automatic import of bids-schemaHEADmaster

6 files changed, 498 insertions, 0 deletions

diff --git a/.gitignore b/.gitignore
index e69de29..d175be6 100644
--- a/.gitignore
+++ b/.gitignore
@@ -0,0 +1,3 @@
+/bids-error-examples-ac0a2f58f34ce284847dde5bd3b90d7ea048c141-filtered.tar.zst
+/bids-examples-f21306744fd57bfd5c8e8e91d907fa8448f9eca5-filtered.tar.zst
+/bids-specification-schema-1.0.5.tar.gz
diff --git a/bids-schema.spec b/bids-schema.spec
new file mode 100644
index 0000000..77cfb2c
--- /dev/null
+++ b/bids-schema.spec
@@ -0,0 +1,363 @@
+## START: Set by rpmautospec
+## (rpmautospec version 0.7.3)
+## RPMAUTOSPEC: autorelease, autochangelog
+%define autorelease(e:s:pb:n) %{?-p:0.}%{lua:
+    release_number = 1;
+    base_release_number = tonumber(rpm.expand("%{?-b*}%{!?-b:1}"));
+    print(release_number + base_release_number - 1);
+}%{?-e:.%{-e*}}%{?-s:.%{-s*}}%{!?-n:%{?dist}}
+## END: Set by rpmautospec
+
+Name:           bids-schema
+Version:        1.0.5
+Release:        %autorelease
+Summary:        BIDS schema description
+
+%global srcversion %(echo '%{version}' | tr '^' '.')
+# Installation paths imitate the structure of
+# https://github.com/bids-standard/bids-schema/ in case we start packaging from
+# that in the future. Schemas are installed under directories versioned by the
+# BIDS specification version, not the schema version. If the following is set
+# correctly, then
+#   https://github.com/bids-standard/bids-schema/raw/refs/heads/main/…
+#   versions/%%{bidsversion}/schema/SCHEMA_VERSION
+# should match or nearly match the schema version packaged here.
+%global bidsversion 1.10.0
+
+# The specification, and the schema data derived from it, are CC-BY-4.0.
+#
+# The Python library in tools/schemacode/, packaged as python3-bidsschematools,
+# is MIT.
+License:        CC-BY-4.0
+# CC0-1.0 comes from the filtered test datasets, Source2 and Source3
+SourceLicense:  CC0-1.0 AND CC-BY-4.0 AND MIT
+URL:            https://github.com/bids-standard/bids-specification
+# The PyPI sdist corresponds to the tools/schemacode directory in git.
+Source0:        %{url}/archive/schema-%{srcversion}/bids-specification-schema-%{srcversion}.tar.gz
+
+# Tests would like to use the following datasets from
+# https://github.com/bids-standard/bids-examples:
+#   CC0-1.0:
+#   - asl003/ ds000248/ micr_SEMzarr/ micr_SPIM/ pet003/ qmri_tb1tfl/
+#   CC-BY-4.0:
+#   - eeg_cbm/
+#   Unclear licensing (no license specified or "Custom" with no text or details):
+#   - hcp_example_bids/ qmri_vfa/
+#   ODC-By-1.0 (not-allowed in Fedora)
+#   - fnirs_automaticity/
+#
+# Also, the following from https://github.com/bids-standard/bids-error-examples:
+#   CC0-1.0:
+#   - invalid_asl003/ invalid_pet001/
+#
+# See BIDS_SELECTION and BIDS_ERROR_SELECTION in
+# tools/schemacode/src/bidsschematools/conftest.py.
+#
+# We use the latest commits from each repository at the time of packaging; see
+# tools/schemacode/src/bidsschematools/conftest.py, which contains code to download
+# these if they are not present.
+%global examples_url https://github.com/bids-standard/bids-examples
+%global examples_commit f21306744fd57bfd5c8e8e91d907fa8448f9eca5
+%global error_examples_url https://github.com/bids-standard/bids-error-examples
+%global error_examples_commit ac0a2f58f34ce284847dde5bd3b90d7ea048c141
+#
+# We use a script to create archives containing only the test datasets that
+# fall under clearly-acceptable content license terms *and* are used in the
+# tests. The script requires that each of the following macros occupies a
+# single (long, if necessary) line.
+%global examples asl003 ds000248 eeg_cbm micr_SEMzarr micr_SPIM pet003 qmri_tb1tfl
+%global error_examples invalid_asl003 invalid_pet001
+# Run this script with no arguments to parse the spec file (in the same
+# directory) for commits, URLs, and whitelisted datasets, and create two
+# corresponding source archives in the current working directory.
+Source1:        get_test_data
+# License: CC0-1.0 AND CC-BY-4.0
+# (does not contribute to the licenses of the binary RPMs)
+Source2:        bids-examples-%{examples_commit}-filtered.tar.zst
+# License: CC0-1.0
+# (does not contribute to the licenses of the binary RPMs)
+Source3:        bids-error-examples-%{error_examples_commit}-filtered.tar.zst
+
+# Man pages hand-written for Fedora in groff_man(7) format based on --help
+Source10:       bst.1
+Source11:       bst-export.1
+
+BuildArch:      noarch
+
+BuildRequires:  symlinks
+BuildRequires:  python3-devel
+# The tests extra includes mostly linting/coverage tools; considering
+# https://docs.fedoraproject.org/en-US/packaging-guidelines/Python/#_linters,
+# it is easier to enumerate test dependencies by hand.
+BuildRequires:  %{py3_dist pytest}
+
+%description
+Portions of the BIDS specification are defined using YAML files in order to
+make the specification machine-readable.
+
+Currently the portions of the specification that rely on this schema are:
+
+  • the entity tables,
+  • entity definitions,
+  • filename templates,
+  • metadata tables.
+
+Any changes to the specification should be mirrored in the schema.
+
+
+%package -n python3-bidsschematools
+Summary:        Python tools for working with the BIDS schema
+License:        MIT
+
+Requires:       %{name} = %{version}-%{release}
+
+%description -n python3-bidsschematools
+A Python library (available after installation in the Python interpreter as
+bidsschematools) for working with the Brain Imaging Data Structure (BIDS)
+schema.
+
+Features: 
+
+  • lightweight
+  • reference schema parsing implementation used for schema testing
+  • simple CLI bindings (e.g. bst export)
+
+
+%pyproject_extras_subpkg -n python3-bidsschematools render expressions
+
+
+%prep
+%autosetup -n bids-specification-schema-%{srcversion}
+%setup -q -T -D -a 2 -c -n bids-specification-schema-%{srcversion}
+%setup -q -T -D -a 3 -c -n bids-specification-schema-%{srcversion}
+
+# Remove JavaScript sources used for building the specification documents
+# (which we don’t do anyway); these include a bundled pre-compiled/minified
+# version of JQuery, which is (license-wise) allowable in the source RPM, but
+# must not be shipped in the binary RPMs. Removing it confirms that it is not
+# used or shipped. We also preemptively remove the CSS sources, which currently
+# don’t contain anything bundled or pre-minified, but are unused and might
+# contain something objectionable in a future release.
+rm -rf src/js/ src/css/
+
+
+%generate_buildrequires
+pushd tools/schemacode >/dev/null
+%pyproject_buildrequires -x render,expressions
+popd >/dev/null
+
+
+%build
+pushd tools/schemacode >/dev/null
+%pyproject_wheel
+popd
+
+
+%install
+# Imitate the structure of https://github.com/bids-standard/bids-schema/ in
+# case we start packaging from that in the future.
+install -d '%{buildroot}%{_datadir}/bids-schema/versions/%{bidsversion}'
+ln -s '%{bidsversion}' '%{buildroot}%{_datadir}/bids-schema/versions/latest'
+cp -rvp src/schema \
+    '%{buildroot}%{_datadir}/bids-schema/versions/%{bidsversion}/schema'
+# While https://github.com/bids-standard/bids-schema does not install
+# metaschema.json alongside the schema/ directory, it *is* included in the PyPI
+# sdist for bidsschematools.
+install -t '%{buildroot}%{_datadir}/bids-schema/versions/%{bidsversion}' \
+    -p -m 0644 src/metaschema.json
+
+pushd tools/schemacode >/dev/null
+%pyproject_install
+%pyproject_save_files -l bidsschematools
+popd
+
+# Unbundle the schema data from the Python library.
+# Since the schema directory is replaced by a symbolic link into the base
+# package, we must remove its contents from the files list, and we must remove
+# the directory itself so that we can list it manually without %%dir.
+sed -r -i '/\/bidsschematools\/data\/schema(\/|$)/d' %{pyproject_files}
+for thing in metaschema.json schema
+do
+  rm -rv "%{buildroot}%{python3_sitelib}/bidsschematools/data/${thing}"
+  # Create an absolute symlink into the buildroot and then convert it to a
+  # relative one; the relative symlink works both in %%check and after the
+  # package is actually installed.
+  ln -s \
+      "%{buildroot}%{_datadir}/bids-schema/versions/%{bidsversion}/${thing}" \
+      "%{buildroot}%{python3_sitelib}/bidsschematools/data/${thing}"
+  symlinks -c -o "%{buildroot}%{python3_sitelib}/bidsschematools/data/${thing}"
+done
+
+# Generate and include a copy of the “exported” JSON version of the schema to
+# imitate the structure of https://github.com/bids-standard/bids-schema. See
+# readthedocs.yml. We do this in %%install rather than %%build because we need
+# to use the generated “bst” entry point.
+PYTHONDONTWRITEBYTECODE=1 PYTHONPATH='%{buildroot}%{python3_sitelib}' \
+    %{buildroot}%{_bindir}/bst -v export --output \
+        '%{buildroot}%{_datadir}/bids-schema/versions/%{bidsversion}/schema.json'
+
+# Do not ship the tests.
+sed -r -i '/\/bidsschematools\/tests(\/|$)/d' %{pyproject_files}
+sed -r -i '/bidsschematools\.tests(\.|$)/d' '%{_pyproject_modules}'
+rm -rvf '%{buildroot}%{python3_sitelib}/bidsschematools/tests'
+
+# Install the man pages
+install -t '%{buildroot}%{_mandir}/man1' -D -p -m 0644 \
+    '%{SOURCE10}' '%{SOURCE11}'
+
+# Install documentation. (Since we use %%doc with an absolute path for the
+# README.md file in the schema directory, we must use absolute paths for all
+# documentation; see
+# https://docs.fedoraproject.org/en-US/packaging-guidelines/#_documentation.)
+install -t '%{buildroot}%{_pkgdocdir}' -D -p -m 0644 \
+    CITATION.cff
+# The top-level README.md in the source tree is really for the *specification*,
+# and this package is for the *schema*. We therefore form a relative symlink to
+# the README.md in the schema directory (in two steps).
+ln -s \
+    '%{buildroot}%{_datadir}/bids-schema/versions/%{bidsversion}/schema/README.md' \
+    '%{buildroot}%{_pkgdocdir}/README.md'
+symlinks -c -o '%{buildroot}%{_pkgdocdir}/README.md'
+install -t '%{buildroot}%{_docdir}/python3-bidsschematools' -D -p -m 0644 \
+    tools/schemacode/README.md
+
+
+%check
+# Sanity check
+verfile='%{_datadir}/bids-schema/versions/%{bidsversion}/schema/SCHEMA_VERSION'
+[ '%{srcversion}' = "$(cat "%{buildroot}${verfile}")" ]
+
+%pyproject_check_import
+
+# These tests require example files that were filtered out for license reasons.
+k="${k-}${k+ and }not test_bids_datasets[hcp_example_bids]"
+k="${k-}${k+ and }not test_bids_datasets[qmri_vfa]"
+k="${k-}${k+ and }not test_bids_datasets[fnirs_automaticity]"
+
+# Since we removed the tests from the installed package, we now link the
+# example data into the original source copy of the library for testing.
+ln -s "${PWD}/bids-examples-%{examples_commit}" \
+    tools/schemacode/tests/data/bids-examples
+ln -s "${PWD}/bids-error-examples-%{error_examples_commit}" \
+    tools/schemacode/tests/data/bids-error-examples
+# We also link the actual schema data, as unbundled and installed in the
+# buildroot.
+rm -rvf 'tools/schemacode/src/bidsschematools/data'
+ln -s '%{buildroot}%{python3_sitelib}/bidsschematools/data' \
+    'tools/schemacode/src/bidsschematools/data'
+# All of this manipulation is OK here in %%check because we already built the
+# wheel and installed the library to the buildroot.
+
+%pytest ${ignore-} -k "${k-}" -v
+
+
+# https://docs.fedoraproject.org/en-US/packaging-guidelines/Directory_Replacement/#_scriptlet_to_replace_a_directory
+# Added for F42; can be removed in F45 (upgrade path for three releases)
+%pretrans -p <lua> -n python3-bidsschematools
+path = "%{python3_sitelib}/bidsschematools/data/schema"
+st = posix.stat(path)
+if st and st.type == "directory" then
+  status = os.rename(path, path .. ".rpmmoved")
+  if not status then
+    suffix = 0
+    while not status do
+      suffix = suffix + 1
+      status = os.rename(path .. ".rpmmoved", path .. ".rpmmoved." .. suffix)
+    end
+    os.rename(path, path .. ".rpmmoved")
+  end
+end
+
+
+%files
+%license LICENSE
+%doc %dir %{_pkgdocdir}
+%doc %{_pkgdocdir}/CITATION.cff
+# This is a symbolic link to the README.md in the schema directory:
+%doc %{_pkgdocdir}/README.md
+
+%dir %{_datadir}/bids-schema/
+%dir %{_datadir}/bids-schema/versions/
+# Symbolic link to the current version
+%{_datadir}/bids-schema/versions/latest
+%dir %{_datadir}/bids-schema/versions/%{bidsversion}/
+%{_datadir}/bids-schema/versions/%{bidsversion}/metaschema.json
+%{_datadir}/bids-schema/versions/%{bidsversion}/schema.json
+%dir %{_datadir}/bids-schema/versions/%{bidsversion}/schema
+%doc %{_datadir}/bids-schema/versions/%{bidsversion}/schema/README.md
+# Version files
+%{_datadir}/bids-schema/versions/%{bidsversion}/schema/BIDS_VERSION
+%{_datadir}/bids-schema/versions/%{bidsversion}/schema/SCHEMA_VERSION
+# Directories (or directory trees) filled with YAML files
+%{_datadir}/bids-schema/versions/%{bidsversion}/schema/meta/
+%{_datadir}/bids-schema/versions/%{bidsversion}/schema/objects/
+%{_datadir}/bids-schema/versions/%{bidsversion}/schema/rules/
+
+
+%files -n python3-bidsschematools -f %{pyproject_files}
+%doc %dir %{_docdir}/python3-bidsschematools
+%doc %{_docdir}/python3-bidsschematools/README.md
+
+# Symbolic link into the appropriate directory in the base package:
+%{python3_sitelib}/bidsschematools/data/schema
+# https://docs.fedoraproject.org/en-US/packaging-guidelines/Directory_Replacement/#_scriptlet_to_replace_a_directory
+# Added for F42; can be removed in F45 (upgrade path for three releases)
+%ghost %{python3_sitelib}/bidsschematools/data/schema.rpmmoved
+
+%{_bindir}/bst
+%{_mandir}/man1/bst.1*
+%{_mandir}/man1/bst-*.1*
+
+
+%changelog
+## START: Generated by rpmautospec
+* Tue Apr 15 2025 Benjamin A. Beasley <code@musicinmybrain.net> - 1.0.5-1
+- Update to 1.0.5 (close RHBZ#2359774)
+
+* Sat Mar 22 2025 Benjamin A. Beasley <code@musicinmybrain.net> - 1.0.4-1
+- Update to 1.0.4 (close RHBZ#2353951)
+
+* Fri Feb 21 2025 Benjamin A. Beasley <code@musicinmybrain.net> - 1.0.3-1
+- Update to 1.0.3 (close RHBZ#2346980)
+
+* Fri Feb 21 2025 Benjamin A. Beasley <code@musicinmybrain.net> - 1.0.2-2
+- De-conditionalize the "render" extra
+
+* Mon Feb 10 2025 Benjamin A. Beasley <code@musicinmybrain.net> - 1.0.2-1
+- Update to 1.0.2 (close RHBZ#2344674)
+
+* Wed Feb 05 2025 Benjamin A. Beasley <code@musicinmybrain.net> - 1.0.1-1
+- Update to 1.0.1 (close RHBZ#2344086)
+
+* Thu Jan 16 2025 Fedora Release Engineering <releng@fedoraproject.org> - 1.0.0-4
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_42_Mass_Rebuild
+
+* Wed Dec 11 2024 Benjamin A. Beasley <code@musicinmybrain.net> - 1.0.0-2
+- Add a SourceLicense field
+
+* Fri Dec 06 2024 Benjamin A. Beasley <code@musicinmybrain.net> - 1.0.0-1
+- Update to 1.0.0 (close RHBZ#2330678)
+
+* Thu Nov 14 2024 Benjamin A. Beasley <code@musicinmybrain.net> - 0.11.3^post3-2
+- Fix the upgrade path for corrected schema unbundling
+
+* Thu Nov 14 2024 Benjamin A. Beasley <code@musicinmybrain.net> - 0.11.3^post3-1
+- Update to 0.11.3^post3 (close RHBZ#2326272)
+- Fix schema unbundling in python3-bidsschematools
+
+* Mon Nov 11 2024 Benjamin A. Beasley <code@musicinmybrain.net> - 0.11.3^post2-1
+- Update to 0.11.3^post2 (close RHBZ#2325251)
+
+* Sat Nov 09 2024 Benjamin A. Beasley <code@musicinmybrain.net> - 0.11.3^post1-2
+- Install schema in a dir. based on the BIDS version (not the schema
+  version)
+
+* Sat Nov 09 2024 Benjamin A. Beasley <code@musicinmybrain.net> - 0.11.3^post1-1
+- Update to 0.11.3^post1 (close RHBZ#2324764)
+
+* Thu Oct 31 2024 Benjamin A. Beasley <code@musicinmybrain.net> - 0.11.3-2
+- Add conditionals for EPEL10
+
+* Sat Sep 14 2024 Benjamin A. Beasley <code@musicinmybrain.net> - 0.11.3-1
+- Initial package (close RHBZ#2303543)
+## END: Generated by rpmautospec
diff --git a/bst-export.1 b/bst-export.1
new file mode 100644
index 0000000..f1bb017
--- /dev/null
+++ b/bst-export.1
@@ -0,0 +1,17 @@
+.TH BST\-EXPORT "1" "August 2024" "" "User Commands"
+.SH NAME
+.B bst\ export
+\(en Export BIDS schema to JSON document
+.SH SYNOPSIS
+.B bst\ export
+.RI [ OPTIONS ]
+.SH OPTIONS
+.TP
+.B \-\-schema\ \fITEXT
+.TP
+.B \-\-output\ \fITEXT
+.TP
+.B \-h\fR, \fB\-\-help
+Show a help message and exit
+.SH "SEE ALSO"
+.BR bst (1)
diff --git a/bst.1 b/bst.1
new file mode 100644
index 0000000..3029b2a
--- /dev/null
+++ b/bst.1
@@ -0,0 +1,21 @@
+.TH BST "1" "August 2024" "" "User Commands"
+.SH NAME
+.B bst
+\(en BIDS Schema Tools
+.SH SYNOPSIS
+.B bst
+.RI [ OPTIONS ]
+.I COMMAND
+.RI [ ARGS ]...
+.SH OPTIONS
+.TP
+.B \-v\fR,\ \fB\-\-verbose
+.TP
+.B \-h\fR,\ \fB\-\-help
+Show a help message and exit.
+.SS "COMMANDS"
+.TP
+.B export
+Export BIDS schema to JSON document
+.SH "SEE ALSO"
+.BR bst\-export (1)
diff --git a/get_test_data b/get_test_data
new file mode 100755
index 0000000..b399b9c
--- /dev/null
+++ b/get_test_data
@@ -0,0 +1,91 @@
+#!/bin/sh
+set -o errexit
+set -o nounset
+
+if [ "$#" != '0' ]
+then
+	cat 1>&2 <<EOF
+Usage: $0
+
+Parses bids-schema.spec in the same directory as this script; downloads test
+data and produces two archives, filtered to include only selected datasets with
+audited license terms, in the current working directory.
+EOF
+	exit 1
+fi
+
+OUTDIR="${PWD}"
+TMPDIR="$(mktemp -d)"
+trap "rm -rf '${TMPDIR}'" INT TERM EXIT
+
+SPEC="$(cd "$(dirname "${0}")"; echo "${PWD}")/bids-schema.spec"
+MACROS="$(grep -E '^%global' "${SPEC}")"
+get_macro()
+{
+  rpm -E "${MACROS}
+%{${1}}"
+}
+
+EX_URL="$(get_macro examples_url)"
+EX_COMMIT="$(get_macro examples_commit)"
+EX_LIST="$(get_macro examples)"
+ERREX_URL="$(get_macro error_examples_url)"
+ERREX_COMMIT="$(get_macro error_examples_commit)"
+ERREX_LIST="$(get_macro error_examples)"
+
+cd "${TMPDIR}"
+EX_ARCHIVE="bids-examples-${EX_COMMIT}.tar.gz"
+EX_DL="${EX_URL}/archive/${EX_COMMIT}/${EX_ARCHIVE}"
+echo "--> Downloading: ${EX_DL}" 1>&2
+curl -L -O "${EX_DL}"
+ERREX_ARCHIVE="bids-error-examples-${ERREX_COMMIT}.tar.gz"
+ERREX_DL="${ERREX_URL}/archive/${ERREX_COMMIT}/${ERREX_ARCHIVE}"
+echo "--> Downloading: ${ERREX_DL}" 1>&2
+curl -L -O "${ERREX_DL}"
+
+echo "--> Extracting: ${EX_ARCHIVE})" 1>&2
+tar -xzf "${EX_ARCHIVE}"
+echo "--> Extracting: ${ERREX_ARCHIVE})" 1>&2
+tar -xzf "${ERREX_ARCHIVE}"
+echo '--> Removing all but “whitelisted” datasets' 1>&2
+EX_ARCHDIR="$(basename "${EX_ARCHIVE}" '.tar.gz')"
+ERREX_ARCHDIR="$(basename "${ERREX_ARCHIVE}" '.tar.gz')"
+mv "${EX_ARCHDIR}" "${EX_ARCHDIR}-original"
+mv "${ERREX_ARCHDIR}" "${ERREX_ARCHDIR}-original"
+mkdir "${EX_ARCHDIR}" "${ERREX_ARCHDIR}"
+for ds in ${EX_LIST}
+do
+  mv "${EX_ARCHDIR}-original/${ds}" "${EX_ARCHDIR}"
+done
+for ds in ${ERREX_LIST}
+do
+  mv "${ERREX_ARCHDIR}-original/${ds}" "${ERREX_ARCHDIR}"
+done
+# Restore the original mtimes
+touch -r "${EX_ARCHDIR}-original" "${EX_ARCHDIR}"
+touch -r "${ERREX_ARCHDIR}-original" "${ERREX_ARCHDIR}"
+
+rearchive()
+{
+  ARCHDIR="${1}"
+  FILTERED="${2}"
+  echo "--> Re-archiving: ${FILTERED}" 1>&2
+  # https://www.gnu.org/software/tar/manual/html_section/Reproducibility.html
+  TZ=UTC LC_ALL=C tar \
+      --create \
+      --sort=name \
+      --format=posix \
+      --numeric-owner --owner=0 --group=0 \
+      --mode=go+u,go-w \
+      --pax-option='delete=atime,delete=ctime' \
+      "${ARCHDIR}/" |
+    zstdmt --ultra -22 > "${FILTERED}"
+}
+
+EX_FILTERED="${EX_ARCHDIR}-filtered.tar.zst"
+ERREX_FILTERED="${ERREX_ARCHDIR}-filtered.tar.zst"
+rearchive "${EX_ARCHDIR}" "${EX_FILTERED}"
+rearchive "${ERREX_ARCHDIR}" "${ERREX_FILTERED}"
+
+mv "${EX_FILTERED}" "${ERREX_FILTERED}" "${OUTDIR}"
+echo 'Done.' 1>&2
diff --git a/sources b/sources
new file mode 100644
index 0000000..a8e3827
--- /dev/null
+++ b/sources
@@ -0,0 +1,3 @@
+49905a88b1329b4860744e1599f98c75  bids-error-examples-ac0a2f58f34ce284847dde5bd3b90d7ea048c141-filtered.tar.zst
+d51766320c9f26a59d365ba0891e1d27  bids-examples-f21306744fd57bfd5c8e8e91d907fa8448f9eca5-filtered.tar.zst
+4142214259722dcf07fc31e268ceaa7b  bids-specification-schema-1.0.5.tar.gz