diff --git a/cwl_utils/parser/cwl_v1_0.py b/cwl_utils/parser/cwl_v1_0.py index 7f3110dd..312c87f7 100644 --- a/cwl_utils/parser/cwl_v1_0.py +++ b/cwl_utils/parser/cwl_v1_0.py @@ -4035,7 +4035,7 @@ class Directory(Saveable): the same Directory. When executing a CommandLineTool, Directories must be recursively staged - first and have local values of `path` assigend. + first and have local values of `path` assigned. Directory objects in CommandLineTool output must provide either a `location` URI or a `path` property in the context of the tool execution @@ -16266,7 +16266,7 @@ class ShellCommandRequirement(ProcessRequirement): Modify the behavior of CommandLineTool to generate a single string containing a shell command line. Each item in the argument list must be joined into a string separated by single spaces and quoted to prevent - intepretation by the shell, unless `CommandLineBinding` for that argument + interpretation by the shell, unless `CommandLineBinding` for that argument contains `shellQuote: false`. If `shellQuote: false` is specified, the argument is joined into the command string without quoting, which allows the use of shell metacharacters such as `|` for pipes. @@ -20275,7 +20275,7 @@ class Workflow(Process): The `source` field expresses the dependency of one parameter on another such that when a value is associated with the parameter specified by `source`, that value is propagated to the destination parameter. When all - data links inbound to a given step are fufilled, the step is ready to + data links inbound to a given step are fulfilled, the step is ready to execute. ## Workflow success and failure diff --git a/cwl_utils/parser/cwl_v1_1.py b/cwl_utils/parser/cwl_v1_1.py index 744cba7f..a6a833f9 100644 --- a/cwl_utils/parser/cwl_v1_1.py +++ b/cwl_utils/parser/cwl_v1_1.py @@ -4035,7 +4035,7 @@ class Directory(Saveable): the same Directory. When executing a CommandLineTool, Directories must be recursively staged - first and have local values of `path` assigend. + first and have local values of `path` assigned. Directory objects in CommandLineTool output must provide either a `location` URI or a `path` property in the context of the tool execution @@ -17590,7 +17590,7 @@ class ShellCommandRequirement(ProcessRequirement): Modify the behavior of CommandLineTool to generate a single string containing a shell command line. Each item in the argument list must be joined into a string separated by single spaces and quoted to prevent - intepretation by the shell, unless `CommandLineBinding` for that argument + interpretation by the shell, unless `CommandLineBinding` for that argument contains `shellQuote: false`. If `shellQuote: false` is specified, the argument is joined into the command string without quoting, which allows the use of shell metacharacters such as `|` for pipes. @@ -18331,7 +18331,7 @@ class WorkReuse(ProcessRequirement): For implementations that support reusing output from past work (on the assumption that same code and same input produce same results), control whether to enable or disable the reuse behavior - for a particular tool or step (to accomodate situations where that + for a particular tool or step (to accommodate situations where that assumption is incorrect). A reused step is not executed but instead returns the same output as the original execution. @@ -18529,7 +18529,7 @@ class NetworkAccess(ProcessRequirement): may apply their own security policies to restrict what is accessible by the tool. - Enabling network access does not imply a publically routable IP + Enabling network access does not imply a publicly routable IP address or the ability to accept inbound connections. """ @@ -18727,7 +18727,7 @@ class InplaceUpdateRequirement(ProcessRequirement): read-only in every step. Workflow steps which modify a file must produce the modified file - as output. Downstream steps which futher process the file must + as output. Downstream steps which further process the file must use the output of previous steps, and not refer to a common input (this is necessary for both ordering and correctness). @@ -21672,7 +21672,7 @@ class WorkflowStepInput(IdentifierRequired, Sink, LoadContents, Labeled): workflow inputs, or the outputs of other workflows steps) with the input parameters of the process specified by the `run` field. Only input parameters declared by the target process will be passed through at runtime to the process - though additonal parameters may be specified (for use within `valueFrom` + though additional parameters may be specified (for use within `valueFrom` expressions for instance) - unconnected or unused parameters do not represent an error condition. @@ -23210,7 +23210,7 @@ class Workflow(Process): The `source` field expresses the dependency of one parameter on another such that when a value is associated with the parameter specified by `source`, that value is propagated to the destination parameter. When all - data links inbound to a given step are fufilled, the step is ready to + data links inbound to a given step are fulfilled, the step is ready to execute. ## Workflow success and failure diff --git a/cwl_utils/templates/WorkflowInputJsonSchemaTemplate.md b/cwl_utils/templates/WorkflowInputJsonSchemaTemplate.md index 74e7db0b..0554fed6 100644 --- a/cwl_utils/templates/WorkflowInputJsonSchemaTemplate.md +++ b/cwl_utils/templates/WorkflowInputJsonSchemaTemplate.md @@ -717,7 +717,7 @@ def add_cwl_metadata_to_schema(schema_dict: Dict) -> Dict: # Always do a deepcopy on the input schema_dict = deepcopy(schema_dict) - # Assert defintions + # Assert definitions assert_definitions_key(schema_dict) # Add in the CWL metadata to the definitions @@ -1059,7 +1059,7 @@ def fix_hints(schema_dict, definition_key): def add_file_and_directory_to_schema(schema_dict: Dict) -> Dict: """ - Add file and directory defintions to schema + Add file and directory definitions to schema :param schema_dict: :return: """ diff --git a/cwl_utils/testdata/EDAM_subset.owl b/cwl_utils/testdata/EDAM_subset.owl index 8678f5b8..a56e2d90 100644 --- a/cwl_utils/testdata/EDAM_subset.owl +++ b/cwl_utils/testdata/EDAM_subset.owl @@ -39,7 +39,7 @@ data "EDAM types of data" relations "EDAM relations" edam "EDAM" - EDAM editors: Jon Ison, Matus Kalas, and Herve Menager. Contributors: Inge Jonassen, Dan Bolser, Hamish McWilliam, Mahmut Uludag, James Malone, Rodrigo Lopez, Steve Pettifer, and Peter Rice. Contibutions from these projects: EMBRACE, ELIXIR, and BioMedBridges (EU); EMBOSS (BBSRC, UK); eSysbio, FUGE Bioinformatics Platform, and ELIXIR.NO/Norwegian Bioinformatics Platform (Research Council of Norway). See http://edamontology.org for documentation and licence. + EDAM editors: Jon Ison, Matus Kalas, and Herve Menager. Contributors: Inge Jonassen, Dan Bolser, Hamish McWilliam, Mahmut Uludag, James Malone, Rodrigo Lopez, Steve Pettifer, and Peter Rice. Contributions from these projects: EMBRACE, ELIXIR, and BioMedBridges (EU); EMBOSS (BBSRC, UK); eSysbio, FUGE Bioinformatics Platform, and ELIXIR.NO/Norwegian Bioinformatics Platform (Research Council of Norway). See http://edamontology.org for documentation and licence. operations "EDAM operations" EDAM http://edamontology.org/ "EDAM relations and concept properties" application/rdf+xml @@ -97,7 +97,7 @@ Example - 'Example' concept property ('example' metadat tag) lists examples of valid values of types of identifiers (accessions). Applicable to some other types of data, too. + 'Example' concept property ('example' metadata tag) lists examples of valid values of types of identifiers (accessions). Applicable to some other types of data, too. true concept_properties diff --git a/cwl_utils/testdata/revsort-run-1-packed.cwl b/cwl_utils/testdata/revsort-run-1-packed.cwl index a8d96664..3ec4e9ce 100755 --- a/cwl_utils/testdata/revsort-run-1-packed.cwl +++ b/cwl_utils/testdata/revsort-run-1-packed.cwl @@ -24,7 +24,7 @@ { "type": "boolean", "default": true, - "doc": "If true, reverse (decending) sort", + "doc": "If true, reverse (descending) sort", "id": "#main/reverse_sort" } ], diff --git a/lint-requirements.txt b/lint-requirements.txt index 1800b69b..fd859c96 100644 --- a/lint-requirements.txt +++ b/lint-requirements.txt @@ -1,4 +1,4 @@ -flake8-bugbear < 25.12 black == 25.* -codespell +codespell == 2.4.1 +flake8-bugbear < 25.12 isort >= 5 diff --git a/pyproject.toml b/pyproject.toml index 133b5929..c8450681 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -142,3 +142,6 @@ ignore = [ [tool.bandit] exclude_dirs = ["cwl_utils/tests"] + +[tool.codespell] +ignore-words-list = "afile" diff --git a/tox.ini b/tox.ini index 7807d810..d7b7efc1 100644 --- a/tox.ini +++ b/tox.ini @@ -41,8 +41,7 @@ commands = py3{10,11,12,13,14}-unit: python -m pip install -U pip setuptools wheel py3{10,11,12,13,14}-unit: make coverage-report coverage.xml PYTEST_EXTRA={posargs} py3{10,11,12,13,14}-bandit: bandit --configfile pyproject.toml --recursive cwl_utils - py3{10,11,12,13,14}-lint: make flake8 - py3{10,11,12,13,14}-lint: make format-check + py3{10,11,12,13,14}-lint: make flake8 format-check codespell-check py3{10,11,12,13,14}-mypy: make mypy allowlist_externals =