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Duckdb query engine #10

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merged 45 commits into from
Feb 22, 2024
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8e6032f
added basic interface for query engine
Mittmich Nov 19, 2023
3e8c4f1
Added explanations
Mittmich Nov 19, 2023
942e946
added query step protocol to query engine interface
Mittmich Nov 21, 2023
28fad15
Update duckdb version to 0.9.1
Mittmich Nov 21, 2023
6992d26
Add support for DuckDBPyRelation in dataframe
Mittmich Nov 21, 2023
96cf7f7
added examples to query engine interface
Mittmich Nov 24, 2023
bf5c53e
Refactor RegionFilter to Snipper
Mittmich Nov 26, 2023
e965eeb
Add GenomicDataSchema protocol and implement
Mittmich Nov 26, 2023
d990363
added single region selection implementation
Mittmich Dec 8, 2023
c06a7f4
Add anchor validation in Snipper class
Mittmich Dec 8, 2023
a45b1e5
blackify
Mittmich Dec 8, 2023
5d5347f
Refactor code and fix imports
Mittmich Dec 8, 2023
7d9cfd6
pixels snipping tests passing
Mittmich Dec 8, 2023
f056b3a
Refactor code formatting
Mittmich Dec 8, 2023
bef26e6
pylint and black
Mittmich Dec 8, 2023
a16f6e6
added documentation for snipping
Mittmich Dec 27, 2023
dac123f
updated documentation
Mittmich Dec 27, 2023
9c335d2
renamed region columns
Mittmich Dec 28, 2023
17f8ad8
untested offset transformation
Mittmich Dec 28, 2023
59b9765
regionoffset working
Mittmich Dec 29, 2023
fb58f9b
Remove unused imports and fixtures
Mittmich Dec 29, 2023
8f3be96
Refactor imports and fix formatting issues
Mittmich Dec 29, 2023
e1376b5
Update imports and ignore additional flake8 warnings
Mittmich Dec 29, 2023
540fc43
Add tests for offset aggregation functions in query engine
Mittmich Jan 3, 2024
be90c4f
added additional test for column name
Mittmich Jan 3, 2024
fb543ed
added tests for aggregation on dense input
Mittmich Jan 3, 2024
8add40d
added addiitonal tests for offsetaggregation
Mittmich Jan 7, 2024
50e0a83
Add region_number attribute to QueryStepDataSchema and ContactSchema;…
Mittmich Jan 13, 2024
9249542
added documentation
Mittmich Jan 21, 2024
430630b
updated documenatation page
Mittmich Jan 25, 2024
37cd211
added use case for contact counting
Mittmich Jan 28, 2024
cf0672e
implemented PR changes
Mittmich Feb 4, 2024
a073331
added duckdb parquet reader function
Mittmich Feb 4, 2024
93aeb22
added check for data mode
Mittmich Feb 4, 2024
92b24f1
Merge branch 'duckdb-transform-aggregation' into duckdb-query-engine
Mittmich Feb 4, 2024
b738f8e
added case whne regions are nested
Mittmich Feb 4, 2024
c58a7b2
renamed BasicQuery, QueryResult and Snipper
Mittmich Feb 4, 2024
e679062
fixed typos in query_engine_interface
Mittmich Feb 11, 2024
da256e1
code review comments for uery engine usage
Mittmich Feb 11, 2024
0218326
added string parsing for enums
Mittmich Feb 11, 2024
555e64e
added capability to specify a subset of positions for offsetaggregation
Mittmich Feb 11, 2024
a5c60b1
added explicit rejection of contacts to offsetaggregation
Mittmich Feb 20, 2024
2582252
added expliict windowsize handling
Mittmich Feb 20, 2024
6b2ad66
renamed window size
Mittmich Feb 21, 2024
94c8825
Renamed offset to distance
Mittmich Feb 21, 2024
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35 changes: 35 additions & 0 deletions .pre-commit-config.yaml
dmitrymyl marked this conversation as resolved.
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Original file line number Diff line number Diff line change
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repos:
- repo: https://github.com/asottile/reorder-python-imports
rev: v3.12.0
hooks:
- id: reorder-python-imports
exclude: ^(pre_commit/resources/|testing/resources/python3_hooks_repo/)
args: [--py38-plus]
- repo: https://github.com/PyCQA/flake8
rev: 6.1.0
hooks:
- id: flake8
args: ["--ignore=E501,W503,W291"]
- repo: https://github.com/pre-commit/mirrors-mypy
rev: v1.7.1
hooks:
- id: mypy
additional_dependencies: [types-all]
exclude: ^testing/resources/
- repo: https://github.com/psf/black-pre-commit-mirror
rev: 23.12.1
hooks:
- id: black
# It is recommended to specify the latest version of Python
# supported by your project here, or alternatively use
# pre-commit's default_language_version, see
# https://pre-commit.com/#top_level-default_language_version
language_version: python3.11
- repo: local
hooks:
- id: pylint
name: pylint
entry: pylint
language: system
types: [python]
args: ["--disable=C0301,W0511"]
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