commit: e0e02abb64e2a95d94baff5bf8a3fac1f5878a95 Author: Horea Christian <chr <AT> chymera <DOT> eu> AuthorDate: Mon Jan 30 11:42:48 2023 +0000 Commit: Horea Christian <horea.christ <AT> gmail <DOT> com> CommitDate: Mon Jan 30 11:42:48 2023 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e0e02abb
dev-python/hdmf: add 3.4.7, 3.5.0_p1, 3.5.1 Signed-off-by: Horea Christian <chr <AT> chymera.eu> dev-python/hdmf/files/hdmf-3.5.0-open_links.patch | 170 ++++++++++++++++++++++ dev-python/hdmf/hdmf-3.4.7.ebuild | 32 ++++ dev-python/hdmf/hdmf-3.5.0_p1.ebuild | 37 +++++ dev-python/hdmf/hdmf-3.5.1.ebuild | 32 ++++ 4 files changed, 271 insertions(+) diff --git a/dev-python/hdmf/files/hdmf-3.5.0-open_links.patch b/dev-python/hdmf/files/hdmf-3.5.0-open_links.patch new file mode 100644 index 000000000..544bf8f4b --- /dev/null +++ b/dev-python/hdmf/files/hdmf-3.5.0-open_links.patch @@ -0,0 +1,170 @@ +From 184b4a6711c60d90e073828ddcd3a6d328ee6a5e Mon Sep 17 00:00:00 2001 +From: Oliver Ruebel <[email protected]> +Date: Wed, 18 Jan 2023 16:05:57 -0800 +Subject: [PATCH 1/5] Fix #817 Check that __open_links exists before trying to + clsoe links + +--- + src/hdmf/backends/hdf5/h5tools.py | 13 +++++++++---- + 1 file changed, 9 insertions(+), 4 deletions(-) + +diff --git a/src/hdmf/backends/hdf5/h5tools.py b/src/hdmf/backends/hdf5/h5tools.py +index ba8946c60..acf2061ad 100644 +--- a/src/hdmf/backends/hdf5/h5tools.py ++++ b/src/hdmf/backends/hdf5/h5tools.py +@@ -746,10 +746,15 @@ def close_linked_files(self): + not, which prevents the linked-to file from being deleted or truncated. Use this method to close all opened, + linked-to files. + """ +- for obj in self.__open_links: +- if obj: +- obj.file.close() +- self.__open_links = [] ++ # Make sure ++ try: ++ for obj in self.__open_links: ++ if obj: ++ obj.file.close() ++ except AttributeError: # In case that self.__open_links does not exist on delete ++ pass ++ finally: ++ self.__open_links = [] + + @docval({'name': 'builder', 'type': GroupBuilder, 'doc': 'the GroupBuilder object representing the HDF5 file'}, + {'name': 'link_data', 'type': bool, + +From c12ea0851f4632c59ecdd626556bee6ddc22b632 Mon Sep 17 00:00:00 2001 +From: Oliver Ruebel <[email protected]> +Date: Wed, 18 Jan 2023 17:32:20 -0800 +Subject: [PATCH 2/5] Catch possible missing HDF5IO.__file error + +--- + src/hdmf/backends/hdf5/h5tools.py | 19 +++++++++++++++---- + 1 file changed, 15 insertions(+), 4 deletions(-) + +diff --git a/src/hdmf/backends/hdf5/h5tools.py b/src/hdmf/backends/hdf5/h5tools.py +index acf2061ad..75044a64a 100644 +--- a/src/hdmf/backends/hdf5/h5tools.py ++++ b/src/hdmf/backends/hdf5/h5tools.py +@@ -736,8 +736,15 @@ def close(self, close_links=True): + """ + if close_links: + self.close_linked_files() +- if self.__file is not None: +- self.__file.close() ++ try: ++ if self.__file is not None: ++ self.__file.close() ++ except AttributeError: ++ # Do not do anything in case that self._file does not exist. This ++ # may happen in case that an error occurs before HDF5IO has been fully ++ # setup in __init__, e.g,. if a child class such as NWBHDF5IO raises ++ # and error before self.__file has been created ++ warnings.warn("HDF5IO was not fully initialized before close. Missing self.__file") + + def close_linked_files(self): + """Close all opened, linked-to files. +@@ -751,8 +758,12 @@ def close_linked_files(self): + for obj in self.__open_links: + if obj: + obj.file.close() +- except AttributeError: # In case that self.__open_links does not exist on delete +- pass ++ except AttributeError: ++ # Do not do anything in case that self.__open_links does not exist. This ++ # may happen in case that an error occurs before HDF5IO has been fully ++ # setup in __init__, e.g,. if a child class such as NWBHDF5IO raises ++ # and error before self.__open_links has been created. ++ warnings.warn("HDF5IO was not fully initialized before close. Missing self.__open_links.") + finally: + self.__open_links = [] + + +From a43e65d13726936aa2ab49169e265a42c5a1be7f Mon Sep 17 00:00:00 2001 +From: Oliver Ruebel <[email protected]> +Date: Wed, 18 Jan 2023 17:32:55 -0800 +Subject: [PATCH 3/5] Add unit test for case where HDF5IO.close is called + before HDF5IO.__init__ is complete + +--- + tests/unit/test_io_hdf5_h5tools.py | 34 ++++++++++++++++++++++++++++++ + 1 file changed, 34 insertions(+) + +diff --git a/tests/unit/test_io_hdf5_h5tools.py b/tests/unit/test_io_hdf5_h5tools.py +index 8c03e72f8..0f2f81e31 100644 +--- a/tests/unit/test_io_hdf5_h5tools.py ++++ b/tests/unit/test_io_hdf5_h5tools.py +@@ -826,6 +826,40 @@ def test_constructor(self): + self.assertEqual(io.manager, self.manager) + self.assertEqual(io.source, self.path) + ++ def test_delete_with_incomplete_construction_missing_file(self): ++ """ ++ Here we test what happens when close is called before HDF5IO.__init__ has ++ bee completed. In this case self.__file is missing ++ """ ++ class MyHDF5IO(HDF5IO): ++ def __init__(self): ++ raise ValueError("test error") ++ with self.assertWarnsWith(warn_type=UserWarning, ++ exc_msg="HDF5IO was not fully initialized before close. Missing self.__file"): ++ try: ++ with MyHDF5IO() as _: ++ pass ++ except ValueError: ++ pass ++ ++ def test_delete_with_incomplete_construction_missing_open_files(self): ++ """ ++ Here we test what happens when close is called before HDF5IO.__init__ has ++ bee completed. In this case self.__open_file is missing ++ """ ++ ++ class MyHDF5IO(HDF5IO): ++ def __init__(self): ++ raise ValueError("test error") ++ ++ with self.assertWarnsWith(warn_type=UserWarning, ++ exc_msg="HDF5IO was not fully initialized before close. Missing self.__open_links."): ++ try: ++ with MyHDF5IO() as _: ++ pass ++ except ValueError: ++ pass ++ + def test_set_file_mismatch(self): + self.file_obj = File(get_temp_filepath(), 'w') + err_msg = ("You argued %s as this object's path, but supplied a file with filename: %s" + +From f79b3a26bdfaee22b8d24bd3094c93be77e5595f Mon Sep 17 00:00:00 2001 +From: Oliver Ruebel <[email protected]> +Date: Thu, 19 Jan 2023 13:54:33 -0800 +Subject: [PATCH 5/5] Move init of __file and __openlink up to prevent warning + during close + +--- + src/hdmf/backends/hdf5/h5tools.py | 4 +++- + 1 file changed, 3 insertions(+), 1 deletion(-) + +diff --git a/src/hdmf/backends/hdf5/h5tools.py b/src/hdmf/backends/hdf5/h5tools.py +index 75044a64a..44b9c612c 100644 +--- a/src/hdmf/backends/hdf5/h5tools.py ++++ b/src/hdmf/backends/hdf5/h5tools.py +@@ -55,6 +55,9 @@ def __init__(self, **kwargs): + path, manager, mode, comm, file_obj, driver = popargs('path', 'manager', 'mode', 'comm', 'file', 'driver', + kwargs) + ++ self.__open_links = [] # keep track of other files opened from links in this file ++ self.__file = None # This will be set below, but set to None first in case an error occurs and we need to close ++ + if path is None and file_obj is None: + raise ValueError("You must supply either a path or a file.") + +@@ -89,7 +92,6 @@ def __init__(self, **kwargs): + self.__dci_queue = HDF5IODataChunkIteratorQueue() # a queue of DataChunkIterators that need to be exhausted + ObjectMapper.no_convert(Dataset) + self._written_builders = WriteStatusTracker() # track which builders were written (or read) by this IO object +- self.__open_links = [] # keep track of other files opened from links in this file + + @property + def comm(self): diff --git a/dev-python/hdmf/hdmf-3.4.7.ebuild b/dev-python/hdmf/hdmf-3.4.7.ebuild new file mode 100644 index 000000000..4e9d47921 --- /dev/null +++ b/dev-python/hdmf/hdmf-3.4.7.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_10 ) +inherit distutils-r1 + +DESCRIPTION="The Hierarchical Data Modeling Framework" +HOMEPAGE="https://github.com/hdmf-dev/hdmf"; +SRC_URI="https://github.com/hdmf-dev/hdmf/releases/download/${PV}/${P}.tar.gz"; + +SLOT="0" +LICENSE="BSD" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-python/h5py[${PYTHON_USEDEP}] + dev-python/jsonschema[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/ruamel-yaml[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + " +BDEPEND="" + +#PATCHES=( +# "${FILESDIR}/${P}-versions.patch" +#) + +distutils_enable_tests pytest diff --git a/dev-python/hdmf/hdmf-3.5.0_p1.ebuild b/dev-python/hdmf/hdmf-3.5.0_p1.ebuild new file mode 100644 index 000000000..6e63271cd --- /dev/null +++ b/dev-python/hdmf/hdmf-3.5.0_p1.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_10 ) +inherit distutils-r1 + +MY_PV="${PV//_p*/}" +MY_P="${PN}-${MY_PV}" + +DESCRIPTION="The Hierarchical Data Modeling Framework" +HOMEPAGE="https://github.com/hdmf-dev/hdmf"; +SRC_URI="https://github.com/hdmf-dev/hdmf/releases/download/${MY_PV}/${MY_P}.tar.gz"; + +SLOT="0" +LICENSE="BSD" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-python/h5py[${PYTHON_USEDEP}] + dev-python/jsonschema[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/ruamel-yaml[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + " +BDEPEND="" + +PATCHES=( + "${FILESDIR}/${MY_P}-open_links.patch" +) + +distutils_enable_tests pytest + +S="${WORKDIR}/${MY_P}" diff --git a/dev-python/hdmf/hdmf-3.5.1.ebuild b/dev-python/hdmf/hdmf-3.5.1.ebuild new file mode 100644 index 000000000..4e9d47921 --- /dev/null +++ b/dev-python/hdmf/hdmf-3.5.1.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_10 ) +inherit distutils-r1 + +DESCRIPTION="The Hierarchical Data Modeling Framework" +HOMEPAGE="https://github.com/hdmf-dev/hdmf"; +SRC_URI="https://github.com/hdmf-dev/hdmf/releases/download/${PV}/${P}.tar.gz"; + +SLOT="0" +LICENSE="BSD" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-python/h5py[${PYTHON_USEDEP}] + dev-python/jsonschema[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/ruamel-yaml[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + " +BDEPEND="" + +#PATCHES=( +# "${FILESDIR}/${P}-versions.patch" +#) + +distutils_enable_tests pytest
