Add option to update modules with linting

CHANGELOG.md

@@ -9,6 +9,8 @@
 ### Linting
 
 - Check that the `.prettierignore` file exists and that starts with the same content.
+- Add isort configuration and GitHub workflow ([#1538](https://github.com/nf-core/tools/pull/1538))
+- Add `fix` flag to `nf-core modules lint` command to update modules to the latest version ([#1588](https://github.com/nf-core/tools/pull/1588))
 
 ### General
 
@@ -18,12 +20,9 @@
 
 ### Modules
 
+- Add `--fix-version` flag to `nf-core modules lint` command to update modules to the latest version ([#1588](https://github.com/nf-core/tools/pull/1588))
 - Fix a bug in the regex extracting the version from biocontainers URLs [#1598](https://github.com/nf-core/tools/pull/1598)
 
-### Linting
-
-- Add isort configuration and GitHub workflow ([#1538](https://github.com/nf-core/tools/pull/1538))
-
 ## [v2.4.1 - Cobolt Koala Patch](https://github.com/nf-core/tools/releases/tag/2.4) - [2022-05-16]
 
 - Patch release to try to fix the template sync ([#1585](https://github.com/nf-core/tools/pull/1585))

nf_core/__main__.py

@@ -596,7 +596,8 @@ def create_test_yml(ctx, tool, run_tests, output, force, no_prompts):
 @click.option("-a", "--all", is_flag=True, help="Run on all modules")
 @click.option("--local", is_flag=True, help="Run additional lint tests for local modules")
 @click.option("--passed", is_flag=True, help="Show passed tests")
-def lint(ctx, tool, dir, key, all, local, passed):
+@click.option("--fix-version", is_flag=True, help="Fix the module version if a newer version is available")
+def lint(ctx, tool, dir, key, all, local, passed, fix_version):
  """
  Lint one or more modules in a directory.
 
@@ -609,7 +610,15 @@ def lint(ctx, tool, dir, key, all, local, passed):
  try:
  module_lint = nf_core.modules.ModuleLint(dir=dir)
  module_lint.modules_repo = ctx.obj["modules_repo_obj"]
- module_lint.lint(module=tool, key=key, all_modules=all, print_results=True, local=local, show_passed=passed)
+ module_lint.lint(
+ module=tool,
+ key=key,
+ all_modules=all,
+ print_results=True,
+ local=local,
+ show_passed=passed,
+ fix_version=fix_version,
+ )
  if len(module_lint.failed) > 0:
  sys.exit(1)
  except nf_core.modules.lint.ModuleLintException as e:

nf_core/modules/lint/__init__.py

@@ -101,7 +101,16 @@ def __init__(self, dir):
  def _get_all_lint_tests():
  return ["main_nf", "meta_yml", "module_todos", "module_deprecations"]
 
- def lint(self, module=None, key=(), all_modules=False, print_results=True, show_passed=False, local=False):
+ def lint(
+ self,
+ module=None,
+ key=(),
+ all_modules=False,
+ print_results=True,
+ show_passed=False,
+ local=False,
+ fix_version=False,
+ ):
  """
  Lint all or one specific module
 
@@ -118,6 +127,7 @@ def lint(self, module=None, key=(), all_modules=False, print_results=True, show_
  :param module: A specific module to lint
  :param print_results: Whether to print the linting results
  :param show_passed: Whether passed tests should be shown as well
+ :param fix_version: Update the module version if a newer version is available
 
  :returns: A ModuleLint object containing information of
  the passed, warned and failed tests
@@ -174,11 +184,11 @@ def lint(self, module=None, key=(), all_modules=False, print_results=True, show_
 
  # Lint local modules
  if local and len(local_modules) > 0:
- self.lint_modules(local_modules, local=True)
+ self.lint_modules(local_modules, local=True, fix_version=fix_version)
 
  # Lint nf-core modules
  if len(nfcore_modules) > 0:
- self.lint_modules(nfcore_modules, local=False)
+ self.lint_modules(nfcore_modules, local=False, fix_version=fix_version)
 
  if print_results:
  self._print_results(show_passed=show_passed)
@@ -282,19 +292,21 @@ def get_installed_modules(self):
 
  return local_modules, nfcore_modules
 
- def lint_modules(self, modules, local=False):
+ def lint_modules(self, modules, local=False, fix_version=False):
  """
  Lint a list of modules
 
  Args:
  modules ([NFCoreModule]): A list of module objects
  local (boolean): Whether the list consist of local or nf-core modules
+ fix_version (boolean): Fix the module version if a newer version is available
  """
  progress_bar = rich.progress.Progress(
  "[bold blue]{task.description}",
  rich.progress.BarColumn(bar_width=None),
  "[magenta]{task.completed} of {task.total}[reset] » [bold yellow]{task.fields[test_name]}",
  transient=True,
+ console=console,
  )
  with progress_bar:
  lint_progress = progress_bar.add_task(
@@ -305,9 +317,9 @@ def lint_modules(self, modules, local=False):
 
  for mod in modules:
  progress_bar.update(lint_progress, advance=1, test_name=mod.module_name)
- self.lint_module(mod, local=local)
+ self.lint_module(mod, progress_bar, local=local, fix_version=fix_version)
 
- def lint_module(self, mod, local=False):
+ def lint_module(self, mod, progress_bar, local=False, fix_version=False):
  """
  Perform linting on one module
 
@@ -326,14 +338,17 @@ def lint_module(self, mod, local=False):
 
  # Only check the main script in case of a local module
  if local:
- self.main_nf(mod)
+ self.main_nf(mod, fix_version, progress_bar)
  self.passed += [LintResult(mod, *m) for m in mod.passed]
  self.warned += [LintResult(mod, *m) for m in (mod.warned + mod.failed)]
 
  # Otherwise run all the lint tests
  else:
  for test_name in self.lint_tests:
- getattr(self, test_name)(mod)
+ if test_name == "main_nf":
+ getattr(self, test_name)(mod, fix_version, progress_bar)
+ else:
+ getattr(self, test_name)(mod)
 
  self.passed += [LintResult(mod, *m) for m in mod.passed]
  self.warned += [LintResult(mod, *m) for m in mod.warned]

nf_core/modules/lint/main_nf.py

@@ -3,12 +3,19 @@
 Lint the main.nf file of a module
 """
 
+import logging
 import re
 
+import requests
+from galaxy.tool_util.deps.mulled.util import build_target
+
 import nf_core
+import nf_core.modules.module_utils
+
+log = logging.getLogger(__name__)
 
 
-def main_nf(module_lint_object, module):
+def main_nf(module_lint_object, module, fix_version, progress_bar):
  """
  Lint a ``main.nf`` module file
 
@@ -100,7 +107,7 @@ def main_nf(module_lint_object, module):
  module.passed.append(("main_nf_script_outputs", "Process 'output' block found", module.main_nf))
 
  # Check the process definitions
- if check_process_section(module, process_lines):
+ if check_process_section(module, process_lines, fix_version, progress_bar):
  module.passed.append(("main_nf_container", "Container versions match", module.main_nf))
  else:
  module.warned.append(("main_nf_container", "Container versions do not match", module.main_nf))
@@ -190,7 +197,7 @@ def check_when_section(self, lines):
  self.passed.append(("when_condition", "when: condition is unchanged", self.main_nf))
 
 
-def check_process_section(self, lines):
+def check_process_section(self, lines, fix_version, progress_bar):
  """
  Lint the section of a module between the process definition
  and the 'input:' definition
@@ -236,14 +243,14 @@ def check_process_section(self, lines):
  self.warned.append(("process_standard_label", "Process label unspecified", self.main_nf))
 
  for l in lines:
- if re.search("bioconda::", l):
+ if _container_type(l) == "bioconda":
  bioconda_packages = [b for b in l.split() if "bioconda::" in b]
  l = l.strip(" '\"")
- if l.startswith("https://containers") or l.startswith("https://depot"):
+ if _container_type(l) == "singularity":
  # e.g. "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :" -> v1.2.0_cv1
  # e.g. "https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' :" -> 0.11.9--0
  singularity_tag = re.search(r"(?:/)?(?:biocontainers_)?(?::)?([A-Za-z\d\-_.]+?)(?:\.img)?['\"]", l).group(1)
- if l.startswith("biocontainers/") or l.startswith("quay.io/"):
+ if _container_type(l) == "docker":
  # e.g. "quay.io/biocontainers/krona:2.7.1--pl526_5' }" -> 2.7.1--pl526_5
  # e.g. "biocontainers/biocontainers:v1.2.0_cv1' }" -> v1.2.0_cv1
  docker_tag = re.search(r"(?:[/])?(?::)?([A-Za-z\d\-_.]+)['\"]", l).group(1)
@@ -272,9 +279,30 @@ def check_process_section(self, lines):
  last_ver = response.get("latest_version")
  if last_ver is not None and last_ver != bioconda_version:
  package, ver = bp.split("=", 1)
- self.warned.append(
- ("bioconda_latest", f"Conda update: {package} `{ver}` -> `{last_ver}`", self.main_nf)
- )
+ # If a new version is available and fix is True, update the version
+ if fix_version:
+ if _fix_module_version(self, bioconda_version, last_ver, singularity_tag, response):
+ progress_bar.print(f"[blue]INFO[/blue]\t Updating package '{package}' {ver} -> {last_ver}")
+ log.debug(f"Updating package {package} {ver} -> {last_ver}")
+ self.passed.append(
+ (
+ "bioconda_latest",
+ f"Conda package has been updated to the latest available: `{bp}`",
+ self.main_nf,
+ )
+ )
+ else:
+ progress_bar.print(
+ f"[blue]INFO[/blue]\t Tried to update package. Unable to update package '{package}' {ver} -> {last_ver}"
+ )
+ log.debug(f"Unable to update package {package} {ver} -> {last_ver}")
+ self.warned.append(
+ ("bioconda_latest", f"Conda update: {package} `{ver}` -> `{last_ver}`", self.main_nf)
+ )
+ else:
+ self.warned.append(
+ ("bioconda_latest", f"Conda update: {package} `{ver}` -> `{last_ver}`", self.main_nf)
+ )
  else:
  self.passed.append(("bioconda_latest", f"Conda package is the latest available: `{bp}`", self.main_nf))
 
@@ -341,3 +369,70 @@ def _is_empty(self, line):
  if line.strip().replace(" ", "") == "":
  empty = True
  return empty
+
+
+def _fix_module_version(self, current_version, latest_version, singularity_tag, response):
+ """Updates the module version
+
+ Changes the bioconda current version by the latest version.
+ Obtains the latest build from bioconda response
+ Checks that the new URLs for docker and singularity with the tag [version]--[build] are valid
+ Changes the docker and singularity URLs
+ """
+ # Get latest build
+ build = _get_build(response)
+
+ with open(self.main_nf, "r") as source:
+ lines = source.readlines()
+
+ # Check if the new version + build exist and replace
+ new_lines = []
+ for line in lines:
+ l = line.strip(" '\"")
+ 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":
+ # Check that the new url is valid
+ new_url = re.search(
+ "(?:')(.+)(?:')", re.sub(rf"{singularity_tag}", f"{latest_version}--{build}", line)
+ ).group(1)
+ response_new_container = requests.get(
+ "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}"
+ )
+ if response_new_container.status_code != 200:
+ return False
+ new_lines.append(re.sub(rf"{singularity_tag}", f"{latest_version}--{build}", line))
+ else:
+ new_lines.append(line)
+
+ # Replace outdated versions by the latest one
+ with open(self.main_nf, "w") as source:
+ for line in new_lines:
+ source.write(line)
+
+ return True
+
+
+def _get_build(response):
+ """Get the latest build of the container version"""
+ build_times = []
+ latest_v = response.get("latest_version")
+ files = response.get("files")
+ for f in files:
+ if f.get("version") == latest_v:
+ build_times.append((f.get("upload_time"), f.get("attrs").get("build")))
+ return sorted(build_times, key=lambda tup: tup[0], reverse=True)[0][1]
+
+
+def _container_type(line):
+ """Returns the container type of a build."""
+ if re.search("bioconda::", line):
+ return "bioconda"
+ if line.startswith("https://containers") or line.startswith("https://depot"):
+ return "singularity"
+ if line.startswith("biocontainers/") or line.startswith("quay.io/"):
+ return "docker"

nf_core/modules/update.py

@@ -433,12 +433,6 @@ class DiffEnum(enum.Enum):
  if not dry_run:
  self.update_modules_json(modules_json, modules_repo.name, module, version)
 
- # Don't save to a file, just iteratively update the variable
- else:
- modules_json = self.update_modules_json(
- modules_json, modules_repo.name, module, version, write_file=False
- )
-
  if self.save_diff_fn:
  # Compare the new modules.json and build a diff
  modules_json_diff = difflib.unified_diff(