From 43b476bf1089120053356b749e17b98010f91fc0 Mon Sep 17 00:00:00 2001 From: Josh Seese Date: Thu, 2 Apr 2026 17:24:36 -0400 Subject: [PATCH 1/4] Boilerplate Code. --- .dockerignore | 2 +- .github/pull_request_template.md | 2 +- .github/workflows/ci.yml | 5 +- .pre-commit-config.yaml | 67 +- LICENSE | 0 README.md | 55 +- README_orig.md | 30 + dataconnect/__init__.py | 23 + dataconnect/_encoding.py | 16 + dataconnect/auth.py | 16 + dataconnect/client.py | 93 ++ dataconnect/exceptions.py | 19 + dataconnect/framework/__init__.py | 0 dataconnect/framework/pyarrow_transport.py | 100 ++ dataconnect/framework/transport.py | 44 + dataconnect/models.py | 28 + dataconnect/py.typed | 0 poetry.lock | 1427 ++++++++++++-------- pyproject.toml | 50 +- pyproject_orig.toml | 68 + python_template/__init__.py | 1 - python_template/reverse.py | 27 - scripts/benchmark.sh | 0 scripts/install.sh | 0 scripts/lint.sh | 0 scripts/test.sh | 0 scripts/typecheck.sh | 2 +- tests/conftest.py | 28 - tests/mocks/words.yml | 4 - tests/test_benchmark_reverser.py | 13 - tests/test_client.py | 11 + tests/test_python_template.py | 5 - tests/test_reversers.py | 38 - 33 files changed, 1437 insertions(+), 737 deletions(-) create mode 100644 LICENSE create mode 100644 README_orig.md create mode 100644 dataconnect/__init__.py create mode 100644 dataconnect/_encoding.py create mode 100644 dataconnect/auth.py create mode 100644 dataconnect/client.py create mode 100644 dataconnect/exceptions.py create mode 100644 dataconnect/framework/__init__.py create mode 100644 dataconnect/framework/pyarrow_transport.py create mode 100644 dataconnect/framework/transport.py create mode 100644 dataconnect/models.py create mode 100644 dataconnect/py.typed create mode 100644 pyproject_orig.toml delete mode 100644 python_template/__init__.py delete mode 100644 python_template/reverse.py mode change 100755 => 100644 scripts/benchmark.sh mode change 100755 => 100644 scripts/install.sh mode change 100755 => 100644 scripts/lint.sh mode change 100755 => 100644 scripts/test.sh delete mode 100644 tests/conftest.py delete mode 100644 tests/mocks/words.yml delete mode 100644 tests/test_benchmark_reverser.py create mode 100644 tests/test_client.py delete mode 100644 tests/test_python_template.py delete mode 100644 tests/test_reversers.py diff --git a/.dockerignore b/.dockerignore index 6541362..ae0c2b1 100644 --- a/.dockerignore +++ b/.dockerignore @@ -14,4 +14,4 @@ **/.git* **/.*project **/.DS_Store -**/._* \ No newline at end of file +**/._* diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md index 86d7758..e2d2831 100644 --- a/.github/pull_request_template.md +++ b/.github/pull_request_template.md @@ -9,7 +9,7 @@ - [ ] Make sure the pull request does not have excessive number of unnecessary commits. Utilize the `git commit --amend --no-edit` command to reduce commit messages when making small file changes (*like changing linespacing*). - [ ] Make sure you have added unit tests for the code changes. Tests should be added in the `tests/` folder. - [ ] Modify docs, if required. Add any new documentation in the `doc/` folder. -- [ ] Rebase on latest active development branch (develop/main). +- [ ] Rebase on latest active development branch (develop/main). ### Changes Summary diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index c270622..c503b3f 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -29,7 +29,9 @@ jobs: key: ${{ runner.os }}-precommit-${{ hashFiles('.pre-commit-config.yaml') }} - name: lint - run: scripts/lint.sh + run: | + chmod +x scripts/lint.sh + scripts/lint.sh - name: build docker image working-directory: ${{ github.workspace }} @@ -50,4 +52,3 @@ jobs: - name: typecheck run: docker run dataconnect-library-python "scripts/typecheck.sh" - diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 5f3c57a..86ded94 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,29 +1,44 @@ +# Pre-commit hook configuration +# Docs: https://pre-commit.com/ +# +# Install: +# pip install pre-commit # or: poetry install --with lint +# pre-commit install # register the git hook +# +# Run manually against all files: +# pre-commit run --all-files +# +# Update hook revisions to latest: +# pre-commit autoupdate + +default_language_version: + python: python3.11 + repos: - - repo: https://github.com/ambv/black - # rev must match pyproject.toml - rev: 23.3.0 + # --------------------------------------------------------------------------- + # General hygiene + # --------------------------------------------------------------------------- + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v5.0.0 hooks: - - id: black - args: ["-l", "100"] - - repo: https://github.com/myint/autoflake - # rev must match pyproject.toml - rev: v1.4 # rev depends on tag name in git not pip version number (thus the v prefix is required here) + - id: trailing-whitespace # strip trailing whitespace + - id: end-of-file-fixer # ensure files end with a newline + - id: check-yaml # validate YAML syntax + - id: check-toml # validate TOML syntax + - id: check-json # validate JSON syntax + - id: check-merge-conflict # forbid merge-conflict markers + - id: check-added-large-files # warn on large committed files + args: ["--maxkb=1024"] + - id: debug-statements # catch leftover debugger imports + - id: mixed-line-ending + args: ["--fix=lf"] + + # --------------------------------------------------------------------------- + # Ruff – fast Python linter (replaces flake8, isort, pyupgrade, …) + # --------------------------------------------------------------------------- + - repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.15.11 hooks: - - id: autoflake - args: - [ - "--in-place", - "--remove-all-unused-imports", - "--ignore-init-module-imports", - ] - - repo: https://github.com/PyCQA/isort - # rev must match pyproject.toml - rev: 5.12.0 - hooks: - - id: isort - args: ["--profile", "black", "-l", "100"] -# - repo: git@github.com:mdsol/git-config-checker.git -# rev: 0.1.1 -# hooks: -# - id: git-config-checker -# args: ["--checks", "emailDomain"] + - id: ruff # lint + auto-fix + args: ["--fix", "--exit-non-zero-on-fix"] + - id: ruff-format # format (Black-compatible) diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..e69de29 diff --git a/README.md b/README.md index 90d7577..3f61f5e 100644 --- a/README.md +++ b/README.md @@ -1,30 +1,49 @@ -# Data Connect Python Library -Python library built by Medidata for connecting to Data Connect and programmatically querying and retrieving data. +from dataconnect import DataConnectClientfrom dataconnect import DataConnectClient +# dataconnect-library-python + +Python SDK for the [Medidata DataConnect](https://github.com/mdsol/dataconnect-library-r) service. + +--- + +## Transport note + +The DataConnect service uses **Apache Arrow Flight** (gRPC binary protocol), +**not** a plain REST/HTTP API. `pyarrow.flight` is the primary transport +dependency. + +--- ## Installation -See [CONTRIBUTING.md](./CONTRIBUTING.md) for installation instructions. +```bash +pip install dataconnect # core (pyarrow + pydantic + httpx) +pip install dataconnect[pandas] # + pandas for .to_pandas() on results +``` -## To Dos +Requires **Python ≥ 3.10**. -The following actions are needed when using this as the template for a new python project: +--- -- [ ] Update `readme.md` for new project -- [ ] Update `factbook.yaml` for new project -- [ ] Update `pyproject.toml` with relevant `name`, `description`, and `authors` and remove unneeded dep groups +## Quick start -- [ ] Remove all example code files (leave `__init__.py` in place) -- [X] Rename all references to `python-template` and `python_template` to new module/folder names -- [ ] Remove all example test files and all code from `conftest.py` (leave the docstring in place) -- [ ] Add placeholder tests so PR passes -- [ ] Get GH Admins to add mdsol robot key so PR passes -- [ ] Add Artifactory robot account info so PR passes +```python +import pyarrow as pa +from dataconnect import DataConnectClient -## Contributing -See [CONTRIBUTING](CONTRIBUTING.md). +with DataConnectClient.connect( + host="dataconnect.example.com", + port=443, + token="your-bearer-token", +) as client: -## Contact + studies = client.studies(search_study_name="ACME", page=1, page_size=10) + study = studies[0] +``` +## Development -See the [factbook](factbook.yaml). +```bash +pip install -e ".[dev]" +pytest +``` diff --git a/README_orig.md b/README_orig.md new file mode 100644 index 0000000..0b97bcd --- /dev/null +++ b/README_orig.md @@ -0,0 +1,30 @@ +# Python Template + +This repository is meant to establish useful practices for python projects. + +## Installation + +See [CONTRIBUTING.md](./CONTRIBUTING.md) for installation instructions. + +## To Dos + +The following actions are needed when using this as the template for a new python project: + +- [ ] Update `readme.md` for new project +- [ ] Update `factbook.yaml` for new project +- [ ] Update `pyproject.toml` with relevant `name`, `description`, and `authors` and remove unneeded dep groups +- [ ] Update `python_template` folder to match new project name +- [ ] Remove all example code files (leave `__init__.py` in place) +- [ ] Rename all references to `python-template` and `python_template` to new module/folder names +- [ ] Remove all example test files and all code from `conftest.py` (leave the docstring in place) +- [ ] Add placeholder tests so PR passes +- [ ] Get GH Admins to add mdsol robot key so PR passes +- [ ] Add Artifactory robot account info so PR passes + +## Contributing + +See [CONTRIBUTING](CONTRIBUTING.md). + +## Contact + +See the [factbook](factbook.yaml). diff --git a/dataconnect/__init__.py b/dataconnect/__init__.py new file mode 100644 index 0000000..3907ded --- /dev/null +++ b/dataconnect/__init__.py @@ -0,0 +1,23 @@ +"""dataconnect — Python SDK for the Medidata DataConnect service.""" + +from __future__ import annotations + +from dataconnect.client import DataConnectClient +from dataconnect.exceptions import AuthenticationError, ConnectionError, DataConnectError +from dataconnect.models import ( + Dataset, + DatasetVersion, + Study, + StudyEnvironment, +) + +__all__ = [ + "DataConnectClient", + "Study", + "StudyEnvironment", + "Dataset", + "DatasetVersion", + "DataConnectError", + "ConnectionError", + "AuthenticationError", +] diff --git a/dataconnect/_encoding.py b/dataconnect/_encoding.py new file mode 100644 index 0000000..bd6bdcb --- /dev/null +++ b/dataconnect/_encoding.py @@ -0,0 +1,16 @@ +"""Encoding utilities for DataConnect.""" + +from __future__ import annotations + +import json +from typing import Any + + +def dumps(obj: Any) -> bytes: + """Serialize *obj* to JSON (bytes).""" + return json.dumps(obj, separators=(",", ":")).encode("utf-8") + + +def loads(data: bytes) -> Any: + """Deserialize JSON from *data* (bytes).""" + return json.loads(data.decode("utf-8")) diff --git a/dataconnect/auth.py b/dataconnect/auth.py new file mode 100644 index 0000000..61f722f --- /dev/null +++ b/dataconnect/auth.py @@ -0,0 +1,16 @@ +"""Authentication and authorization utilities for DataConnect.""" + +from __future__ import annotations + +from dataclasses import dataclass + + +class Credentials: + """Marker base class for all credentials types.""" + + +@dataclass(frozen=True) +class BearerTokenAuth(Credentials): + """Bearer token authentication credentials (OAuth access token).""" + + token: str diff --git a/dataconnect/client.py b/dataconnect/client.py new file mode 100644 index 0000000..9a6f270 --- /dev/null +++ b/dataconnect/client.py @@ -0,0 +1,93 @@ +"""Public API for the DataConnect client library.""" + +from __future__ import annotations + +import json +from types import TracebackType +from typing import Any + +import pyarrow as pa + +from dataconnect import _encoding +from dataconnect.auth import BearerTokenAuth +from dataconnect.framework.pyarrow_transport import PyArrowFlightTransport +from dataconnect.framework.transport import FlightTransport +from dataconnect.models import Dataset, Study + +# Flight actions / commands +_ACTION_LIST_STUDIES = "studies.list" +_ACTION_LIST_DATASETS = "datasets.list" +_ACTION_LIST_DATASET_VERSIONS = "dataset_versions.list" +_ACTION_FETCH_TICKET = "data.fetch_ticket" +_CMD_PUBLISH = "publish" +_CMD_DRY_PUBLISH = "dry_publish" + +_DEFAULT_HOST = "enodia-gateway.platform.imedidata.com" +_DEFAULT_PORT = 443 + + +class DataConnectClient: + """Client for interacting with DataConnect services.""" + + def __init__(self, transport: FlightTransport) -> None: + """Initialize the DataConnect client with a specified transport.""" + self._transport = transport + + @classmethod + def connect( + cls, + host: str = _DEFAULT_HOST, + port: int = _DEFAULT_PORT, + use_tls: bool = True, + token: str = "", + ) -> DataConnectClient: + """Open connection to a Flight server.""" + location = f"grpc+tls://{host}:{port}" + transport = PyArrowFlightTransport( + location=location, + credentials=BearerTokenAuth(token), + ) + return cls(transport) + + def studies(self) -> list[Study]: + """List the studies the client is authorized to access.""" + rows = self._action_json(_ACTION_LIST_STUDIES, None) + return [Study(**r) for r in rows] + + def datasets(self, study_uuid: str) -> list[Dataset]: + """List the datasets available for a given study.""" + body = {"study_uuid": study_uuid} + rows = self._action_json(_ACTION_LIST_DATASETS, {"study_uuid": body}) + return [Dataset(**r) for r in rows] + + def fetch_data(self, dataset_uuid: str) -> pa.Table: + """Fetch the data for a given dataset as a PyArrow Table.""" + body = {"dataset_uuid": dataset_uuid} + results = self._transport.do_action(_ACTION_FETCH_TICKET, _encoding.dumps(body)) + if not results: + raise RuntimeError("Server returned no data for the fetch_data action.") + return self._transport.do_get(results).read_all() + + # Lifecycle + def close(self) -> None: + """Close the underlying transport connection.""" + self._transport.close() + + def __enter__(self) -> DataConnectClient: + return self + + def __exit__( + self, + exc_type: type[BaseException] | None, + exc_value: BaseException | None, + traceback: TracebackType | None, + ) -> None: + self._transport.close() + + # Helpers + def _action_json(self, action: str, body: dict[str, Any] | None) -> Any: + """Execute a Flight action and return the result as JSON.""" + results = self._transport.do_action(action, _encoding.dumps(body or {})) + if not results: + return [] + return json.loads(results.decode("utf-8")) diff --git a/dataconnect/exceptions.py b/dataconnect/exceptions.py new file mode 100644 index 0000000..b686ce7 --- /dev/null +++ b/dataconnect/exceptions.py @@ -0,0 +1,19 @@ +"""Public exceptions for DataConnect.""" + +from __future__ import annotations + + +class DataConnectError(Exception): + """Base exception for all DataConnect client errors.""" + + +class ConnectionError(DataConnectError): + """Error connecting to the DataConnect server.""" + + +class AuthenticationError(DataConnectError): + """Error authenticating with the DataConnect server.""" + + +class QueryError(DataConnectError): + """Error executing a query.""" diff --git a/dataconnect/framework/__init__.py b/dataconnect/framework/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/dataconnect/framework/pyarrow_transport.py b/dataconnect/framework/pyarrow_transport.py new file mode 100644 index 0000000..ee6efd5 --- /dev/null +++ b/dataconnect/framework/pyarrow_transport.py @@ -0,0 +1,100 @@ +"""Default Flight transport implementation using pyarrow.""" + +from __future__ import annotations + +from collections.abc import Iterator + +import pyarrow as pa +from pyarrow import flight + +from dataconnect import AuthenticationError, DataConnectError +from dataconnect.auth import BearerTokenAuth, Credentials +from dataconnect.exceptions import QueryError +from dataconnect.framework.transport import FlightTransport, RecordBatchStream + + +class PyArrowFlightTransport(FlightTransport): + """Flight transport implementation using pyarrow.""" + + def __init__( + self, + location: str, + *, + credentials: Credentials | None = None, + tls_root_certs: bytes | None = None, + headers: dict[str, str] | None = None, + ) -> None: + try: + self._client = flight.FlightClient( # type: ignore[attr-defined] + location, + tls_root_certs=tls_root_certs, + ) + except Exception as exc: + raise ConnectionError(f"Failed to connect to {location}: {exc}") from exc + + self._call_headers: list[tuple[bytes, bytes]] = [ + (k.lower().encode("ascii"), v.encode("utf-8")) for k, v in (headers or {}).items() + ] + + if credentials is not None: + self._apply_credentials(credentials) + + # Auth + def _apply_credentials(self, credentials: Credentials) -> None: + try: + if isinstance(credentials, BearerTokenAuth): + self._call_headers.append((b"authorization", f"Bearer {credentials.token}".encode())) + else: + raise DataConnectError(f"Unsupported credentials type: {type(credentials)}") + except flight.FlightUnauthenticatedError as exc: # type: ignore[attr-defined] + raise AuthenticationError(f"Authentication failed: {exc}") from exc + except flight.FlightError as exc: # type: ignore[attr-defined] + raise ConnectionError(str(exc)) from exc + + def __options(self) -> flight.FlightCallOptions: # type: ignore + return flight.FlightCallOptions(headers=self._call_headers) # type: ignore[attr-defined] + + # FlightTransport + def do_get(self, ticket: bytes) -> RecordBatchStream: + try: + reader = self._client.do_get(flight.Ticket(ticket), self.__options()) # type: ignore[attr-defined] + except flight.FlightUnauthenticatedError as exc: # type: ignore[attr-defined] + raise AuthenticationError(f"Authentication failed: {exc}") from exc + except flight.FlightError as exc: # type: ignore[attr-defined] + raise QueryError(str(exc)) from exc + return _PyArrowRecordBatchStream(reader) + + def do_put(self, command: bytes, table: pa.Table) -> bytes | None: + """Upload a table via DoPut with a command descriptor.""" + return b"" + + def do_action(self, action: str, body: bytes = b"") -> bytes: + """Invoke a Flight action and return a response.""" + return b"" + + def close(self) -> None: + self._client.close() + + +class _PyArrowRecordBatchStream(RecordBatchStream): + """Adapter for pyarrow RecordBatchReader to implement RecordBatchStream.""" + + def __init__(self, reader: flight.FlightStreamReader) -> None: # type: ignore + self._reader = reader + + def read_all(self) -> pa.Table: + """Read all record batches into a single PyArrow Table.""" + try: + return self._reader.read_all() + except flight.FlightError as exc: # type: ignore[attr-defined] + raise QueryError(str(exc)) from exc + + def __iter__(self) -> Iterator[pa.RecordBatch]: + try: + while True: + chunk = self._reader.read_chunk() + yield chunk.data + except StopIteration: + return + except flight.FlightError as exc: # type: ignore[attr-defined] + raise QueryError(str(exc)) from exc diff --git a/dataconnect/framework/transport.py b/dataconnect/framework/transport.py new file mode 100644 index 0000000..09d8986 --- /dev/null +++ b/dataconnect/framework/transport.py @@ -0,0 +1,44 @@ +"""Abstract transport interface.""" + +from __future__ import annotations + +from abc import ABC, abstractmethod +from collections.abc import Iterator + +import pyarrow as pa + + +class FlightTransport(ABC): + """Minimal abstract transport interface for DataConnect Flight operations.""" + + @abstractmethod + def do_action(self, action: str, body: bytes = b"") -> bytes: + """Invoke a Flight action and return a response.""" + + @abstractmethod + def do_get(self, ticket: bytes) -> RecordBatchStream: + """Open a DoGet stream for ticket.""" + + @abstractmethod + def do_put( + self, + command: bytes, + table: pa.Table, + ) -> bytes | None: + """Upload a table via DoPut with a command descriptor.""" + + @abstractmethod + def close(self) -> None: + """Close the transport connection.""" + + +class RecordBatchStream(ABC): + """Minimal abstract stream interface for Flight record batches.""" + + @abstractmethod + def read_all(self) -> pa.Table: + """Read all record batches into a single PyArrow Table.""" + + @abstractmethod + def __iter__(self) -> Iterator[pa.RecordBatch]: + """Iterate over record batches.""" diff --git a/dataconnect/models.py b/dataconnect/models.py new file mode 100644 index 0000000..c003133 --- /dev/null +++ b/dataconnect/models.py @@ -0,0 +1,28 @@ +from __future__ import annotations + +from dataclasses import dataclass + + +@dataclass(frozen=True) +class Study: + id: str + name: str + + +@dataclass(frozen=True) +class StudyEnvironment: + """Environment variables for a study.""" + + +@dataclass(frozen=True) +class Dataset: + id: str + study_id: str + name: str + + +@dataclass(frozen=True) +class DatasetVersion: + id: str + dataset_id: str + name: str diff --git a/dataconnect/py.typed 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+version = "21.3.0" description = "Virtual Python Environment builder" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" +groups = ["dev"] files = [ - {file = "virtualenv-20.21.0-py3-none-any.whl", hash = "sha256:31712f8f2a17bd06234fa97fdf19609e789dd4e3e4bf108c3da71d710651adbc"}, - {file = "virtualenv-20.21.0.tar.gz", hash = "sha256:f50e3e60f990a0757c9b68333c9fdaa72d7188caa417f96af9e52407831a3b68"}, + {file = "virtualenv-21.3.0-py3-none-any.whl", hash = "sha256:4d28ee41f6d9ec8f1f00cd472b9ffbcedda1b3d3b9a575b5c94a2d004fd51bd7"}, + {file = "virtualenv-21.3.0.tar.gz", hash = "sha256:733750db978ec95c2d8eb4feadaa57091002bce404cb39ba69899cf7bd28944e"}, ] [package.dependencies] -distlib = ">=0.3.6,<1" -filelock = ">=3.4.1,<4" -platformdirs = ">=2.4,<4" - -[package.extras] -docs = ["furo (>=2022.12.7)", "proselint (>=0.13)", "sphinx (>=6.1.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=22.12)"] -test = ["covdefaults (>=2.2.2)", "coverage (>=7.1)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23)", "pytest (>=7.2.1)", "pytest-env (>=0.8.1)", "pytest-freezegun (>=0.4.2)", "pytest-mock (>=3.10)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)"] - -[package.source] -type = "legacy" -url = "https://mdsol.jfrog.io/artifactory/api/pypi/pypi-prod-virtual/simple" -reference = "mdsol" - -[[package]] -name = "wmctrl" -version = "0.4" -description = "A tool to programmatically control windows inside X" -optional = false -python-versions = "*" -files = [ - {file = "wmctrl-0.4.tar.gz", hash = "sha256:66cbff72b0ca06a22ec3883ac3a4d7c41078bdae4fb7310f52951769b10e14e0"}, -] +distlib = ">=0.3.7,<1" +filelock = {version = ">=3.24.2,<4", markers = "python_version >= \"3.10\""} +platformdirs = ">=3.9.1,<5" +python-discovery = ">=1.2.2" +typing-extensions = {version = ">=4.13.2", markers = "python_version < \"3.11\""} [package.source] type = "legacy" @@ -1104,6 +1409,6 @@ url = "https://mdsol.jfrog.io/artifactory/api/pypi/pypi-prod-virtual/simple" reference = "mdsol" [metadata] -lock-version = "2.0" -python-versions = "^3.8" -content-hash = "475db98a20df04d903a433c0e98d8c9f9f5522c9c603b9ddca2a715eaa4b538e" +lock-version = "2.1" +python-versions = "^3.10" +content-hash = "78e667319654d56c4d1e9d88f314bf9ed5f8a1f0c70d463f45985ed1c148f936" diff --git a/pyproject.toml b/pyproject.toml index 0ce5632..9e6c95b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,20 +7,17 @@ authors = ["Team 348 (SDK) "] [[tool.poetry.source]] # Needs AUTH in ENV (using UPPERCASE name): # https://python-poetry.org/docs/repositories/#configuring-credentials -# # export POETRY_HTTP_BASIC_MDSOL_PASSWORD=$ARTIFACTORY_PASSWORD # export POETRY_HTTP_BASIC_MDSOL_USERNAME=$ARTIFACTORY_USERNAME name = "mdsol" url = "https://mdsol.jfrog.io/artifactory/api/pypi/pypi-prod-virtual/simple" -secondary = false # # Dependancies # [tool.poetry.dependencies] -python = "^3.8" -pyyaml = "^6.0" -astinus = "^0.7.0" +python = "^3.10" +pyarrow = "^14.0" # SERVICE [tool.poetry.group.service] @@ -41,13 +38,11 @@ pandas = "^2.0.2" optional = true [tool.poetry.group.dev.dependencies] -mypy = "^1.3" -pdbpp = "^0.10.3" +mypy = "^1.20.2" pre-commit = "^3.3.2" -# below revs must exactly match .pre-commit-config.yaml -black = "23.3.0" -autoflake = "2.1.1" -isort = "5.12.0" +pytest = "^7.3.2" +pytest-cov = "^4.1.0" +ruff = "0.15.11" # TEST [tool.poetry.group.test] @@ -64,5 +59,38 @@ requires = ["poetry-core>=1.0.0"] build-backend = "poetry.core.masonry.api" [tool.pytest.ini_options] +testpaths = ["tests"] addopts = "--strict-markers" markers = "benchmark: mark tests that run performance benchmarks" + +[tool.ruff] +target-version = "py310" +line-length = 120 +exclude = [ + ".venv", + ".git", + ".github", + "__pycache__", + "site-packages", + "build", + "dist", + "*.egg-info", + ".mypy_cache", + "doc/", + ".deploy", + "*.md", + "*.sql", + "*.yaml" +] + +[tool.ruff.lint] +select = ["B", "E", "W", "F", "I", "UP", "ANN"] +ignore = ["ANN401"] # allow Any in public API + +# ----------------------------------------------------------------------- +# mypy +# ----------------------------------------------------------------------- +[tool.mypy] +python_version = "3.10" +strict = true +ignore_missing_imports = true diff --git a/pyproject_orig.toml b/pyproject_orig.toml new file mode 100644 index 0000000..cac8f97 --- /dev/null +++ b/pyproject_orig.toml @@ -0,0 +1,68 @@ +[tool.poetry] +name = "python-template" +version = "0.1.0" +description = "" +authors = ["Jeremy Mann "] + +[[tool.poetry.source]] +# Needs AUTH in ENV (using UPPERCASE name): +# https://python-poetry.org/docs/repositories/#configuring-credentials +# +# export POETRY_HTTP_BASIC_MDSOL_PASSWORD=$ARTIFACTORY_PASSWORD +# export POETRY_HTTP_BASIC_MDSOL_USERNAME=$ARTIFACTORY_USERNAME +name = "mdsol" +url = "https://mdsol.jfrog.io/artifactory/api/pypi/pypi-prod-virtual/simple" +secondary = false + +# +# Dependancies +# +[tool.poetry.dependencies] +python = "^3.8" +pyyaml = "^6.0" +astinus = "^0.7.0" + +# SERVICE +[tool.poetry.group.service] +optional = true + +[tool.poetry.group.service.dependencies] +gunicorn ="^20.1.0" + +# ML +[tool.poetry.group.ml] +optional = true + +[tool.poetry.group.ml.dependencies] +pandas = "^2.0.2" + +# DEV +[tool.poetry.group.dev] +optional = true + +[tool.poetry.group.dev.dependencies] +mypy = "^1.3" +pdbpp = "^0.10.3" +pre-commit = "^3.3.2" +# below revs must exactly match .pre-commit-config.yaml +black = "23.3.0" +autoflake = "2.1.1" +isort = "5.12.0" + +# TEST +[tool.poetry.group.test] +optional = true + +[tool.poetry.group.test.dependencies] +pytest = "^7.3.2" +pytest-xdist = "^3.3.1" +pytest-cov = "^4.1.0" +pytest-benchmark = "^4.0.0" + +[build-system] +requires = ["poetry-core>=1.0.0"] +build-backend = "poetry.core.masonry.api" + +[tool.pytest.ini_options] +addopts = "--strict-markers" +markers = "benchmark: mark tests that run performance benchmarks" diff --git a/python_template/__init__.py b/python_template/__init__.py deleted file mode 100644 index 2a08aec..0000000 --- a/python_template/__init__.py +++ /dev/null @@ -1 +0,0 @@ -__version__ = "0.1.0" # pragma: no cover diff --git a/python_template/reverse.py b/python_template/reverse.py deleted file mode 100644 index 357c407..0000000 --- a/python_template/reverse.py +++ /dev/null @@ -1,27 +0,0 @@ -""" -Reverse the letters in a string -""" - -from typing import Callable, List - - -def for_loop_reverse(word: str) -> str: - n_letters = len(word) - ans = "" - for index in range(n_letters): - reverse_index = n_letters - (index + 1) - ans += word[reverse_index] - return ans - - -def slice_reverse(word: str) -> str: - ans = word[::-1] - return ans - - -def reverse_word(word: str, reverser: Callable[[str], str] = for_loop_reverse) -> str: - return reverser(word) - - -def get_reversers() -> List[Callable[[str], str]]: - return [slice_reverse, for_loop_reverse] diff --git a/scripts/benchmark.sh b/scripts/benchmark.sh old mode 100755 new mode 100644 diff --git a/scripts/install.sh b/scripts/install.sh old mode 100755 new mode 100644 diff --git a/scripts/lint.sh b/scripts/lint.sh old mode 100755 new mode 100644 diff --git a/scripts/test.sh b/scripts/test.sh old mode 100755 new mode 100644 diff --git a/scripts/typecheck.sh b/scripts/typecheck.sh index e976549..c523c14 100644 --- a/scripts/typecheck.sh +++ b/scripts/typecheck.sh @@ -1,4 +1,4 @@ #!/bin/bash -mypy --strict python_template +mypy --strict "$(pwd)/dataconnect" diff --git a/tests/conftest.py b/tests/conftest.py deleted file mode 100644 index 71fc287..0000000 --- a/tests/conftest.py +++ /dev/null @@ -1,28 +0,0 @@ -""" -This file contains fixtures that will be used in multiple test modules. - -See: -https://docs.pytest.org/en/latest/how-to/fixtures.html?highlight=conftest -https://stackoverflow.com/questions/34466027/in-pytest-what-is-the-use-of-conftest-py-files -""" -from typing import List - -import pytest -import yaml - -from python_template.reverse import get_reversers - - -def get_words() -> List[str]: - with open("./tests/mocks/words.yml", "r") as f: - return yaml.safe_load(f) - - -@pytest.fixture(params=get_words(), scope="module") -def word(request): - return request.param - - -@pytest.fixture(params=get_reversers(), scope="module") -def reverser(request): - return request.param diff --git a/tests/mocks/words.yml b/tests/mocks/words.yml deleted file mode 100644 index 1979dce..0000000 --- a/tests/mocks/words.yml +++ /dev/null @@ -1,4 +0,0 @@ -- foo -- bardslj -- bazalksjdfl -- bakerylkasdjflasjdflkja diff --git a/tests/test_benchmark_reverser.py b/tests/test_benchmark_reverser.py deleted file mode 100644 index f2264d5..0000000 --- a/tests/test_benchmark_reverser.py +++ /dev/null @@ -1,13 +0,0 @@ -import os - -import pytest - -from python_template.reverse import reverse_word - -SKIP_BENCHMARK = len(os.environ.get("SKIP_BENCHMARK", "")) > 0 -SKIP_REASON = "Environment doesn't want to run the benchmark" - - -@pytest.mark.benchmark -def test_benchmark(benchmark, reverser, word): - benchmark(reverse_word, word, reverser) diff --git a/tests/test_client.py b/tests/test_client.py new file mode 100644 index 0000000..cb45e43 --- /dev/null +++ b/tests/test_client.py @@ -0,0 +1,11 @@ +import pytest + + +def test_client() -> None: + assert True + + +@pytest.mark.benchmark +def test_dummy_benchmark() -> None: + # Dummy benchmark test to satisfy CI + assert True diff --git a/tests/test_python_template.py b/tests/test_python_template.py deleted file mode 100644 index 8407ecb..0000000 --- a/tests/test_python_template.py +++ /dev/null @@ -1,5 +0,0 @@ -def test_import(): - import python_template - - # assert that this module has a name so autoflake doesn't remove the import - assert python_template.__name__ diff --git a/tests/test_reversers.py b/tests/test_reversers.py deleted file mode 100644 index b17a654..0000000 --- a/tests/test_reversers.py +++ /dev/null @@ -1,38 +0,0 @@ -import pytest - -from python_template.reverse import get_reversers, reverse_word - - -@pytest.fixture(scope="module") -def reversed_word(word, reverser): - return reverse_word(word, reverser) - - -def test_reversed_string_same_length(word, reversed_word): - assert len(word) == len(reversed_word) - - -def test_last_letter_of_reversed_word_is_first_letter_of_word(word, reversed_word): - assert word[0] == reversed_word[-1] - - -def test_reverse_empty_string(): - word = "" - reversed_word = reverse_word(word) - assert word == reversed_word - - -def test_reversers_all_agree(word, reversed_word): - first_reverser = get_reversers()[0] - assert reversed_word == first_reverser(word) - - -def test_reversers_palindrome(word, reverser, reversed_word): - palindrome = word + reversed_word - assert palindrome == reverser(palindrome) - - -def test_reverse_asdfjkl_correctly(): - word = "asdfjkl" - reversed_word = reverse_word(word) - assert reversed_word == "lkjfdsa" From 733fb0ce8661e092498e45ba101b807e39cf99a6 Mon Sep 17 00:00:00 2001 From: Irfan Baig Date: Tue, 28 Apr 2026 18:15:05 -0500 Subject: [PATCH 2/4] Fixing CI issue. --- .dockerignore | 2 +- README_orig.md | 6 +++--- scripts/typecheck.sh | 5 ++++- 3 files changed, 8 insertions(+), 5 deletions(-) diff --git a/.dockerignore b/.dockerignore index ae0c2b1..c50d9f9 100644 --- a/.dockerignore +++ b/.dockerignore @@ -2,7 +2,7 @@ * # Add back just needed directories -!python_template +!dataconnect !scripts !tests !pyproject.toml diff --git a/README_orig.md b/README_orig.md index 0b97bcd..3f8b7f6 100644 --- a/README_orig.md +++ b/README_orig.md @@ -12,11 +12,11 @@ The following actions are needed when using this as the template for a new pytho - [ ] Update `readme.md` for new project - [ ] Update `factbook.yaml` for new project -- [ ] Update `pyproject.toml` with relevant `name`, `description`, and `authors` and remove unneeded dep groups +- [X] Update `pyproject.toml` with relevant `name`, `description`, and `authors` and remove unneeded dep groups - [ ] Update `python_template` folder to match new project name - [ ] Remove all example code files (leave `__init__.py` in place) -- [ ] Rename all references to `python-template` and `python_template` to new module/folder names -- [ ] Remove all example test files and all code from `conftest.py` (leave the docstring in place) +- [X] Rename all references to `python-template` and `python_template` to new module/folder names +- [X] Remove all example test files and all code from `conftest.py` (leave the docstring in place) - [ ] Add placeholder tests so PR passes - [ ] Get GH Admins to add mdsol robot key so PR passes - [ ] Add Artifactory robot account info so PR passes diff --git a/scripts/typecheck.sh b/scripts/typecheck.sh index c523c14..693d290 100644 --- a/scripts/typecheck.sh +++ b/scripts/typecheck.sh @@ -1,4 +1,7 @@ #!/bin/bash +set -e -mypy --strict "$(pwd)/dataconnect" +PROJECT_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)" + +mypy --strict "$PROJECT_ROOT/dataconnect" From 5b09655545b489932d0d2c4a2a273a3e9d5b0691 Mon Sep 17 00:00:00 2001 From: Irfan Baig Date: Tue, 28 Apr 2026 18:56:11 -0500 Subject: [PATCH 3/4] Fixing CI issue. --- scripts/test.sh | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/scripts/test.sh b/scripts/test.sh index b46a255..82af140 100644 --- a/scripts/test.sh +++ b/scripts/test.sh @@ -1,8 +1,13 @@ #!/bin/bash +set -e + +PROJECT_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)" + +cd "$PROJECT_ROOT" pytest \ -m "not benchmark" \ - --cov dataconnect_library_python \ + --cov dataconnect \ --cov-report term \ --cov-report html \ From 86f877e295604206f134311392179aea41d2dd27 Mon Sep 17 00:00:00 2001 From: Irfan Baig Date: Tue, 28 Apr 2026 19:07:55 -0500 Subject: [PATCH 4/4] feat: unused-ignore --- dataconnect/framework/pyarrow_transport.py | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/dataconnect/framework/pyarrow_transport.py b/dataconnect/framework/pyarrow_transport.py index ee6efd5..0a6bf2b 100644 --- a/dataconnect/framework/pyarrow_transport.py +++ b/dataconnect/framework/pyarrow_transport.py @@ -25,7 +25,7 @@ def __init__( headers: dict[str, str] | None = None, ) -> None: try: - self._client = flight.FlightClient( # type: ignore[attr-defined] + self._client = flight.FlightClient( location, tls_root_certs=tls_root_certs, ) @@ -46,21 +46,21 @@ def _apply_credentials(self, credentials: Credentials) -> None: self._call_headers.append((b"authorization", f"Bearer {credentials.token}".encode())) else: raise DataConnectError(f"Unsupported credentials type: {type(credentials)}") - except flight.FlightUnauthenticatedError as exc: # type: ignore[attr-defined] + except flight.FlightUnauthenticatedError as exc: raise AuthenticationError(f"Authentication failed: {exc}") from exc - except flight.FlightError as exc: # type: ignore[attr-defined] + except flight.FlightError as exc: raise ConnectionError(str(exc)) from exc - def __options(self) -> flight.FlightCallOptions: # type: ignore - return flight.FlightCallOptions(headers=self._call_headers) # type: ignore[attr-defined] + def __options(self) -> flight.FlightCallOptions: + return flight.FlightCallOptions(headers=self._call_headers) # FlightTransport def do_get(self, ticket: bytes) -> RecordBatchStream: try: - reader = self._client.do_get(flight.Ticket(ticket), self.__options()) # type: ignore[attr-defined] - except flight.FlightUnauthenticatedError as exc: # type: ignore[attr-defined] + reader = self._client.do_get(flight.Ticket(ticket), self.__options()) + except flight.FlightUnauthenticatedError as exc: raise AuthenticationError(f"Authentication failed: {exc}") from exc - except flight.FlightError as exc: # type: ignore[attr-defined] + except flight.FlightError as exc: raise QueryError(str(exc)) from exc return _PyArrowRecordBatchStream(reader) @@ -79,14 +79,14 @@ def close(self) -> None: class _PyArrowRecordBatchStream(RecordBatchStream): """Adapter for pyarrow RecordBatchReader to implement RecordBatchStream.""" - def __init__(self, reader: flight.FlightStreamReader) -> None: # type: ignore + def __init__(self, reader: flight.FlightStreamReader) -> None: self._reader = reader def read_all(self) -> pa.Table: """Read all record batches into a single PyArrow Table.""" try: return self._reader.read_all() - except flight.FlightError as exc: # type: ignore[attr-defined] + except flight.FlightError as exc: raise QueryError(str(exc)) from exc def __iter__(self) -> Iterator[pa.RecordBatch]: @@ -96,5 +96,5 @@ def __iter__(self) -> Iterator[pa.RecordBatch]: yield chunk.data except StopIteration: return - except flight.FlightError as exc: # type: ignore[attr-defined] + except flight.FlightError as exc: raise QueryError(str(exc)) from exc