lint¶

Recipe Linter

Writing additional checks¶

Lint checks are defined in bioconda_utils.lint.checks as subclasses of LintCheck. It might be easiest to have a look at that module and the already existing checks and go from there.

Briefly, each class becomes a check by:

The class name becomes the name of the check in the documentation and when skipping lints. The convention is to use lower case separated by underscore.
The docstring is used to describe the check on the command line, on Github when the check fails and in the documentation.

The first line is considered a title or one line summary used where a brief description is needed. The remainder is a long desription and should include brief help on how to fix the detected issue.
The class property severity defaults to ERROR but can be set to INFO or WARNING for informative checks that should not cause linting to fail.
The class property requires may contain a list of other check classes that are required to have passed before this check is executed. Use this to avoid duplicate errors presented, or to ensure that asumptions made by your check are met by the recipe.
Each class is instantiated once per linting run. Do slow preparation work in the constructor. E.g. the recipe_is_blacklisted check loads and parses the blacklist here.
As each recipe is linted, your check will get called on three functions: check_recipe, check_deps and check_source.

The first is simply passed the Recipe object, which you can use to inspect the recipe in question. The latter two are for convenience and performance. The check_deps call receives a mapping of all dependencies mentioned in the recipe to a list of locations in which the dependency occurred. E.g.:
```
{'setuptools': ['requirements/run',
                'outputs/0/requirements/run']}
```
The check_sources is called for each source listed in the recipe, whether source: is a dict or a source, eliminating the need to repeat handling of these two cases in each check. The value source passed is a dictionary of the source, the value section a path to the source section.
When a check encounters an issue, it should use self.message() to record the issue. The message is commonly modified with a path in the meta data to point to the part of the meta.yaml that lead to the error. This will be used to position annotations on github.

If a check never calls self.message(), it is assumed to have passed (=no errors generated).

You can also provide an alternate filename (fname) and/or specify the line number directly (line).

Module Autodocs¶

Environment Variables

LINT_SKIP¶

If set, will be parsed instead of the most recent commit. To skip checks for specific recipes, add strings of the following form:

[lint skip <check_name> for <recipe_name>]

`check_build_help`	Build tool usage
`check_completeness`	Completeness
`check_deprecation`	Deprecated packages and syntax
`check_noarch`	Use of `noarch` and `skip`
`check_policy`	Policy compliance
`check_repo`	Repository checks
`check_syntax`	Syntax checks

Functions

get_checks()

Loads and returns the available lint checks

Classes

`LintCheck`(_linter)	Base class for lint checks
`LintCheckMeta`	Meta class for lint checks
`LintMessage`	Message issued by LintChecks
`Linter`(config, recipe_folder[, exclude, nocatch])	Lint executor
`Severity`	Severities for lint checks
`conda_render_failure`(_linter)	The recipe was not understood by conda-build
`duplicate_key_in_meta_yaml`(_linter)	The recipe meta.yaml contains a duplicate key
`empty_meta_yaml`(_linter)	The recipe has an empty meta.yaml!?
`jinja_render_failure`(_linter)	The recipe could not be rendered by Jinja2
`linter_failure`(_linter)	An unexpected exception was raised during linting
`missing_build`(_linter)	The recipe is missing a build section.
`missing_meta_yaml`(_linter)	The recipe is missing a meta.yaml file
`missing_version_or_name`(_linter)	The recipe is missing name and/or version
`unknown_check`(_linter)	Something went wrong inside the linter
`unknown_selector`(_linter)	The recipe failed to parse due to selector lines

Documentation

class bioconda_utils.lint.LintCheck(_linter)[source]¶

Bases: object

Base class for lint checks

check_deps(deps)[source]¶

Execute check on recipe dependencies

Example format for deps:

{
  'setuptools': ['requirements/run',
                 'outputs/0/requirements/run/1'],
  'compiler_cxx': ['requirements/build/0']
}

You can use the values in the list directly as section parameter to self.message().

Parameters: deps (Dict[str, List[str]]) – Dictionary mapping requirements occurring in the recipe to their locations within the recipe.
Return type: None

check_recipe(recipe)[source]¶

Execute check on recipe

Override this method in subclasses, using self.message() to issue LintMessage as failures are encountered.

Parameters: recipe (Recipe) – The recipe under test.
Return type: None

check_source(source, section)[source]¶

Execute check on each source

Parameters

source (Dict[~KT, ~VT]) – Dictionary containing the source section
section (str) – Path to the section. Can be source or source/0 (1,2,3…).

Return type

None

fix(message, data)[source]¶

Attempt to fix the problem

Return type: LintMessage

classmethod make_message(recipe, section=None, fname=None, line=None, canfix=False)[source]¶

Create a LintMessage

Parameters

section (Optional[str]) – If specified, a lint location within the recipe meta.yaml pointing to this section/subsection will be added to the message
fname (Optional[str]) – If specified, the message will apply to this file, rather than the recipe meta.yaml
line – If specified, sets the line number for the message directly

Return type

LintMessage

message(section=None, fname=None, line=None, data=None)[source]¶

Add a message to the lint results

Also calls fix if we are supposed to be fixing.

Parameters

section (Optional[str]) – If specified, a lint location within the recipe meta.yaml pointing to this section/subsection will be added to the message
fname (Optional[str]) – If specified, the message will apply to this file, rather than the recipe meta.yaml
line (Optional[int]) – If specified, sets the line number for the message directly
data (Optional[Any]) – Data to be passed to fix. If check can fix, set this to something other than None.

Return type

None

messages = None¶: Messages collected running tests

recipe = None¶: Recipe currently being checked

requires = []¶: Checks that must have passed for this check to be executed.

run(recipe, fix=False)[source]¶

Run the check on a recipe. Called by Linter

Parameters

recipe (Recipe) – The recipe to be linted
fix (bool) – Whether to attempt to fix the recipe

Return type

List[LintMessage]

severity = 30¶: Severity of this check. Only ERROR causes a lint failure.

try_fix = None¶: Whether we are supposed to fix

class bioconda_utils.lint.LintCheckMeta[source]¶

Bases: abc.ABCMeta

Meta class for lint checks

Handles registry

Creates LintCheck classes

class bioconda_utils.lint.LintMessage[source]¶

Bases: tuple

Message issued by LintChecks

Create new instance of LintMessage(recipe, check, severity, title, body, start_line, end_line, fname, canfix)

property body¶: Message body to be presented to user

property canfix¶: Whether the problem can be auto fixed

property check¶: The check issuing the message

property end_line¶: Line at which problem ends

property fname¶: Name of file in which error was found

get_level()[source]¶: Return level string as required by github

property recipe¶: The recipe this message refers to

property severity¶: The severity of the message

property start_line¶: Line at which problem begins

property title¶: Message title to be presented to user

class bioconda_utils.lint.Linter(config, recipe_folder, exclude=None, nocatch=False)[source]¶

Bases: object

Lint executor

Parameters

config (Dict[~KT, ~VT]) – Configuration dict as provided by utils.load_config().
recipe_folder (str) – Folder which recipes are located.
exclude (Optional[List[str]]) – List of function names in registry to skip globally. When running on CI, this will be merged with anything else detected from the commit message or LINT_SKIP environment variable using the special string “[skip lint <function name> for <recipe name>]”. While those other mechanisms define skipping on a recipe-specific basis, this argument can be used to skip tests for all recipes. Use sparingly.
nocatch (bool) – Don’t catch exceptions in lint checks and turn them into linter_error lint messages. Used by tests.

clear_messages()[source]¶: Clears the lint messages stored in linter

get_blacklist()[source]¶

Loads the blacklist as per linter configuration

Return type: Set[str]

get_messages()[source]¶

Returns the lint messages collected during linting

Return type: List[LintMessage]

lint(recipe_names, fix=False)[source]¶

Run linter on multiple recipes

Lint messages are collected in the linter. They can be retrieved with get_messages and the list cleared with clear_messages.

Parameters

recipe_names (List[str]) – List of names of recipes to lint
fix (bool) – Whether checks should attempt to fix detected issues

Return type

bool

Returns

True if issues with errors were found

lint_one(recipe_name, fix=False)[source]¶

Run the linter on a single recipe

Parameters

recipe_name (str) – Mames of recipe to lint
fix (bool) – Whether checks should attempt to fix detected issues

Return type

List[LintMessage]

Returns

List of collected messages

load_skips()[source]¶

Parses lint skips

If LINT_SKIP or the most recent commit contains [ lint skip <check_name> for <recipe_name> ], that particular check will be skipped.

class bioconda_utils.lint.Severity[source]¶

Bases: enum.IntEnum

Severities for lint checks

ERROR = 30¶: Checks of this severity must be fixed and will fail a recipe.

INFO = 10¶: Checks of this severity are purely informational

WARNING = 20¶: Checks of this severity indicate possible problems

class bioconda_utils.lint.conda_render_failure(_linter)[source]¶

Bases: bioconda_utils.lint.LintCheck

The recipe was not understood by conda-build

Please request help from @bioconda/core.

class bioconda_utils.lint.duplicate_key_in_meta_yaml(_linter)[source]¶

Bases: bioconda_utils.lint.LintCheck

The recipe meta.yaml contains a duplicate key

This is invalid YAML, as it’s unclear what the structure should become. Please merge the two offending sections

class bioconda_utils.lint.empty_meta_yaml(_linter)[source]¶

Bases: bioconda_utils.lint.LintCheck

The recipe has an empty meta.yaml!?

Please check if you forgot to commit its contents.

bioconda_utils.lint.get_checks()[source]¶: Loads and returns the available lint checks

class bioconda_utils.lint.jinja_render_failure(_linter)[source]¶

Bases: bioconda_utils.lint.LintCheck

The recipe could not be rendered by Jinja2

Check if you are missing quotes or curly braces in Jinja2 template expressions. (The parts with {{ something }} or {% set var="value" %}).

class bioconda_utils.lint.linter_failure(_linter)[source]¶

Bases: bioconda_utils.lint.LintCheck

An unexpected exception was raised during linting

Please file an issue at the bioconda-utils repo

class bioconda_utils.lint.missing_build(_linter)[source]¶

Bases: bioconda_utils.lint.LintCheck

The recipe is missing a build section.

Please add:

build:
  number: 0

class bioconda_utils.lint.missing_meta_yaml(_linter)[source]¶

Bases: bioconda_utils.lint.LintCheck

The recipe is missing a meta.yaml file

Most commonly, this is because the file was accidentally named meta.yml. If so, rename it to meta.yaml.

class bioconda_utils.lint.missing_version_or_name(_linter)[source]¶

Bases: bioconda_utils.lint.LintCheck

The recipe is missing name and/or version

Please make sure the recipe has at least:

package:
  name: package_name
  version: 0.12.34

bioconda_utils.lint.recipe_error_to_lint_check = {<class 'bioconda_utils.recipe.DuplicateKey'>: <class 'bioconda_utils.lint.duplicate_key_in_meta_yaml'>, <class 'bioconda_utils.recipe.MissingKey'>: <class 'bioconda_utils.lint.missing_version_or_name'>, <class 'bioconda_utils.recipe.EmptyRecipe'>: <class 'bioconda_utils.lint.empty_meta_yaml'>, <class 'bioconda_utils.recipe.MissingBuild'>: <class 'bioconda_utils.lint.missing_build'>, <class 'bioconda_utils.recipe.HasSelector'>: <class 'bioconda_utils.lint.unknown_selector'>, <class 'bioconda_utils.recipe.MissingMetaYaml'>: <class 'bioconda_utils.lint.missing_meta_yaml'>, <class 'bioconda_utils.recipe.CondaRenderFailure'>: <class 'bioconda_utils.lint.conda_render_failure'>, <class 'bioconda_utils.recipe.RenderFailure'>: <class 'bioconda_utils.lint.jinja_render_failure'>}¶: Maps _recipe.RecipeError to LintCheck

class bioconda_utils.lint.unknown_check(_linter)[source]¶

Bases: bioconda_utils.lint.LintCheck

Something went wrong inside the linter

Please request help from @bioconda/core

class bioconda_utils.lint.unknown_selector(_linter)[source]¶

Bases: bioconda_utils.lint.LintCheck

The recipe failed to parse due to selector lines

Please request help from @bioconda/core.