Merge pull request #228171 from bcdarwin/unbreak-pybids-nipype-heudiconv

python310Packages.nipype: unbreak

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

@@ -1,7 +1,8 @@
 { lib, stdenv
 , buildPythonPackage
 , fetchPypi
-, isPy27
+, pythonOlder
+, pythonRelaxDepsHook
 # python dependencies
 , click
 , python-dateutil
@@ -9,6 +10,7 @@
 , filelock
 , funcsigs
 , future
+, looseversion
 , mock
 , networkx
 , nibabel
@@ -26,9 +28,7 @@
 , simplejson
 , traits
 , xvfbwrapper
-, pytest-cov
 , codecov
-, sphinx
 # other dependencies
 , which
 , bash
@@ -40,17 +40,11 @@
 , useNeurdflib ? false
 }:
 
-let
-
- # This is a temporary convenience package for changes waiting to be merged into the primary rdflib repo.
- neurdflib = callPackage ./neurdflib.nix { };
-
-in
-
 buildPythonPackage rec {
   pname = "nipype";
   version = "1.8.5";
-  disabled = isPy27;
+  disabled = pythonOlder "3.7";
+  format = "setuptools";
 
   src = fetchPypi {
     inherit pname version;
@@ -63,9 +57,11 @@ buildPythonPackage rec {
   '';
 
   nativeBuildInputs = [
-    sphinx
+    pythonRelaxDepsHook
   ];
 
+  pythonRelaxDeps = [ "traits" ];
+
   propagatedBuildInputs = [
     click
     python-dateutil
@@ -73,6 +69,7 @@ buildPythonPackage rec {
     filelock
     funcsigs
     future
+    looseversion
     networkx
     nibabel
     numpy
@@ -80,11 +77,12 @@ buildPythonPackage rec {
     prov
     psutil
     pydot
+    rdflib
     scipy
     simplejson
     traits
     xvfbwrapper
-  ] ++ [ (if useNeurdflib then neurdflib else rdflib) ];
+  ];
 
   nativeCheckInputs = [
     pybids
@@ -94,7 +92,6 @@ buildPythonPackage rec {
     pytest
     pytest-forked
     pytest-xdist
-    pytest-cov
     which
   ];
 
@@ -102,7 +99,7 @@ buildPythonPackage rec {
   doCheck = !stdenv.isDarwin;
   # ignore tests which incorrect fail to detect xvfb
   checkPhase = ''
-    LC_ALL="en_US.UTF-8" pytest nipype/tests -k 'not display'
+    LC_ALL="en_US.UTF-8" pytest nipype/tests -k 'not display and not test_no_et_multiproc'
   '';
   pythonImportsCheck = [ "nipype" ];
 

pkgs/development/python-modules/nipype/neurdflib.nix

@@ -1,38 +0,0 @@
-{ lib
-, buildPythonPackage
-, fetchPypi
-, isodate
-, html5lib
-, sparqlwrapper
-, networkx
-, nose
-, python
-}:
-
-buildPythonPackage rec {
-  pname = "neurdflib";
-  version = "5.0.1";
-
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "d34493cee15029ff5db16157429585ff863ba5542675a4d8a94a0da1bc6e3a50";
-  };
-
-  propagatedBuildInputs = [ isodate html5lib sparqlwrapper ];
-
-  nativeCheckInputs = [ networkx nose ];
-
-  # Python 2 syntax
-  # Failing doctest
-  doCheck = false;
-
-  checkPhase = ''
-    ${python.interpreter} run_tests.py
-  '';
-
-  meta = with lib; {
-    description = "A temporary convenience package for changes waiting to be merged into the primary rdflib repo";
-    homepage = "https://pypi.org/project/neurdflib";
-    license = licenses.bsd3;
-  };
-}

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

@@ -1,6 +1,8 @@
 { buildPythonPackage
 , lib
 , fetchPypi
+, fetchpatch
+, formulaic
 , click
 , num2words
 , numpy
@@ -11,19 +13,36 @@
 , bids-validator
 , sqlalchemy
 , pytestCheckHook
+, versioneer
+, pythonRelaxDepsHook
 }:
 
 buildPythonPackage rec {
-  version = "0.15.5";
+  version = "0.15.6";
   pname = "pybids";
 
   src = fetchPypi {
     inherit pname version;
-    hash = "sha256-ryIiWpFoh0KSmyLI4LDn+EkXEYwDIr8/A7opoZJ+bo4=";
+    hash = "sha256-OjWW08tyVDHkF0X3Pa+10HYD/7Gysp5DkEt9LaVxsdM=";
   };
 
+  patches = [
+    # remove after next release
+    (fetchpatch {
+      name = "fix-pybids-sqlalchemy-dep";
+      url = "https://github.com/bids-standard/pybids/commit/5f008dfc282394ef94a68d47dba37ceead9eac9a.patch";
+      hash = "sha256-gx6w35XqDBZ8cTGHeY/mz2xNQqza9E5z8bRJR7mbPcg=";
+      excludes = [ "pyproject.toml" ];  # not in PyPI dist
+    })
+  ];
+
+  nativeBuildInputs = [ pythonRelaxDepsHook ];
+
+  pythonRelaxDeps = [ "sqlalchemy" ];
+
   propagatedBuildInputs = [
     click
+    formulaic
     num2words
     numpy
     scipy
@@ -32,18 +51,18 @@ buildPythonPackage rec {
     patsy
     bids-validator
     sqlalchemy
+    versioneer
   ];
 
   nativeCheckInputs = [ pytestCheckHook ];
   pythonImportsCheck = [ "bids" ];
+  # looks for missing data:
+  disabledTests = [ "test_config_filename" ];
 
   meta = with lib; {
     description = "Python tools for querying and manipulating BIDS datasets";
     homepage = "https://github.com/bids-standard/pybids";
     license = licenses.mit;
     maintainers = with maintainers; [ jonringer ];
-    # Doesn't support sqlalchemy >=1.4
-    # See https://github.com/bids-standard/pybids/issues/680
-    broken = true;
   };
 }