Drop python 3.8, add tests with python 3.13

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -38,4 +38,4 @@ body:
         * Executor _(eg. slurm, local, awsbatch)_
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
         * Version of nf-core/tools _(eg. 1.10, 1.12.1, 1.13)_
-        * Python version _(eg. 3.11, 3.12)_
+        * Python version _(eg. 3.12, 3.13)_

.github/workflows/changelog.py

@@ -19,7 +19,6 @@
 import re
 import sys
 from pathlib import Path
-from typing import List, Tuple
 
 REPO_URL = "https://github.com/nf-core/tools"
 
@@ -51,7 +50,7 @@
     sys.exit(0)
 
 
-def _determine_change_type(pr_title) -> Tuple[str, str]:
+def _determine_change_type(pr_title) -> tuple[str, str]:
     """
     Determine the type of the PR: Template, Download, Linting, Modules, Subworkflows, or General
     Returns a tuple of the section name and the module info.
@@ -99,7 +98,7 @@ def _determine_change_type(pr_title) -> Tuple[str, str]:
 # entry, corresponding to this new PR.
 with changelog_path.open("r") as f:
     orig_lines = f.readlines()
-updated_lines: List[str] = []
+updated_lines: list[str] = []
 
 
 def _skip_existing_entry_for_this_pr(line: str, same_section: bool = True) -> str:
@@ -189,7 +188,7 @@ def _skip_existing_entry_for_this_pr(line: str, same_section: bool = True) -> st
             sys.exit(1)
         updated_lines.append(line)
         # Collecting lines until the next section.
-        section_lines: List[str] = []
+        section_lines: list[str] = []
         while True:
             line = orig_lines.pop(0)
             if line.startswith("#"):
@@ -215,7 +214,7 @@ def _skip_existing_entry_for_this_pr(line: str, same_section: bool = True) -> st
         updated_lines.append(line)
 
 
-def collapse_newlines(lines: List[str]) -> List[str]:
+def collapse_newlines(lines: list[str]) -> list[str]:
     updated = []
     for idx in range(len(lines)):
         if idx != 0 and not lines[idx].strip() and not lines[idx - 1].strip():

.github/workflows/changelog.yml

@@ -64,7 +64,7 @@ jobs:
           git diff --exit-code ${GITHUB_WORKSPACE}/CHANGELOG.md || echo "changed=YES" >> $GITHUB_ENV
           echo "File changed: ${{ env.changed }}"
 
-      - name: Set up Python 3.12
+      - name: Set up Python 3.13
         uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
         with:
           python-version: "3.13"

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

@@ -46,7 +46,7 @@ jobs:
         name: Check out source-code repository
 
       # Set up nf-core/tools
-      - name: Set up Python 3.12
+      - name: Set up Python 3.13
         uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
         with:
           python-version: "3.13"

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

@@ -44,7 +44,7 @@ jobs:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         name: Check out source-code repository
 
-      - name: Set up Python 3.12
+      - name: Set up Python 3.13
         uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
         with:
           python-version: "3.13"

.github/workflows/deploy-pypi.yml

@@ -16,7 +16,7 @@ jobs:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         name: Check out source-code repository
 
-      - name: Set up Python 3.12
+      - name: Set up Python 3.13
         uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
         with:
           python-version: "3.13"

.github/workflows/lint-code.yml

@@ -22,7 +22,7 @@ jobs:
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
-      - name: Set up Python 3.12
+      - name: Set up Python 3.13
         uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
         with:
           python-version: "3.13"

.github/workflows/pytest.yml

@@ -34,16 +34,13 @@ jobs:
     runs-on: "ubuntu-latest"
     strategy:
       matrix:
-        python-version: ["3.8", "3.12"]
+        python-version: ["3.9", "3.13"]
         runner: ["ubuntu-latest"]
-        include:
-          - python-version: "3.8"
-            runner: "ubuntu-20.04"
 
     steps:
       - name: Check conditions
         id: conditions
-        run: echo "run-tests=${{ github.ref == 'refs/heads/main' || (matrix.runner == 'ubuntu-20.04' && matrix.python-version == '3.8') }}" >> "$GITHUB_OUTPUT"
+        run: echo "run-tests=${{ github.ref == 'refs/heads/main' || (matrix.runner == 'ubuntu-20.04' && matrix.python-version == '3.9') }}" >> "$GITHUB_OUTPUT"
 
     outputs:
       python-version: ${{ matrix.python-version }}
@@ -97,14 +94,6 @@ jobs:
           python -m pip install --upgrade pip -r requirements-dev.txt
           pip install -e .
 
-      - name: Downgrade git to the Ubuntu official repository's version
-        if: ${{ needs.setup.outputs.runner == 'ubuntu-20.04' && needs.setup.outputs.python-version == '3.8' }}
-        run: |
-          sudo apt update
-          sudo apt remove -y git git-man
-          sudo add-apt-repository --remove ppa:git-core/ppa
-          sudo apt install -y git
-
       - name: Set up Singularity
         if: ${{ matrix.test == 'test_download.py'}}
         uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
@@ -169,7 +158,7 @@ jobs:
           cd pytest
 
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
-      - name: Set up Python 3.12
+      - name: Set up Python 3.13
         uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
         env:
           AGENT_TOOLSDIRECTORY: /opt/actions-runner/_work/tools/tools/

.github/workflows/sync.yml

@@ -72,7 +72,7 @@ jobs:
           path: nf-core/${{ matrix.pipeline }}
           fetch-depth: "0"
 
-      - name: Set up Python 3.12
+      - name: Set up Python 3.13
         uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
         with:
           python-version: "3.13"

CHANGELOG.md

@@ -18,6 +18,7 @@
 ### General
 
 - Add conda cache dir ([#3610](https://github.com/nf-core/tools/pull/3610))
+- Drop python 3.8, add tests with python 3.13 ([#3538](https://github.com/nf-core/tools/pull/3538))
 - Fixes a bug with the test-datasets subcommand [#3617](https://github.com/nf-core/tools/issues/3617)
 
 ## [v3.3.1 - Tungsten Tamarin Patch](https://github.com/nf-core/tools/releases/tag/3.3.1) - [2025-06-02]

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.12-slim@sha256:fd95fa221297a88e1cf49c55ec1828edd7c5a428187e67b5d1805692d11588db
+FROM python:3.13-slim
 LABEL authors="phil.ewels@seqera.io,erik.danielsson@scilifelab.se" \
     description="Docker image containing requirements for nf-core/tools"
 

README.md

@@ -35,7 +35,7 @@ conda install nf-core
 Alternatively, you can create a new environment with both nf-core/tools and nextflow:
 
 ```bash
-conda create --name nf-core python=3.12 nf-core nextflow
+conda create --name nf-core python=3.13 nf-core nextflow
 conda activate nf-core
 ```
 

docs/api/_src/conf.py

@@ -13,7 +13,6 @@
 #
 import os
 import sys
-from typing import Dict
 
 import nf_core
 
@@ -114,7 +113,7 @@
 
 # -- Options for LaTeX output ------------------------------------------------
 
-latex_elements: Dict[str, str] = {
+latex_elements: dict[str, str] = {
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',

nf_core/components/components_command.py

@@ -3,7 +3,7 @@
 import os
 import shutil
 from pathlib import Path
-from typing import Dict, List, Optional, Union
+from typing import Optional, Union
 
 import nf_core.utils
 from nf_core.modules.modules_json import ModulesJson
@@ -65,7 +65,7 @@ def _configure_repo_and_paths(self, nf_dir_req: bool = True) -> None:
         self.default_subworkflows_path = Path("subworkflows", self.org)
         self.default_subworkflows_tests_path = Path("tests", "subworkflows", self.org)
 
-    def get_local_components(self) -> List[str]:
+    def get_local_components(self) -> list[str]:
         """
         Get the local modules/subworkflows in a pipeline
         """
@@ -78,7 +78,7 @@ def get_local_components(self) -> List[str]:
             str(path.relative_to(local_component_dir)) for path in local_component_dir.iterdir() if path.suffix == ".nf"
         ]
 
-    def get_components_clone_modules(self) -> List[str]:
+    def get_components_clone_modules(self) -> list[str]:
         """
         Get the modules/subworkflows repository available in a clone of nf-core/modules
         """
@@ -142,7 +142,7 @@ def clear_component_dir(self, component_name: str, component_dir: Union[str, Pat
             log.error(f"Could not remove {self.component_type[:-1]} {component_name}: {e}")
             return False
 
-    def components_from_repo(self, install_dir: str) -> List[str]:
+    def components_from_repo(self, install_dir: str) -> list[str]:
         """
         Gets the modules/subworkflows installed from a certain repository
 
@@ -200,7 +200,7 @@ def check_modules_structure(self) -> None:
             modules/nf-core/modules/TOOL/SUBTOOL
         """
         if self.repo_type == "pipeline":
-            wrong_location_modules: List[Path] = []
+            wrong_location_modules: list[Path] = []
             for directory, _, files in os.walk(Path(self.directory, "modules")):
                 if "main.nf" in files:
                     module_path = Path(directory).relative_to(Path(self.directory, "modules"))
@@ -263,7 +263,7 @@ def check_patch_paths(self, patch_path: Path, module_name: str) -> None:
                     ][module_name]["patch"] = str(patch_path.relative_to(self.directory.resolve()))
                 modules_json.dump()
 
-    def check_if_in_include_stmts(self, component_path: str) -> Dict[str, List[Dict[str, Union[int, str]]]]:
+    def check_if_in_include_stmts(self, component_path: str) -> dict[str, list[dict[str, Union[int, str]]]]:
         """
         Checks for include statements in the main.nf file of the pipeline and a list of line numbers where the component is included
         Args:
@@ -272,7 +272,7 @@ def check_if_in_include_stmts(self, component_path: str) -> Dict[str, List[Dict[
         Returns:
             (list): A list of dictionaries, with the workflow file and the line number where the component is included
         """
-        include_stmts: Dict[str, List[Dict[str, Union[int, str]]]] = {}
+        include_stmts: dict[str, list[dict[str, Union[int, str]]]] = {}
         if self.repo_type == "pipeline":
             workflow_files = Path(self.directory, "workflows").glob("*.nf")
             for workflow_file in workflow_files:

nf_core/components/components_differ.py

@@ -4,7 +4,7 @@
 import logging
 import os
 from pathlib import Path
-from typing import Dict, List, Union
+from typing import Union
 
 from rich import box
 from rich.console import Console, Group, RenderableType
@@ -308,7 +308,7 @@ def print_diff(
             )
 
     @staticmethod
-    def per_file_patch(patch_fn: Union[str, Path]) -> Dict[str, List[str]]:
+    def per_file_patch(patch_fn: Union[str, Path]) -> dict[str, list[str]]:
         """
         Splits a patch file for several files into one patch per file.
 
@@ -324,7 +324,7 @@ def per_file_patch(patch_fn: Union[str, Path]) -> Dict[str, List[str]]:
 
         patches = {}
         i = 0
-        patch_lines: List[str] = []
+        patch_lines: list[str] = []
         key = "preamble"
         while i < len(lines):
             line = lines[i]
@@ -470,7 +470,7 @@ def try_apply_patch(
         patch_path: Union[str, Path],
         component_dir: Path,
         reverse: bool = False,
-    ) -> Dict[str, List[str]]:
+    ) -> dict[str, list[str]]:
         """
         Try applying a full patch file to a module or subworkflow
 

nf_core/components/components_test.py

@@ -6,7 +6,7 @@
 import os
 import re
 from pathlib import Path
-from typing import List, Optional
+from typing import Optional
 
 import questionary
 from rich import print
@@ -79,7 +79,7 @@ def __init__(
         self.component_name = component_name
         self.remote_url = remote_url
         self.branch = branch
-        self.errors: List[str] = []
+        self.errors: list[str] = []
         self.verbose = verbose
         self.obsolete_snapshots: bool = False
         self.update = update

nf_core/components/components_utils.py

@@ -1,7 +1,7 @@
 import logging
 import re
 from pathlib import Path
-from typing import Dict, List, Optional, Tuple, Union
+from typing import Optional, Union
 
 import questionary
 import requests
@@ -22,7 +22,7 @@
 yaml.indent(mapping=2, sequence=2, offset=0)
 
 
-def get_repo_info(directory: Path, use_prompt: Optional[bool] = True) -> Tuple[Path, Optional[str], str]:
+def get_repo_info(directory: Path, use_prompt: Optional[bool] = True) -> tuple[Path, Optional[str], str]:
     """
     Determine whether this is a pipeline repository or a clone of
     nf-core/modules
@@ -147,12 +147,12 @@ def prompt_component_version_sha(
 
 def get_components_to_install(
     subworkflow_dir: Union[str, Path],
-) -> Tuple[List[Dict[str, str]], List[Dict[str, str]]]:
+) -> tuple[list[dict[str, str]], list[dict[str, str]]]:
     """
     Parse the subworkflow main.nf file to retrieve all imported modules and subworkflows.
     """
-    modules: Dict[str, Dict[str, str]] = {}
-    subworkflows: Dict[str, Dict[str, str]] = {}
+    modules: dict[str, dict[str, str]] = {}
+    subworkflows: dict[str, dict[str, str]] = {}
 
     with open(Path(subworkflow_dir, "main.nf")) as fh:
         for line in fh:
@@ -165,7 +165,7 @@ def get_components_to_install(
                 if link.startswith("../../../"):
                     name_split = name.lower().split("_")
                     component_name = "/".join(name_split)
-                    component_dict: Dict[str, str] = {
+                    component_dict: dict[str, str] = {
                         "name": component_name,
                     }
                     modules[component_name] = component_dict
@@ -198,7 +198,7 @@ def get_components_to_install(
     return list(modules.values()), list(subworkflows.values())
 
 
-def get_biotools_response(tool_name: str) -> Optional[Dict]:
+def get_biotools_response(tool_name: str) -> Optional[dict]:
     """
     Try to get bio.tools information for 'tool'
     """
@@ -232,12 +232,12 @@ def get_biotools_id(data: dict, tool_name: str) -> str:
     return ""
 
 
-DictWithStrAndTuple = Dict[str, Tuple[List[str], List[str], List[str]]]
+DictWithStrAndTuple = dict[str, tuple[list[str], list[str], list[str]]]
 
 
 def get_channel_info_from_biotools(
     data: dict, tool_name: str
-) -> Optional[Tuple[DictWithStrAndTuple, DictWithStrAndTuple]]:
+) -> Optional[tuple[DictWithStrAndTuple, DictWithStrAndTuple]]:
     """
     Try to find input and output channels and the respective EDAM ontology terms
 

nf_core/components/create.py

@@ -9,7 +9,7 @@
 import shutil
 import subprocess
 from pathlib import Path
-from typing import Dict, Optional
+from typing import Optional
 
 import jinja2
 import questionary
@@ -59,7 +59,7 @@ def __init__(
         self.bioconda = None
         self.singularity_container = None
         self.docker_container = None
-        self.file_paths: Dict[str, Path] = {}
+        self.file_paths: dict[str, Path] = {}
         self.not_empty_template = not empty_template
         self.migrate_pytest = migrate_pytest
         self.tool_identifier = ""
@@ -357,7 +357,7 @@ def _collect_name_prompt(self):
                 elif self.component_type == "subworkflows":
                     self.component = rich.prompt.Prompt.ask("[violet]Name of subworkflow").strip()
 
-    def _get_component_dirs(self) -> Dict[str, Path]:
+    def _get_component_dirs(self) -> dict[str, Path]:
         """Given a directory and a tool/subtool or subworkflow, set the file paths and check if they already exist
 
         Returns dict: keys are relative paths to template files, vals are target paths.