Run pre-commit on all files (#202)

Author: jparismorgan

.clang-format

@@ -1,12 +1,12 @@
 ---
-Language:        Cpp
+Language: Cpp
 # BasedOnStyle:  Google
 AccessModifierOffset: -1
 AlignAfterOpenBracket: AlwaysBreak
 AlignConsecutiveAssignments: false
 AlignConsecutiveDeclarations: false
 AlignEscapedNewlinesLeft: true
-AlignOperands:   true
+AlignOperands: true
 AlignTrailingComments:
   Kind: Always
   OverEmptyLines: 0
@@ -22,54 +22,54 @@ AlwaysBreakBeforeMultilineStrings: true
 AlwaysBreakTemplateDeclarations: true
 BinPackArguments: false
 BinPackParameters: false
-BraceWrapping:   
-  AfterClass:      false
+BraceWrapping:
+  AfterClass: false
   AfterControlStatement: false
-  AfterEnum:       false
-  AfterFunction:   false
-  AfterNamespace:  false
+  AfterEnum: false
+  AfterFunction: false
+  AfterNamespace: false
   AfterObjCDeclaration: false
-  AfterStruct:     false
-  AfterUnion:      false
-  BeforeCatch:     false
-  BeforeElse:      false
-  IndentBraces:    false
+  AfterStruct: false
+  AfterUnion: false
+  BeforeCatch: false
+  BeforeElse: false
+  IndentBraces: false
 BreakBeforeBinaryOperators: None
 BreakBeforeBraces: Attach
 BreakBeforeTernaryOperators: false
 BreakConstructorInitializersBeforeComma: true
 BreakAfterJavaFieldAnnotations: false
 BreakStringLiterals: true
-ColumnLimit:     80
-CommentPragmas:  '^ IWYU pragma:'
+ColumnLimit: 80
+CommentPragmas: "^ IWYU pragma:"
 BreakBeforeInheritanceComma: false
 ConstructorInitializerAllOnOneLineOrOnePerLine: false
 ConstructorInitializerIndentWidth: 4
 ContinuationIndentWidth: 4
 Cpp11BracedListStyle: true
 DerivePointerAlignment: false
-DisableFormat:   false
+DisableFormat: false
 ExperimentalAutoDetectBinPacking: false
 FixNamespaceComments: true
-ForEachMacros:   [ foreach, Q_FOREACH, BOOST_FOREACH ]
-IncludeCategories: 
-  - Regex:           '^<.*\.h>'
-    Priority:        1
-  - Regex:           '^<.*'
-    Priority:        2
-  - Regex:           '.*'
-    Priority:        3
-IncludeIsMainRegex: '([-_](test|unittest))?$'
+ForEachMacros: [foreach, Q_FOREACH, BOOST_FOREACH]
+IncludeCategories:
+  - Regex: '^<.*\.h>'
+    Priority: 1
+  - Regex: "^<.*"
+    Priority: 2
+  - Regex: ".*"
+    Priority: 3
+IncludeIsMainRegex: "([-_](test|unittest))?$"
 IndentCaseLabels: true
 IndentRequiresClause: true
-IndentWidth:     2
+IndentWidth: 2
 IndentWrappedFunctionNames: false
 InsertNewlineAtEOF: true
 JavaScriptQuotes: Leave
 JavaScriptWrapImports: true
 KeepEmptyLinesAtTheStartOfBlocks: false
-MacroBlockBegin: ''
-MacroBlockEnd:   ''
+MacroBlockBegin: ""
+MacroBlockEnd: ""
 MaxEmptyLinesToKeep: 1
 NamespaceIndentation: None
 PenaltyBreakBeforeFirstCallParameter: 1
@@ -79,22 +79,21 @@ PenaltyBreakString: 1000
 PenaltyExcessCharacter: 1000000
 PenaltyReturnTypeOnItsOwnLine: 200
 PointerAlignment: Left
-ReflowComments:  true
+ReflowComments: true
 RequiresClausePosition: OwnLine
 RequiresExpressionIndentation: OuterScope
-SortIncludes:    true
+SortIncludes: true
 SpaceAfterCStyleCast: false
 SpaceAfterTemplateKeyword: true
 SpaceBeforeAssignmentOperators: true
 SpaceBeforeParens: ControlStatements
 SpaceInEmptyParentheses: false
 SpacesBeforeTrailingComments: 2
-SpacesInAngles:  false
+SpacesInAngles: false
 SpacesInContainerLiterals: true
 SpacesInCStyleCastParentheses: false
 SpacesInParentheses: false
 SpacesInSquareBrackets: false
-Standard:        Cpp11
-TabWidth:        8
-UseTab:          Never
-...
+Standard: Cpp11
+TabWidth: 8
+UseTab: Never

.github/workflows/build-wheels.yml

@@ -5,12 +5,12 @@ on:
   push:
     branches:
       - release-*
-      - '*wheel*'  # must quote since "*" is a YAML reserved character; we want a string
+      - "*wheel*" # must quote since "*" is a YAML reserved character; we want a string
     tags:
-      - '*'
+      - "*"
   pull_request:
     branches:
-      - '*wheel*'  # must quote since "*" is a YAML reserved character; we want a string
+      - "*wheel*" # must quote since "*" is a YAML reserved character; we want a string
 
 jobs:
   generate_backwards_compatibility_data:
@@ -19,7 +19,7 @@ jobs:
     steps:
       - name: Checkout code
         uses: actions/checkout@v3
-      
+
       # Based on https://github.com/TileDB-Inc/conda-forge-nightly-controller/blob/51519a0f8340b32cf737fcb59b76c6a91c42dc47/.github/workflows/activity.yml#L19C10-L19C10
       - name: Setup git
         run: |
@@ -74,7 +74,7 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
-      - name: 'Brew setup on macOS' # x-ref c8e49ba8f8b9ce
+      - name: "Brew setup on macOS" # x-ref c8e49ba8f8b9ce
         if: ${{ startsWith(matrix.os, 'macos-') == true }}
         run: |
           set -e pipefail
@@ -94,7 +94,6 @@ jobs:
       - uses: actions/upload-artifact@v3
         with:
           path: ./wheelhouse/*.whl
-
 # TODO: Needs support for pulling in the root directory
 #  build_sdist:
 #    name: Build source distribution

.github/workflows/check-formatting.yml

@@ -5,23 +5,23 @@ on:
     branches:
       - main
     paths-ignore:
-      - '_quarto.yml'
-      - 'quarto-materials/*'
-      - '**/.md'
+      - "_quarto.yml"
+      - "quarto-materials/*"
+      - "**/.md"
   pull_request:
     branches:
       - main
     paths-ignore:
-      - '_quarto.yml'
-      - 'quarto-materials/*'
-      - '**/.md'
+      - "_quarto.yml"
+      - "quarto-materials/*"
+      - "**/.md"
 
 jobs:
   check-formatting:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
-      - name: 'Check clang-format'
+      - name: "Check clang-format"
         run: |
           source $GITHUB_WORKSPACE/scripts/ci/check_clang_format.sh
-        shell: bash
+        shell: bash

.gitignore

@@ -105,4 +105,4 @@ documentation/reference
 *DS_Store
 
 # CMake
-*/cmake-build-*
+*/cmake-build-*

.pre-commit-config.yaml

@@ -26,6 +26,7 @@ repos:
       - id: black
 
   - repo: https://github.com/pre-commit/mirrors-clang-format
-    rev: 'v17.0.6'
+    rev: "v17.0.6"
     hooks:
-      - id: clang-format
+      - id: clang-format
+        exclude: '\.ipynb$'

README.md

@@ -1,23 +1,21 @@
 <a href="https://tiledb.com"><img src="https://github.com/TileDB-Inc/TileDB/raw/dev/doc/source/_static/[email protected]" alt="TileDB logo" width="400"></a>
 
-
-
 # TileDB Vector Search
 
-*TileDB-Vector-Search* is a C++ library and Python API for vector search built on top of the [TileDB Storage Engine](https://github.com/TileDB-Inc/TileDB).
+_TileDB-Vector-Search_ is a C++ library and Python API for vector search built on top of the [TileDB Storage Engine](https://github.com/TileDB-Inc/TileDB).
 
 Please see the following blog posts for background:
 
-* [Why TileDB as a Vector Database](https://tiledb.com/blog/why-tiledb-as-a-vector-database)
-* [TileDB Vector Search 101](https://tiledb.com/blog/tiledb-101-vector-search/)
+- [Why TileDB as a Vector Database](https://tiledb.com/blog/why-tiledb-as-a-vector-database)
+- [TileDB Vector Search 101](https://tiledb.com/blog/tiledb-101-vector-search/)
 
 We have released a [LangChain integration](https://python.langchain.com/docs/integrations/vectorstores/tiledb), with others to come soon.
 
 # Quick Links
 
-* [Build Instructions](https://tiledb-inc.github.io/TileDB-Vector-Search/documentation/Building.html)
-* [Documentation](https://tiledb-inc.github.io/TileDB-Vector-Search/)
-* [Python API reference](https://tiledb-inc.github.io/TileDB-Vector-Search/documentation/reference/)
+- [Build Instructions](https://tiledb-inc.github.io/TileDB-Vector-Search/documentation/Building.html)
+- [Documentation](https://tiledb-inc.github.io/TileDB-Vector-Search/)
+- [Python API reference](https://tiledb-inc.github.io/TileDB-Vector-Search/documentation/reference/)
 
 # Quick Installation
 
@@ -40,4 +38,4 @@ We welcome contributions. Please see [`Building`](./documentation/Building.md) f
 development-build instructions. For large new
 features, please open an issue to discuss goals and approach in order
 to ensure a smooth PR integration and review process. All contributions
-must be licensed under the repository's [MIT License](./LICENSE).
+must be licensed under the repository's [MIT License](./LICENSE).

_quarto.yml

@@ -36,10 +36,10 @@ quartodoc:
     - title: "tiledb.vector_search"
       desc: ""
       contents:
-          - index.Index
-          - flat_index.FlatIndex
-          - ivf_flat_index.IVFFlatIndex
-          - ingestion
+        - index.Index
+        - flat_index.FlatIndex
+        - ivf_flat_index.IVFFlatIndex
+        - ingestion
 
 website:
   favicon: "documentation/assets/tiledb.ico"

apis/python/MANIFEST.in

@@ -5,4 +5,4 @@
 global-exclude *
 include pyproject.toml
 include MANIFEST.in
-recursive-include src *.py
+recursive-include src *.py

apis/python/requirements-py.txt

@@ -1,3 +1,3 @@
 numpy==1.24.3
 tiledb-cloud==0.10.24
-tiledb==0.25.0
+tiledb==0.25.0

apis/python/src/tiledb/vector_search/__init__.py

@@ -6,11 +6,19 @@
 from .index import Index
 from .ingestion import ingest
 from .ivf_flat_index import IVFFlatIndex
-from .module import (array_to_matrix, ivf_index, ivf_index_tdb, ivf_query,
-                     ivf_query_ram, load_as_array, load_as_matrix,
-                     partition_ivf_index, query_vq_heap, query_vq_nth,
-                     validate_top_k)
-from .storage_formats import STORAGE_VERSION, storage_formats
+from .module import array_to_matrix
+from .module import ivf_index
+from .module import ivf_index_tdb
+from .module import ivf_query
+from .module import ivf_query_ram
+from .module import load_as_array
+from .module import load_as_matrix
+from .module import partition_ivf_index
+from .module import query_vq_heap
+from .module import query_vq_nth
+from .module import validate_top_k
+from .storage_formats import STORAGE_VERSION
+from .storage_formats import storage_formats
 
 from  ._tiledbvspy import FeatureVector
 from  ._tiledbvspy import FeatureVectorArray
@@ -41,4 +49,6 @@
     "array_to_matrix",
     "partition_ivf_index",
     "utils",
+    "STORAGE_VERSION",
+    "storage_formats",
 ]