Merge branch 'dev' into componentscommand

CHANGELOG.md

@@ -26,6 +26,7 @@
 - Bump promoted Python version from 3.7 to 3.8 ([#1971](https://github.com/nf-core/tools/pull/1971))
 - Fix incorrect file deletion in `nf-core launch` when `--params_in` has the same name as `--params_out`
 - Updated GitHub actions ([#1998](https://github.com/nf-core/tools/pull/1998), [#2001](https://github.com/nf-core/tools/pull/2001))
+- Track from where modules and subworkflows are installed ([#1999](https://github.com/nf-core/tools/pull/1999))
 - Substitute ModulesCommand and SubworkflowsCommand by ComponentsCommand ([#2000](https://github.com/nf-core/tools/pull/2000))
 
 ### Modules

nf_core/components/components_install.py

@@ -100,4 +100,4 @@ def clean_modules_json(component, component_type, modules_repo, modules_json):
                         f"Removing {component_type[:-1]} '{modules_repo.repo_path}/{component}' from repo '{repo_to_remove}' from modules.json"
                     )
                     modules_json.remove_entry(component_type, component, repo_to_remove, modules_repo.repo_path)
-                    return component_values["installed"]
+                    return component_values["installed_by"]

nf_core/modules/modules_json.py

@@ -277,7 +277,7 @@ def determine_module_branches_and_shas(self, install_dir, remote_url, modules):
                 repo_entry[module] = {
                     "branch": modules_repo.branch,
                     "git_sha": correct_commit_sha,
-                    "installed": "modules",
+                    "installed_by": "modules",
                 }
 
         # Clean up the modules we were unable to find the sha for
@@ -481,8 +481,8 @@ def check_up_to_date(self):
         If a module/subworkflow is installed but the entry in 'modules.json' is missing we iterate through
         the commit log in the remote to try to determine the SHA.
 
-        Check that we have the "installed" value in 'modules.json', otherwise add it.
-        Assume that the modules/subworkflows were installed by and nf-core command (don't track installed by subworkflows).
+        Check that we have the "installed_by" value in 'modules.json', otherwise add it.
+        Assume that the modules/subworkflows were installed by an nf-core command (don't track installed by subworkflows).
         """
         try:
             self.load()
@@ -517,13 +517,13 @@ def check_up_to_date(self):
         if len(subworkflows_missing_from_modules_json) > 0:
             self.resolve_missing_from_modules_json(subworkflows_missing_from_modules_json, "subworkflows")
 
-        # If the "installed" value is not present for modules/subworkflows, add it.
+        # If the "installed_by" value is not present for modules/subworkflows, add it.
         for repo, repo_content in self.modules_json["repos"].items():
             for component_type, dir_content in repo_content.items():
                 for install_dir, installed_components in dir_content.items():
                     for component, component_features in installed_components.items():
-                        if "installed" not in component_features:
-                            self.modules_json["repos"][repo][component_type][install_dir][component]["installed"] = [
+                        if "installed_by" not in component_features:
+                            self.modules_json["repos"][repo][component_type][install_dir][component]["installed_by"] = [
                                 component_type
                             ]
 
@@ -572,12 +572,12 @@ def update(self, modules_repo, module_name, module_version, installed_by, instal
         repo_modules_entry[module_name]["git_sha"] = module_version
         repo_modules_entry[module_name]["branch"] = branch
         try:
-            if installed_by not in repo_modules_entry[module_name]["installed"]:
-                repo_modules_entry[module_name]["installed"].append(installed_by)
+            if installed_by not in repo_modules_entry[module_name]["installed_by"]:
+                repo_modules_entry[module_name]["installed_by"].append(installed_by)
         except KeyError:
-            repo_modules_entry[module_name]["installed"] = [installed_by]
+            repo_modules_entry[module_name]["installed_by"] = [installed_by]
         finally:
-            repo_modules_entry[module_name]["installed"].extend(installed_by_log)
+            repo_modules_entry[module_name]["installed_by"].extend(installed_by_log)
 
         # Sort the 'modules.json' repo entries
         self.modules_json["repos"] = nf_core.utils.sort_dictionary(self.modules_json["repos"])
@@ -616,12 +616,12 @@ def update_subworkflow(
         repo_subworkflows_entry[subworkflow_name]["git_sha"] = subworkflow_version
         repo_subworkflows_entry[subworkflow_name]["branch"] = branch
         try:
-            if installed_by not in repo_subworkflows_entry[subworkflow_name]["installed"]:
-                repo_subworkflows_entry[subworkflow_name]["installed"].append(installed_by)
+            if installed_by not in repo_subworkflows_entry[subworkflow_name]["installed_by"]:
+                repo_subworkflows_entry[subworkflow_name]["installed_by"].append(installed_by)
         except KeyError:
-            repo_subworkflows_entry[subworkflow_name]["installed"] = [installed_by]
+            repo_subworkflows_entry[subworkflow_name]["installed_by"] = [installed_by]
         finally:
-            repo_subworkflows_entry[subworkflow_name]["installed"].extend(installed_by_log)
+            repo_subworkflows_entry[subworkflow_name]["installed_by"].extend(installed_by_log)
 
         # Sort the 'modules.json' repo entries
         self.modules_json["repos"] = nf_core.utils.sort_dictionary(self.modules_json["repos"])

nf_core/pipeline-template/modules.json

@@ -8,17 +8,17 @@
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
-                        "installed": ["modules"]
+                        "installed_by": ["modules"]
                     },
                     "fastqc": {
                         "branch": "master",
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
-                        "installed": ["modules"]
+                        "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
-                        "installed": ["modules"]
+                        "installed_by": ["modules"]
                     }
                 }
             }

tests/modules/modules_json.py

@@ -41,7 +41,7 @@ def test_mod_json_update(self):
         NF_CORE_MODULES_DEFAULT_BRANCH
         == mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["MODULE_NAME"]["branch"]
     )
-    assert "modules" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["MODULE_NAME"]["installed"]
+    assert "modules" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["MODULE_NAME"]["installed_by"]
 
 
 def test_mod_json_create(self):