refactor(api): update for CE protobuf refactoring and Python 3.13 support

[pinglin]

Because

• The protobuf definitions were refactored in CE, renaming Catalog to KnowledgeBase and restructuring the artifact service APIs
• Credit and subscription management endpoints were removed from the CE version of the mgmt API
• Python 3.13 support is needed for the SDK
• Multiple dependency conflicts existed between newer packages required for Python 3.13 and older transitive dependencies

This commit

• Refactors ArtifactClient (instill/clients/artifact.py):

  • Renames all catalog methods to knowledge_base methods
  • Updates imports to reflect new protobuf file structure (artifact_pb2 → file_pb2, knowledge_base_pb2)
  • Adds new methods: list_knowledge_base_runs(), get_chunk()
  • Removes deprecated methods: process_catalog_files(), question_answering(), get_file_catalog()
  • Updates search_chunks() with new parameters: chunk_type, file_media_type, file_ids, tags
  • Fixes mypy type errors by properly constructing protobuf requests instead of using dict unpacking
  • Adds type ignore comments for protobuf enum assignments

• Updates MgmtClient (instill/clients/mgmt.py):

  • Removes CE-specific credit endpoints: get_remaining_credit(), list_credit_consumption_chart_records()
  • Removes CE-specific subscription endpoints: get_authenticated_subscription(), get_organization_subscription()

• Fixes file processing utility (instill/utils/process_file.py):

  • Updates imports from artifact_pb2 to file_pb2 for File message
  • Changes enum handling from string format ("FILE_TYPE_TEXT") to protobuf enum constants (file_interface.File.TYPE_TEXT)
  • Fixes field name from name to filename in File construction
  • Returns proper enum values instead of strings from get_file_type()

• Updates tests (instill/tests/test_utils.py):

  • Adds file_interface import for protobuf enums
  • Updates all assertions to use enum constants instead of string values
  • Fixes field references from result.name to result.filename
  • Separates CSV type testing from TEXT type (CSV has its own TYPE_CSV)
  • Adds pylint disable comment for protobuf module false positives

• Upgrades dependencies for Python 3.13 support (pyproject.toml):

  • Updates Python version constraint: >=3.9,<3.13 → >=3.9,<3.14
  • Updates core dependencies:
    • grpcio: ^1.59.0 → ^1.68.0 (Python 3.13 support)
    • grpcio-tools: 1.62.0 → ^1.68.0 (Python 3.13 build support)
    • protobuf: 4.25.8 → ^5.28.0 (required by grpcio 1.68+)
    • types-protobuf: ^4.24.0.1 → ^5.28.0
    • numpy: ^1.21.0 → >=1.26,<1.28 (Python 3.13 support while avoiding scipy/cupy conflicts)
    • pillow: ^10.1.0 → ^11.0.0
    • pyinstaller: 6.0.0 → ^6.16.0
    • google-api-core: ^2.11.1 → {version = "^2.22.0", extras = ["grpc"]}
    • ray: 2.47.0 → {version = "^2.47.0", extras = ["default"]}
  • Restricts incompatible macOS dev dependencies to Python < 3.13:
    • MacFSEvents = {version = "*", platform = "darwin", python = "<3.13"}
    • sniffer = {version = "*", python = "<3.13"}
  • Explicitly upgrades opentelemetry packages to resolve protobuf 5.x conflicts:
    • opentelemetry-proto = "^1.29.0"
    • opentelemetry-exporter-otlp = "^1.29.0"
    • opentelemetry-exporter-otlp-proto-common = "^1.29.0"
    • opentelemetry-exporter-otlp-proto-grpc = "^1.29.0"
    • opentelemetry-exporter-otlp-proto-http = "^1.29.0"

• Resolves all dependency conflicts:

  • Eliminates numpy version warnings from scipy/cupy by using numpy 1.26-1.27
  • Fixes opentelemetry-proto protobuf <5.0 requirement by upgrading to 1.29+
  • Ensures all opentelemetry exporters are compatible versions

Testing

• All mypy type checks pass
• All pylint checks pass (excluding pre-existing warnings)
• File type enum handling verified through test updates
• Dependency installation completes without conflicts

Breaking Changes

• Method names in ArtifactClient changed from *_catalog* to *_knowledge_base*
• Removed methods: process_catalog_files(), question_answering(), get_file_catalog()
• Removed methods in MgmtClient: get_remaining_credit(), list_credit_consumption_chart_records(), get_authenticated_subscription(), get_organization_subscription()
• process_file() utility now returns protobuf enum values instead of strings for file types