diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index c01047e..5a65e24 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -23,7 +23,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"] + python-version: ["3.9", "3.10", "3.11", "3.12"] steps: - uses: actions/checkout@v3 - name: Set up Python ${{ matrix.python-version }} diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 30de9d8..7ab93aa 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -6,7 +6,7 @@ sphinx: build: os: ubuntu-20.04 tools: - python: "3.8" + python: "3.12" jobs: post_install: # See https://github.com/pdm-project/pdm/discussions/1365 diff --git a/CHANGELOG.md b/CHANGELOG.md index 8a08cdb..19460c1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,17 @@ All notable changes to this project will be documented here. ## [Unreleased] +### Added +- Official support for NumPy 2.0. +- Support for write-through memory-mapping. Thanks to @nh2 and + @chpatrick for the original implementation. + +### Fixed +- A small unit test bug. + +### Removed +- Official support for Python 3.8. +- Official support for NumPy < 1.21. ## [1.0.3] - 2024-01-06 ### Fixed diff --git a/doc/usage.md b/doc/usage.md index 7eeeccb..742527e 100644 --- a/doc/usage.md +++ b/doc/usage.md @@ -70,8 +70,8 @@ Concretely: ```Python Console >>> plydata.elements[0].name 'vertex' ->>> plydata.elements[0].data[0] -(0., 0., 0.) +>>> plydata.elements[0].data[0].tolist() +(0.0, 0.0, 0.0) >>> plydata.elements[0].data['x'] array([0., 0., 1., 1.], dtype=float32) >>> plydata['face'].data['vertex_indices'][0] @@ -91,8 +91,8 @@ and elements can be indexed directly without explicitly going through the `data` attribute: ```Python Console ->>> plydata['vertex'][0] -(0., 0., 0.) +>>> plydata['vertex'][0].tolist() +(0.0, 0.0, 0.0) >>> ``` @@ -138,21 +138,40 @@ two cases to consider. If an element in a binary PLY file has no list properties, then it will be memory-mapped by default, subject to the capabilities of the -underlying file object. Memory mapping can be disabled using the -`mmap` argument: +underlying file object. +- Memory mapping can be disabled or fine-tuned using the `mmap` argument + of `PlyData.read`. +- To confirm whether a given element has been memory-mapped or not, + check the type of `element.data`. + +This is all illustrated below: ```Python Console >>> plydata.text = False >>> plydata.byte_order = '<' >>> plydata.write('tet_binary.ply') >>> ->>> # `mmap=True` is the default: +>>> # Memory-mapping is enabled by default. >>> plydata = PlyData.read('tet_binary.ply') >>> isinstance(plydata['vertex'].data, numpy.memmap) True +>>> # Any falsy value disables memory-mapping here. >>> plydata = PlyData.read('tet_binary.ply', mmap=False) >>> isinstance(plydata['vertex'].data, numpy.memmap) False +>>> # Strings can also be given to fine-tune memory-mapping. +>>> # For example, with 'r+', changes can be written back to the file. +>>> # In this case, the file must be explicitly opened with read-write +>>> # access. +>>> with open('tet_binary.ply', 'r+b') as f: +... plydata = PlyData.read(f, mmap='r+') +>>> isinstance(plydata['vertex'].data, numpy.memmap) +True +>>> plydata['vertex']['x'] = 100 +>>> plydata['vertex'].data.flush() +>>> plydata = PlyData.read('tet_binary.ply') +>>> all(plydata['vertex']['x'] == 100) +True >>> ``` diff --git a/pdm.lock b/pdm.lock index 595139f..7084011 100644 --- a/pdm.lock +++ b/pdm.lock @@ -1,120 +1,258 @@ # This file is @generated by PDM. # It is not intended for manual editing. +[metadata] +groups = ["default", "doc", "lint", "test"] +strategy = [] +lock_version = "4.5.0" +content_hash = "sha256:a6e572200c4c7aa2be3ae20ce275ff7c81bddcf514b6f8373fd41dfe6bd0fc31" + +[[metadata.targets]] +requires_python = ">=3.9" + [[package]] name = "alabaster" -version = "0.7.13" -requires_python = ">=3.6" -summary = "A configurable sidebar-enabled Sphinx theme" +version = "0.7.16" +requires_python = ">=3.9" +summary = "A light, configurable Sphinx theme" +files = [ + {file = "alabaster-0.7.16-py3-none-any.whl", hash = "sha256:b46733c07dce03ae4e150330b975c75737fa60f0a7c591b6c8bf4928a28e2c92"}, + {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"}, +] [[package]] name = "babel" -version = "2.12.1" -requires_python = ">=3.7" +version = "2.15.0" +requires_python = ">=3.8" summary = "Internationalization utilities" dependencies = [ "pytz>=2015.7; python_version < \"3.9\"", ] +files = [ + {file = "Babel-2.15.0-py3-none-any.whl", hash = "sha256:08706bdad8d0a3413266ab61bd6c34d0c28d6e1e7badf40a2cebe67644e2e1fb"}, + {file = "babel-2.15.0.tar.gz", hash = "sha256:8daf0e265d05768bc6c7a314cf1321e9a123afc328cc635c18622a2f30a04413"}, +] [[package]] name = "cachetools" -version = "5.3.1" +version = "5.4.0" requires_python = ">=3.7" summary = "Extensible memoizing collections and decorators" +files = [ + {file = "cachetools-5.4.0-py3-none-any.whl", hash = "sha256:3ae3b49a3d5e28a77a0be2b37dbcb89005058959cb2323858c2657c4a8cab474"}, + {file = "cachetools-5.4.0.tar.gz", hash = "sha256:b8adc2e7c07f105ced7bc56dbb6dfbe7c4a00acce20e2227b3f355be89bc6827"}, +] [[package]] name = "certifi" -version = "2023.5.7" +version = "2024.7.4" requires_python = ">=3.6" summary = "Python package for providing Mozilla's CA Bundle." +files = [ + {file = "certifi-2024.7.4-py3-none-any.whl", hash = "sha256:c198e21b1289c2ab85ee4e67bb4b4ef3ead0892059901a8d5b622f24a1101e90"}, + {file = "certifi-2024.7.4.tar.gz", hash = "sha256:5a1e7645bc0ec61a09e26c36f6106dd4cf40c6db3a1fb6352b0244e7fb057c7b"}, +] [[package]] name = "chardet" -version = "5.1.0" +version = "5.2.0" requires_python = ">=3.7" summary = "Universal encoding detector for Python 3" +files = [ + {file = "chardet-5.2.0-py3-none-any.whl", hash = "sha256:e1cf59446890a00105fe7b7912492ea04b6e6f06d4b742b2c788469e34c82970"}, + {file = "chardet-5.2.0.tar.gz", hash = "sha256:1b3b6ff479a8c414bc3fa2c0852995695c4a026dcd6d0633b2dd092ca39c1cf7"}, +] [[package]] name = "charset-normalizer" -version = "3.1.0" +version = "3.3.2" requires_python = ">=3.7.0" summary = "The Real First Universal Charset Detector. 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f2f06fc..7db1dec 100644 --- a/plyfile.py +++ b/plyfile.py @@ -128,18 +128,17 @@ def _parse_header(stream): ) @staticmethod - def read(stream, mmap=True, known_list_len={}): + def read(stream, mmap='c', known_list_len={}): """ Read PLY data from a readable file-like object or filename. Parameters ---------- stream : str or readable open file - mmap : bool, optional (default=True) - Whether to allow element data to be memory-mapped when - possible. The default is `True`, which allows memory - mapping. Using `False` will prevent memory mapping. - + mmap : {'c', 'r', 'r+'} or bool, optional (default='c') + Configures memory-mapping. Any falsy value disables + memory mapping, and any non-string truthy value is + equivalent to 'c', for copy-on-write mapping. known_list_len : dict, optional Mapping from element names to mappings from list property names to their fixed lengths. This optional argument is @@ -507,7 +506,7 @@ def _read(self, stream, text, byte_order, mmap, stream : readable open file text : bool byte_order : {'<', '>', '='} - mmap : bool + mmap : {'c', 'r', 'r+'} or bool known_list_len : dict """ if text: @@ -519,7 +518,9 @@ def _read(self, stream, text, byte_order, mmap, if mmap and _can_mmap(stream) and can_mmap_lists: # Loading the data is straightforward. We will memory # map the file in copy-on-write mode. - self._read_mmap(stream, byte_order, known_list_len) + mmap_mode = mmap if isinstance(mmap, str) else 'c' + self._read_mmap(stream, byte_order, mmap_mode, + known_list_len) else: # A simple load is impossible. self._read_bin(stream, byte_order) @@ -549,7 +550,7 @@ def _write(self, stream, text, byte_order): stream.write(self.data.astype(self.dtype(byte_order), copy=False).data) - def _read_mmap(self, stream, byte_order, known_list_len): + def _read_mmap(self, stream, byte_order, mmap_mode, known_list_len): """ Memory-map an input file as `self.data`. @@ -557,6 +558,7 @@ def _read_mmap(self, stream, byte_order, known_list_len): ---------- stream : readable open file byte_order : {'<', '>', '='} + mmap_mode: str known_list_len : dict """ list_len_props = {} @@ -581,7 +583,7 @@ def _read_mmap(self, stream, byte_order, known_list_len): if max_bytes < num_bytes: raise PlyElementParseError("early end-of-file", self, max_bytes // dtype.itemsize) - self._data = _np.memmap(stream, dtype, 'c', offset, self.count) + self._data = _np.memmap(stream, dtype, mmap_mode, offset, self.count) # Fix stream position stream.seek(offset + self.count * dtype.itemsize) # remove any extra properties added diff --git a/pyproject.toml b/pyproject.toml index 4032aed..d82a113 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -23,8 +23,8 @@ description = "PLY file reader/writer" authors = [ {name = "Darsh Ranjan", email = "dranjan@berkeley.edu"}, ] -dependencies = ["numpy>=1.17"] -requires-python = ">=3.8" +dependencies = ["numpy>=1.21"] +requires-python = ">=3.9" readme = "README.md" license = {file = "COPYING"} keywords = ["ply", "numpy"] @@ -33,7 +33,6 @@ classifiers = [ "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)", "Operating System :: OS Independent", "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.8", "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", diff --git a/test/test_plyfile.py b/test/test_plyfile.py index 35aaa76..cf15d46 100644 --- a/test/test_plyfile.py +++ b/test/test_plyfile.py @@ -376,15 +376,32 @@ def test_memmap(tmpdir, tet_ply_txt): def test_copy_on_write(tmpdir, tet_ply_txt): ply0 = tet_ply_txt + ply0.text = False filename = str(tmpdir.join('test.ply')) ply0.write(filename) ply1 = PlyData.read(filename) + assert isinstance(ply1['vertex'].data, numpy.memmap) ply1['vertex']['x'] += 1 ply2 = PlyData.read(filename) verify(ply0, ply2) +def test_memmap_rw(tmpdir, tet_ply_txt): + ply0 = tet_ply_txt + ply0.text = False + filename = str(tmpdir.join('test.ply')) + ply0.write(filename) + with open(filename, 'r+b') as f: + ply1 = PlyData.read(f, mmap='r+') + assert isinstance(ply1['vertex'].data, numpy.memmap) + ply1['vertex']['x'][:] = 100 + ply1['vertex'].data.flush() + ply2 = PlyData.read(filename) + + assert (ply2['vertex']['x'] == 100).all() + + def test_write_invalid_filename(tet_ply_txt): with Raises(TypeError) as e: tet_ply_txt.write(None) diff --git a/tox.ini b/tox.ini index ae1e5bd..04f6e65 100644 --- a/tox.ini +++ b/tox.ini @@ -1,9 +1,8 @@ [tox] -envlist = global-init,py38-numpy1.{17,19,21,22,23,24},py39-numpy1.{17,19,21,22,23,24,25},py310-numpy1.{21,22,23,24,25},py311-numpy1.{23,24,25},py312-numpy1.26,global-finalize +envlist = global-init,py39-numpy{1.21,1.22,1.23,1.24,1.25,1.26,2.0},py310-numpy{1.21,1.22,1.23,1.24,1.25,1.26,2.0},py311-numpy{1.23,1.24,1.25,1.26,2.0},py312-numpy{1.26,2.0},global-finalize [gh-actions] python = - 3.8: py38 3.9: py39 3.10: py310 3.11: py311 @@ -21,14 +20,13 @@ usedevelop = True deps = pytest pytest-cov - numpy1.17: numpy>=1.17,<1.18 - numpy1.19: numpy>=1.19,<1.20 numpy1.21: numpy>=1.21,<1.22 numpy1.22: numpy>=1.22,<1.23 numpy1.23: numpy>=1.23,<1.24 numpy1.24: numpy>=1.24,<1.25 numpy1.25: numpy>=1.25,<1.26 numpy1.26: numpy>=1.26,<1.27 + numpy2.0: numpy>=2.0,<2.1 setenv = COVERAGE_FILE = {toxworkdir}/.coverage.{envname} commands = py.test test -v --cov=plyfile