diff env/lib/python3.9/site-packages/planemo/conda_lint.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/planemo/conda_lint.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,209 @@
+"""Logic for linting conda recipes."""
+
+from __future__ import absolute_import
+
+from functools import wraps
+
+from galaxy.tool_util.deps.conda_compat import raw_metadata
+from galaxy.util import unicodify
+
+from planemo.conda_verify.recipe import (
+    check_build_number,
+    check_dir_content,
+    check_license_family,
+    check_name,
+    check_requirements,
+    check_source,
+    check_url,
+    check_version,
+    FIELDS,
+    get_field,
+    RecipeError,
+)
+from planemo.exit_codes import (
+    EXIT_CODE_GENERIC_FAILURE,
+    EXIT_CODE_OK,
+)
+from planemo.io import (
+    coalesce_return_codes,
+    find_matching_directories,
+    info,
+)
+from planemo.lint import (
+    handle_lint_complete,
+    setup_lint,
+)
+
+
+def lint_recipes_on_paths(ctx, paths, **kwds):
+    """Apply conda linting procedure to recipes on supplied paths."""
+    assert_tools = kwds.get("assert_recipes", True)
+    recursive = kwds.get("recursive", False)
+    exit_codes = []
+    for recipe_dir in yield_recipes_on_paths(ctx, paths, recursive):
+        if lint_conda_recipe(ctx, recipe_dir, **kwds) != 0:
+            exit_codes.append(EXIT_CODE_GENERIC_FAILURE)
+        else:
+            exit_codes.append(EXIT_CODE_OK)
+    return coalesce_return_codes(exit_codes, assert_at_least_one=assert_tools)
+
+
+def lint_conda_recipe(ctx, recipe_dir, **kwds):
+    info("Linting conda recipe %s" % recipe_dir)
+    lint_args, lint_ctx = setup_lint(ctx, **kwds)
+
+    def apply(f):
+        lint_ctx.lint(f.__name__, f, recipe_dir)
+
+    apply(lint_name)
+    apply(lint_version)
+    apply(lint_summary)
+    apply(lint_build_number)
+    apply(lint_directory_content)
+    apply(lint_license_family)
+    apply(lint_about_urls)
+    apply(lint_source)
+    apply(lint_fields)
+    apply(lint_requirements)
+
+    return handle_lint_complete(lint_ctx, lint_args)
+
+
+def wraps_recipe_error(is_error=True):
+
+    def outer_wrapper(f):
+
+        @wraps(f)
+        def wrapper(recipe_dir, lint_ctx):
+            try:
+                f(recipe_dir, lint_ctx)
+            except RecipeError as e:
+                if is_error:
+                    lint_ctx.error(unicodify(e))
+                else:
+                    lint_ctx.warn(unicodify(e))
+            except TypeError as e:  # Errors in recipe checking code from YAML.
+                lint_ctx.error(unicodify(e))
+
+        return wrapper
+
+    return outer_wrapper
+
+
+def lints_metadata(f):
+
+    @wraps(f)
+    def wrapper(recipe_dir, lint_ctx):
+        meta = raw_metadata(recipe_dir)
+        f(meta, lint_ctx)
+
+    return wrapper
+
+
+@wraps_recipe_error(is_error=False)
+def lint_directory_content(recipe_dir, lint_ctx):
+    check_dir_content(recipe_dir)
+    lint_ctx.info("Directory content seems okay.")
+
+
+@lints_metadata
+@wraps_recipe_error(is_error=False)
+def lint_license_family(meta, lint_ctx):
+    check_license_family(meta)
+    lint_ctx.info("License from vaild license family.")
+
+
+@lints_metadata
+def lint_summary(meta, lint_ctx):
+    summary = get_field(meta, 'about/summary')
+
+    if not summary:
+        lint_ctx.warn("No summary supplied in about metadata.")
+
+    if summary and len(summary) > 80:
+        msg = "summary exceeds 80 characters"
+        lint_ctx.warn(msg)
+
+
+@lints_metadata
+@wraps_recipe_error(is_error=False)
+def lint_about_urls(meta, lint_ctx):
+    for field in ('about/home', 'about/dev_url', 'about/doc_url',
+                  'about/license_url'):
+        url = get_field(meta, field)
+        if url:
+            check_url(url)
+    lint_ctx.info("About urls (if present) are valid")
+
+
+@lints_metadata
+@wraps_recipe_error(is_error=True)
+def lint_source(meta, lint_ctx):
+    check_source(meta)
+    lint_ctx.info("Source (if present) is valid")
+
+
+@lints_metadata
+@wraps_recipe_error(is_error=True)
+def lint_build_number(meta, lint_ctx):
+    build_number = get_field(meta, 'build/number', 0)
+    check_build_number(build_number)
+    lint_ctx.info("Valid build number [%s]" % build_number)
+
+
+@lints_metadata
+@wraps_recipe_error(is_error=True)
+def lint_version(meta, lint_ctx):
+    version = get_field(meta, 'package/version')
+    check_version(version)
+    lint_ctx.info("Valid version number [%s]" % version)
+
+
+@lints_metadata
+@wraps_recipe_error(is_error=True)
+def lint_name(meta, lint_ctx):
+    name = get_field(meta, 'package/name')
+    check_name(name)
+    lint_ctx.info("Valid recipe name [%s]" % name)
+
+
+@lints_metadata
+@wraps_recipe_error(is_error=False)
+def lint_fields(meta, lint_ctx):
+    # Taken from validate_meta
+    for section in meta:
+        if section not in FIELDS:
+            raise RecipeError("Unknown section: %s" % section)
+        submeta = meta.get(section)
+        if submeta is None:
+            submeta = {}
+        for key in submeta:
+            # Next two lines added for planemo since we don't do the
+            # select lines thing.
+            if key == "skip":
+                continue
+
+            if key not in FIELDS[section]:
+                raise RecipeError("in section %r: unknown key %r" %
+                                  (section, key))
+
+
+@lints_metadata
+@wraps_recipe_error(is_error=False)
+def lint_requirements(meta, lint_ctx):
+    check_requirements(meta)
+    lint_ctx.info("Reference recipe files appear valid")
+
+
+def yield_recipes_on_paths(ctx, paths, recursive):
+    for path in paths:
+        recipe_dirs = find_matching_directories(
+            path, "meta.yaml", recursive=recursive
+        )
+        for recipe_dir in recipe_dirs:
+            yield recipe_dir
+
+
+__all__ = (
+    "lint_recipes_on_paths",
+)