sci-biology/bidsschematools: updated source hashes
Signed-off-by: Horea Christian <chr@chymera.eu>
This commit is contained in:
Horea Christian
parent
ac7f4982a8
commit
5dd7ebe2c2
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@ -1,2 +1,5 @@
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DIST bidsschematools-0.3.0_pre20220801.tar.gz 5716585 SHA256 b91e5707786704c6a0ee13489d78fdc0d274b334ea435bb375498c07d40933eb SHA512 524206d54a04587180dd3b150bb4e88282d62cf1273717d3caedb6b227e74102b9b5d4e68cb2b1725ad6e19641e0fbcb5ee1b2b5931fa7025f918d72e8a591a9 WHIRLPOOL 8a732807ee307fe96093c1fa9b4943d8bf5bbe07a24258460c23d2f35adb91c8cce08516dcd8c8e61d0fe2be2a34ca0d8063612697031520fa5fba083cf4be7c
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DIST bidsschematools-0.3.0_rc1.tar.gz 5717759 SHA256 3789692e42d975eda76c680b53a8057c4d15b05983e879c09ab43291effa99fa SHA512 f250fd9fd88524d6d35ecd446e1b9abd7c80aa845ed08ee281f996a52e36f6e9d9eee855b752e1c7b35ae5c456eae94ca29b81e4585637286c1f535a5ec93105 WHIRLPOOL 4c6e42969a43c391af691784f4272603b0f26f173704add71891c6d9a255ae0e91444e538089c81368fdb5cc003e534425c9b95dd8f1888af3341f68cf48d613
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DIST bids-error-examples-4dee93e8dc75ea7b63c94e1657bbc94e3e77dfd0.tar.gz 666982 BLAKE2B 08f3ec9734d323dae3bcabb5a22f0bfdb3cfff114523f73aa162fb0d62145dcb1c82315b729ced59a20edc4d896247bdbfd8dbd2aa1ec293160d2c6c1b469c16 SHA512 0cd1e3d1a5e5ecb29d5fb00293910f417b5fb0e787eed42d5242c94fcdf7871b8702ef5e1125474df32c077bc7ec810c1eeec236dbca6c9f7bb6998cf2b37a9c
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DIST bids-examples-252449184b532ba08c26e53e422f1e05366ac102.tar.gz 35118815 BLAKE2B d0a8f50f362158bfa200f3db56d52e88d206d667660b65533e637078b1ca8061df751d50fcf4933336e4afd32a19b76e99d6034270b0121410d0ac4046d17a26 SHA512 c4ec6b77cae211572ade803520b07ea9d49a6d2ab8ad8f2cd3f9028ea70bd1bf8e92bbdb294aaf058f1095182bfa1ff1e0e6c138508a1dd0a9879c3ab325dc36
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DIST bidsschematools-0.3.1.tar.gz 109064 BLAKE2B 9432ad8723975b20d8e64e50c44657a6fb97a01a640de8f56e32b29f6c806b3f5317c4761e9b5b567e38cdb69ae461c3e745c4de4f6f2cf648299d9376365369 SHA512 334200722d2d936abf44ea202253a46dfd6120d6dc2ce7a638abd721fdc6810e2f2172ab474883c1dcbba0de1d0e8edf8ab572af0955087375147a6d3ed76f48
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DIST bidsschematools-0.3.1_p2.tar.gz 5725503 BLAKE2B bd3722a1d89d7788317a13931756200915c868c48dce9cd7ef45fa80bbe70861b38c93f9fedb95b73fb0467654c344b1d668865032528dbf5a8ef081a80bd0f8 SHA512 b1771124c0f4b81a8c36a72fba927531b202cabd043c187115cd46826e583486727e313709c41b3b3a5e3ff8a86f18066f24d48e41505019cd1e499e7afece38
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DIST bidsschematools-0.4.0.tar.gz 1158341 BLAKE2B a47ad610936e8bb9f91ade6f234f258535364d5cd3c188544dbb25f2540138596455656a25f167b1b6417cd896e15b4e1baf140999d0dbccdfa01432b2e88783 SHA512 c42dd337a0f2402de2c4794b85382b0e422ffbd9dbc814e943f32bc95cb1d7d2bc31dc40aeef6fd792d14ec09617de289ecdb794c0d22f1154f23e2f04bd5fdd
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@ -1,34 +0,0 @@
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# Copyright 2022 Gentoo Authors
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# Distributed under the terms of the GNU General Public License v2
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EAPI=8
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DISTUTILS_USE_PEP517=setuptools
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PYTHON_COMPAT=( python3_{8..11} )
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MY_HASH="54e7990387166fd206cb1f4ec4eb2187b42c08b3"
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inherit distutils-r1
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DESCRIPTION="A Python library for working with the BIDS schema"
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HOMEPAGE="https://github.com/bids-standard/bids-specification"
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SRC_URI="https://github.com/bids-standard/bids-specification/archive/${MY_HASH}.tar.gz -> ${P}.tar.gz"
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LICENSE="CC-BY-SA-4.0"
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SLOT="0"
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KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
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RDEPEND="dev-python/tabulate"
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DEPEND=""
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S="${WORKDIR}/bids-specification-${MY_HASH}/tools/schemacode"
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distutils_enable_tests pytest
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python_test() {
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# Ideally we should package the testdata packages:
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# https://github.com/bids-standard/bids-examples
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# https://github.com/bids-standard/bids-error-examples
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export SCHEMACODE_TESTS_NONETWORK=1
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epytest
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}
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@ -6,22 +6,20 @@ EAPI=8
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DISTUTILS_USE_PEP517=setuptools
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PYTHON_COMPAT=( python3_{8..11} )
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MY_HASH="14302430895d2f52d33b0e9a2c8e957c86187ce4"
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inherit distutils-r1
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DESCRIPTION="A Python library for working with the BIDS schema"
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HOMEPAGE="https://github.com/bids-standard/bids-specification"
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SRC_URI="https://github.com/TheChymera/bids-specification/archive/${MY_HASH}.tar.gz -> ${P}.tar.gz"
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SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
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LICENSE="CC-BY-SA-4.0"
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LICENSE="MIT"
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SLOT="0"
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KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
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RDEPEND="dev-python/tabulate"
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DEPEND=""
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S="${WORKDIR}/bids-specification-${MY_HASH}/tools/schemacode"
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#S="${WORKDIR}/bids-specification-${MY_HASH}/tools/schemacode"
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distutils_enable_tests pytest
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@ -0,0 +1,65 @@
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# Copyright 2022 Gentoo Authors
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# Distributed under the terms of the GNU General Public License v2
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EAPI=8
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DISTUTILS_USE_PEP517=setuptools
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PYTHON_COMPAT=( python3_{8..10} )
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#MY_PV=${PV%%_*}
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#MY_P="${PN}-${MY_PV}"
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MY_HASH="a87f8955b48d663eab08d7706c7302215c0e36d3"
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EXAMPLES_HASH="252449184b532ba08c26e53e422f1e05366ac102"
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ERROR_EXAMPLES_HASH="4dee93e8dc75ea7b63c94e1657bbc94e3e77dfd0"
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inherit distutils-r1
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DESCRIPTION="A Python library for working with the BIDS schema"
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HOMEPAGE="https://github.com/bids-standard/bids-specification"
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SRC_URI="
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https://github.com/bids-standard/bids-specification/archive/${MY_HASH}.tar.gz -> ${P}.tar.gz
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test? (
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https://github.com/bids-standard/bids-examples/archive/${EXAMPLES_HASH}.tar.gz -> bids-examples-${EXAMPLES_HASH}.tar.gz
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https://github.com/bids-standard/bids-error-examples/archive/${ERROR_EXAMPLES_HASH}.tar.gz -> bids-error-examples-${ERROR_EXAMPLES_HASH}.tar.gz
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)
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"
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LICENSE="MIT"
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SLOT="0"
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KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
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IUSE="render"
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RDEPEND="
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dev-python/pyyaml[${PYTHON_USEDEP}]
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render? (
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dev-python/tabulate[${PYTHON_USEDEP}]
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dev-python/pandas[${PYTHON_USEDEP}]
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)
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"
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DEPEND=""
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#S="${WORKDIR}/${MY_P}"
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S="${WORKDIR}/bids-specification-${MY_HASH}/tools/schemacode/"
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#PATCHES=(
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# "${FILESDIR}/${P}-static_testdata.patch"
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#)
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distutils_enable_tests pytest
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src_prepare() {
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if use test; then
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mkdir "${S}/testdata" || die "Failed to create testdata directory."
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cp -rf "${WORKDIR}/bids-examples-${EXAMPLES_HASH}" "${S}/testdata/bids-examples" || die "Failed to copy testdata into tree."
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cp -rf "${WORKDIR}/bids-error-examples-${ERROR_EXAMPLES_HASH}" "${S}/testdata/bids-error-examples" || die "Failed to copy testdata into tree."
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fi
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if ! use render; then
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rm "${S}/bidsschematools/render.py"
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rm "${S}/bidsschematools/tests/test_render.py"
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fi
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default
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}
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python_test() {
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# We want to display INFO logging explicitly stating whether static data was used.
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epytest --log-level=INFO
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}
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@ -0,0 +1,37 @@
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# Copyright 2022 Gentoo Authors
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# Distributed under the terms of the GNU General Public License v2
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EAPI=8
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DISTUTILS_USE_PEP517=setuptools
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PYTHON_COMPAT=( python3_{8..10} )
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inherit distutils-r1
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DESCRIPTION="A Python library for working with the BIDS schema"
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HOMEPAGE="https://github.com/bids-standard/bids-specification"
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SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
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LICENSE="MIT"
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SLOT="0"
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KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
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IUSE="render"
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RDEPEND="
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dev-python/pyyaml[${PYTHON_USEDEP}]
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render? (
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dev-python/tabulate[${PYTHON_USEDEP}]
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dev-python/pandas[${PYTHON_USEDEP}]
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)
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"
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DEPEND=""
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distutils_enable_tests pytest
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src_prepare() {
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if ! use render; then
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rm "${S}/bidsschematools/render.py"
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rm "${S}/bidsschematools/tests/test_render.py"
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fi
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default
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}
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@ -1,33 +0,0 @@
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# Copyright 2022 Gentoo Authors
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# Distributed under the terms of the GNU General Public License v2
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EAPI=8
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DISTUTILS_USE_PEP517=setuptools
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PYTHON_COMPAT=( python3_{8..11} )
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inherit distutils-r1 git-r3
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DESCRIPTION="A Python library for working with the BIDS schema"
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HOMEPAGE="https://github.com/bids-standard/bids-specification"
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EGIT_REPO_URI="git@github.com:TheChymera/bids-specification.git"
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EGIT_BRANCH="release_candidate"
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LICENSE="CC-BY-SA-4.0"
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SLOT="0"
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KEYWORDS=""
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RDEPEND="dev-python/tabulate"
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DEPEND=""
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S="${WORKDIR}/bids-specification-${MY_HASH}/tools/schemacode"
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distutils_enable_tests pytest
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python_test() {
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# Ideally we should package the testdata packages:
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# https://github.com/bids-standard/bids-examples
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# https://github.com/bids-standard/bids-error-examples
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export SCHEMACODE_TESTS_NONETWORK=1
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epytest
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}
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@ -0,0 +1,98 @@
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--- a/bidsschematools/tests/conftest.py
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+++ b/bidsschematools/tests/conftest.py
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@@ -35,29 +35,38 @@ BIDS_ERROR_SELECTION = [
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def get_gitrepo_fixture(url, whitelist):
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@pytest.fixture(scope="session")
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def fixture():
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- with tempfile.TemporaryDirectory() as path:
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- assert os.path.exists(path)
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- lgr.debug("Cloning %r into %r", url, path)
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- runout = run(
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- [
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- "git",
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- "clone",
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- "--depth=1",
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- "--filter=blob:none",
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- "--sparse",
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- url,
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- path,
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- ],
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- capture_output=True,
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- )
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- if runout.returncode:
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- raise RuntimeError(f"Failed to clone {url} into {path}")
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- # cwd specification is VERY important, not only to achieve the correct
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- # effects, but also to avoid dropping files from your repository if you
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- # were to run `git sparse-checkout` inside the software repo.
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- _ = run(["git", "sparse-checkout", "init", "--cone"], cwd=path)
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- _ = run(["git", "sparse-checkout", "set"] + whitelist, cwd=path)
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- yield path
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+ archive_name = url.rsplit("/",1)[-1]
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+ testdata_archive = os.path.join(os.getcwd(),"testdata",archive_name)
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+ if os.path.isdir(testdata_archive):
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+ lgr.info("Found static testdata archive under `%s`. "
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+ "Not downloading latest data from version control.", testdata_archive)
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+ yield testdata_archive
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+ else:
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+ lgr.info("No static testdata available under `%s`. "
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+ "Attempting to fetch live data from version control.", testdata_archive)
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+ with tempfile.TemporaryDirectory() as path:
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+ assert os.path.exists(path)
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+ lgr.debug("Cloning %r into %r", url, path)
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+ runout = run(
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+ [
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+ "git",
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+ "clone",
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+ "--depth=1",
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+ "--filter=blob:none",
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+ "--sparse",
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+ url,
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+ path,
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+ ],
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+ capture_output=True,
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+ )
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+ if runout.returncode:
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+ raise RuntimeError(f"Failed to clone {url} into {path}")
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+ # cwd specification is VERY important, not only to achieve the correct
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+ # effects, but also to avoid dropping files from your repository if you
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+ # were to run `git sparse-checkout` inside the software repo.
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+ _ = run(["git", "sparse-checkout", "init", "--cone"], cwd=path)
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+ _ = run(["git", "sparse-checkout", "set"] + whitelist, cwd=path)
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+ yield path
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return fixture
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--- a/bidsschematools/tests/test_validator.py
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+++ b/bidsschematools/tests/test_validator.py
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@@ -377,7 +377,6 @@ def test_bids_datasets(bids_examples, tmp_path, dataset):
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result = validate_bids(
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target,
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schema_version=schema_path,
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- report_path=True,
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)
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# Have all files been validated?
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assert len(result["path_tracking"]) == 0
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--- a/bidsschematools/validator.py
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+++ b/bidsschematools/validator.py
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@@ -451,7 +451,7 @@ def validate_all(
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def write_report(
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validation_result,
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- report_path="/var/tmp/bids-validator/report_{datetime}-{pid}.log",
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+ report_path="~/.cache/bidsschematools/validator-report_{datetime}-{pid}.log",
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datetime_format="%Y%m%d%H%M%SZ",
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):
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"""Write a human-readable report based on the validation result.
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@@ -481,8 +481,9 @@ def write_report(
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pid=os.getpid(),
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)
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report_path = os.path.abspath(os.path.expanduser(report_path))
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+ report_dir = os.path.dirname(report_path)
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try:
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- os.makedirs(os.path.dirname(report_path))
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+ os.makedirs(report_dir)
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except OSError:
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pass
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@ -2,11 +2,18 @@
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<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
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<pkgmetadata>
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<maintainer type="person">
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<email>chr@chymera.eu</email>
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<email>gentoo@chymera.eu</email>
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<name>Horea Christian</name>
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</maintainer>
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<maintainer type="project">
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<email>sci@gentoo.org</email>
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<name>Gentoo Science Project</name>
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</maintainer>
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<upstream>
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<remote-id type="github">bids-standard/bids-specification</remote-id>
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<remote-id type="pypi">bidsschematools</remote-id>
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</upstream>
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<use>
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<flag name="render">Support for schema table rendering</flag>
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</use>
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</pkgmetadata>
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