pipeline_todos.py

import fnmatch
import logging
import os
from pathlib import Path

log = logging.getLogger(__name__)


def pipeline_todos(self, root_dir=None):
    """Check for nf-core *TODO* lines.

    The nf-core workflow template contains a number of comment lines to help developers
    of new pipelines know where they need to edit files and add content.
    They typically have the following format:

    .. code-block:: groovy

        // TODO nf-core: Make some kind of change to the workflow here

    ..or in markdown:

    .. code-block:: html

        <!-- TODO nf-core: Add some detail to the docs here -->

    This lint test runs through all files in the pipeline and searches for these lines.
    If any are found they will throw a warning.

    .. tip:: Note that many GUI code editors have plugins to list all instances of *TODO*
              in a given project directory. This is a very quick and convenient way to get
              started on your pipeline!
    """
    passed = []
    warned = []
    file_paths = []

    # Pipelines don't provide a path, so use the workflow path.
    # Modules run this function twice and provide a string path
    if root_dir is None:
        root_dir = self.wf_path

    # Ignore ro-crate-metadata.json to avoid warnings when TODOs are not deleted.
    ignore = [".git", "ro-crate-metadata.json"]
    if Path(root_dir, ".gitignore").is_file():
        with open(Path(root_dir, ".gitignore"), encoding="latin1") as fh:
            for line in fh:
                ignore.append(Path(line.strip().rstrip("/")).name)
            # add ignore to the ro crate
    for root, dirs, files in os.walk(root_dir, topdown=True):
        # Ignore files
        for i_base in ignore:
            i = str(Path(root, i_base))
            dirs[:] = [d for d in dirs if not fnmatch.fnmatch(str(Path(root, d)), i)]
            files[:] = [f for f in files if not fnmatch.fnmatch(str(Path(root, f)), i)]
        for fname in files:
            try:
                with open(Path(root, fname), encoding="latin1") as fh:
                    for line in fh:
                        if "TODO nf-core" in line:
                            line = (
                                line.replace("<!--", "")
                                .replace("-->", "")
                                .replace("# TODO nf-core: ", "")
                                .replace("// TODO nf-core: ", "")
                                .replace("TODO nf-core: ", "")
                                .strip()
                            )
                            warned.append(f"TODO string in `{fname}`: _{line}_")
                            file_paths.append(Path(root, fname))
            except FileNotFoundError:
                log.debug(f"Could not open file {fname} in pipeline_todos lint test")

    if len(warned) == 0:
        passed.append("No TODO strings found")

    # HACK file paths are returned to allow usage of this function in modules/lint.py
    # Needs to be refactored!
    return {"passed": passed, "warned": warned, "file_paths": file_paths}