Merge pull request #3228 from mashehu/fix-yml-config-type

allow mixed str and dict in lint config

CHANGELOG.md

@@ -24,7 +24,7 @@
 
 ### Linting
 
-- General: Run pre-commit when testing linting the template pipeline ([#3280](https://github.com/nf-core/tools/pull/3280))
+- allow mixed `str` and `dict` entries in lint config ([#3228](https://github.com/nf-core/tools/pull/3228))
 
 ### Modules
 
@@ -55,6 +55,7 @@
 - Update python:3.12-slim Docker digest to 2a6386a ([#3284](https://github.com/nf-core/tools/pull/3284))
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.8.0 ([#3299](https://github.com/nf-core/tools/pull/3299))
 - Update gitpod/workspace-base Docker digest to 12853f7 ([#3309](https://github.com/nf-core/tools/pull/3309))
+- Run pre-commit when testing linting the template pipeline ([#3280](https://github.com/nf-core/tools/pull/3280))
 
 ## [v3.0.2 - Titanium Tapir Patch](https://github.com/nf-core/tools/releases/tag/3.0.2) - [2024-10-11]
 

nf_core/components/lint/__init__.py

@@ -22,7 +22,7 @@
 from nf_core.components.nfcore_component import NFCoreComponent
 from nf_core.modules.modules_json import ModulesJson
 from nf_core.pipelines.lint_utils import console
-from nf_core.utils import LintConfigType
+from nf_core.utils import NFCoreYamlLintConfig
 from nf_core.utils import plural_s as _s
 
 log = logging.getLogger(__name__)
@@ -80,7 +80,7 @@ def __init__(
         self.failed: List[LintResult] = []
         self.all_local_components: List[NFCoreComponent] = []
 
-        self.lint_config: Optional[LintConfigType] = None
+        self.lint_config: Optional[NFCoreYamlLintConfig] = None
         self.modules_json: Optional[ModulesJson] = None
 
         if self.component_type == "modules":

nf_core/pipelines/create/create.py

@@ -8,7 +8,7 @@
 import re
 import shutil
 from pathlib import Path
-from typing import Dict, List, Optional, Tuple, Union, cast
+from typing import Dict, List, Optional, Tuple, Union
 
 import git
 import git.config
@@ -22,7 +22,7 @@
 from nf_core.pipelines.create_logo import create_logo
 from nf_core.pipelines.lint_utils import run_prettier_on_file
 from nf_core.pipelines.rocrate import ROCrate
-from nf_core.utils import LintConfigType, NFCoreTemplateConfig
+from nf_core.utils import NFCoreTemplateConfig, NFCoreYamlLintConfig
 
 log = logging.getLogger(__name__)
 
@@ -68,7 +68,7 @@ def __init__(
                 _, config_yml = nf_core.utils.load_tools_config(outdir if outdir else Path().cwd())
                 # Obtain a CreateConfig object from `.nf-core.yml` config file
                 if config_yml is not None and getattr(config_yml, "template", None) is not None:
-                    self.config = CreateConfig(**config_yml["template"].model_dump())
+                    self.config = CreateConfig(**config_yml["template"].model_dump(exclude_none=True))
                 else:
                     raise UserWarning("The template configuration was not provided in '.nf-core.yml'.")
                 # Update the output directory
@@ -206,7 +206,7 @@ def obtain_jinja_params_dict(
             config_yml = None
 
         # Set the parameters for the jinja template
-        jinja_params = self.config.model_dump()
+        jinja_params = self.config.model_dump(exclude_none=True)
 
         # Add template areas to jinja params and create list of areas with paths to skip
         skip_areas = []
@@ -369,8 +369,8 @@ def render_template(self) -> None:
             config_fn, config_yml = nf_core.utils.load_tools_config(self.outdir)
             if config_fn is not None and config_yml is not None:
                 with open(str(config_fn), "w") as fh:
-                    config_yml.template = NFCoreTemplateConfig(**self.config.model_dump())
-                    yaml.safe_dump(config_yml.model_dump(), fh)
+                    config_yml.template = NFCoreTemplateConfig(**self.config.model_dump(exclude_none=True))
+                    yaml.safe_dump(config_yml.model_dump(exclude_none=True), fh)
                     log.debug(f"Dumping pipeline template yml to pipeline config file '{config_fn.name}'")
 
         # Run prettier on files
@@ -401,9 +401,9 @@ def fix_linting(self):
         # Add the lint content to the preexisting nf-core config
         config_fn, nf_core_yml = nf_core.utils.load_tools_config(self.outdir)
         if config_fn is not None and nf_core_yml is not None:
-            nf_core_yml.lint = cast(LintConfigType, lint_config)
+            nf_core_yml.lint = NFCoreYamlLintConfig(**lint_config)
             with open(self.outdir / config_fn, "w") as fh:
-                yaml.dump(nf_core_yml.model_dump(), fh, default_flow_style=False, sort_keys=False)
+                yaml.dump(nf_core_yml.model_dump(exclude_none=True), fh, default_flow_style=False, sort_keys=False)
 
     def make_pipeline_logo(self):
         """Fetch a logo for the new pipeline from the nf-core website"""

nf_core/pipelines/lint/__init__.py

@@ -27,8 +27,8 @@
 from nf_core import __version__
 from nf_core.components.lint import ComponentLint
 from nf_core.pipelines.lint_utils import console
+from nf_core.utils import NFCoreYamlConfig, NFCoreYamlLintConfig, strip_ansi_codes
 from nf_core.utils import plural_s as _s
-from nf_core.utils import strip_ansi_codes
 
 from .actions_awsfulltest import actions_awsfulltest
 from .actions_awstest import actions_awstest
@@ -112,7 +112,7 @@ def __init__(
         # Initialise the parent object
         super().__init__(wf_path)
 
-        self.lint_config = {}
+        self.lint_config: Optional[NFCoreYamlLintConfig] = None
         self.release_mode = release_mode
         self.fail_ignored = fail_ignored
         self.fail_warned = fail_warned
@@ -173,13 +173,12 @@ def _load_lint_config(self) -> bool:
         Add parsed config to the `self.lint_config` class attribute.
         """
         _, tools_config = nf_core.utils.load_tools_config(self.wf_path)
-        self.lint_config = getattr(tools_config, "lint", {}) or {}
+        self.lint_config = getattr(tools_config, "lint", None) or None
         is_correct = True
-
         # Check if we have any keys that don't match lint test names
         if self.lint_config is not None:
-            for k in self.lint_config:
-                if k != "nfcore_components" and k not in self.lint_tests:
+            for k, v in self.lint_config:
+                if v is not None and k != "nfcore_components" and k not in self.lint_tests:
                     # nfcore_components is an exception to allow custom pipelines without nf-core components
                     log.warning(f"Found unrecognised test name '{k}' in pipeline lint config")
                     is_correct = False
@@ -594,7 +593,7 @@ def run_linting(
     lint_obj._load_lint_config()
     lint_obj.load_pipeline_config()
 
-    if "nfcore_components" in lint_obj.lint_config and not lint_obj.lint_config["nfcore_components"]:
+    if lint_obj.lint_config and not lint_obj.lint_config["nfcore_components"]:
         module_lint_obj = None
         subworkflow_lint_obj = None
     else:
@@ -679,5 +678,4 @@ def run_linting(
     if len(lint_obj.failed) > 0:
         if release_mode:
             log.info("Reminder: Lint tests were run in --release mode.")
-
     return lint_obj, module_lint_obj, subworkflow_lint_obj

nf_core/pipelines/lint/multiqc_config.py

@@ -31,6 +31,15 @@ def multiqc_config(self) -> Dict[str, List[str]]:
             lint:
                 multiqc_config: False
 
+        To disable this test only for specific sections, you can specify a list of section names.
+        For example:
+
+        .. code-block:: yaml
+        lint:
+                multiqc_config:
+                    - report_section_order
+                    - report_comment
+
     """
 
     passed: List[str] = []

nf_core/pipelines/lint/nfcore_yml.py

@@ -1,7 +1,8 @@
-import re
 from pathlib import Path
 from typing import Dict, List
 
+from ruamel.yaml import YAML
+
 from nf_core import __version__
 
 REPOSITORY_TYPES = ["pipeline", "modules"]
@@ -26,21 +27,23 @@ def nfcore_yml(self) -> Dict[str, List[str]]:
     failed: List[str] = []
     ignored: List[str] = []
 
+    yaml = YAML()
+
     # Remove field that should be ignored according to the linting config
     ignore_configs = self.lint_config.get(".nf-core", []) if self.lint_config is not None else []
-    try:
-        with open(Path(self.wf_path, ".nf-core.yml")) as fh:
-            content = fh.read()
-    except FileNotFoundError:
-        with open(Path(self.wf_path, ".nf-core.yaml")) as fh:
-            content = fh.read()
+    for ext in (".yml", ".yaml"):
+        try:
+            nf_core_yml = yaml.load(Path(self.wf_path) / f".nf-core{ext}")
+            break
+        except FileNotFoundError:
+            continue
+    else:
+        raise FileNotFoundError("No `.nf-core.yml` file found.")
 
     if "repository_type" not in ignore_configs:
         # Check that the repository type is set in the .nf-core.yml
-        repo_type_re = r"repository_type: (.+)"
-        match = re.search(repo_type_re, content)
-        if match:
-            repo_type = match.group(1)
+        if "repository_type" in nf_core_yml:
+            repo_type = nf_core_yml["repository_type"]
             if repo_type not in REPOSITORY_TYPES:
                 failed.append(
                     f"Repository type in `.nf-core.yml` is not valid. "
@@ -55,10 +58,8 @@ def nfcore_yml(self) -> Dict[str, List[str]]:
 
     if "nf_core_version" not in ignore_configs:
         # Check that the nf-core version is set in the .nf-core.yml
-        nf_core_version_re = r"nf_core_version: (.+)"
-        match = re.search(nf_core_version_re, content)
-        if match:
-            nf_core_version = match.group(1).strip('"')
+        if "nf_core_version" in nf_core_yml:
+            nf_core_version = nf_core_yml["nf_core_version"]
             if nf_core_version != __version__ and "dev" not in nf_core_version:
                 warned.append(
                     f"nf-core version in `.nf-core.yml` is not set to the latest version. "

nf_core/pipelines/lint/readme.py

@@ -23,6 +23,21 @@ def readme(self):
 
         * If pipeline is released but still contains a 'zenodo.XXXXXXX' tag, the test fails
 
+    To disable this test, add the following to the pipeline's ``.nf-core.yml`` file:
+
+    .. code-block:: yaml
+        lint:
+            readme: False
+
+    To disable subsets of these tests, add the following to the pipeline's ``.nf-core.yml`` file:
+
+    .. code-block:: yaml
+
+            lint:
+                readme:
+                    - nextflow_badge
+                    - zenodo_release
+
     """
     passed = []
     warned = []

nf_core/pipelines/lint/template_strings.py

@@ -39,8 +39,8 @@ def template_strings(self):
     ignored = []
     # Files that should be ignored according to the linting config
     ignore_files = self.lint_config.get("template_strings", []) if self.lint_config is not None else []
-    files = self.list_files()
 
+    files = self.list_files()
     # Loop through files, searching for string
     num_matches = 0
     for fn in files:

nf_core/pipelines/sync.py

@@ -6,7 +6,7 @@
 import re
 import shutil
 from pathlib import Path
-from typing import Dict, Optional, Union
+from typing import Any, Dict, Optional, Tuple, Union
 
 import git
 import questionary
@@ -105,7 +105,7 @@ def __init__(
                 with open(template_yaml_path) as f:
                     self.config_yml.template = yaml.safe_load(f)
                 with open(self.config_yml_path, "w") as fh:
-                    yaml.safe_dump(self.config_yml.model_dump(), fh)
+                    yaml.safe_dump(self.config_yml.model_dump(exclude_none=True), fh)
                 log.info(f"Saved pipeline creation settings to '{self.config_yml_path}'")
                 raise SystemExit(
                     f"Please commit your changes and delete the {template_yaml_path} file. Then run the sync command again."
@@ -120,7 +120,7 @@ def __init__(
                 requests.auth.HTTPBasicAuth(self.gh_username, os.environ["GITHUB_AUTH_TOKEN"])
             )
 
-    def sync(self):
+    def sync(self) -> None:
         """Find workflow attributes, create a new template pipeline on TEMPLATE"""
 
         # Clear requests_cache so that we don't get stale API responses
@@ -271,7 +271,7 @@ def make_template_pipeline(self):
 
             self.config_yml.template.force = True
             with open(self.config_yml_path, "w") as config_path:
-                yaml.safe_dump(self.config_yml.model_dump(), config_path)
+                yaml.safe_dump(self.config_yml.model_dump(exclude_none=True), config_path)
 
         try:
             pipeline_create_obj = nf_core.pipelines.create.create.PipelineCreate(
@@ -291,7 +291,7 @@ def make_template_pipeline(self):
                 self.config_yml.template.outdir = "."
                 # Update nf-core version
                 self.config_yml.nf_core_version = nf_core.__version__
-                dump_yaml_with_prettier(self.config_yml_path, self.config_yml.model_dump())
+                dump_yaml_with_prettier(self.config_yml_path, self.config_yml.model_dump(exclude_none=True))
 
         except Exception as err:
             # Reset to where you were to prevent git getting messed up.
@@ -416,12 +416,8 @@ def close_open_template_merge_prs(self):
         list_prs_url = f"https://api.github.com/repos/{self.gh_repo}/pulls"
         with self.gh_api.cache_disabled():
             list_prs_request = self.gh_api.get(list_prs_url)
-        try:
-            list_prs_json = json.loads(list_prs_request.content)
-            list_prs_pp = json.dumps(list_prs_json, indent=4)
-        except Exception:
-            list_prs_json = list_prs_request.content
-            list_prs_pp = list_prs_request.content
+
+        list_prs_json, list_prs_pp = self._parse_json_response(list_prs_request)
 
         log.debug(f"GitHub API listing existing PRs:\n{list_prs_url}\n{list_prs_pp}")
         if list_prs_request.status_code != 200:
@@ -462,12 +458,8 @@ def close_open_pr(self, pr) -> bool:
         # Update the PR status to be closed
         with self.gh_api.cache_disabled():
             pr_request = self.gh_api.patch(url=pr["url"], data=json.dumps({"state": "closed"}))
-        try:
-            pr_request_json = json.loads(pr_request.content)
-            pr_request_pp = json.dumps(pr_request_json, indent=4)
-        except Exception:
-            pr_request_json = pr_request.content
-            pr_request_pp = pr_request.content
+
+        pr_request_json, pr_request_pp = self._parse_json_response(pr_request)
 
         # PR update worked
         if pr_request.status_code == 200:
@@ -481,6 +473,22 @@ def close_open_pr(self, pr) -> bool:
             log.warning(f"Could not close PR ('{pr_request.status_code}'):\n{pr['url']}\n{pr_request_pp}")
             return False
 
+    @staticmethod
+    def _parse_json_response(response) -> Tuple[Any, str]:
+        """Helper method to parse JSON response and create pretty-printed string.
+
+        Args:
+            response: requests.Response object
+
+        Returns:
+            Tuple of (parsed_json, pretty_printed_str)
+        """
+        try:
+            json_data = json.loads(response.content)
+            return json_data, json.dumps(json_data, indent=4)
+        except Exception:
+            return response.content, str(response.content)
+
     def reset_target_dir(self):
         """
         Reset the target pipeline directory. Check out the original branch.