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setup.py
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setup.py
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from itertools import chain
from setuptools import setup
# at least 1.3 to be able to use XMLDataSet and pandas integration with fsspec
PANDAS = "pandas>=1.3, <3.0"
SPARK = "pyspark>=2.2, <4.0"
HDFS = "hdfs>=2.5.8, <3.0"
S3FS = "s3fs>=0.3.0, <0.5"
POLARS = "polars>=0.18.0"
DELTA = "delta-spark~=1.2.1"
def _collect_requirements(requires):
return sorted(set(chain.from_iterable(requires.values())))
api_require = {"api.APIDataSet": ["requests~=2.20"]}
biosequence_require = {"biosequence.BioSequenceDataSet": ["biopython~=1.73"]}
dask_require = {
"dask.ParquetDataSet": ["dask[complete]>=2021.10", "triad>=0.6.7, <1.0"]
}
databricks_require = {"databricks.ManagedTableDataSet": [SPARK, PANDAS, DELTA]}
geopandas_require = {
"geopandas.GeoJSONDataSet": ["geopandas>=0.6.0, <1.0", "pyproj~=3.0"]
}
holoviews_require = {"holoviews.HoloviewsWriter": ["holoviews~=1.13.0"]}
matplotlib_require = {"matplotlib.MatplotlibWriter": ["matplotlib>=3.0.3, <4.0"]}
networkx_require = {"networkx.NetworkXDataSet": ["networkx~=2.4"]}
pandas_require = {
"pandas.CSVDataSet": [PANDAS],
"pandas.ExcelDataSet": [PANDAS, "openpyxl>=3.0.6, <4.0"],
"pandas.DeltaTableDataSet": [PANDAS, "deltalake>=0.10.0"],
"pandas.FeatherDataSet": [PANDAS],
"pandas.GBQTableDataSet": [PANDAS, "pandas-gbq>=0.12.0, <0.18.0"],
"pandas.GBQQueryDataSet": [PANDAS, "pandas-gbq>=0.12.0, <0.18.0"],
"pandas.HDFDataSet": [
PANDAS,
"tables~=3.6.0; platform_system == 'Windows'",
"tables~=3.6, <3.9; platform_system != 'Windows' and python_version<'3.9'",
"tables~=3.6; platform_system != 'Windows' and python_version>='3.9'",
],
"pandas.JSONDataSet": [PANDAS],
"pandas.ParquetDataSet": [PANDAS, "pyarrow>=6.0"],
"pandas.SQLTableDataSet": [PANDAS, "SQLAlchemy>=1.4, <3.0"],
"pandas.SQLQueryDataSet": [PANDAS, "SQLAlchemy>=1.4, <3.0", "pyodbc~=4.0"],
"pandas.XMLDataSet": [PANDAS, "lxml~=4.6"],
"pandas.GenericDataSet": [PANDAS],
}
pickle_require = {"pickle.PickleDataSet": ["compress-pickle[lz4]~=2.1.0"]}
pillow_require = {"pillow.ImageDataSet": ["Pillow~=9.0"]}
plotly_require = {
"plotly.PlotlyDataSet": [PANDAS, "plotly>=4.8.0, <6.0"],
"plotly.JSONDataSet": ["plotly>=4.8.0, <6.0"],
}
polars_require = {
"polars.CSVDataSet": [POLARS],
"polars.GenericDataSet":
[
POLARS, "pyarrow>=4.0", "xlsx2csv>=0.8.0", "deltalake >= 0.6.2"
],
"polars.EagerPolarsDataset":
[
POLARS, "pyarrow>=4.0", "xlsx2csv>=0.8.0", "deltalake >= 0.6.2"
],
"polars.LazyPolarsDataset":
[
# Note: there is no Lazy read Excel option, so we exclude xlsx2csv here.
POLARS, "pyarrow>=4.0", "deltalake >= 0.6.2"
],
}
redis_require = {"redis.PickleDataSet": ["redis~=4.1"]}
snowflake_require = {
"snowflake.SnowparkTableDataSet": [
"snowflake-snowpark-python~=1.0.0",
"pyarrow~=8.0",
]
}
spark_require = {
"spark.SparkDataSet": [SPARK, HDFS, S3FS],
"spark.SparkHiveDataSet": [SPARK, HDFS, S3FS],
"spark.SparkJDBCDataSet": [SPARK, HDFS, S3FS],
"spark.DeltaTableDataSet": [SPARK, HDFS, S3FS, "delta-spark>=1.0, <3.0"],
}
svmlight_require = {"svmlight.SVMLightDataSet": ["scikit-learn~=1.0.2", "scipy~=1.7.3"]}
tensorflow_require = {
"tensorflow.TensorFlowModelDataSet": [
# currently only TensorFlow V2 supported for saving and loading.
# V1 requires HDF5 and serialises differently
"tensorflow~=2.0; platform_system != 'Darwin' or platform_machine != 'arm64'",
# https://developer.apple.com/metal/tensorflow-plugin/
"tensorflow-macos~=2.0; platform_system == 'Darwin' and platform_machine == 'arm64'",
]
}
video_require = {"video.VideoDataSet": ["opencv-python~=4.5.5.64"]}
yaml_require = {"yaml.YAMLDataSet": [PANDAS, "PyYAML>=4.2, <7.0"]}
extras_require = {
"api": _collect_requirements(api_require),
"biosequence": _collect_requirements(biosequence_require),
"dask": _collect_requirements(dask_require),
"databricks": _collect_requirements(databricks_require),
"geopandas": _collect_requirements(geopandas_require),
"holoviews": _collect_requirements(holoviews_require),
"matplotlib": _collect_requirements(matplotlib_require),
"networkx": _collect_requirements(networkx_require),
"pandas": _collect_requirements(pandas_require),
"pickle": _collect_requirements(pickle_require),
"pillow": _collect_requirements(pillow_require),
"plotly": _collect_requirements(plotly_require),
"polars": _collect_requirements(polars_require),
"redis": _collect_requirements(redis_require),
"snowflake": _collect_requirements(snowflake_require),
"spark": _collect_requirements(spark_require),
"svmlight": _collect_requirements(svmlight_require),
"tensorflow": _collect_requirements(tensorflow_require),
"video": _collect_requirements(video_require),
"yaml": _collect_requirements(yaml_require),
**api_require,
**biosequence_require,
**dask_require,
**databricks_require,
**geopandas_require,
**holoviews_require,
**matplotlib_require,
**networkx_require,
**pandas_require,
**pickle_require,
**pillow_require,
**plotly_require,
**polars_require,
**snowflake_require,
**spark_require,
**svmlight_require,
**tensorflow_require,
**video_require,
**yaml_require,
}
extras_require["all"] = _collect_requirements(extras_require)
extras_require["docs"] = [
# docutils>=0.17 changed the HTML
# see https://github.com/readthedocs/sphinx_rtd_theme/issues/1115
"docutils==0.16",
"sphinx~=5.3.0",
"sphinx_rtd_theme==1.2.0",
# Regression on sphinx-autodoc-typehints 1.21
# that creates some problematic docstrings
"sphinx-autodoc-typehints==1.20.2",
"sphinx_copybutton==0.3.1",
"sphinx-notfound-page",
"ipykernel>=5.3, <7.0",
"sphinxcontrib-mermaid~=0.7.1",
"myst-parser~=1.0.0",
"Jinja2<3.1.0",
]
extras_require["test"] = [
"adlfs>=2021.7.1, <=2022.2; python_version == '3.7'",
"adlfs~=2023.1; python_version >= '3.8'",
"bandit>=1.6.2, <2.0",
"behave==1.2.6",
"biopython~=1.73",
"blacken-docs==1.9.2",
"black~=22.0",
"cloudpickle<=2.0.0",
"compress-pickle[lz4]~=2.1.0",
"coverage[toml]",
"dask[complete]~=2021.10", # pinned by Snyk to avoid a vulnerability
"delta-spark>=1.2.1; python_version >= '3.11'", # 1.2.0 has a bug that breaks some of our tests: https://github.com/delta-io/delta/issues/1070
"delta-spark~=1.2.1; python_version < '3.11'",
"deltalake>=0.10.0",
"dill~=0.3.1",
"filelock>=3.4.0, <4.0",
"gcsfs>=2021.4, <=2023.1; python_version == '3.7'",
"gcsfs>=2023.1, <2023.3; python_version >= '3.8'",
"geopandas>=0.6.0, <1.0",
"hdfs>=2.5.8, <3.0",
"holoviews>=1.13.0",
"import-linter[toml]==1.2.6",
"ipython>=7.31.1, <8.0",
"Jinja2<3.1.0",
"joblib>=0.14",
"jupyterlab~=3.0",
"jupyter~=1.0",
"lxml~=4.6",
"matplotlib>=3.0.3, <3.4; python_version < '3.10'", # 3.4.0 breaks holoviews
"matplotlib>=3.5, <3.6; python_version >= '3.10'",
"memory_profiler>=0.50.0, <1.0",
"moto==1.3.7; python_version < '3.10'",
"moto==4.1.12; python_version >= '3.10'",
"networkx~=2.4",
"opencv-python~=4.5.5.64",
"openpyxl>=3.0.3, <4.0",
"pandas-gbq>=0.12.0, <0.18.0; python_version < '3.11'",
"pandas-gbq>=0.18.0; python_version >= '3.11'",
"pandas~=1.3 # 1.3 for read_xml/to_xml",
"Pillow~=9.0",
"plotly>=4.8.0, <6.0",
"polars[xlsx2csv, deltalake]~=0.18.0",
"pre-commit>=2.9.2",
"pyarrow>=1.0; python_version < '3.11'",
"pyarrow>=7.0; python_version >= '3.11'", # Adding to avoid numpy build errors
"pyodbc~=4.0.35",
"pyproj~=3.0",
"pyspark>=2.2, <3.4; python_version < '3.11'",
"pyspark>=3.4; python_version >= '3.11'",
"pytest-cov~=3.0",
"pytest-mock>=1.7.1, <2.0",
"pytest-xdist[psutil]~=2.2.1",
"pytest~=7.2",
"redis~=4.1",
"requests-mock~=1.6",
"requests~=2.20",
"ruff~=0.0.290",
"s3fs>=0.3.0, <0.5", # Needs to be at least 0.3.0 to make use of `cachable` attribute on S3FileSystem.
"snowflake-snowpark-python~=1.0.0; python_version == '3.8'",
"scikit-learn>=1.0.2,<2",
"scipy>=1.7.3",
"packaging",
"SQLAlchemy~=1.2",
"tables~=3.6.0; platform_system == 'Windows' and python_version<'3.8'",
"tables~=3.8.0; platform_system == 'Windows' and python_version>='3.8'", # Import issues with python 3.8 with pytables pinning to 3.8.0 fixes this https://github.com/PyTables/PyTables/issues/933#issuecomment-1555917593
"tables~=3.6, <3.9; platform_system != 'Windows' and python_version<'3.9'",
"tables~=3.6; platform_system != 'Windows' and python_version>='3.9'",
"tensorflow-macos~=2.0; platform_system == 'Darwin' and platform_machine == 'arm64'",
"tensorflow~=2.0; platform_system != 'Darwin' or platform_machine != 'arm64'",
"triad>=0.6.7, <1.0",
"trufflehog~=2.1",
"xlsxwriter~=1.0",
]
setup(
extras_require=extras_require,
)