pyAFQ 1.2__tar.gz → 1.3__tar.gz

{pyAFQ-1.2 → pyAFQ-1.3}/.github/workflows/docbuild.yml

@@ -8,7 +8,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: [3.9, 3.8]
+        python-version: ["3.9", "3.10", "3.11"]
 
     steps:
     - name: Checkout repo
@@ -21,11 +21,13 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install .[all]
-        conda install -c conda-forge xvfbwrapper
+        sudo apt-get install -y xvfb
     - name: Build docs
       env:
         XVFB: 1
+        DISPLAY: :99
       run: |
+        Xvfb :99 -screen 0 1280x1024x24 &
         cd docs
         make html
     - name: Upload docs

{pyAFQ-1.2 → pyAFQ-1.3}/.github/workflows/docker_pyafq.yml

@@ -1,6 +1,6 @@
 name: Build and Push pyAFQ Docker Image
 
-on: [push, pull_request]
+on: [push]
 
 jobs:
   build:
@@ -27,13 +27,13 @@ jobs:
 
     - name: Build pyAFQ GPU docker image
       run: sh ./gpu_docker/docker-build.sh \
-        "${{github.sha}}" "nrdg" "11.0.3-devel" "11"
+        "${{github.sha}}" "nrdg" "11.4.3-devel-ubuntu20.04" "11"
 
     - name: Build a tagged GPU image
       if: startsWith(github.event.ref, 'refs/tags')
       run: |
         sh ./gpu_docker/docker-build.sh \
-          "${GITHUB_REF:10}" "nrdg" "11.0.3-devel" "11"
+          "${GITHUB_REF:10}" "nrdg" "11.4.3-devel-ubuntu20.04" "11"
 
     - name: Login to GHCR 
       if: github.ref == 'refs/heads/master' || startsWith(github.event.ref, 'refs/tags')

{pyAFQ-1.2 → pyAFQ-1.3}/.github/workflows/docker_pyafq_cuda12.yml

@@ -1,6 +1,6 @@
 name: Build and Push pyAFQ CUDA12 Image
 
-on: [push, pull_request]
+on: [push]
 
 jobs:
   build:

{pyAFQ-1.2 → pyAFQ-1.3}/.github/workflows/nightly_anisotropic_test.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: [3.9, 3.8]
+        python-version: ["3.9", "3.10", "3.11"]
 
     steps:
     - name: Checkout repo

{pyAFQ-1.2 → pyAFQ-1.3}/.github/workflows/nightly_basic_test.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: [3.9, 3.8]
+        python-version: ["3.9", "3.10", "3.11"]
 
     steps:
     - name: Checkout repo

{pyAFQ-1.2 → pyAFQ-1.3}/.github/workflows/nightly_custom_test.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: [3.9, 3.8]
+        python-version: ["3.9", "3.10", "3.11"]
 
     steps:
     - name: Checkout repo

{pyAFQ-1.2 → pyAFQ-1.3}/.github/workflows/nightly_pft_test.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: [3.9, 3.8]
+        python-version: ["3.9", "3.10", "3.11"]
 
     steps:
     - name: Checkout repo

{pyAFQ-1.2 → pyAFQ-1.3}/.github/workflows/nightly_reco80_test.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: [3.9, 3.8]
+        python-version: ["3.9", "3.10", "3.11"]
 
     steps:
     - name: Checkout repo

{pyAFQ-1.2 → pyAFQ-1.3}/.github/workflows/nightly_reco_test.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: [3.9, 3.8]
+        python-version: ["3.9", "3.10", "3.11"]
 
     steps:
     - name: Checkout repo

{pyAFQ-1.2 → pyAFQ-1.3}/.github/workflows/nightly_test.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: [3.9, 3.8]
+        python-version: ["3.9", "3.10", "3.11"]
 
     steps:
     - name: Checkout repo

{pyAFQ-1.2 → pyAFQ-1.3}/.github/workflows/test.yml

@@ -9,7 +9,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: [3.9, 3.8]
+        python-version: ["3.9", "3.10", "3.11"]
         nibabel-pre: [true, false]
 
     steps:

{pyAFQ-1.2 → pyAFQ-1.3}/AFQ/_fixes.py

@@ -3,11 +3,6 @@ import numpy as np
 from scipy.special import lpmv, gammaln
 
 from tqdm import tqdm
-from dipy.align import Bunch
-from dipy.tracking.local_tracking import (LocalTracking,
-                                          ParticleFilteringTracking)
-from dipy.tracking.stopping_criterion import StreamlineStatus
-import random
 
 import math
 
@@ -43,80 +38,6 @@ def spherical_harmonics(m, n, theta, phi):
     return val
 
 
-TissueTypes = Bunch(OUTSIDEIMAGE=-1, INVALIDPOINT=0, TRACKPOINT=1, ENDPOINT=2)
-
-
-def _verbose_generate_tractogram(self):
-    """A streamline generator"""
-
-    # Get inverse transform (lin/offset) for seeds
-    inv_A = np.linalg.inv(self.affine)
-    lin = inv_A[:3, :3]
-    offset = inv_A[:3, 3]
-
-    F = np.empty((self.max_length + 1, 3), dtype=float)
-    B = F.copy()
-    for s in tqdm(self.seeds):
-        s = np.dot(lin, s) + offset
-        # Set the random seed in numpy and random
-        if self.random_seed is not None:
-            s_random_seed = hash(np.abs((np.sum(s)) + self.random_seed)) \
-                % (2**32 - 1)
-            random.seed(s_random_seed)
-            np.random.seed(s_random_seed)
-        directions = self.direction_getter.initial_direction(s)
-        if directions.size == 0 and self.return_all:
-            # only the seed position
-            if self.save_seeds:
-                yield [s], s
-            else:
-                yield [s]
-        directions = directions[:self.max_cross]
-        for first_step in directions:
-            stepsF, stream_status = self._tracker(s, first_step, F)
-            if not (self.return_all
-                    or stream_status == StreamlineStatus.ENDPOINT
-                    or stream_status == StreamlineStatus.OUTSIDEIMAGE):
-                continue
-            first_step = -first_step
-            stepsB, stream_status = self._tracker(s, first_step, B)
-            if not (self.return_all
-                    or stream_status == StreamlineStatus.ENDPOINT
-                    or stream_status == StreamlineStatus.OUTSIDEIMAGE):
-                continue
-            if stepsB == 1:
-                streamline = F[:stepsF].copy()
-            else:
-                parts = (B[stepsB - 1:0:-1], F[:stepsF])
-                streamline = np.concatenate(parts, axis=0)
-
-            # move to the next streamline if only the seed position
-            # and not return all
-            len_sl = len(streamline)
-            if len_sl >= self.min_length:
-                if len_sl <= self.max_length:
-                    if self.save_seeds:
-                        yield streamline, s
-                    else:
-                        yield streamline
-
-
-class VerboseLocalTracking(LocalTracking):
-    def __init__(self, *args, min_length=10, max_length=1000, **kwargs):
-        super().__init__(*args, **kwargs)
-        self.min_length = min_length
-        self.max_length = max_length
-    _generate_tractogram = _verbose_generate_tractogram
-
-
-class VerboseParticleFilteringTracking(ParticleFilteringTracking):
-    def __init__(self, *args, min_length=10, max_length=1000, **kwargs):
-        super().__init__(*args, **kwargs)
-        self.min_length = min_length
-        self.max_length = max_length
-    _generate_tractogram = _verbose_generate_tractogram
-
-
 def in_place_norm(vec, axis=-1, keepdims=False, delvec=True):
     """ Return Vectors with Euclidean (L2) norm