[CI] Update CI to be more efficient (#814)

* try smaller image

* use home

* use more cpus

* don't be implicit

* actually increase cpus

* remove recon packages

pyproject.toml

@@ -19,7 +19,6 @@ requires-python = ">=3.10"
 dependencies = [
     'importlib_resources; python_version < "3.11"',
     "dipy>=1.8.0,<1.9.0",
-    "dmri-amico == 1.5.4",
     "fury",
     "indexed_gzip <= 1.8.7",
     "jinja2 < 3.1",
@@ -33,7 +32,6 @@ dependencies = [
     "numpy <= 1.26.3",
     "pandas < 2.0.0",
     "psutil <= 5.9.8",
-    "pyAFQ == 1.3.2",
     "pybids",
     "pyyaml",
     "scikit-image",

qsiprep/data/boilerplate.bib

@@ -25,26 +25,6 @@ @article{dipy
   publisher={Frontiers}
 }
 
-
-@article{pyafq,
-  title = {Evaluating the reliability of human brain white matter tractometry},
-  author = {Kruper, J. and Yeatman, J.D. and Richie-Halford, A. and Bloom, D. and Grotheer, M. and Caffarra, S. and Kiar, G. and Karipidis, I.I. and Roy, E. and Chandio, B.Q. and Garyfallidis, E. and Rokem, A.},
-  journal = {Aperture Neuro},
-  volume = {1},
-  pages = {1-25},
-  year = {2021},
-}
-
-@article{pyafq2,
-  title = {Tract profiles of White Matter Properties: Automating fiber-tract quantification},
-  volume = {7},
-  doi = {10.1371/journal.pone.0049790},
-  number = {11},
-  journal = {PLoS ONE},
-  author = {Yeatman, Jason D. and Dougherty, Robert F. and Myall, Nathaniel J. and Wandell, Brian A. and Feldman, Heidi M.},
-  year = {2012}
-}
-
 @article{nipype1,
     author = {Gorgolewski, K. and Burns, C. D. and Madison, C. and Clark, D. and Halchenko, Y. O. and Waskom, M. L. and Ghosh, S.},
     doi = {10.3389/fninf.2011.00013},
@@ -556,16 +536,6 @@ @article{noddi
   publisher={Elsevier}
 }
 
-@article{amico,
-  title={Accelerated microstructure imaging via convex optimization (AMICO) from diffusion MRI data},
-  author={Daducci, Alessandro and Canales-Rodr{\'\i}guez, Erick J and Zhang, Hui and Dyrby, Tim B and Alexander, Daniel C and Thiran, Jean-Philippe},
-  journal={NeuroImage},
-  volume={105},
-  pages={32--44},
-  year={2015},
-  publisher={Elsevier}
-}
-
 @article{drbuddi,
   title={DR-BUDDI (Diffeomorphic Registration for Blip-Up blip-Down Diffusion Imaging) method for correcting echo planar imaging distortions},
   author={Irfanoglu, M Okan and Modi, Pooja and Nayak, Amritha and Hutchinson, Elizabeth B and Sarlls, Joelle and Pierpaoli, Carlo},

qsiprep/tests/test_cli.py

@@ -2,7 +2,7 @@
 
 import os
 import sys
-from unittest.mock import patch
+from unittest.mock import DEFAULT, patch
 
 import pytest
 from nipype import config as nipype_config
@@ -20,6 +20,8 @@
 
 nipype_config.enable_debug_mode()
 
+DEFAULT_NUM_CPUS = 4
+
 
 @pytest.mark.integration
 @pytest.mark.dsdti_fmap
@@ -181,7 +183,6 @@ def test_drbuddi_rpe(data_dir, output_dir, working_dir):
         "participant",
         f"-w={work_dir}",
         "--sloppy",
-        "--nthreads=4",
         "--anat-modality=none",
         "--denoise-method=none",
         "--b1_biascorrect_stage=none",
@@ -224,7 +225,6 @@ def test_drbuddi_shoreline_epi(data_dir, output_dir, working_dir):
         "--hmc-model=none",
         "--output-resolution=2",
         "--shoreline-iters=1",
-        "--nthreads=1",
     ]
 
     _run_and_generate(TEST_NAME, parameters, test_main=True)
@@ -259,9 +259,8 @@ def test_drbuddi_tensorline_epi(data_dir, output_dir, working_dir):
         "--b1-biascorrect-stage=none",
         "--pepolar-method=DRBUDDI",
         "--hmc-model=tensor",
-        "--output-resolution=2",
+        "--output-resolution=5",
         "--shoreline-iters=1",
-        "--nthreads=1",
     ]
 
     _run_and_generate(TEST_NAME, parameters, test_main=True)
@@ -307,7 +306,6 @@ def test_dscsdsi(data_dir, output_dir, working_dir):
         "--hmc-transform=Rigid",
         "--output-resolution=5",
         "--shoreline-iters=1",
-        "--nthreads=1",
     ]
 
     _run_and_generate(TEST_NAME, parameters, test_main=True)
@@ -350,7 +348,6 @@ def test_dsdti_nofmap(data_dir, output_dir, working_dir):
         "--unringing-method=rpg",
         "--b1-biascorrect-stage=none",
         "--output-resolution=5",
-        "--nthreads=1",
     ]
 
     _run_and_generate(TEST_NAME, parameters, test_main=True)
@@ -393,7 +390,6 @@ def test_dsdti_synfmap(data_dir, output_dir, working_dir):
         "--force-syn",
         "--b1-biascorrect-stage=final",
         "--output-resolution=5",
-        "--nthreads=1",
     ]
 
     _run_and_generate(TEST_NAME, parameters, test_main=True)
@@ -505,8 +501,6 @@ def test_maternal_brain_project(data_dir, output_dir, working_dir):
         "--output-resolution=5",
         "--hmc-model=3dSHORE",
         f"--bids-filter-file={bids_filter}",
-        "--nthreads=4",
-        "--omp-nthreads=4",
     ]
 
     _run_and_generate(TEST_NAME, parameters, test_main=True)
@@ -541,13 +535,34 @@ def test_forrest_gump(data_dir, output_dir, working_dir):
         "--write-graph",
         "--output-resolution=5",
         f"--bids-filter-file={bids_filter}",
-        "--nthreads=4",
-        "--omp-nthreads=4",
     ]
 
     _run_and_generate(TEST_NAME, parameters, test_main=True)
 
 
+def _check_arg_specified(argname, arglist):
+    for arg in arglist:
+        if arg.startswith(argname):
+            return True
+    return False
+
+
+def _update_resources(parameters):
+    """We should use all the available CPUs for testing.
+
+    Sometimes a test will set a specific amount of cpus. In that
+    case, the number should be kept. Otherwise, try to read the
+    env variable (specified in each job in config.yml). If
+    this variable doesn't work, just set it to 4.
+    """
+    nthreads = int(os.environ.get("CIRCLECPUS", DEFAULT_NUM_CPUS))
+    if not _check_arg_specified("--nthreads", parameters):
+        parameters.append(f"--nthreads={nthreads}")
+    if not _check_arg_specified("--omp-nthreads", parameters):
+        parameters.append(f"--omp-nthreads={nthreads}")
+    return parameters
+
+
 def _run_and_generate(test_name, parameters, test_main=True):
     from qsiprep import config
 
@@ -556,6 +571,9 @@ def _run_and_generate(test_name, parameters, test_main=True):
     parameters.append("--notrack")
     parameters.append("-vv")
 
+    # Update resource parameters
+    parameters = _update_resources(parameters)
+
     if test_main:
         # This runs, but for some reason doesn't count toward coverage.
         argv = ["qsiprep"] + parameters