From 9e462c88b1a2f1cf746645827a3dc9c037a0ce4a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lu=C3=A3=20Bida=20Vacaro?= Date: Tue, 26 May 2026 12:12:56 -0300 Subject: [PATCH 1/3] feat(package): remove the need of the libffi-dev requirement on pyreaddbc --- .github/workflows/python-package.yml | 6 +- README.md | 7 - docker/Dockerfile | 2 +- docs/source/installation.rst | 8 - poetry.lock | 4912 ++++++++++++++------------ pyproject.toml | 10 +- pysus/api/extensions.py | 17 +- 7 files changed, 2678 insertions(+), 2284 deletions(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index d6e8f17..b901d7e 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -5,7 +5,7 @@ on: [push, pull_request] jobs: tests: runs-on: ${{ matrix.os }} - timeout-minutes: ${{ (matrix.os == 'windows-latest' && 30) || 15 }} + timeout-minutes: ${{ (matrix.os == 'windows-latest' && 45) || 15 }} strategy: matrix: @@ -34,7 +34,7 @@ jobs: pip install poetry poetry-plugin-export poetry config virtualenvs.create false if [ "${{ runner.os }}" = "Linux" ]; then - poetry install --without dev --extras dbc + poetry install --without dev pip install pre-commit else poetry install --without dev @@ -57,7 +57,7 @@ jobs: shell: bash -l {0} run: | export DUCKDB_NO_THREADS=1 - poetry run pytest -vv pysus/tests/ --retries 3 --retry-delay 15 --timeout=480 -p no:cacheprovider -p no:asyncio + poetry run pytest -vv pysus/tests/ --timeout=480 -p no:cacheprovider -p no:asyncio - name: Upload coverage to Codecov if: matrix.os == 'ubuntu-latest' diff --git a/README.md b/README.md index f491f43..f12070d 100644 --- a/README.md +++ b/README.md @@ -20,13 +20,6 @@ PySUS is a Python package for accessing and analyzing Brazil's public health dat pip install pysus ``` -For DBC file support (requires libffi): -```bash -# Ubuntu/Debian -sudo apt install libffi-dev -pip install pysus[dbc] -``` - For the terminal user interface (TUI): ```bash pip install pysus[tui] diff --git a/docker/Dockerfile b/docker/Dockerfile index 00d3a3a..5956df3 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -29,7 +29,7 @@ COPY docker/scripts/entrypoint.sh /entrypoint.sh COPY docker/notebooks/ /home/pysus/Notebooks/ RUN pip install poetry \ - && cd /usr/src && poetry config virtualenvs.create false && poetry install --with docs --extras dbc \ + && cd /usr/src && poetry config virtualenvs.create false && poetry install --with docs \ && pip install 'httpx<0.28' \ && chown -R pysus:pysus /home/pysus diff --git a/docs/source/installation.rst b/docs/source/installation.rst index bbf7762..d4d64c5 100644 --- a/docs/source/installation.rst +++ b/docs/source/installation.rst @@ -14,14 +14,6 @@ The simplest way to install PySUS is via pip: Extras ^^^^^^ -For DBC file support (requires ``libffi``): - -.. code-block:: bash - - # Ubuntu/Debian - sudo apt install libffi-dev - pip install pysus[dbc] - For the terminal user interface (TUI): .. code-block:: bash diff --git a/poetry.lock b/poetry.lock index e430014..076d6c5 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 2.1.3 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.4.1 and should not be changed by hand. 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{file = "websocket_client-1.8.0-py3-none-any.whl", hash = "sha256:17b44cc997f5c498e809b22cdf2d9c7a9e71c02c8cc2b6c56e7c2d1239bfa526"}, - {file = "websocket_client-1.8.0.tar.gz", hash = "sha256:3239df9f44da632f96012472805d40a23281a991027ce11d2f45a6f24ac4c3da"}, + {file = "websocket_client-1.9.0-py3-none-any.whl", hash = "sha256:af248a825037ef591efbf6ed20cc5faa03d3b47b9e5a2230a529eeee1c1fc3ef"}, + {file = "websocket_client-1.9.0.tar.gz", hash = "sha256:9e813624b6eb619999a97dc7958469217c3176312b3a16a4bd1bc7e08a46ec98"}, ] [package.extras] -docs = ["Sphinx (>=6.0)", "myst-parser (>=2.0.0)", "sphinx-rtd-theme (>=1.1.0)"] +docs = ["Sphinx (>=6.0)", "myst-parser (>=2.0.0)", "sphinx_rtd_theme (>=1.1.0)"] optional = ["python-socks", "wsaccel"] -test = ["websockets"] +test = ["pytest", "websockets"] [[package]] name = "wget" @@ -5468,25 +5889,24 @@ files = [ [[package]] name = "win32-setctime" -version = "1.1.0" +version = "1.2.0" description = "A small Python utility to set file creation time on Windows" optional = false python-versions = ">=3.5" groups = ["main"] markers = "sys_platform == \"win32\"" files = [ - {file = "win32_setctime-1.1.0-py3-none-any.whl", hash = "sha256:231db239e959c2fe7eb1d7dc129f11172354f98361c4fa2d6d2d7e278baa8aad"}, - {file = "win32_setctime-1.1.0.tar.gz", hash = "sha256:15cf5750465118d6929ae4de4eb46e8edae9a5634350c01ba582df868e932cb2"}, + {file = "win32_setctime-1.2.0-py3-none-any.whl", hash = "sha256:95d644c4e708aba81dc3704a116d8cbc974d70b3bdb8be1d150e36be6e9d1390"}, + {file = "win32_setctime-1.2.0.tar.gz", hash = "sha256:ae1fdf948f5640aae05c511ade119313fb6a30d7eabe25fef9764dca5873c4c0"}, ] [package.extras] dev = ["black (>=19.3b0) ; python_version >= \"3.6\"", "pytest (>=4.6.2)"] [extras] -dbc = ["pycparser", "pyreaddbc"] tui = ["humanize", "textual"] [metadata] lock-version = "2.1" python-versions = ">=3.10,<3.14" -content-hash = "c5bb87c75524bd9021f501a4662d090deaafda0974abf48dcf542a23221b8b66" +content-hash = "61b754b1f0f7a86375c7a562f830223b029a2c5594747dc7082eb99b2da021b9" diff --git a/pyproject.toml b/pyproject.toml index 53d5184..5412c6d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -38,17 +38,15 @@ httpx = ">=0.28.0" aioftp = "^0.21.4" dbfread = "2.0.7" bigtree = "^0.12.2" - -pyreaddbc = { version = ">=1.1.0", optional = true } -pycparser = { version = "2.21", optional = true } -textual = { extras = ["syntax"], version = "^8.2.1", optional = true } -humanize = { version = "^4.8.0", optional = true } +pyreaddbc = ">=2.0.4" dotenv = "^0.9.9" boto3 = "^1.42.89" typer = "^0.24.1" +humanize = { version = "^4.8.0", optional = true } +textual = { extras = ["syntax"], version = "^8.2.1", optional = true } + [tool.poetry.extras] -dbc = ["pyreaddbc", "pycparser"] tui = ["textual", "humanize"] [tool.poetry.group.dev.dependencies] diff --git a/pysus/api/extensions.py b/pysus/api/extensions.py index d918817..b81d1b1 100644 --- a/pysus/api/extensions.py +++ b/pysus/api/extensions.py @@ -2,10 +2,8 @@ import asyncio import csv -import ctypes.util import gzip import shutil -import sys import tarfile import zipfile from collections.abc import AsyncGenerator, Callable @@ -26,16 +24,9 @@ from .types import FileType try: - LIBFFI = True - if sys.platform.startswith("linux"): - LIBFFI = ctypes.util.find_library("ffi") is not None + from pyreaddbc import dbc2dbf - if LIBFFI: - from pyreaddbc import dbc2dbf - - DBC_IMPORT = True - else: - DBC_IMPORT = False + DBC_IMPORT = True except ImportError: DBC_IMPORT = False @@ -781,7 +772,7 @@ def _extract(): return list(await asyncio.gather(*tasks)) -class FTPNotImported(BaseTabularFile): +class DBCNotImported(BaseTabularFile): """Placeholder for DBC files when optional dependency is not installed.""" path: Path = Field(default_factory=lambda: Path("...")) @@ -872,7 +863,7 @@ class ExtensionFactory: ".csv": CSV, ".parquet": Parquet, ".dbf": DBF, - ".dbc": DBC if DBC_IMPORT else FTPNotImported, # type: ignore + ".dbc": DBC if DBC_IMPORT else DBCNotImported, # type: ignore ".pdf": PDF, ".json": JSON, } From 515ea1bd53d31dcdf74f038db8c003bd2168fefa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lu=C3=A3=20Bida=20Vacaro?= Date: Tue, 26 May 2026 14:40:44 -0300 Subject: [PATCH 2/3] chore(CI): remove the conda installation from the runners --- .github/workflows/python-package.yml | 19 +++++++------------ .github/workflows/release.yaml | 14 +++----------- pysus/api/extensions.py | 25 ++++++++++++++++--------- 3 files changed, 26 insertions(+), 32 deletions(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index b901d7e..c1c57fe 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -19,17 +19,12 @@ jobs: steps: - uses: actions/checkout@v4 - - uses: conda-incubator/setup-miniconda@v3 + - uses: actions/setup-python@v5 with: - miniforge-version: latest - environment-file: conda/dev.yaml - channels: conda-forge,nodefaults - activate-environment: pysus - auto-update-conda: true - conda-solver: libmamba + python-version: ${{ matrix.python-version }} - name: Install dependencies - shell: bash -l {0} + shell: bash run: | pip install poetry poetry-plugin-export poetry config virtualenvs.create false @@ -43,21 +38,21 @@ jobs: - name: Linting if: matrix.os == 'ubuntu-latest' - shell: bash -l {0} + shell: bash run: pre-commit run --files pysus/**/* - name: Tests (Linux) if: matrix.os != 'windows-latest' - shell: bash -l {0} + shell: bash run: | poetry run pytest -vv pysus/tests/ --retries 3 --retry-delay 15 --cov=pysus --cov-report=xml:coverage.xml --cov-report=term-missing - name: Tests (Windows) if: matrix.os == 'windows-latest' - shell: bash -l {0} + shell: bash run: | export DUCKDB_NO_THREADS=1 - poetry run pytest -vv pysus/tests/ --timeout=480 -p no:cacheprovider -p no:asyncio + poetry run pytest -vv pysus/tests/ --timeout=480 -p no:cacheprovider - name: Upload coverage to Codecov if: matrix.os == 'ubuntu-latest' diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml index 6d9418a..fcf654e 100644 --- a/.github/workflows/release.yaml +++ b/.github/workflows/release.yaml @@ -84,25 +84,17 @@ jobs: if: ${{ !startsWith(github.ref, 'refs/tags/') }} runs-on: ubuntu-latest - defaults: - run: - shell: bash -l {0} - steps: - uses: actions/checkout@v4 - - uses: conda-incubator/setup-miniconda@v3 + - uses: actions/setup-python@v5 with: - miniforge-version: latest - environment-file: conda/dev.yaml - channels: conda-forge,nodefaults - activate-environment: pysus - auto-update-conda: true - conda-solver: libmamba + python-version: "3.12" - name: Install dependencies run: | pip install poetry wget + poetry config virtualenvs.create false poetry install --no-root --with docs - name: Build docs diff --git a/pysus/api/extensions.py b/pysus/api/extensions.py index b81d1b1..51d8b67 100644 --- a/pysus/api/extensions.py +++ b/pysus/api/extensions.py @@ -868,22 +868,29 @@ class ExtensionFactory: ".json": JSON, } + _magic_available: bool = True + _magic_lock: asyncio.Lock = asyncio.Lock() + @classmethod async def _identify(cls, path: Path) -> type[BaseLocalFile] | None: """Identify the file class by its MIME type.""" + if not cls._magic_available: + return None try: import magic except (ImportError, OSError): + cls._magic_available = False return None - try: - mime = await to_thread.run_sync( - magic.from_file, - str(path), - True, - ) - return cls._mime.get(mime) - except (magic.MagicException, OSError): - return None + async with cls._magic_lock: + try: + mime = await to_thread.run_sync( + magic.from_file, + str(path), + True, + ) + return cls._mime.get(mime) + except (magic.MagicException, OSError): + return None @classmethod async def get_file_class(cls, path: Path) -> type[BaseLocalFile]: From 7fafe63c59c3c4d33d10a7769a48307331619dec Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lu=C3=A3=20Bida=20Vacaro?= Date: Tue, 26 May 2026 15:22:32 -0300 Subject: [PATCH 3/3] fix: apparently MIME magic typing doesnt work on Windows OS --- pysus/api/client.py | 12 ++++--- pysus/api/extensions.py | 23 ++++++------ pysus/tests/api/ftp/test_models.py | 4 +-- pysus/tests/api/test_client.py | 37 ++++++++++--------- pysus/tests/api/test_databases.py | 57 ++++++++++++++++++++---------- 5 files changed, 80 insertions(+), 53 deletions(-) diff --git a/pysus/api/client.py b/pysus/api/client.py index 89f8ff1..70ba6bc 100644 --- a/pysus/api/client.py +++ b/pysus/api/client.py @@ -6,7 +6,7 @@ import enum from collections.abc import Callable -from datetime import datetime +from datetime import datetime, timezone from pathlib import Path from typing import TYPE_CHECKING, Literal @@ -16,6 +16,7 @@ from pysus import CACHEPATH from sqlalchemy import DateTime, Enum, Integer, String, create_engine from sqlalchemy.orm import DeclarativeBase, Mapped, mapped_column, sessionmaker +from sqlalchemy.pool import NullPool from .dadosgov import DadosGovClient from .ducklake.client import DuckLake @@ -61,7 +62,7 @@ class LocalFileState(Base): sha256: Mapped[str | None] = mapped_column(String, nullable=True) last_synced: Mapped[datetime] = mapped_column( DateTime, - default=datetime.utcnow, + default=lambda: datetime.now(timezone.utc).replace(tzinfo=None), ) @@ -85,7 +86,10 @@ def __init__(self, db_path: Path = CACHEPATH / "config.db"): db_path.parent.mkdir(parents=True, exist_ok=True) self.cachepath = db_path.parent - self.engine = create_engine(f"duckdb:///{db_path}") + self.engine = create_engine( + f"duckdb:///{db_path.resolve().as_posix()}", + poolclass=NullPool, + ) Base.metadata.create_all(self.engine) self.Session = sessionmaker(bind=self.engine) @@ -239,7 +243,7 @@ async def _update_state( session.add(record) record.status = status - record.last_synced = datetime.utcnow() + record.last_synced = datetime.now(timezone.utc).replace(tzinfo=None) session.commit() async def download( diff --git a/pysus/api/extensions.py b/pysus/api/extensions.py index 51d8b67..59de4dd 100644 --- a/pysus/api/extensions.py +++ b/pysus/api/extensions.py @@ -4,6 +4,7 @@ import csv import gzip import shutil +import sys import tarfile import zipfile from collections.abc import AsyncGenerator, Callable @@ -868,8 +869,7 @@ class ExtensionFactory: ".json": JSON, } - _magic_available: bool = True - _magic_lock: asyncio.Lock = asyncio.Lock() + _magic_available: bool = sys.platform != "win32" @classmethod async def _identify(cls, path: Path) -> type[BaseLocalFile] | None: @@ -881,16 +881,15 @@ async def _identify(cls, path: Path) -> type[BaseLocalFile] | None: except (ImportError, OSError): cls._magic_available = False return None - async with cls._magic_lock: - try: - mime = await to_thread.run_sync( - magic.from_file, - str(path), - True, - ) - return cls._mime.get(mime) - except (magic.MagicException, OSError): - return None + try: + mime = await to_thread.run_sync( + magic.from_file, + str(path), + True, + ) + return cls._mime.get(mime) + except (magic.MagicException, OSError): + return None @classmethod async def get_file_class(cls, path: Path) -> type[BaseLocalFile]: diff --git a/pysus/tests/api/ftp/test_models.py b/pysus/tests/api/ftp/test_models.py index 64bb46e..136577f 100644 --- a/pysus/tests/api/ftp/test_models.py +++ b/pysus/tests/api/ftp/test_models.py @@ -128,7 +128,7 @@ def formatter(self, f): @pytest.mark.asyncio -async def test_file_download_calls_client(mock_client, mock_dataset): +async def test_file_download_calls_client(mock_client, mock_dataset, tmp_path): file = File( path="/root/test.dbc", _info={"path": "/root/test.dbc", "name": "test.dbc"}, @@ -136,7 +136,7 @@ async def test_file_download_calls_client(mock_client, mock_dataset): dataset=mock_dataset, ) - dest = Path("/tmp/test.dbc") + dest = Path(tmp_path / "test.dbc") await file._download(output=dest) mock_client._download_file.assert_called_once_with(file, dest, None) diff --git a/pysus/tests/api/test_client.py b/pysus/tests/api/test_client.py index 3662737..0de234b 100644 --- a/pysus/tests/api/test_client.py +++ b/pysus/tests/api/test_client.py @@ -77,11 +77,13 @@ def test_download_status_values(self): class TestLocalFileState: @pytest.mark.asyncio - async def test_update_state_creates_record(self, test_db_path): + async def test_update_state_creates_record(self, test_db_path, tmp_path): client = PySUS(db_path=test_db_path) + local = pathlib.Path(tmp_path / "test.dbc") + await client._update_state( - local_path=pathlib.Path("/tmp/test.dbc"), + local_path=local, remote_path="/remote/test.dbc", client_name="ftp", status=DownloadStatus.COMPLETED, @@ -93,9 +95,7 @@ async def test_update_state_creates_record(self, test_db_path): with client.Session() as session: record = ( - session.query(LocalFileState) - .filter_by(path="/tmp/test.dbc") - .first() + session.query(LocalFileState).filter_by(path=str(local)).first() ) assert record is not None assert record.remote_path == "/remote/test.dbc" @@ -109,34 +109,36 @@ async def test_update_state_creates_record(self, test_db_path): await client.__aexit__(None, None, None) @pytest.mark.asyncio - async def test_delete_record_removes_entry(self, test_db_path): + async def test_delete_record_removes_entry(self, test_db_path, tmp_path): client = PySUS(db_path=test_db_path) + local = pathlib.Path(tmp_path / "test.dbc") + await client._update_state( - local_path=pathlib.Path("/tmp/test.dbc"), + local_path=local, remote_path="/remote/test.dbc", client_name="ftp", status=DownloadStatus.COMPLETED, ) - await client._delete_record("/tmp/test.dbc") + await client._delete_record(str(local)) with client.Session() as session: record = ( - session.query(LocalFileState) - .filter_by(path="/tmp/test.dbc") - .first() + session.query(LocalFileState).filter_by(path=str(local)).first() ) assert record is None await client.__aexit__(None, None, None) @pytest.mark.asyncio - async def test_get_local_file_finds_existing(self, test_db_path): + async def test_get_local_file_finds_existing(self, test_db_path, tmp_path): client = PySUS(db_path=test_db_path) + local = pathlib.Path(tmp_path / "test.dbc") + await client._update_state( - local_path=pathlib.Path("/tmp/test.dbc"), + local_path=local, remote_path="/remote/test.dbc", client_name="ftp", status=DownloadStatus.COMPLETED, @@ -158,17 +160,20 @@ async def test_get_local_file_finds_existing(self, test_db_path): class TestGetCompletedRemotePaths: @pytest.mark.asyncio - async def test_get_completed_remote_paths(self, test_db_path): + async def test_get_completed_remote_paths(self, test_db_path, tmp_path): client = PySUS(db_path=test_db_path) + local1 = pathlib.Path(tmp_path / "test1.dbc") + local2 = pathlib.Path(tmp_path / "test2.dbc") + await client._update_state( - local_path=pathlib.Path("/tmp/test1.dbc"), + local_path=local1, remote_path="/remote/test1.dbc", client_name="ftp", status=DownloadStatus.COMPLETED, ) await client._update_state( - local_path=pathlib.Path("/tmp/test2.dbc"), + local_path=local2, remote_path="/remote/test2.dbc", client_name="ftp", status=DownloadStatus.PENDING, diff --git a/pysus/tests/api/test_databases.py b/pysus/tests/api/test_databases.py index 4f84f5b..7bd37c4 100644 --- a/pysus/tests/api/test_databases.py +++ b/pysus/tests/api/test_databases.py @@ -303,14 +303,27 @@ def test_fetch_data_no_files(self): class TestListFiles: + def _mock_asyncio_run(self, return_value): + import asyncio + + def _run(coro): + if asyncio.iscoroutine(coro): + coro.close() + return return_value + + return _run + def test_list_files_returns_dataframe(self): import pandas as pd - with patch("pysus.api._impl.databases.asyncio.run") as mock_run: - mock_run.return_value = pd.DataFrame( - {"name": ["test.parquet"], "path": ["/test.parquet"]} - ) + ret = pd.DataFrame( + {"name": ["test.parquet"], "path": ["/test.parquet"]} + ) + with patch( + "pysus.api._impl.databases.asyncio.run", + side_effect=self._mock_asyncio_run(ret), + ): from pysus.api._impl.databases import list_files result = list_files(dataset="SINAN") @@ -321,19 +334,22 @@ def test_list_files_returns_dataframe(self): def test_list_files_with_filters(self): import pandas as pd - with patch("pysus.api._impl.databases.asyncio.run") as mock_run: - mock_run.return_value = pd.DataFrame( - { - "name": ["test1.parquet", "test2.parquet"], - "path": ["/test1.parquet", "/test2.parquet"], - "dataset": ["sinan", "sinan"], - "year": [2024, 2023], - "month": [1, 2], - "state": ["SP", "RJ"], - "modify": ["2024-01-01", "2024-01-02"], - } - ) - + ret = pd.DataFrame( + { + "name": ["test1.parquet", "test2.parquet"], + "path": ["/test1.parquet", "/test2.parquet"], + "dataset": ["sinan", "sinan"], + "year": [2024, 2023], + "month": [1, 2], + "state": ["SP", "RJ"], + "modify": ["2024-01-01", "2024-01-02"], + } + ) + + with patch( + "pysus.api._impl.databases.asyncio.run", + side_effect=self._mock_asyncio_run(ret), + ): from pysus.api._impl.databases import list_files result = list_files( @@ -357,9 +373,12 @@ def test_list_files_with_filters(self): def test_list_files_empty_result(self): import pandas as pd - with patch("pysus.api._impl.databases.asyncio.run") as mock_run: - mock_run.return_value = pd.DataFrame() + ret = pd.DataFrame() + with patch( + "pysus.api._impl.databases.asyncio.run", + side_effect=self._mock_asyncio_run(ret), + ): from pysus.api._impl.databases import list_files result = list_files(dataset="SINAN")