Merge pull request nf-core#3608 from nf-core/feat/bump-versions-for-sub-modules

Author: mashehu

CHANGELOG.md

@@ -8,6 +8,8 @@
 
 ### Modules
 
+- feat: nf-core modules bump-version supports specifying the toolkit ([#3608](https://github.com/nf-core/tools/pull/3608))
+
 ### Subworkflows
 
 ### General

nf_core/__main__.py

@@ -1398,7 +1398,7 @@ def command_modules_info(ctx, tool, directory):
     type=str,
     callback=normalize_case,
     required=False,
-    metavar="<tool> or <tool/subtool>",
+    metavar="<tool> or <tool/subtool>. Module to bump versions for. If <tool> is provided and <tool/subtool> exists, all subtools will be bumped.",
     shell_complete=autocomplete_modules,
 )
 @click.option(
@@ -1411,12 +1411,13 @@ def command_modules_info(ctx, tool, directory):
 )
 @click.option("-a", "--all", is_flag=True, help="Run on all modules")
 @click.option("-s", "--show-all", is_flag=True, help="Show up-to-date modules in results too")
-def command_modules_bump_versions(ctx, tool, directory, all, show_all):
+@click.option("-r", "--dry-run", is_flag=True, help="Dry run the command")
+def command_modules_bump_versions(ctx, tool, directory, all, show_all, dry_run):
     """
     Bump versions for one or more modules in a clone of
     the nf-core/modules repo.
     """
-    modules_bump_versions(ctx, tool, directory, all, show_all)
+    modules_bump_versions(ctx, tool, directory, all, show_all, dry_run)
 
 
 # nf-core subworkflows click command

nf_core/commands_modules.py

@@ -334,7 +334,7 @@ def modules_info(ctx, tool, directory):
         sys.exit(1)
 
 
-def modules_bump_versions(ctx, tool, directory, all, show_all):
+def modules_bump_versions(ctx, tool, directory, all, show_all, dry_run):
     """
     Bump versions for one or more modules in a clone of
     the nf-core/modules repo.
@@ -349,7 +349,7 @@ def modules_bump_versions(ctx, tool, directory, all, show_all):
             ctx.obj["modules_repo_branch"],
             ctx.obj["modules_repo_no_pull"],
         )
-        version_bumper.bump_versions(module=tool, all_modules=all, show_uptodate=show_all)
+        version_bumper.bump_versions(module=tool, all_modules=all, show_up_to_date=show_all, dry_run=dry_run)
     except ModuleExceptionError as e:
         log.error(e)
         sys.exit(1)

nf_core/modules/bump_versions.py

@@ -46,10 +46,16 @@ def __init__(
         self.tools_config: Optional[NFCoreYamlConfig]
 
     def bump_versions(
-        self, module: Union[str, None] = None, all_modules: bool = False, show_uptodate: bool = False
-    ) -> None:
+        self,
+        module: Optional[str] = None,
+        all_modules: bool = False,
+        show_up_to_date: bool = False,
+        dry_run: bool = False,
+    ) -> list[NFCoreComponent]:
         """
-        Bump the container and conda version of single module or all modules
+        Bump the container and conda version of single module or all modules.
+
+        If module is the name of a directory in the modules directory, all modules in that directory will be bumped.
 
         Looks for a bioconda tool version in the `main.nf` file of the module and checks whether
         are more recent version is available. If yes, then tries to get docker/singularity
@@ -59,12 +65,17 @@ def bump_versions(
         Args:
             module: a specific module to update
             all_modules: whether to bump versions for all modules
+            show_up_to_date: whether to show up-to-date modules as well
+            dry_run: whether to dry run the command
+
+        Returns:
+            list[NFCoreComponent]: the updated modules
         """
         self.up_to_date = []
         self.updated = []
         self.failed = []
         self.ignored = []
-        self.show_up_to_date = show_uptodate
+        self.show_up_to_date = show_up_to_date
 
         # Check modules directory structure
         self.check_modules_structure()
@@ -105,12 +116,23 @@ def bump_versions(
                 raise nf_core.modules.modules_utils.ModuleExceptionError(
                     "You cannot specify a tool and request all tools to be bumped."
                 )
-            nfcore_modules = [m for m in nfcore_modules if m.component_name == module]
+            # First try to find an exact match
+            exact_matches = [m for m in nfcore_modules if m.component_name == module]
+            if exact_matches:
+                nfcore_modules = exact_matches
+            else:
+                # If no exact match, look for modules that start with the given name (subtools)
+                nfcore_modules = [m for m in nfcore_modules if m.component_name.startswith(module + "/")]
+
             if len(nfcore_modules) == 0:
                 raise nf_core.modules.modules_utils.ModuleExceptionError(
                     f"Could not find the specified module: '{module}'"
                 )
 
+        # mainly used for testing, return the list of nfcore_modules selected
+        if dry_run:
+            return nfcore_modules
+
         progress_bar = Progress(
             "[bold blue]{task.description}",
             BarColumn(bar_width=None),
@@ -130,6 +152,8 @@ def bump_versions(
 
         self._print_results()
 
+        return nfcore_modules
+
     def bump_module_version(self, module: NFCoreComponent) -> bool:
         """
         Bump the bioconda and container version of a single NFCoreComponent
@@ -160,9 +184,9 @@ def bump_module_version(self, module: NFCoreComponent) -> bool:
             return False
 
         # Don't update if blocked in blacklist
-        self.bump_versions_config = getattr(self.tools_config, "bump-versions", {}) or {}
-        if module.component_name in self.bump_versions_config:
-            config_version = self.bump_versions_config[module.component_name]
+        bump_versions_config: dict[str, str] = getattr(self.tools_config, "bump-versions", {}) or {}
+        if module.component_name in bump_versions_config:
+            config_version = bump_versions_config[module.component_name]
             if not config_version:
                 self.ignored.append(("Omitting module due to config.", module.component_name))
                 return False

tests/modules/test_bump_versions.py

@@ -1,10 +1,15 @@
 import os
 import re
+import tempfile
+from pathlib import Path
 
 import pytest
+import ruamel.yaml
 
 import nf_core.modules.bump_versions
+from nf_core import __version__
 from nf_core.modules.modules_utils import ModuleExceptionError
+from nf_core.utils import NFCoreYamlConfig
 
 from ..test_modules import TestModules
 
@@ -20,14 +25,68 @@ def test_modules_bump_versions_single_module(self):
         with open(env_yml_path, "w") as fh:
             fh.write(new_content)
         version_bumper = nf_core.modules.bump_versions.ModuleVersionBumper(pipeline_dir=self.nfcore_modules)
-        version_bumper.bump_versions(module="bpipe/test")
+        modules = version_bumper.bump_versions(module="bpipe/test")
         assert len(version_bumper.failed) == 0
+        assert [m.component_name for m in modules] == ["bpipe/test"]
 
     def test_modules_bump_versions_all_modules(self):
         """Test updating all modules"""
         version_bumper = nf_core.modules.bump_versions.ModuleVersionBumper(pipeline_dir=self.nfcore_modules)
-        version_bumper.bump_versions(all_modules=True)
+        modules = version_bumper.bump_versions(all_modules=True)
         assert len(version_bumper.failed) == 0
+        assert [m.component_name for m in modules] == ["bpipe/test"]
+
+    @staticmethod
+    def _mock_nf_core_yml(root_dir: Path) -> None:
+        """Mock the .nf_core.yml"""
+        yaml = ruamel.yaml.YAML()
+        yaml.preserve_quotes = True
+        yaml.indent(mapping=2, sequence=2, offset=0)
+        nf_core_yml = NFCoreYamlConfig(nf_core_version=__version__, repository_type="modules", org_path="nf-core")
+        with open(Path(root_dir, ".nf-core.yml"), "w") as fh:
+            yaml.dump(nf_core_yml.model_dump(), fh)
+
+    @staticmethod
+    def _mock_modules(root_dir: Path, modules: list[str]) -> None:
+        """Mock the directory for a given module (or sub-module) for use with `dry_run`"""
+        nf_core_dir = root_dir / "modules" / "nf-core"
+        for module in modules:
+            if "/" in module:
+                module, sub_module = module.split("/")
+                module_dir = nf_core_dir / module / sub_module
+            else:
+                module_dir = nf_core_dir / module
+            module_dir.mkdir(parents=True)
+            module_main = module_dir / "main.nf"
+            with module_main.open("w"):
+                pass
+
+    def test_modules_bump_versions_multiple_modules(self):
+        """Test updating all modules when multiple modules are present"""
+        # mock the fgbio directory
+        root_dir = Path(tempfile.TemporaryDirectory().name)
+        self._mock_modules(root_dir=root_dir, modules=["fqgrep", "fqtk"])
+        # mock the ".nf-core.yml"
+        self._mock_nf_core_yml(root_dir=root_dir)
+
+        # run it with dryrun to return the modules that it found
+        version_bumper = nf_core.modules.bump_versions.ModuleVersionBumper(pipeline_dir=root_dir)
+        modules = version_bumper.bump_versions(all_modules=True, dry_run=True)
+        assert sorted([m.component_name for m in modules]) == sorted(["fqgrep", "fqtk"])
+
+    def test_modules_bump_versions_submodules(self):
+        """Test updating a submodules"""
+        # mock the fgbio directory
+        root_dir = Path(tempfile.TemporaryDirectory().name)
+        in_modules = ["fgbio/callduplexconsensusreads", "fgbio/groupreadsbyumi"]
+        self._mock_modules(root_dir=root_dir, modules=in_modules)
+        # mock the ".nf-core.yml"
+        self._mock_nf_core_yml(root_dir=root_dir)
+
+        # run it with dryrun to return the modules that it found
+        version_bumper = nf_core.modules.bump_versions.ModuleVersionBumper(pipeline_dir=root_dir)
+        out_modules = version_bumper.bump_versions(module="fgbio", dry_run=True)
+        assert sorted([m.component_name for m in out_modules]) == sorted(in_modules)
 
     def test_modules_bump_versions_fail(self):
         """Fail updating a module with wrong name"""