--- a/env/lib/python3.7/site-packages/planemo/lint.py	Thu May 14 16:47:39 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,178 +0,0 @@
-"""Utilities to help linting various targets."""
-from __future__ import absolute_import
-
-import os
-
-import requests
-from galaxy.tool_util.lint import LintContext
-from six.moves.urllib.request import urlopen
-
-import planemo.linters.biocontainer_registered
-import planemo.linters.conda_requirements
-import planemo.linters.doi
-import planemo.linters.urls
-import planemo.linters.xsd
-from planemo.io import error
-from planemo.shed import find_urls_for_xml
-from planemo.xml import validation
-
-
-def build_lint_args(ctx, **kwds):
-    """Handle common report, error, and skip linting arguments."""
-    report_level = kwds.get("report_level", "all")
-    fail_level = kwds.get("fail_level", "warn")
-    skip = kwds.get("skip", None)
-    if skip is None:
-        skip = ctx.global_config.get("lint_skip", "")
-        if isinstance(skip, list):
-            skip = ",".join(skip)
-
-    skip_types = [s.strip() for s in skip.split(",")]
-    lint_args = dict(
-        level=report_level,
-        fail_level=fail_level,
-        extra_modules=_lint_extra_modules(**kwds),
-        skip_types=skip_types,
-    )
-    return lint_args
-
-
-# TODO: Move this back to tool_lint.
-def _lint_extra_modules(**kwds):
-    linters = []
-    if kwds.get("xsd", True):
-        linters.append(planemo.linters.xsd)
-
-    if kwds.get("doi", False):
-        linters.append(planemo.linters.doi)
-
-    if kwds.get("urls", False):
-        linters.append(planemo.linters.urls)
-
-    if kwds.get("conda_requirements", False):
-        linters.append(planemo.linters.conda_requirements)
-
-    if kwds.get("biocontainer", False):
-        linters.append(planemo.linters.biocontainer_registered)
-
-    return linters
-
-
-def setup_lint(ctx, **kwds):
-    """Setup lint_args and lint_ctx to begin linting a target."""
-    lint_args = build_lint_args(ctx, **kwds)
-    lint_ctx = LintContext(lint_args["level"])
-    return lint_args, lint_ctx
-
-
-def handle_lint_complete(lint_ctx, lint_args, failed=False):
-    """Complete linting of a target and decide exit code."""
-    if not failed:
-        failed = lint_ctx.failed(lint_args["fail_level"])
-    if failed:
-        error("Failed linting")
-    return 1 if failed else 0
-
-
-def lint_dois(tool_xml, lint_ctx):
-    """Find referenced DOIs and check they have valid with https://doi.org."""
-    dois = find_dois_for_xml(tool_xml)
-    for publication in dois:
-        is_doi(publication, lint_ctx)
-
-
-def find_dois_for_xml(tool_xml):
-    dois = []
-    for element in tool_xml.getroot().findall("citations"):
-        for citation in list(element):
-            if citation.tag == 'citation' and citation.attrib.get('type', '') == 'doi':
-                dois.append(citation.text)
-    return dois
-
-
-def is_doi(publication_id, lint_ctx):
-    """Check if dx.doi knows about the ``publication_id``."""
-    base_url = "https://doi.org"
-    if publication_id is None:
-        lint_ctx.error('Empty DOI citation')
-        return
-    publication_id = publication_id.strip()
-    doiless_publication_id = publication_id.split("doi:", 1)[-1]
-    if not doiless_publication_id:
-        lint_ctx.error('Empty DOI citation')
-        return
-    url = "%s/%s" % (base_url, doiless_publication_id)
-    r = requests.get(url)
-    if r.status_code == 200:
-        if publication_id != doiless_publication_id:
-            lint_ctx.error("%s is valid, but Galaxy expects DOI without 'doi:' prefix" % publication_id)
-        else:
-            lint_ctx.info("%s is a valid DOI" % publication_id)
-    elif r.status_code == 404:
-        lint_ctx.error("%s is not a valid DOI" % publication_id)
-    else:
-        lint_ctx.warn("dx.doi returned unexpected status code %d" % r.status_code)
-
-
-def lint_xsd(lint_ctx, schema_path, path):
-    """Lint XML at specified path with supplied schema."""
-    name = lint_ctx.object_name or os.path.basename(path)
-    validator = validation.get_validator(require=True)
-    validation_result = validator.validate(schema_path, path)
-    if not validation_result.passed:
-        msg = "Invalid XML found in file: %s. Errors [%s]"
-        msg = msg % (name, validation_result.output)
-        lint_ctx.error(msg)
-    else:
-        lint_ctx.info("File validates against XML schema.")
-
-
-def lint_urls(root, lint_ctx):
-    """Find referenced URLs and verify they are valid."""
-    urls, docs = find_urls_for_xml(root)
-
-    # This is from Google Chome on macOS, current at time of writing:
-    BROWSER_USER_AGENT = "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_12_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.75 Safari/537.36"
-
-    def validate_url(url, lint_ctx, user_agent=None):
-        is_valid = True
-        if url.startswith('http://') or url.startswith('https://'):
-            if user_agent:
-                headers = {"User-Agent": user_agent, 'Accept': '*/*'}
-            else:
-                headers = None
-            r = None
-            try:
-                r = requests.get(url, headers=headers, stream=True)
-                r.raise_for_status()
-                next(r.iter_content(1000))
-            except Exception as e:
-                if r and r.status_code == 429:
-                    # too many requests
-                    pass
-                else:
-                    is_valid = False
-                    lint_ctx.error("Error '%s' accessing %s" % (e, url))
-        else:
-            try:
-                with urlopen(url) as handle:
-                    handle.read(100)
-            except Exception as e:
-                is_valid = False
-                lint_ctx.error("Error '%s' accessing %s" % (e, url))
-        if is_valid:
-            lint_ctx.info("URL OK %s" % url)
-
-    for url in urls:
-        validate_url(url, lint_ctx)
-    for url in docs:
-        validate_url(url, lint_ctx, BROWSER_USER_AGENT)
-
-
-__all__ = (
-    "build_lint_args",
-    "handle_lint_complete",
-    "lint_dois",
-    "lint_urls",
-    "lint_xsd",
-)