Merge pull request #2573 from mashehu/make-tests-faster

make tests faster

nf_core/components/install.py

@@ -127,6 +127,8 @@ def install(self, component, silent=False):
  self.install_included_components(component_dir)
 
  if not silent:
+ modules_json.load()
+ modules_json.dump(run_prettier=True)
  # Print include statement
  component_name = "_".join(component.upper().split("/"))
  log.info(f"Use the following statement to include this {self.component_type[:-1]}:")

nf_core/components/update.py

@@ -288,20 +288,21 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr
  updated.append(component)
  recursive_update = True
  modules_to_update, subworkflows_to_update = self.get_components_to_update(component)
- if not silent and not self.update_all and len(modules_to_update + subworkflows_to_update) > 0:
- log.warning(
- f"All modules and subworkflows linked to the updated {self.component_type[:-1]} will be {'asked for update' if self.show_diff else 'automatically updated'}.\n"
- "It is advised to keep all your modules and subworkflows up to date.\n"
- "It is not guaranteed that a subworkflow will continue working as expected if all modules/subworkflows used in it are not up to date.\n"
- )
- if self.update_deps:
- recursive_update = True
- else:
- recursive_update = questionary.confirm(
- "Would you like to continue updating all modules and subworkflows?",
- default=True,
- style=nf_core.utils.nfcore_question_style,
- ).unsafe_ask()
+ if not silent and len(modules_to_update + subworkflows_to_update) > 0:
+ if not self.update_all:
+ log.warning(
+ f"All modules and subworkflows linked to the updated {self.component_type[:-1]} will be {'asked for update' if self.show_diff else 'automatically updated'}.\n"
+ "It is advised to keep all your modules and subworkflows up to date.\n"
+ "It is not guaranteed that a subworkflow will continue working as expected if all modules/subworkflows used in it are not up to date.\n"
+ )
+ if self.update_deps:
+ recursive_update = True
+ else:
+ recursive_update = questionary.confirm(
+ "Would you like to continue updating all modules and subworkflows?",
+ default=True,
+ style=nf_core.utils.nfcore_question_style,
+ ).unsafe_ask()
  if recursive_update and len(modules_to_update + subworkflows_to_update) > 0:
  # Update linked components
  self.update_linked_components(modules_to_update, subworkflows_to_update, updated)
@@ -323,8 +324,12 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr
  )
  elif not all_patches_successful and not silent:
  log.info(f"Updates complete. Please apply failed patch{plural_es(components_info)} manually.")
+ self.modules_json.load()
+ self.modules_json.dump(run_prettier=True)
  elif not silent:
  log.info("Updates complete :sparkles:")
+ self.modules_json.load()
+ self.modules_json.dump(run_prettier=True)
 
  return exit_value
 

nf_core/modules/modules_json.py

@@ -6,6 +6,7 @@
 import shutil
 import tempfile
 from pathlib import Path
+from typing import Union
 
 import git
 import questionary
@@ -41,7 +42,7 @@ def __init__(self, pipeline_dir):
  self.modules_dir = Path(self.dir, "modules")
  self.subworkflows_dir = Path(self.dir, "subworkflows")
  self.modules_json_path = Path(self.dir, "modules.json")
- self.modules_json = None
+ self.modules_json: Union(dict, None) = None
  self.pipeline_modules = None
  self.pipeline_subworkflows = None
  self.pipeline_components = None
@@ -1035,13 +1036,17 @@ def get_component_branch(self, component_type, component, repo_url, install_dir)
  )
  return branch
 
- def dump(self):
+ def dump(self, run_prettier: bool = False):
  """
  Sort the modules.json, and write it to file
  """
  # Sort the modules.json
  self.modules_json["repos"] = nf_core.utils.sort_dictionary(self.modules_json["repos"])
- dump_json_with_prettier(self.modules_json_path, self.modules_json)
+ if run_prettier:
+ dump_json_with_prettier(self.modules_json_path, self.modules_json)
+ else:
+ with open(self.modules_json_path, "w") as fh:
+ json.dump(self.modules_json, fh, indent=4)
 
  def resolve_missing_installation(self, missing_installation, component_type):
  missing_but_in_mod_json = [