clean up unused arguments

Remove unused arguments

CHANGELOG.md

@@ -27,6 +27,7 @@
 - Bump promoted Python version from 3.7 to 3.8 ([#1971](https://github.com/nf-core/tools/pull/1971))
 - Fix incorrect file deletion in `nf-core launch` when `--params_in` has the same name as `--params_out`
 - Updated GitHub actions ([#1998](https://github.com/nf-core/tools/pull/1998), [#2001](https://github.com/nf-core/tools/pull/2001))
+- Code maintenance ([#1818](https://github.com/nf-core/tools/pull/1818))
 - Track from where modules and subworkflows are installed ([#1999](https://github.com/nf-core/tools/pull/1999))
 - Substitute ModulesCommand and SubworkflowsCommand by ComponentsCommand ([#2000](https://github.com/nf-core/tools/pull/2000))
 - Don't print source file + line number on logging messages (except when verbose) ([#2015](https://github.com/nf-core/tools/pull/2015))
@@ -55,7 +56,7 @@
 - Update MultiQC module, update supplying MultiQC default and custom config and logo files to module
 - Add a 'recommend' methods description text to MultiQC to help pipeline users report pipeline usage in publications ([#1749](https://github.com/nf-core/tools/pull/1749))
 - Fix template spacing modified by JINJA ([#1830](https://github.com/nf-core/tools/pull/1830))
-- Fix MultiQC execution on template [#1855](https://github.com/nf-core/tools/pull/1855)
+- Fix MultiQC execution on template ([#1855](https://github.com/nf-core/tools/pull/1855))
 - Don't skip including `base.config` when skipping nf-core/configs
 
 ### Linting

nf_core/lint/__init__.py

@@ -123,7 +123,7 @@ def run_linting(
     lint_obj._print_results(show_passed)
     module_lint_obj._print_results(show_passed)
     nf_core.lint_utils.print_joint_summary(lint_obj, module_lint_obj)
-    nf_core.lint_utils.print_fixes(lint_obj, module_lint_obj)
+    nf_core.lint_utils.print_fixes(lint_obj)
 
     # Save results to Markdown file
     if md_fn is not None:

nf_core/lint_utils.py

@@ -34,19 +34,21 @@ def print_joint_summary(lint_obj, module_lint_obj):
     console.print(table)
 
 
-def print_fixes(lint_obj, module_lint_obj):
+def print_fixes(lint_obj):
     """Prints available and applied fixes"""
 
-    if len(lint_obj.could_fix):
-        fix_cmd = "nf-core lint {} --fix {}".format(
-            "" if lint_obj.wf_path == "." else f"--dir {lint_obj.wf_path}", " --fix ".join(lint_obj.could_fix)
-        )
+    if lint_obj.could_fix:
+        fix_flags = "".join([f" --fix {fix}" for fix in lint_obj.could_fix])
+        wf_dir = "" if lint_obj.wf_path == "." else f"--dir {lint_obj.wf_path}"
+        fix_cmd = f"nf-core lint {wf_dir} {fix_flags}"
         console.print(
-            f"\nTip: Some of these linting errors can automatically be resolved with the following command:\n\n[blue]    {fix_cmd}\n"
+            "\nTip: Some of these linting errors can automatically be resolved with the following command:\n\n"
+            f"[blue]    {fix_cmd}\n"
         )
     if len(lint_obj.fix):
         console.print(
-            "Automatic fixes applied. Please check with 'git diff' and revert any changes you do not want with 'git checkout <file>'."
+            "Automatic fixes applied. "
+            "Please check with 'git diff' and revert any changes you do not want with 'git checkout <file>'."
         )
 
 

nf_core/modules/lint/__init__.py

@@ -134,7 +134,6 @@ def lint(
         module=None,
         key=(),
         all_modules=False,
-        hide_progress=False,
         print_results=True,
         show_passed=False,
         local=False,

nf_core/modules/lint/main_nf.py

@@ -99,18 +99,18 @@ def main_nf(module_lint_object, module, fix_version, progress_bar):
             continue
 
         # Perform state-specific linting checks
-        if state == "process" and not _is_empty(module, l):
+        if state == "process" and not _is_empty(l):
             process_lines.append(l)
-        if state == "input" and not _is_empty(module, l):
+        if state == "input" and not _is_empty(l):
             inputs.extend(_parse_input(module, l))
-        if state == "output" and not _is_empty(module, l):
+        if state == "output" and not _is_empty(l):
             outputs += _parse_output(module, l)
             outputs = list(set(outputs))  # remove duplicate 'meta's
-        if state == "when" and not _is_empty(module, l):
+        if state == "when" and not _is_empty(l):
             when_lines.append(l)
-        if state == "script" and not _is_empty(module, l):
+        if state == "script" and not _is_empty(l):
             script_lines.append(l)
-        if state == "shell" and not _is_empty(module, l):
+        if state == "shell" and not _is_empty(l):
             shell_lines.append(l)
 
     # Check that we have required sections
@@ -390,7 +390,7 @@ def _parse_output(self, line):
     return output
 
 
-def _is_empty(self, line):
+def _is_empty(line):
     """Check whether a line is empty or a comment"""
     empty = False
     if line.strip().startswith("//"):
@@ -421,7 +421,7 @@ def _fix_module_version(self, current_version, latest_version, singularity_tag,
         build_type = _container_type(l)
         if build_type == "bioconda":
             new_lines.append(re.sub(rf"{current_version}", f"{latest_version}", line))
-        elif build_type == "singularity" or build_type == "docker":
+        elif build_type in ("singularity", "docker"):
             # Check that the new url is valid
             new_url = re.search(
                 "(?:['\"])(.+)(?:['\"])", re.sub(rf"{singularity_tag}", f"{latest_version}--{build}", line)
@@ -431,7 +431,8 @@ def _fix_module_version(self, current_version, latest_version, singularity_tag,
                     "https://" + new_url if not new_url.startswith("https://") else new_url, stream=True
                 )
                 log.debug(
-                    f"Connected to URL: {'https://' + new_url if not new_url.startswith('https://') else new_url}, status_code: {response_new_container.status_code}"
+                    f"Connected to URL: {'https://' + new_url if not new_url.startswith('https://') else new_url}, "
+                    f"status_code: {response_new_container.status_code}"
                 )
             except (requests.exceptions.RequestException, sqlite3.InterfaceError) as e:
                 log.debug(f"Unable to connect to url '{new_url}' due to error: {e}")

nf_core/modules/lint/module_deprecations.py

@@ -4,7 +4,7 @@
 log = logging.getLogger(__name__)
 
 
-def module_deprecations(module_lint_object, module):
+def module_deprecations(_, module):
     """
     Check that the modules are up to the latest nf-core standard
     """

nf_core/modules/lint/module_tests.py

@@ -9,7 +9,7 @@
 log = logging.getLogger(__name__)
 
 
-def module_tests(module_lint_object, module):
+def module_tests(_, module):
     """
     Lint the tests of a module in ``nf-core/modules``
 

nf_core/modules/lint/module_todos.py

@@ -5,7 +5,7 @@
 log = logging.getLogger(__name__)
 
 
-def module_todos(module_lint_object, module):
+def module_todos(_, module):
     """
     Look for TODO statements in the module files
 

nf_core/modules/test_yml_builder.py

@@ -56,7 +56,8 @@ def run(self):
         """Run build steps"""
         if not self.no_prompts:
             log.info(
-                "[yellow]Press enter to use default values [cyan bold](shown in brackets) [yellow]or type your own responses"
+                "[yellow]Press enter to use default values "
+                "[cyan bold](shown in brackets) [yellow]or type your own responses"
             )
         self.check_inputs()
         self.scrape_workflow_entry_points()
@@ -170,7 +171,10 @@ def build_single_test(self, entry_point):
         while ep_test["command"] == "":
             # Don't think we need the last `-c` flag, but keeping to avoid having to update 100s modules.
             # See https://github.com/nf-core/tools/issues/1562
-            default_val = f"nextflow run ./tests/modules/nf-core/{self.module_name} -entry {entry_point} -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/{self.module_name}/nextflow.config"
+            default_val = (
+                f"nextflow run ./tests/modules/nf-core/{self.module_name} -entry {entry_point} "
+                f"-c ./tests/config/nextflow.config -c ./tests/modules/nf-core/{self.module_name}/nextflow.config"
+            )
             if self.no_prompts:
                 ep_test["command"] = default_val
             else:
@@ -192,7 +196,7 @@ def build_single_test(self, entry_point):
                     ).strip()
                     ep_test["tags"] = [t.strip() for t in prompt_tags.split(",")]
 
-        ep_test["files"] = self.get_md5_sums(entry_point, ep_test["command"])
+        ep_test["files"] = self.get_md5_sums(ep_test["command"])
 
         return ep_test
 
@@ -253,7 +257,7 @@ def create_test_file_dict(self, results_dir, is_repeat=False):
 
         return test_files
 
-    def get_md5_sums(self, entry_point, command, results_dir=None, results_dir_repeat=None):
+    def get_md5_sums(self, command, results_dir=None, results_dir_repeat=None):
         """
         Recursively go through directories and subdirectories
         and generate tuples of (<file_path>, <md5sum>)

nf_core/utils.py

@@ -338,22 +338,22 @@ def setup_requests_cachedir():
     return config
 
 
-def wait_cli_function(poll_func, poll_every=20):
+def wait_cli_function(poll_func, refresh_per_second=20):
     """
     Display a command-line spinner while calling a function repeatedly.
 
     Keep waiting until that function returns True
 
     Arguments:
        poll_func (function): Function to call
-       poll_every (int): How many tenths of a second to wait between function calls. Default: 20.
+       refresh_per_second (int): Refresh this many times per second. Default: 20.
 
     Returns:
        None. Just sits in an infite loop until the function returns True.
     """
     try:
         spinner = Spinner("dots2", "Use ctrl+c to stop waiting and force exit.")
-        with Live(spinner, refresh_per_second=20):
+        with Live(spinner, refresh_per_second=refresh_per_second):
             while True:
                 if poll_func():
                     break

tests/modules/create_test_yml.py

@@ -35,9 +35,7 @@ def test_modules_create_test_yml_get_md5(self, test_file_dir):
     meta_builder = nf_core.modules.ModulesTestYmlBuilder("test/tool", self.pipeline_dir, False, "./", False, True)
     with open(os.path.join(test_file_dir, "test_file.txt"), "w") as fh:
         fh.write("this line is just for testing")
-    test_files = meta_builder.get_md5_sums(
-        entry_point="dummy", command="dummy", results_dir=test_file_dir, results_dir_repeat=test_file_dir
-    )
+    test_files = meta_builder.get_md5_sums(command="dummy", results_dir=test_file_dir, results_dir_repeat=test_file_dir)
     assert test_files[0]["md5sum"] == "2191e06b28b5ba82378bcc0672d01786"