Substitute ModulesCommand and SubworkflowsCommand by ComponentsCommand

nf_core/components/components_command.py

@@ -158,22 +158,22 @@ def load_lint_config(self):
         except FileNotFoundError:
             log.debug(f"No lint config file found: {config_fn}")
 
-    def check_component_structure(self, component_name):
+    def check_modules_structure(self):
         """
-        Check that the structure of the modules/subworkflow directory in a pipeline is the correct one:
-            modules/nf-core/TOOL/SUBTOOL | subworkflows/nf-core/SUBWORKFLOW
+        Check that the structure of the modules directory in a pipeline is the correct one:
+            modules/nf-core/TOOL/SUBTOOL
 
         Prior to nf-core/tools release 2.6 the directory structure had an additional level of nesting:
             modules/nf-core/modules/TOOL/SUBTOOL
         """
         if self.repo_type == "pipeline":
             wrong_location_modules = []
-            for directory, _, files in os.walk(Path(self.dir, component_name)):
+            for directory, _, files in os.walk(Path(self.dir, "modules")):
                 if "main.nf" in files:
-                    module_path = Path(directory).relative_to(Path(self.dir, component_name))
+                    module_path = Path(directory).relative_to(Path(self.dir, "modules"))
                     parts = module_path.parts
                     # Check that there are modules installed directly under the 'modules' directory
-                    if parts[1] == component_name:
+                    if parts[1] == "modules":
                         wrong_location_modules.append(module_path)
             # If there are modules installed in the wrong location
             if len(wrong_location_modules) > 0:
@@ -185,12 +185,43 @@ def check_component_structure(self, component_name):
                 )
                 # Move wrong modules to the right directory
                 for module in wrong_location_modules:
-                    modules_dir = Path(component_name).resolve()
+                    modules_dir = Path("modules").resolve()
                     correct_dir = Path(modules_dir, self.modules_repo.repo_path, Path(*module.parts[2:]))
                     wrong_dir = Path(modules_dir, module)
                     shutil.move(wrong_dir, correct_dir)
                     log.info(f"Moved {wrong_dir} to {correct_dir}.")
-                shutil.rmtree(Path(self.dir, component_name, self.modules_repo.repo_path, component_name))
+                shutil.rmtree(Path(self.dir, "modules", self.modules_repo.repo_path, "modules"))
                 # Regenerate modules.json file
                 modules_json = ModulesJson(self.dir)
                 modules_json.check_up_to_date()
+
+    def check_patch_paths(self, patch_path, module_name):
+        """
+        Check that paths in patch files are updated to the new modules path
+        """
+        if patch_path.exists():
+            log.info(f"Modules {module_name} contains a patch file.")
+            rewrite = False
+            with open(patch_path, "r") as fh:
+                lines = fh.readlines()
+                for index, line in enumerate(lines):
+                    # Check if there are old paths in the patch file and replace
+                    if f"modules/{self.modules_repo.repo_path}/modules/{module_name}/" in line:
+                        rewrite = True
+                        lines[index] = line.replace(
+                            f"modules/{self.modules_repo.repo_path}/modules/{module_name}/",
+                            f"modules/{self.modules_repo.repo_path}/{module_name}/",
+                        )
+            if rewrite:
+                log.info(f"Updating paths in {patch_path}")
+                with open(patch_path, "w") as fh:
+                    for line in lines:
+                        fh.write(line)
+                # Update path in modules.json if the file is in the correct format
+                modules_json = ModulesJson(self.dir)
+                modules_json.load()
+                if modules_json.has_git_url_and_modules():
+                    modules_json.modules_json["repos"][self.modules_repo.remote_url]["modules"][
+                        self.modules_repo.repo_path
+                    ][module_name]["patch"] = str(patch_path.relative_to(Path(self.dir).resolve()))
+                modules_json.dump()

nf_core/components/components_test.py

@@ -1,3 +1,6 @@
+from nf_core.components.components_command import ComponentCommand
+
+
 class ComponentsTest(ComponentCommand):
     """
     Class to run module pytests.
@@ -38,7 +41,7 @@ def __init__(
         self.no_prompts = no_prompts
         self.pytest_args = pytest_args
 
-        super().__init__(".", remote_url, branch, no_pull)
+        super().__init__("component_type", ".", remote_url, branch, no_pull)
 
     def run(self):
         """Run test steps"""

nf_core/components/list.py

@@ -6,8 +6,6 @@
 import nf_core.modules.modules_utils
 from nf_core.components.components_command import ComponentCommand
 from nf_core.modules.modules_json import ModulesJson
-
-# from .modules_command import ModulesRepo
 from nf_core.modules.modules_repo import ModulesRepo
 
 log = logging.getLogger(__name__)

nf_core/modules/bump_versions.py

@@ -18,17 +18,16 @@
 
 import nf_core.modules.modules_utils
 import nf_core.utils
+from nf_core.components.components_command import ComponentCommand
 from nf_core.utils import plural_s as _s
 from nf_core.utils import rich_force_colors
 
-from .modules_command import ModuleCommand
-
 log = logging.getLogger(__name__)
 
 
-class ModuleVersionBumper(ModuleCommand):
+class ModuleVersionBumper(ComponentCommand):
     def __init__(self, pipeline_dir, remote_url=None, branch=None, no_pull=False):
-        super().__init__(pipeline_dir, remote_url, branch, no_pull)
+        super().__init__("modules", pipeline_dir, remote_url, branch, no_pull)
 
         self.up_to_date = None
         self.updated = None

nf_core/modules/create.py

@@ -17,13 +17,12 @@
 import nf_core.components.components_create
 import nf_core.modules.modules_utils
 import nf_core.utils
-
-from .modules_command import ModuleCommand
+from nf_core.components.components_command import ComponentCommand
 
 log = logging.getLogger(__name__)
 
 
-class ModuleCreate(ModuleCommand):
+class ModuleCreate(ComponentCommand):
     def __init__(
         self,
         directory=".",
@@ -36,7 +35,7 @@ def __init__(
         conda_version=None,
         repo_type=None,
     ):
-        super().__init__(directory)
+        super().__init__("modules", directory)
         self.directory = directory
         self.tool = tool
         self.author = author
@@ -157,7 +156,7 @@ 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/modules/info.py

@@ -11,16 +11,16 @@
 from rich.text import Text
 
 import nf_core.utils
+from nf_core.components.components_command import ComponentCommand
 from nf_core.modules.modules_json import ModulesJson
 
-from .modules_command import ModuleCommand
 from .modules_repo import NF_CORE_MODULES_REMOTE
 from .modules_utils import get_repo_type
 
 log = logging.getLogger(__name__)
 
 
-class ModuleInfo(ModuleCommand):
+class ModuleInfo(ComponentCommand):
     """
     Class to print information of a module.
 
@@ -56,7 +56,7 @@ class ModuleInfo(ModuleCommand):
     """
 
     def __init__(self, pipeline_dir, tool, remote_url, branch, no_pull):
-        super().__init__(pipeline_dir, remote_url, branch, no_pull)
+        super().__init__("modules", pipeline_dir, remote_url, branch, no_pull)
         self.meta = None
         self.local_path = None
         self.remote_location = None
@@ -139,7 +139,6 @@ def get_local_yaml(self):
 
         if self.repo_type == "pipeline":
             # Try to find and load the meta.yml file
-            repo_name = self.modules_repo.repo_path
             module_base_path = os.path.join(self.dir, "modules")
             # Check that we have any modules installed from this repo
             modules = self.modules_json.get_all_modules().get(self.modules_repo.remote_url)

nf_core/modules/install.py

@@ -6,12 +6,12 @@
 import nf_core.utils
 from nf_core.modules.modules_json import ModulesJson
 
-from .modules_command import ModuleCommand
+from nf_core.components.components_command import ComponentCommand
 
 log = logging.getLogger(__name__)
 
 
-class ModuleInstall(ModuleCommand):
+class ModuleInstall(ComponentCommand):
     def __init__(
         self,
         pipeline_dir,
@@ -23,7 +23,7 @@ def __init__(
         no_pull=False,
         installed_by=False,
     ):
-        super().__init__(pipeline_dir, remote_url, branch, no_pull)
+        super().__init__("modules", pipeline_dir, remote_url, branch, no_pull)
         self.force = force
         self.prompt = prompt
         self.sha = sha

nf_core/modules/lint/__init__.py

@@ -21,10 +21,9 @@
 
 import nf_core.modules.modules_utils
 import nf_core.utils
+from nf_core.components.components_command import ComponentCommand
 from nf_core.lint_utils import console
-from nf_core.modules.modules_command import ModuleCommand
 from nf_core.modules.modules_json import ModulesJson
-from nf_core.modules.modules_repo import ModulesRepo
 from nf_core.modules.nfcore_module import NFCoreModule
 from nf_core.utils import plural_s as _s
 
@@ -48,7 +47,7 @@ def __init__(self, mod, lint_test, message, file_path):
         self.module_name = mod.module_name
 
 
-class ModuleLint(ModuleCommand):
+class ModuleLint(ComponentCommand):
     """
     An object for linting modules either in a clone of the 'nf-core/modules'
     repository or in any nf-core pipeline directory
@@ -73,7 +72,7 @@ def __init__(
         no_pull=False,
         hide_progress=False,
     ):
-        super().__init__(dir=dir, remote_url=remote_url, branch=branch, no_pull=no_pull, hide_progress=False)
+        super().__init__("modules", dir=dir, remote_url=remote_url, branch=branch, no_pull=no_pull, hide_progress=False)
 
         self.fail_warned = fail_warned
         self.passed = []

nf_core/modules/modules_test.py

@@ -15,13 +15,13 @@
 
 import nf_core.modules.modules_utils
 import nf_core.utils
-from nf_core.modules.modules_command import ModuleCommand
+from nf_core.components.components_command import ComponentCommand
 from nf_core.modules.modules_json import ModulesJson
 
 log = logging.getLogger(__name__)
 
 
-class ModulesTest(ModuleCommand):
+class ModulesTest(ComponentCommand):
     """
     Class to run module pytests.
 
@@ -61,7 +61,7 @@ def __init__(
         self.no_prompts = no_prompts
         self.pytest_args = pytest_args
 
-        super().__init__(".", remote_url, branch, no_pull)
+        super().__init__("modules", ".", remote_url, branch, no_pull)
 
     def run(self):
         """Run test steps"""

nf_core/modules/patch.py

@@ -7,17 +7,17 @@
 import questionary
 
 import nf_core.utils
+from nf_core.components.components_command import ComponentCommand
 
-from .modules_command import ModuleCommand
 from .modules_differ import ModulesDiffer
 from .modules_json import ModulesJson
 
 log = logging.getLogger(__name__)
 
 
-class ModulePatch(ModuleCommand):
+class ModulePatch(ComponentCommand):
     def __init__(self, dir, remote_url=None, branch=None, no_pull=False):
-        super().__init__(dir, remote_url, branch, no_pull)
+        super().__init__("modules", dir, remote_url, branch, no_pull)
 
         self.modules_json = ModulesJson(dir)
 

nf_core/modules/remove.py

@@ -4,14 +4,17 @@
 import questionary
 
 import nf_core.utils
+from nf_core.components.components_command import ComponentCommand
 
-from .modules_command import ModuleCommand
 from .modules_json import ModulesJson
 
 log = logging.getLogger(__name__)
 
 
-class ModuleRemove(ModuleCommand):
+class ModuleRemove(ComponentCommand):
+    def __init__(self, pipeline_dir):
+        super().__init__("modules", pipeline_dir)
+
     def remove(self, module):
         """
         Remove an already installed module