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fix: update package manager to uv, gh-workflow and bugfix (#39)
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* add: uv packaging

- update github workflow
- run linter

* fix: F821 Undefined name `AnnotationTypesProcess`

* fix: readthedocs.yaml

* fix: add dep to docs group

* update: fix some issues

* update: license on pyproject.toml

---------

Co-authored-by: David Martínez Millán <[email protected]>
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@FedericaBrando @dmartmillan
FedericaBrando and dmartmillan authored Dec 16, 2024
1 parent a5ea7a9 commit 921af6d
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37 changes: 20 additions & 17 deletions .github/workflows/openvariant_tester.yml
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Expand Up @@ -24,27 +24,30 @@ jobs:
build:

runs-on: ubuntu-latest
env:
UV_LINK_MODE: copy
RUFF_FORMAT: github

steps:
- uses: actions/checkout@v3
- name: Set up the latest Python
uses: actions/setup-python@v3
- uses: actions/checkout@v4

- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: "3.x"
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install flake8 pytest pytest-cov
pip install -e .
- name: Lint with flake8
python-version-file: "pyproject.toml"

- uses: astral-sh/setup-uv@v4

- name: Lint with Ruff
run: |
# stop the build if there are Python syntax errors or undefined names
# flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
- name: Test with pytest
uv sync --extra linting --frozen
uv run ruff check openvariant
- name: Test
run: |
pytest --cov .
uv sync --extra tests --frozen
uv run pytest --cov .
- name: Upload coverage reports to Codecov with GitHub Action
uses: codecov/codecov-action@v3

15 changes: 8 additions & 7 deletions .readthedocs.yaml
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Expand Up @@ -3,17 +3,18 @@ version: 2
build:
os: "ubuntu-22.04"
tools:
python: "3.12"
python: "3.10"
apt_packages:
- build-essential
- libzmq3-dev
- gcc
- g++
- python3-dev
commands:
- asdf plugin add uv
- asdf install uv latest
- asdf global uv latest
- uv sync --extra docs --frozen
- uv run -m sphinx -T -b html -d docs/_build/doctrees -D language=en docs $READTHEDOCS_OUTPUT/html

sphinx:
configuration: docs/conf.py

python:
install:
- requirements: requirements-docs.txt
configuration: docs/conf.py
72 changes: 36 additions & 36 deletions openvariant/tasks/plugin.py
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Expand Up @@ -31,49 +31,49 @@ def _add_action(name: str) -> None:
init_file.write(f"import .{name} from {context_name}\n")
init_file.close()
with open(f"{path}/{name}/{name}.py", 'w') as plugin_file:
plugin_file.write(f"from openvariant.plugins.context import Context\n")
plugin_file.write(f"from openvariant.plugins.plugin import Plugin\n\n\n")
plugin_file.write("from openvariant.plugins.context import Context\n")
plugin_file.write("from openvariant.plugins.plugin import Plugin\n\n\n")
plugin_file.write(f"class {context_name}(Context):\n")
plugin_file.write(f"\t\"\"\"\n")
plugin_file.write("\t\"\"\"\n")
plugin_file.write(f"\t{context_name} class generated by OpenVariant\n\n")
plugin_file.write(f"\tAttributes\n")
plugin_file.write(f"\t-------\n")
plugin_file.write(f"\trow : dict\n")
plugin_file.write(f"\t\tMain method to execute data transformation in each row.\n")
plugin_file.write(f"\tfield_name : str\n")
plugin_file.write(f"\t\tName of the corresponding column that was described on the annotation schema.\n")
plugin_file.write(f"\tfile_path : str\n")
plugin_file.write(f"\t\tPath of the Input file that is being parsed.\n")
plugin_file.write(f"\t\"\"\"\n\n")
plugin_file.write(f"\tdef __init__(self, row: dict, field_name: str, file_path: str) -> None:\n")
plugin_file.write(f"\t\tsuper().__init__(row, field_name, file_path)\n")
plugin_file.write(f"\n\n")
plugin_file.write("\tAttributes\n")
plugin_file.write("\t-------\n")
plugin_file.write("\trow : dict\n")
plugin_file.write("\t\tMain method to execute data transformation in each row.\n")
plugin_file.write("\tfield_name : str\n")
plugin_file.write("\t\tName of the corresponding column that was described on the annotation schema.\n")
plugin_file.write("\tfile_path : str\n")
plugin_file.write("\t\tPath of the Input file that is being parsed.\n")
plugin_file.write("\t\"\"\"\n\n")
plugin_file.write("\tdef __init__(self, row: dict, field_name: str, file_path: str) -> None:\n")
plugin_file.write("\t\tsuper().__init__(row, field_name, file_path)\n")
plugin_file.write("\n\n")
plugin_file.write(f"class {plugin_name}(Plugin):\n")
plugin_file.write(f"\t\"\"\"\n")
plugin_file.write("\t\"\"\"\n")
plugin_file.write(f"\t{plugin_name} class generated by OpenVariant\n\n")
plugin_file.write(f"\tMethods\n")
plugin_file.write(f"\t-------\n")
plugin_file.write("\tMethods\n")
plugin_file.write("\t-------\n")
plugin_file.write(f"\trun(context: {context_name})\n")
plugin_file.write(f"\t\tMain method to execute data transformation in each row.\n")
plugin_file.write(f"\t\"\"\"\n\n")
plugin_file.write("\t\tMain method to execute data transformation in each row.\n")
plugin_file.write("\t\"\"\"\n\n")
plugin_file.write(f"\tdef run(self, context: {context_name}) -> dict:\n")
plugin_file.write(f"\t\t\"\"\"\n")
plugin_file.write(f"\t\tData transformation of a single row\n\n")
plugin_file.write(f"\t\tParameters\n")
plugin_file.write(f"\t\t-------\n")
plugin_file.write("\t\t\"\"\"\n")
plugin_file.write("\t\tData transformation of a single row\n\n")
plugin_file.write("\t\tParameters\n")
plugin_file.write("\t\t-------\n")
plugin_file.write(f"\t\tcontext : {context_name}\n")
plugin_file.write(f"\t\t\tRepresentation of the row to be parsed.\n")
plugin_file.write(f"\t\t\n")
plugin_file.write(f"\t\tReturns\n")
plugin_file.write(f"\t\t-------\n")
plugin_file.write(f"\t\tfloat or int or str\n")
plugin_file.write(f"\t\t\tThe value of the field transformed.\n")
plugin_file.write(f"\t\t\"\"\"\n")
plugin_file.write(f"\n")
plugin_file.write(f"\t\t# This is an example code, modify if as you wish\n")
plugin_file.write(f"\t\tcontext.row[context.field_name] = \"Hello world! file:\" + context.file_path\n")
plugin_file.write(f"\n")
plugin_file.write(f"\t\treturn context.row[context.field_name]\n")
plugin_file.write("\t\t\tRepresentation of the row to be parsed.\n")
plugin_file.write("\t\t\n")
plugin_file.write("\t\tReturns\n")
plugin_file.write("\t\t-------\n")
plugin_file.write("\t\tfloat or int or str\n")
plugin_file.write("\t\t\tThe value of the field transformed.\n")
plugin_file.write("\t\t\"\"\"\n")
plugin_file.write("\n")
plugin_file.write("\t\t# This is an example code, modify if as you wish\n")
plugin_file.write("\t\tcontext.row[context.field_name] = \"Hello world! file:\" + context.file_path\n")
plugin_file.write("\n")
plugin_file.write("\t\treturn context.row[context.field_name]\n")


class PluginActions(Enum):
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11 changes: 8 additions & 3 deletions openvariant/variant/variant.py
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Expand Up @@ -94,13 +94,18 @@ def _extract_header(file_path: str, original_header: list, annotation: Annotatio

for field, ann in mapping_fields:
ann_type = ann[0]
header_schema.update({field: AnnotationTypesProcess[ann_type].value(ann, original_header, file_path,
header_schema)})

class_name = ann_type
module_name = "openvariant.annotation.process"
ClassAnnotation = import_class_from_module(module_name, class_name)
instance = ClassAnnotation()

header_schema.update({field: instance(ann, original_header, file_path, header_schema)})
return header_schema, annotation.columns


@lru_cache(maxsize=256)
def _parse_field(value: float or int or str, func: Callable) -> str:
def _parse_field(value: float | int | str, func: Callable) -> str:
"""Getting the value of a specific annotation field. Cached with LRU policy"""
result = func(value)
return result if result is not None else str(float('nan'))
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4 changes: 2 additions & 2 deletions openvariant/variant/where.py
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Expand Up @@ -52,9 +52,9 @@ def _parse_where(where: str or None) -> List:
WhereAttributesKeys.FIELD.value: wh[0],
WhereAttributesKeys.VALUE.value: wh[2]}
except KeyError:
raise ValueError(f"Unknown \"where\" syntax.")
raise ValueError("Unknown \"where\" syntax.")
else:
raise ValueError(f"Unknown where syntax.")
raise ValueError("Unknown where syntax.")
return [stmt]


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142 changes: 142 additions & 0 deletions pyproject.toml
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@@ -0,0 +1,142 @@
[build-system]
requires = ["hatchling", "setuptools"]
build-backend = "hatchling.build"

[project]
name = "open-variant"
version = "1.0.1"
description = "OpenVariant provides different functionalities to read, parse and operate different multiple input file formats, being able to customize the output."
authors = [
{ name = "BBGLab (Barcelona Biomedical Genomics Lab)", email = "[email protected]" }
]
dependencies = [
"pyyaml==6.0.1",
"tqdm==4.66.3",
"click==8.1.3",
"pyliftover==0.4.1",
"appdirs==1.4.4",
]
readme = "README.md"
requires-python = ">=3.10"
license = { file = "LICENSE" }
keywords = ["bioinformatics", "openvariant", "openvar", "bbglab"]


[project.urls]
Homepage = "https://github.com/bbglab/openvariant"
Documentation = "https://openvariant.readthedocs.io/"
Repository = "https://github.com/bbglab/openvariant"
Issues = "https://github.com/bbglab/openvariant/issues"


[project.scripts]
"openvar" = "openvariant.commands.openvar:openvar"

[project.optional-dependencies]
docs = [
"alabaster==0.7.12",
"asttokens==2.0.5",
"attrs==22.1.0",
"babel==2.10.3",
"backcall==0.2.0",
"beautifulsoup4==4.11.1",
"bleach==5.0.1",
"charset-normalizer==2.1.0",
"click==8.1.3",
"decorator==5.1.1",
"defusedxml==0.7.1",
"docutils==0.17.1",
"entrypoints==0.4",
"executing==0.9.1",
"fastjsonschema==2.16.1",
"idna==3.7",
"imagesize==1.4.1",
"jedi==0.18.1",
"jinja2==3.1.4",
"jsonschema==4.8.0",
"jupyter-client==7.3.4",
"jupyter-core==4.11.2",
"jupyterlab-pygments==0.2.2",
"markupsafe==2.1.1",
"matplotlib-inline==0.1.3",
"nbclient==0.6.6",
"nbformat==5.4.0",
"nbsphinx==0.8.9",
"nest-asyncio==1.5.5",
"open-variant==1.0.0",
"packaging==21.3",
"pandocfilters==1.5.0",
"parso==0.8.3",
"pexpect==4.8.0",
"pickleshare==0.7.5",
"prompt-toolkit==3.0.30",
"ptyprocess==0.7.0",
"pure-eval==0.2.2",
"pydata-sphinx-theme==0.8.1",
"pygments==2.15.0",
"pyparsing==3.0.9",
"pyrsistent==0.18.1",
"python-dateutil==2.8.2",
"pytz==2022.1",
"pyyaml==6.0.1",
"pyzmq==26.2.0",
"requests==2.32.2",
"ruamel-yaml==0.16.13",
"six==1.16.0",
"snowballstemmer==2.2.0",
"soupsieve==2.3.2.post1",
"sphinx-copybutton==0.5.0",
"sphinx==4.5.0",
"sphinx-gallery==0.10.1",
"sphinx-panels==0.6.0",
"sphinxcontrib-applehelp==1.0.2",
"sphinxcontrib-autoyaml==1.0.0",
"sphinxcontrib-devhelp==1.0.2",
"sphinxcontrib-htmlhelp==2.0.0",
"sphinxcontrib-jsmath==1.0.1",
"sphinxcontrib-qthelp==1.0.3",
"sphinxcontrib-serializinghtml==1.1.5",
"stack-data==0.3.0",
"tinycss2==1.1.1",
"tornado==6.4.2",
"tqdm==4.66.3",
"traitlets==5.3.0",
"urllib3==1.26.19",
"wcwidth==0.2.5",
"webencodings==0.5.1",
"ipython>=8.18.0",
"nbconvert==7.0.0rc0",
"mistune==2.0.3",
"sphinxcontrib-bibtex==2.6.3",
"setuptools>=58.2.0",
]
linting = [
"flake8>=7.1.1",
"ruff>=0.8.3",
]
tests = [
"coverage>=7.6.9",
"pytest-cov>=6.0.0",
"pytest>=8.3.4",
]

[tool.hatch.metadata]
allow-direct-references = true

[tool.hatch.build.targets.wheel]
packages = ["openvariant"]

[tool.uv.sources]
open-variant = { workspace = true }

[tool.ruff.lint]
select = ["F"]
ignore = ["F401"]

[tool.ruff]
line-length = 127

[tool.ruff.format]
quote-style = "single"
indent-style = "space"
docstring-code-format = true
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