add mypy to pre-commit config, fix mypy errors

.github/workflows/create-lint-wf.yml

@@ -27,7 +27,7 @@ jobs:
           - "latest-everything"
     steps:
       # Get the repo code
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Check out source-code repository
 
       # Set up nf-core/tools
@@ -48,7 +48,7 @@ jobs:
           version: ${{ matrix.NXF_VER }}
 
       # Install the Prettier linting tools
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
 
       - name: Install Prettier
         run: npm install -g prettier

.github/workflows/create-test-lint-wf-template.yml

@@ -33,7 +33,7 @@ jobs:
           - "template_skip_nf_core_configs.yml"
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Check out source-code repository
 
       - name: Set up Python 3.12
@@ -52,7 +52,7 @@ jobs:
           version: latest-everything
 
       # Install the Prettier linting tools
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
 
       - name: Install Prettier
         run: npm install -g prettier

.github/workflows/create-test-wf.yml

@@ -26,7 +26,7 @@ jobs:
           - "23.04.0"
           - "latest-everything"
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Check out source-code repository
 
       - name: Set up Python 3.12

.github/workflows/deploy-pypi.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Check out source-code repository
 
       - name: Set up Python 3.12

.github/workflows/fix-linting.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -24,7 +24,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
 
       - name: Install Prettier
         run: npm install -g prettier @prettier/plugin-php

.github/workflows/lint-code.yml

@@ -16,9 +16,9 @@ jobs:
   EditorConfig:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
 
       - name: Install editorconfig-checker
         run: npm install -g editorconfig-checker
@@ -30,9 +30,9 @@ jobs:
   Prettier:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
 
       - name: Install Prettier
         run: npm install -g prettier
@@ -43,7 +43,7 @@ jobs:
   PythonBlack:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Check code lints with Black
         uses: psf/black@stable
@@ -74,7 +74,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out source-code repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Set up Python 3.12
         uses: actions/setup-python@v4
@@ -89,8 +89,8 @@ jobs:
   static-type-check:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v3
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
         with:
           python-version: 3.12
           cache: "pip"

.github/workflows/push_dockerhub_dev.yml

@@ -23,7 +23,7 @@ jobs:
       fail-fast: false
     steps:
       - name: Check out code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Build nfcore/tools:dev docker image
         run: docker build --no-cache . -t nfcore/tools:dev

.github/workflows/push_dockerhub_release.yml

@@ -23,7 +23,7 @@ jobs:
       fail-fast: false
     steps:
       - name: Check out code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Build nfcore/tools:latest docker image
         run: docker build --no-cache . -t nfcore/tools:latest

.github/workflows/rich-codex.yml

@@ -6,7 +6,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Set up Python
         uses: actions/setup-python@v4
         with:

.github/workflows/sync.yml

@@ -36,10 +36,10 @@ jobs:
       matrix: ${{fromJson(needs.get-pipelines.outputs.matrix)}}
       fail-fast: false
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Check out nf-core/tools
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Check out nf-core/${{ matrix.pipeline }}
         with:
           repository: nf-core/${{ matrix.pipeline }}

.github/workflows/tools-api-docs-dev.yml

@@ -24,7 +24,7 @@ jobs:
 
     steps:
       - name: Check out source-code repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Set up Python 3.12
         uses: actions/setup-python@v4

.github/workflows/tools-api-docs-release.yml

@@ -19,7 +19,7 @@ jobs:
           - ${{ github.event.release.tag_name }}
     steps:
       - name: Check out source-code repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Set up Python 3.12
         uses: actions/setup-python@v4

.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

CHANGELOG.md

@@ -31,6 +31,7 @@
 - Change testing framework for modules and subworkflows from pytest to nf-test ([#2490](https://github.com/nf-core/tools/pull/2490))
 - `bump_version` keeps now the indentation level of the updated version entries ([#2514](https://github.com/nf-core/tools/pull/2514))
 - Run tests with Python 3.12 ([#2522](https://github.com/nf-core/tools/pull/2522)).
+- Add mypy to pre-commit config for the tools repo ([#2545](https://github.com/nf-core/tools/pull/2545))
 
 # [v2.10 - Nickel Ostrich](https://github.com/nf-core/tools/releases/tag/2.10) + [2023-09-25]
 

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