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c6d1665: install_sct (fail vs pass)

Created 4 years agoDiff never expires

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non-interactive mode

Full verbose!

+ getopts :iydbcvh opt

+ trap detectKeyboardInterrupt INT

+ trap finish EXIT

+ print info '

*******************************

* Welcome to SCT installation *

*******************************

+ type=info

+ shift

+ case "$type" in

+ echo -e '\n\033[0;32m

*******************************

* Welcome to SCT installation *

*******************************

\033[0m\n'

*******************************

* Welcome to SCT installation *

*******************************

+ fetch_os_type

+ print info 'Checking OS type and version...'

+ type=info

+ shift

+ case "$type" in

+ echo -e '\n\033[0;32mChecking OS type and version...\033[0m\n'

Checking OS type and version...

+ OSver=unknown

++ uname -a

+ uname_output='Linux fv-az31-656 5.4.0-1063-azure #66~18.04.1-Ubuntu SMP Thu Oct 21 09:59:28 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux'

+ uname_output='Linux fv-az82-661 5.4.0-1063-azure #66~18.04.1-Ubuntu SMP Thu Oct 21 09:59:28 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux'

+ echo 'Linux fv-az31-656 5.4.0-1063-azure #66~18.04.1-Ubuntu SMP Thu Oct 21 09:59:28 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux'

+ echo 'Linux fv-az82-661 5.4.0-1063-azure #66~18.04.1-Ubuntu SMP Thu Oct 21 09:59:28 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux'

Linux fv-az31-656 5.4.0-1063-azure #66~18.04.1-Ubuntu SMP Thu Oct 21 09:59:28 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

Linux fv-az82-661 5.4.0-1063-azure #66~18.04.1-Ubuntu SMP Thu Oct 21 09:59:28 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

+ echo 'Linux fv-az82-661 5.4.0-1063-azure #66~18.04.1-Ubuntu SMP Thu Oct 21 09:59:28 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux'

+ grep -i darwin

+ echo 'Linux fv-az31-656 5.4.0-1063-azure #66~18.04.1-Ubuntu SMP Thu Oct 21 09:59:28 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux'

+ grep -i linux

+ echo 'Linux fv-az31-656 5.4.0-1063-azure #66~18.04.1-Ubuntu SMP Thu Oct 21 09:59:28 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux'

+ echo 'Linux fv-az82-661 5.4.0-1063-azure #66~18.04.1-Ubuntu SMP Thu Oct 21 09:59:28 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux'

+ OS=linux

+ check_requirements

+ print info 'Checking requirements...'

+ type=info

+ shift

+ case "$type" in

+ echo -e '\n\033[0;32mChecking requirements...\033[0m\n'

Checking requirements...

++ command -v curl

+ [[ -n /usr/bin/curl ]]

+ gcc --version

+ print info 'OK!'

+ type=info

+ shift

+ case "$type" in

+ echo -e '\n\033[0;32mOK!\033[0m\n'

OK!

+ [[ -e spinalcordtoolbox/version.txt ]]

++ cat spinalcordtoolbox/version.txt

+ SCT_VERSION=dev

+ [[ -z '' ]]

+ [[ -d .git ]]

+ SCT_INSTALL_TYPE=in-place

+ get_shell_rc_path

+ [[ /bin/bash == *\b\a\s\h* ]]

+ THE_RC=bash

+ RC_FILE_PATH=/home/runner/.bashrc

+ echo -e '\nSCT version ......... dev'

SCT version ......... dev

+ echo -e 'Installation type ... in-place'

Installation type ... in-place

+ echo -e 'Operating system .... linux (unknown)'

Operating system .... linux (unknown)

+ echo -e 'Shell config ........ /home/runner/.bashrc'

Shell config ........ /home/runner/.bashrc

+ REPORT_STATS=no

+ '[' -z yes ']'

+ [[ no =~ [Yy](es)? ]]

+ print info '--> Crash reports will not be sent.'

+ type=info

+ shift

+ case "$type" in

+ echo -e '\n\033[0;32m--> Crash reports will not be sent.\033[0m\n'

--> Crash reports will not be sent.

+ [[ in-place == \i\n\-\p\l\a\c\e ]]

+ SCT_DIR=/home/runner/work/spinalcordtoolbox/spinalcordtoolbox

+ true

+ keep_default_path=

+ [[ ! '' =~ ^([Yy](es)?|[Nn]o?)$ ]]

+ print info 'SCT will be installed here: [/home/runner/work/spinalcordtoolbox/spinalcordtoolbox]'

+ type=info

+ shift

+ case "$type" in

+ echo -e '\n\033[0;32mSCT will be installed here: [/home/runner/work/spinalcordtoolbox/spinalcordtoolbox]\033[0m\n'

SCT will be installed here: [/home/runner/work/spinalcordtoolbox/spinalcordtoolbox]

+ keep_default_path=yes

+ '[' -z yes ']'

+ [[ ! yes =~ ^([Yy](es)?|[Nn]o?)$ ]]

+ [[ yes =~ ^[Yy] ]]

+ break

+ space_regex='[[:space:]]+'

+ [[ /home/runner/work/spinalcordtoolbox/spinalcordtoolbox =~ [[:space:]]+ ]]

+ add_to_path=

+ [[ ! '' =~ ^([Yy](es)?|[Nn]o?)$ ]]

+ add_to_path=yes

+ '[' -z yes ']'

+ [[ ! yes =~ ^([Yy](es)?|[Nn]o?)$ ]]

+ mkdir -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox

+ [[ -d /home/runner/work/spinalcordtoolbox/spinalcordtoolbox ]]

+ [[ ! -w /home/runner/work/spinalcordtoolbox/spinalcordtoolbox ]]

+ [[ bash == \b\a\s\h ]]

+ DISPLAY_UPDATE_PATH='export PATH="/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin:$PATH"'

+ [[ /home/runner/work/spinalcordtoolbox/spinalcordtoolbox != \/\h\o\m\e\/\r\u\n\n\e\r\/\w\o\r\k\/\s\p\i\n\a\l\c\o\r\d\t\o\o\l\b\o\x\/\s\p\i\n\a\l\c\o\r\d\t\o\o\l\b\o\x ]]

+ print info 'Skipping copy of source files (source and destination folders are the same)'

+ type=info

+ shift

+ case "$type" in

+ echo -e '\n\033[0;32mSkipping copy of source files (source and destination folders are the same)\033[0m\n'

Skipping copy of source files (source and destination folders are the same)

+ [[ -x /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin ]]

+ cd /home/runner/work/spinalcordtoolbox/spinalcordtoolbox

+ [[ ! -f spinalcordtoolbox/version.txt ]]

+ run rm -rf /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python

+ print code rm -rf /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python

+ type=code

+ shift

+ case "$type" in

+ echo -e '\n\033[0;34mrm -rf /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python\033[0m\n'

rm -rf /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python

+ rm -rf /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python

+ run mkdir -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python

+ print code mkdir -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python

+ type=code

+ shift

+ case "$type" in

+ echo -e '\n\033[0;34mmkdir -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python\033[0m\n'

mkdir -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python

+ mkdir -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python

+ print info 'Downloading Miniconda...'

+ type=info

+ shift

+ case "$type" in

+ echo -e '\n\033[0;32mDownloading Miniconda...\033[0m\n'

Downloading Miniconda...

+ case $OS in

+ download /tmp/tmp.T01PPSHXCC/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

+ download /tmp/tmp.out2FZ4doz/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

+ command -v wget

+ run wget -nv -O /tmp/tmp.T01PPSHXCC/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

+ run wget -nv -O /tmp/tmp.out2FZ4doz/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

+ print code wget -nv -O /tmp/tmp.T01PPSHXCC/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

+ print code wget -nv -O /tmp/tmp.out2FZ4doz/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

+ type=code

+ shift

+ case "$type" in

+ echo -e '\n\033[0;34mwget -nv -O /tmp/tmp.T01PPSHXCC/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh\033[0m\n'

+ echo -e '\n\033[0;34mwget -nv -O /tmp/tmp.out2FZ4doz/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh\033[0m\n'

wget -nv -O /tmp/tmp.T01PPSHXCC/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

wget -nv -O /tmp/tmp.out2FZ4doz/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

+ wget -nv -O /tmp/tmp.T01PPSHXCC/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

+ wget -nv -O /tmp/tmp.out2FZ4doz/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

2021-11-19 20:23:20 URL:https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh [66709754/66709754] -> "/tmp/tmp.T01PPSHXCC/miniconda.sh" [1]

2021-11-19 19:35:10 URL:https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh [66709754/66709754] -> "/tmp/tmp.out2FZ4doz/miniconda.sh" [1]

+ print info 'Installing Miniconda...'

+ type=info

+ shift

+ case "$type" in

+ echo -e '\n\033[0;32mInstalling Miniconda...\033[0m\n'

Installing Miniconda...

+ run bash /tmp/tmp.T01PPSHXCC/miniconda.sh -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python -b -f

+ run bash /tmp/tmp.out2FZ4doz/miniconda.sh -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python -b -f

+ print code bash /tmp/tmp.T01PPSHXCC/miniconda.sh -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python -b -f

+ print code bash /tmp/tmp.out2FZ4doz/miniconda.sh -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python -b -f

+ type=code

+ shift

+ case "$type" in

+ echo -e '\n\033[0;34mbash /tmp/tmp.T01PPSHXCC/miniconda.sh -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python -b -f\033[0m\n'

+ echo -e '\n\033[0;34mbash /tmp/tmp.out2FZ4doz/miniconda.sh -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python -b -f\033[0m\n'

bash /tmp/tmp.T01PPSHXCC/miniconda.sh -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python -b -f

bash /tmp/tmp.out2FZ4doz/miniconda.sh -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python -b -f

+ bash /tmp/tmp.T01PPSHXCC/miniconda.sh -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python -b -f

+ bash /tmp/tmp.out2FZ4doz/miniconda.sh -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python -b -f

PREFIX=/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python

Unpacking payload ...

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Extracting : libgomp-9.3.0-h5101ec6_17.conda: 0%| | 0/38 [00:00<?, ?it/s]

Extracting : pycparser-2.20-py_2.conda: 3%|▎ | 1/38 [00:00<00:01, 30.87it/s]

Extracting : libgomp-9.3.0-h5101ec6_17.conda: 3%|▎ | 1/38 [00:00<00:07, 4.84it/s]

Extracting : tzdata-2021a-h52ac0ba_0.conda: 5%|▌ | 2/38 [00:00<00:01, 32.44it/s]

Extracting : pycparser-2.20-py_2.conda: 3%|▎ | 1/38 [00:00<00:07, 4.84it/s]

Extracting : tk-8.6.10-hbc83047_0.conda: 8%|▊ | 3/38 [00:00<00:03, 10.22it/s]

Extracting : tzdata-2021a-h52ac0ba_0.conda: 5%|▌ | 2/38 [00:00<00:07, 4.84it/s]

Extracting : tk-8.6.10-hbc83047_0.conda: 11%|█ | 4/38 [00:00<00:02, 13.61it/s]

Extracting : tk-8.6.10-hbc83047_0.conda: 8%|▊ | 3/38 [00:00<00:07, 4.84it/s]

Extracting : six-1.16.0-pyhd3eb1b0_0.conda: 11%|█ | 4/38 [00:00<00:02, 13.61it/s]

Extracting : six-1.16.0-pyhd3eb1b0_0.conda: 11%|█ | 4/38 [00:00<00:07, 4.84it/s]

Extracting : yaml-0.2.5-h7b6447c_0.conda: 13%|█▎ | 5/38 [00:00<00:02, 13.61it/s]

Extracting : yaml-0.2.5-h7b6447c_0.conda: 13%|█▎ | 5/38 [00:00<00:06, 4.84it/s]

Extracting : libgcc-ng-9.3.0-h5101ec6_17.conda: 16%|█▌ | 6/38 [00:00<00:02, 13.61it/s]

Extracting : libgcc-ng-9.3.0-h5101ec6_17.conda: 16%|█▌ | 6/38 [00:00<00:06, 4.84it/s]

Extracting : zlib-1.2.11-h7b6447c_3.conda: 18%|█▊ | 7/38 [00:00<00:02, 13.61it/s]

Extracting : libgcc-ng-9.3.0-h5101ec6_17.conda: 18%|█▊ | 7/38 [00:00<00:04, 6.51it/s]

Extracting : setuptools-52.0.0-py39h06a4308_0.conda: 21%|██ | 8/38 [00:00<00:02, 13.61it/s]

Extracting : zlib-1.2.11-h7b6447c_3.conda: 18%|█▊ | 7/38 [00:00<00:04, 6.51it/s]

Extracting : chardet-4.0.0-py39h06a4308_1003.conda: 24%|██▎ | 9/38 [00:00<00:02, 13.61it/s]

Extracting : setuptools-52.0.0-py39h06a4308_0.conda: 21%|██ | 8/38 [00:00<00:04, 6.51it/s]

Extracting : cffi-1.14.6-py39h400218f_0.conda: 26%|██▋ | 10/38 [00:00<00:02, 13.61it/s]

Extracting : chardet-4.0.0-py39h06a4308_1003.conda: 24%|██▎ | 9/38 [00:00<00:04, 6.51it/s]

Extracting : ruamel_yaml-0.15.100-py39h27cfd23_0.conda: 29%|██▉ | 11/38 [00:00<00:01, 13.61it/s]

Extracting : cffi-1.14.6-py39h400218f_0.conda: 26%|██▋ | 10/38 [00:00<00:04, 6.51it/s]

Extracting : libstdcxx-ng-9.3.0-hd4cf53a_17.conda: 32%|███▏ | 12/38 [00:00<00:01, 13.61it/s]

Extracting : ruamel_yaml-0.15.100-py39h27cfd23_0.conda: 29%|██▉ | 11/38 [00:00<00:04, 6.51it/s]

Extracting : certifi-2021.5.30-py39h06a4308_0.conda: 34%|███▍ | 13/38 [00:00<00:01, 13.61it/s]

Extracting : libstdcxx-ng-9.3.0-hd4cf53a_17.conda: 32%|███▏ | 12/38 [00:00<00:03, 6.51it/s]

Extracting : urllib3-1.26.6-pyhd3eb1b0_1.conda: 37%|███▋ | 14/38 [00:00<00:01, 13.61it/s]

Extracting : certifi-2021.5.30-py39h06a4308_0.conda: 34%|███▍ | 13/38 [00:00<00:03, 6.51it/s]

Extracting : brotlipy-0.7.0-py39h27cfd23_1003.conda: 39%|███▉ | 15/38 [00:00<00:01, 13.61it/s]

Extracting : urllib3-1.26.6-pyhd3eb1b0_1.conda: 37%|███▋ | 14/38 [00:00<00:03, 6.51it/s]

Extracting : brotlipy-0.7.0-py39h27cfd23_1003.conda: 42%|████▏ | 16/38 [00:00<00:01, 18.01it/s]

Extracting : brotlipy-0.7.0-py39h27cfd23_1003.conda: 39%|███▉ | 15/38 [00:00<00:03, 6.51it/s]

Extracting : sqlite-3.36.0-hc218d9a_0.conda: 42%|████▏ | 16/38 [00:00<00:01, 18.01it/s]

Extracting : brotlipy-0.7.0-py39h27cfd23_1003.conda: 42%|████▏ | 16/38 [00:00<00:02, 8.85it/s]

Extracting : readline-8.1-h27cfd23_0.conda: 45%|████▍ | 17/38 [00:00<00:01, 18.01it/s]

Extracting : sqlite-3.36.0-hc218d9a_0.conda: 42%|████▏ | 16/38 [00:00<00:02, 8.85it/s]

Extracting : ld_impl_linux-64-2.35.1-h7274673_9.conda: 47%|████▋ | 18/38 [00:00<00:01, 18.01it/s]

Extracting : readline-8.1-h27cfd23_0.conda: 45%|████▍ | 17/38 [00:00<00:02, 8.85it/s]

Extracting : pyopenssl-20.0.1-pyhd3eb1b0_1.conda: 50%|█████ | 19/38 [00:00<00:01, 18.01it/s]

Extracting : ld_impl_linux-64-2.35.1-h7274673_9.conda: 47%|████▋ | 18/38 [00:00<00:02, 8.85it/s]

Extracting : openssl-1.1.1k-h27cfd23_0.conda: 53%|█████▎ | 20/38 [00:00<00:00, 18.01it/s]

Extracting : pyopenssl-20.0.1-pyhd3eb1b0_1.conda: 50%|█████ | 19/38 [00:00<00:02, 8.85it/s]

Extracting : libffi-3.3-he6710b0_2.conda: 55%|█████▌ | 21/38 [00:00<00:00, 18.01it/s]

Extracting : openssl-1.1.1k-h27cfd23_0.conda: 53%|█████▎ | 20/38 [00:00<00:02, 8.85it/s]

Extracting : ncurses-6.2-he6710b0_1.conda: 58%|█████▊ | 22/38 [00:00<00:00, 18.01it/s]

Extracting : openssl-1.1.1k-h27cfd23_0.conda: 55%|█████▌ | 21/38 [00:00<00:01, 11.52it/s]

Extracting : ncurses-6.2-he6710b0_1.conda: 61%|██████ | 23/38 [00:00<00:00, 20.40it/s]

Extracting : libffi-3.3-he6710b0_2.conda: 55%|█████▌ | 21/38 [00:00<00:01, 11.52it/s]

Extracting : xz-5.2.5-h7b6447c_0.conda: 61%|██████ | 23/38 [00:00<00:00, 20.40it/s]

Extracting : ncurses-6.2-he6710b0_1.conda: 58%|█████▊ | 22/38 [00:00<00:01, 11.52it/s]

Extracting : pip-21.1.3-py39h06a4308_0.conda: 63%|██████▎ | 24/38 [00:00<00:00, 20.40it/s]

Extracting : xz-5.2.5-h7b6447c_0.conda: 61%|██████ | 23/38 [00:00<00:01, 11.52it/s]

Extracting : pysocks-1.7.1-py39h06a4308_0.conda: 66%|██████▌ | 25/38 [00:00<00:00, 20.40it/s]

Extracting : pip-21.1.3-py39h06a4308_0.conda: 63%|██████▎ | 24/38 [00:00<00:01, 11.52it/s]

Extracting : requests-2.25.1-pyhd3eb1b0_0.conda: 68%|██████▊ | 26/38 [00:00<00:00, 20.40it/s]

Extracting : pip-21.1.3-py39h06a4308_0.conda: 66%|██████▌ | 25/38 [00:00<00:00, 13.75it/s]

Extracting : ca-certificates-2021.7.5-h06a4308_1.conda: 71%|███████ | 27/38 [00:00<00:00, 20.40it/s]

Extracting : pysocks-1.7.1-py39h06a4308_0.conda: 66%|██████▌ | 25/38 [00:00<00:00, 13.75it/s]

Extracting : cryptography-3.4.7-py39hd23ed53_0.conda: 74%|███████▎ | 28/38 [00:00<00:00, 20.40it/s]

Extracting : requests-2.25.1-pyhd3eb1b0_0.conda: 68%|██████▊ | 26/38 [00:00<00:00, 13.75it/s]

Extracting : tqdm-4.61.2-pyhd3eb1b0_1.conda: 76%|███████▋ | 29/38 [00:00<00:00, 20.40it/s]

Extracting : ca-certificates-2021.7.5-h06a4308_1.conda: 71%|███████ | 27/38 [00:00<00:00, 13.75it/s]

Extracting : wheel-0.36.2-pyhd3eb1b0_0.conda: 79%|███████▉ | 30/38 [00:00<00:00, 20.40it/s]

Extracting : cryptography-3.4.7-py39hd23ed53_0.conda: 74%|███████▎ | 28/38 [00:00<00:00, 13.75it/s]

Extracting : conda-package-handling-1.7.3-py39h27cfd23_1.conda: 82%|████████▏ | 31/38 [00:00<00:00, 20.40it/s]

Extracting : tqdm-4.61.2-pyhd3eb1b0_1.conda: 76%|███████▋ | 29/38 [00:00<00:00, 13.75it/s]

Extracting : _libgcc_mutex-0.1-main.conda: 84%|████████▍ | 32/38 [00:00<00:00, 20.40it/s]

Extracting : tqdm-4.61.2-pyhd3eb1b0_1.conda: 79%|███████▉ | 30/38 [00:00<00:00, 17.13it/s]

Extracting : pycosat-0.6.3-py39h27cfd23_0.conda: 87%|████████▋ | 33/38 [00:00<00:00, 20.40it/s]

Extracting : wheel-0.36.2-pyhd3eb1b0_0.conda: 79%|███████▉ | 30/38 [00:00<00:00, 17.13it/s]

Extracting : pycosat-0.6.3-py39h27cfd23_0.conda: 89%|████████▉ | 34/38 [00:00<00:00, 26.55it/s]

Extracting : conda-package-handling-1.7.3-py39h27cfd23_1.conda: 82%|████████▏ | 31/38 [00:00<00:00, 17.13it/s]

Extracting : python-3.9.5-h12debd9_4.tar.bz2: 89%|████████▉ | 34/38 [00:03<00:00, 26.55it/s]

Extracting : _libgcc_mutex-0.1-main.conda: 84%|████████▍ | 32/38 [00:00<00:00, 17.13it/s]

Extracting : _openmp_mutex-4.5-1_gnu.tar.bz2: 92%|█████████▏| 35/38 [00:03<00:00, 26.55it/s]

Extracting : pycosat-0.6.3-py39h27cfd23_0.conda: 87%|████████▋ | 33/38 [00:00<00:00, 17.13it/s]

Extracting : idna-2.10-pyhd3eb1b0_0.tar.bz2: 95%|█████████▍| 36/38 [00:03<00:00, 26.55it/s]

Extracting : python-3.9.5-h12debd9_4.tar.bz2: 89%|████████▉ | 34/38 [00:03<00:00, 17.13it/s]

Extracting : conda-4.10.3-py39h06a4308_0.tar.bz2: 97%|█████████▋| 37/38 [00:03<00:00, 26.55it/s]

Extracting : python-3.9.5-h12debd9_4.tar.bz2: 92%|█████████▏| 35/38 [00:03<00:00, 4.55it/s]

Extracting : _openmp_mutex-4.5-1_gnu.tar.bz2: 92%|█████████▏| 35/38 [00:03<00:00, 4.55it/s]

Extracting : idna-2.10-pyhd3eb1b0_0.tar.bz2: 95%|█████████▍| 36/38 [00:03<00:00, 4.55it/s]

Extracting : conda-4.10.3-py39h06a4308_0.tar.bz2: 97%|█████████▋| 37/38 [00:03<00:00, 4.55it/s]

Collecting package metadata (current_repodata.json): ...working... done

Solving environment: ...working... done

## Package Plan ##

environment location: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python

added / updated specs:

- _libgcc_mutex==0.1=main

- _openmp_mutex==4.5=1_gnu

- brotlipy==0.7.0=py39h27cfd23_1003

- ca-certificates==2021.7.5=h06a4308_1

- certifi==2021.5.30=py39h06a4308_0

- cffi==1.14.6=py39h400218f_0

- chardet==4.0.0=py39h06a4308_1003

- conda-package-handling==1.7.3=py39h27cfd23_1

- conda==4.10.3=py39h06a4308_0

- cryptography==3.4.7=py39hd23ed53_0

- idna==2.10=pyhd3eb1b0_0

- ld_impl_linux-64==2.35.1=h7274673_9

- libffi==3.3=he6710b0_2

- libgcc-ng==9.3.0=h5101ec6_17

- libgomp==9.3.0=h5101ec6_17

- libstdcxx-ng==9.3.0=hd4cf53a_17

- ncurses==6.2=he6710b0_1

- openssl==1.1.1k=h27cfd23_0

- pip==21.1.3=py39h06a4308_0

- pycosat==0.6.3=py39h27cfd23_0

- pycparser==2.20=py_2

- pyopenssl==20.0.1=pyhd3eb1b0_1

- pysocks==1.7.1=py39h06a4308_0

- python==3.9.5=h12debd9_4

- readline==8.1=h27cfd23_0

- requests==2.25.1=pyhd3eb1b0_0

- ruamel_yaml==0.15.100=py39h27cfd23_0

- setuptools==52.0.0=py39h06a4308_0

- six==1.16.0=pyhd3eb1b0_0

- sqlite==3.36.0=hc218d9a_0

- tk==8.6.10=hbc83047_0

- tqdm==4.61.2=pyhd3eb1b0_1

- tzdata==2021a=h52ac0ba_0

- urllib3==1.26.6=pyhd3eb1b0_1

- wheel==0.36.2=pyhd3eb1b0_0

- xz==5.2.5=h7b6447c_0

- yaml==0.2.5=h7b6447c_0

- zlib==1.2.11=h7b6447c_3

The following NEW packages will be INSTALLED:

_libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main

_openmp_mutex pkgs/main/linux-64::_openmp_mutex-4.5-1_gnu

brotlipy pkgs/main/linux-64::brotlipy-0.7.0-py39h27cfd23_1003

ca-certificates pkgs/main/linux-64::ca-certificates-2021.7.5-h06a4308_1

certifi pkgs/main/linux-64::certifi-2021.5.30-py39h06a4308_0

cffi pkgs/main/linux-64::cffi-1.14.6-py39h400218f_0

chardet pkgs/main/linux-64::chardet-4.0.0-py39h06a4308_1003

conda pkgs/main/linux-64::conda-4.10.3-py39h06a4308_0

conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.7.3-py39h27cfd23_1

cryptography pkgs/main/linux-64::cryptography-3.4.7-py39hd23ed53_0

idna pkgs/main/noarch::idna-2.10-pyhd3eb1b0_0

ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.35.1-h7274673_9

libffi pkgs/main/linux-64::libffi-3.3-he6710b0_2

libgcc-ng pkgs/main/linux-64::libgcc-ng-9.3.0-h5101ec6_17

libgomp pkgs/main/linux-64::libgomp-9.3.0-h5101ec6_17

libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-9.3.0-hd4cf53a_17

ncurses pkgs/main/linux-64::ncurses-6.2-he6710b0_1

openssl pkgs/main/linux-64::openssl-1.1.1k-h27cfd23_0

pip pkgs/main/linux-64::pip-21.1.3-py39h06a4308_0

pycosat pkgs/main/linux-64::pycosat-0.6.3-py39h27cfd23_0

pycparser pkgs/main/noarch::pycparser-2.20-py_2

pyopenssl pkgs/main/noarch::pyopenssl-20.0.1-pyhd3eb1b0_1

pysocks pkgs/main/linux-64::pysocks-1.7.1-py39h06a4308_0

python pkgs/main/linux-64::python-3.9.5-h12debd9_4

readline pkgs/main/linux-64::readline-8.1-h27cfd23_0

requests pkgs/main/noarch::requests-2.25.1-pyhd3eb1b0_0

ruamel_yaml pkgs/main/linux-64::ruamel_yaml-0.15.100-py39h27cfd23_0

setuptools pkgs/main/linux-64::setuptools-52.0.0-py39h06a4308_0

six pkgs/main/noarch::six-1.16.0-pyhd3eb1b0_0

sqlite pkgs/main/linux-64::sqlite-3.36.0-hc218d9a_0

tk pkgs/main/linux-64::tk-8.6.10-hbc83047_0

tqdm pkgs/main/noarch::tqdm-4.61.2-pyhd3eb1b0_1

tzdata pkgs/main/noarch::tzdata-2021a-h52ac0ba_0

urllib3 pkgs/main/noarch::urllib3-1.26.6-pyhd3eb1b0_1

wheel pkgs/main/noarch::wheel-0.36.2-pyhd3eb1b0_0

xz pkgs/main/linux-64::xz-5.2.5-h7b6447c_0

yaml pkgs/main/linux-64::yaml-0.2.5-h7b6447c_0

zlib pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3

Preparing transaction: ...working... done

Executing transaction: ...working... done

installation finished.

+ find /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python -type f -exec touch '{}' +

+ print info 'Creating conda environment...'

+ type=info

+ shift

+ case "$type" in

+ echo -e '\n\033[0;32mCreating conda environment...\033[0m\n'

Creating conda environment...

+ python/bin/conda create -y -n venv_sct python=3.7

Collecting package metadata (current_repodata.json): ...working... done

Solving environment: ...working... done

## Package Plan ##

environment location: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct

added / updated specs:

- python=3.7

The following packages will be downloaded:

package | build

---------------------------|-----------------

ca-certificates-2021.10.26 | h06a4308_2 115 KB

certifi-2021.10.8 | py37h06a4308_0 151 KB

ncurses-6.3 | h7f8727e_2 782 KB

openssl-1.1.1l | h7f8727e_0 2.5 MB

pip-21.2.2 | py37h06a4308_0 1.8 MB

python-3.7.11 | h12debd9_0 45.3 MB

setuptools-58.0.4 | py37h06a4308_0 775 KB

tk-8.6.11 | h1ccaba5_0 3.0 MB

wheel-0.37.0 | pyhd3eb1b0_1 33 KB

------------------------------------------------------------

Total: 54.5 MB

The following NEW packages will be INSTALLED:

_libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main

_openmp_mutex pkgs/main/linux-64::_openmp_mutex-4.5-1_gnu

ca-certificates pkgs/main/linux-64::ca-certificates-2021.10.26-h06a4308_2

certifi pkgs/main/linux-64::certifi-2021.10.8-py37h06a4308_0

ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.35.1-h7274673_9

libffi pkgs/main/linux-64::libffi-3.3-he6710b0_2

libgcc-ng pkgs/main/linux-64::libgcc-ng-9.3.0-h5101ec6_17

libgomp pkgs/main/linux-64::libgomp-9.3.0-h5101ec6_17

libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-9.3.0-hd4cf53a_17

ncurses pkgs/main/linux-64::ncurses-6.3-h7f8727e_2

openssl pkgs/main/linux-64::openssl-1.1.1l-h7f8727e_0

pip pkgs/main/linux-64::pip-21.2.2-py37h06a4308_0

python pkgs/main/linux-64::python-3.7.11-h12debd9_0

readline pkgs/main/linux-64::readline-8.1-h27cfd23_0

setuptools pkgs/main/linux-64::setuptools-58.0.4-py37h06a4308_0

sqlite pkgs/main/linux-64::sqlite-3.36.0-hc218d9a_0

tk pkgs/main/linux-64::tk-8.6.11-h1ccaba5_0

wheel pkgs/main/noarch::wheel-0.37.0-pyhd3eb1b0_1

xz pkgs/main/linux-64::xz-5.2.5-h7b6447c_0

zlib pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3

Downloading and Extracting Packages

wheel-0.37.0 | 33 KB | | 0%

wheel-0.37.0 | 33 KB | ####8 | 49%

wheel-0.37.0 | 33 KB | ########## | 100%

ncurses-6.3 | 782 KB | | 0%

ncurses-6.3 | 782 KB | 8 | 8%

ncurses-6.3 | 782 KB | ########## | 100%

tk-8.6.11 | 3.0 MB | | 0%

python-3.7.11 | 45.3 MB | | 0%

tk-8.6.11 | 3.0 MB | 9 | 9%

python-3.7.11 | 45.3 MB | 2 | 3%

tk-8.6.11 | 3.0 MB | ######3 | 64%

python-3.7.11 | 45.3 MB | ##3 | 23%

tk-8.6.11 | 3.0 MB | ########## | 100%

python-3.7.11 | 45.3 MB | ####8 | 48%

tk-8.6.11 | 3.0 MB | ########## | 100%

python-3.7.11 | 45.3 MB | ######5 | 65%

python-3.7.11 | 45.3 MB | ########2 | 83%

python-3.7.11 | 45.3 MB | #########9 | 100%

python-3.7.11 | 45.3 MB | ########## | 100%

setuptools-58.0.4 | 775 KB | | 0%

setuptools-58.0.4 | 775 KB | ########## | 100%

tk-8.6.11 | 3.0 MB | | 0%

tk-8.6.11 | 3.0 MB | ########## | 100%

pip-21.2.2 | 1.8 MB | | 0%

pip-21.2.2 | 1.8 MB | ########## | 100%

ca-certificates-2021 | 115 KB | | 0%

ca-certificates-2021 | 115 KB | ########## | 100%

wheel-0.37.0 | 33 KB | | 0%

wheel-0.37.0 | 33 KB | ########## | 100%

openssl-1.1.1l | 2.5 MB | | 0%

openssl-1.1.1l | 2.5 MB | #######2 | 72%

openssl-1.1.1l | 2.5 MB | ########## | 100%

pip-21.2.2 | 1.8 MB | | 0%

pip-21.2.2 | 1.8 MB | ########2 | 82%

pip-21.2.2 | 1.8 MB | ########## | 100%

certifi-2021.10.8 | 151 KB | | 0%

certifi-2021.10.8 | 151 KB | ########## | 100%

python-3.7.11 | 45.3 MB | | 0%

python-3.7.11 | 45.3 MB | 1 | 2%

python-3.7.11 | 45.3 MB | #2 | 13%

python-3.7.11 | 45.3 MB | #9 | 20%

python-3.7.11 | 45.3 MB | ##7 | 27%

python-3.7.11 | 45.3 MB | ###3 | 34%

python-3.7.11 | 45.3 MB | ###9 | 40%

python-3.7.11 | 45.3 MB | #####4 | 55%

python-3.7.11 | 45.3 MB | #######1 | 71%

python-3.7.11 | 45.3 MB | ########6 | 86%

python-3.7.11 | 45.3 MB | ########## | 100%

Preparing transaction: ...working... done

Verifying transaction: ...working... done

Executing transaction: ...working... done

# To activate this environment, use

# $ conda activate venv_sct

# To deactivate an active environment, use

# $ conda deactivate

+ find /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python -type f -exec touch '{}' +

+ perl -pi -e 's/^ENABLE_USER_SITE.*$/ENABLE_USER_SITE = False/' /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/lib/python3.7/site.py

+ source python/etc/profile.d/conda.sh

++ export CONDA_EXE=/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/bin/conda

++ CONDA_EXE=/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/bin/conda

++ export _CE_M=

++ _CE_M=

++ export _CE_CONDA=

++ _CE_CONDA=

++ export CONDA_PYTHON_EXE=/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/bin/python

++ CONDA_PYTHON_EXE=/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/bin/python

++ '[' -z '' ']'

++ export CONDA_SHLVL=0

++ CONDA_SHLVL=0

++ '[' -n '' ']'

++++ dirname /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/bin/conda

+++ dirname /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/bin

++ PATH=/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/condabin:/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin:/home/runner/.local/bin:/opt/pipx_bin:/usr/share/rust/.cargo/bin:/home/runner/.config/composer/vendor/bin:/usr/local/.ghcup/bin:/home/runner/.dotnet/tools:/snap/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin

++ export PATH

++ '[' -z '' ']'

++ PS1=

+ set +u

+ conda activate venv_sct

+ local cmd=activate

+ case "$cmd" in

+ __conda_activate activate venv_sct

+ '[' -n '' ']'

+ local ask_conda

++ PS1=

++ __conda_exe shell.posix activate venv_sct

++ __add_sys_prefix_to_path

++ '[' -n '' ']'

+++ dirname /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/bin/conda

++ SYSP=/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/bin

+++ dirname /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/bin

++ SYSP=/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python

++ '[' -n '' ']'

++ PATH=/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/bin:/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/condabin:/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin:/home/runner/.local/bin:/opt/pipx_bin:/usr/share/rust/.cargo/bin:/home/runner/.config/composer/vendor/bin:/usr/local/.ghcup/bin:/home/runner/.dotnet/tools:/snap/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin

++ export PATH

++ /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/bin/conda shell.posix activate venv_sct

+ ask_conda='PS1='\''(venv_sct) '\''

export PATH='\''/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin:/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/condabin:/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin:/home/runner/.local/bin:/opt/pipx_bin:/usr/share/rust/.cargo/bin:/home/runner/.config/composer/vendor/bin:/usr/local/.ghcup/bin:/home/runner/.dotnet/tools:/snap/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin'\''

export CONDA_PREFIX='\''/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct'\''

export CONDA_SHLVL='\''1'\''

export CONDA_DEFAULT_ENV='\''venv_sct'\''

export CONDA_PROMPT_MODIFIER='\''(venv_sct) '\''

export CONDA_EXE='\''/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/bin/conda'\''

export _CE_M='\'''\''

export _CE_CONDA='\'''\''

export CONDA_PYTHON_EXE='\''/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/bin/python'\'''

+ eval 'PS1='\''(venv_sct) '\''

export CONDA_PREFIX='\''/home/runner/work/spin

Différences enregistrées

Texte d'origine

Ouvrir un fichier

non-interactive mode
 Full verbose!
+ getopts :iydbcvh opt
+ trap detectKeyboardInterrupt INT
+ trap finish EXIT
+ print info '
*******************************
* Welcome to SCT installation *
*******************************
'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32m
*******************************
* Welcome to SCT installation *
*******************************
\033[0m\n'

*******************************
* Welcome to SCT installation *
*******************************

+ fetch_os_type
+ print info 'Checking OS type and version...'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mChecking OS type and version...\033[0m\n'

Checking OS type and version...

+ OSver=unknown
++ uname -a
+ uname_output='Linux fv-az31-656 5.4.0-1063-azure #66~18.04.1-Ubuntu SMP Thu Oct 21 09:59:28 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux'
+ echo 'Linux fv-az31-656 5.4.0-1063-azure #66~18.04.1-Ubuntu SMP Thu Oct 21 09:59:28 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux'
Linux fv-az31-656 5.4.0-1063-azure #66~18.04.1-Ubuntu SMP Thu Oct 21 09:59:28 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
+ grep -i darwin
+ echo 'Linux fv-az31-656 5.4.0-1063-azure #66~18.04.1-Ubuntu SMP Thu Oct 21 09:59:28 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux'
+ grep -i linux
+ echo 'Linux fv-az31-656 5.4.0-1063-azure #66~18.04.1-Ubuntu SMP Thu Oct 21 09:59:28 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux'
+ OS=linux
+ check_requirements
+ print info 'Checking requirements...'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mChecking requirements...\033[0m\n'

Checking requirements...

++ command -v curl
+ [[ -n /usr/bin/curl ]]
+ gcc --version
+ print info 'OK!'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mOK!\033[0m\n'

OK!

+ [[ -e spinalcordtoolbox/version.txt ]]
++ cat spinalcordtoolbox/version.txt
+ SCT_VERSION=dev
+ [[ -z '' ]]
+ [[ -d .git ]]
+ SCT_INSTALL_TYPE=in-place
+ get_shell_rc_path
+ [[ /bin/bash == *\b\a\s\h* ]]
+ THE_RC=bash
+ RC_FILE_PATH=/home/runner/.bashrc
+ echo -e '\nSCT version ......... dev'

SCT version ......... dev
+ echo -e 'Installation type ... in-place'
Installation type ... in-place
+ echo -e 'Operating system .... linux (unknown)'
Operating system .... linux (unknown)
+ echo -e 'Shell config ........ /home/runner/.bashrc'
Shell config ........ /home/runner/.bashrc
+ REPORT_STATS=no
+ '[' -z yes ']'
+ [[ no =~ [Yy](es)? ]]
+ print info '--> Crash reports will not be sent.'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32m--> Crash reports will not be sent.\033[0m\n'

--> Crash reports will not be sent.

+ [[ in-place == \i\n\-\p\l\a\c\e ]]
+ SCT_DIR=/home/runner/work/spinalcordtoolbox/spinalcordtoolbox
+ true
+ keep_default_path=
+ [[ ! '' =~ ^([Yy](es)?|[Nn]o?)$ ]]
+ print info 'SCT will be installed here: [/home/runner/work/spinalcordtoolbox/spinalcordtoolbox]'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mSCT will be installed here: [/home/runner/work/spinalcordtoolbox/spinalcordtoolbox]\033[0m\n'

SCT will be installed here: [/home/runner/work/spinalcordtoolbox/spinalcordtoolbox]

+ keep_default_path=yes
+ '[' -z yes ']'
+ [[ ! yes =~ ^([Yy](es)?|[Nn]o?)$ ]]
+ [[ yes =~ ^[Yy] ]]
+ break
+ space_regex='[[:space:]]+'
+ [[ /home/runner/work/spinalcordtoolbox/spinalcordtoolbox =~ [[:space:]]+ ]]
+ add_to_path=
+ [[ ! '' =~ ^([Yy](es)?|[Nn]o?)$ ]]
+ add_to_path=yes
+ '[' -z yes ']'
+ [[ ! yes =~ ^([Yy](es)?|[Nn]o?)$ ]]
+ mkdir -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox
+ [[ -d /home/runner/work/spinalcordtoolbox/spinalcordtoolbox ]]
+ [[ ! -w /home/runner/work/spinalcordtoolbox/spinalcordtoolbox ]]
+ [[ bash == \b\a\s\h ]]
+ DISPLAY_UPDATE_PATH='export PATH="/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin:$PATH"'
+ [[ /home/runner/work/spinalcordtoolbox/spinalcordtoolbox != \/\h\o\m\e\/\r\u\n\n\e\r\/\w\o\r\k\/\s\p\i\n\a\l\c\o\r\d\t\o\o\l\b\o\x\/\s\p\i\n\a\l\c\o\r\d\t\o\o\l\b\o\x ]]
+ print info 'Skipping copy of source files (source and destination folders are the same)'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mSkipping copy of source files (source and destination folders are the same)\033[0m\n'

Skipping copy of source files (source and destination folders are the same)

+ [[ -x /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin ]]
+ cd /home/runner/work/spinalcordtoolbox/spinalcordtoolbox
+ [[ ! -f spinalcordtoolbox/version.txt ]]
+ run rm -rf /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python
+ print code rm -rf /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python
+ type=code
+ shift
+ case "$type" in
+ echo -e '\n\033[0;34mrm -rf /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python\033[0m\n'

rm -rf /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python

+ rm -rf /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python
+ run mkdir -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python
+ print code mkdir -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python
+ type=code
+ shift
+ case "$type" in
+ echo -e '\n\033[0;34mmkdir -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python\033[0m\n'

mkdir -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python

+ mkdir -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python
+ print info 'Downloading Miniconda...'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mDownloading Miniconda...\033[0m\n'

Downloading Miniconda...

+ case $OS in
+ download /tmp/tmp.T01PPSHXCC/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
+ command -v wget
+ run wget -nv -O /tmp/tmp.T01PPSHXCC/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
+ print code wget -nv -O /tmp/tmp.T01PPSHXCC/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
+ type=code
+ shift
+ case "$type" in
+ echo -e '\n\033[0;34mwget -nv -O /tmp/tmp.T01PPSHXCC/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh\033[0m\n'

wget -nv -O /tmp/tmp.T01PPSHXCC/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

+ wget -nv -O /tmp/tmp.T01PPSHXCC/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
2021-11-19 20:23:20 URL:https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh [66709754/66709754] -> "/tmp/tmp.T01PPSHXCC/miniconda.sh" [1]
+ print info 'Installing Miniconda...'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mInstalling Miniconda...\033[0m\n'

Installing Miniconda...

+ run bash /tmp/tmp.T01PPSHXCC/miniconda.sh -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python -b -f
+ print code bash /tmp/tmp.T01PPSHXCC/miniconda.sh -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python -b -f
+ type=code
+ shift
+ case "$type" in
+ echo -e '\n\033[0;34mbash /tmp/tmp.T01PPSHXCC/miniconda.sh -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python -b -f\033[0m\n'

bash /tmp/tmp.T01PPSHXCC/miniconda.sh -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python -b -f

+ bash /tmp/tmp.T01PPSHXCC/miniconda.sh -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python -b -f
PREFIX=/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python
Unpacking payload ...

0%|          | 0/38 [00:00<?, ?it/s]
Extracting : libgomp-9.3.0-h5101ec6_17.conda:   0%|          | 0/38 [00:00<?, ?it/s]
Extracting : pycparser-2.20-py_2.conda:   3%|▎         | 1/38 [00:00<00:01, 30.87it/s]
Extracting : tzdata-2021a-h52ac0ba_0.conda:   5%|▌         | 2/38 [00:00<00:01, 32.44it/s]
Extracting : tk-8.6.10-hbc83047_0.conda:   8%|▊         | 3/38 [00:00<00:03, 10.22it/s]   
Extracting : tk-8.6.10-hbc83047_0.conda:  11%|█         | 4/38 [00:00<00:02, 13.61it/s]
Extracting : six-1.16.0-pyhd3eb1b0_0.conda:  11%|█         | 4/38 [00:00<00:02, 13.61it/s]
Extracting : yaml-0.2.5-h7b6447c_0.conda:  13%|█▎        | 5/38 [00:00<00:02, 13.61it/s]  
Extracting : libgcc-ng-9.3.0-h5101ec6_17.conda:  16%|█▌        | 6/38 [00:00<00:02, 13.61it/s]
Extracting : zlib-1.2.11-h7b6447c_3.conda:  18%|█▊        | 7/38 [00:00<00:02, 13.61it/s]     
Extracting : setuptools-52.0.0-py39h06a4308_0.conda:  21%|██        | 8/38 [00:00<00:02, 13.61it/s]
Extracting : chardet-4.0.0-py39h06a4308_1003.conda:  24%|██▎       | 9/38 [00:00<00:02, 13.61it/s] 
Extracting : cffi-1.14.6-py39h400218f_0.conda:  26%|██▋       | 10/38 [00:00<00:02, 13.61it/s]    
Extracting : ruamel_yaml-0.15.100-py39h27cfd23_0.conda:  29%|██▉       | 11/38 [00:00<00:01, 13.61it/s]
Extracting : libstdcxx-ng-9.3.0-hd4cf53a_17.conda:  32%|███▏      | 12/38 [00:00<00:01, 13.61it/s]     
Extracting : certifi-2021.5.30-py39h06a4308_0.conda:  34%|███▍      | 13/38 [00:00<00:01, 13.61it/s]
Extracting : urllib3-1.26.6-pyhd3eb1b0_1.conda:  37%|███▋      | 14/38 [00:00<00:01, 13.61it/s]     
Extracting : brotlipy-0.7.0-py39h27cfd23_1003.conda:  39%|███▉      | 15/38 [00:00<00:01, 13.61it/s]
Extracting : brotlipy-0.7.0-py39h27cfd23_1003.conda:  42%|████▏     | 16/38 [00:00<00:01, 18.01it/s]
Extracting : sqlite-3.36.0-hc218d9a_0.conda:  42%|████▏     | 16/38 [00:00<00:01, 18.01it/s]        
Extracting : readline-8.1-h27cfd23_0.conda:  45%|████▍     | 17/38 [00:00<00:01, 18.01it/s] 
Extracting : ld_impl_linux-64-2.35.1-h7274673_9.conda:  47%|████▋     | 18/38 [00:00<00:01, 18.01it/s]
Extracting : pyopenssl-20.0.1-pyhd3eb1b0_1.conda:  50%|█████     | 19/38 [00:00<00:01, 18.01it/s]     
Extracting : openssl-1.1.1k-h27cfd23_0.conda:  53%|█████▎    | 20/38 [00:00<00:00, 18.01it/s]    
Extracting : libffi-3.3-he6710b0_2.conda:  55%|█████▌    | 21/38 [00:00<00:00, 18.01it/s]    
Extracting : ncurses-6.2-he6710b0_1.conda:  58%|█████▊    | 22/38 [00:00<00:00, 18.01it/s]
Extracting : ncurses-6.2-he6710b0_1.conda:  61%|██████    | 23/38 [00:00<00:00, 20.40it/s]
Extracting : xz-5.2.5-h7b6447c_0.conda:  61%|██████    | 23/38 [00:00<00:00, 20.40it/s]   
Extracting : pip-21.1.3-py39h06a4308_0.conda:  63%|██████▎   | 24/38 [00:00<00:00, 20.40it/s]
Extracting : pysocks-1.7.1-py39h06a4308_0.conda:  66%|██████▌   | 25/38 [00:00<00:00, 20.40it/s]
Extracting : requests-2.25.1-pyhd3eb1b0_0.conda:  68%|██████▊   | 26/38 [00:00<00:00, 20.40it/s]
Extracting : ca-certificates-2021.7.5-h06a4308_1.conda:  71%|███████   | 27/38 [00:00<00:00, 20.40it/s]
Extracting : cryptography-3.4.7-py39hd23ed53_0.conda:  74%|███████▎  | 28/38 [00:00<00:00, 20.40it/s]  
Extracting : tqdm-4.61.2-pyhd3eb1b0_1.conda:  76%|███████▋  | 29/38 [00:00<00:00, 20.40it/s]         
Extracting : wheel-0.36.2-pyhd3eb1b0_0.conda:  79%|███████▉  | 30/38 [00:00<00:00, 20.40it/s]
Extracting : conda-package-handling-1.7.3-py39h27cfd23_1.conda:  82%|████████▏ | 31/38 [00:00<00:00, 20.40it/s]
Extracting : _libgcc_mutex-0.1-main.conda:  84%|████████▍ | 32/38 [00:00<00:00, 20.40it/s]                     
Extracting : pycosat-0.6.3-py39h27cfd23_0.conda:  87%|████████▋ | 33/38 [00:00<00:00, 20.40it/s]
Extracting : pycosat-0.6.3-py39h27cfd23_0.conda:  89%|████████▉ | 34/38 [00:00<00:00, 26.55it/s]
Extracting : python-3.9.5-h12debd9_4.tar.bz2:  89%|████████▉ | 34/38 [00:03<00:00, 26.55it/s]   
Extracting : _openmp_mutex-4.5-1_gnu.tar.bz2:  92%|█████████▏| 35/38 [00:03<00:00, 26.55it/s]
Extracting : idna-2.10-pyhd3eb1b0_0.tar.bz2:  95%|█████████▍| 36/38 [00:03<00:00, 26.55it/s] 
Extracting : conda-4.10.3-py39h06a4308_0.tar.bz2:  97%|█████████▋| 37/38 [00:03<00:00, 26.55it/s]
                                                                                                 
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

environment location: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python

added / updated specs:
    - _libgcc_mutex==0.1=main
    - _openmp_mutex==4.5=1_gnu
    - brotlipy==0.7.0=py39h27cfd23_1003
    - ca-certificates==2021.7.5=h06a4308_1
    - certifi==2021.5.30=py39h06a4308_0
    - cffi==1.14.6=py39h400218f_0
    - chardet==4.0.0=py39h06a4308_1003
    - conda-package-handling==1.7.3=py39h27cfd23_1
    - conda==4.10.3=py39h06a4308_0
    - cryptography==3.4.7=py39hd23ed53_0
    - idna==2.10=pyhd3eb1b0_0
    - ld_impl_linux-64==2.35.1=h7274673_9
    - libffi==3.3=he6710b0_2
    - libgcc-ng==9.3.0=h5101ec6_17
    - libgomp==9.3.0=h5101ec6_17
    - libstdcxx-ng==9.3.0=hd4cf53a_17
    - ncurses==6.2=he6710b0_1
    - openssl==1.1.1k=h27cfd23_0
    - pip==21.1.3=py39h06a4308_0
    - pycosat==0.6.3=py39h27cfd23_0
    - pycparser==2.20=py_2
    - pyopenssl==20.0.1=pyhd3eb1b0_1
    - pysocks==1.7.1=py39h06a4308_0
    - python==3.9.5=h12debd9_4
    - readline==8.1=h27cfd23_0
    - requests==2.25.1=pyhd3eb1b0_0
    - ruamel_yaml==0.15.100=py39h27cfd23_0
    - setuptools==52.0.0=py39h06a4308_0
    - six==1.16.0=pyhd3eb1b0_0
    - sqlite==3.36.0=hc218d9a_0
    - tk==8.6.10=hbc83047_0
    - tqdm==4.61.2=pyhd3eb1b0_1
    - tzdata==2021a=h52ac0ba_0
    - urllib3==1.26.6=pyhd3eb1b0_1
    - wheel==0.36.2=pyhd3eb1b0_0
    - xz==5.2.5=h7b6447c_0
    - yaml==0.2.5=h7b6447c_0
    - zlib==1.2.11=h7b6447c_3

The following NEW packages will be INSTALLED:

_libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  _openmp_mutex      pkgs/main/linux-64::_openmp_mutex-4.5-1_gnu
  brotlipy           pkgs/main/linux-64::brotlipy-0.7.0-py39h27cfd23_1003
  ca-certificates    pkgs/main/linux-64::ca-certificates-2021.7.5-h06a4308_1
  certifi            pkgs/main/linux-64::certifi-2021.5.30-py39h06a4308_0
  cffi               pkgs/main/linux-64::cffi-1.14.6-py39h400218f_0
  chardet            pkgs/main/linux-64::chardet-4.0.0-py39h06a4308_1003
  conda              pkgs/main/linux-64::conda-4.10.3-py39h06a4308_0
  conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.7.3-py39h27cfd23_1
  cryptography       pkgs/main/linux-64::cryptography-3.4.7-py39hd23ed53_0
  idna               pkgs/main/noarch::idna-2.10-pyhd3eb1b0_0
  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.35.1-h7274673_9
  libffi             pkgs/main/linux-64::libffi-3.3-he6710b0_2
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.3.0-h5101ec6_17
  libgomp            pkgs/main/linux-64::libgomp-9.3.0-h5101ec6_17
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.3.0-hd4cf53a_17
  ncurses            pkgs/main/linux-64::ncurses-6.2-he6710b0_1
  openssl            pkgs/main/linux-64::openssl-1.1.1k-h27cfd23_0
  pip                pkgs/main/linux-64::pip-21.1.3-py39h06a4308_0
  pycosat            pkgs/main/linux-64::pycosat-0.6.3-py39h27cfd23_0
  pycparser          pkgs/main/noarch::pycparser-2.20-py_2
  pyopenssl          pkgs/main/noarch::pyopenssl-20.0.1-pyhd3eb1b0_1
  pysocks            pkgs/main/linux-64::pysocks-1.7.1-py39h06a4308_0
  python             pkgs/main/linux-64::python-3.9.5-h12debd9_4
  readline           pkgs/main/linux-64::readline-8.1-h27cfd23_0
  requests           pkgs/main/noarch::requests-2.25.1-pyhd3eb1b0_0
  ruamel_yaml        pkgs/main/linux-64::ruamel_yaml-0.15.100-py39h27cfd23_0
  setuptools         pkgs/main/linux-64::setuptools-52.0.0-py39h06a4308_0
  six                pkgs/main/noarch::six-1.16.0-pyhd3eb1b0_0
  sqlite             pkgs/main/linux-64::sqlite-3.36.0-hc218d9a_0
  tk                 pkgs/main/linux-64::tk-8.6.10-hbc83047_0
  tqdm               pkgs/main/noarch::tqdm-4.61.2-pyhd3eb1b0_1
  tzdata             pkgs/main/noarch::tzdata-2021a-h52ac0ba_0
  urllib3            pkgs/main/noarch::urllib3-1.26.6-pyhd3eb1b0_1
  wheel              pkgs/main/noarch::wheel-0.36.2-pyhd3eb1b0_0
  xz                 pkgs/main/linux-64::xz-5.2.5-h7b6447c_0
  yaml               pkgs/main/linux-64::yaml-0.2.5-h7b6447c_0
  zlib               pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3

Preparing transaction: ...working... done
Executing transaction: ...working... done
installation finished.
+ find /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python -type f -exec touch '{}' +
+ print info 'Creating conda environment...'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mCreating conda environment...\033[0m\n'

Creating conda environment...

+ python/bin/conda create -y -n venv_sct python=3.7
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

environment location: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct

added / updated specs:
    - python=3.7

The following packages will be downloaded:

package                    |            build
    ---------------------------|-----------------
    ca-certificates-2021.10.26 |       h06a4308_2         115 KB
    certifi-2021.10.8          |   py37h06a4308_0         151 KB
    ncurses-6.3                |       h7f8727e_2         782 KB
    openssl-1.1.1l             |       h7f8727e_0         2.5 MB
    pip-21.2.2                 |   py37h06a4308_0         1.8 MB
    python-3.7.11              |       h12debd9_0        45.3 MB
    setuptools-58.0.4          |   py37h06a4308_0         775 KB
    tk-8.6.11                  |       h1ccaba5_0         3.0 MB
    wheel-0.37.0               |     pyhd3eb1b0_1          33 KB
    ------------------------------------------------------------
                                           Total:        54.5 MB

The following NEW packages will be INSTALLED:

_libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  _openmp_mutex      pkgs/main/linux-64::_openmp_mutex-4.5-1_gnu
  ca-certificates    pkgs/main/linux-64::ca-certificates-2021.10.26-h06a4308_2
  certifi            pkgs/main/linux-64::certifi-2021.10.8-py37h06a4308_0
  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.35.1-h7274673_9
  libffi             pkgs/main/linux-64::libffi-3.3-he6710b0_2
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.3.0-h5101ec6_17
  libgomp            pkgs/main/linux-64::libgomp-9.3.0-h5101ec6_17
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.3.0-hd4cf53a_17
  ncurses            pkgs/main/linux-64::ncurses-6.3-h7f8727e_2
  openssl            pkgs/main/linux-64::openssl-1.1.1l-h7f8727e_0
  pip                pkgs/main/linux-64::pip-21.2.2-py37h06a4308_0
  python             pkgs/main/linux-64::python-3.7.11-h12debd9_0
  readline           pkgs/main/linux-64::readline-8.1-h27cfd23_0
  setuptools         pkgs/main/linux-64::setuptools-58.0.4-py37h06a4308_0
  sqlite             pkgs/main/linux-64::sqlite-3.36.0-hc218d9a_0
  tk                 pkgs/main/linux-64::tk-8.6.11-h1ccaba5_0
  wheel              pkgs/main/noarch::wheel-0.37.0-pyhd3eb1b0_1
  xz                 pkgs/main/linux-64::xz-5.2.5-h7b6447c_0
  zlib               pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3

Downloading and Extracting Packages

wheel-0.37.0         | 33 KB     |            |   0% 
wheel-0.37.0         | 33 KB     | ####8      |  49% 
wheel-0.37.0         | 33 KB     | ########## | 100%

ncurses-6.3          | 782 KB    |            |   0% 
ncurses-6.3          | 782 KB    | 8          |   8% 
ncurses-6.3          | 782 KB    | ########## | 100% 
ncurses-6.3          | 782 KB    | ########## | 100%

tk-8.6.11            | 3.0 MB    |            |   0% 
tk-8.6.11            | 3.0 MB    | 9          |   9% 
tk-8.6.11            | 3.0 MB    | ######3    |  64% 
tk-8.6.11            | 3.0 MB    | ########## | 100% 
tk-8.6.11            | 3.0 MB    | ########## | 100%

setuptools-58.0.4    | 775 KB    |            |   0% 
setuptools-58.0.4    | 775 KB    | ########## | 100% 
setuptools-58.0.4    | 775 KB    | ########## | 100%

ca-certificates-2021 | 115 KB    |            |   0% 
ca-certificates-2021 | 115 KB    | ########## | 100%

openssl-1.1.1l       | 2.5 MB    |            |   0% 
openssl-1.1.1l       | 2.5 MB    | #######2   |  72% 
openssl-1.1.1l       | 2.5 MB    | ########## | 100%

pip-21.2.2           | 1.8 MB    |            |   0% 
pip-21.2.2           | 1.8 MB    | ########2  |  82% 
pip-21.2.2           | 1.8 MB    | ########## | 100%

certifi-2021.10.8    | 151 KB    |            |   0% 
certifi-2021.10.8    | 151 KB    | ########## | 100%

python-3.7.11        | 45.3 MB   |            |   0% 
python-3.7.11        | 45.3 MB   | 1          |   2% 
python-3.7.11        | 45.3 MB   | #2         |  13% 
python-3.7.11        | 45.3 MB   | #9         |  20% 
python-3.7.11        | 45.3 MB   | ##7        |  27% 
python-3.7.11        | 45.3 MB   | ###3       |  34% 
python-3.7.11        | 45.3 MB   | ###9       |  40% 
python-3.7.11        | 45.3 MB   | #####4     |  55% 
python-3.7.11        | 45.3 MB   | #######1   |  71% 
python-3.7.11        | 45.3 MB   | ########6  |  86% 
python-3.7.11        | 45.3 MB   | ########## | 100% 
python-3.7.11        | 45.3 MB   | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
#
# To activate this environment, use
#
#     $ conda activate venv_sct
#
# To deactivate an active environment, use
#
#     $ conda deactivate

+ find /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python -type f -exec touch '{}' +
+ perl -pi -e 's/^ENABLE_USER_SITE.*$/ENABLE_USER_SITE = False/' /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/lib/python3.7/site.py
+ source python/etc/profile.d/conda.sh
++ export CONDA_EXE=/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/bin/conda
++ CONDA_EXE=/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/bin/conda
++ export _CE_M=
++ _CE_M=
++ export _CE_CONDA=
++ _CE_CONDA=
++ export CONDA_PYTHON_EXE=/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/bin/python
++ CONDA_PYTHON_EXE=/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/bin/python
++ '[' -z '' ']'
++ export CONDA_SHLVL=0
++ CONDA_SHLVL=0
++ '[' -n '' ']'
++++ dirname /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/bin/conda
+++ dirname /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/bin
++ PATH=/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/condabin:/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin:/home/runner/.local/bin:/opt/pipx_bin:/usr/share/rust/.cargo/bin:/home/runner/.config/composer/vendor/bin:/usr/local/.ghcup/bin:/home/runner/.dotnet/tools:/snap/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
++ export PATH
++ '[' -z '' ']'
++ PS1=
+ set +u
+ conda activate venv_sct
+ local cmd=activate
+ case "$cmd" in
+ __conda_activate activate venv_sct
+ '[' -n '' ']'
+ local ask_conda
++ PS1=
++ __conda_exe shell.posix activate venv_sct
++ __add_sys_prefix_to_path
++ '[' -n '' ']'
+++ dirname /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/bin/conda
++ SYSP=/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/bin
+++ dirname /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/bin
++ SYSP=/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python
++ '[' -n '' ']'
++ PATH=/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/bin:/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/condabin:/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin:/home/runner/.local/bin:/opt/pipx_bin:/usr/share/rust/.cargo/bin:/home/runner/.config/composer/vendor/bin:/usr/local/.ghcup/bin:/home/runner/.dotnet/tools:/snap/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
++ export PATH
++ /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/bin/conda shell.posix activate venv_sct
+ ask_conda='PS1='\''(venv_sct) '\''
export PATH='\''/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin:/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/condabin:/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin:/home/runner/.local/bin:/opt/pipx_bin:/usr/share/rust/.cargo/bin:/home/runner/.config/composer/vendor/bin:/usr/local/.ghcup/bin:/home/runner/.dotnet/tools:/snap/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin'\''
export CONDA_PREFIX='\''/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct'\''
export CONDA_SHLVL='\''1'\''
export CONDA_DEFAULT_ENV='\''venv_sct'\''
export CONDA_PROMPT_MODIFIER='\''(venv_sct) '\''
export CONDA_EXE='\''/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/bin/conda'\''
export _CE_M='\'''\''
export _CE_CONDA='\'''\''
export CONDA_PYTHON_EXE='\''/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/bin/python'\'''
+ eval 'PS1='\''(venv_sct) '\''
export PATH='\''/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin:/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/condabin:/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin:/home/runner/.local/bin:/opt/pipx_bin:/usr/share/rust/.cargo/bin:/home/runner/.config/composer/vendor/bin:/usr/local/.ghcup/bin:/home/runner/.dotnet/tools:/snap/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin'\''
export CONDA_PREFIX='\''/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct'\''
export CONDA_SHLVL='\''1'\''
export CONDA_DEFAULT_ENV='\''venv_sct'\''
export CONDA_PROMPT_MODIFIER='\''(venv_sct) '\''
export CONDA_EXE='\''/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/bin/conda'\''
export _CE_M='\'''\''
export _CE_CONDA='\'''\''
export CONDA_PYTHON_EXE='\''/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/bin/python'\'''
++ PS1='(venv_sct) '
++ export PATH=/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin:/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/condabin:/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin:/home/runner/.local/bin:/opt/pipx_bin:/usr/share/rust/.cargo/bin:/home/runner/.config/composer/vendor/bin:/usr/local/.ghcup/bin:/home/runner/.dotnet/tools:/snap/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
++ PATH=/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin:/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/condabin:/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin:/home/runner/.local/bin:/opt/pipx_bin:/usr/share/rust/.cargo/bin:/home/runner/.config/composer/vendor/bin:/usr/local/.ghcup/bin:/home/runner/.dotnet/tools:/snap/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
++ export CONDA_PREFIX=/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct
++ CONDA_PREFIX=/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct
++ export CONDA_SHLVL=1
++ CONDA_SHLVL=1
++ export CONDA_DEFAULT_ENV=venv_sct
++ CONDA_DEFAULT_ENV=venv_sct
++ export 'CONDA_PROMPT_MODIFIER=(venv_sct) '
++ CONDA_PROMPT_MODIFIER='(venv_sct) '
++ export CONDA_EXE=/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/bin/conda
++ CONDA_EXE=/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/bin/conda
++ export _CE_M=
++ _CE_M=
++ export _CE_CONDA=
++ _CE_CONDA=
++ export CONDA_PYTHON_EXE=/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/bin/python
++ CONDA_PYTHON_EXE=/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/bin/python
+ __conda_hashr
+ '[' -n '' ']'
+ '[' -n '' ']'
+ hash -r
+ set -u
+ print info 'Validating that conda environment can be activated...'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mValidating that conda environment can be activated...\033[0m\n'

Validating that conda environment can be activated...

+++ command -v python/envs/venv_sct/bin/python
++ realpath python/envs/venv_sct/bin/python
+ EXPECTED_PYTHON=/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/python3.7
+++ command -v python
++ realpath /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/python
+ ACTUAL_PYTHON=/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/python3.7
+ '[' /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/python3.7 '!=' /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/python3.7 ']'
+ python -m pip install -U 'pip!=21.2.*'
Collecting pip!=21.2.*
  Downloading pip-21.3.1-py3-none-any.whl (1.7 MB)
Installing collected packages: pip
  Attempting uninstall: pip
    Found existing installation: pip 21.2.2
    Uninstalling pip-21.2.2:
      Successfully uninstalled pip-21.2.2
Successfully installed pip-21.3.1
+ print info 'Installing Python dependencies...'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mInstalling Python dependencies...\033[0m\n'

Installing Python dependencies...

+ [[ -f requirements-freeze.txt ]]
+ print info 'Using requirements.txt (git installation)'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mUsing requirements.txt (git installation)\033[0m\n'

Using requirements.txt (git installation)

+ REQUIREMENTS_FILE=requirements.txt
+ pip install -r requirements.txt
Looking in links: https://download.pytorch.org/whl/cpu/torch_stable.html
Ignoring torch: markers 'sys_platform == "darwin"' don't match your environment
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  Downloading https://download.pytorch.org/whl/cpu/torch-1.5.0%2Bcpu-cp37-cp37m-linux_x86_64.whl (127.3 MB)
Collecting torchvision==0.6.0+cpu
  Downloading https://download.pytorch.org/whl/cpu/torchvision-0.6.0%2Bcpu-cp37-cp37m-linux_x86_64.whl (5.7 MB)
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  Downloading future-0.18.2.tar.gz (829 kB)
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Collecting pillow>=4.1.1
  Downloading Pillow-8.4.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB)
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Collecting loguru~=0.5
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Requirement already satisfied: certifi>=2017.4.17 in ./python/envs/venv_sct/lib/python3.7/site-packages (from requests->-r requirements.txt (line 21)) (2021.10.8)
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Collecting wrapt>=1.11.1
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Requirement already satisfied: wheel>=0.26 in ./python/envs/venv_sct/lib/python3.7/site-packages (from tensorflow~=1.15.0->-r requirements.txt (line 26)) (0.37.0)
INFO: pip is looking at multiple versions of scikit-learn to determine which version is compatible with other requirements. This could take a while.
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  Downloading scikit_learn-1.0-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (23.1 MB)
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  Downloading scikit_image-0.18.2-cp37-cp37m-manylinux1_x86_64.whl (29.2 MB)
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  Downloading scipy-1.7.1-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (28.5 MB)
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Collecting pandas
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Collecting matplotlib
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  Preparing metadata (setup.py): finished with status 'done'
Collecting pytest-ordering
  Downloading pytest_ordering-0.6-py3-none-any.whl (4.6 kB)
Collecting identify>=1.0.0
  Downloading identify-2.4.0-py2.py3-none-any.whl (98 kB)
Collecting virtualenv>=20.0.8
  Downloading virtualenv-20.10.0-py2.py3-none-any.whl (5.6 MB)
Collecting nodeenv>=0.11.1
  Downloading nodeenv-1.6.0-py2.py3-none-any.whl (21 kB)
Collecting cfgv>=2.0.0
  Downloading cfgv-3.3.1-py2.py3-none-any.whl (7.3 kB)
Collecting tensorboard
  Downloading tensorboard-1.15.0-py3-none-any.whl (3.8 MB)
Collecting grpcio>=1.8.6
  Downloading grpcio-1.42.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.0 MB)
Collecting numpy
  Downloading numpy-1.18.5-cp37-cp37m-manylinux1_x86_64.whl (20.1 MB)
Collecting gast==0.2.2
  Downloading gast-0.2.2.tar.gz (10 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting google-pasta>=0.1.6
  Downloading google_pasta-0.2.0-py3-none-any.whl (57 kB)
Requirement already satisfied: setuptools>=41.0.0 in ./python/envs/venv_sct/lib/python3.7/site-packages (from tensorboard->ivadomed->-r requirements.txt (line 7)) (58.0.4)
Collecting werkzeug>=0.11.15
  Downloading Werkzeug-2.0.2-py3-none-any.whl (288 kB)
Collecting markdown>=2.6.8
  Downloading Markdown-3.3.6-py3-none-any.whl (97 kB)
Collecting cryptography>=1.3.4
  Downloading cryptography-35.0.0-cp36-abi3-manylinux_2_24_x86_64.whl (3.5 MB)
Collecting pyOpenSSL>=0.14
  Downloading pyOpenSSL-21.0.0-py2.py3-none-any.whl (55 kB)
Collecting mock>=2.0.0
  Downloading mock-4.0.3-py3-none-any.whl (28 kB)
Collecting tomli
  Using cached tomli-1.2.2-py3-none-any.whl (12 kB)
Collecting cffi>=1.12
  Downloading cffi-1.15.0-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (427 kB)
Collecting dictdiffer
  Downloading dictdiffer-0.9.0-py2.py3-none-any.whl (16 kB)
Collecting click
  Downloading click-8.0.3-py3-none-any.whl (97 kB)
Collecting zipp>=0.5
  Downloading zipp-3.6.0-py3-none-any.whl (5.3 kB)
Collecting typing-extensions>=3.6.4
  Downloading typing_extensions-4.0.0-py3-none-any.whl (22 kB)
Collecting formulaic~=0.2.4
  Downloading formulaic-0.2.4-py3-none-any.whl (55 kB)
Collecting sqlalchemy<1.4.0.dev0
  Downloading SQLAlchemy-1.3.24-cp37-cp37m-manylinux2010_x86_64.whl (1.3 MB)
Collecting num2words
  Downloading num2words-0.5.10-py3-none-any.whl (101 kB)
Collecting bids-validator
  Downloading bids_validator-1.8.4-py2.py3-none-any.whl (19 kB)
Collecting docutils
  Downloading docutils-0.18-py2.py3-none-any.whl (569 kB)
Collecting jsonpointer
  Downloading jsonpointer-2.2-py2.py3-none-any.whl (7.5 kB)
Collecting pycparser
  Downloading pycparser-2.21-py2.py3-none-any.whl (118 kB)
Collecting interface-meta>=1.2
  Downloading interface_meta-1.2.4-py2.py3-none-any.whl (14 kB)
Collecting distlib<1,>=0.3.1
  Downloading distlib-0.3.3-py2.py3-none-any.whl (496 kB)
Collecting backports.entry-points-selectable>=1.0.4
  Downloading backports.entry_points_selectable-1.1.1-py2.py3-none-any.whl (6.2 kB)
Collecting filelock<4,>=3.2
  Downloading filelock-3.4.0-py3-none-any.whl (9.8 kB)
Collecting platformdirs<3,>=2
  Downloading platformdirs-2.4.0-py3-none-any.whl (14 kB)
Collecting docopt>=0.6.2
  Downloading docopt-0.6.2.tar.gz (25 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Building wheels for collected packages: colored, gast, requirements-parser, transforms3d, pytest-console-scripts, termcolor, future, sphinx-jsonschema, docopt
  Building wheel for colored (setup.py): started
  Building wheel for colored (setup.py): finished with status 'done'
  Created wheel for colored: filename=colored-1.4.3-py3-none-any.whl size=14341 sha256=18630b6266cd86b19346eaa06bb91232b7b23504b00938f42ef4142491b6bb12
  Stored in directory: /home/runner/.cache/pip/wheels/4a/f6/00/835e81851bc345428a253721c8bdad0062721dfb861bc6e752
  Building wheel for gast (setup.py): started
  Building wheel for gast (setup.py): finished with status 'done'
  Created wheel for gast: filename=gast-0.2.2-py3-none-any.whl size=7554 sha256=bc99c1b16595562d5d90644794440a4ed5ab0bb7157bcd5c1010260afbdd3ab9
  Stored in directory: /home/runner/.cache/pip/wheels/21/7f/02/420f32a803f7d0967b48dd823da3f558c5166991bfd204eef3
  Building wheel for requirements-parser (setup.py): started
  Building wheel for requirements-parser (setup.py): finished with status 'done'
  Created wheel for requirements-parser: filename=requirements_parser-0.2.0-py3-none-any.whl size=7688 sha256=ece62aad7a52f9ee3f0e3241c960ba9e64fbe7f5e298e1b575be5a0e9dc81f33
  Stored in directory: /home/runner/.cache/pip/wheels/40/e4/ca/8af24ee94c3863d620d6a52793d82930f4d1d3515a5121d495
  Building wheel for transforms3d (setup.py): started
  Building wheel for transforms3d (setup.py): finished with status 'done'
  Created wheel for transforms3d: filename=transforms3d-0.3.1-py3-none-any.whl size=59373 sha256=1cbe628447f3f17d516fcbbacd8fd460f5b544003a9dc31291ce54a7871beb98
  Stored in directory: /home/runner/.cache/pip/wheels/b5/b7/93/8985551f83720ce37548a5b543c75380bb707955a9c2c5d28c
  Building wheel for pytest-console-scripts (setup.py): started
  Building wheel for pytest-console-scripts (setup.py): finished with status 'done'
  Created wheel for pytest-console-scripts: filename=pytest_console_scripts-1.2.1-py3-none-any.whl size=9138 sha256=7bdfb14f9b49ca714f32eb00684ab1b7a693999b6e127aa1194d38c696288d03
  Stored in directory: /home/runner/.cache/pip/wheels/0c/8d/86/30a5d0717aa57680c1c7a42fabc750923abf5e2574515dff19
  Building wheel for termcolor (setup.py): started
  Building wheel for termcolor (setup.py): finished with status 'done'
  Created wheel for termcolor: filename=termcolor-1.1.0-py3-none-any.whl size=4847 sha256=b4472c415844498203c51f52b4a7aecf9ef9295e967ac6c35586d2a8966fcf26
  Stored in directory: /home/runner/.cache/pip/wheels/3f/e3/ec/8a8336ff196023622fbcb36de0c5a5c218cbb24111d1d4c7f2
  Building wheel for future (setup.py): started
  Building wheel for future (setup.py): finished with status 'done'
  Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491070 sha256=97aa3373800c0af56b8b115fe43b2f0a08940bf2fd62533cf1c2723e6a39548d
  Stored in directory: /home/runner/.cache/pip/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0
  Building wheel for sphinx-jsonschema (setup.py): started
  Building wheel for sphinx-jsonschema (setup.py): finished with status 'done'
  Created wheel for sphinx-jsonschema: filename=sphinx_jsonschema-1.17.1-py3-none-any.whl size=14000 sha256=f0b016d511724fe3b9eb6ac4a1ef90524a6aac19d3571432e51f236e4fb06d2d
  Stored in directory: /home/runner/.cache/pip/wheels/4d/d8/24/17b5acc06ae865851a662e96babab02d34f025665d7650540d
  Building wheel for docopt (setup.py): started
  Building wheel for docopt (setup.py): finished with status 'done'
  Created wheel for docopt: filename=docopt-0.6.2-py2.py3-none-any.whl size=13724 sha256=9571dc77bf63748c7939f6ec2736c873f0d7441feed664c8e695ed65e795a983
  Stored in directory: /home/runner/.cache/pip/wheels/72/b0/3f/1d95f96ff986c7dfffe46ce2be4062f38ebd04b506c77c81b9
Successfully built colored gast requirements-parser transforms3d pytest-console-scripts termcolor future sphinx-jsonschema docopt
Installing collected packages: six, zipp, typing-extensions, pytz, python-dateutil, pyparsing, numpy, wrapt, tomli, scipy, pycparser, pandas, packaging, interface-meta, importlib-metadata, docopt, astor, urllib3, toml, sqlalchemy, setuptools-scm, py, pluggy, platformdirs, pillow, num2words, nibabel, kiwisolver, iniconfig, idna, future, formulaic, fonttools, filelock, distlib, cycler, click, charset-normalizer, cffi, bids-validator, backports.entry-points-selectable, attrs, werkzeug, virtualenv, torch, tifffile, threadpoolctl, requests, pyyaml, PyWavelets, pytest, pybids, protobuf, nodeenv, networkx, mock, matplotlib, markdown, jsonpointer, joblib, imageio, identify, h5py, grpcio, docutils, dictdiffer, cryptography, coverage, cfgv, absl-py, tqdm, torchvision, termcolor, tensorflow-estimator, tensorboard, sphinx-jsonschema, seaborn, scikit-learn, scikit-image, pytest-ordering, pytest-console-scripts, PyQt5-sip, pyOpenSSL, pre-commit, opt-einsum, onnxruntime, keras-preprocessing, keras-applications, google-pasta, gast, csv-diff, bids-neuropoly, xlwt, wquantiles, transforms3d, tensorflow, requirements-parser, raven, pytest-cov, pyqt5, psutil, Keras, ivadomed, dipy, colored
Successfully installed Keras-2.3.1 PyQt5-sip-4.19.19 PyWavelets-1.2.0 absl-py-1.0.0 astor-0.8.1 attrs-21.2.0 backports.entry-points-selectable-1.1.1 bids-neuropoly-0.2 bids-validator-1.8.4 cffi-1.15.0 cfgv-3.3.1 charset-normalizer-2.0.7 click-8.0.3 colored-1.4.3 coverage-6.1.2 cryptography-35.0.0 csv-diff-1.1 cycler-0.11.0 dictdiffer-0.9.0 dipy-1.4.1 distlib-0.3.3 docopt-0.6.2 docutils-0.18 filelock-3.4.0 fonttools-4.28.1 formulaic-0.2.4 future-0.18.2 gast-0.2.2 google-pasta-0.2.0 grpcio-1.42.0 h5py-2.10.0 identify-2.4.0 idna-3.3 imageio-2.11.0 importlib-metadata-4.8.2 iniconfig-1.1.1 interface-meta-1.2.4 ivadomed-2.7.4 joblib-1.1.0 jsonpointer-2.2 keras-applications-1.0.8 keras-preprocessing-1.1.2 kiwisolver-1.3.2 markdown-3.3.6 matplotlib-3.5.0 mock-4.0.3 networkx-2.6.3 nibabel-3.2.1 nodeenv-1.6.0 num2words-0.5.10 numpy-1.18.5 onnxruntime-1.4.0 opt-einsum-3.3.0 packaging-21.3 pandas-1.3.4 pillow-8.4.0 platformdirs-2.4.0 pluggy-1.0.0 pre-commit-2.10.1 protobuf-3.19.1 psutil-5.8.0 py-1.11.0 pyOpenSSL-21.0.0 pybids-0.14.0 pycparser-2.21 pyparsing-3.0.6 pyqt5-5.11.3 pytest-6.2.5 pytest-console-scripts-1.2.1 pytest-cov-3.0.0 pytest-ordering-0.6 python-dateutil-2.8.2 pytz-2021.3 pyyaml-6.0 raven-6.10.0 requests-2.26.0 requirements-parser-0.2.0 scikit-image-0.18.3 scikit-learn-1.0.1 scipy-1.7.2 seaborn-0.11.2 setuptools-scm-6.3.2 six-1.16.0 sphinx-jsonschema-1.17.1 sqlalchemy-1.3.24 tensorboard-1.15.0 tensorflow-1.15.5 tensorflow-estimator-1.15.1 termcolor-1.1.0 threadpoolctl-3.0.0 tifffile-2021.11.2 toml-0.10.2 tomli-1.2.2 torch-1.5.0+cpu torchvision-0.6.0+cpu tqdm-4.62.3 transforms3d-0.3.1 typing-extensions-4.0.0 urllib3-1.26.7 virtualenv-20.10.0 werkzeug-2.0.2 wquantiles-0.6 wrapt-1.13.3 xlwt-1.3.0 zipp-3.6.0
+ print info 'Installing spinalcordtoolbox...'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mInstalling spinalcordtoolbox...\033[0m\n'

Installing spinalcordtoolbox...

+ pip install -e .
Obtaining file:///home/runner/work/spinalcordtoolbox/spinalcordtoolbox
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Installing collected packages: spinalcordtoolbox
  Running setup.py develop for spinalcordtoolbox
Successfully installed spinalcordtoolbox-dev
+ grep -q 'The TensorFlow library was compiled to use'
+ python3 -c 'import keras; print(keras.__version__)'
+ print info 'Creating launchers for Python scripts...'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mCreating launchers for Python scripts...\033[0m\n'

Creating launchers for Python scripts...

+ mkdir -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/isct_convert_binary_to_trilinear /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/isct_minc2volume-viewer /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/isct_test_ants /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_analyze_lesion /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_analyze_texture /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_apply_transfo /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_check_dependencies /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_compute_ernst_angle /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_compute_hausdorff_distance /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_compute_mscc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_compute_mtr /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_compute_mtsat /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_compute_snr /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_concat_transfo /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_convert /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_create_mask /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_crop_image /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_deepseg /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_deepseg_gm /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_deepseg_lesion /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_deepseg_sc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_denoising_onlm /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_detect_pmj /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_dice_coefficient /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_dmri_compute_bvalue /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_dmri_compute_dti /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_dmri_concat_b0_and_dwi /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_dmri_concat_bvals /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_dmri_concat_bvecs /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_dmri_display_bvecs /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_dmri_moco /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_dmri_separate_b0_and_dwi /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_dmri_transpose_bvecs /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_download_data /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_extract_metric /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_flatten_sagittal /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_fmri_compute_tsnr /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_fmri_moco /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_get_centerline /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_image /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_label_utils /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_label_vertebrae /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_maths /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_merge_images /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_process_segmentation /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_propseg /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_qc /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_register_multimodal /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_register_to_template /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_resample /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_run_batch /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_smooth_spinalcord /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_straighten_spinalcord /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_version /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ for file in "$SCT_DIR"/python/envs/venv_sct/bin/*sct*
+ cp /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/sct_warp_template /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin/
+ export PATH=/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin:/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin:/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/condabin:/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin:/home/runner/.local/bin:/opt/pipx_bin:/usr/share/rust/.cargo/bin:/home/runner/.config/composer/vendor/bin:/usr/local/.ghcup/bin:/home/runner/.dotnet/tools:/snap/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
+ PATH=/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin:/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin:/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/condabin:/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin:/home/runner/.local/bin:/opt/pipx_bin:/usr/share/rust/.cargo/bin:/home/runner/.config/composer/vendor/bin:/usr/local/.ghcup/bin:/home/runner/.dotnet/tools:/snap/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
+ [[ -n '' ]]
+ print info 'Installing binaries...'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mInstalling binaries...\033[0m\n'

Installing binaries...

+ run sct_download_data -d binaries_linux -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin -k
+ print code sct_download_data -d binaries_linux -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin -k
+ type=code
+ shift
+ case "$type" in
+ echo -e '\n\033[0;34msct_download_data -d binaries_linux -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin -k\033[0m\n'

sct_download_data -d binaries_linux -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin -k

+ sct_download_data -d binaries_linux -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin -k

--
Spinal Cord Toolbox (git-HEAD-13b65d231ba9f68e78d1b1c13c996d2fbc1c6ec1)

sct_download_data -d binaries_linux -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin -k
--

Trying URL: https://osf.io/cs6zt/?action=download
Downloading: 20200801_sct_binaries_linux.tar.gz
Creating temporary folder (/tmp/sct-20211119202538.288555-6876ec48)
Unzip data to: /tmp/sct-20211119202538.288555-6876ec48
Removing temporary folders...
Done!

+ print info 'All requirements installed!'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mAll requirements installed!\033[0m\n'

All requirements installed!

+ [[ -n '' ]]
+ print info 'Installing data...'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mInstalling data...\033[0m\n'

Installing data...

+ run rm -rf /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data
+ print code rm -rf /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data
+ type=code
+ shift
+ case "$type" in
+ echo -e '\n\033[0;34mrm -rf /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data\033[0m\n'

rm -rf /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data

+ rm -rf /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data
+ run mkdir -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data
+ print code mkdir -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data
+ type=code
+ shift
+ case "$type" in
+ echo -e '\n\033[0;34mmkdir -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data\033[0m\n'

mkdir -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data

+ mkdir -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data
+ for data in PAM50 gm_model optic_models pmj_models deepseg_sc_models deepseg_gm_models deepseg_lesion_models c2c3_disc_models
+ run sct_download_data -d PAM50 -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50
+ print code sct_download_data -d PAM50 -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50
+ type=code
+ shift
+ case "$type" in
+ echo -e '\n\033[0;34msct_download_data -d PAM50 -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50\033[0m\n'

sct_download_data -d PAM50 -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50

+ sct_download_data -d PAM50 -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50

--
Spinal Cord Toolbox (git-HEAD-13b65d231ba9f68e78d1b1c13c996d2fbc1c6ec1)

sct_download_data -d PAM50 -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50
--

Removing existing destination folder '/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50'
Trying URL: https://github.com/sct-data/PAM50/releases/download/r20201104/PAM50-r20201104.zip
Downloading: PAM50-r20201104.zip
Creating temporary folder (/tmp/sct-20211119202542.233490-resxhtfc)
Unzip data to: /tmp/sct-20211119202542.233490-resxhtfc
Removing temporary folders...
Done!

+ for data in PAM50 gm_model optic_models pmj_models deepseg_sc_models deepseg_gm_models deepseg_lesion_models c2c3_disc_models
+ run sct_download_data -d gm_model -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/gm_model
+ print code sct_download_data -d gm_model -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/gm_model
+ type=code
+ shift
+ case "$type" in
+ echo -e '\n\033[0;34msct_download_data -d gm_model -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/gm_model\033[0m\n'

sct_download_data -d gm_model -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/gm_model

+ sct_download_data -d gm_model -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/gm_model

--
Spinal Cord Toolbox (git-HEAD-13b65d231ba9f68e78d1b1c13c996d2fbc1c6ec1)

sct_download_data -d gm_model -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/gm_model
--

Removing existing destination folder '/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/gm_model'
Trying URL: https://osf.io/ugscu/?action=download
Downloading: 20160922_gm_model.zip
Creating temporary folder (/tmp/sct-20211119202544.813556-47rk4gi2)
Unzip data to: /tmp/sct-20211119202544.813556-47rk4gi2
Removing temporary folders...
Done!

+ for data in PAM50 gm_model optic_models pmj_models deepseg_sc_models deepseg_gm_models deepseg_lesion_models c2c3_disc_models
+ run sct_download_data -d optic_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/optic_models
+ print code sct_download_data -d optic_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/optic_models
+ type=code
+ shift
+ case "$type" in
+ echo -e '\n\033[0;34msct_download_data -d optic_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/optic_models\033[0m\n'

sct_download_data -d optic_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/optic_models

+ sct_download_data -d optic_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/optic_models

--
Spinal Cord Toolbox (git-HEAD-13b65d231ba9f68e78d1b1c13c996d2fbc1c6ec1)

sct_download_data -d optic_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/optic_models
--

Removing existing destination folder '/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/optic_models'
Trying URL: https://github.com/sct-data/optic_models/releases/download/r20170413/20170413_optic_models.zip
Downloading: 20170413_optic_models.zip
Creating temporary folder (/tmp/sct-20211119202545.579859-utych52p)
Unzip data to: /tmp/sct-20211119202545.579859-utych52p
Removing temporary folders...
Done!

+ for data in PAM50 gm_model optic_models pmj_models deepseg_sc_models deepseg_gm_models deepseg_lesion_models c2c3_disc_models
+ run sct_download_data -d pmj_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/pmj_models
+ print code sct_download_data -d pmj_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/pmj_models
+ type=code
+ shift
+ case "$type" in
+ echo -e '\n\033[0;34msct_download_data -d pmj_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/pmj_models\033[0m\n'

sct_download_data -d pmj_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/pmj_models

+ sct_download_data -d pmj_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/pmj_models

--
Spinal Cord Toolbox (git-HEAD-13b65d231ba9f68e78d1b1c13c996d2fbc1c6ec1)

sct_download_data -d pmj_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/pmj_models
--

Removing existing destination folder '/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/pmj_models'
Trying URL: https://github.com/sct-data/pmj_models/releases/download/r20170922/20170922_pmj_models.zip
Downloading: 20170922_pmj_models.zip
Creating temporary folder (/tmp/sct-20211119202546.221617-76658p4n)
Unzip data to: /tmp/sct-20211119202546.221617-76658p4n
Removing temporary folders...
Done!

+ for data in PAM50 gm_model optic_models pmj_models deepseg_sc_models deepseg_gm_models deepseg_lesion_models c2c3_disc_models
+ run sct_download_data -d deepseg_sc_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/deepseg_sc_models
+ print code sct_download_data -d deepseg_sc_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/deepseg_sc_models
+ type=code
+ shift
+ case "$type" in
+ echo -e '\n\033[0;34msct_download_data -d deepseg_sc_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/deepseg_sc_models\033[0m\n'

sct_download_data -d deepseg_sc_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/deepseg_sc_models

+ sct_download_data -d deepseg_sc_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/deepseg_sc_models

--
Spinal Cord Toolbox (git-HEAD-13b65d231ba9f68e78d1b1c13c996d2fbc1c6ec1)

sct_download_data -d deepseg_sc_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/deepseg_sc_models
--

Removing existing destination folder '/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/deepseg_sc_models'
Trying URL: https://github.com/sct-data/deepseg_sc_models/releases/download/r20180610/20180610_deepseg_sc_models.zip
Downloading: 20180610_deepseg_sc_models.zip
Creating temporary folder (/tmp/sct-20211119202547.802493-pdxpflqq)
Unzip data to: /tmp/sct-20211119202547.802493-pdxpflqq
Removing temporary folders...
Done!

+ for data in PAM50 gm_model optic_models pmj_models deepseg_sc_models deepseg_gm_models deepseg_lesion_models c2c3_disc_models
+ run sct_download_data -d deepseg_gm_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/deepseg_gm_models
+ print code sct_download_data -d deepseg_gm_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/deepseg_gm_models
+ type=code
+ shift
+ case "$type" in
+ echo -e '\n\033[0;34msct_download_data -d deepseg_gm_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/deepseg_gm_models\033[0m\n'

sct_download_data -d deepseg_gm_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/deepseg_gm_models

+ sct_download_data -d deepseg_gm_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/deepseg_gm_models

--
Spinal Cord Toolbox (git-HEAD-13b65d231ba9f68e78d1b1c13c996d2fbc1c6ec1)

sct_download_data -d deepseg_gm_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/deepseg_gm_models
--

Removing existing destination folder '/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/deepseg_gm_models'
Trying URL: https://github.com/sct-data/deepseg_gm_models/releases/download/r20180205/20180205_deepseg_gm_models.zip
Downloading: 20180205_deepseg_gm_models.zip
Creating temporary folder (/tmp/sct-20211119202549.209853-xr9egjth)
Unzip data to: /tmp/sct-20211119202549.209853-xr9egjth
Removing temporary folders...
Done!

+ for data in PAM50 gm_model optic_models pmj_models deepseg_sc_models deepseg_gm_models deepseg_lesion_models c2c3_disc_models
+ run sct_download_data -d deepseg_lesion_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/deepseg_lesion_models
+ print code sct_download_data -d deepseg_lesion_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/deepseg_lesion_models
+ type=code
+ shift
+ case "$type" in
+ echo -e '\n\033[0;34msct_download_data -d deepseg_lesion_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/deepseg_lesion_models\033[0m\n'

sct_download_data -d deepseg_lesion_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/deepseg_lesion_models

+ sct_download_data -d deepseg_lesion_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/deepseg_lesion_models

--
Spinal Cord Toolbox (git-HEAD-13b65d231ba9f68e78d1b1c13c996d2fbc1c6ec1)

sct_download_data -d deepseg_lesion_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/deepseg_lesion_models
--

Removing existing destination folder '/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/deepseg_lesion_models'
Trying URL: https://github.com/sct-data/deepseg_lesion_models/releases/download/r20180613/20180613_deepseg_lesion_models.zip
Downloading: 20180613_deepseg_lesion_models.zip
Creating temporary folder (/tmp/sct-20211119202550.336541-k1uvgvr6)
Unzip data to: /tmp/sct-20211119202550.336541-k1uvgvr6
Removing temporary folders...
Done!

+ for data in PAM50 gm_model optic_models pmj_models deepseg_sc_models deepseg_gm_models deepseg_lesion_models c2c3_disc_models
+ run sct_download_data -d c2c3_disc_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/c2c3_disc_models
+ print code sct_download_data -d c2c3_disc_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/c2c3_disc_models
+ type=code
+ shift
+ case "$type" in
+ echo -e '\n\033[0;34msct_download_data -d c2c3_disc_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/c2c3_disc_models\033[0m\n'

sct_download_data -d c2c3_disc_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/c2c3_disc_models

+ sct_download_data -d c2c3_disc_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/c2c3_disc_models

--
Spinal Cord Toolbox (git-HEAD-13b65d231ba9f68e78d1b1c13c996d2fbc1c6ec1)

sct_download_data -d c2c3_disc_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/c2c3_disc_models
--

Removing existing destination folder '/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/c2c3_disc_models'
Trying URL: https://github.com/sct-data/c2c3_disc_models/releases/download/r20190117/20190117_c2c3_disc_models.zip
Downloading: 20190117_c2c3_disc_models.zip
Creating temporary folder (/tmp/sct-20211119202551.123895-5r_7z84l)
Unzip data to: /tmp/sct-20211119202551.123895-5r_7z84l
Removing temporary folders...
Done!

+ python -c 'import spinalcordtoolbox.deepseg.models; spinalcordtoolbox.deepseg.models.install_default_models()'
+ conda deactivate
+ [[ -e /home/runner/.bashrc ]]
+ grep sct_env /home/runner/.bashrc
+ grep '^export MPLBACKEND=Agg' /home/runner/.bashrc
+ [[ yes =~ ^[Yy] ]]
+ edit_shellrc
+ echo
+ echo ''
++ date '+%Y-%m-%d %H:%M:%S'
+ echo '# SPINALCORDTOOLBOX (installed on 2021-11-19 20:25:52)'
+ echo 'export PATH="/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin:$PATH"'
+ [[ bash == \b\a\s\h ]]
+ echo 'export SCT_DIR=/home/runner/work/spinalcordtoolbox/spinalcordtoolbox'
+ echo ''
+ [[ -n '' ]]
+ print info 'Validate installation...'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mValidate installation...\033[0m\n'

Validate installation...

+ sct_check_dependencies

--
Spinal Cord Toolbox (git-HEAD-13b65d231ba9f68e78d1b1c13c996d2fbc1c6ec1)

sct_check_dependencies 
--

SCT info:
- version: git-HEAD-13b65d231ba9f68e78d1b1c13c996d2fbc1c6ec1
- path: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox
OS: linux (Linux-5.4.0-1063-azure-x86_64-with-debian-buster-sid)
CPU cores: Available: 2, Used by ITK functions: 2
RAM: Total: 6954MB, Used: 511MB, Available: 6112MB
Check Python executable.............................[OK]
  Using bundled python 3.7.11 (default, Jul 27 2021, 14:32:16) 
[GCC 7.5.0] at /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/python
Check if data are installed.........................[OK]
generated new fontManager
Check if colored is installed.......................[OK] (1.4.3)
Check if dipy is installed..........................[OK] (1.4.1)
Check if h5py is installed..........................[OK] (2.10.0)
Check if Keras (2.3.1) is installed.................[OK] (2.3.1)
Check if ivadomed is installed......................[OK] (2.7.4)
Check if matplotlib is installed....................[OK] (3.5.0)
Check if nibabel is installed.......................[OK] (3.2.1)
Check if numpy is installed.........................[OK] (1.18.5)
Check if onnxruntime (1.4.0) is installed...........[OK] (1.4.0)
Check if pandas is installed........................[OK] (1.3.4)
Check if psutil is installed........................[OK] (5.8.0)
Check if pyqt5 (5.11.3) is installed................[OK] (5.11.3)
Check if pytest is installed........................[OK] (6.2.5)
Check if pytest-cov is installed....................[OK] (3.0.0)
Check if raven is installed.........................[OK]
Check if requests is installed......................[OK] (2.26.0)
Check if requirements-parser is installed...........[OK] (0.2.0)
Check if scipy is installed.........................[OK] (1.7.2)
Check if scikit-image is installed..................[OK] (0.18.3)
Check if scikit-learn is installed..................[OK] (1.0.1)
Check if tensorflow is installed....................[OK] (1.15.5)
Check if torch (1.5.0+cpu) is installed.............[OK] (1.5.0+cpu)
Check if torchvision (0.6.0+cpu) is installed.......[OK] (0.6.0+cpu)
Check if xlwt is installed..........................[OK] (1.3.0)
Check if tqdm is installed..........................[OK] (4.62.3)
Check if transforms3d is installed..................[OK] (0.3.1)
Check if urllib3 is installed.......................[OK] (1.26.7)
Check if pytest_console_scripts is installed........[OK]
Check if wquantiles is installed....................[OK] (0.4)
Check if spinalcordtoolbox is installed.............[OK]
Check ANTs compatibility with OS ...................[OK]
Check PropSeg compatibility with OS ................[OK]
Check if figure can be opened with matplotlib.......[FAIL] (Using non-GUI backend 'agg')
Check if figure can be opened with PyQt.............[FAIL] ($DISPLAY not set on X11-supporting system)
Check FSLeyes version...............................Command not found. If you installed FSLeyes as part of FSL package, please check that FSL is included in $PATH variable. If you installed FSLeyes using conda environment, make sure that the environment is activated. If you do not have FSLeyes installed, consider its installation to easily visualize processing outputs and/or to use SCT within FSLeyes. More info at: https://spinalcordtoolbox.com/en/latest/user_section/fsleyes.html

+ [[ yes =~ ^[Nn] ]]
+ print info 'Open a new Terminal window to load environment variables, or run:
  source /home/runner/.bashrc'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mOpen a new Terminal window to load environment variables, or run:
  source /home/runner/.bashrc\033[0m\n'

Open a new Terminal window to load environment variables, or run:
  source /home/runner/.bashrc

++ finish
++ value=0
++ cd /home/runner/work/spinalcordtoolbox/spinalcordtoolbox
++ [[ 0 -eq 0 ]]
++ print info 'Installation finished successfully!'
++ type=info
++ shift
++ case "$type" in
++ echo -e '\n\033[0;32mInstallation finished successfully!\033[0m\n'

Installation finished successfully!

++ rm -rf /tmp/tmp.T01PPSHXCC
++ exit 0

Texte modifié

Ouvrir un fichier

*******************************
* Welcome to SCT installation *
*******************************

+ fetch_os_type
+ print info 'Checking OS type and version...'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mChecking OS type and version...\033[0m\n'

Checking OS type and version...

+ OSver=unknown
++ uname -a
+ uname_output='Linux fv-az82-661 5.4.0-1063-azure #66~18.04.1-Ubuntu SMP Thu Oct 21 09:59:28 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux'
+ echo 'Linux fv-az82-661 5.4.0-1063-azure #66~18.04.1-Ubuntu SMP Thu Oct 21 09:59:28 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux'
Linux fv-az82-661 5.4.0-1063-azure #66~18.04.1-Ubuntu SMP Thu Oct 21 09:59:28 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
+ echo 'Linux fv-az82-661 5.4.0-1063-azure #66~18.04.1-Ubuntu SMP Thu Oct 21 09:59:28 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux'
+ grep -i darwin
+ grep -i linux
+ echo 'Linux fv-az82-661 5.4.0-1063-azure #66~18.04.1-Ubuntu SMP Thu Oct 21 09:59:28 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux'
+ OS=linux
+ check_requirements
+ print info 'Checking requirements...'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mChecking requirements...\033[0m\n'

Checking requirements...

++ command -v curl
+ [[ -n /usr/bin/curl ]]
+ gcc --version
+ print info 'OK!'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mOK!\033[0m\n'

OK!

--> Crash reports will not be sent.

SCT will be installed here: [/home/runner/work/spinalcordtoolbox/spinalcordtoolbox]

Skipping copy of source files (source and destination folders are the same)

rm -rf /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python

mkdir -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python

Downloading Miniconda...

+ case $OS in
+ download /tmp/tmp.out2FZ4doz/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
+ command -v wget
+ run wget -nv -O /tmp/tmp.out2FZ4doz/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
+ print code wget -nv -O /tmp/tmp.out2FZ4doz/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
+ type=code
+ shift
+ case "$type" in
+ echo -e '\n\033[0;34mwget -nv -O /tmp/tmp.out2FZ4doz/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh\033[0m\n'

wget -nv -O /tmp/tmp.out2FZ4doz/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

+ wget -nv -O /tmp/tmp.out2FZ4doz/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
2021-11-19 19:35:10 URL:https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh [66709754/66709754] -> "/tmp/tmp.out2FZ4doz/miniconda.sh" [1]
+ print info 'Installing Miniconda...'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mInstalling Miniconda...\033[0m\n'

Installing Miniconda...

+ run bash /tmp/tmp.out2FZ4doz/miniconda.sh -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python -b -f
+ print code bash /tmp/tmp.out2FZ4doz/miniconda.sh -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python -b -f
+ type=code
+ shift
+ case "$type" in
+ echo -e '\n\033[0;34mbash /tmp/tmp.out2FZ4doz/miniconda.sh -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python -b -f\033[0m\n'

bash /tmp/tmp.out2FZ4doz/miniconda.sh -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python -b -f

+ bash /tmp/tmp.out2FZ4doz/miniconda.sh -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python -b -f
PREFIX=/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python
Unpacking payload ...

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Extracting : libgomp-9.3.0-h5101ec6_17.conda:   0%|          | 0/38 [00:00<?, ?it/s]
Extracting : libgomp-9.3.0-h5101ec6_17.conda:   3%|▎         | 1/38 [00:00<00:07,  4.84it/s]
Extracting : pycparser-2.20-py_2.conda:   3%|▎         | 1/38 [00:00<00:07,  4.84it/s]      
Extracting : tzdata-2021a-h52ac0ba_0.conda:   5%|▌         | 2/38 [00:00<00:07,  4.84it/s]
Extracting : tk-8.6.10-hbc83047_0.conda:   8%|▊         | 3/38 [00:00<00:07,  4.84it/s]   
Extracting : six-1.16.0-pyhd3eb1b0_0.conda:  11%|█         | 4/38 [00:00<00:07,  4.84it/s]
Extracting : yaml-0.2.5-h7b6447c_0.conda:  13%|█▎        | 5/38 [00:00<00:06,  4.84it/s]  
Extracting : libgcc-ng-9.3.0-h5101ec6_17.conda:  16%|█▌        | 6/38 [00:00<00:06,  4.84it/s]
Extracting : libgcc-ng-9.3.0-h5101ec6_17.conda:  18%|█▊        | 7/38 [00:00<00:04,  6.51it/s]
Extracting : zlib-1.2.11-h7b6447c_3.conda:  18%|█▊        | 7/38 [00:00<00:04,  6.51it/s]     
Extracting : setuptools-52.0.0-py39h06a4308_0.conda:  21%|██        | 8/38 [00:00<00:04,  6.51it/s]
Extracting : chardet-4.0.0-py39h06a4308_1003.conda:  24%|██▎       | 9/38 [00:00<00:04,  6.51it/s] 
Extracting : cffi-1.14.6-py39h400218f_0.conda:  26%|██▋       | 10/38 [00:00<00:04,  6.51it/s]    
Extracting : ruamel_yaml-0.15.100-py39h27cfd23_0.conda:  29%|██▉       | 11/38 [00:00<00:04,  6.51it/s]
Extracting : libstdcxx-ng-9.3.0-hd4cf53a_17.conda:  32%|███▏      | 12/38 [00:00<00:03,  6.51it/s]     
Extracting : certifi-2021.5.30-py39h06a4308_0.conda:  34%|███▍      | 13/38 [00:00<00:03,  6.51it/s]
Extracting : urllib3-1.26.6-pyhd3eb1b0_1.conda:  37%|███▋      | 14/38 [00:00<00:03,  6.51it/s]     
Extracting : brotlipy-0.7.0-py39h27cfd23_1003.conda:  39%|███▉      | 15/38 [00:00<00:03,  6.51it/s]
Extracting : brotlipy-0.7.0-py39h27cfd23_1003.conda:  42%|████▏     | 16/38 [00:00<00:02,  8.85it/s]
Extracting : sqlite-3.36.0-hc218d9a_0.conda:  42%|████▏     | 16/38 [00:00<00:02,  8.85it/s]        
Extracting : readline-8.1-h27cfd23_0.conda:  45%|████▍     | 17/38 [00:00<00:02,  8.85it/s] 
Extracting : ld_impl_linux-64-2.35.1-h7274673_9.conda:  47%|████▋     | 18/38 [00:00<00:02,  8.85it/s]
Extracting : pyopenssl-20.0.1-pyhd3eb1b0_1.conda:  50%|█████     | 19/38 [00:00<00:02,  8.85it/s]     
Extracting : openssl-1.1.1k-h27cfd23_0.conda:  53%|█████▎    | 20/38 [00:00<00:02,  8.85it/s]    
Extracting : openssl-1.1.1k-h27cfd23_0.conda:  55%|█████▌    | 21/38 [00:00<00:01, 11.52it/s]
Extracting : libffi-3.3-he6710b0_2.conda:  55%|█████▌    | 21/38 [00:00<00:01, 11.52it/s]    
Extracting : ncurses-6.2-he6710b0_1.conda:  58%|█████▊    | 22/38 [00:00<00:01, 11.52it/s]
Extracting : xz-5.2.5-h7b6447c_0.conda:  61%|██████    | 23/38 [00:00<00:01, 11.52it/s]   
Extracting : pip-21.1.3-py39h06a4308_0.conda:  63%|██████▎   | 24/38 [00:00<00:01, 11.52it/s]
Extracting : pip-21.1.3-py39h06a4308_0.conda:  66%|██████▌   | 25/38 [00:00<00:00, 13.75it/s]
Extracting : pysocks-1.7.1-py39h06a4308_0.conda:  66%|██████▌   | 25/38 [00:00<00:00, 13.75it/s]
Extracting : requests-2.25.1-pyhd3eb1b0_0.conda:  68%|██████▊   | 26/38 [00:00<00:00, 13.75it/s]
Extracting : ca-certificates-2021.7.5-h06a4308_1.conda:  71%|███████   | 27/38 [00:00<00:00, 13.75it/s]
Extracting : cryptography-3.4.7-py39hd23ed53_0.conda:  74%|███████▎  | 28/38 [00:00<00:00, 13.75it/s]  
Extracting : tqdm-4.61.2-pyhd3eb1b0_1.conda:  76%|███████▋  | 29/38 [00:00<00:00, 13.75it/s]         
Extracting : tqdm-4.61.2-pyhd3eb1b0_1.conda:  79%|███████▉  | 30/38 [00:00<00:00, 17.13it/s]
Extracting : wheel-0.36.2-pyhd3eb1b0_0.conda:  79%|███████▉  | 30/38 [00:00<00:00, 17.13it/s]
Extracting : conda-package-handling-1.7.3-py39h27cfd23_1.conda:  82%|████████▏ | 31/38 [00:00<00:00, 17.13it/s]
Extracting : _libgcc_mutex-0.1-main.conda:  84%|████████▍ | 32/38 [00:00<00:00, 17.13it/s]                     
Extracting : pycosat-0.6.3-py39h27cfd23_0.conda:  87%|████████▋ | 33/38 [00:00<00:00, 17.13it/s]
Extracting : python-3.9.5-h12debd9_4.tar.bz2:  89%|████████▉ | 34/38 [00:03<00:00, 17.13it/s]   
Extracting : python-3.9.5-h12debd9_4.tar.bz2:  92%|█████████▏| 35/38 [00:03<00:00,  4.55it/s]
Extracting : _openmp_mutex-4.5-1_gnu.tar.bz2:  92%|█████████▏| 35/38 [00:03<00:00,  4.55it/s]
Extracting : idna-2.10-pyhd3eb1b0_0.tar.bz2:  95%|█████████▍| 36/38 [00:03<00:00,  4.55it/s] 
Extracting : conda-4.10.3-py39h06a4308_0.tar.bz2:  97%|█████████▋| 37/38 [00:03<00:00,  4.55it/s]
                                                                                                 
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

environment location: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python

The following NEW packages will be INSTALLED:

Creating conda environment...

+ python/bin/conda create -y -n venv_sct python=3.7
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

environment location: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct

added / updated specs:
    - python=3.7

The following packages will be downloaded:

The following NEW packages will be INSTALLED:

Downloading and Extracting Packages

ncurses-6.3          | 782 KB    |            |   0% 
ncurses-6.3          | 782 KB    | ########## | 100% 
ncurses-6.3          | 782 KB    | ########## | 100%

python-3.7.11        | 45.3 MB   |            |   0% 
python-3.7.11        | 45.3 MB   | 2          |   3% 
python-3.7.11        | 45.3 MB   | ##3        |  23% 
python-3.7.11        | 45.3 MB   | ####8      |  48% 
python-3.7.11        | 45.3 MB   | ######5    |  65% 
python-3.7.11        | 45.3 MB   | ########2  |  83% 
python-3.7.11        | 45.3 MB   | #########9 | 100% 
python-3.7.11        | 45.3 MB   | ########## | 100%

setuptools-58.0.4    | 775 KB    |            |   0% 
setuptools-58.0.4    | 775 KB    | ########## | 100% 
setuptools-58.0.4    | 775 KB    | ########## | 100%

tk-8.6.11            | 3.0 MB    |            |   0% 
tk-8.6.11            | 3.0 MB    | ########## | 100% 
tk-8.6.11            | 3.0 MB    | ########## | 100%

pip-21.2.2           | 1.8 MB    |            |   0% 
pip-21.2.2           | 1.8 MB    | ########## | 100% 
pip-21.2.2           | 1.8 MB    | ########## | 100%

ca-certificates-2021 | 115 KB    |            |   0% 
ca-certificates-2021 | 115 KB    | ########## | 100%

wheel-0.37.0         | 33 KB     |            |   0% 
wheel-0.37.0         | 33 KB     | ########## | 100%

openssl-1.1.1l       | 2.5 MB    |            |   0% 
openssl-1.1.1l       | 2.5 MB    | ########## | 100% 
openssl-1.1.1l       | 2.5 MB    | ########## | 100%

certifi-2021.10.8    | 151 KB    |            |   0% 
certifi-2021.10.8    | 151 KB    | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
#
# To activate this environment, use
#
#     $ conda activate venv_sct
#
# To deactivate an active environment, use
#
#     $ conda deactivate

Validating that conda environment can be activated...

Installing Python dependencies...

Using requirements.txt (git installation)

+ REQUIREMENTS_FILE=requirements.txt
+ pip install -r requirements.txt
Looking in links: https://download.pytorch.org/whl/cpu/torch_stable.html
Ignoring torch: markers 'sys_platform == "darwin"' don't match your environment
Ignoring torchvision: markers 'sys_platform == "darwin"' don't match your environment
Collecting colored
  Downloading colored-1.4.3.tar.gz (29 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting dipy
  Downloading dipy-1.4.1-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (7.7 MB)
Collecting h5py~=2.10.0
  Downloading h5py-2.10.0-cp37-cp37m-manylinux1_x86_64.whl (2.9 MB)
Collecting Keras==2.3.1
  Downloading Keras-2.3.1-py2.py3-none-any.whl (377 kB)
Collecting ivadomed
  Downloading ivadomed-2.9.0-py3-none-any.whl (215 kB)
Collecting matplotlib
  Downloading matplotlib-3.5.0-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (11.2 MB)
Collecting nibabel
  Downloading nibabel-3.2.1-py3-none-any.whl (3.3 MB)
Collecting numpy
  Downloading numpy-1.21.4-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (15.7 MB)
Collecting onnxruntime==1.4.0
  Downloading onnxruntime-1.4.0-cp37-cp37m-manylinux2010_x86_64.whl (4.4 MB)
Collecting pandas
  Downloading pandas-1.3.4-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.3 MB)
Collecting psutil
  Downloading psutil-5.8.0-cp37-cp37m-manylinux2010_x86_64.whl (296 kB)
Collecting pyqt5==5.11.3
  Downloading PyQt5-5.11.3-5.11.2-cp35.cp36.cp37.cp38-abi3-manylinux1_x86_64.whl (117.8 MB)
Collecting pytest
  Downloading pytest-6.2.5-py3-none-any.whl (280 kB)
Collecting pytest-cov
  Downloading pytest_cov-3.0.0-py3-none-any.whl (20 kB)
Collecting raven
  Downloading raven-6.10.0-py2.py3-none-any.whl (284 kB)
Collecting requests
  Downloading requests-2.26.0-py2.py3-none-any.whl (62 kB)
Collecting requirements-parser
  Downloading requirements-parser-0.2.0.tar.gz (6.3 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting scipy
  Downloading scipy-1.7.2-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (38.2 MB)
Collecting scikit-image
  Downloading scikit_image-0.18.3-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (29.2 MB)
Collecting scikit-learn
  Downloading scikit_learn-1.0.1-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (23.2 MB)
Collecting tensorflow~=1.15.0
  Downloading tensorflow-1.15.5-cp37-cp37m-manylinux2010_x86_64.whl (110.5 MB)
Collecting torch==1.5.0+cpu
  Downloading https://download.pytorch.org/whl/cpu/torch-1.5.0%2Bcpu-cp37-cp37m-linux_x86_64.whl (127.3 MB)
Collecting torchvision==0.6.0+cpu
  Downloading https://download.pytorch.org/whl/cpu/torchvision-0.6.0%2Bcpu-cp37-cp37m-linux_x86_64.whl (5.7 MB)
Collecting xlwt
  Downloading xlwt-1.3.0-py2.py3-none-any.whl (99 kB)
Collecting tqdm
  Downloading tqdm-4.62.3-py2.py3-none-any.whl (76 kB)
Collecting transforms3d
  Downloading transforms3d-0.3.1.tar.gz (62 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting urllib3[secure]
  Downloading urllib3-1.26.7-py2.py3-none-any.whl (138 kB)
Collecting pytest_console_scripts
  Downloading pytest-console-scripts-1.2.1.tar.gz (13 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting wquantiles
  Downloading wquantiles-0.6-py3-none-any.whl (3.3 kB)
Collecting pyyaml
  Downloading PyYAML-6.0-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (596 kB)
Collecting six>=1.9.0
  Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting keras-preprocessing>=1.0.5
  Downloading Keras_Preprocessing-1.1.2-py2.py3-none-any.whl (42 kB)
Collecting keras-applications>=1.0.6
  Downloading Keras_Applications-1.0.8-py3-none-any.whl (50 kB)
Collecting protobuf
  Downloading protobuf-3.19.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.1 MB)
Collecting PyQt5_sip<4.20,>=4.19.11
  Downloading PyQt5_sip-4.19.19-cp37-cp37m-manylinux1_x86_64.whl (67 kB)
Collecting future
  Downloading future-0.18.2.tar.gz (829 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting pillow>=4.1.1
  Downloading Pillow-8.4.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB)
Collecting joblib~=1.0
  Downloading joblib-1.1.0-py2.py3-none-any.whl (306 kB)
Collecting pybids>=0.12.4
  Downloading pybids-0.14.0-py3-none-any.whl (3.2 MB)
Collecting pyparsing<3,>=2.0.2
  Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB)
Collecting seaborn~=0.11
  Downloading seaborn-0.11.2-py3-none-any.whl (292 kB)
Collecting ivadomed
  Downloading ivadomed-2.8.0-py3-none-any.whl (226 kB)
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Requirement already satisfied: certifi>=2017.4.17 in ./python/envs/venv_sct/lib/python3.7/site-packages (from requests->-r requirements.txt (line 21)) (2021.10.8)
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Requirement already satisfied: wheel>=0.26 in ./python/envs/venv_sct/lib/python3.7/site-packages (from tensorflow~=1.15.0->-r requirements.txt (line 26)) (0.37.0)
Collecting grpcio>=1.8.6
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Collecting wrapt>=1.11.1
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  Preparing metadata (setup.py): started
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INFO: pip is looking at multiple versions of scikit-learn to determine which version is compatible with other requirements. This could take a while.
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  Downloading scikit_learn-1.0-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (23.1 MB)
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  Downloading scipy-1.7.1-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (28.5 MB)
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Collecting requirements-parser
  Downloading requirements-parser-0.1.0.tar.gz (4.9 kB)
  Preparing metadata (setup.py): started
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  Downloading raven-6.9.0-py2.py3-none-any.whl (287 kB)
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Collecting psutil
  Downloading psutil-5.7.3.tar.gz (465 kB)
  Preparing metadata (setup.py): started
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Collecting pandas
  Downloading pandas-1.3.3-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.3 MB)
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Collecting numpy
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INFO: pip is looking at multiple versions of nibabel to determine which version is compatible with other requirements. This could take a while.
Collecting nibabel
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Collecting matplotlib
  Downloading matplotlib-3.4.3-cp37-cp37m-manylinux1_x86_64.whl (10.3 MB)
INFO: pip is looking at multiple versions of ivadomed to determine which version is compatible with other requirements. This could take a while.
Collecting ivadomed
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Collecting bids-neuropoly>=0.2
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Collecting pre-commit==2.10.1
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Collecting sphinx-jsonschema
  Downloading sphinx-jsonschema-1.17.1.tar.gz (17 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting nodeenv>=0.11.1
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Collecting identify>=1.0.0
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Collecting cfgv>=2.0.0
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Collecting absl-py>=0.7.0
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Requirement already satisfied: setuptools>=41.0.0 in ./python/envs/venv_sct/lib/python3.7/site-packages (from tensorboard->ivadomed->-r requirements.txt (line 7)) (58.0.4)
Collecting werkzeug>=0.11.15
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Collecting markdown>=2.6.8
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Collecting cryptography>=1.3.4
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Collecting pyOpenSSL>=0.14
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Collecting mock>=2.0.0
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Collecting tomli
  Using cached tomli-1.2.2-py3-none-any.whl (12 kB)
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Collecting filelock<4,>=3.2
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Collecting docopt>=0.6.2
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  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Building wheels for collected packages: colored, gast, requirements-parser, transforms3d, pytest-console-scripts, termcolor, future, sphinx-jsonschema, docopt
  Building wheel for colored (setup.py): started
  Building wheel for colored (setup.py): finished with status 'done'
  Created wheel for colored: filename=colored-1.4.3-py3-none-any.whl size=14341 sha256=6b77204e6ceee8d78376836f9b4cdfff3546f8f07399674ad44816883a058125
  Stored in directory: /home/runner/.cache/pip/wheels/4a/f6/00/835e81851bc345428a253721c8bdad0062721dfb861bc6e752
  Building wheel for gast (setup.py): started
  Building wheel for gast (setup.py): finished with status 'done'
  Created wheel for gast: filename=gast-0.2.2-py3-none-any.whl size=7554 sha256=f0cc01e60aa49a3206e6477889ea74f5fc09285f2069856516a027deae43e857
  Stored in directory: /home/runner/.cache/pip/wheels/21/7f/02/420f32a803f7d0967b48dd823da3f558c5166991bfd204eef3
  Building wheel for requirements-parser (setup.py): started
  Building wheel for requirements-parser (setup.py): finished with status 'done'
  Created wheel for requirements-parser: filename=requirements_parser-0.2.0-py3-none-any.whl size=7688 sha256=af169c5f169101499803590289540a060428999963edbd383f2d53398e1a8dd0
  Stored in directory: /home/runner/.cache/pip/wheels/40/e4/ca/8af24ee94c3863d620d6a52793d82930f4d1d3515a5121d495
  Building wheel for transforms3d (setup.py): started
  Building wheel for transforms3d (setup.py): finished with status 'done'
  Created wheel for transforms3d: filename=transforms3d-0.3.1-py3-none-any.whl size=59373 sha256=26054e65fd290b2d003b8c8a801b8ac5e4b05dae37f02f61dee89469cf45642a
  Stored in directory: /home/runner/.cache/pip/wheels/b5/b7/93/8985551f83720ce37548a5b543c75380bb707955a9c2c5d28c
  Building wheel for pytest-console-scripts (setup.py): started
  Building wheel for pytest-console-scripts (setup.py): finished with status 'done'
  Created wheel for pytest-console-scripts: filename=pytest_console_scripts-1.2.1-py3-none-any.whl size=9138 sha256=6032b88f8688d05d06d9f388b4fc85323cdd05ab0cbc06518c1db2ad82a90bf6
  Stored in directory: /home/runner/.cache/pip/wheels/0c/8d/86/30a5d0717aa57680c1c7a42fabc750923abf5e2574515dff19
  Building wheel for termcolor (setup.py): started
  Building wheel for termcolor (setup.py): finished with status 'done'
  Created wheel for termcolor: filename=termcolor-1.1.0-py3-none-any.whl size=4847 sha256=61cc5d8a666b3f8e6fe9a5efc1f215786675a452ab39ce204792aeec8a907c52
  Stored in directory: /home/runner/.cache/pip/wheels/3f/e3/ec/8a8336ff196023622fbcb36de0c5a5c218cbb24111d1d4c7f2
  Building wheel for future (setup.py): started
  Building wheel for future (setup.py): finished with status 'done'
  Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491070 sha256=f71c5473e69ac59ab0a649fe87dacfde404a28c6fe62bf7baa9a8970db860bbb
  Stored in directory: /home/runner/.cache/pip/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0
  Building wheel for sphinx-jsonschema (setup.py): started
  Building wheel for sphinx-jsonschema (setup.py): finished with status 'done'
  Created wheel for sphinx-jsonschema: filename=sphinx_jsonschema-1.17.1-py3-none-any.whl size=14000 sha256=1414eaf7a45426e713d9fd67ef8aab460ed34ec52f19613647c96cdef78b3848
  Stored in directory: /home/runner/.cache/pip/wheels/4d/d8/24/17b5acc06ae865851a662e96babab02d34f025665d7650540d
  Building wheel for docopt (setup.py): started
  Building wheel for docopt (setup.py): finished with status 'done'
  Created wheel for docopt: filename=docopt-0.6.2-py2.py3-none-any.whl size=13724 sha256=0c352c26c906e93da1b2d84dd8d59612ecd8f09db3de5383b60c1376b1123657
  Stored in directory: /home/runner/.cache/pip/wheels/72/b0/3f/1d95f96ff986c7dfffe46ce2be4062f38ebd04b506c77c81b9
Successfully built colored gast requirements-parser transforms3d pytest-console-scripts termcolor future sphinx-jsonschema docopt
Installing collected packages: six, zipp, typing-extensions, pytz, python-dateutil, pyparsing, numpy, wrapt, tomli, scipy, pycparser, pandas, packaging, interface-meta, importlib-metadata, docopt, astor, urllib3, toml, sqlalchemy, setuptools-scm, py, pluggy, platformdirs, pillow, num2words, nibabel, kiwisolver, iniconfig, idna, future, formulaic, fonttools, filelock, distlib, cycler, click, charset-normalizer, cffi, bids-validator, backports.entry-points-selectable, attrs, werkzeug, virtualenv, torch, tifffile, threadpoolctl, requests, pyyaml, PyWavelets, pytest, pybids, protobuf, nodeenv, networkx, mock, matplotlib, markdown, jsonpointer, joblib, imageio, identify, h5py, grpcio, docutils, dictdiffer, cryptography, coverage, cfgv, absl-py, tqdm, torchvision, termcolor, tensorflow-estimator, tensorboard, sphinx-jsonschema, seaborn, scikit-learn, scikit-image, pytest-ordering, pytest-console-scripts, PyQt5-sip, pyOpenSSL, pre-commit, opt-einsum, onnxruntime, keras-preprocessing, keras-applications, google-pasta, gast, csv-diff, bids-neuropoly, xlwt, wquantiles, transforms3d, tensorflow, requirements-parser, raven, pytest-cov, pyqt5, psutil, Keras, ivadomed, dipy, colored
Successfully installed Keras-2.3.1 PyQt5-sip-4.19.19 PyWavelets-1.2.0 absl-py-1.0.0 astor-0.8.1 attrs-21.2.0 backports.entry-points-selectable-1.1.1 bids-neuropoly-0.2 bids-validator-1.8.4 cffi-1.15.0 cfgv-3.3.1 charset-normalizer-2.0.7 click-8.0.3 colored-1.4.3 coverage-6.1.2 cryptography-35.0.0 csv-diff-1.1 cycler-0.11.0 dictdiffer-0.9.0 dipy-1.4.1 distlib-0.3.3 docopt-0.6.2 docutils-0.18 filelock-3.4.0 fonttools-4.28.1 formulaic-0.2.4 future-0.18.2 gast-0.2.2 google-pasta-0.2.0 grpcio-1.42.0 h5py-2.10.0 identify-2.4.0 idna-3.3 imageio-2.11.0 importlib-metadata-4.8.2 iniconfig-1.1.1 interface-meta-1.2.4 ivadomed-2.7.4 joblib-1.1.0 jsonpointer-2.2 keras-applications-1.0.8 keras-preprocessing-1.1.2 kiwisolver-1.3.2 markdown-3.3.6 matplotlib-3.5.0 mock-4.0.3 networkx-2.6.3 nibabel-3.2.1 nodeenv-1.6.0 num2words-0.5.10 numpy-1.18.5 onnxruntime-1.4.0 opt-einsum-3.3.0 packaging-21.3 pandas-1.3.4 pillow-8.4.0 platformdirs-2.4.0 pluggy-1.0.0 pre-commit-2.10.1 protobuf-3.19.1 psutil-5.8.0 py-1.11.0 pyOpenSSL-21.0.0 pybids-0.14.0 pycparser-2.21 pyparsing-3.0.6 pyqt5-5.11.3 pytest-6.2.5 pytest-console-scripts-1.2.1 pytest-cov-3.0.0 pytest-ordering-0.6 python-dateutil-2.8.2 pytz-2021.3 pyyaml-6.0 raven-6.10.0 requests-2.26.0 requirements-parser-0.2.0 scikit-image-0.18.3 scikit-learn-1.0.1 scipy-1.7.2 seaborn-0.11.2 setuptools-scm-6.3.2 six-1.16.0 sphinx-jsonschema-1.17.1 sqlalchemy-1.3.24 tensorboard-1.15.0 tensorflow-1.15.5 tensorflow-estimator-1.15.1 termcolor-1.1.0 threadpoolctl-3.0.0 tifffile-2021.11.2 toml-0.10.2 tomli-1.2.2 torch-1.5.0+cpu torchvision-0.6.0+cpu tqdm-4.62.3 transforms3d-0.3.1 typing-extensions-4.0.0 urllib3-1.26.7 virtualenv-20.10.0 werkzeug-2.0.2 wquantiles-0.6 wrapt-1.13.3 xlwt-1.3.0 zipp-3.6.0
+ print info 'Installing spinalcordtoolbox...'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mInstalling spinalcordtoolbox...\033[0m\n'

Installing spinalcordtoolbox...

Creating launchers for Python scripts...

Installing binaries...

sct_download_data -d binaries_linux -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin -k

+ sct_download_data -d binaries_linux -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin -k

--
Spinal Cord Toolbox (git-HEAD-13b65d231ba9f68e78d1b1c13c996d2fbc1c6ec1)

sct_download_data -d binaries_linux -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin -k
--

Trying URL: https://osf.io/cs6zt/?action=download
Downloading: 20200801_sct_binaries_linux.tar.gz
Creating temporary folder (/tmp/sct-20211119193735.381296-7go18ak2)
Unzip data to: /tmp/sct-20211119193735.381296-7go18ak2
Removing temporary folders...
Done!

+ print info 'All requirements installed!'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mAll requirements installed!\033[0m\n'

All requirements installed!

+ [[ -n '' ]]
+ print info 'Installing data...'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mInstalling data...\033[0m\n'

Installing data...

rm -rf /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data

mkdir -p /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data

sct_download_data -d PAM50 -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50

+ sct_download_data -d PAM50 -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50

--
Spinal Cord Toolbox (git-HEAD-13b65d231ba9f68e78d1b1c13c996d2fbc1c6ec1)

sct_download_data -d PAM50 -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50
--

Removing existing destination folder '/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/PAM50'
Trying URL: https://github.com/sct-data/PAM50/releases/download/r20201104/PAM50-r20201104.zip
Downloading: PAM50-r20201104.zip
Creating temporary folder (/tmp/sct-20211119193739.189069-8624aqyp)
Unzip data to: /tmp/sct-20211119193739.189069-8624aqyp
Removing temporary folders...
Done!

sct_download_data -d gm_model -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/gm_model

+ sct_download_data -d gm_model -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/gm_model

--
Spinal Cord Toolbox (git-HEAD-13b65d231ba9f68e78d1b1c13c996d2fbc1c6ec1)

sct_download_data -d gm_model -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/gm_model
--

Removing existing destination folder '/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/gm_model'
Trying URL: https://osf.io/ugscu/?action=download
Downloading: 20160922_gm_model.zip
Creating temporary folder (/tmp/sct-20211119193742.856478-o0_k2hew)
Unzip data to: /tmp/sct-20211119193742.856478-o0_k2hew
Removing temporary folders...
Done!

sct_download_data -d optic_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/optic_models

+ sct_download_data -d optic_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/optic_models

--
Spinal Cord Toolbox (git-HEAD-13b65d231ba9f68e78d1b1c13c996d2fbc1c6ec1)

sct_download_data -d optic_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/optic_models
--

Removing existing destination folder '/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/optic_models'
Trying URL: https://github.com/sct-data/optic_models/releases/download/r20170413/20170413_optic_models.zip
Downloading: 20170413_optic_models.zip
Creating temporary folder (/tmp/sct-20211119193743.652856-pf7nvtp6)
Unzip data to: /tmp/sct-20211119193743.652856-pf7nvtp6
Removing temporary folders...
Done!

sct_download_data -d pmj_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/pmj_models

+ sct_download_data -d pmj_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/pmj_models

--
Spinal Cord Toolbox (git-HEAD-13b65d231ba9f68e78d1b1c13c996d2fbc1c6ec1)

sct_download_data -d pmj_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/pmj_models
--

Removing existing destination folder '/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/pmj_models'
Trying URL: https://github.com/sct-data/pmj_models/releases/download/r20170922/20170922_pmj_models.zip
Downloading: 20170922_pmj_models.zip
Creating temporary folder (/tmp/sct-20211119193744.718840-9ttune52)
Unzip data to: /tmp/sct-20211119193744.718840-9ttune52
Removing temporary folders...
Done!

sct_download_data -d deepseg_sc_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/deepseg_sc_models

+ sct_download_data -d deepseg_sc_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/deepseg_sc_models

--
Spinal Cord Toolbox (git-HEAD-13b65d231ba9f68e78d1b1c13c996d2fbc1c6ec1)

sct_download_data -d deepseg_sc_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/deepseg_sc_models
--

Removing existing destination folder '/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/deepseg_sc_models'
Trying URL: https://github.com/sct-data/deepseg_sc_models/releases/download/r20180610/20180610_deepseg_sc_models.zip
Downloading: 20180610_deepseg_sc_models.zip
Creating temporary folder (/tmp/sct-20211119193746.914556-_b42o79v)
Unzip data to: /tmp/sct-20211119193746.914556-_b42o79v
Removing temporary folders...
Done!

sct_download_data -d deepseg_gm_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/deepseg_gm_models

+ sct_download_data -d deepseg_gm_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/deepseg_gm_models

--
Spinal Cord Toolbox (git-HEAD-13b65d231ba9f68e78d1b1c13c996d2fbc1c6ec1)

sct_download_data -d deepseg_gm_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/deepseg_gm_models
--

Removing existing destination folder '/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/deepseg_gm_models'
Trying URL: https://github.com/sct-data/deepseg_gm_models/releases/download/r20180205/20180205_deepseg_gm_models.zip
Downloading: 20180205_deepseg_gm_models.zip
Creating temporary folder (/tmp/sct-20211119193748.264683-1onk7yh0)
Unzip data to: /tmp/sct-20211119193748.264683-1onk7yh0
Removing temporary folders...
Done!

sct_download_data -d deepseg_lesion_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/deepseg_lesion_models

+ sct_download_data -d deepseg_lesion_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/deepseg_lesion_models

--
Spinal Cord Toolbox (git-HEAD-13b65d231ba9f68e78d1b1c13c996d2fbc1c6ec1)

sct_download_data -d deepseg_lesion_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/deepseg_lesion_models
--

Removing existing destination folder '/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/deepseg_lesion_models'
Trying URL: https://github.com/sct-data/deepseg_lesion_models/releases/download/r20180613/20180613_deepseg_lesion_models.zip
Downloading: 20180613_deepseg_lesion_models.zip
Creating temporary folder (/tmp/sct-20211119193749.397964-5w4w3f06)
Unzip data to: /tmp/sct-20211119193749.397964-5w4w3f06
Removing temporary folders...
Done!

sct_download_data -d c2c3_disc_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/c2c3_disc_models

+ sct_download_data -d c2c3_disc_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/c2c3_disc_models

--
Spinal Cord Toolbox (git-HEAD-13b65d231ba9f68e78d1b1c13c996d2fbc1c6ec1)

sct_download_data -d c2c3_disc_models -o /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/c2c3_disc_models
--

Removing existing destination folder '/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/data/c2c3_disc_models'
Trying URL: https://github.com/sct-data/c2c3_disc_models/releases/download/r20190117/20190117_c2c3_disc_models.zip
Downloading: 20190117_c2c3_disc_models.zip
Creating temporary folder (/tmp/sct-20211119193750.325035-li_8zgkm)
Unzip data to: /tmp/sct-20211119193750.325035-li_8zgkm
Removing temporary folders...
Done!

+ python -c 'import spinalcordtoolbox.deepseg.models; spinalcordtoolbox.deepseg.models.install_default_models()'
+ conda deactivate
+ [[ -e /home/runner/.bashrc ]]
+ grep sct_env /home/runner/.bashrc
+ grep '^export MPLBACKEND=Agg' /home/runner/.bashrc
+ [[ yes =~ ^[Yy] ]]
+ edit_shellrc
+ echo
+ echo ''
++ date '+%Y-%m-%d %H:%M:%S'
+ echo '# SPINALCORDTOOLBOX (installed on 2021-11-19 19:37:51)'
+ echo 'export PATH="/home/runner/work/spinalcordtoolbox/spinalcordtoolbox/bin:$PATH"'
+ [[ bash == \b\a\s\h ]]
+ echo 'export SCT_DIR=/home/runner/work/spinalcordtoolbox/spinalcordtoolbox'
+ echo ''
+ [[ -n '' ]]
+ print info 'Validate installation...'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mValidate installation...\033[0m\n'

Validate installation...

+ sct_check_dependencies

--
Spinal Cord Toolbox (git-HEAD-13b65d231ba9f68e78d1b1c13c996d2fbc1c6ec1)

sct_check_dependencies 
--

SCT info:
- version: git-HEAD-13b65d231ba9f68e78d1b1c13c996d2fbc1c6ec1
- path: /home/runner/work/spinalcordtoolbox/spinalcordtoolbox
OS: linux (Linux-5.4.0-1063-azure-x86_64-with-debian-buster-sid)
CPU cores: Available: 2, Used by ITK functions: 2
RAM: Total: 6954MB, Used: 490MB, Available: 6134MB
Check Python executable.............................[OK]
  Using bundled python 3.7.11 (default, Jul 27 2021, 14:32:16) 
[GCC 7.5.0] at /home/runner/work/spinalcordtoolbox/spinalcordtoolbox/python/envs/venv_sct/bin/python
Check if data are installed.........................[OK]
generated new fontManager
Check if colored is installed.......................[OK] (1.4.3)
Check if dipy is installed..........................[OK] (1.4.1)
Check if h5py is installed..........................[OK] (2.10.0)
Check if Keras (2.3.1) is installed.................[OK] (2.3.1)
Check if ivadomed is installed......................[OK] (2.7.4)
Check if matplotlib is installed....................[OK] (3.5.0)
Check if nibabel is installed.......................[OK] (3.2.1)
Check if numpy is installed.........................[OK] (1.18.5)
Check if onnxruntime (1.4.0) is installed...........[OK] (1.4.0)
Check if pandas is installed........................[OK] (1.3.4)
Check if psutil is installed........................[OK] (5.8.0)
Check if pyqt5 (5.11.3) is installed................[OK] (5.11.3)
Check if pytest is installed........................[OK] (6.2.5)
Check if pytest-cov is installed....................[OK] (3.0.0)
Check if raven is installed.........................[OK]
Check if requests is installed......................[OK] (2.26.0)
Check if requirements-parser is installed...........[OK] (0.2.0)
Check if scipy is installed.........................[OK] (1.7.2)
Check if scikit-image is installed..................[OK] (0.18.3)
Check if scikit-learn is installed..................[OK] (1.0.1)
Check if tensorflow is installed....................[OK] (1.15.5)
Check if torch (1.5.0+cpu) is installed.............[OK] (1.5.0+cpu)
Check if torchvision (0.6.0+cpu) is installed.......[OK] (0.6.0+cpu)
Check if xlwt is installed..........................[OK] (1.3.0)
Check if tqdm is installed..........................[OK] (4.62.3)
Check if transforms3d is installed..................[OK] (0.3.1)
Check if urllib3 is installed.......................[OK] (1.26.7)
Check if pytest_console_scripts is installed........[OK]
Check if wquantiles is installed....................[OK] (0.4)
Check if spinalcordtoolbox is installed.............[OK]
Check ANTs compatibility with OS ...................[OK]
Check PropSeg compatibility with OS ................[OK]
Check if figure can be opened with matplotlib.......[FAIL] (Using non-GUI backend 'agg')
Check if figure can be opened with PyQt.............[FAIL] ($DISPLAY not set on X11-supporting system)
Check FSLeyes version...............................Command not found. If you installed FSLeyes as part of FSL package, please check that FSL is included in $PATH variable. If you installed FSLeyes using conda environment, make sure that the environment is activated. If you do not have FSLeyes installed, consider its installation to easily visualize processing outputs and/or to use SCT within FSLeyes. More info at: https://spinalcordtoolbox.com/en/latest/user_section/fsleyes.html

Open a new Terminal window to load environment variables, or run:
  source /home/runner/.bashrc

Installation finished successfully!

++ rm -rf /tmp/tmp.out2FZ4doz
++ exit 0