.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:

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)
 

src/nextflow_file.py

@@ -23,8 +23,7 @@ from .bioflowinsighterror import BioFlowInsightError
 class Nextflow_File(Nextflow_Building_Blocks):
     def __init__(self, address, duplicate = True, DSL="", author = None, name = None, origin=None, output_dir='./results', display_info = True):
         self.file = address 
-        print(self.get_file_address())
-        if(self.get_file_address().find('/')!=-1):
+        if(self.get_file_address().find('/')==-1):
             raise BioFlowInsightError(f"BioFlow-Insight cannot directly analyse a workflow from its directory. Please analyse the workflow from the parent directory instead.", num = -1)
         
         self.output_dir = Path(output_dir)