add new command modules test

nf_core/__main__.py

@@ -48,7 +48,7 @@
         },
         {
             "name": "Developing new modules",
-            "commands": ["create", "create-test-yml", "lint", "bump-versions", "mulled"],
+            "commands": ["create", "create-test-yml", "lint", "bump-versions", "mulled", "test"],
         },
     ],
 }
@@ -709,6 +709,26 @@ def mulled(specifications, build_number):
         sys.exit(1)
 
 
+# nf-core modules test
+@modules.command("test")
+@click.pass_context
+@click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
+@click.option("-p", "--no-prompts", is_flag=True, default=False, help="Use defaults without prompting")
+@click.option("-a", "--pytest_args", type=str, required=False, multiple=True, help="Additional pytest arguments")
+def test_module(ctx, tool, no_prompts, pytest_args):
+    """
+    Run module tests locally.
+
+    Given the name of a module, runs the Nextflow test command.
+    """
+    try:
+        meta_builder = nf_core.modules.ModulesTest(tool, no_prompts, pytest_args)
+        meta_builder.run()
+    except UserWarning as e:
+        log.critical(e)
+        sys.exit(1)
+
+
 # nf-core schema subcommands
 @nf_core_cli.group()
 def schema():

nf_core/modules/__init__.py

@@ -10,3 +10,4 @@
 from .remove import ModuleRemove
 from .info import ModuleInfo
 from .mulled import MulledImageNameGenerator
+from .module_test import ModulesTest

nf_core/modules/module_test.py

@@ -0,0 +1,126 @@
+#!/usr/bin/env python
+"""
+The ModulesTest class runs the tests locally
+"""
+
+import logging
+import questionary
+import os
+import pytest
+import sys
+import rich
+
+import nf_core.utils
+from .modules_repo import ModulesRepo
+
+log = logging.getLogger(__name__)
+
+
+class ModulesTest(object):
+    """
+    Class to run module pytests.
+
+    ...
+
+    Attributes
+    ----------
+    module_name : str
+        name of the tool to run tests for
+    no_prompts : bool
+        flat indicating if prompts are used
+    pytest_args : tuple
+        additional arguments passed to pytest command
+
+    Methods
+    -------
+    run():
+        Run test steps
+    __check_inputs():
+        Check inputs. Ask for module_name if not provided and check that the directory exists
+    __set_profile():
+        Set software profile
+    __run_pytests(self):
+        Run pytest
+    """
+
+    def __init__(
+        self,
+        module_name=None,
+        no_prompts=False,
+        pytest_args="",
+    ):
+        self.module_name = module_name
+        self.no_prompts = no_prompts
+        self.pytest_args = pytest_args
+        self.module_dir = None
+
+    def run(self):
+        """Run test steps"""
+        if not self.no_prompts:
+            log.info(
+                "[yellow]Press enter to use default values [cyan bold](shown in brackets) [yellow]or type your own responses"
+            )
+        self.__check_inputs()
+        self.__set_profile()
+        self.__run_pytests()
+
+    def __check_inputs(self):
+        """Do more complex checks about supplied flags."""
+
+        # Get the tool name if not specified
+        if self.module_name is None:
+            if self.no_prompts:
+                raise UserWarning(
+                    f"Tool name not provided and prompts deactivated. Please provide the tool name as TOOL/SUBTOOL or TOOL."
+                )
+            modules_repo = ModulesRepo()
+            modules_repo.get_modules_file_tree()
+            self.module_name = questionary.autocomplete(
+                "Tool name:",
+                choices=modules_repo.modules_avail_module_names,
+                style=nf_core.utils.nfcore_question_style,
+            ).ask()
+        self.module_dir = os.path.join("modules", *self.module_name.split("/"))
+
+        # First, sanity check that the module directory exists
+        if not os.path.isdir(self.module_dir):
+            raise UserWarning(f"Cannot find directory '{self.module_dir}'. Should be TOOL/SUBTOOL or TOOL")
+
+    def __set_profile(self):
+        """Set $PROFILE env variable.
+        The config expects $PROFILE and Nextflow fails if it's not set.
+        """
+        if os.environ.get("PROFILE") is None:
+            os.environ["PROFILE"] = ""
+            if self.no_prompts:
+                log.info(
+                    "Setting env var '$PROFILE' to an empty string as not set.\n"
+                    "Tests will run with Docker by default. "
+                    "To use Singularity set 'export PROFILE=singularity' in your shell before running this command."
+                )
+            else:
+                question = {
+                    "type": "list",
+                    "name": "profile",
+                    "message": "Choose software profile",
+                    "choices": ["Docker", "Singularity", "Conda"],
+                }
+                answer = questionary.unsafe_prompt([question], style=nf_core.utils.nfcore_question_style)
+                profile = answer["profile"].lower()
+                if profile in ["singularity", "conda"]:
+                    os.environ["PROFILE"] = profile
+                    log.info(f"Setting env var '$PROFILE' to '{profile}'")
+
+    def __run_pytests(self):
+        """Given a module name, run tests."""
+        # Print nice divider line
+        console = rich.console.Console()
+        console.print("[black]" + "─" * console.width)
+
+        # Set pytest arguments
+        command_args = ["--tag", f"{self.module_name}", "--symlink", "--keep-workflow-wd"]
+        command_args += self.pytest_args
+
+        # Run pytest
+        log.info(f"Running pytest for module '{self.module_name}'")
+        sys.exit(pytest.main(command_args))

tests/modules/module_test.py

@@ -0,0 +1,16 @@
+"""Test the 'modules test' command which runs module pytests."""
+import os
+import pytest
+
+import nf_core.modules
+
+
+def test_modules_test_check_inputs(self):
+    """Test the check_inputs() function - raise UserWarning because module doesn't exist"""
+    cwd = os.getcwd()
+    os.chdir(self.nfcore_modules)
+    meta_builder = nf_core.modules.ModulesTest("none", True, "")
+    with pytest.raises(UserWarning) as excinfo:
+        meta_builder.check_inputs()
+    os.chdir(cwd)
+    assert "Cannot find directory" in str(excinfo.value)

tests/test_modules.py

@@ -113,3 +113,7 @@ def test_modulesrepo_class(self):
         test_modules_bump_versions_fail,
         test_modules_bump_versions_fail_unknown_version,
     )
+
+    from .modules.module_test import (
+        test_modules_test_check_inputs,
+    )