Commit 9bef3bc5 authored by Cage, Gregory's avatar Cage, Gregory
Browse files

Merge branch '3-sammy-release-impl' into 'main' 

Initial implementation of Nova library

Closes #3

See merge request ndip/public-packages/nova-galaxy!1
parents 40cb78dd 117cb5ce

.gitlab-ci.yml

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@@ -86,7 +86,8 @@ package-build: 
      ${IMAGE_NAME}:src-${CI_COMMIT_SHA}

      bash -c "

      poetry config repositories.gitlab_repo ${CI_API_V4_URL}/projects/${CI_PROJECT_ID}/packages/pypi &&

      poetry publish -u gitlab-ci-token -p ${CI_JOB_TOKEN} -r gitlab_repo

      poetry publish -u gitlab-ci-token -p ${CI_JOB_TOKEN} -r gitlab_repo &&

      poetry publish -u __token__ -p ${PYPI_API_TOKEN}

      "

  when: manual

  tags:

poetry.lock

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pyproject.toml

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[tool.poetry]

name = "nova-galaxy"

version = "0.1.0"

version = "0.3.0"

description = "Utilties for accessing the ORNL Galaxy instance"

authors = ["Greg Watson <watsongr@ornl.gov>"]

authors = ["Greg Watson <watsongr@ornl.gov>", "Gregory Cage <cagege@ornl.gov>"]

readme = "README.md"

license = "MIT"

keywords = ["NOVA", "Galaxy", "python"]

packages = [

	{include = "src/nova"}

    {include = "nova", from ="src"}

]





[tool.poetry.dependencies]

python = "^3.10"

bioblend = "^1.3.0"
@@ -20,9 +21,6 @@ build-backend = "poetry.core.masonry.api" 




[tool.pytest.ini_options]

pythonpath = [

  ".", "src"

]

testpaths = ["tests"]

python_files = ["test*.py"]

norecursedirs = [".git", "tmp*", "_tmp*", "__pycache__"]
@@ -82,6 +80,3 @@ coverage = ">=6.4.3" 
pytest = "*"

ruff = ">=0.6.2"

copier=">=9.3"
 


[tool.poetry.scripts]

nova_galaxy = "nova_galaxy:main"

src/nova/galaxy/__init__.py

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import importlib.metadata



from .nova import NOVA

from .data_store import Datastore

from .dataset import Dataset, DatasetCollection, upload_datasets

from .nova import Nova, NovaConnection

from .outputs import Outputs

from .parameters import Parameters

from .tool import Tool



__all__ = ["NOVA"]

__all__ = [

    "Nova",

    "NovaConnection",

    "Datastore",

    "Dataset",

    "DatasetCollection",

    "upload_datasets",

    "Outputs",

    "Parameters",

    "Tool",

]



__version__ = importlib.metadata.version(__package__)
 
__version__ = importlib.metadata.version("nova-galaxy")

src/nova/galaxy/data_store.py

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"""DataStore is used to configure Galaxy to group outputs of a tool together."""



from typing import TYPE_CHECKING



if TYPE_CHECKING:

    from .nova import NovaConnection  # Only imports for type checking





class Datastore:

    """Groups tool outputs together.



    The constructor is not intended for external use. Use nova.galaxy.Nova.create_data_store() instead.

    """



    def __init__(self, name: str, nova_connection: "NovaConnection", history_id: str) -> None:

        self.name = name

        self.nova_connection = nova_connection

        self.history_id = history_id

        self.persist_store = False



    def persist(self) -> None:

        self.persist_store = True