diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 461b629d1e33b28fa76a14515c1a751254466565..f15b634502fef608302d7b32b4edfacac058acd1 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -11,6 +11,17 @@ run_tests: +black_cli: + needs: [] + image: python:3.10 + stage: test + script: + - python -m pip install --upgrade pip + - pip install -r requirements-dev.txt + - black bioflow_insight_cli/ --check --diff + + + upload: stage: deploy rules: diff --git a/bioflow_insight_cli/main.py b/bioflow_insight_cli/main.py index 00e35d1e2660dedbdf28f287eb9539e25deb611b..7f9d32e14e929b556aa1367d1e79105da751f06d 100644 --- a/bioflow_insight_cli/main.py +++ b/bioflow_insight_cli/main.py @@ -7,8 +7,11 @@ from src.workflow import Workflow @click.command() @click.version_option(bioflow_insight_src.__version__) @click.argument('main_workflow_path') - -@click.option('--output-dir', default='./results', help='Where the results will be written.') +@click.option( + '--output-dir', + default='./results', + help='Where the results will be written.', +) @click.option( '--duplicate', 'duplicate', @@ -19,15 +22,14 @@ from src.workflow import Workflow 'When processes and subworkflows are duplicated in the workflow by the \'include as\' option, ' 'this option will duplicate the task in the graph output.', ) - @click.option( '--processes-to-remove', 'processes_2_remove', required=False, help='' - 'List of processes which are to be removed from the different structural representations (format "process1, process2, ...").', + 'List of processes which are to be removed from the different structural representations ' + '(format "process1, process2, ...").', ) - @click.option( '--no-render-graphs', 'render_graphs', @@ -37,30 +39,66 @@ from src.workflow import Workflow help='Don\'t generate the graphs output in png format using graphviz (faster),' 'the mermaid and dot formats are always generated.', ) - - -@click.option('--name', 'name', required=False, help='Workflow name, extracted otherwise (in the case of a Git repo).') +@click.option( + '--name', + 'name', + required=False, + help='Workflow name, extracted otherwise (in the case of a Git repo).', +) @click.option( '--authors', 'authors', required=False, - help='' - 'Authors of workflow (format "author1, author2, ..."), ' - 'extracted otherwise (in the case of a Git repo).', + help='Authors of workflow (format "author1, author2, ..."), extracted otherwise (in the case of a Git repo).', +) +@click.option( + '--keywords', + 'keywords', + required=False, + help='Keywords of workflow (fomat "keyword1, keyword2, ..."), extracted otherwise (in the case of a Git repo).', +) +@click.option( + '--description', + 'description', + required=False, + help='Description of workflow, extracted otherwise (in the case of a Git repo).', +) +@click.option( + '--date-published', + 'datePublished', + required=False, + help='Publication date (format "yyyy-mm-dd"), extracted otherwise (in the case of a Git repo).', +) +@click.option( + '--license', + 'license', + required=False, + help='License of workflow, extracted otherwise (in the case of a Git repo).', +) +@click.option( + '--creative-work-status', + 'creativeWorkStatus', + required=False, + help='Creative work status of workflow, extracted otherwise (in the case of a Git repo).', +) +@click.option( + '--version', + 'version', + required=False, + help='Version of workflow, extracted otherwise (in the case of a Git repo).', +) +@click.option( + '--producer', + 'producer', + required=False, + help='Producer of workflow, extracted otherwise (in the case of a Git repo).', +) +@click.option( + '--publisher', + 'publisher', + required=False, + help='Publisher of workflow, extracted otherwise (in the case of a Git repo).', ) - -@click.option('--keywords', 'keywords', required=False, help='Keywords of workflow (fomat "keyword1, keyword2, ..."), extracted otherwise (in the case of a Git repo).') -@click.option('--description', 'description', required=False, help='Description of workflow, extracted otherwise (in the case of a Git repo).') -@click.option('--date-published', 'datePublished', required=False, help='Publication date (format "yyyy-mm-dd"), extracted otherwise (in the case of a Git repo).') - -@click.option('--license', 'license', required=False, help='License of workflow, extracted otherwise (in the case of a Git repo).') -@click.option('--creative-work-status', 'creativeWorkStatus', required=False, help='Creative work status of workflow, extracted otherwise (in the case of a Git repo).') -@click.option('--version', 'version', required=False, help='Version of workflow, extracted otherwise (in the case of a Git repo).') -@click.option('--producer', 'producer', required=False, help='Producer of workflow, extracted otherwise (in the case of a Git repo).') -@click.option('--publisher', 'publisher', required=False, help='Publisher of workflow, extracted otherwise (in the case of a Git repo).') - - - @click.option( '--display-info', 'display_info', @@ -69,7 +107,6 @@ from src.workflow import Workflow is_flag=True, help='Option to show a visual summary of the analysis.', ) - def cli_command(main_workflow_path, **kwargs): return cli(main_workflow_path, **kwargs)