Duckdb query engine (#10)

* added basic interface for query engine

* Added explanations

* added query step protocol to query engine interface

* Update duckdb version to 0.9.1

* Add support for DuckDBPyRelation in dataframe
models and query engine

* added examples to query engine interface

* Refactor RegionFilter to Snipper

* Add GenomicDataSchema protocol and implement
position field and contact order methods

* added single region selection implementation

* Add anchor validation in Snipper class

* blackify

* Refactor code and fix imports

* pixels snipping tests passing

* Refactor code formatting

* pylint and black

* added documentation for snipping

* updated documentation

* renamed region columns

* untested offset transformation

* regionoffset working

* Remove unused imports and fixtures

* Refactor imports and fix formatting issues

* Update imports and ignore additional flake8 warnings

* Add tests for offset aggregation functions in query engine

* added additional test for column name

* added tests for aggregation on dense input

* added addiitonal tests for offsetaggregation

* Add region_number attribute to QueryStepDataSchema and ContactSchema; implemented new aggregation method

* added documentation

* updated documenatation page

* added use case for contact counting

* implemented PR changes

* added duckdb parquet reader function

* added check for data mode

* added case whne regions are nested

* renamed BasicQuery, QueryResult and Snipper

* fixed typos in query_engine_interface

* code review comments for uery engine usage

* added string parsing for enums

* added capability to specify a subset of positions for offsetaggregation

* added explicit rejection of contacts to offsetaggregation

* added expliict windowsize handling

* renamed window size

* Renamed offset to distance

.pre-commit-config.yaml

@@ -0,0 +1,35 @@
+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"]