add tests for subworkflows install command

CHANGELOG.md

@@ -17,9 +17,7 @@
 - Fix bug when updating modules from old version in old folder structure
 - Don't remove local copy of modules repo, only update it with fetch ([#1881](https://github.com/nf-core/tools/pull/1881))
 - Add subworkflow commands create-test-yml, create and install ([#1897](https://github.com/nf-core/tools/pull/1897))
-- Update subworkflows install so it installs also imported modules and subworkflows ([#1904](https://github.com/nf-core/tools/pull/1904))
 - Improve test coverage of `sync.py` and `__main__.py` ([#1936](https://github.com/nf-core/tools/pull/1936), [#1965](https://github.com/nf-core/tools/pull/1965))
-- `check_up_to_date()` function from `modules_json` also checks for subworkflows.
 - The default branch can now be specified when creating a new pipeline repo [#1959](https://github.com/nf-core/tools/pull/1959).
 - Only warn when checking that the pipeline directory contains a `main.nf` and a `nextflow.config` file if the pipeline is not an nf-core pipeline [#1964](https://github.com/nf-core/tools/pull/1964)
 - Add file `versions.yml` when generating `test.yml` with `nf-core modules create-test-yml` but don't check for md5sum [#1963](https://github.com/nf-core/tools/pull/1963)
@@ -32,6 +30,12 @@
 
 - Update patch file paths if the modules directory has the old structure ([#1878](https://github.com/nf-core/tools/pull/1878))
 
+### Subworkflows
+
+- Add tests for subworkflows install command ([#1996](https://github.com/nf-core/tools/pull/1996))
+- `check_up_to_date()` function from `modules_json` also checks for subworkflows.
+- Update subworkflows install so it installs also imported modules and subworkflows ([#1904](https://github.com/nf-core/tools/pull/1904))
+
 ## [v2.6 - Tin Octopus](https://github.com/nf-core/tools/releases/tag/2.6) - [2022-10-04]
 
 ### Template

nf_core/components/components_install.py

@@ -42,19 +42,20 @@ def collect_and_verify_name(component_type, component, modules_repo):
     return component
 
 
-def check_component_installed(component_type, component, current_version, component_dir, modules_repo, force):
+def check_component_installed(component_type, component, current_version, component_dir, modules_repo, force, prompt):
     """
     Check that the module/subworkflow is not already installed
     """
     if (current_version is not None and os.path.exists(component_dir)) and not force:
         log.info(f"{component_type[:-1].title()} is already installed.")
 
-        message = "?" if component_type == "modules" else " of this subworkflow and all it's imported modules?"
-        force = questionary.confirm(
-            f"{component_type[:-1].title()} {component} is already installed. \nDo you want to force the reinstallation{message}",
-            style=nf_core.utils.nfcore_question_style,
-            default=False,
-        ).unsafe_ask()
+        if prompt:
+            message = "?" if component_type == "modules" else " of this subworkflow and all it's imported modules?"
+            force = questionary.confirm(
+                f"{component_type[:-1].title()} {component} is already installed. \nDo you want to force the reinstallation{message}",
+                style=nf_core.utils.nfcore_question_style,
+                default=False,
+            ).unsafe_ask()
 
         if not force:
             repo_flag = "" if modules_repo.repo_path == NF_CORE_MODULES_NAME else f"-g {modules_repo.remote_url} "

nf_core/modules/install.py

@@ -69,7 +69,7 @@ def install(self, module, silent=False):
 
         # Check that the module is not already installed
         if not nf_core.components.components_install.check_component_installed(
-            self.component_type, module, current_version, module_dir, self.modules_repo, self.force
+            self.component_type, module, current_version, module_dir, self.modules_repo, self.force, self.prompt
         ):
             return False
 

nf_core/modules/modules_json.py

@@ -806,9 +806,9 @@ def get_all_components(self, component_type):
 
         return self.pipeline_components
 
-    def get_module_branch(self, module, repo_url, install_dir):
+    def get_component_branch(self, component_type, component, repo_url, install_dir):
         """
-        Gets the branch from which the module was installed
+        Gets the branch from which the module/subworkflow was installed
 
         Returns:
             (str): The branch name
@@ -820,14 +820,14 @@ def get_module_branch(self, module, repo_url, install_dir):
         branch = (
             self.modules_json["repos"]
             .get(repo_url, {})
-            .get("modules", {})
+            .get(component_type, {})
             .get(install_dir, {})
-            .get(module, {})
+            .get(component, {})
             .get("branch")
         )
         if branch is None:
             raise LookupError(
-                f"Could not find branch information for module '{Path(install_dir, module)}'."
+                f"Could not find branch information for component '{Path(install_dir, component)}'."
                 f"Please remove the 'modules.json' and rerun the command to recreate it"
             )
         return branch

nf_core/modules/patch.py

@@ -62,7 +62,9 @@ def patch(self, module=None):
                 f"The '{module_fullname}' module does not have a valid version in the 'modules.json' file. Cannot compute patch"
             )
         # Get the module branch and reset it in the ModulesRepo object
-        module_branch = self.modules_json.get_module_branch(module, self.modules_repo.remote_url, module_dir)
+        module_branch = self.modules_json.get_component_branch(
+            self.component_type, module, self.modules_repo.remote_url, module_dir
+        )
         if module_branch != self.modules_repo.branch:
             self.modules_repo.setup_branch(module_branch)
 

nf_core/modules/update.py

@@ -315,7 +315,9 @@ def get_single_module_info(self, module):
                 log.info(f"Updating module to ({sha})")
 
         # Check if the update branch is the same as the installation branch
-        current_branch = self.modules_json.get_module_branch(module, self.modules_repo.remote_url, install_dir)
+        current_branch = self.modules_json.get_component_branch(
+            self.component_type, module, self.modules_repo.remote_url, install_dir
+        )
         new_branch = self.modules_repo.branch
         if current_branch != new_branch:
             log.warning(
@@ -361,11 +363,23 @@ def get_all_modules_info(self, branch=None):
                 for module_dir, module in modules:
                     try:
                         modules_info[repo_name][module_dir].append(
-                            (module, self.sha, self.modules_json.get_module_branch(module, repo_name, module_dir))
+                            (
+                                module,
+                                self.sha,
+                                self.modules_json.get_component_branch(
+                                    self.component_type, module, repo_name, module_dir
+                                ),
+                            )
                         )
                     except KeyError:
                         modules_info[repo_name][module_dir] = [
-                            (module, self.sha, self.modules_json.get_module_branch(module, repo_name, module_dir))
+                            (
+                                module,
+                                self.sha,
+                                self.modules_json.get_component_branch(
+                                    self.component_type, module, repo_name, module_dir
+                                ),
+                            )
                         ]
             elif isinstance(self.update_config[repo_name], dict):
                 # If it is a dict, then there are entries for individual modules or module directories
@@ -381,15 +395,19 @@ def get_all_modules_info(self, branch=None):
                                         (
                                             module,
                                             custom_sha,
-                                            self.modules_json.get_module_branch(module, repo_name, module_dir),
+                                            self.modules_json.get_component_branch(
+                                                self.component_type, module, repo_name, module_dir
+                                            ),
                                         )
                                     )
                                 except KeyError:
                                     modules_info[repo_name][module_dir] = [
                                         (
                                             module,
                                             custom_sha,
-                                            self.modules_json.get_module_branch(module, repo_name, module_dir),
+                                            self.modules_json.get_component_branch(
+                                                self.component_type, module, repo_name, module_dir
+                                            ),
                                         )
                                     ]
                         if self.sha is not None:
@@ -409,15 +427,19 @@ def get_all_modules_info(self, branch=None):
                                         (
                                             module,
                                             self.sha,
-                                            self.modules_json.get_module_branch(module, repo_name, module_dir),
+                                            self.modules_json.get_component_branch(
+                                                self.component_type, module, repo_name, module_dir
+                                            ),
                                         )
                                     )
                                 except KeyError:
                                     modules_info[repo_name][module_dir] = [
                                         (
                                             module,
                                             self.sha,
-                                            self.modules_json.get_module_branch(module, repo_name, module_dir),
+                                            self.modules_json.get_component_branch(
+                                                self.component_type, module, repo_name, module_dir
+                                            ),
                                         )
                                     ]
                             elif isinstance(dir_config[module], str):
@@ -428,15 +450,19 @@ def get_all_modules_info(self, branch=None):
                                         (
                                             module,
                                             custom_sha,
-                                            self.modules_json.get_module_branch(module, repo_name, module_dir),
+                                            self.modules_json.get_component_branch(
+                                                self.component_type, module, repo_name, module_dir
+                                            ),
                                         )
                                     )
                                 except KeyError:
                                     modules_info[repo_name][module_dir] = [
                                         (
                                             module,
                                             custom_sha,
-                                            self.modules_json.get_module_branch(module, repo_name, module_dir),
+                                            self.modules_json.get_component_branch(
+                                                self.component_type, module, repo_name, module_dir
+                                            ),
                                         )
                                     ]
                                 if self.sha is not None:
@@ -455,11 +481,23 @@ def get_all_modules_info(self, branch=None):
                 for module_dir, module in modules:
                     try:
                         modules_info[repo_name][module_dir].append(
-                            (module, custom_sha, self.modules_json.get_module_branch(module, repo_name, module_dir))
+                            (
+                                module,
+                                custom_sha,
+                                self.modules_json.get_component_branch(
+                                    self.component_type, module, repo_name, module_dir
+                                ),
+                            )
                         )
                     except KeyError:
                         modules_info[repo_name][module_dir] = [
-                            (module, custom_sha, self.modules_json.get_module_branch(module, repo_name, module_dir))
+                            (
+                                module,
+                                custom_sha,
+                                self.modules_json.get_component_branch(
+                                    self.component_type, module, repo_name, module_dir
+                                ),
+                            )
                         ]
                 if self.sha is not None:
                     overridden_repos.append(repo_name)

nf_core/subworkflows/create.py

@@ -9,7 +9,6 @@
 import os
 
 import yaml
-from packaging.version import parse as parse_version
 
 import nf_core
 import nf_core.components.components_create
@@ -114,7 +113,7 @@ def create(self):
                 pytest_modules_yml = dict(sorted(pytest_modules_yml.items()))
                 with open(os.path.join(self.directory, "tests", "config", "pytest_modules.yml"), "w") as fh:
                     yaml.dump(pytest_modules_yml, fh, sort_keys=True, Dumper=nf_core.utils.custom_yaml_dumper())
-            except FileNotFoundError as e:
+            except FileNotFoundError:
                 raise UserWarning("Could not open 'tests/config/pytest_modules.yml' file!")
 
         new_files = list(self.file_paths.values())

nf_core/subworkflows/install.py

@@ -69,7 +69,13 @@ def install(self, subworkflow, silent=False):
 
         # Check that the subworkflow is not already installed
         if not nf_core.components.components_install.check_component_installed(
-            self.component_type, subworkflow, current_version, subworkflow_dir, self.modules_repo, self.force
+            self.component_type,
+            subworkflow,
+            current_version,
+            subworkflow_dir,
+            self.modules_repo,
+            self.force,
+            self.prompt,
         ):
             return False
 

tests/modules/install.py

@@ -67,4 +67,7 @@ def test_modules_install_different_branch_succeed(self):
 
     # Verify that the branch entry was added correctly
     modules_json = ModulesJson(self.pipeline_dir)
-    assert modules_json.get_module_branch("fastp", GITLAB_URL, GITLAB_REPO) == GITLAB_BRANCH_TEST_BRANCH
+    assert (
+        modules_json.get_component_branch(self.component_type, "fastp", GITLAB_URL, GITLAB_REPO)
+        == GITLAB_BRANCH_TEST_BRANCH
+    )

tests/modules/update.py

@@ -231,7 +231,10 @@ def test_update_different_branch_single_module(self):
 
     # Verify that the branch entry was updated correctly
     modules_json = ModulesJson(self.pipeline_dir)
-    assert modules_json.get_module_branch("fastp", GITLAB_URL, GITLAB_REPO) == GITLAB_BRANCH_TEST_BRANCH
+    assert (
+        modules_json.get_component_branch(self.component_type, "fastp", GITLAB_URL, GITLAB_REPO)
+        == GITLAB_BRANCH_TEST_BRANCH
+    )
     assert modules_json.get_module_version("fastp", GITLAB_URL, GITLAB_REPO) == GITLAB_BRANCH_TEST_NEW_SHA
 
 
@@ -249,10 +252,16 @@ def test_update_different_branch_mixed_modules_main(self):
 
     modules_json = ModulesJson(self.pipeline_dir)
     # Verify that the branch entry was updated correctly
-    assert modules_json.get_module_branch("fastp", GITLAB_URL, GITLAB_REPO) == GITLAB_BRANCH_TEST_BRANCH
+    assert (
+        modules_json.get_component_branch(self.component_type, "fastp", GITLAB_URL, GITLAB_REPO)
+        == GITLAB_BRANCH_TEST_BRANCH
+    )
     assert modules_json.get_module_version("fastp", GITLAB_URL, GITLAB_REPO) == GITLAB_BRANCH_TEST_NEW_SHA
     # MultiQC is present in both branches but should've been updated using the 'main' branch
-    assert modules_json.get_module_branch("multiqc", GITLAB_URL, GITLAB_REPO) == GITLAB_DEFAULT_BRANCH
+    assert (
+        modules_json.get_component_branch(self.component_type, "multiqc", GITLAB_URL, GITLAB_REPO)
+        == GITLAB_DEFAULT_BRANCH
+    )
 
 
 def test_update_different_branch_mix_modules_branch_test(self):
@@ -272,7 +281,10 @@ def test_update_different_branch_mix_modules_branch_test(self):
     )
     assert update_obj.update()
 
-    assert modules_json.get_module_branch("multiqc", GITLAB_URL, GITLAB_REPO) == GITLAB_BRANCH_TEST_BRANCH
+    assert (
+        modules_json.get_component_branch(self.component_type, "multiqc", GITLAB_URL, GITLAB_REPO)
+        == GITLAB_BRANCH_TEST_BRANCH
+    )
     assert modules_json.get_module_version("multiqc", GITLAB_URL, GITLAB_REPO) == GITLAB_BRANCH_TEST_NEW_SHA