add mypy to pre-commit config, fix mypy errors

.pre-commit-config.yaml

@@ -11,3 +11,13 @@ repos:
     rev: "v2.7.1"
     hooks:
       - id: prettier
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: "v1.7.1" # Use the sha / tag you want to point at
+    hooks:
+      - id: mypy
+        additional_dependencies:
+          - types-PyYAML
+          - types-requests
+          - types-jsonschema
+          - types-Markdown
+          - types-setuptools

docs/api/_src/conf.py

@@ -14,6 +14,7 @@
 #
 import os
 import sys
+from typing import Dict
 
 sys.path.insert(0, os.path.abspath("../../../nf_core"))
 import nf_core
@@ -58,7 +59,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language: str = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -113,7 +114,7 @@
 
 # -- Options for LaTeX output ------------------------------------------------
 
-latex_elements = {
+latex_elements: Dict[str, str] = {
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',

mypy.ini

@@ -1,2 +1,3 @@
 [mypy]
 warn_unused_configs = True
+ignore_missing_imports = true

nf_core/__main__.py

@@ -151,7 +151,7 @@ def nf_core_cli(ctx, verbose, hide_progress, log_file):
 
 
 # nf-core list
-@nf_core_cli.command()
+@nf_core_cli.command("list")
 @click.argument("keywords", required=False, nargs=-1, metavar="<filter keywords>")
 @click.option(
     "-s",
@@ -162,7 +162,7 @@ def nf_core_cli(ctx, verbose, hide_progress, log_file):
 )
 @click.option("--json", is_flag=True, default=False, help="Print full output as JSON")
 @click.option("--show-archived", is_flag=True, default=False, help="Print archived workflows")
-def list(keywords, sort, json, show_archived):
+def list_pipelines(keywords, sort, json, show_archived):
     """
     List available nf-core pipelines with local info.
 
@@ -553,21 +553,21 @@ def subworkflows(ctx, git_remote, branch, no_pull):
 
 
 # nf-core modules list subcommands
-@modules.group()
+@modules.group("list")
 @click.pass_context
-def list(ctx):
+def modules_list(ctx):
     """
     List modules in a local pipeline or remote repository.
     """
     pass
 
 
 # nf-core modules list remote
-@list.command()
+@modules_list.command("remote")
 @click.pass_context
 @click.argument("keywords", required=False, nargs=-1, metavar="<filter keywords>")
 @click.option("-j", "--json", is_flag=True, help="Print as JSON to stdout")
-def remote(ctx, keywords, json):
+def modules_list_remote(ctx, keywords, json):
     """
     List modules in a remote GitHub repo [dim i](e.g [link=https://github.com/nf-core/modules]nf-core/modules[/])[/].
     """
@@ -588,7 +588,7 @@ def remote(ctx, keywords, json):
 
 
 # nf-core modules list local
-@list.command()
+@modules_list.command("local")
 @click.pass_context
 @click.argument("keywords", required=False, nargs=-1, metavar="<filter keywords>")
 @click.option("-j", "--json", is_flag=True, help="Print as JSON to stdout")
@@ -599,7 +599,7 @@ def remote(ctx, keywords, json):
     default=".",
     help=r"Pipeline directory. [dim]\[default: Current working directory][/]",
 )
-def local(ctx, keywords, json, dir):  # pylint: disable=redefined-builtin
+def modules_list_local(ctx, keywords, json, dir):  # pylint: disable=redefined-builtin
     """
     List modules installed locally in a pipeline
     """
@@ -620,7 +620,7 @@ def local(ctx, keywords, json, dir):  # pylint: disable=redefined-builtin
 
 
 # nf-core modules install
-@modules.command()
+@modules.command("install")
 @click.pass_context
 @click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
 @click.option(
@@ -633,7 +633,7 @@ def local(ctx, keywords, json, dir):  # pylint: disable=redefined-builtin
 @click.option("-p", "--prompt", is_flag=True, default=False, help="Prompt for the version of the module")
 @click.option("-f", "--force", is_flag=True, default=False, help="Force reinstallation of module if it already exists")
 @click.option("-s", "--sha", type=str, metavar="<commit sha>", help="Install module at commit SHA")
-def install(ctx, tool, dir, prompt, force, sha):
+def modules_install(ctx, tool, dir, prompt, force, sha):
     """
     Install DSL2 modules within a pipeline.
 
@@ -660,7 +660,7 @@ def install(ctx, tool, dir, prompt, force, sha):
 
 
 # nf-core modules update
-@modules.command()
+@modules.command("update")
 @click.pass_context
 @click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
 @click.option(
@@ -699,7 +699,7 @@ def install(ctx, tool, dir, prompt, force, sha):
     default=False,
     help="Automatically update all linked modules and subworkflows without asking for confirmation",
 )
-def update(ctx, tool, directory, force, prompt, sha, install_all, preview, save_diff, update_deps):
+def modules_update(ctx, tool, directory, force, prompt, sha, install_all, preview, save_diff, update_deps):
     """
     Update DSL2 modules within a pipeline.
 
@@ -767,7 +767,7 @@ def patch(ctx, tool, dir, remove):
 
 
 # nf-core modules remove
-@modules.command()
+@modules.command("remove")
 @click.pass_context
 @click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
 @click.option(
@@ -777,7 +777,7 @@ def patch(ctx, tool, dir, remove):
     default=".",
     help=r"Pipeline directory. [dim]\[default: current working directory][/]",
 )
-def remove(ctx, dir, tool):
+def modules_remove(ctx, dir, tool):
     """
     Remove a module from a pipeline.
     """
@@ -887,7 +887,7 @@ def test_module(ctx, tool, dir, no_prompts, update, once):
 
 
 # nf-core modules lint
-@modules.command()
+@modules.command("lint")
 @click.pass_context
 @click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
 @click.option("-d", "--dir", type=click.Path(exists=True), default=".", metavar="<pipeline/modules directory>")
@@ -912,9 +912,7 @@ def test_module(ctx, tool, dir, no_prompts, update, once):
     show_default=True,
 )
 @click.option("--fix-version", is_flag=True, help="Fix the module version if a newer version is available")
-def lint(
-    ctx, tool, dir, registry, key, all, fail_warned, local, passed, sort_by, fix_version
-):  # pylint: disable=redefined-outer-name
+def modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed, sort_by, fix_version):
     """
     Lint one or more modules in a directory.
 
@@ -959,7 +957,7 @@ def lint(
 
 
 # nf-core modules info
-@modules.command()
+@modules.command("info")
 @click.pass_context
 @click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
 @click.option(
@@ -969,7 +967,7 @@ def lint(
     default=".",
     help=r"Pipeline directory. [dim]\[default: Current working directory][/]",
 )
-def info(ctx, tool, dir):
+def modules_info(ctx, tool, dir):
     """
     Show developer usage information about a given module.
 
@@ -1095,17 +1093,17 @@ def test_subworkflow(ctx, subworkflow, dir, no_prompts, update, once):
 
 
 # nf-core subworkflows list subcommands
-@subworkflows.group()
+@subworkflows.group("list")
 @click.pass_context
-def list(ctx):
+def subworkflows_list(ctx):
     """
     List subworkflows in a local pipeline or remote repository.
     """
     pass
 
 
 # nf-core subworkflows list remote
-@list.command()
+@subworkflows_list.command("remote")
 @click.pass_context
 @click.argument("keywords", required=False, nargs=-1, metavar="<filter keywords>")
 @click.option("-j", "--json", is_flag=True, help="Print as JSON to stdout")
@@ -1131,7 +1129,7 @@ def remote(ctx, keywords, json):
 
 
 # nf-core subworkflows list local
-@list.command()
+@subworkflows_list.command("local")
 @click.pass_context
 @click.argument("keywords", required=False, nargs=-1, metavar="<filter keywords>")
 @click.option("-j", "--json", is_flag=True, help="Print as JSON to stdout")
@@ -1163,7 +1161,7 @@ def local(ctx, keywords, json, dir):  # pylint: disable=redefined-builtin
 
 
 # nf-core subworkflows lint
-@subworkflows.command()
+@subworkflows.command("lint")
 @click.pass_context
 @click.argument("subworkflow", type=str, required=False, metavar="subworkflow name")
 @click.option("-d", "--dir", type=click.Path(exists=True), default=".", metavar="<pipeline/modules directory>")
@@ -1187,9 +1185,7 @@ def local(ctx, keywords, json, dir):  # pylint: disable=redefined-builtin
     help="Sort lint output by subworkflow or test name.",
     show_default=True,
 )
-def lint(
-    ctx, subworkflow, dir, registry, key, all, fail_warned, local, passed, sort_by
-):  # pylint: disable=redefined-outer-name
+def subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, local, passed, sort_by):
     """
     Lint one or more subworkflows in a directory.
 
@@ -1496,11 +1492,11 @@ def build(dir, no_prompts, web_only, url):
 
 
 # nf-core schema lint
-@schema.command()
+@schema.command("lint")
 @click.argument(
     "schema_path", type=click.Path(exists=True), default="nextflow_schema.json", metavar="<pipeline schema>"
 )
-def lint(schema_path):
+def schema_lint(schema_path):
     """
     Check that a given pipeline schema is valid.
 

nf_core/params_file.py

@@ -89,7 +89,7 @@ def __init__(
         self,
         pipeline=None,
         revision=None,
-    ):
+    ) -> None:
         """Initialise the ParamFileBuilder class
 
         Args:

nf_core/subworkflows/lint/__init__.py

@@ -29,12 +29,12 @@ class SubworkflowLint(ComponentLint):
     """
 
     # Import lint functions
-    from .main_nf import main_nf
-    from .meta_yml import meta_yml
-    from .subworkflow_changes import subworkflow_changes
-    from .subworkflow_tests import subworkflow_tests
-    from .subworkflow_todos import subworkflow_todos
-    from .subworkflow_version import subworkflow_version
+    from .main_nf import main_nf  # type: ignore[misc]
+    from .meta_yml import meta_yml  # type: ignore[misc]
+    from .subworkflow_changes import subworkflow_changes  # type: ignore[misc]
+    from .subworkflow_tests import subworkflow_tests  # type: ignore[misc]
+    from .subworkflow_todos import subworkflow_todos  # type: ignore[misc]
+    from .subworkflow_version import subworkflow_version  # type: ignore[misc]
 
     def __init__(
         self,

pyproject.toml

@@ -20,8 +20,3 @@ norecursedirs = [ ".*", "build", "dist", "*.egg", "data", "__pycache__", ".githu
 profile = "black"
 known_first_party = ["nf_core"]
 multi_line_output = 3
-
-[tool.mypy]
-ignore_missing_imports = true
-follow_imports = "skip"
-disable_error_code = "no-redef"

requirements-dev.txt

@@ -11,3 +11,4 @@ types-PyYAML
 types-requests
 types-jsonschema
 types-Markdown
+types-setuptools

tests/test_lint.py

@@ -178,44 +178,44 @@ def test_sphinx_md_files(self):
     #######################
     # SPECIFIC LINT TESTS #
     #######################
-    from .lint.actions_awsfulltest import (
+    from .lint.actions_awsfulltest import (  # type: ignore[misc]
         test_actions_awsfulltest_fail,
         test_actions_awsfulltest_pass,
         test_actions_awsfulltest_warn,
     )
-    from .lint.actions_awstest import (
+    from .lint.actions_awstest import (  # type: ignore[misc]
         test_actions_awstest_fail,
         test_actions_awstest_pass,
     )
-    from .lint.actions_ci import (
+    from .lint.actions_ci import (  # type: ignore[misc]
         test_actions_ci_fail_wrong_nf,
         test_actions_ci_fail_wrong_trigger,
         test_actions_ci_pass,
     )
-    from .lint.actions_schema_validation import (
+    from .lint.actions_schema_validation import (  # type: ignore[misc]
         test_actions_schema_validation_fails_for_additional_property,
         test_actions_schema_validation_missing_jobs,
         test_actions_schema_validation_missing_on,
     )
-    from .lint.files_exist import (
+    from .lint.files_exist import (  # type: ignore[misc]
         test_files_exist_depreciated_file,
         test_files_exist_missing_config,
         test_files_exist_missing_main,
         test_files_exist_pass,
     )
-    from .lint.files_unchanged import (
+    from .lint.files_unchanged import (  # type: ignore[misc]
         test_files_unchanged_fail,
         test_files_unchanged_pass,
     )
-    from .lint.merge_markers import test_merge_markers_found
-    from .lint.modules_json import test_modules_json_pass
-    from .lint.nextflow_config import (
+    from .lint.merge_markers import test_merge_markers_found  # type: ignore[misc]
+    from .lint.modules_json import test_modules_json_pass  # type: ignore[misc]
+    from .lint.nextflow_config import (  # type: ignore[misc]
         test_nextflow_config_bad_name_fail,
         test_nextflow_config_dev_in_release_mode_failed,
         test_nextflow_config_example_pass,
         test_nextflow_config_missing_test_profile_failed,
     )
-    from .lint.version_consistency import test_version_consistency
+    from .lint.version_consistency import test_version_consistency  # type: ignore[misc]
 
 
 # TODO nf-core: Assess and strip out if no longer required for DSL2