From 9953d6dd7c5488a5a9b98e687b546ce1f41dcf6a Mon Sep 17 00:00:00 2001
From: bjlang <>
Date: Wed, 18 Oct 2023 11:32:50 +0200
Subject: [PATCH 1/5] refactor code in preparation of a future 'subworkflows
 patch' command

---
 nf_core/components/patch.py | 221 ++++++++++++++++++++++++++++++++++++
 nf_core/modules/patch.py    | 209 +---------------------------------
 2 files changed, 225 insertions(+), 205 deletions(-)
 create mode 100644 nf_core/components/patch.py

diff --git a/nf_core/components/patch.py b/nf_core/components/patch.py
new file mode 100644
index 0000000000..aaa5c3dd10
--- /dev/null
+++ b/nf_core/components/patch.py
@@ -0,0 +1,221 @@
+import logging
+import os
+import shutil
+import tempfile
+from pathlib import Path
+
+import questionary
+
+import nf_core.utils
+from nf_core.components.components_command import ComponentCommand
+
+from nf_core.modules.modules_differ import ModulesDiffer
+from nf_core.modules.modules_json import ModulesJson
+
+log = logging.getLogger(__name__)
+
+
+class ComponentPatch(ComponentCommand):
+    def __init__(self, pipeline_dir, component_type, remote_url=None, branch=None, no_pull=False, installed_by=False):
+        super().__init__(component_type, pipeline_dir, remote_url, branch, no_pull)
+
+        self.modules_json = ModulesJson(dir)
+
+    def _parameter_checks(self, component):
+        """Checks the compatibility of the supplied parameters.
+
+        Raises:
+            UserWarning: if any checks fail.
+        """
+        if not self.has_valid_directory():
+            raise UserWarning("The command was not run in a valid pipeline directory.")
+
+        components = self.modules_json.get_all_components(self.component_type).get(self.modules_repo.remote_url)
+        component_names = [component for _, component in components]
+
+        if component is not None and component not in component_names:
+            component_dir = [dir for dir, m in components if m == component][0]
+            raise UserWarning(f"{self.component_type[:-1].title()} '{Path(self.component_type, component_dir, module)}' does not exist in the pipeline")
+
+    def patch(self, component=None):
+        # Check modules directory structure
+        self.check_modules_structure()
+
+        # Verify that 'modules.json' is consistent with the installed modules
+        self.modules_json.check_up_to_date()
+        self._parameter_checks(component)
+        components = self.modules_json.get_all_components(self.component_type).get(self.modules_repo.remote_url)
+
+        if component is None:
+            choices = [
+                component if directory == self.modules_repo.repo_path else f"{directory}/{component}"
+                for directory, component in components
+            ]
+            component = questionary.autocomplete(
+                f"{self.component_type[:-1].title()} name:",
+                choices=sorted(choices),
+                style=nf_core.utils.nfcore_question_style,
+            ).unsafe_ask()
+        component_dir = [dir for dir, m in components if m == component][0]
+        component_fullname = str(Path(self.component_type, self.modules_repo.repo_path, component))
+
+        # Verify that the component has an entry in the modules.json file
+        if not self.modules_json.module_present(component, self.modules_repo.remote_url, component_dir):
+            raise UserWarning(
+                f"The '{component_fullname}' {self.component_type[:-1]} does not have an entry in the 'modules.json' file. Cannot compute patch"
+            )
+
+        component_version = self.modules_json.get_component_version(
+            self.component_type, component, self.modules_repo.remote_url, self.modules_repo.repo_path
+        )
+        if component_version is None:
+            raise UserWarning(
+                f"The '{component_fullname}' {self.component_type[:-1]} does not have a valid version in the 'modules.json' file. Cannot compute patch"
+            )
+        # Get the component branch and reset it in the ModulesRepo object
+        component_branch = self.modules_json.get_component_branch(
+            self.component_type, component, self.modules_repo.remote_url, component_dir
+        )
+        if component_branch != self.modules_repo.branch:
+            self.modules_repo.setup_branch(component_branch)
+
+        # Set the diff filename based on the module name
+        patch_filename = f"{component.replace('/', '-')}.diff"
+        component_relpath = Path("modules", component_dir, component)
+        patch_relpath = Path(component_relpath, patch_filename)
+        component_current_dir = Path(self.dir, component_relpath)
+        patch_path = Path(self.dir, patch_relpath)
+
+        if patch_path.exists():
+            remove = questionary.confirm(
+                f"Patch exists for {self.component_type[:-1]} '{component_fullname}'. Do you want to regenerate it?",
+                style=nf_core.utils.nfcore_question_style,
+            ).unsafe_ask()
+            if remove:
+                os.remove(patch_path)
+            else:
+                return
+
+        # Create a temporary directory for storing the unchanged version of the module
+        install_dir = tempfile.mkdtemp()
+        component_install_dir = Path(install_dir, component)
+        if not self.install_component_files(component, component_version, self.modules_repo, install_dir):
+            raise UserWarning(
+                f"Failed to install files of {self.component_type[:-1]} '{component}' from remote ({self.modules_repo.remote_url})."
+            )
+
+        # Write the patch to a temporary location (otherwise it is printed to the screen later)
+        patch_temp_path = tempfile.mktemp()
+        try:
+            ModulesDiffer.write_diff_file(
+                patch_temp_path,
+                component,
+                self.modules_repo.repo_path,
+                component_install_dir,
+                component_current_dir,
+                for_git=False,
+                dsp_from_dir=component_relpath,
+                dsp_to_dir=component_relpath,
+            )
+            log.debug(f"Patch file wrote to a temporary directory {patch_temp_path}")
+        except UserWarning:
+            raise UserWarning(f"{self.component_type[:-1]} '{component_fullname}' is unchanged. No patch to compute")
+
+        # Write changes to modules.json
+        self.modules_json.add_patch_entry(component, self.modules_repo.remote_url, component_dir, patch_relpath)
+        log.debug(f"Wrote patch path for {self.component_type[:-1]} {component} to modules.json")
+
+        # Show the changes made to the module
+        ModulesDiffer.print_diff(
+            component,
+            self.modules_repo.repo_path,
+            component_install_dir,
+            component_current_dir,
+            dsp_from_dir=component_current_dir,
+            dsp_to_dir=component_current_dir,
+        )
+
+        # Finally move the created patch file to its final location
+        shutil.move(patch_temp_path, patch_path)
+        log.info(f"Patch file of '{component_fullname}' written to '{patch_path}'")
+
+    def remove(self, component):
+        # Check modules directory structure
+        self.check_modules_structure()
+
+        self.modules_json.check_up_to_date()
+        self._parameter_checks(component)
+        components = self.modules_json.get_all_components(self.component_type).get(self.modules_repo.remote_url)
+
+        if component is None:
+            choices = [
+                component if directory == self.modules_repo.repo_path else f"{directory}/{component}"
+                for directory, component in components
+            ]
+            component = questionary.autocomplete(
+                f"{self.component_type[:-1]} name:",
+                choices,
+                style=nf_core.utils.nfcore_question_style,
+            ).unsafe_ask()
+        component_dir = [dir for dir, m in components if m == component][0]
+        component_fullname = str(Path("modules", component_dir, component))
+
+        # Verify that the component has an entry in the modules.json file
+        if not self.modules_json.module_present(component, self.modules_repo.remote_url, component_dir):
+            raise UserWarning(
+                f"The '{component_fullname}' {self.component_type[:-1]} does not have an entry in the 'modules.json' file. Cannot compute patch"
+            )
+
+        component_version = self.modules_json.get_component_version(
+            self.component_type, component, self.modules_repo.remote_url, self.modules_repo.repo_path
+        )
+        if component_version is None:
+            raise UserWarning(
+                f"The '{component_fullname}' {self.component_type[:-1]} 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
+        component_branch = self.modules_json.get_component_branch(
+            self.component_type, component, self.modules_repo.remote_url, component_dir
+        )
+        if component_branch != self.modules_repo.branch:
+            self.modules_repo.setup_branch(component_branch)
+
+        # Set the diff filename based on the component name
+        patch_filename = f"{component.replace('/', '-')}.diff"
+        component_relpath = Path("modules", component_dir, component)
+        patch_relpath = Path(component_relpath, patch_filename)
+        patch_path = Path(self.dir, patch_relpath)
+        component_path = Path(self.dir, component_relpath)
+
+        if patch_path.exists():
+            remove = questionary.confirm(
+                f"Patch exists for {self.component_type[:-1]} '{component_fullname}'. Are you sure you want to remove?",
+                style=nf_core.utils.nfcore_question_style,
+            ).unsafe_ask()
+            if not remove:
+                return
+
+        # Try to apply the patch in reverse and move resulting files to module dir
+        temp_component_dir = self.modules_json.try_apply_patch_reverse(
+            component, self.modules_repo.repo_path, patch_relpath, component_path
+        )
+        try:
+            for file in Path(temp_component_dir).glob("*"):
+                file.rename(component_path.joinpath(file.name))
+            os.rmdir(temp_component_dir)
+        except Exception as err:
+            raise UserWarning(f"There was a problem reverting the patched file: {err}")
+
+        log.info(f"Patch for {component} reverted!")
+        # Remove patch file if we could revert the patch
+        patch_path.unlink()
+        # Write changes to module.json
+        self.modules_json.remove_patch_entry(component, self.modules_repo.remote_url, component_dir)
+
+        if not all(
+            self.modules_repo.component_files_identical(component, component_path, component_version, "modules").values()
+        ):
+            log.error(
+                f"Module files do not appear to match the remote for the commit sha in the 'module.json': {component_version}\n"
+                f"Recommend reinstalling with 'nf-core modules install --force --sha {component_version} {module}' "
+            )
diff --git a/nf_core/modules/patch.py b/nf_core/modules/patch.py
index 198bb70de5..b4e86f2d19 100644
--- a/nf_core/modules/patch.py
+++ b/nf_core/modules/patch.py
@@ -1,211 +1,10 @@
 import logging
-import os
-import shutil
-import tempfile
-from pathlib import Path
 
-import questionary
-
-import nf_core.utils
-from nf_core.components.components_command import ComponentCommand
-
-from .modules_differ import ModulesDiffer
-from .modules_json import ModulesJson
+from nf_core.components.patch import ComponentPatch
 
 log = logging.getLogger(__name__)
 
 
-class ModulePatch(ComponentCommand):
-    def __init__(self, dir, remote_url=None, branch=None, no_pull=False):
-        super().__init__("modules", dir, remote_url, branch, no_pull)
-
-        self.modules_json = ModulesJson(dir)
-
-    def param_check(self, module):
-        if not self.has_valid_directory():
-            raise UserWarning()
-
-        modules = self.modules_json.get_all_components(self.component_type)[self.modules_repo.remote_url]
-        module_names = [module for _, module in modules]
-
-        if module is not None and module not in module_names:
-            module_dir = [dir for dir, m in modules if m == module][0]
-            raise UserWarning(f"Module '{Path('modules', module_dir, module)}' does not exist in the pipeline")
-
-    def patch(self, module=None):
-        # Check modules directory structure
-        self.check_modules_structure()
-
-        self.modules_json.check_up_to_date()
-        self.param_check(module)
-        modules = self.modules_json.get_all_components(self.component_type)[self.modules_repo.remote_url]
-
-        if module is None:
-            choices = [
-                module if directory == self.modules_repo.repo_path else f"{directory}/{module}"
-                for directory, module in modules
-            ]
-            module = questionary.autocomplete(
-                "Tool:",
-                choices,
-                style=nf_core.utils.nfcore_question_style,
-            ).unsafe_ask()
-        module_dir = [dir for dir, m in modules if m == module][0]
-        module_fullname = str(Path("modules", module_dir, module))
-
-        # Verify that the module has an entry in the modules.json file
-        if not self.modules_json.module_present(module, self.modules_repo.remote_url, module_dir):
-            raise UserWarning(
-                f"The '{module_fullname}' module does not have an entry in the 'modules.json' file. Cannot compute patch"
-            )
-
-        module_version = self.modules_json.get_module_version(module, self.modules_repo.remote_url, module_dir)
-        if module_version is None:
-            raise UserWarning(
-                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_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)
-
-        # Set the diff filename based on the module name
-        patch_filename = f"{module.replace('/', '-')}.diff"
-        module_relpath = Path("modules", module_dir, module)
-        patch_relpath = Path(module_relpath, patch_filename)
-        module_current_dir = Path(self.dir, module_relpath)
-        patch_path = Path(self.dir, patch_relpath)
-
-        if patch_path.exists():
-            remove = questionary.confirm(
-                f"Patch exists for module '{module_fullname}'. Do you want to regenerate it?",
-                style=nf_core.utils.nfcore_question_style,
-            ).unsafe_ask()
-            if remove:
-                os.remove(patch_path)
-            else:
-                return
-
-        # Create a temporary directory for storing the unchanged version of the module
-        install_dir = tempfile.mkdtemp()
-        module_install_dir = Path(install_dir, module)
-        if not self.install_component_files(module, module_version, self.modules_repo, install_dir):
-            raise UserWarning(
-                f"Failed to install files of module '{module}' from remote ({self.modules_repo.remote_url})."
-            )
-
-        # Write the patch to a temporary location (otherwise it is printed to the screen later)
-        patch_temp_path = tempfile.mktemp()
-        try:
-            ModulesDiffer.write_diff_file(
-                patch_temp_path,
-                module,
-                self.modules_repo.repo_path,
-                module_install_dir,
-                module_current_dir,
-                for_git=False,
-                dsp_from_dir=module_relpath,
-                dsp_to_dir=module_relpath,
-            )
-            log.debug(f"Patch file wrote to a temporary directory {patch_temp_path}")
-        except UserWarning:
-            raise UserWarning(f"Module '{module_fullname}' is unchanged. No patch to compute")
-
-        # Write changes to modules.json
-        self.modules_json.add_patch_entry(module, self.modules_repo.remote_url, module_dir, patch_relpath)
-        log.debug(f"Wrote patch path for module {module} to modules.json")
-
-        # Show the changes made to the module
-        ModulesDiffer.print_diff(
-            module,
-            self.modules_repo.repo_path,
-            module_install_dir,
-            module_current_dir,
-            dsp_from_dir=module_current_dir,
-            dsp_to_dir=module_current_dir,
-        )
-
-        # Finally move the created patch file to its final location
-        shutil.move(patch_temp_path, patch_path)
-        log.info(f"Patch file of '{module_fullname}' written to '{patch_path}'")
-
-    def remove(self, module):
-        # Check modules directory structure
-        self.check_modules_structure()
-
-        self.modules_json.check_up_to_date()
-        self.param_check(module)
-        modules = self.modules_json.get_all_components(self.component_type)[self.modules_repo.remote_url]
-
-        if module is None:
-            choices = [
-                module if directory == self.modules_repo.repo_path else f"{directory}/{module}"
-                for directory, module in modules
-            ]
-            module = questionary.autocomplete(
-                "Tool:",
-                choices,
-                style=nf_core.utils.nfcore_question_style,
-            ).unsafe_ask()
-        module_dir = [dir for dir, m in modules if m == module][0]
-        module_fullname = str(Path("modules", module_dir, module))
-
-        # Verify that the module has an entry in the modules.json file
-        if not self.modules_json.module_present(module, self.modules_repo.remote_url, module_dir):
-            raise UserWarning(
-                f"The '{module_fullname}' module does not have an entry in the 'modules.json' file. Cannot compute patch"
-            )
-
-        module_version = self.modules_json.get_module_version(module, self.modules_repo.remote_url, module_dir)
-        if module_version is None:
-            raise UserWarning(
-                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_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)
-
-        # Set the diff filename based on the module name
-        patch_filename = f"{module.replace('/', '-')}.diff"
-        module_relpath = Path("modules", module_dir, module)
-        patch_relpath = Path(module_relpath, patch_filename)
-        patch_path = Path(self.dir, patch_relpath)
-        module_path = Path(self.dir, module_relpath)
-
-        if patch_path.exists():
-            remove = questionary.confirm(
-                f"Patch exists for module '{module_fullname}'. Are you sure you want to remove?",
-                style=nf_core.utils.nfcore_question_style,
-            ).unsafe_ask()
-            if not remove:
-                return
-
-        # Try to apply the patch in reverse and move resulting files to module dir
-        temp_module_dir = self.modules_json.try_apply_patch_reverse(
-            module, self.modules_repo.repo_path, patch_relpath, module_path
-        )
-        try:
-            for file in Path(temp_module_dir).glob("*"):
-                file.rename(module_path.joinpath(file.name))
-            os.rmdir(temp_module_dir)
-        except Exception as err:
-            raise UserWarning(f"There was a problem reverting the patched file: {err}")
-
-        log.info(f"Patch for {module} reverted!")
-        # Remove patch file if we could revert the patch
-        patch_path.unlink()
-        # Write changes to module.json
-        self.modules_json.remove_patch_entry(module, self.modules_repo.remote_url, module_dir)
-
-        if not all(
-            self.modules_repo.component_files_identical(module, module_path, module_version, "modules").values()
-        ):
-            log.error(
-                f"Module files do not appear to match the remote for the commit sha in the 'module.json': {module_version}\n"
-                f"Recommend reinstalling with 'nf-core modules install --force --sha {module_version} {module}' "
-            )
+class ModulePatch(ComponentPatch):
+    def __init__(self, pipeline_dir, remote_url=None, branch=None, no_pull=False, installed_by=False):
+        super().__init__(pipeline_dir, "modules", remote_url, branch, no_pull, installed_by)

From 3bae03e5859c5c5f93e28997b2a2be98466235fa Mon Sep 17 00:00:00 2001
From: bjlang <>
Date: Wed, 18 Oct 2023 12:34:24 +0200
Subject: [PATCH 2/5] correct paths

---
 nf_core/components/patch.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/nf_core/components/patch.py b/nf_core/components/patch.py
index aaa5c3dd10..0f93b2081b 100644
--- a/nf_core/components/patch.py
+++ b/nf_core/components/patch.py
@@ -19,7 +19,7 @@ class ComponentPatch(ComponentCommand):
     def __init__(self, pipeline_dir, component_type, remote_url=None, branch=None, no_pull=False, installed_by=False):
         super().__init__(component_type, pipeline_dir, remote_url, branch, no_pull)
 
-        self.modules_json = ModulesJson(dir)
+        self.modules_json = ModulesJson(pipeline_dir)
 
     def _parameter_checks(self, component):
         """Checks the compatibility of the supplied parameters.
@@ -81,7 +81,7 @@ def patch(self, component=None):
 
         # Set the diff filename based on the module name
         patch_filename = f"{component.replace('/', '-')}.diff"
-        component_relpath = Path("modules", component_dir, component)
+        component_relpath = Path(self.component_type, component_dir, component)
         patch_relpath = Path(component_relpath, patch_filename)
         component_current_dir = Path(self.dir, component_relpath)
         patch_path = Path(self.dir, patch_relpath)
@@ -158,7 +158,7 @@ def remove(self, component):
                 style=nf_core.utils.nfcore_question_style,
             ).unsafe_ask()
         component_dir = [dir for dir, m in components if m == component][0]
-        component_fullname = str(Path("modules", component_dir, component))
+        component_fullname = str(Path(self.component_type, component_dir, component))
 
         # Verify that the component has an entry in the modules.json file
         if not self.modules_json.module_present(component, self.modules_repo.remote_url, component_dir):
@@ -182,7 +182,7 @@ def remove(self, component):
 
         # Set the diff filename based on the component name
         patch_filename = f"{component.replace('/', '-')}.diff"
-        component_relpath = Path("modules", component_dir, component)
+        component_relpath = Path(self.component_type, component_dir, component)
         patch_relpath = Path(component_relpath, patch_filename)
         patch_path = Path(self.dir, patch_relpath)
         component_path = Path(self.dir, component_relpath)
@@ -213,7 +213,7 @@ def remove(self, component):
         self.modules_json.remove_patch_entry(component, self.modules_repo.remote_url, component_dir)
 
         if not all(
-            self.modules_repo.component_files_identical(component, component_path, component_version, "modules").values()
+            self.modules_repo.component_files_identical(component, component_path, component_version, self.component_type).values()
         ):
             log.error(
                 f"Module files do not appear to match the remote for the commit sha in the 'module.json': {component_version}\n"

From 5582012d318446b1130a8abd6db5e31465b3e1f3 Mon Sep 17 00:00:00 2001
From: bjlang <>
Date: Wed, 18 Oct 2023 12:50:37 +0200
Subject: [PATCH 3/5] Make isort happy

---
 nf_core/components/patch.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/nf_core/components/patch.py b/nf_core/components/patch.py
index 0f93b2081b..e17c05713a 100644
--- a/nf_core/components/patch.py
+++ b/nf_core/components/patch.py
@@ -8,7 +8,6 @@
 
 import nf_core.utils
 from nf_core.components.components_command import ComponentCommand
-
 from nf_core.modules.modules_differ import ModulesDiffer
 from nf_core.modules.modules_json import ModulesJson
 

From 6c1d2700f2560f515ed8feeb1e2aa82f53967793 Mon Sep 17 00:00:00 2001
From: bjlang <>
Date: Mon, 23 Oct 2023 11:51:57 +0200
Subject: [PATCH 4/5] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 04a40a48c7..0f10292826 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,6 +14,7 @@
 ### Modules
 
 - Added stub test creation to `create_test_yml` ([#2476](https://github.com/nf-core/tools/pull/2476))
+- Replace ModulePatch by ComponentPatch ([#2482](https://github.com/nf-core/tools/pull/2482))
 
 ### Subworkflows
 

From bf77d8872c71e363d372a9575267a0b2e7bda921 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Mon, 23 Oct 2023 09:58:54 +0000
Subject: [PATCH 5/5] [automated] Fix code linting

---
 nf_core/components/patch.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/nf_core/components/patch.py b/nf_core/components/patch.py
index e17c05713a..28f2f886b1 100644
--- a/nf_core/components/patch.py
+++ b/nf_core/components/patch.py
@@ -34,7 +34,9 @@ def _parameter_checks(self, component):
 
         if component is not None and component not in component_names:
             component_dir = [dir for dir, m in components if m == component][0]
-            raise UserWarning(f"{self.component_type[:-1].title()} '{Path(self.component_type, component_dir, module)}' does not exist in the pipeline")
+            raise UserWarning(
+                f"{self.component_type[:-1].title()} '{Path(self.component_type, component_dir, module)}' does not exist in the pipeline"
+            )
 
     def patch(self, component=None):
         # Check modules directory structure
@@ -212,7 +214,9 @@ def remove(self, component):
         self.modules_json.remove_patch_entry(component, self.modules_repo.remote_url, component_dir)
 
         if not all(
-            self.modules_repo.component_files_identical(component, component_path, component_version, self.component_type).values()
+            self.modules_repo.component_files_identical(
+                component, component_path, component_version, self.component_type
+            ).values()
         ):
             log.error(
                 f"Module files do not appear to match the remote for the commit sha in the 'module.json': {component_version}\n"