Merge pull request #18063 from galaxybot/dev_auto_update_dependencies

Update Python dependencies

config/plugins/webhooks/demo/tour_generator/__init__.py

@@ -59,7 +59,7 @@ def _upload_test_data(self):
                 filename = test_datasets[input_name]
                 input_path = self._tool.test_data_path(filename)
                 if not input_path:
-                    raise ValueError('Test dataset "%s" doesn\'t exist.' % input_name)
+                    raise ValueError(f'Test dataset "{input_name}" doesn\'t exist.')
                 upload_tool = self._trans.app.toolbox.get_tool("upload1")
                 filename = os.path.basename(input_path)
                 with open(input_path, "rb") as f:
@@ -92,12 +92,12 @@ def _upload_test_data(self):
 
     def _generate_tour(self):
         """Generate a tour."""
-        tour_name = self._tool.name + " Tour"
+        tour_name = f"{self._tool.name} Tour"
         test_inputs = self._test.inputs.keys()
         steps = [
             {
                 "title": tour_name,
-                "content": "This short tour will guide you through the <b>" + self._tool.name + "</b> tool.",
+                "content": f"This short tour will guide you through the <b>{self._tool.name}</b> tool.",
                 "orphan": True,
             }
         ]
@@ -107,26 +107,26 @@ def _generate_tour(self):
                 continue
             step = {
                 "title": input.label,
-                "element": "[id='form-element-%s']" % name,
+                "element": f"[id='form-element-{name}']",
                 "placement": "right",
                 "content": "",
             }
             if input.type == "text":
                 if name in test_inputs:
                     param = self._test.inputs[name]
-                    step["content"] = "Enter value(s): <b>%s</b>" % param
+                    step["content"] = f"Enter value(s): <b>{param}</b>"
                 else:
                     step["content"] = "Enter a value"
             elif input.type == "integer" or input.type == "float":
                 if name in test_inputs:
                     num_param = self._test.inputs[name][0]
-                    step["content"] = "Enter number: <b>%s</b>" % num_param
+                    step["content"] = f"Enter number: <b>{num_param}</b>"
                 else:
                     step["content"] = "Enter a number"
             elif input.type == "boolean":
                 if name in test_inputs:
                     choice = "Yes" if self._test.inputs[name][0] is True else "No"
-                    step["content"] = "Choose <b>%s</b>" % choice
+                    step["content"] = f"Choose <b>{choice}</b>"
                 else:
                     step["content"] = "Choose Yes/No"
             elif input.type == "select":
@@ -138,7 +138,7 @@ def _generate_tour(self):
                                 params.append(option[0])
                 if params:
                     select_param = ", ".join(params)
-                    step["content"] = "Select parameter(s): <b>%s</b>" % select_param
+                    step["content"] = f"Select parameter(s): <b>{select_param}</b>"
                 else:
                     step["content"] = "Select a parameter"
             elif input.type == "data":
@@ -151,7 +151,7 @@ def _generate_tour(self):
             elif input.type == "conditional":
                 param_id = f"{input.name}|{input.test_param.name}"
                 step["title"] = input.test_param.label
-                step["element"] = "[id='form-element-%s']" % param_id
+                step["element"] = f"[id='form-element-{param_id}']"
                 params = []
                 if param_id in self._test.inputs.keys():
                     for option in input.test_param.static_options:
@@ -173,24 +173,24 @@ def _generate_tour(self):
                                 step_msg = f"Select dataset: <b>{hid}: {dataset}</b>"
                             else:
                                 case_params = ", ".join(self._test.inputs[tour_id])
-                                step_msg = "Select parameter(s): " + "<b>%s</b>" % case_params
+                                step_msg = f"Select parameter(s): <b>{case_params}</b>"
                             cond_case_steps.append(
                                 {
                                     "title": case_title,
-                                    "element": "[id='form-element-%s']" % tour_id,
+                                    "element": f"[id='form-element-{tour_id}']",
                                     "placement": "right",
                                     "content": step_msg,
                                 }
                             )
                 if params:
                     cond_param = ", ".join(params)
-                    step["content"] = "Select parameter(s): <b>%s</b>" % cond_param
+                    step["content"] = f"Select parameter(s): <b>{cond_param}</b>"
                 else:
                     step["content"] = "Select a parameter"
             elif input.type == "data_column":
                 if name in test_inputs:
                     column_param = self._test.inputs[name][0]
-                    step["content"] = "Select <b>Column: %s</b>" % column_param
+                    step["content"] = f"Select <b>Column: {column_param}</b>"
                 else:
                     step["content"] = "Select a column"
             else:
@@ -210,7 +210,7 @@ def _generate_tour(self):
         self._tour = {
             "title_default": tour_name,
             "name": tour_name,
-            "description": self._tool.name + " " + self._tool.description,
+            "description": f"{self._tool.name} {self._tool.description}",
             "steps": steps,
         }
 

doc/parse_gx_xsd.py

@@ -34,7 +34,7 @@ def main():
 
 
 class Tag:
-    def __init__(self, line):
+    def __init__(self, line: str):
         assert line.startswith("$tag:")
         line_parts = line.split(" ")
         first_part = line_parts[0]
@@ -52,12 +52,12 @@ def __init__(self, line):
 
     @property
     def _pretty_title(self):
-        return " > ".join("``%s``" % p for p in self.title.split("|"))
+        return " > ".join(f"``{p}``" for p in self.title.split("|"))
 
     def build_help(self):
         tag = xmlschema_doc.find(self.xpath)
         if tag is None:
-            raise Exception("Could not find xpath for %s" % self.xpath)
+            raise Exception(f"Could not find xpath for {self.xpath}")
 
         tag_help = StringIO()
         tag_help.write("## " + self._pretty_title)
@@ -98,7 +98,7 @@ def _build_tag(tag, hide_attributes):
                     doc = _doc_or_none(element)
                     if doc is None:
                         doc = _doc_or_none(_type_el(element))
-                    assert doc is not None, "Documentation for %s is empty" % element.attrib["name"]
+                    assert doc is not None, f"Documentation for {element.attrib['name']} is empty"
                     doc = doc.strip()
 
                     element_el = _find_tag_el(element)
@@ -110,10 +110,9 @@ def _build_tag(tag, hide_attributes):
     if best_practices := _get_bp_link(annotation_el):
         tag_help.write("\n\n### Best Practices\n")
         tag_help.write(
-            """
-Find the Intergalactic Utilities Commision suggested best practices for this
-element [here](%s)."""
-            % best_practices
+            f"""
+Find the Intergalactic Utilities Commission suggested best practices for this
+element [here]({best_practices})."""
         )
     tag_help.write(_build_attributes_table(tag, attributes, hide_attributes))
 
@@ -140,7 +139,7 @@ def _get_bp_link(annotation_el):
     anchor = annotation_el.attrib.get("{http://galaxyproject.org/xml/1.0}best_practices", None)
     link = None
     if anchor:
-        link = "https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html#%s" % anchor
+        link = f"https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html#{anchor}"
     return link
 
 
@@ -149,7 +148,7 @@ def _build_attributes_table(tag, attributes, hide_attributes=False, attribute_na
     attribute_table.write("\n\n")
     if attributes and not hide_attributes:
         header_prefix = "#" * header_level
-        attribute_table.write("\n%s Attributes\n\n" % header_prefix)
+        attribute_table.write(f"\n{header_prefix} Attributes\n\n")
         attribute_table.write("Attribute | Details | Required\n")
         attribute_table.write("--- | --- | ---\n")
         for attribute in attributes:
@@ -159,7 +158,7 @@ def _build_attributes_table(tag, attributes, hide_attributes=False, attribute_na
             details = _doc_or_none(attribute)
             if details is None:
                 type_el = _type_el(attribute)
-                assert type_el is not None, "No details or type found for %s" % name
+                assert type_el is not None, f"No details or type found for {name}"
                 details = _doc_or_none(type_el)
                 annotation_el = type_el.find("{http://www.w3.org/2001/XMLSchema}annotation")
             else:
@@ -170,10 +169,7 @@ def _build_attributes_table(tag, attributes, hide_attributes=False, attribute_na
             details = details.replace("|", "\\|").strip()
             best_practices = _get_bp_link(annotation_el)
             if best_practices:
-                details += (
-                    """ Find the Intergalactic Utilities Commision suggested best practices for this element [here](%s)."""
-                    % best_practices
-                )
+                details += f""" Find the Intergalactic Utilities Commission suggested best practices for this element [here]({best_practices})."""
 
             attribute_table.write(f"``{name}`` | {details} | {use}\n")
     return attribute_table.getvalue()
@@ -204,7 +200,7 @@ def _find_attributes(tag):
     for attribute_group in attribute_groups:
         attribute_group_name = attribute_group.get("ref")
         attribute_group_def = xmlschema_doc.find(
-            "//{http://www.w3.org/2001/XMLSchema}attributeGroup/[@name='%s']" % attribute_group_name
+            f"//{{http://www.w3.org/2001/XMLSchema}}attributeGroup/[@name='{attribute_group_name}']"
         )
         attributes.extend(_find_attributes(attribute_group_def))
     return attributes
@@ -219,9 +215,9 @@ def _find_tag_el(tag):
 
 def _type_el(tag):
     element_type = tag.attrib["type"]
-    type_el = xmlschema_doc.find("//{http://www.w3.org/2001/XMLSchema}complexType/[@name='%s']" % element_type)
+    type_el = xmlschema_doc.find(f"//{{http://www.w3.org/2001/XMLSchema}}complexType/[@name='{element_type}']")
     if type_el is None:
-        type_el = xmlschema_doc.find("//{http://www.w3.org/2001/XMLSchema}simpleType/[@name='%s']" % element_type)
+        type_el = xmlschema_doc.find(f"//{{http://www.w3.org/2001/XMLSchema}}simpleType/[@name='{element_type}']")
     return type_el
 
 

lib/galaxy/actions/library.py

@@ -265,7 +265,7 @@ def _check_path_paste_params(self, params):
             if not os.path.exists(path):
                 bad_paths.append(path)
         if bad_paths:
-            message = 'Invalid paths: "%s".' % '", "'.join(bad_paths)
+            message = 'Invalid paths: "{}".'.format('", "'.join(bad_paths))
             response_code = 400
             return None, response_code, message
         return None

lib/galaxy/auth/providers/ldap_ad.py

@@ -135,8 +135,8 @@ def check_config(self, username, email, options):
         self.role_search_attribute = options.get(self.role_search_option)
         if self.auto_create_roles_or_groups and self.role_search_attribute is None:
             raise ConfigurationError(
-                "If 'auto-create-roles' or 'auto-create-groups' is True, a '%s' attribute has to"
-                " be provided." % self.role_search_option
+                f"If 'auto-create-roles' or 'auto-create-groups' is True, a '{self.role_search_option}' attribute has to"
+                " be provided."
             )
 
         return ok, failure_mode

lib/galaxy/config/__init__.py

@@ -944,7 +944,8 @@ def _process_config(self, kwargs: Dict[str, Any]) -> None:
                     log.warning(
                         "The path '%s' for the 'sanitize_allowlist_file' config option is "
                         "deprecated and will be no longer checked in a future release. Please consult "
-                        "the latest version of the sample configuration file." % deprecated
+                        "the latest version of the sample configuration file.",
+                        deprecated,
                     )
                     _sanitize_allowlist_path = deprecated
                     break
@@ -965,7 +966,7 @@ def _process_config(self, kwargs: Dict[str, Any]) -> None:
         )
         # Searching data libraries
         self.ftp_upload_dir_template = kwargs.get(
-            "ftp_upload_dir_template", "${ftp_upload_dir}%s${ftp_upload_dir_identifier}" % os.path.sep
+            "ftp_upload_dir_template", f"${{ftp_upload_dir}}{os.path.sep}${{ftp_upload_dir_identifier}}"
         )
         # Support older library-specific path paste option but just default to the new
         # allow_path_paste value.

lib/galaxy/datatypes/binary.py

@@ -2089,7 +2089,7 @@ def display_peek(self, dataset: DatasetProtocol) -> str:
         try:
             return dataset.peek
         except Exception:
-            return "HDF5 Model (%s)" % (nice_size(dataset.get_size()))
+            return f"HDF5 Model ({nice_size(dataset.get_size())})"
 
     def display_data(
         self,
@@ -4258,7 +4258,7 @@ def display_peek(self, dataset: DatasetProtocol) -> str:
         try:
             return dataset.peek
         except Exception:
-            return "Binary pretext file (%s)" % (nice_size(dataset.get_size()))
+            return f"Binary pretext file ({nice_size(dataset.get_size())})"
 
 
 class JP2(Binary):
@@ -4302,7 +4302,7 @@ def display_peek(self, dataset: DatasetProtocol) -> str:
         try:
             return dataset.peek
         except Exception:
-            return "Binary JPEG 2000 file (%s)" % (nice_size(dataset.get_size()))
+            return f"Binary JPEG 2000 file ({nice_size(dataset.get_size())})"
 
 
 class Npz(CompressedArchive):
@@ -4356,7 +4356,7 @@ def display_peek(self, dataset: DatasetProtocol) -> str:
         try:
             return dataset.peek
         except Exception:
-            return "Binary Numpy npz file (%s)" % (nice_size(dataset.get_size()))
+            return f"Binary Numpy npz file ({nice_size(dataset.get_size())})"
 
 
 class HexrdImagesNpz(Npz):
@@ -4433,7 +4433,7 @@ def display_peek(self, dataset: DatasetProtocol) -> str:
         try:
             return dataset.peek
         except Exception:
-            return "Binary Numpy npz file (%s)" % (nice_size(dataset.get_size()))
+            return f"Binary Numpy npz file ({nice_size(dataset.get_size())})"
 
 
 class HexrdEtaOmeNpz(Npz):
@@ -4495,7 +4495,7 @@ def display_peek(self, dataset: DatasetProtocol) -> str:
         try:
             return dataset.peek
         except Exception:
-            return "Binary Numpy npz file (%s)" % (nice_size(dataset.get_size()))
+            return f"Binary Numpy npz file ({nice_size(dataset.get_size())})"
 
 
 class FITS(Binary):
@@ -4624,4 +4624,4 @@ def display_peek(self, dataset: DatasetProtocol) -> str:
         try:
             return dataset.peek
         except Exception:
-            return "Binary numpy file (%s)" % (nice_size(dataset.get_size()))
+            return f"Binary numpy file ({nice_size(dataset.get_size())})"

lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py

@@ -181,7 +181,7 @@ def __main__():
                     fields = [str(item) for item in (region.chrom, region.start, region.end, name, 0, region.strand)]
                     if force_num_columns is not None and len(fields) != force_num_columns:
                         fields = force_bed_field_count(fields, count, force_num_columns)
-                    out.write("%s\n" % "\t".join(fields))
+                    out.write("{}\n".format("\t".join(fields)))
                 except Exception:
                     skipped_lines += 1
                     if first_skipped_line is None:

lib/galaxy/datatypes/converters/maf_to_fasta_converter.py

@@ -24,11 +24,12 @@ def __main__():
                 else:
                     spec_counts[spec] += 1
                 out.write(
-                    "%s\n"
-                    % maf_utilities.get_fasta_header(
-                        c,
-                        {"block_index": count, "species": spec, "sequence_index": spec_counts[spec]},
-                        suffix="%s_%i_%i" % (spec, count, spec_counts[spec]),
+                    "{}\n".format(
+                        maf_utilities.get_fasta_header(
+                            c,
+                            {"block_index": count, "species": spec, "sequence_index": spec_counts[spec]},
+                            suffix="%s_%i_%i" % (spec, count, spec_counts[spec]),
+                        )
                     )
                 )
                 out.write(f"{c.text}\n")

lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py

@@ -20,7 +20,7 @@ def main():
     with open(sys.argv[1]) as in_file, open(sys.argv[2], "w") as out_file:
         try:
             for fields in bx.wiggle.IntervalReader(UCSCOutWrapper(in_file)):
-                out_file.write("%s\n" % "\t".join(map(str, fields)))
+                out_file.write("{}\n".format("\t".join(map(str, fields))))
         except UCSCLimitException:
             # Wiggle data was truncated, at the very least need to warn the user.
             sys.stderr.write(

lib/galaxy/datatypes/interval.py

@@ -289,18 +289,18 @@ def as_ucsc_display_file(self, dataset: DatasetProtocol, **kwd) -> Union[FileObj
                     if t < len(elems):
                         strand = cast(str, elems[t])
                     tmp = [elems[c], elems[s], elems[e], name, "0", strand]
-                    fh.write("%s\n" % "\t".join(tmp))
+                    fh.write("{}\n".format("\t".join(tmp)))
             elif n >= 0:  # name column (should) exists
                 for i, elems in enumerate(compression_utils.file_iter(dataset.get_file_name())):
                     name = "region_%i" % i
                     if n >= 0 and n < len(elems):
                         name = cast(str, elems[n])
                     tmp = [elems[c], elems[s], elems[e], name]
-                    fh.write("%s\n" % "\t".join(tmp))
+                    fh.write("{}\n".format("\t".join(tmp)))
             else:
                 for elems in compression_utils.file_iter(dataset.get_file_name()):
                     tmp = [elems[c], elems[s], elems[e]]
-                    fh.write("%s\n" % "\t".join(tmp))
+                    fh.write("{}\n".format("\t".join(tmp)))
             return compression_utils.get_fileobj(fh.name, mode="rb")
 
     def display_peek(self, dataset: DatasetProtocol) -> str:

lib/galaxy/datatypes/neo4j.py

@@ -30,9 +30,8 @@ def generate_primary_file(self, dataset: HasExtraFilesAndMetadata) -> str:
         """
         # self.regenerate_primary_file(dataset)
         rval = [
-            "<html><head><title>Files for Composite Dataset (%s)</title></head><p/>\
+            f"<html><head><title>Files for Composite Dataset ({self.file_ext})</title></head><p/>\
             This composite dataset is composed of the following files:<p/><ul>"
-            % (self.file_ext)
         ]
         for composite_name, composite_file in self.get_composite_files(dataset=dataset).items():
             opt_text = ""

lib/galaxy/datatypes/proteomics.py

@@ -714,7 +714,7 @@ def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
             if not line.startswith("<?"):
                 break
         # pattern match <root or <ns:root for any ns string
-        pattern = r"<(\w*:)?%s" % self.root
+        pattern = rf"<(\w*:)?{self.root}"
         return re.search(pattern, line) is not None
 
     def set_peek(self, dataset: DatasetProtocol, **kwd) -> None: