run pyupgrade for python 3.8 compatibility

docs/api/_src/conf.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 #
 # Configuration file for the Sphinx documentation builder.
 #

nf_core/bump_version.py

@@ -187,7 +187,7 @@ def update_file_version(filename: Union[str, Path], pipeline_obj: Pipeline, patt
     fn = pipeline_obj._fp(filename)
     content = ""
     try:
-        with open(fn, "r") as fh:
+        with open(fn) as fh:
             content = fh.read()
     except FileNotFoundError:
         log.warning(f"File not found: '{fn}'")

nf_core/components/components_command.py

@@ -227,7 +227,7 @@ def check_patch_paths(self, patch_path: Path, module_name: str) -> None:
         if patch_path.exists():
             log.info(f"Modules {module_name} contains a patch file.")
             rewrite = False
-            with open(patch_path, "r") as fh:
+            with open(patch_path) as fh:
                 lines = fh.readlines()
                 for index, line in enumerate(lines):
                     # Check if there are old paths in the patch file and replace
@@ -264,7 +264,7 @@ def check_if_in_include_stmts(self, component_path: str) -> Dict[str, List[Dict[
         if self.repo_type == "pipeline":
             workflow_files = Path(self.dir, "workflows").glob("*.nf")
             for workflow_file in workflow_files:
-                with open(workflow_file, "r") as fh:
+                with open(workflow_file) as fh:
                     # Check if component path is in the file using mmap
                     with mmap.mmap(fh.fileno(), 0, access=mmap.ACCESS_READ) as s:
                         if s.find(component_path.encode()) != -1:

nf_core/components/components_utils.py

@@ -138,7 +138,7 @@ def get_components_to_install(subworkflow_dir: str) -> Tuple[List[str], List[str
     """
     modules = []
     subworkflows = []
-    with open(Path(subworkflow_dir, "main.nf"), "r") as fh:
+    with open(Path(subworkflow_dir, "main.nf")) as fh:
         for line in fh:
             regex = re.compile(
                 r"include(?: *{ *)([a-zA-Z\_0-9]*)(?: *as *)?(?:[a-zA-Z\_0-9]*)?(?: *})(?: *from *)(?:'|\")(.*)(?:'|\")"

nf_core/components/create.py

@@ -2,7 +2,6 @@
 The ComponentCreate class handles generating of module and subworkflow templates
 """
 
-from __future__ import print_function
 
 import glob
 import json
@@ -440,7 +439,7 @@ def _copy_old_files(self, component_old_path):
         pytest_dir = Path(self.directory, "tests", self.component_type, self.org, self.component_dir)
         nextflow_config = pytest_dir / "nextflow.config"
         if nextflow_config.is_file():
-            with open(nextflow_config, "r") as fh:
+            with open(nextflow_config) as fh:
                 config_lines = ""
                 for line in fh:
                     if "publishDir" not in line:
@@ -460,7 +459,7 @@ def _print_and_delete_pytest_files(self):
             "[violet]Do you want to delete the pytest files?[/]\nPytest file 'main.nf' will be printed to standard output to allow migrating the tests manually to 'main.nf.test'.",
             default=False,
         ):
-            with open(pytest_dir / "main.nf", "r") as fh:
+            with open(pytest_dir / "main.nf") as fh:
                 log.info(fh.read())
             shutil.rmtree(pytest_dir)
             log.info(
@@ -475,7 +474,7 @@ def _print_and_delete_pytest_files(self):
             )
         # Delete tags from pytest_modules.yml
         modules_yml = Path(self.directory, "tests", "config", "pytest_modules.yml")
-        with open(modules_yml, "r") as fh:
+        with open(modules_yml) as fh:
             yml_file = yaml.safe_load(fh)
         yml_key = str(self.component_dir) if self.component_type == "modules" else f"subworkflows/{self.component_dir}"
         if yml_key in yml_file:

nf_core/components/info.py

@@ -184,7 +184,7 @@ def get_local_yaml(self):
                 meta_fn = Path(comp_dir, "meta.yml")
                 if meta_fn.exists():
                     log.debug(f"Found local file: {meta_fn}")
-                    with open(meta_fn, "r") as fh:
+                    with open(meta_fn) as fh:
                         self.local_path = comp_dir
                         return yaml.safe_load(fh)
 
@@ -196,7 +196,7 @@ def get_local_yaml(self):
                 meta_fn = Path(comp_dir, "meta.yml")
                 if meta_fn.exists():
                     log.debug(f"Found local file: {meta_fn}")
-                    with open(meta_fn, "r") as fh:
+                    with open(meta_fn) as fh:
                         self.local_path = comp_dir
                         return yaml.safe_load(fh)
             log.debug(f"{self.component_type[:-1].title()} '{self.component}' meta.yml not found locally")

nf_core/components/lint/__init__.py

@@ -3,7 +3,6 @@
 in nf-core pipelines
 """
 
-from __future__ import print_function
 
 import logging
 import operator

nf_core/components/nfcore_component.py

@@ -81,7 +81,7 @@ def __init__(
     def _get_main_nf_tags(self, test_main_nf: Union[Path, str]):
         """Collect all tags from the main.nf.test file."""
         tags = []
-        with open(test_main_nf, "r") as fh:
+        with open(test_main_nf) as fh:
             for line in fh:
                 if line.strip().startswith("tag"):
                     tags.append(line.strip().split()[1].strip('"'))
@@ -90,7 +90,7 @@ def _get_main_nf_tags(self, test_main_nf: Union[Path, str]):
     def _get_included_components(self, main_nf: Union[Path, str]):
         """Collect all included components from the main.nf file."""
         included_components = []
-        with open(main_nf, "r") as fh:
+        with open(main_nf) as fh:
             for line in fh:
                 if line.strip().startswith("include"):
                     # get tool/subtool or subworkflow name from include statement, can be in the form
@@ -107,7 +107,7 @@ def _get_included_components(self, main_nf: Union[Path, str]):
     def _get_included_components_in_chained_tests(self, main_nf_test: Union[Path, str]):
         """Collect all included components from the main.nf file."""
         included_components = []
-        with open(main_nf_test, "r") as fh:
+        with open(main_nf_test) as fh:
             for line in fh:
                 if line.strip().startswith("script"):
                     # get tool/subtool or subworkflow name from script statement, can be:
@@ -151,7 +151,7 @@ def _get_included_components_in_chained_tests(self, main_nf_test: Union[Path, st
     def get_inputs_from_main_nf(self):
         """Collect all inputs from the main.nf file."""
         inputs = []
-        with open(self.main_nf, "r") as f:
+        with open(self.main_nf) as f:
             data = f.read()
         # get input values from main.nf after "input:", which can be formatted as tuple val(foo) path(bar) or val foo or val bar or path bar or path foo
         # regex matches:
@@ -178,7 +178,7 @@ def get_inputs_from_main_nf(self):
 
     def get_outputs_from_main_nf(self):
         outputs = []
-        with open(self.main_nf, "r") as f:
+        with open(self.main_nf) as f:
             data = f.read()
         # get output values from main.nf after "output:". the names are always after "emit:"
         if "output:" not in data:

nf_core/components/update.py

@@ -499,7 +499,7 @@ def get_all_components_info(self, branch=None):
                         ]
             elif isinstance(self.update_config[repo_name], dict):
                 # If it is a dict, then there are entries for individual components or component directories
-                for component_dir in set([dir for dir, _ in components]):
+                for component_dir in {dir for dir, _ in components}:
                     if isinstance(self.update_config[repo_name][component_dir], str):
                         # If a string is given it is the commit SHA to which we should update to
                         custom_sha = self.update_config[repo_name][component_dir]

nf_core/create.py

@@ -75,7 +75,7 @@ def __init__(
             ],
         }
         # Get list of files we're skipping with the supplied skip keys
-        self.skip_paths = set(sp for k in skip_paths_keys for sp in skippable_paths[k])
+        self.skip_paths = {sp for k in skip_paths_keys for sp in skippable_paths[k]}
 
         # Set convenience variables
         self.name = self.template_params["name"]
@@ -108,7 +108,7 @@ def create_param_dict(self, name, description, author, version, template_yaml_pa
         # Obtain template customization info from template yaml file or `.nf-core.yml` config file
         try:
             if template_yaml_path is not None:
-                with open(template_yaml_path, "r") as f:
+                with open(template_yaml_path) as f:
                     template_yaml = yaml.safe_load(f)
             elif "template" in config_yml:
                 template_yaml = config_yml["template"]
@@ -395,7 +395,7 @@ def remove_nf_core_in_bug_report_template(self):
         """
         bug_report_path = self.outdir / ".github" / "ISSUE_TEMPLATE" / "bug_report.yml"
 
-        with open(bug_report_path, "r") as fh:
+        with open(bug_report_path) as fh:
             contents = yaml.load(fh, Loader=yaml.FullLoader)
 
         # Remove the first item in the body, which is the information about the docs

nf_core/download.py

@@ -1,6 +1,5 @@
 """Downloads a nf-core pipeline to the local file system."""
 
-from __future__ import print_function
 
 import concurrent.futures
 import io
@@ -640,7 +639,7 @@ def wf_use_local_configs(self, revision_dirname):
         log.debug(f"Editing 'params.custom_config_base' in '{nfconfig_fn}'")
 
         # Load the nextflow.config file into memory
-        with open(nfconfig_fn, "r") as nfconfig_fh:
+        with open(nfconfig_fn) as nfconfig_fh:
             nfconfig = nfconfig_fh.read()
 
         # Replace the target string
@@ -700,7 +699,7 @@ def find_container_images(self, workflow_directory):
                 if bool(config_findings_dsl2):
                     # finding fill always be a tuple of length 2, first the quote used and second the enquoted value.
                     for finding in config_findings_dsl2:
-                        config_findings.append((finding + (self.nf_config, "Nextflow configs")))
+                        config_findings.append(finding + (self.nf_config, "Nextflow configs"))
                 else:  # no regex match, likely just plain string
                     """
                     Append string also as finding-like tuple for consistency
@@ -719,7 +718,7 @@ def find_container_images(self, workflow_directory):
             for file in files:
                 if file.endswith(".nf"):
                     file_path = os.path.join(subdir, file)
-                    with open(file_path, "r") as fh:
+                    with open(file_path) as fh:
                         # Look for any lines with container "xxx" or container 'xxx'
                         search_space = fh.read()
                         """
@@ -744,7 +743,7 @@ def find_container_images(self, workflow_directory):
                         for finding in local_module_findings:
                             # append finding since we want to collect them from all modules
                             # also append search_space because we need to start over later if nothing was found.
-                            module_findings.append((finding + (search_space, file_path)))
+                            module_findings.append(finding + (search_space, file_path))
 
         # Not sure if there will ever be multiple container definitions per module, but beware DSL3.
         # Like above run on shallow copy, because length may change at runtime.

nf_core/launch.py

@@ -1,6 +1,5 @@
 """ Launch a pipeline, interactively collecting params """
 
-from __future__ import print_function
 
 import copy
 import json

nf_core/licences.py

@@ -1,6 +1,5 @@
 """Lists software licences for a given workflow."""
 
-from __future__ import print_function
 
 import json
 import logging

nf_core/lint/actions_awsfulltest.py

@@ -32,7 +32,7 @@ def actions_awsfulltest(self):
     fn = os.path.join(self.wf_path, ".github", "workflows", "awsfulltest.yml")
     if os.path.isfile(fn):
         try:
-            with open(fn, "r") as fh:
+            with open(fn) as fh:
                 wf = yaml.safe_load(fh)
         except Exception as e:
             return {"failed": [f"Could not parse yaml file: {fn}, {e}"]}

nf_core/lint/actions_awstest.py

@@ -27,7 +27,7 @@ def actions_awstest(self):
         return {"ignored": [f"'awstest.yml' workflow not found: `{fn}`"]}
 
     try:
-        with open(fn, "r") as fh:
+        with open(fn) as fh:
             wf = yaml.safe_load(fh)
     except Exception as e:
         return {"failed": [f"Could not parse yaml file: {fn}, {e}"]}

nf_core/lint/actions_ci.py

@@ -48,7 +48,7 @@ def actions_ci(self):
         return {"ignored": ["'.github/workflows/ci.yml' not found"]}
 
     try:
-        with open(fn, "r") as fh:
+        with open(fn) as fh:
             ciwf = yaml.safe_load(fh)
     except Exception as e:
         return {"failed": [f"Could not parse yaml file: {fn}, {e}"]}

nf_core/lint/actions_schema_validation.py

@@ -36,7 +36,7 @@ def actions_schema_validation(self):
 
         # load workflow
         try:
-            with open(wf_path, "r") as fh:
+            with open(wf_path) as fh:
                 wf_json = yaml.safe_load(fh)
         except Exception as e:
             failed.append(f"Could not parse yaml file: {wf}, {e}")

nf_core/lint/files_unchanged.py

@@ -187,16 +187,16 @@ def _tf(file_path):
         else:
             for f in files:
                 try:
-                    with open(_pf(f), "r") as fh:
+                    with open(_pf(f)) as fh:
                         pipeline_file = fh.read()
-                    with open(_tf(f), "r") as fh:
+                    with open(_tf(f)) as fh:
                         template_file = fh.read()
                     if template_file in pipeline_file:
                         passed.append(f"`{f}` matches the template")
                     else:
                         if "files_unchanged" in self.fix:
                             # Try to fix the problem by overwriting the pipeline file
-                            with open(_tf(f), "r") as fh:
+                            with open(_tf(f)) as fh:
                                 template_file = fh.read()
                             with open(_pf(f), "w") as fh:
                                 fh.write(template_file)

nf_core/lint/merge_markers.py

@@ -23,7 +23,7 @@ def merge_markers(self):
 
     ignore = [".git"]
     if os.path.isfile(os.path.join(self.wf_path, ".gitignore")):
-        with io.open(os.path.join(self.wf_path, ".gitignore"), "rt", encoding="latin1") as fh:
+        with open(os.path.join(self.wf_path, ".gitignore"), encoding="latin1") as fh:
             for l in fh:
                 ignore.append(os.path.basename(l.strip().rstrip("/")))
     for root, dirs, files in os.walk(self.wf_path, topdown=True):
@@ -41,7 +41,7 @@ def merge_markers(self):
             if nf_core.utils.is_file_binary(os.path.join(root, fname)):
                 continue
             try:
-                with io.open(os.path.join(root, fname), "rt", encoding="latin1") as fh:
+                with open(os.path.join(root, fname), encoding="latin1") as fh:
                     for l in fh:
                         if ">>>>>>>" in l:
                             failed.append(f"Merge marker '>>>>>>>' in `{os.path.join(root, fname)}`: {l[:30]}")

nf_core/lint/multiqc_config.py

@@ -34,7 +34,7 @@ def multiqc_config(self) -> Dict[str, List[str]]:
         return {"ignored": ["'assets/multiqc_config.yml' not found"]}
 
     try:
-        with open(fn, "r") as fh:
+        with open(fn) as fh:
             mqc_yml = yaml.safe_load(fh)
     except Exception as e:
         return {"failed": [f"Could not parse yaml file: {fn}, {e}"]}

nf_core/lint/nextflow_config.py

@@ -190,13 +190,11 @@ def nextflow_config(self):
 
     # Check and warn if the process configuration is done with deprecated syntax
     process_with_deprecated_syntax = list(
-        set(
-            [
-                re.search(r"^(process\.\$.*?)\.+.*$", ck).group(1)
-                for ck in self.nf_config.keys()
-                if re.match(r"^(process\.\$.*?)\.+.*$", ck)
-            ]
-        )
+        {
+            re.search(r"^(process\.\$.*?)\.+.*$", ck).group(1)
+            for ck in self.nf_config.keys()
+            if re.match(r"^(process\.\$.*?)\.+.*$", ck)
+        }
     )
     for pd in process_with_deprecated_syntax:
         warned.append(f"Process configuration is done with deprecated_syntax: {pd}")
@@ -300,7 +298,7 @@ def nextflow_config(self):
         ]
         path = os.path.join(self.wf_path, "nextflow.config")
         i = 0
-        with open(path, "r") as f:
+        with open(path) as f:
             for line in f:
                 if lines[i] in line:
                     i += 1
@@ -320,7 +318,7 @@ def nextflow_config(self):
             )
 
     # Check for the availability of the "test" configuration profile by parsing nextflow.config
-    with open(os.path.join(self.wf_path, "nextflow.config"), "r") as f:
+    with open(os.path.join(self.wf_path, "nextflow.config")) as f:
         content = f.read()
 
         # Remove comments

nf_core/lint/pipeline_todos.py

@@ -41,7 +41,7 @@ def pipeline_todos(self, root_dir=None):
 
     ignore = [".git"]
     if os.path.isfile(os.path.join(root_dir, ".gitignore")):
-        with io.open(os.path.join(root_dir, ".gitignore"), "rt", encoding="latin1") as fh:
+        with open(os.path.join(root_dir, ".gitignore"), encoding="latin1") as fh:
             for l in fh:
                 ignore.append(os.path.basename(l.strip().rstrip("/")))
     for root, dirs, files in os.walk(root_dir, topdown=True):
@@ -52,7 +52,7 @@ def pipeline_todos(self, root_dir=None):
             files[:] = [f for f in files if not fnmatch.fnmatch(os.path.join(root, f), i)]
         for fname in files:
             try:
-                with io.open(os.path.join(root, fname), "rt", encoding="latin1") as fh:
+                with open(os.path.join(root, fname), encoding="latin1") as fh:
                     for l in fh:
                         if "TODO nf-core" in l:
                             l = (

nf_core/lint/readme.py

@@ -31,7 +31,7 @@ def readme(self):
     # Remove field that should be ignored according to the linting config
     ignore_configs = self.lint_config.get("readme", [])
 
-    with open(os.path.join(self.wf_path, "README.md"), "r") as fh:
+    with open(os.path.join(self.wf_path, "README.md")) as fh:
         content = fh.read()
 
     if "nextflow_badge" not in ignore_configs:

nf_core/lint/template_strings.py

@@ -30,7 +30,7 @@ def template_strings(self):
         if encoding is not None or (ftype is not None and any([ftype.startswith(ft) for ft in binary_ftypes])):
             continue
 
-        with io.open(fn, "r", encoding="latin1") as fh:
+        with open(fn, encoding="latin1") as fh:
             lnum = 0
             for l in fh:
                 lnum += 1