From 445eccfd1c2b63e7e38022bbaac778ecb1a7369f Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 31 Jan 2024 16:48:01 +0100 Subject: [PATCH 1/5] handle float values in default value comparison fixes 2710 --- nf_core/lint/nextflow_config.py | 21 ++++++--- nf_core/list.py | 2 +- tests/lint/nextflow_config.py | 74 +++++++++++++++++++++++++++-- tests/test_lint.py | 84 +++++++++++++++++---------------- 4 files changed, 128 insertions(+), 53 deletions(-) diff --git a/nf_core/lint/nextflow_config.py b/nf_core/lint/nextflow_config.py index 15794ef677..40c42b17e4 100644 --- a/nf_core/lint/nextflow_config.py +++ b/nf_core/lint/nextflow_config.py @@ -388,18 +388,27 @@ def nextflow_config(self): ignored.append(f"Config default ignored: {param}") elif param in self.nf_config.keys(): if str(self.nf_config[param]) == schema_default: - passed.append(f"Config default value correct: {param}") + passed.append(f"Config default value correct: {param}= {schema_default}") else: # Handle "number" type if schema_default.endswith(".0") and str(self.nf_config[param]) == schema_default[:-2]: - passed.append(f"Config default value correct: {param}") + passed.append(f"Config default value correct: {param}= {schema_default}") else: - failed.append( - f"Config default value incorrect: `{param}` is set as {self._wrap_quotes(schema_default)} in `nextflow_schema.json` but is {self._wrap_quotes(self.nf_config[param])} in `nextflow.config`." - ) + # try to convert to float + try: + if float(self.nf_config[param]) == float(schema_default): + passed.append(f"Config default value correct: {param}= {schema_default}") + else: + failed.append( + f"Config default value incorrect: `{param}` is set as {self._wrap_quotes(schema_default)} in `nextflow_schema.json` but is {self._wrap_quotes(self.nf_config[param])} in `nextflow.config`." + ) + except ValueError: + failed.append( + f"Config default value incorrect: `{param}` is set as {self._wrap_quotes(schema_default)} in `nextflow_schema.json` but is {self._wrap_quotes(self.nf_config[param])} in `nextflow.config`." + ) else: failed.append( - f"Default value from the Nextflow schema '{param} = {self._wrap_quotes(schema_default)}' not found in `nextflow.config`." + f"Default value from the Nextflow schema `{param} = {self._wrap_quotes(schema_default)}` not found in `nextflow.config`." ) return {"passed": passed, "warned": warned, "failed": failed, "ignored": ignored} diff --git a/nf_core/list.py b/nf_core/list.py index d0b59319a3..b22ca56163 100644 --- a/nf_core/list.py +++ b/nf_core/list.py @@ -39,7 +39,7 @@ def list_workflows(filter_by=None, sort_by="release", as_json=False, show_archiv return wfs.print_summary() -def get_local_wf(workflow, revision=None): +def get_local_wf(workflow, revision=None) -> str: """ Check if this workflow has a local copy and use nextflow to pull it if not """ diff --git a/tests/lint/nextflow_config.py b/tests/lint/nextflow_config.py index 60aaee5243..0ae1b906be 100644 --- a/tests/lint/nextflow_config.py +++ b/tests/lint/nextflow_config.py @@ -64,8 +64,8 @@ def test_default_values_match(self): result = lint_obj.nextflow_config() assert len(result["failed"]) == 0 assert len(result["warned"]) == 0 - assert "Config default value correct: params.max_cpus" in result["passed"] - assert "Config default value correct: params.validate_params" in result["passed"] + assert "Config default value correct: params.max_cpus" in str(result["passed"]) + assert "Config default value correct: params.validate_params" in str(result["passed"]) def test_default_values_fail(self): @@ -75,7 +75,8 @@ def test_default_values_fail(self): nf_conf_file = Path(new_pipeline) / "nextflow.config" with open(nf_conf_file) as f: content = f.read() - fail_content = re.sub(r"\bmax_cpus = 16\b", "max_cpus = 0", content) + fail_content = re.sub(r"\bmax_cpus\s*=\s*16\b", "max_cpus = 0", content) + print(fail_content) with open(nf_conf_file, "w") as f: f.write(fail_content) # Change the default value of max_memory in nextflow_schema.json @@ -115,5 +116,68 @@ def test_default_values_ignored(self): result = lint_obj.nextflow_config() assert len(result["failed"]) == 0 assert len(result["ignored"]) == 1 - assert "Config default value correct: params.max_cpus" not in result["passed"] - assert "Config default ignored: params.max_cpus" in result["ignored"] + assert "Config default value correct: params.max_cpu" not in str(result["passed"]) + assert "Config default ignored: params.max_cpus" in str(result["ignored"]) + + +def test_default_values_float(self): + """Test comparing two float values.""" + new_pipeline = self._make_pipeline_copy() + # Add a float value `dummy=0.0001` to the nextflow.config below `validate_params` + nf_conf_file = Path(new_pipeline) / "nextflow.config" + with open(nf_conf_file) as f: + content = f.read() + fail_content = re.sub( + r"validate_params\s*=\s*true", "params.validate_params = true\ndummy = 0.000000001", content + ) + with open(nf_conf_file, "w") as f: + f.write(fail_content) + # Add a float value `dummy` to the nextflow_schema.json + nf_schema_file = Path(new_pipeline) / "nextflow_schema.json" + with open(nf_schema_file) as f: + content = f.read() + fail_content = re.sub( + r'"validate_params": {', + ' "dummy": {"type": "float","default":0.000000001},\n"validate_params": {', + content, + ) + with open(nf_schema_file, "w") as f: + f.write(fail_content) + + lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj._load_pipeline_config() + result = lint_obj.nextflow_config() + assert len(result["failed"]) == 0 + assert len(result["warned"]) == 0 + assert "Config default value correct: params.dummy" in str(result["passed"]) + + +def test_default_values_float_fail(self): + """Test comparing two float values.""" + new_pipeline = self._make_pipeline_copy() + # Add a float value `dummy=0.0001` to the nextflow.config below `validate_params` + nf_conf_file = Path(new_pipeline) / "nextflow.config" + with open(nf_conf_file) as f: + content = f.read() + fail_content = re.sub( + r"validate_params\s*=\s*true", "params.validate_params = true\ndummy = 0.000000001", content + ) + with open(nf_conf_file, "w") as f: + f.write(fail_content) + # Add a float value `dummy` to the nextflow_schema.json + nf_schema_file = Path(new_pipeline) / "nextflow_schema.json" + with open(nf_schema_file) as f: + content = f.read() + fail_content = re.sub( + r'"validate_params": {', ' "dummy": {"type": "float","default":0.000001},\n"validate_params": {', content + ) + with open(nf_schema_file, "w") as f: + f.write(fail_content) + + lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj._load_pipeline_config() + result = lint_obj.nextflow_config() + + assert len(result["failed"]) == 1 + assert len(result["warned"]) == 0 + assert "Config default value incorrect: `params.dummy" in str(result["failed"]) diff --git a/tests/test_lint.py b/tests/test_lint.py index 2f989aeffb..77b6768b55 100644 --- a/tests/test_lint.py +++ b/tests/test_lint.py @@ -179,49 +179,51 @@ def test_sphinx_md_files(self): ####################### # SPECIFIC LINT TESTS # ####################### - from .lint.actions_awsfulltest import ( # type: ignore[misc] - test_actions_awsfulltest_fail, - test_actions_awsfulltest_pass, - test_actions_awsfulltest_warn, - ) - from .lint.actions_awstest import ( # type: ignore[misc] - test_actions_awstest_fail, - test_actions_awstest_pass, - ) - from .lint.actions_ci import ( # type: ignore[misc] - test_actions_ci_fail_wrong_nf, - test_actions_ci_fail_wrong_trigger, - test_actions_ci_pass, - ) - from .lint.actions_schema_validation import ( # type: ignore[misc] - test_actions_schema_validation_fails_for_additional_property, - test_actions_schema_validation_missing_jobs, - test_actions_schema_validation_missing_on, - ) - from .lint.files_exist import ( # type: ignore[misc] - test_files_exist_depreciated_file, - test_files_exist_fail_conditional, - test_files_exist_missing_config, - test_files_exist_missing_main, - test_files_exist_pass, - test_files_exist_pass_conditional, - ) - from .lint.files_unchanged import ( # type: ignore[misc] - test_files_unchanged_fail, - test_files_unchanged_pass, - ) - from .lint.merge_markers import test_merge_markers_found # type: ignore[misc] - from .lint.modules_json import test_modules_json_pass # type: ignore[misc] - from .lint.multiqc_config import ( # type: ignore[misc] - test_multiqc_config_exists_ignore, - test_multiqc_config_missing_report_section_order, - test_multiqc_config_report_comment_fail, - test_multiqc_config_report_comment_release_fail, - test_multiqc_config_report_comment_release_succeed, - test_multiqc_incorrect_export_plots, - ) + # from .lint.actions_awsfulltest import ( # type: ignore[misc] + # test_actions_awsfulltest_fail, + # test_actions_awsfulltest_pass, + # test_actions_awsfulltest_warn, + # ) + # from .lint.actions_awstest import ( # type: ignore[misc] + # test_actions_awstest_fail, + # test_actions_awstest_pass, + # ) + # from .lint.actions_ci import ( # type: ignore[misc] + # test_actions_ci_fail_wrong_nf, + # test_actions_ci_fail_wrong_trigger, + # test_actions_ci_pass, + # ) + # from .lint.actions_schema_validation import ( # type: ignore[misc] + # test_actions_schema_validation_fails_for_additional_property, + # test_actions_schema_validation_missing_jobs, + # test_actions_schema_validation_missing_on, + # ) + # from .lint.files_exist import ( # type: ignore[misc] + # test_files_exist_depreciated_file, + # test_files_exist_fail_conditional, + # test_files_exist_missing_config, + # test_files_exist_missing_main, + # test_files_exist_pass, + # test_files_exist_pass_conditional, + # ) + # from .lint.files_unchanged import ( # type: ignore[misc] + # test_files_unchanged_fail, + # test_files_unchanged_pass, + # ) + # from .lint.merge_markers import test_merge_markers_found # type: ignore[misc] + # from .lint.modules_json import test_modules_json_pass # type: ignore[misc] + # from .lint.multiqc_config import ( # type: ignore[misc] + # test_multiqc_config_exists_ignore, + # test_multiqc_config_missing_report_section_order, + # test_multiqc_config_report_comment_fail, + # test_multiqc_config_report_comment_release_fail, + # test_multiqc_config_report_comment_release_succeed, + # test_multiqc_incorrect_export_plots, + # ) from .lint.nextflow_config import ( # type: ignore[misc] test_default_values_fail, + test_default_values_float, + test_default_values_float_fail, test_default_values_ignored, test_default_values_match, test_nextflow_config_bad_name_fail, From 04bc025705defb5c9c34570a21f4fa4298dffc06 Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 31 Jan 2024 17:17:16 +0100 Subject: [PATCH 2/5] use type based file default value comparison --- nf_core/lint/nextflow_config.py | 54 ++++++++++++---------- nf_core/schema.py | 48 ++++++++++++------- tests/lint/nextflow_config.py | 2 +- tests/test_lint.py | 82 ++++++++++++++++----------------- 4 files changed, 103 insertions(+), 83 deletions(-) diff --git a/nf_core/lint/nextflow_config.py b/nf_core/lint/nextflow_config.py index 40c42b17e4..68750cd859 100644 --- a/nf_core/lint/nextflow_config.py +++ b/nf_core/lint/nextflow_config.py @@ -373,39 +373,43 @@ def nextflow_config(self): schema.no_prompts = True schema.load_schema() schema.get_schema_defaults() # Get default values from schema + schema.get_schema_types() # Get types from schema self.nf_config.keys() # Params in nextflow.config for param_name in schema.schema_defaults.keys(): param = "params." + param_name - # Convert booleans to strings if needed - schema_default = ( - "true" - if str(schema.schema_defaults[param_name]) == "True" - else "false" - if str(schema.schema_defaults[param_name]) == "False" - else str(schema.schema_defaults[param_name]) - ) if param in ignore_defaults: ignored.append(f"Config default ignored: {param}") elif param in self.nf_config.keys(): - if str(self.nf_config[param]) == schema_default: + config_default = None + schema_default = None + if schema.schema_types[param_name] == "boolean": + schema_default = str(schema.schema_defaults[param_name]).lower() + config_default = str(self.nf_config[param]).lower() + elif schema.schema_types[param_name] == "number": + try: + schema_default = float(schema.schema_defaults[param_name]) + config_default = float(self.nf_config[param]) + except ValueError: + failed.append( + f"Config default value incorrect: `{param}` is set as type `number` in nextflow_schema.json, but is not a number in `nextflow.config`." + ) + elif schema.schema_types[param_name] == "integer": + try: + schema_default = int(schema.schema_defaults[param_name]) + config_default = int(self.nf_config[param]) + except ValueError: + failed.append( + f"Config default value incorrect: `{param}` is set as type `integer` in nextflow_schema.json, but is not an integer in `nextflow.config`." + ) + else: + schema_default = str(schema.schema_defaults[param_name]) + config_default = str(self.nf_config[param]) + if config_default is not None and config_default == schema_default: passed.append(f"Config default value correct: {param}= {schema_default}") else: - # Handle "number" type - if schema_default.endswith(".0") and str(self.nf_config[param]) == schema_default[:-2]: - passed.append(f"Config default value correct: {param}= {schema_default}") - else: - # try to convert to float - try: - if float(self.nf_config[param]) == float(schema_default): - passed.append(f"Config default value correct: {param}= {schema_default}") - else: - failed.append( - f"Config default value incorrect: `{param}` is set as {self._wrap_quotes(schema_default)} in `nextflow_schema.json` but is {self._wrap_quotes(self.nf_config[param])} in `nextflow.config`." - ) - except ValueError: - failed.append( - f"Config default value incorrect: `{param}` is set as {self._wrap_quotes(schema_default)} in `nextflow_schema.json` but is {self._wrap_quotes(self.nf_config[param])} in `nextflow.config`." - ) + failed.append( + f"Config default value incorrect: `{param}` is set as {self._wrap_quotes(schema_default)} in `nextflow_schema.json` but is {self._wrap_quotes(self.nf_config[param])} in `nextflow.config`." + ) else: failed.append( f"Default value from the Nextflow schema `{param} = {self._wrap_quotes(schema_default)}` not found in `nextflow.config`." diff --git a/nf_core/schema.py b/nf_core/schema.py index b0c5dc04b6..df04dc5a1e 100644 --- a/nf_core/schema.py +++ b/nf_core/schema.py @@ -4,9 +4,9 @@ import copy import json import logging -import os import tempfile import webbrowser +from pathlib import Path import jinja2 import jsonschema @@ -30,10 +30,11 @@ class PipelineSchema: def __init__(self): """Initialise the object""" - self.schema = None - self.pipeline_dir = None - self.schema_filename = None + self.schema = {} + self.pipeline_dir = "" + self.schema_filename = "" self.schema_defaults = {} + self.schema_types = {} self.schema_params = {} self.input_params = {} self.pipeline_params = {} @@ -48,29 +49,29 @@ def __init__(self): def get_schema_path(self, path, local_only=False, revision=None): """Given a pipeline name, directory, or path, set self.schema_filename""" - + path = Path(path) # Supplied path exists - assume a local pipeline directory or schema - if os.path.exists(path): + if path.exists(): if revision is not None: log.warning(f"Local workflow supplied, ignoring revision '{revision}'") - if os.path.isdir(path): + if path.is_dir(): self.pipeline_dir = path - self.schema_filename = os.path.join(path, "nextflow_schema.json") + self.schema_filename = path / "nextflow_schema.json" else: - self.pipeline_dir = os.path.dirname(path) + self.pipeline_dir = path.parent self.schema_filename = path # Path does not exist - assume a name of a remote workflow elif not local_only: self.pipeline_dir = nf_core.list.get_local_wf(path, revision=revision) - self.schema_filename = os.path.join(self.pipeline_dir, "nextflow_schema.json") + self.schema_filename = Path(self.pipeline_dir, "nextflow_schema.json") # Only looking for local paths, overwrite with None to be safe else: self.schema_filename = None # Check that the schema file exists - if self.schema_filename is None or not os.path.exists(self.schema_filename): + if self.schema_filename is None or not Path(self.schema_filename).exists(): error = f"Could not find pipeline schema for '{path}': {self.schema_filename}" log.error(error) raise AssertionError(error) @@ -106,6 +107,9 @@ def load_lint_schema(self): def load_schema(self): """Load a pipeline schema from a file""" + if self.schema_filename is None: + raise AssertionError("Pipeline schema filename could not be found.") + with open(self.schema_filename) as fh: self.schema = json.load(fh) self.schema_defaults = {} @@ -147,7 +151,7 @@ def sanitise_param_default(self, param): param["default"] = str(param["default"]) return param - def get_schema_defaults(self): + def get_schema_defaults(self) -> None: """ Generate set of default input parameters from schema. @@ -171,6 +175,16 @@ def get_schema_defaults(self): if param["default"] is not None: self.schema_defaults[p_key] = param["default"] + def get_schema_types(self) -> None: + """Get a list of all parameter types in the schema""" + for name, param in self.schema.get("properties", {}).items(): + if "type" in param: + self.schema_types[name] = param["type"] + for _, definition in self.schema.get("definitions", {}).items(): + for name, param in definition.get("properties", {}).items(): + if "type" in param: + self.schema_types[name] = param["type"] + def save_schema(self, suppress_logging=False): """Save a pipeline schema to a file""" # Write results to a JSON file @@ -486,7 +500,7 @@ def print_documentation( console = rich.console.Console() console.print("\n", Syntax(prettified_docs, format), "\n") else: - if os.path.exists(output_fn) and not force: + if Path(output_fn).exists() and not force: log.error(f"File '{output_fn}' exists! Please delete first, or use '--force'") return with open(output_fn, "w") as fh: @@ -572,7 +586,7 @@ def make_skeleton_schema(self): ) schema_template = env.get_template("nextflow_schema.json") template_vars = { - "name": self.pipeline_manifest.get("name", os.path.dirname(self.schema_filename)).strip("'"), + "name": self.pipeline_manifest.get("name", Path(self.schema_filename).parent).strip("'"), "description": self.pipeline_manifest.get("description", "").strip("'"), } self.schema = json.loads(schema_template.render(template_vars)) @@ -656,9 +670,11 @@ def get_wf_params(self): if len(self.pipeline_params) > 0 and len(self.pipeline_manifest) > 0: log.debug("Skipping get_wf_params as we already have them") return - + if self.schema_filename is None: + log.error("Cannot get workflow params without a schema file") + return log.debug("Collecting pipeline parameter defaults\n") - config = nf_core.utils.fetch_wf_config(os.path.dirname(self.schema_filename)) + config = nf_core.utils.fetch_wf_config(Path(self.schema_filename).parent) skipped_params = [] # Pull out just the params. values for ckey, cval in config.items(): diff --git a/tests/lint/nextflow_config.py b/tests/lint/nextflow_config.py index 0ae1b906be..bc807da00a 100644 --- a/tests/lint/nextflow_config.py +++ b/tests/lint/nextflow_config.py @@ -138,7 +138,7 @@ def test_default_values_float(self): content = f.read() fail_content = re.sub( r'"validate_params": {', - ' "dummy": {"type": "float","default":0.000000001},\n"validate_params": {', + ' "dummy": {"type": "number","default":0.000000001},\n"validate_params": {', content, ) with open(nf_schema_file, "w") as f: diff --git a/tests/test_lint.py b/tests/test_lint.py index 77b6768b55..9839265892 100644 --- a/tests/test_lint.py +++ b/tests/test_lint.py @@ -179,47 +179,47 @@ def test_sphinx_md_files(self): ####################### # SPECIFIC LINT TESTS # ####################### - # from .lint.actions_awsfulltest import ( # type: ignore[misc] - # test_actions_awsfulltest_fail, - # test_actions_awsfulltest_pass, - # test_actions_awsfulltest_warn, - # ) - # from .lint.actions_awstest import ( # type: ignore[misc] - # test_actions_awstest_fail, - # test_actions_awstest_pass, - # ) - # from .lint.actions_ci import ( # type: ignore[misc] - # test_actions_ci_fail_wrong_nf, - # test_actions_ci_fail_wrong_trigger, - # test_actions_ci_pass, - # ) - # from .lint.actions_schema_validation import ( # type: ignore[misc] - # test_actions_schema_validation_fails_for_additional_property, - # test_actions_schema_validation_missing_jobs, - # test_actions_schema_validation_missing_on, - # ) - # from .lint.files_exist import ( # type: ignore[misc] - # test_files_exist_depreciated_file, - # test_files_exist_fail_conditional, - # test_files_exist_missing_config, - # test_files_exist_missing_main, - # test_files_exist_pass, - # test_files_exist_pass_conditional, - # ) - # from .lint.files_unchanged import ( # type: ignore[misc] - # test_files_unchanged_fail, - # test_files_unchanged_pass, - # ) - # from .lint.merge_markers import test_merge_markers_found # type: ignore[misc] - # from .lint.modules_json import test_modules_json_pass # type: ignore[misc] - # from .lint.multiqc_config import ( # type: ignore[misc] - # test_multiqc_config_exists_ignore, - # test_multiqc_config_missing_report_section_order, - # test_multiqc_config_report_comment_fail, - # test_multiqc_config_report_comment_release_fail, - # test_multiqc_config_report_comment_release_succeed, - # test_multiqc_incorrect_export_plots, - # ) + from .lint.actions_awsfulltest import ( # type: ignore[misc] + test_actions_awsfulltest_fail, + test_actions_awsfulltest_pass, + test_actions_awsfulltest_warn, + ) + from .lint.actions_awstest import ( # type: ignore[misc] + test_actions_awstest_fail, + test_actions_awstest_pass, + ) + from .lint.actions_ci import ( # type: ignore[misc] + test_actions_ci_fail_wrong_nf, + test_actions_ci_fail_wrong_trigger, + test_actions_ci_pass, + ) + from .lint.actions_schema_validation import ( # type: ignore[misc] + test_actions_schema_validation_fails_for_additional_property, + test_actions_schema_validation_missing_jobs, + test_actions_schema_validation_missing_on, + ) + from .lint.files_exist import ( # type: ignore[misc] + test_files_exist_depreciated_file, + test_files_exist_fail_conditional, + test_files_exist_missing_config, + test_files_exist_missing_main, + test_files_exist_pass, + test_files_exist_pass_conditional, + ) + from .lint.files_unchanged import ( # type: ignore[misc] + test_files_unchanged_fail, + test_files_unchanged_pass, + ) + from .lint.merge_markers import test_merge_markers_found # type: ignore[misc] + from .lint.modules_json import test_modules_json_pass # type: ignore[misc] + from .lint.multiqc_config import ( # type: ignore[misc] + test_multiqc_config_exists_ignore, + test_multiqc_config_missing_report_section_order, + test_multiqc_config_report_comment_fail, + test_multiqc_config_report_comment_release_fail, + test_multiqc_config_report_comment_release_succeed, + test_multiqc_incorrect_export_plots, + ) from .lint.nextflow_config import ( # type: ignore[misc] test_default_values_fail, test_default_values_float, From 4e9cb73c979e8eb8608a532f145dbd8d8fe576ab Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 31 Jan 2024 16:19:47 +0000 Subject: [PATCH 3/5] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4b6d48ce92..a74457b523 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,6 +16,7 @@ ### General - Update pre-commit hook astral-sh/ruff-pre-commit to v0.1.15 ([#2705](https://github.com/nf-core/tools/pull/2705)) +- use types for default value comparison ([#2712](https://github.com/nf-core/tools/pull/2712)) # [v2.12 - Aluminium Wolf](https://github.com/nf-core/tools/releases/tag/2.11) - [2024-01-29] From 0fe6533a63085f5737c7d7d59623d0e498c21d2d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= Date: Thu, 1 Feb 2024 09:57:50 +0100 Subject: [PATCH 4/5] Update tests/lint/nextflow_config.py MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Júlia Mir Pedrol --- tests/lint/nextflow_config.py | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/lint/nextflow_config.py b/tests/lint/nextflow_config.py index bc807da00a..fa85568f14 100644 --- a/tests/lint/nextflow_config.py +++ b/tests/lint/nextflow_config.py @@ -76,7 +76,6 @@ def test_default_values_fail(self): with open(nf_conf_file) as f: content = f.read() fail_content = re.sub(r"\bmax_cpus\s*=\s*16\b", "max_cpus = 0", content) - print(fail_content) with open(nf_conf_file, "w") as f: f.write(fail_content) # Change the default value of max_memory in nextflow_schema.json From ef65f766160cb1f25e26b728f5b8b214995139c3 Mon Sep 17 00:00:00 2001 From: mashehu Date: Thu, 1 Feb 2024 10:29:22 +0100 Subject: [PATCH 5/5] fix schema tests --- nf_core/list.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/nf_core/list.py b/nf_core/list.py index b22ca56163..67d1a76878 100644 --- a/nf_core/list.py +++ b/nf_core/list.py @@ -6,6 +6,8 @@ import os import re from datetime import datetime +from pathlib import Path +from typing import Union import git import requests @@ -39,12 +41,12 @@ def list_workflows(filter_by=None, sort_by="release", as_json=False, show_archiv return wfs.print_summary() -def get_local_wf(workflow, revision=None) -> str: +def get_local_wf(workflow: Union[str, Path], revision=None) -> Union[str, None]: """ Check if this workflow has a local copy and use nextflow to pull it if not """ # Assume nf-core if no org given - if workflow.count("/") == 0: + if str(workflow).count("/") == 0: workflow = f"nf-core/{workflow}" wfs = Workflows()