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Add stubs to create test yml #2476

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merged 8 commits into from
Oct 18, 2023
Merged

Add stubs to create test yml #2476

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9ab896c
Merge pull request #2440 from nf-core/dev
mirpedrol Sep 25, 2023
ff99f7c
add stub test
nvnieuwk Oct 17, 2023
f7198ef
Merge branch 'dev' into add-stubs-to-create-test-yml
nvnieuwk Oct 17, 2023
2ac9e2c
ignore md5sum and empty file checks for stub
nvnieuwk Oct 17, 2023
9c9ab25
update changelog
nvnieuwk Oct 17, 2023
324110f
added stub to subworkflows
nvnieuwk Oct 17, 2023
f60b6af
make stub the last one
nvnieuwk Oct 18, 2023
efe344a
Merge branch 'dev' into add-stubs-to-create-test-yml
nvnieuwk Oct 18, 2023
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4 changes: 4 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -13,8 +13,12 @@

### Modules

- Added stub test creation to `create_test_yml` ([#2476](https://github.com/nf-core/tools/pull/2476))

### Subworkflows

- Added stub test creation to `create_test_yml` ([#2476](https://github.com/nf-core/tools/pull/2476))

### General

# [v2.10 - Nickel Ostrich](https://github.com/nf-core/tools/releases/tag/2.10) + [2023-09-25]
Expand Down
28 changes: 19 additions & 9 deletions nf_core/modules/test_yml_builder.py
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Original file line number Diff line number Diff line change
Expand Up @@ -142,12 +142,19 @@ def build_all_tests(self):
"""
Go over each entry point and build structure
"""

# Build the stub test
stub_test = self.build_single_test(self.entry_points[0], stub=True)
if stub_test:
self.tests.append(stub_test)

# Build the other tests
for entry_point in self.entry_points:
ep_test = self.build_single_test(entry_point)
if ep_test:
self.tests.append(ep_test)

def build_single_test(self, entry_point):
def build_single_test(self, entry_point, stub=False):
"""Given the supplied cli flags, prompt for any that are missing.

Returns: Test command
Expand All @@ -158,6 +165,8 @@ def build_single_test(self, entry_point):
"tags": [],
"files": [],
}
stub_option = " -stub" if stub else ""
stub_name = " stub" if stub else ""

# Print nice divider line
console = rich.console.Console()
Expand All @@ -166,7 +175,7 @@ def build_single_test(self, entry_point):
log.info(f"Building test meta for entry point '{entry_point}'")

while ep_test["name"] == "":
default_val = f"{self.module_name.replace('/', ' ')} {entry_point}"
default_val = f"{self.module_name.replace('/', ' ')} {entry_point}{stub_name}"
if self.no_prompts:
ep_test["name"] = default_val
else:
Expand All @@ -178,6 +187,7 @@ def build_single_test(self, entry_point):
default_val = (
f"nextflow run ./tests/modules/{self.org}/{self.module_name} -entry {entry_point} "
f"-c ./tests/config/nextflow.config"
f"{stub_option}"
)
if self.no_prompts:
ep_test["command"] = default_val
Expand All @@ -200,7 +210,7 @@ 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(ep_test["command"])
ep_test["files"] = self.get_md5_sums(ep_test["command"], stub=stub)

return ep_test

Expand All @@ -227,7 +237,7 @@ def _md5(self, fname):
md5sum = hash_md5.hexdigest()
return md5sum

def create_test_file_dict(self, results_dir, is_repeat=False):
def create_test_file_dict(self, results_dir, is_repeat=False, stub=False):
"""Walk through directory and collect md5 sums"""
test_files = []
for root, _, files in os.walk(results_dir, followlinks=True):
Expand All @@ -236,13 +246,13 @@ def create_test_file_dict(self, results_dir, is_repeat=False):
# add the key here so that it comes first in the dict
test_file = {"path": file_path}
# Check that this isn't an empty file
if self.check_if_empty_file(file_path):
if self.check_if_empty_file(file_path) and not stub:
if not is_repeat:
self.errors.append(f"Empty file found! '{os.path.basename(file_path)}'")
# Add the md5 anyway, linting should fail later and can be manually removed if needed.
# Originally we skipped this if empty, but then it's too easy to miss the warning.
# Equally, if a file is legitimately empty we don't want to prevent this from working.
if filename != "versions.yml":
if filename != "versions.yml" and not stub:
# Only add md5sum if the file is not versions.yml
file_md5 = self._md5(file_path)
test_file["md5sum"] = file_md5
Expand All @@ -254,7 +264,7 @@ def create_test_file_dict(self, results_dir, is_repeat=False):

return test_files

def get_md5_sums(self, command, results_dir=None, results_dir_repeat=None):
def get_md5_sums(self, command, results_dir=None, results_dir_repeat=None, stub=False):
"""
Recursively go through directories and subdirectories
and generate tuples of (<file_path>, <md5sum>)
Expand All @@ -276,11 +286,11 @@ def get_md5_sums(self, command, results_dir=None, results_dir_repeat=None):
log.error(f"Directory '{results_dir}' does not exist")
results_dir = None

test_files = self.create_test_file_dict(results_dir=results_dir)
test_files = self.create_test_file_dict(results_dir=results_dir, stub=stub)

# If test was repeated, compare the md5 sums
if results_dir_repeat:
test_files_repeat = self.create_test_file_dict(results_dir=results_dir_repeat, is_repeat=True)
test_files_repeat = self.create_test_file_dict(results_dir=results_dir_repeat, is_repeat=True, stub=stub)

# Compare both test.yml files
for i in range(len(test_files)):
Expand Down
32 changes: 21 additions & 11 deletions nf_core/subworkflows/test_yml_builder.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -145,12 +145,19 @@ def build_all_tests(self):
"""
Go over each entry point and build structure
"""

# Build the stub test
stub_test = self.build_single_test(self.entry_points[0], stub=True)
if stub_test:
self.tests.append(stub_test)

# Build the other tests
for entry_point in self.entry_points:
ep_test = self.build_single_test(entry_point)
if ep_test:
self.tests.append(ep_test)

def build_single_test(self, entry_point):
def build_single_test(self, entry_point, stub=False):
"""Given the supplied cli flags, prompt for any that are missing.

Returns: Test command
Expand All @@ -161,6 +168,8 @@ def build_single_test(self, entry_point):
"tags": [],
"files": [],
}
stub_option = " -stub" if stub else ""
stub_name = " stub" if stub else ""

# Print nice divider line
console = rich.console.Console()
Expand All @@ -169,14 +178,14 @@ def build_single_test(self, entry_point):
log.info(f"Building test meta for entry point '{entry_point}'")

while ep_test["name"] == "":
default_val = f"{self.subworkflow} {entry_point}"
default_val = f"{self.subworkflow} {entry_point}{stub_name}"
if self.no_prompts:
ep_test["name"] = default_val
else:
ep_test["name"] = rich.prompt.Prompt.ask("[violet]Test name", default=default_val).strip()

while ep_test["command"] == "":
default_val = f"nextflow run ./tests/subworkflows/{self.modules_repo.repo_path}/{self.subworkflow} -entry {entry_point} -c ./tests/config/nextflow.config"
default_val = f"nextflow run ./tests/subworkflows/{self.modules_repo.repo_path}/{self.subworkflow} -entry {entry_point} -c ./tests/config/nextflow.config{stub_option}"
if self.no_prompts:
ep_test["command"] = default_val
else:
Expand All @@ -195,7 +204,7 @@ 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(ep_test["command"])
ep_test["files"] = self.get_md5_sums(ep_test["command"], stub=stub)

return ep_test

Expand Down Expand Up @@ -244,7 +253,7 @@ def _md5(self, fname):
md5sum = hash_md5.hexdigest()
return md5sum

def create_test_file_dict(self, results_dir, is_repeat=False):
def create_test_file_dict(self, results_dir, is_repeat=False, stub=False):
"""Walk through directory and collect md5 sums"""
test_files = []
for root, _, files in os.walk(results_dir, followlinks=True):
Expand All @@ -256,14 +265,15 @@ def create_test_file_dict(self, results_dir, is_repeat=False):
# add the key here so that it comes first in the dict
test_file = {"path": file_path}
# Check that this isn't an empty file
if self.check_if_empty_file(file_path):
if self.check_if_empty_file(file_path) and not stub:
if not is_repeat:
self.errors.append(f"Empty file found! '{os.path.basename(file_path)}'")
# Add the md5 anyway, linting should fail later and can be manually removed if needed.
# Originally we skipped this if empty, but then it's too easy to miss the warning.
# Equally, if a file is legitimately empty we don't want to prevent this from working.
file_md5 = self._md5(file_path)
test_file["md5sum"] = file_md5
if not stub:
file_md5 = self._md5(file_path)
test_file["md5sum"] = file_md5
# Switch out the results directory path with the expected 'output' directory
test_file["path"] = file_path.replace(results_dir, "output")
test_files.append(test_file)
Expand All @@ -272,7 +282,7 @@ def create_test_file_dict(self, results_dir, is_repeat=False):

return test_files

def get_md5_sums(self, command, results_dir=None, results_dir_repeat=None):
def get_md5_sums(self, command, results_dir=None, results_dir_repeat=None, stub=False):
"""
Recursively go through directories and subdirectories
and generate tuples of (<file_path>, <md5sum>)
Expand All @@ -294,11 +304,11 @@ def get_md5_sums(self, command, results_dir=None, results_dir_repeat=None):
log.error(f"Directory '{results_dir}' does not exist")
results_dir = None

test_files = self.create_test_file_dict(results_dir=results_dir)
test_files = self.create_test_file_dict(results_dir=results_dir, stub=stub)

# If test was repeated, compare the md5 sums
if results_dir_repeat:
test_files_repeat = self.create_test_file_dict(results_dir=results_dir_repeat, is_repeat=True)
test_files_repeat = self.create_test_file_dict(results_dir=results_dir_repeat, is_repeat=True, stub=stub)

# Compare both test.yml files
for i in range(len(test_files)):
Expand Down
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