1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
|
#!/bin/bash
set -eo pipefail
SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
PLATFORM=$(python -c 'import platform; print(platform.system())')
echo "Installing pip-pre dependencies on ${PLATFORM}"
STD_ARGS="--progress-bar off --upgrade --pre"
QT_BINDING="PyQt6"
# Dependencies of scientific-python-nightly-wheels are installed here so that
# we can use strict --index-url (instead of --extra-index-url) below
echo "PyQt6 and scientific-python-nightly-wheels dependencies"
python -m pip install $STD_ARGS pip setuptools packaging \
threadpoolctl cycler fonttools kiwisolver pyparsing pillow python-dateutil \
patsy pytz tzdata nibabel tqdm trx-python joblib numexpr "$QT_BINDING" \
py-cpuinfo blosc2 hatchling
echo "NumPy/SciPy/pandas etc."
python -m pip uninstall -yq numpy
python -m pip install $STD_ARGS --only-binary ":all:" --default-timeout=60 \
--index-url "https://pypi.anaconda.org/scientific-python-nightly-wheels/simple" \
"numpy>=2.1.0.dev0" "scikit-learn>=1.6.dev0" "scipy>=1.15.0.dev0" \
"pandas>=3.0.0.dev0" "matplotlib>=3.10.0.dev0" \
"h5py>=3.12.1" "dipy>=1.10.0.dev0" "pyarrow>=19.0.0.dev0" "tables>=3.10.2.dev0"
# statsmodels requires formulaic@main so we need to use --extra-index-url
echo "statsmodels"
python -m pip install $STD_ARGS --only-binary ":all:" \
--extra-index-url "https://pypi.anaconda.org/scientific-python-nightly-wheels/simple" \
"statsmodels>=0.15.0.dev0"
# No Numba because it forces an old NumPy version
echo "pymatreader"
pip install https://gitlab.com/obob/pymatreader/-/archive/master/pymatreader-master.zip
echo "OpenMEEG"
python -m pip install $STD_ARGS --only-binary ":all:" --extra-index-url "https://test.pypi.org/simple" "openmeeg>=2.6.0.dev4"
echo "nilearn"
# TODO: Revert once settled:
# https://github.com/scikit-learn/scikit-learn/pull/30268#issuecomment-2479701651
python -m pip install $STD_ARGS "git+https://github.com/larsoner/nilearn@sklearn"
echo "VTK"
python -m pip install $STD_ARGS --only-binary ":all:" --extra-index-url "https://wheels.vtk.org" vtk
python -c "import vtk"
echo "PyVista"
python -m pip install $STD_ARGS "git+https://github.com/pyvista/pyvista"
echo "picard"
python -m pip install $STD_ARGS git+https://github.com/pierreablin/picard
echo "pyvistaqt"
pip install $STD_ARGS git+https://github.com/pyvista/pyvistaqt
echo "imageio-ffmpeg, xlrd, mffpy"
pip install $STD_ARGS imageio-ffmpeg xlrd mffpy traitlets pybv eeglabio
echo "mne-qt-browser"
pip install $STD_ARGS git+https://github.com/mne-tools/mne-qt-browser
echo "mne-bids"
pip install $STD_ARGS git+https://github.com/mne-tools/mne-bids
echo "nibabel"
pip install $STD_ARGS git+https://github.com/nipy/nibabel
echo "joblib"
pip install $STD_ARGS git+https://github.com/joblib/joblib
echo "edfio"
# Disable protection for Azure, see
# https://github.com/mne-tools/mne-python/pull/12609#issuecomment-2115639369
GIT_CLONE_PROTECTION_ACTIVE=false pip install $STD_ARGS git+https://github.com/the-siesta-group/edfio
if [[ "${PLATFORM}" == "Linux" ]]; then
echo "h5io"
pip install $STD_ARGS git+https://github.com/h5io/h5io
echo "pysnirf2"
pip install $STD_ARGS git+https://github.com/BUNPC/pysnirf2
fi
# Make sure we're on a NumPy 2.0 variant
echo "Checking NumPy version"
python -c "import numpy as np; assert np.__version__[0] == '2', np.__version__"
# And that Qt works
echo "Checking Qt"
${SCRIPT_DIR}/check_qt_import.sh "$QT_BINDING"
|
