Merge branch 'dev' into modules-lint-sort

nf_core/modules/modules_json.py

@@ -546,6 +546,16 @@ def check_up_to_date(self):
             self.load()
             if not self.has_git_url_and_modules():
                 raise UserWarning
+            # check that all "installed_by" entries are lists and not strings
+            # [these strings come from an older dev version, so this check can probably be removed in a future release]
+            for _, repo_entry in self.modules_json.get("repos", {}).items():
+                for component_type in ["modules", "subworkflows"]:
+                    if component_type in repo_entry:
+                        for install_dir, install_dir_entry in repo_entry[component_type].items():
+                            for _, component in install_dir_entry.items():
+                                if "installed_by" in component and isinstance(component["installed_by"], str):
+                                    log.debug(f"Updating {component} in modules.json")
+                                    component["installed_by"] = [component["installed_by"]]
         except UserWarning:
             log.info("The 'modules.json' file is not up to date. Recreating the 'modules.json' file.")
             self.create()

tests/modules/install.py

@@ -71,3 +71,15 @@ def test_modules_install_different_branch_succeed(self):
         modules_json.get_component_branch(self.component_type, "fastp", GITLAB_URL, GITLAB_REPO)
         == GITLAB_BRANCH_TEST_BRANCH
     )
+
+
+def test_modules_install_tracking(self):
+    """Test installing a module and finding 'modules' in the installed_by section of modules.json"""
+    self.mods_install.install("trimgalore")
+
+    # Verify that the installed_by entry was added correctly
+    modules_json = ModulesJson(self.pipeline_dir)
+    mod_json = modules_json.get_modules_json()
+    assert mod_json["repos"]["https://github.com/nf-core/modules.git"]["modules"]["nf-core"]["trimgalore"][
+        "installed_by"
+    ] == ["modules"]

tests/subworkflows/install.py

@@ -76,3 +76,67 @@ def test_subworkflows_install_different_branch_fail(self):
     install_obj = SubworkflowInstall(self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_BRANCH_TEST_BRANCH)
     # The bam_stats_samtools subworkflow does not exists in the branch-test branch
     assert install_obj.install("bam_stats_samtools") is False
+
+
+def test_subworkflows_install_tracking(self):
+    """Test installing a subworkflow and finding the correct entries in installed_by section of modules.json"""
+    self.subworkflow_install.install("bam_sort_stats_samtools")
+
+    # Verify that the installed_by entry was added correctly
+    modules_json = ModulesJson(self.pipeline_dir)
+    mod_json = modules_json.get_modules_json()
+    assert mod_json["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"]["nf-core"][
+        "bam_sort_stats_samtools"
+    ]["installed_by"] == ["subworkflows"]
+    assert mod_json["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"]["nf-core"]["bam_stats_samtools"][
+        "installed_by"
+    ] == ["bam_sort_stats_samtools"]
+    assert mod_json["repos"]["https://github.com/nf-core/modules.git"]["modules"]["nf-core"]["samtools/stats"][
+        "installed_by"
+    ] == ["bam_stats_samtools"]
+    assert mod_json["repos"]["https://github.com/nf-core/modules.git"]["modules"]["nf-core"]["samtools/sort"][
+        "installed_by"
+    ] == ["bam_sort_stats_samtools"]
+
+    # Clean directory
+    self.subworkflow_remove.remove("bam_sort_stats_samtools")
+
+
+def test_subworkflows_install_tracking_added_already_installed(self):
+    """Test installing a subworkflow and finding the correct entries in installed_by section of modules.json"""
+    self.subworkflow_install.install("bam_sort_stats_samtools")
+    self.subworkflow_install.install("bam_stats_samtools")
+
+    # Verify that the installed_by entry was added correctly
+    modules_json = ModulesJson(self.pipeline_dir)
+    mod_json = modules_json.get_modules_json()
+    assert mod_json["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"]["nf-core"][
+        "bam_sort_stats_samtools"
+    ]["installed_by"] == ["subworkflows"]
+    assert sorted(
+        mod_json["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"]["nf-core"]["bam_stats_samtools"][
+            "installed_by"
+        ]
+    ) == sorted(["bam_sort_stats_samtools", "subworkflows"])
+
+    # Clean directory
+    self.subworkflow_remove.remove("bam_sort_stats_samtools")
+    self.subworkflow_remove.remove("bam_stats_samtools")
+
+
+def test_subworkflows_install_tracking_added_super_subworkflow(self):
+    """Test installing a subworkflow and finding the correct entries in installed_by section of modules.json"""
+    self.subworkflow_install.install("bam_stats_samtools")
+    self.subworkflow_install.install("bam_sort_stats_samtools")
+
+    # Verify that the installed_by entry was added correctly
+    modules_json = ModulesJson(self.pipeline_dir)
+    mod_json = modules_json.get_modules_json()
+    assert mod_json["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"]["nf-core"][
+        "bam_sort_stats_samtools"
+    ]["installed_by"] == ["subworkflows"]
+    assert sorted(
+        mod_json["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"]["nf-core"]["bam_stats_samtools"][
+            "installed_by"
+        ]
+    ) == sorted(["subworkflows", "bam_sort_stats_samtools"])

tests/test_modules.py

@@ -152,6 +152,7 @@ def test_modulesrepo_class(self):
         test_modules_install_from_gitlab,
         test_modules_install_nomodule,
         test_modules_install_nopipeline,
+        test_modules_install_tracking,
         test_modules_install_trimgalore,
         test_modules_install_trimgalore_twice,
     )

tests/test_subworkflows.py

@@ -107,6 +107,9 @@ def tearDown(self):
         test_subworkflows_install_emptypipeline,
         test_subworkflows_install_from_gitlab,
         test_subworkflows_install_nosubworkflow,
+        test_subworkflows_install_tracking,
+        test_subworkflows_install_tracking_added_already_installed,
+        test_subworkflows_install_tracking_added_super_subworkflow,
     )
     from .subworkflows.list import (
         test_subworkflows_install_and_list_subworkflows,