diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml new file mode 100644 index 0000000..fdde68b --- /dev/null +++ b/.github/workflows/docs.yaml @@ -0,0 +1,31 @@ +name: docs +on: + push: + branches: + - conformance-1.2.1 + paths: + # Only rebuild website when docs have changed + - 'README.md' + - 'docs/**' + - 'mkdocs.yml' + - .github/** + +jobs: + deploy: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v2 + + - name: Install Conda environment from environment.yml + uses: mamba-org/provision-with-micromamba@main + with: + environment-file: docs/environment.yml + environment-name: env_docs + channels: conda-forge + channel-priority: flexible + + - name: Install project + run: | + /home/runner/micromamba-root/envs/env_docs/bin/python setup.py install + + - run: /home/runner/micromamba-root/envs/env_docs/bin/mkdocs gh-deploy --force diff --git a/docs/conformance/1.0/conformance.md b/docs/conformance/1.0/conformance.md new file mode 100644 index 0000000..cf15deb --- /dev/null +++ b/docs/conformance/1.0/conformance.md @@ -0,0 +1,30 @@ +## Conformance tests for CWL v1.0 for the latest release + +### Classes + +![test result](https://flat.badgen.net/https/raw.githubusercontent.com/Terradue/calrissian/conformance-1.2.1/conformance/badges/1.0.2/workflow.json?icon=commonwl) +![test result](https://flat.badgen.net/https/raw.githubusercontent.com/Terradue/calrissian/conformance-1.2.1/conformance/badges/1.0.2/command_line_tool.json?icon=commonwl) +![test result](https://flat.badgen.net/https/raw.githubusercontent.com/Terradue/calrissian/conformance-1.2.1/conformance/badges/1.0.2/expression_tool.json?icon=commonwl) + +### Required features + +![test result](https://flat.badgen.net/https/raw.githubusercontent.com/Terradue/calrissian/conformance-1.2.1/conformance/badges/1.0.2/required.json?icon=commonwl) + +### Optional features + +![test result](https://flat.badgen.net/https/raw.githubusercontent.com/Terradue/calrissian/conformance-1.2.1/conformance/badges/1.0.2/docker.json?icon=commonwl) +![test result](https://flat.badgen.net/https/raw.githubusercontent.com/Terradue/calrissian/conformance-1.2.1/conformance/badges/1.0.2/env_var.json?icon=commonwl) +![test result](https://flat.badgen.net/https/raw.githubusercontent.com/Terradue/calrissian/conformance-1.2.1/conformance/badges/1.0.2/initial_work_dir.json?icon=commonwl) +![test result](https://flat.badgen.net/https/raw.githubusercontent.com/Terradue/calrissian/conformance-1.2.1/conformance/badges/1.0.2/inline_javascript.json?icon=commonwl) +![test result](https://flat.badgen.net/https/raw.githubusercontent.com/Terradue/calrissian/conformance-1.2.1/conformance/badges/1.0.2/multiple_input.json?icon=commonwl) +![test result](https://flat.badgen.net/https/raw.githubusercontent.com/Terradue/calrissian/conformance-1.2.1/conformance/badges/1.0.2/resource.json?icon=commonwl) +![test result](https://flat.badgen.net/https/raw.githubusercontent.com/Terradue/calrissian/conformance-1.2.1/conformance/badges/1.0.2/scatter.json?icon=commonwl) +![test result](https://flat.badgen.net/https/raw.githubusercontent.com/Terradue/calrissian/conformance-1.2.1/conformance/badges/1.0.2/schema_def.json?icon=commonwl) +![test result](https://flat.badgen.net/https/raw.githubusercontent.com/Terradue/calrissian/conformance-1.2.1/conformance/badges/1.0.2/shell_command.json?icon=commonwl) +![test result](https://flat.badgen.net/https/raw.githubusercontent.com/Terradue/calrissian/conformance-1.2.1/conformance/badges/1.0.2/step_input.json?icon=commonwl) +![test result](https://flat.badgen.net/https/raw.githubusercontent.com/Terradue/calrissian/conformance-1.2.1/conformance/badges/1.0.2/step_input_expression.json?icon=commonwl) +![test result](https://flat.badgen.net/https/raw.githubusercontent.com/Terradue/calrissian/conformance-1.2.1/conformance/badges/1.0.2/subworkflow.json?icon=commonwl) + +### Conformance output + +[log](../result-1.0.txt) \ No newline at end of file diff --git a/docs/conformance/1.0/result-1-0.txt b/docs/conformance/1.0/result-1-0.txt new file mode 100644 index 0000000..ecf04ce --- /dev/null +++ b/docs/conformance/1.0/result-1-0.txt @@ -0,0 +1,398 @@ +Test [1/197] cl_basic_generation: General test of command line generation + +Test [2/197] nested_prefixes_arrays: Test nested prefixes with arrays + +Test [3/197] nested_cl_bindings: Test nested command line bindings + +Test [4/197] cl_optional_inputs_missing: Test command line with optional input (missing) + +Test [5/197] cl_optional_bindings_provided: Test command line with optional input (provided) + +Test [6/197] initworkdir_expreng_requirements: Test InitialWorkDirRequirement ExpressionEngineRequirement.engineConfig feature + +Test [7/197] stdout_redirect_docker: Test command execution in Docker with stdout redirection + +Test [8/197] stdout_redirect_shortcut_docker: Test command execution in Docker with shortcut stdout redirection + +Test [9/197] stdout_redirect_mediumcut_docker: Test command execution in Docker with mediumcut stdout redirection + +Test [10/197] stderr_redirect: Test command line with stderr redirection + +Test [11/197] stderr_redirect_shortcut: Test command line with stderr redirection, brief syntax + +Test [12/197] stderr_redirect_mediumcut: Test command line with stderr redirection, named brief syntax + +Test [13/197] stdinout_redirect_docker: Test command execution in Docker with stdin and stdout redirection + +Test [14/197] expression_any: Test default usage of Any in expressions. + +Test [15/197] expression_any_null: Test explicitly passing null to Any type inputs with default values. + +Test [16/197] expression_any_string: Testing the string 'null' does not trip up an Any with a default value. + +Test [17/197] expression_any_nodefaultany: Test Any without defaults cannot be unspecified. + +Test [18/197] expression_any_null_nodefaultany: Test explicitly passing null to Any type without a default value. + +Test [19/197] expression_any_nullstring_nodefaultany: Testing the string 'null' does not trip up an Any without a default value. + +Test [20/197] any_outputSource_compatibility: Testing Any type compatibility in outputSource + +Test [21/197] stdinout_redirect: Test command execution in with stdin and stdout redirection + +Test [22/197] expression_parseint: Test ExpressionTool with Javascript engine + +Test [23/197] expression_outputEval: Test outputEval to transform output + +Test [24/197] wf_wc_parseInt: Test two step workflow with imported tools + +Test [25/197] wf_wc_expressiontool: Test two step workflow with inline tools + +Test [26/197] wf_wc_scatter: Test single step workflow with Scatter step + +Test [27/197] wf_wc_scatter_multiple_merge: Test single step workflow with Scatter step and two data links connected to same input, default merge behavior + +Test [28/197] wf_wc_scatter_multiple_nested: Test single step workflow with Scatter step and two data links connected to same input, nested merge behavior + +Test [29/197] wf_wc_scatter_multiple_flattened: Test single step workflow with Scatter step and two data links connected to same input, flattened merge behavior + +Test [30/197] wf_wc_nomultiple: Test that no MultipleInputFeatureRequirement is necessary when workflow step source is a single-item list + +Test [31/197] wf_input_default_missing: Test workflow with default value for input parameter (missing) + +Test [32/197] wf_input_default_provided: Test workflow with default value for input parameter (provided) + +Test [33/197] wf_default_tool_default: Test that workflow defaults override tool defaults + +Test [34/197] envvar_req: Test EnvVarRequirement + +Test [35/197] wf_scatter_single_param: Test workflow scatter with single scatter parameter + +Test [36/197] wf_scatter_two_nested_crossproduct: Test workflow scatter with two scatter parameters and nested_crossproduct join method + +Test [37/197] wf_scatter_two_flat_crossproduct: Test workflow scatter with two scatter parameters and flat_crossproduct join method + +Test [38/197] wf_scatter_two_dotproduct: Test workflow scatter with two scatter parameters and dotproduct join method + +Test [39/197] wf_scatter_emptylist: Test workflow scatter with single empty list parameter + +Test [40/197] wf_scatter_nested_crossproduct_secondempty: Test workflow scatter with two scatter parameters and nested_crossproduct join method with second list empty + +Test [41/197] wf_scatter_nested_crossproduct_firstempty: Test workflow scatter with two scatter parameters and nested_crossproduct join method with first list empty + +Test [42/197] wf_scatter_flat_crossproduct_oneempty: Test workflow scatter with two scatter parameters, one of which is empty and flat_crossproduct join method + +Test [43/197] wf_scatter_dotproduct_twoempty: Test workflow scatter with two empty scatter parameters and dotproduct join method + +Test [44/197] any_input_param: Test Any type input parameter + +Test [45/197] nested_workflow: Test nested workflow + +Test [46/197] requirement_priority: Test requirement priority + +Test [47/197] requirement_override_hints: Test requirements override hints + +Test [48/197] requirement_workflow_steps: Test requirements on workflow steps + +Test [49/197] step_input_default_value: Test default value on step input parameter + +Test [50/197] step_input_default_value_nosource: Test use default value on step input parameter with empty source + +Test [51/197] step_input_default_value_nullsource: Test use default value on step input parameter with null source + +Test [52/197] step_input_default_value_overriden: Test default value on step input parameter overridden by provided source + +Test [53/197] wf_simple: Test simple workflow + +Test [54/197] hints_unknown_ignored: Test unknown hints are ignored. + +Test [55/197] initial_workdir_secondary_files_expr: Test InitialWorkDirRequirement linking input files and capturing secondaryFiles on input and output. Also tests the use of a variety of parameter references and expressions in the secondaryFiles field. + +Test [56/197] rename: Test InitialWorkDirRequirement with expression in filename. + +Test [57/197] initial_workdir_trailingnl: Test if trailing newline is present in file entry in InitialWorkDir + +Test [58/197] inline_expressions: Test inline expressions + +Test [59/197] schemadef_req_tool_param: Test SchemaDefRequirement definition used in tool parameter + +Test [60/197] schemadef_req_wf_param: Test SchemaDefRequirement definition used in workflow parameter + +Test [61/197] param_evaluation_noexpr: Test parameter evaluation, no support for JS expressions + +Test [62/197] param_evaluation_expr: Test parameter evaluation, with support for JS expressions + +Test [63/197] metadata: Test metadata + +Test [64/197] format_checking: Test simple format checking. + +Test [65/197] format_checking_subclass: Test format checking against ontology using subclassOf. + +Test [66/197] format_checking_equivalentclass: Test format checking against ontology using equivalentClass. + +Test [67/197] output_secondaryfile_optional: Test optional output file and optional secondaryFile on output. + +Test [68/197] valuefrom_ignored_null: Test that valueFrom is ignored when the parameter is null + +Test [69/197] valuefrom_secondexpr_ignored: Test that second expression in concatenated valueFrom is not ignored + +Test [70/197] valuefrom_wf_step: Test valueFrom on workflow step. + +Test [71/197] valuefrom_wf_step_multiple: Test valueFrom on workflow step with multiple sources + +Test [72/197] valuefrom_wf_step_other: Test valueFrom on workflow step referencing other inputs + +Test [73/197] record_output_binding: Test record type output binding. + +Test [74/197] docker_json_output_path: Test support for reading cwl.output.json when running in a Docker container and just 'path' is provided. + +Test [75/197] docker_json_output_location: Test support for reading cwl.output.json when running in a Docker container and just 'location' is provided. + +Test [76/197] multiple_glob_expr_list: Test support for returning multiple glob patterns from expression + +Test [77/197] wf_scatter_oneparam_valuefrom: Test workflow scatter with single scatter parameter and two valueFrom on step input (first and current el) + +Test [78/197] wf_scatter_twoparam_nested_crossproduct_valuefrom: Test workflow scatter with two scatter parameters and nested_crossproduct join method and valueFrom on step input + +Test [79/197] wf_scatter_twoparam_flat_crossproduct_valuefrom: Test workflow scatter with two scatter parameters and flat_crossproduct join method and valueFrom on step input + +Test [80/197] wf_scatter_twoparam_dotproduct_valuefrom: Test workflow scatter with two scatter parameters and dotproduct join method and valueFrom on step input + +Test [81/197] wf_scatter_oneparam_valuefrom_twice_current_el: Test workflow scatter with single scatter parameter and two valueFrom on step input (current el twice) + +Test [82/197] wf_scatter_oneparam_valueFrom: Test valueFrom eval on scattered input parameter + +Test [83/197] wf_two_inputfiles_namecollision: Test workflow two input files with same name. + +Test [84/197] directory_input_param_ref: Test directory input with parameter reference + +Test [85/197] directory_input_docker: Test directory input in Docker + +Test [86/197] directory_output: Test directory output + +Test [87/197] directory_secondaryfiles: Test directories in secondaryFiles + +Test [88/197] dynamic_initial_workdir: Test dynamic initial work dir + +Test [89/197] writable_stagedfiles: Test writable staged files. + +Test [90/197] input_file_literal: Test file literal as input + +Test [91/197] initial_workdir_expr: Test expression in InitialWorkDir listing + +Test [92/197] nameroot_nameext_stdout_expr: Test nameroot/nameext expression in arguments, stdout + +Test [93/197] input_dir_inputbinding: Test directory input with inputBinding + +Test [94/197] cl_gen_arrayofarrays: Test command line generation of array-of-arrays + +Test [95/197] env_home_tmpdir: Test $HOME and $TMPDIR are set correctly + +Test [96/197] env_home_tmpdir_docker: Test $HOME and $TMPDIR are set correctly in Docker + +Test [97/197] expressionlib_tool_wf_override: Test that expressionLib requirement of individual tool step overrides expressionLib of workflow. + +Test [98/197] initial_workdir_output: Test output of InitialWorkDir + +Test [99/197] embedded_subworkflow: Test embedded subworkflow + +Test [100/197] filesarray_secondaryfiles: Test secondaryFiles on array of files. + +Test [101/197] exprtool_directory_literal: Test directory literal output created by ExpressionTool + +Test [102/197] exprtool_file_literal: Test file literal output created by ExpressionTool + +Test [103/197] dockeroutputdir: Test dockerOutputDirectory + +Test [104/197] hints_import: Test hints with $import + +Test [105/197] default_path_notfound_warning: Test warning instead of error when default path is not found + +Test [106/197] inlinejs_req_expressions: Test InlineJavascriptRequirement with multiple expressions in the same tool + +Test [107/197] input_dir_recurs_copy_writable: Test if a writable input directory is recursively copied and writable + +Test [108/197] null_missing_params: Test that missing parameters are null (not undefined) in expression + +Test [109/197] param_notnull_expr: Test that provided parameter is not null in expression + +Test [110/197] wf_compound_doc: Test compound workflow document + +Test [111/197] nameroot_nameext_generated: Test that nameroot and nameext are generated from basename at execution time by the runner + +Test [112/197] initialworkpath_output: Test that file path in $(inputs) for initialworkdir is in $(outdir). + +Test [113/197] wf_scatter_twopar_oneinput_flattenedmerge: Test single step workflow with Scatter step and two data links connected to same input, flattened merge behavior. Workflow inputs are set as list + +Test [114/197] wf_multiplesources_multipletypes: Test step input with multiple sources with multiple types + +Test [115/197] shelldir_notinterpreted: Test that shell directives are not interpreted. + +Test [116/197] shelldir_quoted: Test that shell directives are quoted. + +Test [117/197] initial_workdir_empty_writable: Test empty writable dir with InitialWorkDirRequirement + +Test [118/197] initial_workdir_empty_writable_docker: Test empty writable dir with InitialWorkDirRequirement inside Docker + +Test [119/197] dynamic_resreq_inputs: Test dynamic resource reqs referencing inputs + +Test [120/197] fileliteral_input_docker: Test file literal as input without Docker + +Test [121/197] outputbinding_glob_sorted: Test that OutputBinding.glob is sorted as specified by POSIX + +Test [122/197] initialworkdir_nesteddir: Test InitialWorkDirRequirement with a nested directory structure from another step + +Test [123/197] booleanflags_cl_noinputbinding: Test that boolean flags do not appear on command line if inputBinding is empty and not null + +Test [124/197] expr_reference_self_noinput: Test that expression engine does not fail to evaluate reference to self with unprovided input + +Test [125/197] success_codes: Test successCodes + +Test [126/197] dynamic_resreq_wf: Test simple workflow with a dynamic resource requirement + +Test [127/197] cl_empty_array_input: Test that empty array input does not add anything to command line + +Test [128/197] resreq_step_overrides_wf: Test that ResourceRequirement on a step level redefines requirement on the workflow level + +Test [129/197] valuefrom_constant_overrides_inputs: Test valueFrom with constant value overriding provided array inputs + +Test [130/197] dynamic_resreq_filesizes: Test dynamic resource reqs referencing the size of Files inside a Directory + +Test [131/197] wf_step_connect_undeclared_param: Test that it is not an error to connect a parameter to a workflow step, even if the parameter doesn't appear in the `run` process inputs. + +Test [132/197] wf_step_access_undeclared_param: Test that parameters that don't appear in the `run` process inputs are not present in the input object used to run the tool. + +Test [133/197] env_home_tmpdir_docker: Test $HOME and $TMPDIR are set correctly in Docker without using return code + +Test [134/197] wf_scatter_oneparam_valuefrom_inputs: Test workflow scatter with single scatter parameter and two valueFrom using $inputs (first and current el) + +Test [135/197] packed_import_schema: SchemaDefRequirement with $import, and packed + +Test [136/197] job_input_secondary_subdirs: Test specifying secondaryFiles in subdirectories of the job input document. + +Test [137/197] job_input_subdir_primary_and_secondary_subdirs: Test specifying secondaryFiles in same subdirectory of the job input as the primary input file. + +Test [138/197] scatter_embedded_subworkflow: Test simple scatter over an embedded subworkflow + +Test [139/197] scatter_multi_input_embedded_subworkflow: Test simple multiple input scatter over an embedded subworkflow + +Test [140/197] workflow_embedded_subworkflow_embedded_subsubworkflow: Test twice nested subworkflow + +Test [141/197] workflow_embedded_subworkflow_with_tool_and_subsubworkflow: Test subworkflow of mixed depth with tool first + +Test [142/197] workflow_embedded_subworkflow_with_subsubworkflow_and_tool: Test subworkflow of mixed depth with tool after + +Test [143/197] workflow_records_inputs_and_outputs: Test record type inputs to and outputs from workflows. + +Test [144/197] workflow_integer_input: Test integer workflow input and outputs + +Test [145/197] workflow_integer_input_optional_specified: Test optional integer workflow inputs (specified) + +Test [146/197] workflow_integer_input_optional_unspecified: Test optional integer workflow inputs (unspecified) + +Test [147/197] workflow_integer_input_default_specified: Test default integer workflow inputs (specified) + +Test [148/197] workflow_integer_input_default_unspecified: Test default integer workflow inputs (unspecified) + +Test [149/197] workflow_integer_input_default_and_tool_integer_input_default: Test default integer tool and workflow inputs (unspecified) + +Test [150/197] workflow_file_input_default_unspecified: Test File input with default unspecified to workflow + +Test [151/197] workflow_file_input_default_specified: Test File input with default specified to workflow + +Test [152/197] clt_optional_union_input_file_or_files_with_array_of_one_file_provided: Test input union type or File or File array to a tool with one file in array specified. + +Test [153/197] clt_optional_union_input_file_or_files_with_many_files_provided: Test input union type or File or File array to a tool with a few files in array specified. + +Test [154/197] clt_optional_union_input_file_or_files_with_single_file_provided: Test input union type or File or File array to a tool with one file specified. + +Test [155/197] clt_optional_union_input_file_or_files_with_nothing_provided: Test input union type or File or File array to a tool with null specified. + +Test [156/197] clt_any_input_with_integer_provided: Test Any parameter with integer input to a tool + +Test [157/197] clt_any_input_with_string_provided: Test Any parameter with string input to a tool + +Test [158/197] clt_any_input_with_file_provided: Test Any parameter with file input to a tool + +Test [159/197] clt_any_input_with_mixed_array_provided: Test Any parameter with array input to a tool + +Test [160/197] clt_any_input_with_record_provided: Test Any parameter with record input to a tool + +Test [161/197] workflow_any_input_with_integer_provided: Test Any parameter with integer input to a workflow + +Test [162/197] workflow_any_input_with_string_provided: Test Any parameter with string input to a workflow + +Test [163/197] workflow_any_input_with_file_provided: Test Any parameter with file input to a workflow + +Test [164/197] workflow_any_input_with_mixed_array_provided: Test Any parameter with array input to a workflow + +Test [165/197] workflow_any_input_with_record_provided: Test Any parameter with record input to a tool + +Test [166/197] workflow_union_default_input_unspecified: Test union type input to workflow with default unspecified + +Test [167/197] workflow_union_default_input_with_file_provided: Test union type input to workflow with default specified as file + +Test [168/197] workflowstep_valuefrom_string: Test valueFrom on workflow step from literal (string). + +Test [169/197] workflowstep_valuefrom_file_basename: Test valueFrom on workflow step using basename. + +Test [170/197] expression_tool_int_array_output: Test output arrays in a tool (with ints). + +Test [171/197] workflowstep_int_array_input_output: Test output arrays in a workflow (with ints). + +Test [172/197] workflow_file_array_output: Test output arrays in a workflow (with Files). + +Test [173/197] docker_entrypoint: Test Docker ENTRYPOINT usage + +Test 173 failed: calrissian --max-ram 8G --max-cores 4 --default-container debian:stretch-slim --outdir=/output/tmp4i_2wfjf --quiet v1.0/v1.0/docker-run-cmd.cwl v1.0/v1.0/empty.json +Test Docker ENTRYPOINT usage +Returned non-zero +Test [174/197] clt_file_size_property_with_empty_file: Test use of size in expressions for an empty file + +Test [175/197] clt_file_size_property_with_multi_file: Test use of size in expressions for a few files + +Test [176/197] any_without_defaults_unspecified_fails: Test Any without defaults, unspecified, should fail. + +Test [177/197] any_without_defaults_specified_fails: Test Any without defaults, specified, should fail. + +Test [178/197] step_input_default_value_noexp: Test default value on step input parameter, no ExpressionTool + +Test [179/197] step_input_default_value_overriden_noexp: Test default value on step input parameter overridden by provided source, no ExpressionTool + +Test [180/197] nested_workflow_noexp: Test nested workflow, without ExpressionTool + +Test [181/197] wf_multiplesources_multipletypes_noexp: Test step input with multiple sources with multiple types, without ExpressionTool + +Test [182/197] dynamic_resreq_wf_optional_file_default: Within a workflow, test accessing the size attribute of an optional input File as part of a CommandLineTool's ResourceRequirement calculation. The CommandLineTool input has a default value (a local file) and the workflow nor the workflow step does not provide any value for this input. + +Test [183/197] dynamic_resreq_wf_optional_file_step_default: Within a workflow, test accessing the size attribute of an optional input File as part of a CommandLineTool's ResourceRequirement calculation. The workflow step provides a default value (a local file) for this input and the workflow itself does not provide any value for this input. + +Test [184/197] dynamic_resreq_wf_optional_file_wf_default: Within a workflow, test accessing the size attribute of an optional input File as part of a CommandLineTool's ResourceRequirement calculation. The workflow itelf provides a default value (a local file) for this input. + +Test [185/197] step_input_default_value_overriden_2nd_step: Test default value on step input parameter overridden by provided source. With passthrough first step + +Test [186/197] step_input_default_value_overriden_2nd_step_noexp: Test default value on step input parameter overridden by provided source. With passthrough first step and no ExpressionTool + +Test [187/197] step_input_default_value_overriden_2nd_step_null: Test default value on step input parameter overridden by provided source. With null producing first step + +Test [188/197] step_input_default_value_overriden_2nd_step_null_noexp: Test default value on step input parameter overridden by provided source. With null producing first step and no ExpressionTool + +Test [189/197] stdin_from_directory_literal_with_local_file: Pipe to stdin from user provided local File via a Directory literal + +Test [190/197] stdin_from_directory_literal_with_literal_file: Pipe to stdin from literal File via a Directory literal + +Test [191/197] directory_literal_with_literal_file_nostdin: Test non-stdin reference to literal File via a Directory literal + +Test [192/197] no_inputs_commandlinetool: Test CommandLineTool without inputs + +Test [193/197] no_outputs_commandlinetool: Test CommandLineTool without outputs + +Test [194/197] no_inputs_workflow: Test Workflow without inputs + +Test [195/197] no_outputs_workflow: Test Workflow without outputs + +Test [196/197] anonymous_enum_in_array: Test an anonymous enum inside an array inside a record + +Test [197/197] schema-def_anonymous_enum_in_array: Test an anonymous enum inside an array inside a record, SchemaDefRequirement + +195 tests passed, 1 failures, 1 unsupported features diff --git a/docs/conformance/badges/1.0.2/command_line_tool.json b/docs/conformance/badges/1.0.2/command_line_tool.json new file mode 100644 index 0000000..851e9c9 --- /dev/null +++ b/docs/conformance/badges/1.0.2/command_line_tool.json @@ -0,0 +1 @@ +{"subject": "command_line_tool", "status": "97%", "color": "yellow"} \ No newline at end of file diff --git a/docs/conformance/badges/1.0.2/docker.json b/docs/conformance/badges/1.0.2/docker.json new file mode 100644 index 0000000..b48ae9b --- /dev/null +++ b/docs/conformance/badges/1.0.2/docker.json @@ -0,0 +1 @@ +{"subject": "docker", "status": "75%", "color": "yellow"} \ No newline at end of file diff --git a/docs/conformance/badges/1.0.2/env_var.json b/docs/conformance/badges/1.0.2/env_var.json new file mode 100644 index 0000000..94c5ea6 --- /dev/null +++ b/docs/conformance/badges/1.0.2/env_var.json @@ -0,0 +1 @@ +{"subject": "env_var", "status": "100%", "color": "green"} \ No newline at end of file diff --git a/docs/conformance/badges/1.0.2/expression_tool.json b/docs/conformance/badges/1.0.2/expression_tool.json new file mode 100644 index 0000000..0aa7dfc --- /dev/null +++ b/docs/conformance/badges/1.0.2/expression_tool.json @@ -0,0 +1 @@ +{"subject": "expression_tool", "status": "100%", "color": "green"} \ No newline at end of file diff --git a/docs/conformance/badges/1.0.2/initial_work_dir.json b/docs/conformance/badges/1.0.2/initial_work_dir.json new file mode 100644 index 0000000..d9d41f2 --- /dev/null +++ b/docs/conformance/badges/1.0.2/initial_work_dir.json @@ -0,0 +1 @@ +{"subject": "initial_work_dir", "status": "100%", "color": "green"} \ No newline at end of file diff --git a/docs/conformance/badges/1.0.2/inline_javascript.json b/docs/conformance/badges/1.0.2/inline_javascript.json new file mode 100644 index 0000000..cd29e4d --- /dev/null +++ b/docs/conformance/badges/1.0.2/inline_javascript.json @@ -0,0 +1 @@ +{"subject": "inline_javascript", "status": "100%", "color": "green"} \ No newline at end of file diff --git a/docs/conformance/badges/1.0.2/multiple_input.json b/docs/conformance/badges/1.0.2/multiple_input.json new file mode 100644 index 0000000..7c758a4 --- /dev/null +++ b/docs/conformance/badges/1.0.2/multiple_input.json @@ -0,0 +1 @@ +{"subject": "multiple_input", "status": "100%", "color": "green"} \ No newline at end of file diff --git a/docs/conformance/badges/1.0.2/required.json b/docs/conformance/badges/1.0.2/required.json new file mode 100644 index 0000000..720ce59 --- /dev/null +++ b/docs/conformance/badges/1.0.2/required.json @@ -0,0 +1 @@ +{"subject": "required", "status": "100%", "color": "green"} \ No newline at end of file diff --git a/docs/conformance/badges/1.0.2/resource.json b/docs/conformance/badges/1.0.2/resource.json new file mode 100644 index 0000000..8e4c3a1 --- /dev/null +++ b/docs/conformance/badges/1.0.2/resource.json @@ -0,0 +1 @@ +{"subject": "resource", "status": "100%", "color": "green"} \ No newline at end of file diff --git a/docs/conformance/badges/1.0.2/scatter.json b/docs/conformance/badges/1.0.2/scatter.json new file mode 100644 index 0000000..4ea16ca --- /dev/null +++ b/docs/conformance/badges/1.0.2/scatter.json @@ -0,0 +1 @@ +{"subject": "scatter", "status": "100%", "color": "green"} \ No newline at end of file diff --git a/docs/conformance/badges/1.0.2/schema_def.json b/docs/conformance/badges/1.0.2/schema_def.json new file mode 100644 index 0000000..f635d69 --- /dev/null +++ b/docs/conformance/badges/1.0.2/schema_def.json @@ -0,0 +1 @@ +{"subject": "schema_def", "status": "100%", "color": "green"} \ No newline at end of file diff --git a/docs/conformance/badges/1.0.2/shell_command.json b/docs/conformance/badges/1.0.2/shell_command.json new file mode 100644 index 0000000..f74b75a --- /dev/null +++ b/docs/conformance/badges/1.0.2/shell_command.json @@ -0,0 +1 @@ +{"subject": "shell_command", "status": "100%", "color": "green"} \ No newline at end of file diff --git a/docs/conformance/badges/1.0.2/step_input.json b/docs/conformance/badges/1.0.2/step_input.json new file mode 100644 index 0000000..de6c670 --- /dev/null +++ b/docs/conformance/badges/1.0.2/step_input.json @@ -0,0 +1 @@ +{"subject": "step_input", "status": "100%", "color": "green"} \ No newline at end of file diff --git a/docs/conformance/badges/1.0.2/step_input_expression.json b/docs/conformance/badges/1.0.2/step_input_expression.json new file mode 100644 index 0000000..7dff650 --- /dev/null +++ b/docs/conformance/badges/1.0.2/step_input_expression.json @@ -0,0 +1 @@ +{"subject": "step_input_expression", "status": "100%", "color": "green"} \ No newline at end of file diff --git a/docs/conformance/badges/1.0.2/subworkflow.json b/docs/conformance/badges/1.0.2/subworkflow.json new file mode 100644 index 0000000..28c8934 --- /dev/null +++ b/docs/conformance/badges/1.0.2/subworkflow.json @@ -0,0 +1 @@ +{"subject": "subworkflow", "status": "100%", "color": "green"} \ No newline at end of file diff --git a/docs/conformance/badges/1.0.2/workflow.json b/docs/conformance/badges/1.0.2/workflow.json new file mode 100644 index 0000000..4791c72 --- /dev/null +++ b/docs/conformance/badges/1.0.2/workflow.json @@ -0,0 +1 @@ +{"subject": "workflow", "status": "100%", "color": "green"} \ No newline at end of file diff --git a/docs/environment.yml b/docs/environment.yml new file mode 100644 index 0000000..e69de29 diff --git a/mkdocs.yml b/mkdocs.yml new file mode 100644 index 0000000..d90aea9 --- /dev/null +++ b/mkdocs.yml @@ -0,0 +1,28 @@ +site_name: Calrissian +site_description: 'CWL runner for Kubernetes' +# Repository + +repo_name: 'Duke-GCB/calrissian' +repo_url: 'https://github.com/Duke-GCB/calrissian.git' +edit_uri: 'blob/main/docs/' +site_url: 'https://Duke-GCB.github.io/calrissian/' + + +theme: + name: material + +markdown_extensions: +- admonition +- pymdownx.highlight +- pymdownx.superfences +- attr_list + +plugins: +- search +#- mkdocs-jupyter + +nav: +- Introduction: 'index.md' +- Conformance: + - 1.0: 'conformance/1.0/conformance.md' +