sci-biology/bidsschematools: updated source hashes

Signed-off-by: Horea Christian <chr@chymera.eu>

sci-biology/bidsschematools/Manifest

@@ -1,2 +1,5 @@
-DIST bidsschematools-0.3.0_pre20220801.tar.gz 5716585 SHA256 b91e5707786704c6a0ee13489d78fdc0d274b334ea435bb375498c07d40933eb SHA512 524206d54a04587180dd3b150bb4e88282d62cf1273717d3caedb6b227e74102b9b5d4e68cb2b1725ad6e19641e0fbcb5ee1b2b5931fa7025f918d72e8a591a9 WHIRLPOOL 8a732807ee307fe96093c1fa9b4943d8bf5bbe07a24258460c23d2f35adb91c8cce08516dcd8c8e61d0fe2be2a34ca0d8063612697031520fa5fba083cf4be7c
+DIST bids-error-examples-4dee93e8dc75ea7b63c94e1657bbc94e3e77dfd0.tar.gz 666982 BLAKE2B 08f3ec9734d323dae3bcabb5a22f0bfdb3cfff114523f73aa162fb0d62145dcb1c82315b729ced59a20edc4d896247bdbfd8dbd2aa1ec293160d2c6c1b469c16 SHA512 0cd1e3d1a5e5ecb29d5fb00293910f417b5fb0e787eed42d5242c94fcdf7871b8702ef5e1125474df32c077bc7ec810c1eeec236dbca6c9f7bb6998cf2b37a9c
-DIST bidsschematools-0.3.0_rc1.tar.gz 5717759 SHA256 3789692e42d975eda76c680b53a8057c4d15b05983e879c09ab43291effa99fa SHA512 f250fd9fd88524d6d35ecd446e1b9abd7c80aa845ed08ee281f996a52e36f6e9d9eee855b752e1c7b35ae5c456eae94ca29b81e4585637286c1f535a5ec93105 WHIRLPOOL 4c6e42969a43c391af691784f4272603b0f26f173704add71891c6d9a255ae0e91444e538089c81368fdb5cc003e534425c9b95dd8f1888af3341f68cf48d613
+DIST bids-examples-252449184b532ba08c26e53e422f1e05366ac102.tar.gz 35118815 BLAKE2B d0a8f50f362158bfa200f3db56d52e88d206d667660b65533e637078b1ca8061df751d50fcf4933336e4afd32a19b76e99d6034270b0121410d0ac4046d17a26 SHA512 c4ec6b77cae211572ade803520b07ea9d49a6d2ab8ad8f2cd3f9028ea70bd1bf8e92bbdb294aaf058f1095182bfa1ff1e0e6c138508a1dd0a9879c3ab325dc36
+DIST bidsschematools-0.3.1.tar.gz 109064 BLAKE2B 9432ad8723975b20d8e64e50c44657a6fb97a01a640de8f56e32b29f6c806b3f5317c4761e9b5b567e38cdb69ae461c3e745c4de4f6f2cf648299d9376365369 SHA512 334200722d2d936abf44ea202253a46dfd6120d6dc2ce7a638abd721fdc6810e2f2172ab474883c1dcbba0de1d0e8edf8ab572af0955087375147a6d3ed76f48
+DIST bidsschematools-0.3.1_p2.tar.gz 5725503 BLAKE2B bd3722a1d89d7788317a13931756200915c868c48dce9cd7ef45fa80bbe70861b38c93f9fedb95b73fb0467654c344b1d668865032528dbf5a8ef081a80bd0f8 SHA512 b1771124c0f4b81a8c36a72fba927531b202cabd043c187115cd46826e583486727e313709c41b3b3a5e3ff8a86f18066f24d48e41505019cd1e499e7afece38
+DIST bidsschematools-0.4.0.tar.gz 1158341 BLAKE2B a47ad610936e8bb9f91ade6f234f258535364d5cd3c188544dbb25f2540138596455656a25f167b1b6417cd896e15b4e1baf140999d0dbccdfa01432b2e88783 SHA512 c42dd337a0f2402de2c4794b85382b0e422ffbd9dbc814e943f32bc95cb1d7d2bc31dc40aeef6fd792d14ec09617de289ecdb794c0d22f1154f23e2f04bd5fdd

sci-biology/bidsschematools/bidsschematools-0.3.0_pre20220801.ebuild

@@ -1,34 +0,0 @@
-# Copyright 2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{8..11} )
-
-MY_HASH="54e7990387166fd206cb1f4ec4eb2187b42c08b3"
-
-inherit distutils-r1
-
-DESCRIPTION="A Python library for working with the BIDS schema"
-HOMEPAGE="https://github.com/bids-standard/bids-specification"
-SRC_URI="https://github.com/bids-standard/bids-specification/archive/${MY_HASH}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="CC-BY-SA-4.0"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-RDEPEND="dev-python/tabulate"
-DEPEND=""
-
-S="${WORKDIR}/bids-specification-${MY_HASH}/tools/schemacode"
-
-distutils_enable_tests pytest
-
-python_test() {
-	# Ideally we should package the testdata packages:
-	# https://github.com/bids-standard/bids-examples
-	# https://github.com/bids-standard/bids-error-examples
-	export SCHEMACODE_TESTS_NONETWORK=1
-	epytest
-}

sci-biology/bidsschematools/bidsschematools-0.3.1.ebuild

@@ -6,22 +6,20 @@ EAPI=8
 DISTUTILS_USE_PEP517=setuptools
 PYTHON_COMPAT=( python3_{8..11} )
 
-MY_HASH="14302430895d2f52d33b0e9a2c8e957c86187ce4"
-
 inherit distutils-r1
 
 DESCRIPTION="A Python library for working with the BIDS schema"
 HOMEPAGE="https://github.com/bids-standard/bids-specification"
-SRC_URI="https://github.com/TheChymera/bids-specification/archive/${MY_HASH}.tar.gz -> ${P}.tar.gz"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
 
-LICENSE="CC-BY-SA-4.0"
+LICENSE="MIT"
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 
 RDEPEND="dev-python/tabulate"
 DEPEND=""
 
-S="${WORKDIR}/bids-specification-${MY_HASH}/tools/schemacode"
+#S="${WORKDIR}/bids-specification-${MY_HASH}/tools/schemacode"
 
 distutils_enable_tests pytest
 

sci-biology/bidsschematools/bidsschematools-0.3.1_p2.ebuild

@@ -0,0 +1,65 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{8..10} )
+
+#MY_PV=${PV%%_*}
+#MY_P="${PN}-${MY_PV}"
+MY_HASH="a87f8955b48d663eab08d7706c7302215c0e36d3"
+EXAMPLES_HASH="252449184b532ba08c26e53e422f1e05366ac102"
+ERROR_EXAMPLES_HASH="4dee93e8dc75ea7b63c94e1657bbc94e3e77dfd0"
+inherit distutils-r1
+
+DESCRIPTION="A Python library for working with the BIDS schema"
+HOMEPAGE="https://github.com/bids-standard/bids-specification"
+SRC_URI="
+	https://github.com/bids-standard/bids-specification/archive/${MY_HASH}.tar.gz -> ${P}.tar.gz
+	test? (
+		https://github.com/bids-standard/bids-examples/archive/${EXAMPLES_HASH}.tar.gz -> bids-examples-${EXAMPLES_HASH}.tar.gz
+		https://github.com/bids-standard/bids-error-examples/archive/${ERROR_EXAMPLES_HASH}.tar.gz -> bids-error-examples-${ERROR_EXAMPLES_HASH}.tar.gz
+		)
+"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="render"
+
+RDEPEND="
+	dev-python/pyyaml[${PYTHON_USEDEP}]
+	render? (
+		dev-python/tabulate[${PYTHON_USEDEP}]
+		dev-python/pandas[${PYTHON_USEDEP}]
+	)
+"
+DEPEND=""
+
+#S="${WORKDIR}/${MY_P}"
+S="${WORKDIR}/bids-specification-${MY_HASH}/tools/schemacode/"
+
+#PATCHES=(
+#	"${FILESDIR}/${P}-static_testdata.patch"
+#)
+
+distutils_enable_tests pytest
+
+src_prepare() {
+	if use test; then
+		mkdir "${S}/testdata" || die "Failed to create testdata directory."
+		cp -rf "${WORKDIR}/bids-examples-${EXAMPLES_HASH}" "${S}/testdata/bids-examples" || die "Failed to copy testdata into tree."
+		cp -rf "${WORKDIR}/bids-error-examples-${ERROR_EXAMPLES_HASH}" "${S}/testdata/bids-error-examples" || die "Failed to copy testdata into tree."
+	fi
+	if ! use render; then
+		rm "${S}/bidsschematools/render.py"
+		rm "${S}/bidsschematools/tests/test_render.py"
+	fi
+	default
+}
+
+python_test() {
+	# We want to display INFO logging explicitly stating whether static data was used.
+	epytest --log-level=INFO
+}

sci-biology/bidsschematools/bidsschematools-0.4.0.ebuild

@@ -0,0 +1,37 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit distutils-r1
+
+DESCRIPTION="A Python library for working with the BIDS schema"
+HOMEPAGE="https://github.com/bids-standard/bids-specification"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="render"
+
+RDEPEND="
+	dev-python/pyyaml[${PYTHON_USEDEP}]
+	render? (
+		dev-python/tabulate[${PYTHON_USEDEP}]
+		dev-python/pandas[${PYTHON_USEDEP}]
+	)
+"
+DEPEND=""
+
+distutils_enable_tests pytest
+
+src_prepare() {
+	if ! use render; then
+		rm "${S}/bidsschematools/render.py"
+		rm "${S}/bidsschematools/tests/test_render.py"
+	fi
+	default
+}

sci-biology/bidsschematools/bidsschematools-9999.ebuild

@@ -1,33 +0,0 @@
-# Copyright 2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{8..11} )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="A Python library for working with the BIDS schema"
-HOMEPAGE="https://github.com/bids-standard/bids-specification"
-EGIT_REPO_URI="git@github.com:TheChymera/bids-specification.git"
-EGIT_BRANCH="release_candidate"
-
-LICENSE="CC-BY-SA-4.0"
-SLOT="0"
-KEYWORDS=""
-
-RDEPEND="dev-python/tabulate"
-DEPEND=""
-
-S="${WORKDIR}/bids-specification-${MY_HASH}/tools/schemacode"
-
-distutils_enable_tests pytest
-
-python_test() {
-	# Ideally we should package the testdata packages:
-	# https://github.com/bids-standard/bids-examples
-	# https://github.com/bids-standard/bids-error-examples
-	export SCHEMACODE_TESTS_NONETWORK=1
-	epytest
-}

sci-biology/bidsschematools/files/bidsschematools-0.3.1_p1-static_testdata.patch

@@ -0,0 +1,98 @@
+--- a/bidsschematools/tests/conftest.py
++++ b/bidsschematools/tests/conftest.py
+@@ -35,29 +35,38 @@ BIDS_ERROR_SELECTION = [
+ def get_gitrepo_fixture(url, whitelist):
+     @pytest.fixture(scope="session")
+     def fixture():
+-        with tempfile.TemporaryDirectory() as path:
+-            assert os.path.exists(path)
+-            lgr.debug("Cloning %r into %r", url, path)
+-            runout = run(
+-                [
+-                    "git",
+-                    "clone",
+-                    "--depth=1",
+-                    "--filter=blob:none",
+-                    "--sparse",
+-                    url,
+-                    path,
+-                ],
+-                capture_output=True,
+-            )
+-            if runout.returncode:
+-                raise RuntimeError(f"Failed to clone {url} into {path}")
+-            # cwd specification is VERY important, not only to achieve the correct
+-            # effects, but also to avoid dropping files from your repository if you
+-            # were to run `git sparse-checkout` inside the software repo.
+-            _ = run(["git", "sparse-checkout", "init", "--cone"], cwd=path)
+-            _ = run(["git", "sparse-checkout", "set"] + whitelist, cwd=path)
+-            yield path
++        archive_name = url.rsplit("/",1)[-1]
++        testdata_archive = os.path.join(os.getcwd(),"testdata",archive_name)
++        if os.path.isdir(testdata_archive):
++            lgr.info("Found static testdata archive under `%s`. "
++                "Not downloading latest data from version control.", testdata_archive)
++            yield testdata_archive
++        else:
++            lgr.info("No static testdata available under `%s`. "
++                "Attempting to fetch live data from version control.", testdata_archive)
++            with tempfile.TemporaryDirectory() as path:
++                assert os.path.exists(path)
++                lgr.debug("Cloning %r into %r", url, path)
++                runout = run(
++                    [
++                        "git",
++                        "clone",
++                        "--depth=1",
++                        "--filter=blob:none",
++                        "--sparse",
++                        url,
++                        path,
++                    ],
++                    capture_output=True,
++                )
++                if runout.returncode:
++                    raise RuntimeError(f"Failed to clone {url} into {path}")
++                # cwd specification is VERY important, not only to achieve the correct
++                # effects, but also to avoid dropping files from your repository if you
++                # were to run `git sparse-checkout` inside the software repo.
++                _ = run(["git", "sparse-checkout", "init", "--cone"], cwd=path)
++                _ = run(["git", "sparse-checkout", "set"] + whitelist, cwd=path)
++                yield path
+
+     return fixture
+
+
+--- a/bidsschematools/tests/test_validator.py
++++ b/bidsschematools/tests/test_validator.py
+@@ -377,7 +377,6 @@ def test_bids_datasets(bids_examples, tmp_path, dataset):
+     result = validate_bids(
+         target,
+         schema_version=schema_path,
+-        report_path=True,
+     )
+     # Have all files been validated?
+     assert len(result["path_tracking"]) == 0
+--- a/bidsschematools/validator.py
++++ b/bidsschematools/validator.py
+@@ -451,7 +451,7 @@ def validate_all(
+
+ def write_report(
+     validation_result,
+-    report_path="/var/tmp/bids-validator/report_{datetime}-{pid}.log",
++    report_path="~/.cache/bidsschematools/validator-report_{datetime}-{pid}.log",
+     datetime_format="%Y%m%d%H%M%SZ",
+ ):
+     """Write a human-readable report based on the validation result.
+@@ -481,8 +481,9 @@ def write_report(
+         pid=os.getpid(),
+     )
+     report_path = os.path.abspath(os.path.expanduser(report_path))
++    report_dir = os.path.dirname(report_path)
+     try:
+-        os.makedirs(os.path.dirname(report_path))
++        os.makedirs(report_dir)
+     except OSError:
+         pass
+
+

sci-biology/bidsschematools/metadata.xml

@@ -2,11 +2,18 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
 	<maintainer type="person">
-		<email>chr@chymera.eu</email>
+		<email>gentoo@chymera.eu</email>
 		<name>Horea Christian</name>
 	</maintainer>
 	<maintainer type="project">
 		<email>sci@gentoo.org</email>
 		<name>Gentoo Science Project</name>
 	</maintainer>
+	<upstream>
+		<remote-id type="github">bids-standard/bids-specification</remote-id>
+		<remote-id type="pypi">bidsschematools</remote-id>
+	</upstream>
+	<use>
+		<flag name="render">Support for schema table rendering</flag>
+	</use>
 </pkgmetadata>