path.join("pygoslin", "data", "goslin", "testfiles", 'formulas-swiss-lipids.csv') - with open(file_names, newline='') as csvfile: + with open(file_names, newline='', encoding= "utf-8") as csvfile: lipidreader = csv.reader(csvfile, delimiter=',', quotechar='\"') for row in lipidreader: @@ -70,7 +70,7 @@ def test_formulas_swiss_lipids(self): def test_formulas_lipid_maps(self): global lipids_maps_parser file_name = os.path.join("pygoslin", "data", "goslin", "testfiles", 'formulas-lipid-maps.csv') - with open(file_name, newline='') as csvfile: + with open(file_name, newline='', encoding= "utf-8") as csvfile: lipidreader = csv.reader(csvfile, delimiter=',', quotechar='\"') for row in lipidreader: diff --git a/pygoslin/tests/GoslinTest.py b/pygoslin/tests/Goslin_test.py similarity index 97% rename from pygoslin/tests/GoslinTest.py rename to pygoslin/tests/Goslin_test.py index 746a4a5..497d1be 100644 --- a/pygoslin/tests/GoslinTest.py +++ b/pygoslin/tests/Goslin_test.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 @@ -99,7 +99,7 @@ def test_sphingolipids(self): def test_parser(self): lipidnames = [] file_name = os.path.join("pygoslin", "data", "goslin", "testfiles", "goslin-test.csv") - with open(file_name, mode = "rt") as infile: + with open(file_name, mode = "rt", encoding= "utf-8") as infile: for line in infile: line = line.strip().strip(" ") if len(line) > 0: lipidnames.append(line) diff --git a/pygoslin/tests/HmdbTest.py b/pygoslin/tests/Hmdb_test.py similarity index 96% rename from pygoslin/tests/HmdbTest.py rename to pygoslin/tests/Hmdb_test.py index 3fcf87a..59240ff 100644 --- a/pygoslin/tests/HmdbTest.py +++ b/pygoslin/tests/Hmdb_test.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 @@ -96,7 +96,7 @@ def test_sphingolipids(self): def test_parser(self): lipidnames = [] file_name = os.path.join("pygoslin", "data", "goslin", "testfiles", "hmdb-test.csv") - with open(file_name, mode = "rt") as infile: + with open(file_name, mode = "rt", encoding= "utf-8") as infile: for line in infile: line = line.strip().strip(" ") if len(line) > 0: lipidnames.append(line) diff --git a/pygoslin/tests/LipidMapsTest.py b/pygoslin/tests/LipidMaps_test.py similarity index 97% rename from pygoslin/tests/LipidMapsTest.py rename to pygoslin/tests/LipidMaps_test.py index f7c348c..a50f96b 100644 --- a/pygoslin/tests/LipidMapsTest.py +++ b/pygoslin/tests/LipidMaps_test.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 @@ -92,7 +92,7 @@ def test_sphingolipids(self): def test_parser(self): lipidnames = [] file_name = os.path.join("pygoslin", "data", "goslin", "testfiles", "lipid-maps-test.csv") - with open(file_name, mode = "rt") as infile: + with open(file_name, mode = "rt", encoding= "utf-8") as infile: lipidreader = csv.reader(infile, delimiter=',', quotechar='"') for row in lipidreader: lipidnames.append(row) diff --git a/pygoslin/tests/MassesTest.py b/pygoslin/tests/Masses_test.py similarity index 94% rename from pygoslin/tests/MassesTest.py rename to pygoslin/tests/Masses_test.py index d2b6984..09e2fa9 100644 --- a/pygoslin/tests/MassesTest.py +++ b/pygoslin/tests/Masses_test.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 @@ -44,7 +44,7 @@ class TestFormulas(unittest.TestCase): def test_masses(self): global parser file_name = os.path.join("pygoslin", "data", "goslin", "testfiles", 'lipid-masses.csv') - with open(file_name, newline='') as csvfile: + with open(file_name, newline='', encoding= "utf-8") as csvfile: lipidreader = csv.reader(csvfile, delimiter=',', quotechar='\"') for i, row in enumerate(lipidreader): if i == 0: continue diff --git a/pygoslin/tests/ParserTest.py b/pygoslin/tests/Parser_test.py similarity index 99% rename from pygoslin/tests/ParserTest.py rename to pygoslin/tests/Parser_test.py index fa2ebb8..d25fae4 100644 --- a/pygoslin/tests/ParserTest.py +++ b/pygoslin/tests/Parser_test.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 @@ -539,7 +539,7 @@ def test_parser_read(self): global lipid_parser lipidnames = [] file_name = os.path.join("pygoslin", "data", "goslin", "testfiles", "lipidnames.csv") - with open(file_name, mode = "rt") as infile: + with open(file_name, mode = "rt", encoding= "utf-8") as infile: for line in infile: line = line.strip().strip(" ") if len(line) < 2: continue diff --git a/pygoslin/tests/ShorthandTest.py b/pygoslin/tests/Shorthand_test.py similarity index 99% rename from pygoslin/tests/ShorthandTest.py rename to pygoslin/tests/Shorthand_test.py index d7bcd40..f26098e 100644 --- a/pygoslin/tests/ShorthandTest.py +++ b/pygoslin/tests/Shorthand_test.py @@ -172,7 +172,7 @@ def test_sphingolipids(self): def test_nomenclature(self): data = [] file_name = os.path.join("pygoslin", "data", "goslin", "testfiles", "shorthand-test.csv") - with open(file_name, mode = "rt") as infile: + with open(file_name, mode = "rt", encoding= "utf-8") as infile: lipidreader = csv.reader(infile, delimiter=',', quotechar='"') for row in lipidreader: row[-1] = row[-1].strip(" ") diff --git a/pygoslin/tests/SwissLipidsTest.py b/pygoslin/tests/SwissLipids_test.py similarity index 96% rename from pygoslin/tests/SwissLipidsTest.py rename to pygoslin/tests/SwissLipids_test.py index 5f1e959..5cb787a 100644 --- a/pygoslin/tests/SwissLipidsTest.py +++ b/pygoslin/tests/SwissLipids_test.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 @@ -85,7 +85,7 @@ def test_sphingolipids(self): def teset_swiss_lipids_parser(self): lipidnames = [] file_name = os.path.join("pygoslin", "data", "goslin", "testfiles", "swiss-lipids-test.csv") - with open(file_name, mode = "rt") as infile: + with open(file_name, mode = "rt", encoding= "utf-8") as infile: for line in infile: line = line.strip().strip(" ") if len(line) > 0: lipidnames.append(line) diff --git a/pygoslin/tests/__init__.py b/pygoslin/tests/__init__.py index 3310fd2..d9f3c82 100644 --- a/pygoslin/tests/__init__.py +++ b/pygoslin/tests/__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/pyproject.toml b/pyproject.toml index 5f106ab..24ee53d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -5,3 +5,10 @@ requires = [ "cython" ] build-backend = "setuptools.build_meta" + +[tool.pytest.ini_options] +minversion = "6.0" +addopts = "-ra -q" +testpaths = [ + "pygoslin/tests" +] diff --git a/setup.py b/setup.py index 9b7f22f..6d1c0ba 100644 --- a/setup.py +++ b/setup.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 @@ -42,11 +42,11 @@ setup( name = 'pygoslin', - version = '2.0.2', + version = '2.0.3', url = 'https://github.com/lifs-tools/pygoslin', license = 'MIT', author = 'Dominik Kopczynski', - author_email = 'dominik.kopczynski@isas.de', + author_email = 'dominik.kopczynski@univie.ac.at', description = 'Python implementation for Goslin', long_description = open('README.md', encoding='utf-8').read(), long_description_content_type="text/markdown", @@ -59,6 +59,7 @@ #ext_modules= cythonize("pygoslin/parser/ParserCore.pyx", language_level = 3) if pyx_support else None, setup_requires = ["pytest-runner"], tests_require = ["pytest"], + test_suite= "tests", python_requires = '>=3.5', include_package_data = True, package_data = {