Merge branch 'build-package' into 'main'

Build package

See merge request !1

.gitignore

+/.coverage
+*.egg-info
+.DS_Store
+__pycache__
+.venv
+.idea
+dist/
+results*/
\ No newline at end of file

.gitlab-ci.yml

+upload:
+  stage: deploy
+  rules:
+    - if: $CI_COMMIT_TAG
+  needs: []
+  image: python:3.11
+  variables:
+    PRIVATE_REGISTRY_API_URL: "${PRIVATE_REGISTRY_API_URL}"
+    TWINE_PASSWORD: "${PRIVATE_REGISTRY_TOKEN_PASSWORD}"
+    TWINE_USERNAME: "${PRIVATE_REGISTRY_TOKEN_USERNAME}"
+  script:
+    - pip install "setuptools>=62.6"
+    - pip install -e .[dev]
+    - echo "Tag name used ${CI_COMMIT_TAG}"
+    - >
+      if [[ -z "$CI_COMMIT_TAG" ]]; then
+        CI_COMMIT_TAG="v0.0.1a"
+      fi
+    - sed -i "s/v0.0.1-dev/$CI_COMMIT_TAG/g" src/__init__.py
+    - python -m build
+    - python -m twine upload --verbose --repository-url ${PRIVATE_REGISTRY_API_URL} dist/*

bioflow_insight_cli/main.py

+import click
+
+from src.nextflow_file import Nextflow_File
+
+
+@click.command()
+@click.argument('main_workflow_path')
+@click.option('--author', 'author', required=False, help='Author name, extracted otherwise')
+@click.option('--name', 'name', required=False, help='Workflow name, extracted otherwise')
+@click.option('--output-dir', default='./results', help='Where the results will be written')
+@click.option(
+    '--no-duplicate',
+    'duplicate',
+    required=False,
+    default=True,
+    is_flag=True,
+    help=''
+    'When processes and subworkflows are duplicated in the workflows by the \'include as\' option, '
+    'this option will duplicate the procedures in the graph output.',
+)
+@click.option(
+    '--graph-in-dot-only',
+    'render_graphs',
+    required=False,
+    default=True,
+    is_flag=True,
+    help='Generate the graph output only in dot format, not png (faster).',
+)
+def cli_command(main_workflow_path, **kwargs):
+    return cli(main_workflow_path, **kwargs)
+
+
+def cli(main_workflow_path, render_graphs: bool, **kwargs):
+    """
+    The path to main file, subworkflows and modules must be in direct subdir of this file,
+    in folders with eponymous names.
+    """
+
+    w = Nextflow_File(address=main_workflow_path, **kwargs)
+    w.initialise()
+    w.generate_all_graphs(render_graphs=render_graphs)
+
+
+if __name__ == '__main__':
+    cli_command()

pyproject.toml

@@ -15,7 +15,7 @@ classifiers = [
 #    "License :: OSI Approved :: MIT License",
     "Operating System :: OS Independent",
 ]
-dynamic = ["version", "dependencies"]
+dynamic = ["version", "dependencies", "optional-dependencies"]
 
 [tool.setuptools.dynamic]
 dependencies = {file = ["requirements.txt"]}

wf_test/main.nf

+//include { p1 as p1_1; p1 as p1_2} from './modules/p1'
+
+
+//include { wf1 as wf1_1; wf1 as wf1_2 } from './subworkflows/wf1'
+include { wf1 as wf1_1 } from './subworkflows/wf1'
+//include { wf1 as wf1_2 } from './subworkflows/wf1'
+
+
+
+
+
+
+
+workflow {
+
+    a = channel.empty()
+
+    //c = wf1_1(a)
+    //c = wf1_2(b)
+
+    b = wf1_1(a)
+
+
+
+    //c = p1_1(p1_2(wf1_2(wf1_1(a))))
+    //wf1_1(a) 
+    //    | wf1_2 
+    //    | p1_2 
+    //    | p1_1
+
+    //(a, b) = p1_1(a)
+    //(ch1, ch2) = (params.ped ? [a, Channel.empty()]: [Channel.empty(), b])
+    //(ch1, ch2) = a.into(2)
+    
+
+
+}
\ No newline at end of file

wf_test/modules/p1.nf

+
+process p1 {
+    input:
+    file(input)
+    output:
+    file(output_1)
+    file(output_2)
+    
+    """
+    something
+    """
+}
+

wf_test/subworkflows/wf1.nf

+include { p1  } from '../modules/p1'
+
+workflow wf1 {
+    take:
+    input_wf1
+
+    main:
+    output_wf1 = p1(input_wf1)
+
+    emit:
+    //val = output_wf1
+    output_wf1
+}
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