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Fix incorrect assertions for called_with on mocks #2891

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merged 12 commits into from
Mar 27, 2024
Merged

Fix incorrect assertions for called_with on mocks #2891

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faf3a87
fix: assertions for called_with/called_once_with were silently return…
awgymer Mar 20, 2024
a124c14
[automated] Update CHANGELOG.md
nf-core-bot Mar 20, 2024
d29f2ba
Update expected assertion for mock patch calls
awgymer Mar 20, 2024
fb2ded4
fix type hints
mashehu Mar 26, 2024
4fa1514
fix tests
mashehu Mar 26, 2024
72a65b2
Merge branch 'dev' into 2890-fix-ci-3-12
mashehu Mar 26, 2024
016db6d
try to fix the remote schema functionality
mashehu Mar 26, 2024
b69f328
add isolated filesystem to cli tests
mashehu Mar 26, 2024
80c2b16
Merge branch '2890-fix-ci-3-12' of github.com:awgymer/nf-core-tools i…
mashehu Mar 26, 2024
738e4e0
use correct types
mashehu Mar 26, 2024
a7e5593
revert remote changes
mashehu Mar 26, 2024
3fa8131
fix tests
mashehu Mar 26, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -41,6 +41,7 @@
- Fix issue with config resolution that was causing nested configs to behave unexpectedly ([#2862](https://github.com/nf-core/tools/pull/2862))
- Fix schema docs console output truncating ([#2880](https://github.com/nf-core/tools/pull/2880))
- fix: ensure path object converted to string before stripping quotes ([#2878](https://github.com/nf-core/tools/pull/2878))
- Fix incorrect assertions for called_with on mocks ([#2891](https://github.com/nf-core/tools/pull/2891))
- Make cli-provided module/subworkflow names case insensitive ([#2869](https://github.com/nf-core/tools/pull/2869))
- Update pre-commit hook astral-sh/ruff-pre-commit to v0.3.4 ([#2894](https://github.com/nf-core/tools/pull/2894))

Expand Down
296 changes: 148 additions & 148 deletions nf_core/lint/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
import logging
import os
from pathlib import Path
from typing import List, Union
from typing import List, Tuple, Union

import git
import rich
Expand All @@ -25,155 +25,14 @@
import nf_core.subworkflows.lint
import nf_core.utils
from nf_core import __version__
from nf_core.components.lint import ComponentLint
from nf_core.lint_utils import console
from nf_core.utils import plural_s as _s
from nf_core.utils import strip_ansi_codes

log = logging.getLogger(__name__)


def run_linting(
pipeline_dir,
release_mode=False,
fix=(),
key=(),
show_passed=False,
fail_ignored=False,
fail_warned=False,
sort_by="test",
md_fn=None,
json_fn=None,
hide_progress=False,
):
"""Runs all nf-core linting checks on a given Nextflow pipeline project
in either `release` mode or `normal` mode (default). Returns an object
of type :class:`PipelineLint` after finished.

Args:
pipeline_dir (str): The path to the Nextflow pipeline root directory
release_mode (bool): Set this to `True`, if the linting should be run in the `release` mode.
See :class:`PipelineLint` for more information.

Returns:
An object of type :class:`PipelineLint` that contains all the linting results.
An object of type :class:`ComponentLint` that contains all the linting results for the modules.
An object of type :class:`ComponentLint` that contains all the linting results for the subworkflows.
"""

# Verify that the requested tests exist
if key:
all_tests = set(PipelineLint._get_all_lint_tests(release_mode)).union(
set(nf_core.modules.lint.ModuleLint.get_all_module_lint_tests(is_pipeline=True))
)
bad_keys = [k for k in key if k not in all_tests]
if len(bad_keys) > 0:
raise AssertionError(
"Test name{} not recognised: '{}'".format(
_s(bad_keys),
"', '".join(bad_keys),
)
)
log.info("Only running tests: '{}'".format("', '".join(key)))

# Check if we were given any keys, and if they match any pipeline tests
if key:
pipeline_keys = list(set(key).intersection(set(PipelineLint._get_all_lint_tests(release_mode))))
else:
# If no key is supplied, run all tests
pipeline_keys = None

# Create the lint object
lint_obj = PipelineLint(pipeline_dir, release_mode, fix, pipeline_keys, fail_ignored, fail_warned, hide_progress)

# Load the various pipeline configs
lint_obj._load_lint_config()
lint_obj._load_pipeline_config()
lint_obj._list_files()

# Create the modules lint object
module_lint_obj = nf_core.modules.lint.ModuleLint(pipeline_dir, hide_progress=hide_progress)
# Create the subworkflows lint object
try:
subworkflow_lint_obj = nf_core.subworkflows.lint.SubworkflowLint(pipeline_dir, hide_progress=hide_progress)
except LookupError:
subworkflow_lint_obj = None

# Verify that the pipeline is correctly configured and has a modules.json file
module_lint_obj.has_valid_directory()
module_lint_obj.has_modules_file()

# Run only the tests we want
if key:
# Select only the module lint tests
module_lint_tests = list(
set(key).intersection(set(nf_core.modules.lint.ModuleLint.get_all_module_lint_tests(is_pipeline=True)))
)
# Select only the subworkflow lint tests
subworkflow_lint_tests = list(
set(key).intersection(
set(nf_core.subworkflows.lint.SubworkflowLint.get_all_subworkflow_lint_tests(is_pipeline=True))
)
)
else:
# If no key is supplied, run the default modules tests
module_lint_tests = ("module_changes", "module_version")
subworkflow_lint_tests = ("subworkflow_changes", "subworkflow_version")
module_lint_obj.filter_tests_by_key(module_lint_tests)
if subworkflow_lint_obj is not None:
subworkflow_lint_obj.filter_tests_by_key(subworkflow_lint_tests)

# Set up files for component linting test
module_lint_obj.set_up_pipeline_files()
if subworkflow_lint_obj is not None:
subworkflow_lint_obj.set_up_pipeline_files()

# Run the pipeline linting tests
try:
lint_obj._lint_pipeline()
except AssertionError as e:
log.critical(f"Critical error: {e}")
log.info("Stopping tests...")
return lint_obj, module_lint_obj

# Run the module lint tests
if len(module_lint_obj.all_local_components) > 0:
module_lint_obj.lint_modules(module_lint_obj.all_local_components, local=True)
if len(module_lint_obj.all_remote_components) > 0:
module_lint_obj.lint_modules(module_lint_obj.all_remote_components, local=False)
# Run the subworkflows lint tests
if subworkflow_lint_obj is not None:
if len(subworkflow_lint_obj.all_local_components) > 0:
subworkflow_lint_obj.lint_subworkflows(subworkflow_lint_obj.all_local_components, local=True)
if len(subworkflow_lint_obj.all_remote_components) > 0:
subworkflow_lint_obj.lint_subworkflows(subworkflow_lint_obj.all_remote_components, local=False)

# Print the results
lint_obj._print_results(show_passed)
module_lint_obj._print_results(show_passed, sort_by=sort_by)
if subworkflow_lint_obj is not None:
subworkflow_lint_obj._print_results(show_passed, sort_by=sort_by)
nf_core.lint_utils.print_joint_summary(lint_obj, module_lint_obj, subworkflow_lint_obj)
nf_core.lint_utils.print_fixes(lint_obj)

# Save results to Markdown file
if md_fn is not None:
log.info(f"Writing lint results to {md_fn}")
markdown = lint_obj._get_results_md()
with open(md_fn, "w") as fh:
fh.write(markdown)

# Save results to JSON file
if json_fn is not None:
lint_obj._save_json_results(json_fn)

# Reminder about --release mode flag if we had failures
if len(lint_obj.failed) > 0:
if release_mode:
log.info("Reminder: Lint tests were run in --release mode.")

return lint_obj, module_lint_obj, subworkflow_lint_obj


class PipelineLint(nf_core.utils.Pipeline):
"""Object to hold linting information and results.

Expand Down Expand Up @@ -411,7 +270,7 @@ def format_result(test_results):
# Table of passed tests
if len(self.passed) > 0 and show_passed:
console.print(
rich.panel.Panel(
Panel(
format_result(self.passed),
title=rf"[bold][✔] {len(self.passed)} Pipeline Test{_s(self.passed)} Passed",
title_align="left",
Expand All @@ -423,7 +282,7 @@ def format_result(test_results):
# Table of fixed tests
if len(self.fixed) > 0:
console.print(
rich.panel.Panel(
Panel(
format_result(self.fixed),
title=rf"[bold][?] {len(self.fixed)} Pipeline Test{_s(self.fixed)} Fixed",
title_align="left",
Expand All @@ -435,7 +294,7 @@ def format_result(test_results):
# Table of ignored tests
if len(self.ignored) > 0:
console.print(
rich.panel.Panel(
Panel(
format_result(self.ignored),
title=rf"[bold][?] {len(self.ignored)} Pipeline Test{_s(self.ignored)} Ignored",
title_align="left",
Expand All @@ -447,7 +306,7 @@ def format_result(test_results):
# Table of warning tests
if len(self.warned) > 0:
console.print(
rich.panel.Panel(
Panel(
format_result(self.warned),
title=rf"[bold][!] {len(self.warned)} Pipeline Test Warning{_s(self.warned)}",
title_align="left",
Expand All @@ -459,7 +318,7 @@ def format_result(test_results):
# Table of failing tests
if len(self.failed) > 0:
console.print(
rich.panel.Panel(
Panel(
format_result(self.failed),
title=rf"[bold][✗] {len(self.failed)} Pipeline Test{_s(self.failed)} Failed",
title_align="left",
Expand Down Expand Up @@ -640,3 +499,144 @@ def _wrap_quotes(self, files: Union[List[str], List[Path], Path]) -> str:
files = [files]
bfiles = [f"`{str(f)}`" for f in files]
return " or ".join(bfiles)


def run_linting(
pipeline_dir,
release_mode: bool = False,
fix=(),
key=(),
show_passed: bool = False,
fail_ignored: bool = False,
fail_warned: bool = False,
sort_by: str = "test",
md_fn=None,
json_fn=None,
hide_progress: bool = False,
) -> Tuple[PipelineLint, ComponentLint, ComponentLint | None]:
"""Runs all nf-core linting checks on a given Nextflow pipeline project
in either `release` mode or `normal` mode (default). Returns an object
of type :class:`PipelineLint` after finished.

Args:
pipeline_dir (str): The path to the Nextflow pipeline root directory
release_mode (bool): Set this to `True`, if the linting should be run in the `release` mode.
See :class:`PipelineLint` for more information.

Returns:
An object of type :class:`PipelineLint` that contains all the linting results.
An object of type :class:`ComponentLint` that contains all the linting results for the modules.
An object of type :class:`ComponentLint` that contains all the linting results for the subworkflows.
"""

# Verify that the requested tests exist
if key:
all_tests = set(PipelineLint._get_all_lint_tests(release_mode)).union(
set(nf_core.modules.lint.ModuleLint.get_all_module_lint_tests(is_pipeline=True))
)
bad_keys = [k for k in key if k not in all_tests]
if len(bad_keys) > 0:
raise AssertionError(
"Test name{} not recognised: '{}'".format(
_s(bad_keys),
"', '".join(bad_keys),
)
)
log.info("Only running tests: '{}'".format("', '".join(key)))

# Check if we were given any keys, and if they match any pipeline tests
if key:
pipeline_keys = list(set(key).intersection(set(PipelineLint._get_all_lint_tests(release_mode))))
else:
# If no key is supplied, run all tests
pipeline_keys = None

# Create the lint object
lint_obj = PipelineLint(pipeline_dir, release_mode, fix, pipeline_keys, fail_ignored, fail_warned, hide_progress)

# Load the various pipeline configs
lint_obj._load_lint_config()
lint_obj._load_pipeline_config()
lint_obj._list_files()

# Create the modules lint object
module_lint_obj = nf_core.modules.lint.ModuleLint(pipeline_dir, hide_progress=hide_progress)
# Create the subworkflows lint object
try:
subworkflow_lint_obj = nf_core.subworkflows.lint.SubworkflowLint(pipeline_dir, hide_progress=hide_progress)
except LookupError:
subworkflow_lint_obj = None

# Verify that the pipeline is correctly configured and has a modules.json file
module_lint_obj.has_valid_directory()
module_lint_obj.has_modules_file()
# Run only the tests we want
if key:
# Select only the module lint tests
module_lint_tests = list(
set(key).intersection(set(nf_core.modules.lint.ModuleLint.get_all_module_lint_tests(is_pipeline=True)))
)
# Select only the subworkflow lint tests
subworkflow_lint_tests = list(
set(key).intersection(
set(nf_core.subworkflows.lint.SubworkflowLint.get_all_subworkflow_lint_tests(is_pipeline=True))
)
)
else:
# If no key is supplied, run the default modules tests
module_lint_tests = list(("module_changes", "module_version"))
subworkflow_lint_tests = list(("subworkflow_changes", "subworkflow_version"))
module_lint_obj.filter_tests_by_key(module_lint_tests)
if subworkflow_lint_obj is not None:
subworkflow_lint_obj.filter_tests_by_key(subworkflow_lint_tests)

# Set up files for component linting test
module_lint_obj.set_up_pipeline_files()
if subworkflow_lint_obj is not None:
subworkflow_lint_obj.set_up_pipeline_files()

# Run the pipeline linting tests
try:
lint_obj._lint_pipeline()
except AssertionError as e:
log.critical(f"Critical error: {e}")
log.info("Stopping tests...")
return lint_obj, module_lint_obj, subworkflow_lint_obj

# Run the module lint tests
if len(module_lint_obj.all_local_components) > 0:
module_lint_obj.lint_modules(module_lint_obj.all_local_components, local=True)
if len(module_lint_obj.all_remote_components) > 0:
module_lint_obj.lint_modules(module_lint_obj.all_remote_components, local=False)
# Run the subworkflows lint tests
if subworkflow_lint_obj is not None:
if len(subworkflow_lint_obj.all_local_components) > 0:
subworkflow_lint_obj.lint_subworkflows(subworkflow_lint_obj.all_local_components, local=True)
if len(subworkflow_lint_obj.all_remote_components) > 0:
subworkflow_lint_obj.lint_subworkflows(subworkflow_lint_obj.all_remote_components, local=False)

# Print the results
lint_obj._print_results(show_passed)
module_lint_obj._print_results(show_passed, sort_by=sort_by)
if subworkflow_lint_obj is not None:
subworkflow_lint_obj._print_results(show_passed, sort_by=sort_by)
nf_core.lint_utils.print_joint_summary(lint_obj, module_lint_obj, subworkflow_lint_obj)
nf_core.lint_utils.print_fixes(lint_obj)

# Save results to Markdown file
if md_fn is not None:
log.info(f"Writing lint results to {md_fn}")
markdown = lint_obj._get_results_md()
with open(md_fn, "w") as fh:
fh.write(markdown)

# Save results to JSON file
if json_fn is not None:
lint_obj._save_json_results(json_fn)

# Reminder about --release mode flag if we had failures
if len(lint_obj.failed) > 0:
if release_mode:
log.info("Reminder: Lint tests were run in --release mode.")

return lint_obj, module_lint_obj, subworkflow_lint_obj
6 changes: 4 additions & 2 deletions nf_core/schema.py
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Original file line number Diff line number Diff line change
Expand Up @@ -62,8 +62,10 @@ def get_schema_path(self, path, local_only=False, revision=None):

# 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 = Path(self.pipeline_dir, "nextflow_schema.json")
if self.pipeline_dir is not None:
self.schema_filename = Path(self.pipeline_dir, "nextflow_schema.json")
else:
self.schema_filename = None

# Only looking for local paths, overwrite with None to be safe
else:
Expand Down
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