From b1eb5e8563fc963990171d1d3690bb60b129c5c7 Mon Sep 17 00:00:00 2001 From: Felipe Carlos Date: Sun, 9 Aug 2026 02:03:30 -0300 Subject: [PATCH 1/5] backend: enhance arrow compatibility libs Co-authored-by: Felipe Carvalho --- pyproject.toml | 6 ++ pysits/__init__.py | 4 ++ pysits/backend/arrow.py | 106 +++++++++++++++++++++++++++++++++++ pysits/backend/pkgs.py | 6 ++ pysits/conversions/tibble.py | 36 ++++++++++++ 5 files changed, 158 insertions(+) create mode 100644 pysits/backend/arrow.py diff --git a/pyproject.toml b/pyproject.toml index 302fde4..f08bff0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -60,6 +60,9 @@ classifiers = [ dependencies = [ "rpy2>=3.5.17,<4.0.0", "pandas>=2.2.3", + # pandas ships no wheels for Python 3.14 before 3.0. Without this floor pip + # builds pandas from source there, and the result segfaults on basic calls. + "pandas>=3.0.0; python_version>='3.14'", "pillow>=11.1.0", "matplotlib>=3.10.1", "geopandas>=1.1.0", @@ -90,6 +93,9 @@ dev = [ "pytest-cov>=6.1.1", "pytest-randomly>=3.16.0", "cloudpickle>=3.1.1", + # The test suite covers the xarray exporters and reads rasters directly + "pysits[xarray]", + "rasterio>=1.3.0", ] [tool.ruff] diff --git a/pysits/__init__.py b/pysits/__init__.py index 5355f73..a908803 100644 --- a/pysits/__init__.py +++ b/pysits/__init__.py @@ -17,6 +17,10 @@ """pysits module.""" +# Importing `backend.arrow` first selects the libarrow allocator, which must +# happen before anything imports `pyarrow` or loads the R `arrow` package. +# Keep this import above the others. See `pysits.backend.arrow`. +from .backend import arrow as _arrow # noqa: F401 from .conversions.dsl.mask import MaskValue from .conversions.dsl.tuning import hparam from .settings import __version__ diff --git a/pysits/backend/arrow.py b/pysits/backend/arrow.py new file mode 100644 index 0000000..9d24d5b --- /dev/null +++ b/pysits/backend/arrow.py @@ -0,0 +1,106 @@ +# +# Copyright (C) 2025 sits developers. +# +# This program is free software; you can redistribute it and/or modify it +# under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program; if not, see . +# + +"""Arrow interoperability between R and Python. + +``pysits`` moves data between R and Python as Arrow IPC streams. That puts two +independent builds of the libarrow C++ library in a single process: the one +bundled in the R ``arrow`` package and the one bundled in ``pyarrow``. Their +symbols collapse into a single namespace, so a call made through ``pyarrow`` +can be served by R's libarrow. + +Each build keeps a private ``mimalloc`` heap. When the two are mixed, a buffer +allocated by one library is read back as zeroed memory by the other, and every +transfer is silently corrupted instead of failing. Both builds also support the +system allocator, which is shared, so selecting it keeps them interoperable. + +The allocator is chosen by libarrow the first time it initializes, so importing +this module sets ``ARROW_DEFAULT_MEMORY_POOL``. It is imported before anything +that pulls in ``pyarrow`` or the R ``arrow`` package. +""" + +import os + +# +# Allocator selected to keep R libarrow and pyarrow interoperable +# +ARROW_MEMORY_POOL_ENVVAR = "ARROW_DEFAULT_MEMORY_POOL" +ARROW_MEMORY_POOL = "system" + +# Set on import: libarrow reads this once, when it initializes. A value already +# present in the environment is left alone so users can override it. +os.environ.setdefault(ARROW_MEMORY_POOL_ENVVAR, ARROW_MEMORY_POOL) + +# +# Values transferred to R and back to verify the round-trip is lossless. A +# mismatched pair of libarrow builds reads them back as zeros. +# +PROBE_COLUMN = "pysits_arrow_probe" +PROBE_VALUES = [0.5, 1.5, 2.5] + + +def check_arrow_memory_pool() -> None: + """Refuse to load R ``arrow`` package under an unshared allocator. + + Called before the R ``arrow`` package is loaded. Corruption appears only + once both libarrow builds are in use, and is silent when it does, so the + configuration is rejected up front rather than probed for afterwards. + + Raises: + RuntimeError: If the selected allocator is not the shared one. + """ + selected = os.environ.get(ARROW_MEMORY_POOL_ENVVAR) + + if selected == ARROW_MEMORY_POOL: + return + + raise RuntimeError( + f"{ARROW_MEMORY_POOL_ENVVAR} is set to '{selected}', but pysits " + f"requires '{ARROW_MEMORY_POOL}'.\n\n" + "The R `arrow` package and `pyarrow` each bundle their own build of " + "the libarrow C++ library. Loaded together, they must use the system " + "allocator to share buffers. With any other allocator, data sent " + "between R and Python is silently replaced by zeros.\n\n" + f"Unset {ARROW_MEMORY_POOL_ENVVAR}, or set it before starting Python:\n\n" + f" export {ARROW_MEMORY_POOL_ENVVAR}={ARROW_MEMORY_POOL}" + ) + + +def arrow_interop_error(observed: list) -> RuntimeError: + """Build the error raised when an Arrow round-trip loses data. + + Args: + observed (list): Values read back from R for `PROBE_VALUES`. + + Returns: + RuntimeError: Error describing the cause and how to resolve it. + """ + import pyarrow as pa + + pool = pa.default_memory_pool().backend_name + + return RuntimeError( + "Data sent to R is coming back corrupted, so pysits cannot run.\n\n" + f"Sent {PROBE_VALUES}, received {observed}.\n\n" + "The R `arrow` package and `pyarrow` each bundle their own build of " + "the libarrow C++ library. Loaded together, they must use the system " + f"allocator to share buffers, but pyarrow is using '{pool}'.\n\n" + "This happens when pyarrow is initialized before pysits with a " + "different allocator. Either import pysits before pyarrow, or set the " + "environment variable before starting Python:\n\n" + f" export {ARROW_MEMORY_POOL_ENVVAR}={ARROW_MEMORY_POOL}" + ) diff --git a/pysits/backend/pkgs.py b/pysits/backend/pkgs.py index 37c2c90..83d0a29 100644 --- a/pysits/backend/pkgs.py +++ b/pysits/backend/pkgs.py @@ -17,6 +17,7 @@ """backend packages.""" +from pysits.backend.arrow import check_arrow_memory_pool from pysits.backend.loaders import load_package from pysits.settings import __sitsver__ @@ -33,4 +34,9 @@ r_pkg_kohonen = load_package("kohonen") r_pkg_sf = load_package("sf") r_pkg_htmlwidgets = load_package("htmlwidgets") + +# `arrow` brings a second libarrow build into the process, so the allocator has +# to be compatible before it is loaded. See `pysits.backend.arrow`. +check_arrow_memory_pool() + r_pkg_arrow = load_package("arrow") diff --git a/pysits/conversions/tibble.py b/pysits/conversions/tibble.py index db1c5a2..4850d50 100644 --- a/pysits/conversions/tibble.py +++ b/pysits/conversions/tibble.py @@ -36,6 +36,7 @@ from rpy2.robjects.vectors import DataFrame as RDataFrame from shapely import wkt +from pysits.backend.arrow import PROBE_COLUMN, PROBE_VALUES, arrow_interop_error from pysits.backend.functions import r_fnc_class, r_fnc_set_column from pysits.backend.pkgs import r_pkg_base, r_pkg_sf, r_pkg_sits from pysits.models.frame import NestedFrame @@ -90,6 +91,39 @@ def _sf_to_shapely(sf_object: RDataFrame) -> list: # # Arrow IPC helpers # +def _check_arrow_interop() -> None: + """Verify that Arrow data is not corrupted once R's libarrow is loaded. + + R libarrow only initializes on first use, so a probe is sent through R to + force it, and ``pyarrow`` is then re-tested. A mismatched pair of libarrow + builds corrupts the conversion of Python objects to Arrow arrays, returning + zeros instead of raising, which would silently damage every nested column. + + Raises: + RuntimeError: If either transfer loses data. + """ + probe = PandasDataFrame({PROBE_COLUMN: PROBE_VALUES}) + + # Forces R libarrow to initialize, and checks the Python -> R direction + r_probe = rpy2_globalenv["pysits_read_ipc_raw"]( + robjects.vectors.ByteVector(_dataframe_to_ipc_bytes(probe)) + ) + + # Load content from R + observed = list(r_probe.rx2(PROBE_COLUMN)) + + # If it is different, then given an error + if observed != PROBE_VALUES: + raise arrow_interop_error(observed) + + # Both libarrow builds are live now: check the conversion of Python objects + # to Arrow arrays, which is the path nested columns depend on. + observed = pa.array(PROBE_VALUES).to_pylist() + + if observed != PROBE_VALUES: + raise arrow_interop_error(observed) + + def _ensure_r_ipc_functions(): """Define R-side IPC reader/writer/unnester functions once.""" if "pysits_write_ipc_raw" in rpy2_globalenv: @@ -162,6 +196,8 @@ def _ensure_r_ipc_functions(): } """) + _check_arrow_interop() + def _dataframe_to_ipc_bytes(df: PandasDataFrame) -> bytes: """Serialize a pandas DataFrame to Arrow IPC bytes. From ef0e233832840f27954e10ca2a61c2c1ce20c12c Mon Sep 17 00:00:00 2001 From: Felipe Carlos Date: Sun, 9 Aug 2026 02:16:27 -0300 Subject: [PATCH 2/5] package: define minimum rpy2 version Co-authored-by: Felipe Carvalho --- pyproject.toml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index f08bff0..c608490 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -58,11 +58,13 @@ classifiers = [ ] dependencies = [ - "rpy2>=3.5.17,<4.0.0", + # 3.6.0 is the first release distributing wheels. Earlier ones are + # source-only, so pip would compile rpy2 against the local R installation + "rpy2>=3.6.0,<4.0.0", "pandas>=2.2.3", - # pandas ships no wheels for Python 3.14 before 3.0. Without this floor pip - # builds pandas from source there, and the result segfaults on basic calls. - "pandas>=3.0.0; python_version>='3.14'", + # pandas ships no wheels for Python 3.14 before 2.3.3. Without this floor + # pip builds pandas from source there, and the result segfaults. + "pandas>=2.3.3; python_version>='3.14'", "pillow>=11.1.0", "matplotlib>=3.10.1", "geopandas>=1.1.0", From 20e7d16bdb1ccb6eb21d3b4d446e66e298d56122 Mon Sep 17 00:00:00 2001 From: Felipe Carlos Date: Sun, 9 Aug 2026 02:16:42 -0300 Subject: [PATCH 3/5] action: update tests workflow Co-authored-by: Felipe Carvalho --- .github/workflows/tests.yaml | 106 +++++++++++++++++++++++++++++++++++ 1 file changed, 106 insertions(+) create mode 100644 .github/workflows/tests.yaml diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml new file mode 100644 index 0000000..6c8d198 --- /dev/null +++ b/.github/workflows/tests.yaml @@ -0,0 +1,106 @@ +name: Tests + +on: + push: + branches: [main] + pull_request: + branches: [main] + + # Run every Saturday at 3:00 AM + schedule: + # * is a special character in YAML so you have to quote this string + - cron: '0 3 * * 6' + + workflow_dispatch: + inputs: + reason: + required: false + description: 'Reason' + default: 'Manual trigger' + +jobs: + test: + name: Python ${{ matrix.python-version }} + runs-on: ubuntu-latest + + strategy: + # Report every version, so a single break does not hide the others. + fail-fast: false + matrix: + python-version: ['3.10', '3.11', '3.12', '3.13', '3.14'] + + env: + # Fail the build on R warnings that would otherwise pass unnoticed + R_KEEP_PKG_SOURCE: yes + + steps: + - name: Checkout code + uses: actions/checkout@v4 + + - name: Set up R + uses: r-lib/actions/setup-r@v2 + with: + use-public-rspm: true + + - name: Install R dependencies + uses: r-lib/actions/setup-r-dependencies@v2 + with: + # `arrow` and `kohonen` are required by pysits but are not part of a + # default `install.packages("sits")`, so they are listed explicitly. + packages: | + any::sits + any::arrow + any::kohonen + any::jsonlite + + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + + - name: Create a clean virtual environment + # Mirrors how users install pysits, so a broken dependency resolution + # is caught here rather than by them. + run: python -m venv .venv + + - name: Install pysits + # `--only-binary` makes pip fail instead of falling back to a source + # build when no wheel matches this interpreter. Those builds have + # shipped binaries that segfault. Only pysits itself is built here. + run: | + .venv/bin/python -m pip install --upgrade pip + .venv/bin/python -m pip install \ + --only-binary=:all: --no-binary pysits \ + ".[dev]" + + - name: Report resolved dependency versions + run: .venv/bin/python -m pip list + + - name: Verify Arrow interoperability between R and Python + # pyarrow and R arrow package each bundle libarrow. If they stop + # sharing an allocator, transfers are silently corrupted rather than + # failing, so this asserts a known value survives a round-trip. + run: | + .venv/bin/python - <<'EOF' + import pyarrow as pa + + import pysits + from pysits.conversions.tibble import ( + pandas_sits_to_tibble, + tibble_sits_to_pandas, + ) + + probe = [0.5, 1.5, 2.5] + assert pa.array(probe).to_pylist() == probe, "pyarrow returns corrupted data" + + samples = pysits.samples_modis_ndvi + expected = samples["time_series"][0]["NDVI"].tolist() + actual = tibble_sits_to_pandas(pandas_sits_to_tibble(samples.head(1))) + actual = actual["time_series"][0]["NDVI"].tolist() + + assert actual == expected, f"round-trip corrupted data: {actual} != {expected}" + print("Arrow round-trip is lossless.") + EOF + + - name: Run tests + run: .venv/bin/python -m pytest From 0a1e1966f1c0bd8a34c5b8061a3d45e3e1343ff6 Mon Sep 17 00:00:00 2001 From: Felipe Carlos Date: Sun, 9 Aug 2026 03:32:14 -0300 Subject: [PATCH 4/5] package: lock dependencies Co-authored-by: Felipe Carvalho --- uv.lock | 204 +++++++++++++++++++++++++++++++++++++++++++++++++------- 1 file changed, 181 insertions(+), 23 deletions(-) diff --git a/uv.lock b/uv.lock index b8590dd..3a1c9fc 100644 --- a/uv.lock +++ b/uv.lock @@ -2,7 +2,10 @@ version = 1 revision = 3 requires-python = ">=3.10, <4" resolution-markers = [ - "python_full_version >= '3.12'", + "python_full_version >= '3.14' and sys_platform == 'win32'", + "python_full_version >= '3.14' and sys_platform == 'emscripten'", + "python_full_version >= '3.14' and sys_platform != 'emscripten' and sys_platform != 'win32'", + "python_full_version >= '3.12' and python_full_version < '3.14'", "python_full_version == '3.11.*'", "python_full_version < '3.11'", ] @@ -264,7 +267,8 @@ name = "contourpy" version = "1.3.2" source = { registry = "https://pypi.org/simple" } dependencies = [ - { name = "numpy" }, + { name = "numpy", version = "2.2.6", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.14'" }, + { name = "numpy", version = "2.5.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.14'" }, ] sdist = { url = "https://files.pythonhosted.org/packages/66/54/eb9bfc647b19f2009dd5c7f5ec51c4e6ca831725f1aea7a993034f483147/contourpy-1.3.2.tar.gz", hash = "sha256:b6945942715a034c671b7fc54f9588126b0b8bf23db2696e3ca8328f3ff0ab54", size = 13466130, upload-time = "2025-04-15T17:47:53.79Z" } wheels = [ @@ -425,7 +429,8 @@ wheels = [ [package.optional-dependencies] array = [ - { name = "numpy" }, + { name = "numpy", version = "2.2.6", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.14'" }, + { name = "numpy", version = "2.5.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.14'" }, ] [[package]] @@ -513,9 +518,11 @@ name = "geopandas" version = "1.1.0" source = { registry = "https://pypi.org/simple" } dependencies = [ - { name = "numpy" 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cron: '0 3 * * 6' - workflow_dispatch: inputs: reason: