python312Packages.bids-validator: fix build (#353943)

pkgs/development/python-modules/bids-validator/default.nix

@@ -7,6 +7,9 @@
   # build-system
   setuptools,
   versioneer,
+
+  # dependencies
+  bidsschematools,
 }:
 
 buildPythonPackage rec {
@@ -14,7 +17,7 @@ buildPythonPackage rec {
   version = "1.14.7.post0";
   pyproject = true;
 
-  disabled = pythonOlder "3.7";
+  disabled = pythonOlder "3.8";
 
   src = fetchPypi {
     pname = "bids_validator";
@@ -22,21 +25,22 @@ buildPythonPackage rec {
     hash = "sha256-5gBaUAt1+KlhWT+2fUYIUQfa2xFvWaXDtSSqBpeUW2Y=";
   };
 
-  nativeBuildInputs = [
+  build-system = [
     setuptools
     versioneer
   ];
 
-  # needs packages which are not available in nixpkgs
-  doCheck = false;
+  dependencies = [
+    bidsschematools
+  ];
 
   pythonImportsCheck = [ "bids_validator" ];
 
-  meta = with lib; {
+  meta = {
     description = "Validator for the Brain Imaging Data Structure";
     homepage = "https://github.com/bids-standard/bids-validator";
     changelog = "https://github.com/bids-standard/bids-validator/releases/tag/v${version}";
-    license = licenses.mit;
-    maintainers = [ ];
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ wegank ];
   };
 }

pkgs/development/python-modules/bidsschematools/default.nix

@@ -0,0 +1,45 @@
+{
+  lib,
+  buildPythonPackage,
+  pythonOlder,
+  fetchPypi,
+  setuptools,
+  click,
+  pyyaml,
+  jsonschema,
+}:
+
+buildPythonPackage rec {
+  pname = "bidsschematools";
+  version = "0.11.3";
+  pyproject = true;
+
+  disabled = pythonOlder "3.9";
+
+  src = fetchPypi {
+    pname = "bidsschematools";
+    inherit version;
+    hash = "sha256-GvR3pOXXmdpjH2xdL+trhLW6ZdsTpEWUdNUlVQ4gFXo=";
+  };
+
+  build-system = [
+    setuptools
+  ];
+
+  dependencies = [
+    click
+    pyyaml
+    jsonschema
+  ];
+
+  pythonImportsCheck = [
+    "bidsschematools"
+  ];
+
+  meta = {
+    description = "Python tools for working with the BIDS schema";
+    homepage = "https://github.com/bids-standard/bids-specification/tree/master/tools/schemacode";
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ wegank ];
+  };
+}

pkgs/development/python-modules/pybids/default.nix

@@ -12,6 +12,7 @@
   nibabel,
   bids-validator,
   sqlalchemy,
+  universal-pathlib,
   pytestCheckHook,
   versioneer,
 }:
@@ -31,12 +32,12 @@ buildPythonPackage rec {
     "sqlalchemy"
   ];
 
-  nativeBuildInputs = [
+  build-system = [
     setuptools
     versioneer
   ] ++ versioneer.optional-dependencies.toml;
 
-  propagatedBuildInputs = [
+  dependencies = [
     bids-validator
     click
     formulaic
@@ -46,6 +47,7 @@ buildPythonPackage rec {
     pandas
     scipy
     sqlalchemy
+    universal-pathlib
   ];
 
   pythonImportsCheck = [ "bids" ];
@@ -64,12 +66,12 @@ buildPythonPackage rec {
     "test_to_df"
   ];
 
-  meta = with lib; {
+  meta = {
     description = "Python tools for querying and manipulating BIDS datasets";
     homepage = "https://github.com/bids-standard/pybids";
     changelog = "https://github.com/bids-standard/pybids/blob/${version}/CHANGELOG.rst";
-    license = licenses.mit;
-    maintainers = [ ];
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ wegank ];
     mainProgram = "pybids";
   };
 }

pkgs/development/python-modules/templateflow/default.nix

@@ -4,6 +4,8 @@
   fetchFromGitHub,
   pythonOlder,
   setuptools-scm,
+  hatchling,
+  hatch-vcs,
   nipreps-versions,
   pybids,
   requests,
@@ -24,8 +26,13 @@ buildPythonPackage rec {
     hash = "sha256-COS767n2aC65m6AJihZb4NhJ4ZK9YkTAZR7Hcnc/LMs=";
   };
 
-  nativeBuildInputs = [ setuptools-scm ];
-  propagatedBuildInputs = [
+  build-system = [
+    setuptools-scm
+    hatchling
+    hatch-vcs
+  ];
+
+  dependencies = [
     nipreps-versions
     pybids
     requests
@@ -33,7 +40,12 @@ buildPythonPackage rec {
   ];
 
   doCheck = false; # most tests try to download data
-  #pythonImportsCheck = [ "templateflow" ];  # touches $HOME/.cache, hence needs https://github.com/NixOS/nixpkgs/pull/120300
+
+  postFixup = ''
+    export HOME=$(mktemp -d)
+  '';
+
+  pythonImportsCheck = [ "templateflow" ];
 
   meta = with lib; {
     homepage = "https://templateflow.org/python-client";

pkgs/top-level/python-packages.nix

@@ -1603,6 +1603,8 @@ self: super: with self; {
 
   bids-validator = callPackage ../development/python-modules/bids-validator { };
 
+  bidsschematools = callPackage ../development/python-modules/bidsschematools { };
+
   biliass = callPackage ../development/python-modules/biliass { };
 
   bilibili-api-python = callPackage ../development/python-modules/bilibili-api-python { };