Merge pull request #3816 from mashehu/update-to-python-3_10

Author: mashehu

.github/workflows/pytest.yml

@@ -34,13 +34,13 @@ jobs:
     runs-on: "ubuntu-latest"
     strategy:
       matrix:
-        python-version: ["3.9", "3.14"]
+        python-version: ["3.10", "3.14"]
         runner: ["ubuntu-latest"]
 
     steps:
       - name: Check conditions
         id: conditions
-        run: echo "run-tests=${{ github.ref == 'refs/heads/main' || (matrix.runner == 'ubuntu-20.04' && matrix.python-version == '3.9') }}" >> "$GITHUB_OUTPUT"
+        run: echo "run-tests=${{ github.ref == 'refs/heads/main' || (matrix.runner == 'ubuntu-20.04' && matrix.python-version == '3.10') }}" >> "$GITHUB_OUTPUT"
 
     outputs:
       python-version: ${{ matrix.python-version }}

nf_core/commands_pipelines.py

@@ -2,7 +2,6 @@
 import os
 import sys
 from pathlib import Path
-from typing import Optional, Union
 
 import rich
 
@@ -282,9 +281,9 @@ def pipelines_list(ctx, keywords, sort, json, show_archived):
 # nf-core pipelines rocrate
 def pipelines_rocrate(
     ctx,
-    pipeline_dir: Union[str, Path],
-    json_path: Optional[Union[str, Path]],
-    zip_path: Optional[Union[str, Path]],
+    pipeline_dir: str | Path,
+    json_path: str | Path | None,
+    zip_path: str | Path | None,
     pipeline_version: str,
 ) -> None:
     from nf_core.pipelines.rocrate import ROCrate

nf_core/commands_test_datasets.py

@@ -1,5 +1,4 @@
 import logging
-from typing import Optional
 
 import click
 import rich
@@ -30,7 +29,7 @@ def test_datasets_list_remote(ctx: click.Context, branch: str, generate_nf_path:
 
 
 def test_datasets_search(
-    ctx: click.Context, branch: str, generate_nf_path: bool, generate_dl_url: bool, query: Optional[str]
+    ctx: click.Context, branch: str, generate_nf_path: bool, generate_dl_url: bool, query: str | None
 ) -> None:
     """
     Search all files on a given branch in the remote nf-core/testdatasets repository on github

nf_core/components/components_command.py

@@ -3,7 +3,6 @@
 import os
 import shutil
 from pathlib import Path
-from typing import Optional, Union
 
 import nf_core.utils
 from nf_core.modules.modules_json import ModulesJson
@@ -22,9 +21,9 @@ class ComponentCommand:
     def __init__(
         self,
         component_type: str,
-        directory: Union[str, Path] = ".",
-        remote_url: Optional[str] = None,
-        branch: Optional[str] = None,
+        directory: str | Path = ".",
+        remote_url: str | None = None,
+        branch: str | None = None,
         no_pull: bool = False,
         hide_progress: bool = False,
         no_prompts: bool = False,
@@ -37,7 +36,7 @@ def __init__(
         self.modules_repo = ModulesRepo(remote_url, branch, no_pull, hide_progress)
         self.hide_progress: bool = hide_progress
         self.no_prompts: bool = no_prompts
-        self.repo_type: Optional[str] = None
+        self.repo_type: str | None = None
         self.org: str = ""
         self._configure_repo_and_paths()
 
@@ -114,7 +113,7 @@ def has_modules_file(self) -> None:
             log.info("Creating missing 'module.json' file.")
             ModulesJson(self.directory).create()
 
-    def clear_component_dir(self, component_name: str, component_dir: Union[str, Path]) -> bool:
+    def clear_component_dir(self, component_name: str, component_dir: str | Path) -> bool:
         """
         Removes all files in the module/subworkflow directory
 
@@ -161,7 +160,7 @@ def components_from_repo(self, install_dir: str) -> list[str]:
         ]
 
     def install_component_files(
-        self, component_name: str, component_version: str, modules_repo: ModulesRepo, install_dir: Union[str, Path]
+        self, component_name: str, component_version: str, modules_repo: ModulesRepo, install_dir: str | Path
     ) -> bool:
         """
         Installs a module/subworkflow into the given directory
@@ -263,7 +262,7 @@ 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, 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 +271,7 @@ 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, 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 +4,6 @@
 import logging
 import os
 from pathlib import Path
-from typing import Union
 
 from rich import box
 from rich.console import Console, Group, RenderableType
@@ -308,7 +307,7 @@ def print_diff(
         )
 
     @staticmethod
-    def per_file_patch(patch_fn: Union[str, Path]) -> dict[str, list[str]]:
+    def per_file_patch(patch_fn: str | Path) -> dict[str, list[str]]:
         """
         Splits a patch file for several files into one patch per file.
 
@@ -466,8 +465,8 @@ def try_apply_single_patch(file_lines, patch, reverse=False):
     def try_apply_patch(
         component_type: str,
         component: str,
-        repo_path: Union[str, Path],
-        patch_path: Union[str, Path],
+        repo_path: str | Path,
+        patch_path: str | Path,
         component_dir: Path,
         reverse: bool = False,
     ) -> dict[str, list[str]]:

nf_core/components/components_test.py

@@ -6,7 +6,6 @@
 import os
 import re
 from pathlib import Path
-from typing import Optional
 
 import questionary
 from rich import print
@@ -65,15 +64,15 @@ class ComponentsTest(ComponentCommand):  # type: ignore[misc]
     def __init__(
         self,
         component_type: str,
-        component_name: Optional[str] = None,
+        component_name: str | None = None,
         directory: str = ".",
         no_prompts: bool = False,
-        remote_url: Optional[str] = None,
-        branch: Optional[str] = None,
+        remote_url: str | None = None,
+        branch: str | None = None,
         verbose: bool = False,
         update: bool = False,
         once: bool = False,
-        profile: Optional[str] = None,
+        profile: str | None = None,
     ):
         super().__init__(component_type, directory, remote_url, branch, no_prompts=no_prompts)
         self.component_name = component_name

nf_core/components/components_utils.py

@@ -1,7 +1,6 @@
 import logging
 import re
 from pathlib import Path
-from typing import Optional, Union
 
 import questionary
 import requests
@@ -22,7 +21,7 @@
 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: bool | None = True) -> tuple[Path, str | None, str]:
     """
     Determine whether this is a pipeline repository or a clone of
     nf-core/modules
@@ -95,7 +94,7 @@ def prompt_component_version_sha(
     component_name: str,
     component_type: str,
     modules_repo: "ModulesRepo",
-    installed_sha: Optional[str] = None,
+    installed_sha: str | None = None,
 ) -> str:
     """
     Creates an interactive questionary prompt for selecting the module/subworkflow version
@@ -146,7 +145,7 @@ def prompt_component_version_sha(
 
 
 def get_components_to_install(
-    subworkflow_dir: Union[str, Path],
+    subworkflow_dir: str | Path,
 ) -> tuple[list[dict[str, str]], list[dict[str, str]]]:
     """
     Parse the subworkflow main.nf file to retrieve all imported modules and subworkflows.
@@ -198,7 +197,7 @@ 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) -> dict | None:
     """
     Try to get bio.tools information for 'tool'
     """
@@ -237,7 +236,7 @@ def get_biotools_id(data: dict, tool_name: str) -> str:
 
 def get_channel_info_from_biotools(
     data: dict, tool_name: str
-) -> Optional[tuple[DictWithStrAndTuple, DictWithStrAndTuple]]:
+) -> tuple[DictWithStrAndTuple, DictWithStrAndTuple] | None:
     """
     Try to find input and output channels and the respective EDAM ontology terms
 

nf_core/components/create.py

@@ -9,7 +9,6 @@
 import shutil
 import subprocess
 from pathlib import Path
-from typing import Optional, Union
 
 import jinja2
 import questionary
@@ -41,12 +40,12 @@ def __init__(
         component_type: str,
         directory: Path = Path("."),
         component: str = "",
-        author: Optional[str] = None,
-        process_label: Optional[str] = None,
-        has_meta: Optional[str] = None,
+        author: str | None = None,
+        process_label: str | None = None,
+        has_meta: str | None = None,
         force: bool = False,
-        conda_name: Optional[str] = None,
-        conda_version: Optional[str] = None,
+        conda_name: str | None = None,
+        conda_version: str | None = None,
         empty_template: bool = False,
         migrate_pytest: bool = False,  # TODO: Deprecate this flag in the future
     ):
@@ -293,7 +292,7 @@ def _get_module_structure_components(self):
                 default=True,
             )
 
-    def _render_template(self) -> Optional[bool]:
+    def _render_template(self) -> bool | None:
         """
         Create new module/subworkflow files with Jinja2.
         """
@@ -560,7 +559,7 @@ def generate_meta_yml_file(self) -> None:
             )
 
             if hasattr(self, "inputs"):
-                inputs_array: list[Union[dict, list[dict]]] = []
+                inputs_array: list[dict | list[dict]] = []
                 for i, (input_name, ontologies) in enumerate(self.inputs.items()):
                     channel_entry: dict[str, dict] = {
                         input_name: {
@@ -609,9 +608,9 @@ def generate_meta_yml_file(self) -> None:
                 meta_yml["input"][0]["bam"]["ontologies"][2].yaml_add_eol_comment("SAM", "edam")
 
             if hasattr(self, "outputs"):
-                outputs_dict: dict[str, Union[list, dict]] = {}
+                outputs_dict: dict[str, list | dict] = {}
                 for i, (output_name, ontologies) in enumerate(self.outputs.items()):
-                    channel_contents: list[Union[list[dict], dict]] = []
+                    channel_contents: list[list[dict] | dict] = []
                     if self.has_meta:
                         channel_contents.append(
                             [

nf_core/components/info.py

@@ -1,7 +1,6 @@
 import logging
 import os
 from pathlib import Path
-from typing import Optional, Union
 
 import questionary
 import yaml
@@ -59,18 +58,18 @@ class ComponentInfo(ComponentCommand):
     def __init__(
         self,
         component_type: str,
-        pipeline_dir: Union[str, Path],
+        pipeline_dir: str | Path,
         component_name: str,
-        remote_url: Optional[str] = None,
-        branch: Optional[str] = None,
+        remote_url: str | None = None,
+        branch: str | None = None,
         no_pull: bool = False,
     ):
         super().__init__(component_type, pipeline_dir, remote_url, branch, no_pull)
-        self.meta: Optional[dict] = None
-        self.local_path: Optional[Path] = None
-        self.remote_location: Optional[str] = None
+        self.meta: dict | None = None
+        self.local_path: Path | None = None
+        self.remote_location: str | None = None
         self.local: bool = False
-        self.modules_json: Optional[ModulesJson] = None
+        self.modules_json: ModulesJson | None = None
 
         if self.repo_type == "pipeline":
             # Check modules directory structure
@@ -90,7 +89,7 @@ def _configure_repo_and_paths(self, nf_dir_req=False) -> None:
         """
         return super()._configure_repo_and_paths(nf_dir_req)
 
-    def init_mod_name(self, component: Optional[str]) -> str:
+    def init_mod_name(self, component: str | None) -> str:
         """
         Makes sure that we have a module/subworkflow name before proceeding.
 
@@ -170,11 +169,11 @@ def get_component_info(self):
 
         return self.generate_component_info_help()
 
-    def get_local_yaml(self) -> Optional[dict]:
+    def get_local_yaml(self) -> dict | None:
         """Attempt to get the meta.yml file from a locally installed module/subworkflow.
 
         Returns:
-            Optional[dict]: Parsed meta.yml if found, None otherwise
+            dict | None: Parsed meta.yml if found, None otherwise
         """
 
         if self.repo_type == "pipeline":
@@ -213,7 +212,7 @@ def get_local_yaml(self) -> Optional[dict]:
 
         return {}
 
-    def get_remote_yaml(self) -> Optional[dict]:
+    def get_remote_yaml(self) -> dict | None:
         """Attempt to get the meta.yml file from a remote repo.
 
         Returns:

nf_core/components/install.py

@@ -1,7 +1,6 @@
 import logging
 import os
 from pathlib import Path
-from typing import Optional, Union
 
 import questionary
 from rich import print
@@ -30,15 +29,15 @@
 class ComponentInstall(ComponentCommand):
     def __init__(
         self,
-        pipeline_dir: Union[str, Path],
+        pipeline_dir: str | Path,
         component_type: str,
         force: bool = False,
         prompt: bool = False,
-        sha: Optional[str] = None,
-        remote_url: Optional[str] = None,
-        branch: Optional[str] = None,
+        sha: str | None = None,
+        remote_url: str | None = None,
+        branch: str | None = None,
         no_pull: bool = False,
-        installed_by: Optional[list[str]] = None,
+        installed_by: list[str] | None = None,
     ):
         super().__init__(component_type, pipeline_dir, remote_url, branch, no_pull)
         self.current_remote = ModulesRepo(remote_url, branch)
@@ -52,7 +51,7 @@ def __init__(
         else:
             self.installed_by = [self.component_type]
 
-    def install(self, component: Union[str, dict[str, str]], silent: bool = False) -> bool:
+    def install(self, component: str | dict[str, str], silent: bool = False) -> bool:
         if isinstance(component, dict):
             # Override modules_repo when the component to install is a dependency from a subworkflow.
             remote_url = component.get("git_remote", self.current_remote.remote_url)
@@ -211,7 +210,7 @@ def install_included_components(self, subworkflow_dir):
             self.installed_by = original_installed
 
     def collect_and_verify_name(
-        self, component: Optional[str], modules_repo: "nf_core.modules.modules_repo.ModulesRepo"
+        self, component: str | None, modules_repo: "nf_core.modules.modules_repo.ModulesRepo"
     ) -> str:
         """
         Collect component name.