📦️ Restore bids-validator installation in containerized C-PAC images (#2120)

Author: shnizzedy

.github/Dockerfiles/Ubuntu.jammy-non-free.Dockerfile

@@ -29,7 +29,8 @@ FROM neurodebian:jammy-non-free
 LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
 Ubuntu Jammy base image"
 LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
-ARG DEBIAN_FRONTEND=noninteractive
+ARG BIDS_VALIDATOR_VERSION=1.14.6 \
+    DEBIAN_FRONTEND=noninteractive
 ENV TZ=America/New_York \
     PATH=$PATH:/.local/bin \
     PYTHONPATH=$PYTHONPATH:/.local/lib/python3.10/site-packages
@@ -61,7 +62,10 @@ RUN groupadd -r c-pac \
     && echo $TZ > /etc/timezone \
     && sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \
     && dpkg-reconfigure --frontend=noninteractive locales \
-    && update-locale LANG="en_US.UTF-8"
+    && update-locale LANG="en_US.UTF-8" \
+    # # install bids-validator
+    && curl -fsSL https://raw.githubusercontent.com/tj/n/master/bin/n | bash -s lts \
+    && npm install -g "bids-validator@${BIDS_VALIDATOR_VERSION}"
 
 COPY --from=c-pac_templates /cpac_templates /cpac_templates
 COPY --from=dcan-hcp /opt/dcan-tools/pipeline/global /opt/dcan-tools/pipeline/global

CHANGELOG.md

@@ -27,6 +27,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Fixed
 
 - A bug in which AWS S3 encryption was looked for in Nipype config instead of pipeline config (only affected uploading logs).
+- Restored `bids-validator` functionality.
 
 ### Removed
 

CPAC/utils/tests/test_bids_utils.py

@@ -18,6 +18,7 @@
 
 from logging import basicConfig, INFO
 import os
+from subprocess import run
 
 import pytest
 import yaml
@@ -73,6 +74,11 @@ def _prefix_entities(paths, path):
             )
 
 
+def test_bids_validator() -> None:
+    """Test subprocess call to `bids-validator`."""
+    run(["bids-validator", "--version"], check=True)
+
+
 @pytest.mark.parametrize("only_one_anat", [True, False])
 def test_create_cpac_data_config_only_one_anat(tmp_path, only_one_anat):
     """Test 'only_one_anat' parameter of 'create_cpac_data_config' function."""

CPAC/utils/versioning/dependencies.py

@@ -136,6 +136,12 @@ def requirements() -> dict:
 
 REPORTED = sorted_versions(
     {
+        **cli_version(
+            "bids-validator --version",
+            dependency="bids-validator",
+            in_result=False,
+            formatting=first_line,
+        ),
         **cli_version("ldd --version", formatting=first_line),
         "Python": sys.version.replace("\n", " ").replace("  ", " "),
         **cli_version(

pyproject.toml

@@ -1,19 +1,20 @@
 # Copyright (C) 2024  C-PAC Developers
-
+#
 # This file is part of C-PAC.
-
+#
 # C-PAC is free software: you can redistribute it and/or modify it under
 # the terms of the GNU Lesser General Public License as published by the
 # Free Software Foundation, either version 3 of the License, or (at your
 # option) any later version.
-
+#
 # C-PAC is distributed in the hope that it will be useful, but WITHOUT
 # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
 # FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
 # License for more details.
-
+#
 # You should have received a copy of the GNU Lesser General Public
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
+
 [build-system]
-requires = ["nipype", "numpy", "pyyaml", "setuptools", "voluptuous"]
+requires = ["nipype==1.8.6", "numpy==1.25.1", "pyyaml==6.0", "setuptools<60.0", "voluptuous==0.13.1"]
 build-backend = "setuptools.build_meta"

requirements.txt

@@ -45,7 +45,7 @@ h5py==3.8.0
 importlib-metadata==6.8.0
 lxml==4.9.2
 pip==23.3
-setuptools==68.0.0
+setuptools<60.0
 urllib3==1.26.18
 wheel==0.40.0
 zipp==3.16.0