Update python versions we test for

.github/workflows/ci.yml

@@ -9,10 +9,10 @@ jobs:
     strategy:
       matrix:
         python-version:
-          - 3.6
-          - 3.7
-          - 3.8
-          - 3.9
+          - '3.8'
+          - '3.9'
+          - '3.10'
+          - '3.11'
 
     steps:
       - name: Install Python via conda.

CONTRIBUTING.rst

@@ -102,7 +102,7 @@ Before you submit a pull request, check that it meets these guidelines:
 2. If the pull request adds functionality, the docs should be updated. Put
    your new functionality into a function with a docstring, and add the
    feature to the list in README.rst.
-3. The pull request should work for Python 2.7, 3.4, 3.5 and 3.6, and for PyPy. Check
+3. The pull request should work for Python 3.8, 3.9, 3.10, and 3.11 as well as for PyPy. Check
    https://travis-ci.org/bihealth/altamisa/pull_requests
    and make sure that the tests pass for all supported Python versions.
 

altamisa/apps/isatab2dot.py

@@ -19,7 +19,6 @@ def print_dot(
     proc_shape="ellipse",
     proc_color="blue",
 ):
-
     print(indent + "/* materials */", file=outf)
     for name, mat in obj.materials.items():
         label = json.dumps("{}:\n{}\n({})".format(mat.type, mat.name if mat.name else "-", name))

altamisa/constants/investigation_headers.py

@@ -68,11 +68,11 @@
 INVESTIGATION_PUBLICATION_TITLE = "Investigation Publication Title"  #:
 INVESTIGATION_PUBLICATION_STATUS = "Investigation Publication Status"  #:
 INVESTIGATION_PUBLICATION_STATUS_TERM_ACCESSION_NUMBER = (
-    "Investigation Publication Status Term Accession Number"
-)  #:
+    "Investigation Publication Status Term Accession Number"  #:
+)
 INVESTIGATION_PUBLICATION_STATUS_TERM_SOURCE_REF = (
-    "Investigation Publication Status Term Source REF"
-)  #:
+    "Investigation Publication Status Term Source REF"  #:
+)
 #: Collected header keys of INVESTIGATION PUBLICATIONS
 INVESTIGATION_PUBLICATIONS_KEYS = (
     INVESTIGATION_PUBMED_ID,
@@ -96,8 +96,8 @@
 INVESTIGATION_PERSON_AFFILIATION = "Investigation Person Affiliation"  #:
 INVESTIGATION_PERSON_ROLES = "Investigation Person Roles"  #:
 INVESTIGATION_PERSON_ROLES_TERM_ACCESSION_NUMBER = (
-    "Investigation Person Roles Term Accession Number"
-)  #:
+    "Investigation Person Roles Term Accession Number"  #:
+)
 INVESTIGATION_PERSON_ROLES_TERM_SOURCE_REF = "Investigation Person Roles Term Source REF"  #:
 #: Collected header keys of INVESTIGATION CONTACTS section
 INVESTIGATION_CONTACTS_KEYS = (
@@ -152,8 +152,8 @@
 STUDY_PUBLICATION_TITLE = "Study Publication Title"  #:
 STUDY_PUBLICATION_STATUS = "Study Publication Status"  #:
 STUDY_PUBLICATION_STATUS_TERM_ACCESSION_NUMBER = (
-    "Study Publication Status Term Accession Number"
-)  #:
+    "Study Publication Status Term Accession Number"  #:
+)
 STUDY_PUBLICATION_STATUS_TERM_SOURCE_REF = "Study Publication Status Term Source REF"  #:
 #: Collected header keys of STUDY PUBLICATIONS section
 STUDY_PUBLICATIONS_KEYS = (
@@ -185,13 +185,13 @@
 STUDY_ASSAY_FILE_NAME = "Study Assay File Name"  #:
 STUDY_ASSAY_MEASUREMENT_TYPE = "Study Assay Measurement Type"  #:
 STUDY_ASSAY_MEASUREMENT_TYPE_TERM_ACCESSION_NUMBER = (
-    "Study Assay Measurement Type Term Accession Number"
-)  #:
+    "Study Assay Measurement Type Term Accession Number"  #:
+)
 STUDY_ASSAY_MEASUREMENT_TYPE_TERM_SOURCE_REF = "Study Assay Measurement Type Term Source REF"  #:
 STUDY_ASSAY_TECHNOLOGY_TYPE = "Study Assay Technology Type"  #:
 STUDY_ASSAY_TECHNOLOGY_TYPE_TERM_ACCESSION_NUMBER = (
-    "Study Assay Technology Type Term Accession Number"
-)  #:
+    "Study Assay Technology Type Term Accession Number"  #:
+)
 STUDY_ASSAY_TECHNOLOGY_TYPE_TERM_SOURCE_REF = "Study Assay Technology Type Term Source REF"  #:
 STUDY_ASSAY_TECHNOLOGY_PLATFORM = "Study Assay Technology Platform"  #:
 #: Collected header keys of STUDY ASSAYS section
@@ -217,19 +217,19 @@
 STUDY_PROTOCOL_VERSION = "Study Protocol Version"  #:
 STUDY_PROTOCOL_PARAMETERS_NAME = "Study Protocol Parameters Name"  #:
 STUDY_PROTOCOL_PARAMETERS_NAME_TERM_ACCESSION_NUMBER = (
-    "Study Protocol Parameters Name Term Accession Number"
-)  #:
+    "Study Protocol Parameters Name Term Accession Number"  #:
+)
 STUDY_PROTOCOL_PARAMETERS_NAME_TERM_SOURCE_REF = (
-    "Study Protocol Parameters Name Term Source REF"
-)  #:
+    "Study Protocol Parameters Name Term Source REF"  #:
+)
 STUDY_PROTOCOL_COMPONENTS_NAME = "Study Protocol Components Name"  #:
 STUDY_PROTOCOL_COMPONENTS_TYPE = "Study Protocol Components Type"  #:
 STUDY_PROTOCOL_COMPONENTS_TYPE_TERM_ACCESSION_NUMBER = (
-    "Study Protocol Components Type Term Accession Number"
-)  #:
+    "Study Protocol Components Type Term Accession Number"  #:
+)
 STUDY_PROTOCOL_COMPONENTS_TYPE_TERM_SOURCE_REF = (
-    "Study Protocol Components Type Term Source REF"
-)  #:
+    "Study Protocol Components Type Term Source REF"  #:
+)
 #: Collected header keys of STUDY PROTOCOLS section
 STUDY_PROTOCOLS_KEYS = (
     STUDY_PROTOCOL_NAME,

altamisa/constants/table_headers.py

@@ -36,8 +36,8 @@
 METABOLITE_ASSIGNMENT_FILE = "Metabolite Assignment File"  #:
 PEPTIDE_ASSIGNMENT_FILE = "Peptide Assignment File"  #:
 POST_TRANSLATIONAL_MODIFICATION_ASSIGNMENT_FILE = (
-    "Post Translational Modification Assignment File"
-)  #:
+    "Post Translational Modification Assignment File"  #:
+)
 PROTEIN_ASSIGNMENT_FILE = "Protein Assignment File"  #:
 RAW_DATA_FILE = "Raw Data File"  #:
 RAW_SPECTRAL_DATA_FILE = "Raw Spectral Data File"  #:

altamisa/isatab/models.py

@@ -93,8 +93,7 @@ class Comment:
 
 @attr.s(auto_attribs=True, frozen=True)
 class OntologyRef:
-    """Description of an ontology term source, as used for investigation file.
-    """
+    """Description of an ontology term source, as used for investigation file."""
 
     #: The name of the ontology (e.g., ``CEBI``)
     name: str
@@ -112,8 +111,7 @@ class OntologyRef:
 
 @attr.s(auto_attribs=True, frozen=True)
 class BasicInfo:
-    """Basic metadata for an investigation or study (``INVESTIGATION`` or ``STUDY``).
-    """
+    """Basic metadata for an investigation or study (``INVESTIGATION`` or ``STUDY``)."""
 
     #: Path to the investigation or study file
     path: Path
@@ -135,8 +133,7 @@ class BasicInfo:
 
 @attr.s(auto_attribs=True, frozen=True)
 class PublicationInfo:
-    """Information regarding an investigation publication (``INVESTIGATION PUBLICATIONS``).
-    """
+    """Information regarding an investigation publication (``INVESTIGATION PUBLICATIONS``)."""
 
     #: Publication PubMed ID
     pubmed_id: str

altamisa/isatab/parse_investigation.py

@@ -56,7 +56,7 @@ def _split_study_protocols_parameters(
         tpl = "Repeated protocol parameter; found: {}"
         msg = tpl.format(names)
         raise ParseIsatabException(msg)
-    for (name, acc, src) in zip(names, name_term_accs, name_term_srcs):
+    for name, acc, src in zip(names, name_term_accs, name_term_srcs):
         if any((name, acc, src)):  # skips empty parameters
             yield models.OntologyTermRef(name, acc, src)
 
@@ -79,7 +79,7 @@ def _split_study_protocols_components(
         tpl = "Repeated protocol components; found: {}"
         msg = tpl.format(names)
         raise ParseIsatabException(msg)
-    for (name, ctype, acc, src) in zip(
+    for name, ctype, acc, src in zip(
         names, types, type_term_accs, type_term_srcs
     ):  # pragma: no cover
         if not name and any((ctype, acc, src)):

altamisa/isatab/write_assay_study.py

@@ -167,8 +167,7 @@ def run(self):
 
 
 class _WriterBase:
-    """Base class that writes a file from an ``Study`` or ``Assay`` object.
-    """
+    """Base class that writes a file from an ``Study`` or ``Assay`` object."""
 
     #: Note type starting a graph
     _starting_type = None

docs/conf.py

@@ -54,9 +54,9 @@
 master_doc = "index"
 
 # General information about the project.
-project = u"AltamISA"
-copyright = u"2018-2019, Berlin Institute of Health"
-author = u"Mathias Kuhring, Manuel Holtgrewe"
+project = "AltamISA"
+copyright = "2018-2019, Berlin Institute of Health"
+author = "Mathias Kuhring, Manuel Holtgrewe"
 
 # The version info for the project you're documenting, acts as replacement
 # for |version| and |release|, also used in various other places throughout
@@ -132,15 +132,15 @@
 # (source start file, target name, title, author, documentclass
 # [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, "altamisa.tex", u"AltamISA Documentation", u"Core Unit Bioinformatics", "manual")
+    (master_doc, "altamisa.tex", "AltamISA Documentation", "Core Unit Bioinformatics", "manual")
 ]
 
 
 # -- Options for manual page output ------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [(master_doc, "altamisa", u"AltamISA Documentation", [author], 1)]
+man_pages = [(master_doc, "altamisa", "AltamISA Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output ----------------------------------------
@@ -152,7 +152,7 @@
     (
         master_doc,
         "altamisa",
-        u"AltamISA Documentation",
+        "AltamISA Documentation",
         author,
         "altamisa",
         "One line description of project.",

requirements/test_black.txt

@@ -4,4 +4,4 @@
 -r test.txt
 
 # Black for formatting
-black ==18.9b0
+black == 23.10.1

setup.py

@@ -45,10 +45,10 @@ def parse_requirements(path):
         "Natural Language :: English",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
         "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.6",
-        "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: 3.11",
     ],
     entry_points={
         "console_scripts": (

tests/conftest.py

@@ -63,26 +63,23 @@ def small_assay_file():
 
 @pytest.fixture
 def full_investigation_file():
-    """This file contains values for each normal investigation section and key.
-    """
+    """This file contains values for each normal investigation section and key."""
     path = os.path.join(os.path.dirname(__file__), "data/i_fullinvest/i_fullinvest.txt")
     with open(path, "rt") as file:
         yield file
 
 
 @pytest.fixture
 def full2_investigation_file():
-    """This file contains values for each normal investigation section and key.
-    """
+    """This file contains values for each normal investigation section and key."""
     path = os.path.join(os.path.dirname(__file__), "data/i_fullinvest2/i_fullinvest2.txt")
     with open(path, "rt") as file:
         yield file
 
 
 @pytest.fixture
 def comment_investigation_file():
-    """This file contains comments for each investigation section.
-    """
+    """This file contains comments for each investigation section."""
     path = os.path.join(os.path.dirname(__file__), "data/i_comments/i_comments.txt")
     with open(path, "rt") as file:
         yield file
@@ -124,8 +121,7 @@ def small2_study_file():
 
 @pytest.fixture
 def small2_assay_file():
-    """This file contains splitting and pooling examples.
-    """
+    """This file contains splitting and pooling examples."""
     path = os.path.join(os.path.dirname(__file__), "data/i_small2/a_small2.txt")
     with open(path, "rt") as file:
         yield file
@@ -140,8 +136,7 @@ def gelelect_investigation_file():
 
 @pytest.fixture
 def gelelect_assay_file():
-    """This file contains special cases for gel electrophoresis assays.
-    """
+    """This file contains special cases for gel electrophoresis assays."""
     path = os.path.join(
         os.path.dirname(__file__),
         "data/test_gelelect/a_study01_protein_expression_profiling_gel_electrophoresis.txt",

tests/test_exceptions.py

@@ -19,7 +19,7 @@ def test_header_exception_simple_header_not_allowed(assay_file_exception_simple_
 
 
 def test_header_exception_labeled_header_not_allowed(
-    assay_file_exception_labeled_header_not_allowed
+    assay_file_exception_labeled_header_not_allowed,
 ):
     with pytest.raises(ParseIsatabException) as excinfo:
         AssayReader.from_stream("S1", "A1", assay_file_exception_labeled_header_not_allowed)
@@ -35,7 +35,7 @@ def test_header_exception_unknown_header(assay_file_exception_unknown_header):
 
 
 def test_header_exception_term_source_ref_next_column(
-    assay_file_exception_term_source_ref_next_column
+    assay_file_exception_term_source_ref_next_column,
 ):
     with pytest.raises(ParseIsatabException) as excinfo:
         AssayReader.from_stream("S1", "A1", assay_file_exception_term_source_ref_next_column)
@@ -44,7 +44,7 @@ def test_header_exception_term_source_ref_next_column(
 
 
 def test_header_exception_term_source_ref_stop_iteration(
-    assay_file_exception_term_source_ref_stop_iteration
+    assay_file_exception_term_source_ref_stop_iteration,
 ):
     with pytest.raises(ParseIsatabException) as excinfo:
         AssayReader.from_stream("S1", "A1", assay_file_exception_term_source_ref_stop_iteration)