diff options
Diffstat (limited to 'sci-libs/nipype')
| -rw-r--r-- | sci-libs/nipype/Manifest | 3 | ||||
| -rw-r--r-- | sci-libs/nipype/files/nipype-1.5.0-collections.patch | 28 | ||||
| -rw-r--r-- | sci-libs/nipype/files/nipype-1.8.4-dependency_compatibility.patch | 575 | ||||
| -rw-r--r-- | sci-libs/nipype/files/nipype-1.8.4-no_etelemetry.patch | 50 | ||||
| -rw-r--r-- | sci-libs/nipype/nipype-1.8.4-r1.ebuild (renamed from sci-libs/nipype/nipype-1.5.0.ebuild) | 34 | ||||
| -rw-r--r-- | sci-libs/nipype/nipype-1.8.4-r2.ebuild | 96 | ||||
| -rw-r--r-- | sci-libs/nipype/nipype-1.8.6.ebuild | 97 |
7 files changed, 867 insertions, 16 deletions
diff --git a/sci-libs/nipype/Manifest b/sci-libs/nipype/Manifest index a3c77d4ff..6c9059e1c 100644 --- a/sci-libs/nipype/Manifest +++ b/sci-libs/nipype/Manifest @@ -1 +1,2 @@ -DIST nipype-1.5.0.tar.gz 2735317 BLAKE2B d618714b15defde52325bac32a80449846b448d1c141a21f9d950976c8c89624d714dbab10b4cd99fe20d4eb99ceb4095ebc6ddc567f57b3803e2c16ffda155a SHA512 eb11096a090855278c3e76ffe9643ab4de046a017511ba51f59448fd8cf9d67a4f6c552acbbbdd38065cfb456c24fd21299cf698fa05c5be507524622f28ac85 +DIST nipype-1.8.4.tar.gz 2914433 BLAKE2B c25b82c22641f6df2b57c8a07fd318034bb4fe4eaa1037baebc1ffc03d3e1add347d9f0c94139144fc17043a5c97926c88b40755f19794cc71366d76ba339698 SHA512 8949226accd7c158b6a3ec92389a11760a9b306098ccb8ef50844efbddb4e6a9108bb6a32ec7b0402c4ea56881a3548b052fe7f5e757d2771aea5b2eebc9377b +DIST nipype-1.8.6.tar.gz 2921102 BLAKE2B 79a2131b8265f1b0a3a8d2fa6ff56cbbc2d393c79099178cf036d82357a971a72f024b132d7b4d7d4af85165f562192b6cc5cfc9e797105bdc009734e8a89033 SHA512 23140beb02f4c3807d9d0291bde41ce8c1b06e48dc94001b007f193caaa89428387d1528fa20ae328d2c4a781024c9acf07f7be9ce507ecb2f1daf338c092eec diff --git a/sci-libs/nipype/files/nipype-1.5.0-collections.patch b/sci-libs/nipype/files/nipype-1.5.0-collections.patch new file mode 100644 index 000000000..e784ba48b --- /dev/null +++ b/sci-libs/nipype/files/nipype-1.5.0-collections.patch @@ -0,0 +1,28 @@ +--- a/nipype/interfaces/base/traits_extension.py 2020-06-03 11:08:30.000000000 -0400 ++++ b/nipype/interfaces/base/traits_extension.py 2022-07-11 14:09:31.847784312 -0400 +@@ -19,7 +19,10 @@ + (usually by Robert Kern). + + """ +-from collections import Sequence ++try: ++ from collections import Sequence ++except ImportError: ++ from collections.abc import Sequence + + # perform all external trait imports here + from traits import __version__ as traits_version +--- a/nipype/utils/misc.py 2020-06-03 11:08:30.000000000 -0400 ++++ b/nipype/utils/misc.py 2020-06-03 14:08:57.951408897 -0400 +@@ -6,7 +6,10 @@ + import os + import sys + import re +-from collections import Iterator ++try: ++ from collections import Iterator ++except ImportError: ++ from collections.abc import Iterator + from warnings import warn + + from distutils.version import LooseVersion diff --git a/sci-libs/nipype/files/nipype-1.8.4-dependency_compatibility.patch b/sci-libs/nipype/files/nipype-1.8.4-dependency_compatibility.patch new file mode 100644 index 000000000..9811139e7 --- /dev/null +++ b/sci-libs/nipype/files/nipype-1.8.4-dependency_compatibility.patch @@ -0,0 +1,575 @@ +From a31870d0f9dc0e774f1cf9d18351586f78ecb252 Mon Sep 17 00:00:00 2001 +From: Chris Markiewicz <effigies@gmail.com> +Date: Sat, 28 Jan 2023 08:11:54 -0500 +Subject: [PATCH 1/9] FIX: Set dtypes for integer test images + +NiBabel 4 began warning that int64 images would error, and NiBabel 5 +began erroring if not passed an explicit dtype or header. + +We don't need int64 images, just set some sensible dtypes. +--- + nipype/algorithms/tests/test_ErrorMap.py | 2 +- + nipype/algorithms/tests/test_TSNR.py | 3 ++- + nipype/algorithms/tests/test_metrics.py | 2 +- + 3 files changed, 4 insertions(+), 3 deletions(-) + +diff --git a/nipype/algorithms/tests/test_ErrorMap.py b/nipype/algorithms/tests/test_ErrorMap.py +index 98f05d8e17..adac507bad 100644 +--- a/nipype/algorithms/tests/test_ErrorMap.py ++++ b/nipype/algorithms/tests/test_ErrorMap.py +@@ -17,7 +17,7 @@ def test_errormap(tmpdir): + volume1 = np.array([[[2.0, 8.0], [1.0, 2.0]], [[1.0, 9.0], [0.0, 3.0]]]) + # Alan Turing's birthday + volume2 = np.array([[[0.0, 7.0], [2.0, 3.0]], [[1.0, 9.0], [1.0, 2.0]]]) +- mask = np.array([[[1, 0], [0, 1]], [[1, 0], [0, 1]]]) ++ mask = np.array([[[1, 0], [0, 1]], [[1, 0], [0, 1]]], dtype=np.uint8) + + img1 = nb.Nifti1Image(volume1, np.eye(4)) + img2 = nb.Nifti1Image(volume2, np.eye(4)) +diff --git a/nipype/algorithms/tests/test_TSNR.py b/nipype/algorithms/tests/test_TSNR.py +index 26c1019b63..320bec8ab2 100644 +--- a/nipype/algorithms/tests/test_TSNR.py ++++ b/nipype/algorithms/tests/test_TSNR.py +@@ -131,5 +131,6 @@ def assert_unchanged(self, expected_ranges): + [ + [[[2, 4, 3, 9, 1], [3, 6, 4, 7, 4]], [[8, 3, 4, 6, 2], [4, 0, 4, 4, 2]]], + [[[9, 7, 5, 5, 7], [7, 8, 4, 8, 4]], [[0, 4, 7, 1, 7], [6, 8, 8, 8, 7]]], +- ] ++ ], ++ dtype=np.int16, + ) +diff --git a/nipype/algorithms/tests/test_metrics.py b/nipype/algorithms/tests/test_metrics.py +index ad7502992e..3652fc2ce5 100644 +--- a/nipype/algorithms/tests/test_metrics.py ++++ b/nipype/algorithms/tests/test_metrics.py +@@ -45,7 +45,7 @@ def test_fuzzy_overlap(tmpdir): + + # Just considering the mask, the central pixel + # that raised the index now is left aside. +- data = np.zeros((3, 3, 3), dtype=int) ++ data = np.zeros((3, 3, 3), dtype=np.uint8) + data[0, 0, 0] = 1 + data[2, 2, 2] = 1 + nb.Nifti1Image(data, np.eye(4)).to_filename("mask.nii.gz") + +From 443492e82f3b197ad739cb244912ced652853a8d Mon Sep 17 00:00:00 2001 +From: Chris Markiewicz <effigies@gmail.com> +Date: Sat, 28 Jan 2023 08:43:07 -0500 +Subject: [PATCH 2/9] FIX: Coerce depidx to lil_matrix + +--- + nipype/pipeline/plugins/base.py | 18 +++++++++++++----- + 1 file changed, 13 insertions(+), 5 deletions(-) + +diff --git a/nipype/pipeline/plugins/base.py b/nipype/pipeline/plugins/base.py +index a927b24686..3d600dda55 100644 +--- a/nipype/pipeline/plugins/base.py ++++ b/nipype/pipeline/plugins/base.py +@@ -21,6 +21,18 @@ + logger = logging.getLogger("nipype.workflow") + + ++def _graph_to_lil_matrix(graph, nodelist): ++ """Provide a sparse linked list matrix across various NetworkX versions""" ++ import scipy.sparse as ssp ++ ++ try: ++ from networkx import to_scipy_sparse_array ++ except ImportError: # NetworkX < 2.7 ++ from networkx import to_scipy_sparse_matrix as to_scipy_sparse_array ++ ++ return ssp.lil_matrix(to_scipy_sparse_array(graph, nodelist=nodelist, format="lil")) ++ ++ + class PluginBase(object): + """Base class for plugins.""" + +@@ -431,12 +443,8 @@ def _task_finished_cb(self, jobid, cached=False): + + def _generate_dependency_list(self, graph): + """Generates a dependency list for a list of graphs.""" +- import networkx as nx +- + self.procs, _ = topological_sort(graph) +- self.depidx = nx.to_scipy_sparse_matrix( +- graph, nodelist=self.procs, format="lil" +- ) ++ self.depidx = _graph_to_lil_matrix(graph, nodelist=self.procs) + self.refidx = self.depidx.astype(int) + self.proc_done = np.zeros(len(self.procs), dtype=bool) + self.proc_pending = np.zeros(len(self.procs), dtype=bool) + +From 34ef6c2ff89f327fcf2951b792ef38b6d56f8c4e Mon Sep 17 00:00:00 2001 +From: Chris Markiewicz <effigies@gmail.com> +Date: Sat, 28 Jan 2023 11:57:54 -0500 +Subject: [PATCH 3/9] FIX: Accept "str" in dipy type (includes "string") + +--- + nipype/interfaces/dipy/base.py | 6 +++--- + 1 file changed, 3 insertions(+), 3 deletions(-) + +diff --git a/nipype/interfaces/dipy/base.py b/nipype/interfaces/dipy/base.py +index d8a1c0fbf5..161ed33227 100644 +--- a/nipype/interfaces/dipy/base.py ++++ b/nipype/interfaces/dipy/base.py +@@ -110,7 +110,7 @@ def convert_to_traits_type(dipy_type, is_file=False): + """Convert DIPY type to Traits type.""" + dipy_type = dipy_type.lower() + is_mandatory = bool("optional" not in dipy_type) +- if "variable" in dipy_type and "string" in dipy_type: ++ if "variable" in dipy_type and "str" in dipy_type: + return traits.ListStr, is_mandatory + elif "variable" in dipy_type and "int" in dipy_type: + return traits.ListInt, is_mandatory +@@ -120,9 +120,9 @@ def convert_to_traits_type(dipy_type, is_file=False): + return traits.ListBool, is_mandatory + elif "variable" in dipy_type and "complex" in dipy_type: + return traits.ListComplex, is_mandatory +- elif "string" in dipy_type and not is_file: ++ elif "str" in dipy_type and not is_file: + return traits.Str, is_mandatory +- elif "string" in dipy_type and is_file: ++ elif "str" in dipy_type and is_file: + return File, is_mandatory + elif "int" in dipy_type: + return traits.Int, is_mandatory + +From 83c8cf86d6bbb0dc04aa58dbe5119fd864342d9c Mon Sep 17 00:00:00 2001 +From: Chris Markiewicz <effigies@gmail.com> +Date: Sat, 28 Jan 2023 11:55:34 -0500 +Subject: [PATCH 4/9] MNT: Update requirements from info.py + +--- + requirements.txt | 6 +++--- + 1 file changed, 3 insertions(+), 3 deletions(-) + +diff --git a/requirements.txt b/requirements.txt +index afec34ebfd..331e2c5def 100644 +--- a/requirements.txt ++++ b/requirements.txt +@@ -2,8 +2,7 @@ + click>=6.6.0 + networkx>=2.0 + nibabel>=2.1.0 +-numpy>=1.13 ; python_version < "3.7" +-numpy>=1.15.3 ; python_version >= "3.7" ++numpy>=1.17 + packaging + prov>=1.5.2 + pydot>=1.2.3 +@@ -11,6 +10,7 @@ python-dateutil>=2.2 + rdflib>=5.0.0 + scipy>=0.14 + simplejson>=3.8.0 +-traits>=4.6,!=5.0 ++traits>=4.6,<6.4,!=5.0 + filelock>=3.0.0 + etelemetry>=0.2.0 ++looseversion + +From 24c55a6f48aa658320ff35283b6f91ec38b13a40 Mon Sep 17 00:00:00 2001 +From: Horea Christian <chr@chymera.eu> +Date: Thu, 26 Jan 2023 02:28:33 -0500 +Subject: [PATCH 5/9] Writing pickles directly as networkx no longer ships + write_gpickle + +--- + nipype/interfaces/cmtk/cmtk.py | 12 ++++++++---- + nipype/interfaces/cmtk/nbs.py | 7 +++++-- + nipype/interfaces/cmtk/nx.py | 12 ++++++++---- + nipype/interfaces/cmtk/tests/test_nbs.py | 4 +++- + 4 files changed, 24 insertions(+), 11 deletions(-) + +diff --git a/nipype/interfaces/cmtk/cmtk.py b/nipype/interfaces/cmtk/cmtk.py +index 8775a8517e..8df7a1c5ad 100644 +--- a/nipype/interfaces/cmtk/cmtk.py ++++ b/nipype/interfaces/cmtk/cmtk.py +@@ -226,7 +226,8 @@ def cmat( + # Add node information from specified parcellation scheme + path, name, ext = split_filename(resolution_network_file) + if ext == ".pck": +- gp = nx.read_gpickle(resolution_network_file) ++ with open(resolution_network_file, 'rb') as f: ++ gp = pickle.load(f) + elif ext == ".graphml": + gp = nx.read_graphml(resolution_network_file) + else: +@@ -379,7 +380,8 @@ def cmat( + fibdev.add_edge(u, v, weight=di["fiber_length_std"]) + + iflogger.info("Writing network as %s", matrix_name) +- nx.write_gpickle(G, op.abspath(matrix_name)) ++ with open(op.abspath(matrix_name), 'wb') as f: ++ pickle.dump(G, f, pickle.HIGHEST_PROTOCOL) + + numfib_mlab = nx.to_numpy_matrix(numfib, dtype=int) + numfib_dict = {"number_of_fibers": numfib_mlab} +@@ -394,7 +396,8 @@ def cmat( + path, name, ext = split_filename(matrix_name) + intersection_matrix_name = op.abspath(name + "_intersections") + ext + iflogger.info("Writing intersection network as %s", intersection_matrix_name) +- nx.write_gpickle(I, intersection_matrix_name) ++ with open(intersection_matrix_name, 'wb') as f: ++ pickle.dump(I, f, pickle.HIGHEST_PROTOCOL) + + path, name, ext = split_filename(matrix_mat_name) + if not ext == ".mat": +@@ -1070,7 +1073,8 @@ def create_nodes(roi_file, resolution_network_file, out_filename): + ) + ) + G.nodes[int(u)]["dn_position"] = tuple([xyz[0], xyz[2], -xyz[1]]) +- nx.write_gpickle(G, out_filename) ++ with open(out_filename, 'wb') as f: ++ pickle.dump(G, f, pickle.HIGHEST_PROTOCOL) + return out_filename + + +diff --git a/nipype/interfaces/cmtk/nbs.py b/nipype/interfaces/cmtk/nbs.py +index 4e1db9ffb7..57d63897c7 100644 +--- a/nipype/interfaces/cmtk/nbs.py ++++ b/nipype/interfaces/cmtk/nbs.py +@@ -6,6 +6,7 @@ + + import numpy as np + import networkx as nx ++import pickle + + from ... import logging + from ..base import ( +@@ -172,12 +173,14 @@ def _run_interface(self, runtime): + + path = op.abspath("NBS_Result_" + details) + iflogger.info(path) +- nx.write_gpickle(nbsgraph, path) ++ with open(path, 'wb') as f: ++ pickle.dump(nbsgraph, f, pickle.HIGHEST_PROTOCOL) + iflogger.info("Saving output NBS edge network as %s", path) + + pval_path = op.abspath("NBS_P_vals_" + details) + iflogger.info(pval_path) +- nx.write_gpickle(nbs_pval_graph, pval_path) ++ with open(pval_path, 'wb') as f: ++ pickle.dump(nbs_pval_graph, f, pickle.HIGHEST_PROTOCOL) + iflogger.info("Saving output p-value network as %s", pval_path) + return runtime + +diff --git a/nipype/interfaces/cmtk/nx.py b/nipype/interfaces/cmtk/nx.py +index aaf4bece39..a662eb65c6 100644 +--- a/nipype/interfaces/cmtk/nx.py ++++ b/nipype/interfaces/cmtk/nx.py +@@ -200,7 +200,8 @@ def average_networks(in_files, ntwk_res_file, group_id): + + # Writes the networks and returns the name + network_name = group_id + "_average.pck" +- nx.write_gpickle(avg_ntwk, op.abspath(network_name)) ++ with open(op.abspath(network_name), 'wb') as f: ++ pickle.dump(avg_ntwk, f, pickle.HIGHEST_PROTOCOL) + iflogger.info("Saving average network as %s", op.abspath(network_name)) + avg_ntwk = fix_keys_for_gexf(avg_ntwk) + network_name = group_id + "_average.gexf" +@@ -483,7 +484,8 @@ def _run_interface(self, runtime): + for key in list(node_measures.keys()): + newntwk = add_node_data(node_measures[key], ntwk) + out_file = op.abspath(self._gen_outfilename(key, "pck")) +- nx.write_gpickle(newntwk, out_file) ++ with open(out_file, 'wb') as f: ++ pickle.dump(newntwk, f, pickle.HIGHEST_PROTOCOL) + nodentwks.append(out_file) + if isdefined(self.inputs.out_node_metrics_matlab): + node_out_file = op.abspath(self.inputs.out_node_metrics_matlab) +@@ -497,7 +499,8 @@ def _run_interface(self, runtime): + for key in list(edge_measures.keys()): + newntwk = add_edge_data(edge_measures[key], ntwk) + out_file = op.abspath(self._gen_outfilename(key, "pck")) +- nx.write_gpickle(newntwk, out_file) ++ with open(out_file, 'wb') as f: ++ pickle.dump(newntwk, f, pickle.HIGHEST_PROTOCOL) + edgentwks.append(out_file) + if isdefined(self.inputs.out_edge_metrics_matlab): + edge_out_file = op.abspath(self.inputs.out_edge_metrics_matlab) +@@ -521,7 +524,8 @@ def _run_interface(self, runtime): + out_file = op.abspath( + self._gen_outfilename(self.inputs.out_k_crust, "pck") + ) +- nx.write_gpickle(ntwk_measures[key], out_file) ++ with open(out_file, 'wb') as f: ++ pickle.dump(ntwk_measures[key], f, pickle.HIGHEST_PROTOCOL) + kntwks.append(out_file) + gpickled.extend(kntwks) + +diff --git a/nipype/interfaces/cmtk/tests/test_nbs.py b/nipype/interfaces/cmtk/tests/test_nbs.py +index 46da939f1a..7a60b407a4 100644 +--- a/nipype/interfaces/cmtk/tests/test_nbs.py ++++ b/nipype/interfaces/cmtk/tests/test_nbs.py +@@ -2,6 +2,7 @@ + from ....utils.misc import package_check + import numpy as np + import networkx as nx ++import pickle + import pytest + + have_cv = True +@@ -20,7 +21,8 @@ def creating_graphs(tmpdir): + G = nx.from_numpy_matrix(graph) + out_file = tmpdir.strpath + graphnames[idx] + ".pck" + # Save as pck file +- nx.write_gpickle(G, out_file) ++ with open(out_file, 'wb') as f: ++ pickle.dump(G, f, pickle.HIGHEST_PROTOCOL) + graphlist.append(out_file) + return graphlist + + +From b9a8e2000be9ce30a94aca85453d5cf4e32e10ec Mon Sep 17 00:00:00 2001 +From: Horea Christian <chr@chymera.eu> +Date: Thu, 26 Jan 2023 02:03:39 -0500 +Subject: [PATCH 6/9] updating networkx from_numpy_{matrix,array} + +--- + nipype/interfaces/cmtk/cmtk.py | 2 +- + nipype/interfaces/cmtk/nbs.py | 4 ++-- + nipype/interfaces/cmtk/tests/test_nbs.py | 2 +- + 3 files changed, 4 insertions(+), 4 deletions(-) + +diff --git a/nipype/interfaces/cmtk/cmtk.py b/nipype/interfaces/cmtk/cmtk.py +index 8df7a1c5ad..fc730b1166 100644 +--- a/nipype/interfaces/cmtk/cmtk.py ++++ b/nipype/interfaces/cmtk/cmtk.py +@@ -264,7 +264,7 @@ def cmat( + ) + intersection_matrix = np.matrix(intersection_matrix) + I = G.copy() +- H = nx.from_numpy_matrix(np.matrix(intersection_matrix)) ++ H = nx.from_numpy_array(np.matrix(intersection_matrix)) + H = nx.relabel_nodes(H, lambda x: x + 1) # relabel nodes so they start at 1 + I.add_weighted_edges_from( + ((u, v, d["weight"]) for u, v, d in H.edges(data=True)) +diff --git a/nipype/interfaces/cmtk/nbs.py b/nipype/interfaces/cmtk/nbs.py +index 57d63897c7..b0a8b5df33 100644 +--- a/nipype/interfaces/cmtk/nbs.py ++++ b/nipype/interfaces/cmtk/nbs.py +@@ -150,8 +150,8 @@ def _run_interface(self, runtime): + pADJ[x, y] = PVAL[idx] + + # Create networkx graphs from the adjacency matrix +- nbsgraph = nx.from_numpy_matrix(ADJ) +- nbs_pval_graph = nx.from_numpy_matrix(pADJ) ++ nbsgraph = nx.from_numpy_array(ADJ) ++ nbs_pval_graph = nx.from_numpy_array(pADJ) + + # Relabel nodes because they should not start at zero for our convention + nbsgraph = nx.relabel_nodes(nbsgraph, lambda x: x + 1) +diff --git a/nipype/interfaces/cmtk/tests/test_nbs.py b/nipype/interfaces/cmtk/tests/test_nbs.py +index 7a60b407a4..6323546c1e 100644 +--- a/nipype/interfaces/cmtk/tests/test_nbs.py ++++ b/nipype/interfaces/cmtk/tests/test_nbs.py +@@ -18,7 +18,7 @@ def creating_graphs(tmpdir): + graphnames = ["name" + str(i) for i in range(6)] + for idx, name in enumerate(graphnames): + graph = np.random.rand(10, 10) +- G = nx.from_numpy_matrix(graph) ++ G = nx.from_numpy_array(graph) + out_file = tmpdir.strpath + graphnames[idx] + ".pck" + # Save as pck file + with open(out_file, 'wb') as f: + +From 7aa7c5968cf28afed9aca658bca28470afbfeb9f Mon Sep 17 00:00:00 2001 +From: Chris Markiewicz <effigies@gmail.com> +Date: Sat, 28 Jan 2023 12:45:17 -0500 +Subject: [PATCH 7/9] FIX: Purge nx.to_numpy_matrix + +--- + nipype/interfaces/cmtk/cmtk.py | 8 ++++---- + nipype/interfaces/cmtk/nbs.py | 2 +- + 2 files changed, 5 insertions(+), 5 deletions(-) + +diff --git a/nipype/interfaces/cmtk/cmtk.py b/nipype/interfaces/cmtk/cmtk.py +index fc730b1166..00c134fc37 100644 +--- a/nipype/interfaces/cmtk/cmtk.py ++++ b/nipype/interfaces/cmtk/cmtk.py +@@ -383,13 +383,13 @@ def cmat( + with open(op.abspath(matrix_name), 'wb') as f: + pickle.dump(G, f, pickle.HIGHEST_PROTOCOL) + +- numfib_mlab = nx.to_numpy_matrix(numfib, dtype=int) ++ numfib_mlab = nx.to_numpy_array(numfib, dtype=int) + numfib_dict = {"number_of_fibers": numfib_mlab} +- fibmean_mlab = nx.to_numpy_matrix(fibmean, dtype=np.float64) ++ fibmean_mlab = nx.to_numpy_array(fibmean, dtype=np.float64) + fibmean_dict = {"mean_fiber_length": fibmean_mlab} +- fibmedian_mlab = nx.to_numpy_matrix(fibmedian, dtype=np.float64) ++ fibmedian_mlab = nx.to_numpy_array(fibmedian, dtype=np.float64) + fibmedian_dict = {"median_fiber_length": fibmedian_mlab} +- fibdev_mlab = nx.to_numpy_matrix(fibdev, dtype=np.float64) ++ fibdev_mlab = nx.to_numpy_array(fibdev, dtype=np.float64) + fibdev_dict = {"fiber_length_std": fibdev_mlab} + + if intersections: +diff --git a/nipype/interfaces/cmtk/nbs.py b/nipype/interfaces/cmtk/nbs.py +index b0a8b5df33..2560ed8e3c 100644 +--- a/nipype/interfaces/cmtk/nbs.py ++++ b/nipype/interfaces/cmtk/nbs.py +@@ -40,7 +40,7 @@ def ntwks_to_matrices(in_files, edge_key): + raise KeyError( + "the graph edges do not have {} attribute".format(edge_key) + ) +- matrix[:, :, idx] = nx.to_numpy_matrix(graph) # Retrieve the matrix ++ matrix[:, :, idx] = nx.to_numpy_array(graph) # Retrieve the matrix + return matrix + + + +From f20035c303a88fba3e207ac60388397665bb97be Mon Sep 17 00:00:00 2001 +From: Chris Markiewicz <effigies@gmail.com> +Date: Sat, 28 Jan 2023 12:45:38 -0500 +Subject: [PATCH 8/9] FIX: Purge nx.read_gpickle + +--- + nipype/interfaces/cmtk/convert.py | 9 ++++++++- + nipype/interfaces/cmtk/nbs.py | 11 ++++++++--- + nipype/interfaces/cmtk/nx.py | 11 ++++++++--- + 3 files changed, 24 insertions(+), 7 deletions(-) + +diff --git a/nipype/interfaces/cmtk/convert.py b/nipype/interfaces/cmtk/convert.py +index 321a40fbba..a45daddcd6 100644 +--- a/nipype/interfaces/cmtk/convert.py ++++ b/nipype/interfaces/cmtk/convert.py +@@ -18,6 +18,13 @@ + from .base import CFFBaseInterface, have_cfflib + + ++def _read_pickle(fname): ++ import pickle ++ ++ with open(fname, 'rb') as f: ++ return pickle.load(f) ++ ++ + class CFFConverterInputSpec(BaseInterfaceInputSpec): + graphml_networks = InputMultiPath( + File(exists=True), desc="list of graphML networks" +@@ -135,7 +142,7 @@ def _run_interface(self, runtime): + unpickled = [] + for ntwk in self.inputs.gpickled_networks: + _, ntwk_name, _ = split_filename(ntwk) +- unpickled = nx.read_gpickle(ntwk) ++ unpickled = _read_pickle(ntwk) + cnet = cf.CNetwork(name=ntwk_name) + cnet.set_with_nxgraph(unpickled) + a.add_connectome_network(cnet) +diff --git a/nipype/interfaces/cmtk/nbs.py b/nipype/interfaces/cmtk/nbs.py +index 2560ed8e3c..a2bd42abee 100644 +--- a/nipype/interfaces/cmtk/nbs.py ++++ b/nipype/interfaces/cmtk/nbs.py +@@ -24,13 +24,18 @@ + iflogger = logging.getLogger("nipype.interface") + + ++def _read_pickle(fname): ++ with open(fname, 'rb') as f: ++ return pickle.load(f) ++ ++ + def ntwks_to_matrices(in_files, edge_key): +- first = nx.read_gpickle(in_files[0]) ++ first = _read_pickle(in_files[0]) + files = len(in_files) + nodes = len(first.nodes()) + matrix = np.zeros((nodes, nodes, files)) + for idx, name in enumerate(in_files): +- graph = nx.read_gpickle(name) ++ graph = _read_pickle(name) + for u, v, d in graph.edges(data=True): + try: + graph[u][v]["weight"] = d[ +@@ -162,7 +167,7 @@ def _run_interface(self, runtime): + else: + node_ntwk_name = self.inputs.in_group1[0] + +- node_network = nx.read_gpickle(node_ntwk_name) ++ node_network = _read_pickle(node_ntwk_name) + iflogger.info( + "Populating node dictionaries with attributes from %s", node_ntwk_name + ) +diff --git a/nipype/interfaces/cmtk/nx.py b/nipype/interfaces/cmtk/nx.py +index a662eb65c6..991ca89dcf 100644 +--- a/nipype/interfaces/cmtk/nx.py ++++ b/nipype/interfaces/cmtk/nx.py +@@ -24,11 +24,16 @@ + iflogger = logging.getLogger("nipype.interface") + + ++def _read_pickle(fname): ++ with open(fname, 'rb') as f: ++ return pickle.load(f) ++ ++ + def read_unknown_ntwk(ntwk): + if not isinstance(ntwk, nx.classes.graph.Graph): + _, _, ext = split_filename(ntwk) + if ext == ".pck": +- ntwk = nx.read_gpickle(ntwk) ++ ntwk = _read_pickle(ntwk) + elif ext == ".graphml": + ntwk = nx.read_graphml(ntwk) + return ntwk +@@ -121,7 +126,7 @@ def average_networks(in_files, ntwk_res_file, group_id): + counting_ntwk = ntwk.copy() + # Sums all the relevant variables + for index, subject in enumerate(in_files): +- tmp = nx.read_gpickle(subject) ++ tmp = _read_pickle(subject) + iflogger.info("File %s has %i edges", subject, tmp.number_of_edges()) + edges = list(tmp.edges()) + for edge in edges: +@@ -461,7 +466,7 @@ def _run_interface(self, runtime): + edgentwks = list() + kntwks = list() + matlab = list() +- ntwk = nx.read_gpickle(self.inputs.in_file) ++ ntwk = _read_pickle(self.inputs.in_file) + + # Each block computes, writes, and saves a measure + # The names are then added to the output .pck file list + +From f6bf0af19c044709de5be79a4488dcfd4d08f305 Mon Sep 17 00:00:00 2001 +From: Chris Markiewicz <effigies@gmail.com> +Date: Sat, 28 Jan 2023 13:23:33 -0500 +Subject: [PATCH 9/9] FIX: Add dtypes to nilearn interface/tests + +--- + nipype/interfaces/nilearn.py | 2 +- + nipype/interfaces/tests/test_nilearn.py | 5 +++-- + 2 files changed, 4 insertions(+), 3 deletions(-) + +diff --git a/nipype/interfaces/nilearn.py b/nipype/interfaces/nilearn.py +index 053902e2bd..95494e7f5f 100644 +--- a/nipype/interfaces/nilearn.py ++++ b/nipype/interfaces/nilearn.py +@@ -155,7 +155,7 @@ def _process_inputs(self): + if self.inputs.include_global: + global_label_data = label_data.dataobj.sum(axis=3) # sum across all regions + global_label_data = ( +- np.rint(global_label_data).astype(int).clip(0, 1) ++ np.rint(global_label_data).clip(0, 1).astype('u1') + ) # binarize + global_label_data = self._4d(global_label_data, label_data.affine) + global_masker = nl.NiftiLabelsMasker( +diff --git a/nipype/interfaces/tests/test_nilearn.py b/nipype/interfaces/tests/test_nilearn.py +index 2066c00768..4f94bbb87b 100644 +--- a/nipype/interfaces/tests/test_nilearn.py ++++ b/nipype/interfaces/tests/test_nilearn.py +@@ -184,10 +184,11 @@ def assert_expected_output(self, labels, wanted): + [[2, -2, -1, -2, -5], [3, 0, 3, -5, -2]], + [[-4, -2, -2, 1, -2], [3, 1, 4, -3, -2]], + ], +- ] ++ ], ++ np.int16, + ) + +- fake_label_data = np.array([[[1, 0], [3, 1]], [[2, 0], [1, 3]]]) ++ fake_label_data = np.array([[[1, 0], [3, 1]], [[2, 0], [1, 3]]], np.uint8) + + fake_equiv_4d_label_data = np.array( + [ diff --git a/sci-libs/nipype/files/nipype-1.8.4-no_etelemetry.patch b/sci-libs/nipype/files/nipype-1.8.4-no_etelemetry.patch new file mode 100644 index 000000000..b5c223422 --- /dev/null +++ b/sci-libs/nipype/files/nipype-1.8.4-no_etelemetry.patch @@ -0,0 +1,50 @@ +diff --git a/nipype/__init__.py b/nipype/__init__.py +index 06084e823..2e42dcbce 100644 +--- a/nipype/__init__.py ++++ b/nipype/__init__.py +@@ -73,23 +73,6 @@ from .interfaces import ( + ) + + +-def check_latest_version(raise_exception=False): +- """ +- Check for the latest version of the library. +- +- Parameters +- ---------- +- raise_exception: bool +- Raise a RuntimeError if a bad version is being used +- """ +- import etelemetry +- +- logger = logging.getLogger("nipype.utils") +- return etelemetry.check_available_version( +- "nipy/nipype", __version__, logger, raise_exception +- ) +- +- + # Run telemetry on import for interactive sessions, such as IPython, Jupyter notebooks, Python REPL + if config.getboolean("execution", "check_version"): + import __main__ +@@ -98,4 +81,4 @@ if config.getboolean("execution", "check_version"): + from .interfaces.base import BaseInterface + + if BaseInterface._etelemetry_version_data is None: +- BaseInterface._etelemetry_version_data = check_latest_version() or "n/a" ++ BaseInterface._etelemetry_version_data = "n/a" +diff --git a/nipype/interfaces/base/core.py b/nipype/interfaces/base/core.py +index c8099be63..f7770dbfc 100644 +--- a/nipype/interfaces/base/core.py ++++ b/nipype/interfaces/base/core.py +@@ -183,10 +183,9 @@ class BaseInterface(Interface): + config.getboolean("execution", "check_version") + and "NIPYPE_NO_ET" not in os.environ + ): +- from ... import check_latest_version + + if BaseInterface._etelemetry_version_data is None: +- BaseInterface._etelemetry_version_data = check_latest_version() or "n/a" ++ BaseInterface._etelemetry_version_data = "n/a" + + if not self.input_spec: + raise Exception("No input_spec in class: %s" % self.__class__.__name__) diff --git a/sci-libs/nipype/nipype-1.5.0.ebuild b/sci-libs/nipype/nipype-1.8.4-r1.ebuild index 35792adbc..7c2e801ff 100644 --- a/sci-libs/nipype/nipype-1.5.0.ebuild +++ b/sci-libs/nipype/nipype-1.8.4-r1.ebuild @@ -1,20 +1,21 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) PYTHON_REQ_USE="threads(+),sqlite" inherit distutils-r1 DESCRIPTION="Neuroimaging in Python: Pipelines and Interfaces" -HOMEPAGE="http://nipy.sourceforge.net/nipype/" +HOMEPAGE="https://nipype.readthedocs.io/" SRC_URI="https://github.com/nipy/nipype/archive/${PV}.tar.gz -> ${P}.tar.gz" LICENSE="BSD" SLOT="0" -KEYWORDS="~amd64 ~x86" +KEYWORDS="~amd64" IUSE="test" RESTRICT="!test? ( test )" @@ -28,30 +29,28 @@ DEPEND=" ${RDEPEND} ) " -# Dependency disabled as upstream test configuration which requires it fails -#dev-python/pytest-xdist[${PYTHON_USEDEP}] RDEPEND=" - >=dev-python/click-6.6[${PYTHON_USEDEP}] + dev-python/click[${PYTHON_USEDEP}] dev-python/filelock[${PYTHON_USEDEP}] + dev-python/looseversion[${PYTHON_USEDEP}] dev-python/networkx[${PYTHON_USEDEP}] dev-python/packaging[${PYTHON_USEDEP}] dev-python/pydot[${PYTHON_USEDEP}] - dev-python/pydotplus[${PYTHON_USEDEP}] dev-python/python-dateutil[${PYTHON_USEDEP}] - >=dev-python/rdflib-5.0.0[${PYTHON_USEDEP}] + dev-python/rdflib[${PYTHON_USEDEP}] dev-python/scipy[${PYTHON_USEDEP}] dev-python/simplejson[${PYTHON_USEDEP}] - dev-python/traits[${PYTHON_USEDEP}] + <dev-python/traits-6.4.0[${PYTHON_USEDEP}] " PATCHES=( - "${FILESDIR}/${P}"-version_check.patch + "${FILESDIR}/${PN}-1.8.4-dependency_compatibility.patch" ) src_prepare() { # Remove etelemetry - sed -i '/"etelemetry/d' nipype/info.py || die + sed -i '/"etelemetry/d' nipype/info.py requirements.txt || die # Mark failing tests sed -i \ @@ -68,11 +67,16 @@ python_install_all() { doenvd "${FILESDIR}/98nipype" } +# Reported upstream: +# https://github.com/nipy/nipype/issues/3540 +EPYTEST_DESELECT=( + nipype/interfaces/tests/test_io.py::test_s3datagrabber_communication +) + python_test() { # Setting environment variable to disable etelemetry version check: # https://github.com/nipy/nipype/issues/3196#issuecomment-605980044 - NIPYPE_NO_ET=1 pytest -vv\ - || die + NIPYPE_NO_ET=1 epytest # Upstream test configuration fails #-c nipype/pytest.ini\ #--doctest-modules nipype\ diff --git a/sci-libs/nipype/nipype-1.8.4-r2.ebuild b/sci-libs/nipype/nipype-1.8.4-r2.ebuild new file mode 100644 index 000000000..4c3da70b3 --- /dev/null +++ b/sci-libs/nipype/nipype-1.8.4-r2.ebuild @@ -0,0 +1,96 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) +PYTHON_REQ_USE="threads(+),sqlite" + +inherit distutils-r1 + +DESCRIPTION="Neuroimaging in Python: Pipelines and Interfaces" +HOMEPAGE="https://nipype.readthedocs.io/" +SRC_URI="https://github.com/nipy/nipype/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" +RESTRICT="!test? ( test )" + +DEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/prov[${PYTHON_USEDEP}] + sci-libs/nibabel[${PYTHON_USEDEP}] + test? ( + dev-python/mock[${PYTHON_USEDEP}] + dev-python/pytest[${PYTHON_USEDEP}] + ${RDEPEND} + ) +" + +RDEPEND=" + dev-python/click[${PYTHON_USEDEP}] + dev-python/filelock[${PYTHON_USEDEP}] + dev-python/looseversion[${PYTHON_USEDEP}] + dev-python/networkx[${PYTHON_USEDEP}] + dev-python/packaging[${PYTHON_USEDEP}] + dev-python/pydot[${PYTHON_USEDEP}] + dev-python/python-dateutil[${PYTHON_USEDEP}] + dev-python/rdflib[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/simplejson[${PYTHON_USEDEP}] + <dev-python/traits-6.4.0[${PYTHON_USEDEP}] +" + +PATCHES=( + "${FILESDIR}/${PN}-1.8.4-dependency_compatibility.patch" + "${FILESDIR}/${PN}-1.8.4-no_etelemetry.patch" +) + +src_prepare() { + # Remove etelemetry + # Doing this separately since the file is affected by another patch. + sed -i '/"etelemetry/d' nipype/info.py requirements.txt || die + + # Mark failing tests + sed -i \ + -e "/def test_no_et(tmp_path):/i@pytest.mark.skip('Known to fail by upstream: https://github.com/nipy/nipype/issues/3196#issuecomment-606003186')" \ + nipype/tests/test_nipype.py || die + sed -i \ + -e "/def test_fslversion():/i@pytest.mark.skip('Known to fail by upstream: https://github.com/nipy/nipype/issues/3196#issuecomment-605997462')" \ + nipype/interfaces/fsl/tests/test_base.py || die + default +} + +python_install_all() { + distutils-r1_python_install_all + doenvd "${FILESDIR}/98nipype" +} + +# Reported upstream: +# https://github.com/nipy/nipype/issues/3540 +EPYTEST_DESELECT=( + nipype/interfaces/tests/test_io.py::test_s3datagrabber_communication +) + +python_test() { + # Setting environment variable to disable etelemetry version check: + # https://github.com/nipy/nipype/issues/3196#issuecomment-605980044 + NIPYPE_NO_ET=1 epytest + # Upstream test configuration fails + #-c nipype/pytest.ini\ + #--doctest-modules nipype\ + #--cov nipype\ + #--cov-config .coveragerc\ + #--cov-report xml:cov.xml\ +} + +pkg_postinst() { + echo + einfo "Please run the following commands if you" + einfo "intend to use nipype from an existing shell:" + einfo "source /etc/profile" + echo +} diff --git a/sci-libs/nipype/nipype-1.8.6.ebuild b/sci-libs/nipype/nipype-1.8.6.ebuild new file mode 100644 index 000000000..88bc23395 --- /dev/null +++ b/sci-libs/nipype/nipype-1.8.6.ebuild @@ -0,0 +1,97 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) +PYTHON_REQ_USE="threads(+),sqlite" + +inherit distutils-r1 + +DESCRIPTION="Neuroimaging in Python: Pipelines and Interfaces" +HOMEPAGE="https://nipype.readthedocs.io/" +SRC_URI="https://github.com/nipy/nipype/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" +# Tests fail with numpy import error: +# https://github.com/nipy/nipype/issues/3626 +RESTRICT="test" + +DEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/prov[${PYTHON_USEDEP}] + sci-libs/nibabel[${PYTHON_USEDEP}] + test? ( + dev-python/mock[${PYTHON_USEDEP}] + dev-python/pytest[${PYTHON_USEDEP}] + ${RDEPEND} + ) +" + +RDEPEND=" + dev-python/click[${PYTHON_USEDEP}] + dev-python/filelock[${PYTHON_USEDEP}] + dev-python/looseversion[${PYTHON_USEDEP}] + dev-python/networkx[${PYTHON_USEDEP}] + dev-python/packaging[${PYTHON_USEDEP}] + dev-python/pydot[${PYTHON_USEDEP}] + dev-python/python-dateutil[${PYTHON_USEDEP}] + dev-python/rdflib[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/simplejson[${PYTHON_USEDEP}] + <dev-python/traits-6.4.0[${PYTHON_USEDEP}] +" + +PATCHES=( + "${FILESDIR}/${PN}-1.8.4-no_etelemetry.patch" +) + +src_prepare() { + # Remove etelemetry + # Doing this separately since the file is affected by another patch. + sed -i '/"etelemetry/d' nipype/info.py requirements.txt || die + + # Mark failing tests + sed -i \ + -e "/def test_no_et(tmp_path):/i@pytest.mark.skip('Known to fail by upstream: https://github.com/nipy/nipype/issues/3196#issuecomment-606003186')" \ + nipype/tests/test_nipype.py || die + sed -i \ + -e "/def test_fslversion():/i@pytest.mark.skip('Known to fail by upstream: https://github.com/nipy/nipype/issues/3196#issuecomment-605997462')" \ + nipype/interfaces/fsl/tests/test_base.py || die + default +} + +python_install_all() { + distutils-r1_python_install_all + doenvd "${FILESDIR}/98nipype" +} + +# Reported upstream: +# https://github.com/nipy/nipype/issues/3540 +EPYTEST_DESELECT=( + nipype/interfaces/tests/test_io.py::test_s3datagrabber_communication +) + +python_test() { + # Setting environment variable to disable etelemetry version check: + # https://github.com/nipy/nipype/issues/3196#issuecomment-605980044 + NIPYPE_NO_ET=1 epytest + # Upstream test configuration fails + #-c nipype/pytest.ini\ + #--doctest-modules nipype\ + #--cov nipype\ + #--cov-config .coveragerc\ + #--cov-report xml:cov.xml\ +} + +pkg_postinst() { + echo + einfo "Please run the following commands if you" + einfo "intend to use nipype from an existing shell:" + einfo "source /etc/profile" + echo +} |