Compare text

Find the difference between two text files

Real-time editor

Hide whitespace changes

Hide unchanged lines

Disable line wrap

Layout

Diff precision

Text styles

Syntax highlighting

Diffchecker Desktop The most secure way to run Diffchecker. Get the Diffchecker Desktop app: your diffs never leave your computer!Get Desktop

Passing test vs. lchauvin install error

Created 9 months agoDiff never expires

113 removals

Lines
Total
Removed

Characters
Total
Removed

To continue using this feature, upgrade to Diffchecker Pro View Pricing

408 lines

107 additions

Lines
Total
Added

Characters
Total
Added

To continue using this feature, upgrade to Diffchecker Pro View Pricing

416 lines

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

* Welcome to SCT installation *

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

Checking OS type and version...

Linux runnervmnfq8z 6.8.0-1036-azure #42~22.04.1-Ubuntu SMP Fri Sep 12 00:09:41 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux

Linux imaging-gpu-05 5.15.0-153-generic #163-Ubuntu SMP Thu Aug 7 16:37:18 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux

Checking requirements...

OK!

Source files not present. Downloading source files (@ master) to /tmp/tmp.zRQSjifCZQ/spinalcordtoolbox.

Cloning into '/tmp/tmp.zRQSjifCZQ/spinalcordtoolbox'...

SCT version ......... 7.2.dev0

Installation type ... package

Installation type ... in-place

Operating system .... linux (unknown)

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

Shell config ........ /home/lchauvin/.bashrc

Checking permissions on required file /home/runner/.bashrc:

Checking permissions on required file /home/lchauvin/.bashrc:

- File exists: True

- File ownership: True

- Read permissions: True

- Write permissions: True

SCT will be installed here: [/home/runner/sct_7.2.dev0]

WARNING: Directory already exists. Files will be overwritten.

Copying source files from /tmp/tmp.zRQSjifCZQ/spinalcordtoolbox to /home/runner/sct_7.2.dev0

SCT will be installed here: [/scratch/02/lchauvin/workspace/projects/spinalcordtoolbox]

...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................

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

Downloading Miniforge...

wget -nv -O /tmp/tmp.zRQSjifCZQ/miniforge.sh https://github.com/conda-forge/miniforge/releases/download/24.11.2-1/Miniforge3-Linux-x86_64.sh

wget -nv -O /tmp/tmp.fRYleHJK6d/miniforge.sh https://github.com/conda-forge/miniforge/releases/download/24.11.2-1/Miniforge3-Linux-x86_64.sh

2025-10-20 11:03:04 URL:https://release-assets.githubusercontent.com/github-production-release-asset/221584272/81e205c2-1911-4a2d-8b46-066d460f73d6?sp=r&sv=2018-11-09&sr=b&spr=https&se=2025-10-20T11%3A45%3A36Z&rscd=attachment%3B+filename%3DMiniforge3-Linux-x86_64.sh&rsct=application%2Foctet-stream&skoid=96c2d410-5711-43a1-aedd-ab1947aa7ab0&sktid=398a6654-997b-47e9-b12b-9515b896b4de&skt=2025-10-20T10%3A45%3A01Z&ske=2025-10-20T11%3A45%3A36Z&sks=b&skv=2018-11-09&sig=3z7Zh%2FIVP9koICUReSw9uG4idTwebqbqMPC75KwKobo%3D&jwt=*** [77972610/77972610] -> "/tmp/tmp.zRQSjifCZQ/miniforge.sh" [1]

2025-10-15 15:22:51 URL:https://release-assets.githubusercontent.com/github-production-release-asset/221584272/81e205c2-1911-4a2d-8b46-066d460f73d6?sp=r&sv=2018-11-09&sr=b&spr=https&se=2025-10-15T16%3A00%3A24Z&rscd=attachment%3B+filename%3DMiniforge3-Linux-x86_64.sh&rsct=application%2Foctet-stream&skoid=96c2d410-5711-43a1-aedd-ab1947aa7ab0&sktid=398a6654-997b-47e9-b12b-9515b896b4de&skt=2025-10-15T15%3A00%3A07Z&ske=2025-10-15T16%3A00%3A24Z&sks=b&skv=2018-11-09&sig=gZl9lbEIwMEc%2B3uSHIC9rlNA489O46ysRDfTJlg00Ww%3D&jwt=eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzI1NiJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmVsZWFzZS1hc3NldHMuZ2l0aHVidXNlcmNvbnRlbnQuY29tIiwia2V5Ijoia2V5MSIsImV4cCI6MTc2MDU0MzU2NiwibmJmIjoxNzYwNTQxNzY2LCJwYXRoIjoicmVsZWFzZWFzc2V0cHJvZHVjdGlvbi5ibG9iLmNvcmUud2luZG93cy5uZXQifQ.Z6S8dSFr71LHeFj0Asow-z1IvznpiSk3ToCDSq6d0m4&response-content-disposition=attachment%3B%20filename%3DMiniforge3-Linux-x86_64.sh&response-content-type=application%2Foctet-stream [77972610/77972610] -> "/tmp/tmp.fRYleHJK6d/miniforge.sh" [1]

Installing Miniforge...

bash /tmp/tmp.zRQSjifCZQ/miniforge.sh -p /home/runner/sct_7.2.dev0/python -b -f

bash /tmp/tmp.fRYleHJK6d/miniforge.sh -p /scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/python -b -f

PREFIX=/home/runner/sct_7.2.dev0/python

PREFIX=/scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/python

Unpacking payload ...

Extracting _libgcc_mutex-0.1-conda_forge.tar.bz2

Extracting ca-certificates-2024.12.14-hbcca054_0.conda

Extracting ld_impl_linux-64-2.43-h712a8e2_2.conda

Extracting pybind11-abi-4-hd8ed1ab_3.tar.bz2

Extracting python_abi-3.12-5_cp312.conda

Extracting tzdata-2024b-hc8b5060_0.conda

Extracting libgomp-14.2.0-h77fa898_1.conda

Extracting _openmp_mutex-4.5-2_gnu.tar.bz2

Extracting libgcc-14.2.0-h77fa898_1.conda

Extracting c-ares-1.34.4-hb9d3cd8_0.conda

Extracting libexpat-2.6.4-h5888daf_0.conda

Extracting libgcc-ng-14.2.0-h69a702a_1.conda

Extracting liblzma-5.6.3-hb9d3cd8_1.conda

Extracting libstdcxx-14.2.0-hc0a3c3a_1.conda

Extracting libzlib-1.3.1-hb9d3cd8_2.conda

Extracting openssl-3.4.0-hb9d3cd8_0.conda

Extracting reproc-14.2.5.post0-hb9d3cd8_0.conda

Extracting bzip2-1.0.8-h4bc722e_7.conda

Extracting keyutils-1.6.1-h166bdaf_0.tar.bz2

Extracting libev-4.33-hd590300_2.conda

Extracting libffi-3.4.2-h7f98852_5.tar.bz2

Extracting libiconv-1.17-hd590300_2.conda

Extracting libnsl-2.0.1-hd590300_0.conda

Extracting libsqlite-3.47.2-hee588c1_0.conda

Extracting libssh2-1.11.1-hf672d98_0.conda

Extracting libstdcxx-ng-14.2.0-h4852527_1.conda

Extracting libuuid-2.38.1-h0b41bf4_0.conda

Extracting libxcrypt-4.4.36-hd590300_1.conda

Extracting lz4-c-1.10.0-h5888daf_1.conda

Extracting lzo-2.10-hd590300_1001.conda

Extracting ncurses-6.5-he02047a_1.conda

Extracting reproc-cpp-14.2.5.post0-h5888daf_0.conda

Extracting tk-8.6.13-noxft_h4845f30_101.conda

Extracting fmt-11.0.2-h434a139_0.conda

Extracting libedit-3.1.20191231-he28a2e2_2.tar.bz2

Extracting libnghttp2-1.64.0-h161d5f1_0.conda

Extracting libsolv-0.7.30-h3509ff9_0.conda

Extracting libxml2-2.13.5-h0d44e9d_1.conda

Extracting readline-8.2-h8228510_1.conda

Extracting yaml-cpp-0.8.0-h59595ed_0.conda

Extracting zstd-1.5.6-ha6fb4c9_0.conda

Extracting krb5-1.21.3-h659f571_0.conda

Extracting libarchive-3.7.7-h4585015_3.conda

Extracting python-3.12.8-h9e4cc4f_1_cpython.conda

Extracting libcurl-8.11.1-h332b0f4_0.conda

Extracting menuinst-2.2.0-py312h7900ff3_0.conda

Extracting archspec-0.2.3-pyhd8ed1ab_0.conda

Extracting boltons-24.0.0-pyhd8ed1ab_1.conda

Extracting brotli-python-1.1.0-py312h2ec8cdc_2.conda

Extracting certifi-2024.12.14-pyhd8ed1ab_0.conda

Extracting charset-normalizer-3.4.1-pyhd8ed1ab_0.conda

Extracting colorama-0.4.6-pyhd8ed1ab_1.conda

Extracting distro-1.9.0-pyhd8ed1ab_1.conda

Extracting frozendict-2.4.6-py312h66e93f0_0.conda

Extracting hpack-4.0.0-pyhd8ed1ab_1.conda

Extracting hyperframe-6.0.1-pyhd8ed1ab_1.conda

Extracting idna-3.10-pyhd8ed1ab_1.conda

Extracting jsonpointer-3.0.0-py312h7900ff3_1.conda

Extracting libmamba-1.5.12-h49b8a8d_0.conda

Extracting packaging-24.2-pyhd8ed1ab_2.conda

Extracting platformdirs-4.3.6-pyhd8ed1ab_1.conda

Extracting pluggy-1.5.0-pyhd8ed1ab_1.conda

Extracting pycosat-0.6.6-py312h66e93f0_2.conda

Extracting pycparser-2.22-pyh29332c3_1.conda

Extracting pysocks-1.7.1-pyha55dd90_7.conda

Extracting ruamel.yaml.clib-0.2.8-py312h66e93f0_1.conda

Extracting setuptools-75.6.0-pyhff2d567_1.conda

Extracting truststore-0.10.0-pyhd8ed1ab_0.conda

Extracting wheel-0.45.1-pyhd8ed1ab_1.conda

Extracting cffi-1.17.1-py312h06ac9bb_0.conda

Extracting h2-4.1.0-pyhd8ed1ab_1.conda

Extracting jsonpatch-1.33-pyhd8ed1ab_1.conda

Extracting libmambapy-1.5.12-py312hbaee817_0.conda

Extracting pip-24.3.1-pyh8b19718_2.conda

Extracting ruamel.yaml-0.18.8-py312h66e93f0_0.conda

Extracting tqdm-4.67.1-pyhd8ed1ab_1.conda

Extracting zstandard-0.23.0-py312hef9b889_1.conda

Extracting conda-package-streaming-0.11.0-pyhd8ed1ab_0.conda

Extracting urllib3-2.3.0-pyhd8ed1ab_0.conda

Extracting conda-package-handling-2.4.0-pyha770c72_1.conda

Extracting requests-2.32.3-pyhd8ed1ab_1.conda

Extracting conda-24.11.2-py312h7900ff3_1.conda

Extracting conda-libmamba-solver-24.9.0-pyhd8ed1ab_0.conda

Extracting mamba-1.5.12-py312h9460a1c_0.conda

Installing base environment...

Transaction

Prefix: /home/runner/sct_7.2.dev0/python

Prefix: /scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/python

Updating specs:

- conda-forge/linux-64::_libgcc_mutex==0.1=conda_forge[md5=d7c89558ba9fa0495403155b64376d81]

- conda-forge/linux-64::ca-certificates==2024.12.14=hbcca054_0[md5=720523eb0d6a9b0f6120c16b2aa4e7de]

- conda-forge/linux-64::ld_impl_linux-64==2.43=h712a8e2_2[md5=048b02e3962f066da18efe3a21b77672]

- conda-forge/noarch::pybind11-abi==4=hd8ed1ab_3[md5=878f923dd6acc8aeb47a75da6c4098be]

- conda-forge/linux-64::python_abi==3.12=5_cp312[md5=0424ae29b104430108f5218a66db7260]

- conda-forge/noarch::tzdata==2024b=hc8b5060_0[md5=8ac3367aafb1cc0a068483c580af8015]

- conda-forge/linux-64::libgomp==14.2.0=h77fa898_1[md5=cc3573974587f12dda90d96e3e55a702]

- conda-forge/linux-64::_openmp_mutex==4.5=2_gnu[md5=73aaf86a425cc6e73fcf236a5a46396d]

- conda-forge/linux-64::libgcc==14.2.0=h77fa898_1[md5=3cb76c3f10d3bc7f1105b2fc9db984df]

- conda-forge/linux-64::c-ares==1.34.4=hb9d3cd8_0[md5=e2775acf57efd5af15b8e3d1d74d72d3]

- conda-forge/linux-64::libexpat==2.6.4=h5888daf_0[md5=db833e03127376d461e1e13e76f09b6c]

- conda-forge/linux-64::libgcc-ng==14.2.0=h69a702a_1[md5=e39480b9ca41323497b05492a63bc35b]

- conda-forge/linux-64::liblzma==5.6.3=hb9d3cd8_1[md5=2ecf2f1c7e4e21fcfe6423a51a992d84]

- conda-forge/linux-64::libstdcxx==14.2.0=hc0a3c3a_1[md5=234a5554c53625688d51062645337328]

- conda-forge/linux-64::libzlib==1.3.1=hb9d3cd8_2[md5=edb0dca6bc32e4f4789199455a1dbeb8]

- conda-forge/linux-64::openssl==3.4.0=hb9d3cd8_0[md5=23cc74f77eb99315c0360ec3533147a9]

- conda-forge/linux-64::reproc==14.2.5.post0=hb9d3cd8_0[md5=69fbc0a9e42eb5fe6733d2d60d818822]

- conda-forge/linux-64::bzip2==1.0.8=h4bc722e_7[md5=62ee74e96c5ebb0af99386de58cf9553]

- conda-forge/linux-64::keyutils==1.6.1=h166bdaf_0[md5=30186d27e2c9fa62b45fb1476b7200e3]

- conda-forge/linux-64::libev==4.33=hd590300_2[md5=172bf1cd1ff8629f2b1179945ed45055]

- conda-forge/linux-64::libffi==3.4.2=h7f98852_5[md5=d645c6d2ac96843a2bfaccd2d62b3ac3]

- conda-forge/linux-64::libiconv==1.17=hd590300_2[md5=d66573916ffcf376178462f1b61c941e]

- conda-forge/linux-64::libnsl==2.0.1=hd590300_0[md5=30fd6e37fe21f86f4bd26d6ee73eeec7]

- conda-forge/linux-64::libsqlite==3.47.2=hee588c1_0[md5=b58da17db24b6e08bcbf8fed2fb8c915]

- conda-forge/linux-64::libssh2==1.11.1=hf672d98_0[md5=be2de152d8073ef1c01b7728475f2fe7]

- conda-forge/linux-64::libstdcxx-ng==14.2.0=h4852527_1[md5=8371ac6457591af2cf6159439c1fd051]

- conda-forge/linux-64::libuuid==2.38.1=h0b41bf4_0[md5=40b61aab5c7ba9ff276c41cfffe6b80b]

- conda-forge/linux-64::libxcrypt==4.4.36=hd590300_1[md5=5aa797f8787fe7a17d1b0821485b5adc]

- conda-forge/linux-64::lz4-c==1.10.0=h5888daf_1[md5=9de5350a85c4a20c685259b889aa6393]

- conda-forge/linux-64::lzo==2.10=hd590300_1001[md5=ec7398d21e2651e0dcb0044d03b9a339]

- conda-forge/linux-64::ncurses==6.5=he02047a_1[md5=70caf8bb6cf39a0b6b7efc885f51c0fe]

- conda-forge/linux-64::reproc-cpp==14.2.5.post0=h5888daf_0[md5=828302fca535f9cfeb598d5f7c204323]

- conda-forge/linux-64::tk==8.6.13=noxft_h4845f30_101[md5=d453b98d9c83e71da0741bb0ff4d76bc]

- conda-forge/linux-64::fmt==11.0.2=h434a139_0[md5=995f7e13598497691c1dc476d889bc04]

- conda-forge/linux-64::libedit==3.1.20191231=he28a2e2_2[md5=4d331e44109e3f0e19b4cb8f9b82f3e1]

- conda-forge/linux-64::libnghttp2==1.64.0=h161d5f1_0[md5=19e57602824042dfd0446292ef90488b]

- conda-forge/linux-64::libsolv==0.7.30=h3509ff9_0[md5=02539b77d25aa4f65b20246549e256c3]

- conda-forge/linux-64::libxml2==2.13.5=h0d44e9d_1[md5=f5b05674697ae7d2c5932766695945e1]

- conda-forge/linux-64::readline==8.2=h8228510_1[md5=47d31b792659ce70f470b5c82fdfb7a4]

- conda-forge/linux-64::yaml-cpp==0.8.0=h59595ed_0[md5=965eaacd7c18eb8361fd12bb9e7a57d7]

- conda-forge/linux-64::zstd==1.5.6=ha6fb4c9_0[md5=4d056880988120e29d75bfff282e0f45]

- conda-forge/linux-64::krb5==1.21.3=h659f571_0[md5=3f43953b7d3fb3aaa1d0d0723d91e368]

- conda-forge/linux-64::libarchive==3.7.7=h4585015_3[md5=a28808eae584c7f519943719b2a2b386]

- conda-forge/linux-64::python==3.12.8=h9e4cc4f_1_cpython[md5=7fd2fd79436d9b473812f14e86746844]

- conda-forge/linux-64::libcurl==8.11.1=h332b0f4_0[md5=2b3e0081006dc21e8bf53a91c83a055c]

- conda-forge/linux-64::menuinst==2.2.0=py312h7900ff3_0[md5=f22f8e77b36e67297feffe03eefd5375]

- conda-forge/noarch::archspec==0.2.3=pyhd8ed1ab_0[md5=192278292e20704f663b9c766909d67b]

- conda-forge/noarch::boltons==24.0.0=pyhd8ed1ab_1[md5=d88c38e66d85ecc9c7e2c4110676bbf4]

- conda-forge/linux-64::brotli-python==1.1.0=py312h2ec8cdc_2[md5=b0b867af6fc74b2a0aa206da29c0f3cf]

- conda-forge/noarch::certifi==2024.12.14=pyhd8ed1ab_0[md5=6feb87357ecd66733be3279f16a8c400]

- conda-forge/noarch::charset-normalizer==3.4.1=pyhd8ed1ab_0[md5=e83a31202d1c0a000fce3e9cf3825875]

- conda-forge/noarch::colorama==0.4.6=pyhd8ed1ab_1[md5=962b9857ee8e7018c22f2776ffa0b2d7]

- conda-forge/noarch::distro==1.9.0=pyhd8ed1ab_1[md5=0a2014fd9860f8b1eaa0b1f3d3771a08]

- conda-forge/linux-64::frozendict==2.4.6=py312h66e93f0_0[md5=9fa8408745a0621314b7751d11fecc18]

- conda-forge/noarch::hpack==4.0.0=pyhd8ed1ab_1[md5=2aa5ff7fa34a81b9196532c84c10d865]

- conda-forge/noarch::hyperframe==6.0.1=pyhd8ed1ab_1[md5=566e75c90c1d0c8c459eb0ad9833dc7a]

- conda-forge/noarch::idna==3.10=pyhd8ed1ab_1[md5=39a4f67be3286c86d696df570b1201b7]

- conda-forge/linux-64::jsonpointer==3.0.0=py312h7900ff3_1[md5=6b51f7459ea4073eeb5057207e2e1e3d]

- conda-forge/linux-64::libmamba==1.5.12=h49b8a8d_0[md5=d6aec145c4f2473c09c2699d74f6dfc0]

- conda-forge/noarch::packaging==24.2=pyhd8ed1ab_2[md5=3bfed7e6228ebf2f7b9eaa47f1b4e2aa]

- conda-forge/noarch::platformdirs==4.3.6=pyhd8ed1ab_1[md5=577852c7e53901ddccc7e6a9959ddebe]

- conda-forge/noarch::pluggy==1.5.0=pyhd8ed1ab_1[md5=e9dcbce5f45f9ee500e728ae58b605b6]

- conda-forge/linux-64::pycosat==0.6.6=py312h66e93f0_2[md5=08223e6a73e0bca5ade16ec4cebebf23]

- conda-forge/noarch::pycparser==2.22=pyh29332c3_1[md5=12c566707c80111f9799308d9e265aef]

- conda-forge/noarch::pysocks==1.7.1=pyha55dd90_7[md5=461219d1a5bd61342293efa2c0c90eac]

- conda-forge/linux-64::ruamel.yaml.clib==0.2.8=py312h66e93f0_1[md5=532c3e5d0280be4fea52396ec1fa7d5d]

- conda-forge/noarch::setuptools==75.6.0=pyhff2d567_1[md5=fc80f7995e396cbaeabd23cf46c413dc]

- conda-forge/noarch::truststore==0.10.0=pyhd8ed1ab_0[md5=ad1c20cd193e3044bcf17798c33b9d67]

- conda-forge/noarch::wheel==0.45.1=pyhd8ed1ab_1[md5=75cb7132eb58d97896e173ef12ac9986]

- conda-forge/linux-64::cffi==1.17.1=py312h06ac9bb_0[md5=a861504bbea4161a9170b85d4d2be840]

- conda-forge/noarch::h2==4.1.0=pyhd8ed1ab_1[md5=825927dc7b0f287ef8d4d0011bb113b1]

- conda-forge/noarch::jsonpatch==1.33=pyhd8ed1ab_1[md5=cb60ae9cf02b9fcb8004dec4089e5691]

- conda-forge/linux-64::libmambapy==1.5.12=py312hbaee817_0[md5=88dd983e44c86cdde2817ecfa7d84d5a]

- conda-forge/noarch::pip==24.3.1=pyh8b19718_2[md5=04e691b9fadd93a8a9fad87a81d4fd8f]

- conda-forge/linux-64::ruamel.yaml==0.18.8=py312h66e93f0_0[md5=b77952bccd6b8d5c46e2f54354b4296b]

- conda-forge/noarch::tqdm==4.67.1=pyhd8ed1ab_1[md5=9efbfdc37242619130ea42b1cc4ed861]

- conda-forge/linux-64::zstandard==0.23.0=py312hef9b889_1[md5=8b7069e9792ee4e5b4919a7a306d2e67]

- conda-forge/noarch::conda-package-streaming==0.11.0=pyhd8ed1ab_0[md5=bc9533d8616a97551ed144789bf9c1cd]

- conda-forge/noarch::urllib3==2.3.0=pyhd8ed1ab_0[md5=32674f8dbfb7b26410ed580dd3c10a29]

- conda-forge/noarch::conda-package-handling==2.4.0=pyha770c72_1[md5=28b86d110bda4ef40e680d1afa9ddb1d]

- conda-forge/noarch::requests==2.32.3=pyhd8ed1ab_1[md5=a9b9368f3701a417eac9edbcae7cb737]

- conda-forge/linux-64::conda==24.11.2=py312h7900ff3_1[md5=2dff8a88fb65b9c99f6c28aad1126c66]

- conda-forge/noarch::conda-libmamba-solver==24.9.0=pyhd8ed1ab_0[md5=45378d089c5f72c9c0d63d58414c645d]

- conda-forge/linux-64::mamba==1.5.12=py312h9460a1c_0[md5=59a9360536caad98732fdfdc320e41dc]

Package Version Build Channel Size

─────────────────────────────────────────────────────────────────────────────────────

Install:

+ _libgcc_mutex 0.1 conda_forge conda-forge

+ ca-certificates 2024.12.14 hbcca054_0 conda-forge

+ ld_impl_linux-64 2.43 h712a8e2_2 conda-forge

+ pybind11-abi 4 hd8ed1ab_3 conda-forge

+ python_abi 3.12 5_cp312 conda-forge

+ tzdata 2024b hc8b5060_0 conda-forge

+ libgomp 14.2.0 h77fa898_1 conda-forge

+ _openmp_mutex 4.5 2_gnu conda-forge

+ libgcc 14.2.0 h77fa898_1 conda-forge

+ c-ares 1.34.4 hb9d3cd8_0 conda-forge

+ libexpat 2.6.4 h5888daf_0 conda-forge

+ libgcc-ng 14.2.0 h69a702a_1 conda-forge

+ liblzma 5.6.3 hb9d3cd8_1 conda-forge

+ libstdcxx 14.2.0 hc0a3c3a_1 conda-forge

+ libzlib 1.3.1 hb9d3cd8_2 conda-forge

+ openssl 3.4.0 hb9d3cd8_0 conda-forge

+ reproc 14.2.5.post0 hb9d3cd8_0 conda-forge

+ bzip2 1.0.8 h4bc722e_7 conda-forge

+ keyutils 1.6.1 h166bdaf_0 conda-forge

+ libev 4.33 hd590300_2 conda-forge

+ libffi 3.4.2 h7f98852_5 conda-forge

+ libiconv 1.17 hd590300_2 conda-forge

+ libnsl 2.0.1 hd590300_0 conda-forge

+ libsqlite 3.47.2 hee588c1_0 conda-forge

+ libssh2 1.11.1 hf672d98_0 conda-forge

+ libstdcxx-ng 14.2.0 h4852527_1 conda-forge

+ libuuid 2.38.1 h0b41bf4_0 conda-forge

+ libxcrypt 4.4.36 hd590300_1 conda-forge

+ lz4-c 1.10.0 h5888daf_1 conda-forge

+ lzo 2.10 hd590300_1001 conda-forge

+ ncurses 6.5 he02047a_1 conda-forge

+ reproc-cpp 14.2.5.post0 h5888daf_0 conda-forge

+ tk 8.6.13 noxft_h4845f30_101 conda-forge

+ fmt 11.0.2 h434a139_0 conda-forge

+ libedit 3.1.20191231 he28a2e2_2 conda-forge

+ libnghttp2 1.64.0 h161d5f1_0 conda-forge

+ libsolv 0.7.30 h3509ff9_0 conda-forge

+ libxml2 2.13.5 h0d44e9d_1 conda-forge

+ readline 8.2 h8228510_1 conda-forge

+ yaml-cpp 0.8.0 h59595ed_0 conda-forge

+ zstd 1.5.6 ha6fb4c9_0 conda-forge

+ krb5 1.21.3 h659f571_0 conda-forge

+ libarchive 3.7.7 h4585015_3 conda-forge

+ python 3.12.8 h9e4cc4f_1_cpython conda-forge

+ libcurl 8.11.1 h332b0f4_0 conda-forge

+ menuinst 2.2.0 py312h7900ff3_0 conda-forge

+ archspec 0.2.3 pyhd8ed1ab_0 conda-forge

+ boltons 24.0.0 pyhd8ed1ab_1 conda-forge

+ brotli-python 1.1.0 py312h2ec8cdc_2 conda-forge

+ certifi 2024.12.14 pyhd8ed1ab_0 conda-forge

+ charset-normalizer 3.4.1 pyhd8ed1ab_0 conda-forge

+ colorama 0.4.6 pyhd8ed1ab_1 conda-forge

+ distro 1.9.0 pyhd8ed1ab_1 conda-forge

+ frozendict 2.4.6 py312h66e93f0_0 conda-forge

+ hpack 4.0.0 pyhd8ed1ab_1 conda-forge

+ hyperframe 6.0.1 pyhd8ed1ab_1 conda-forge

+ idna 3.10 pyhd8ed1ab_1 conda-forge

+ jsonpointer 3.0.0 py312h7900ff3_1 conda-forge

+ libmamba 1.5.12 h49b8a8d_0 conda-forge

+ packaging 24.2 pyhd8ed1ab_2 conda-forge

+ platformdirs 4.3.6 pyhd8ed1ab_1 conda-forge

+ pluggy 1.5.0 pyhd8ed1ab_1 conda-forge

+ pycosat 0.6.6 py312h66e93f0_2 conda-forge

+ pycparser 2.22 pyh29332c3_1 conda-forge

+ pysocks 1.7.1 pyha55dd90_7 conda-forge

+ ruamel.yaml.clib 0.2.8 py312h66e93f0_1 conda-forge

+ setuptools 75.6.0 pyhff2d567_1 conda-forge

+ truststore 0.10.0 pyhd8ed1ab_0 conda-forge

+ wheel 0.45.1 pyhd8ed1ab_1 conda-forge

+ cffi 1.17.1 py312h06ac9bb_0 conda-forge

+ h2 4.1.0 pyhd8ed1ab_1 conda-forge

+ jsonpatch 1.33 pyhd8ed1ab_1 conda-forge

+ libmambapy 1.5.12 py312hbaee817_0 conda-forge

+ pip 24.3.1 pyh8b19718_2 conda-forge

+ ruamel.yaml 0.18.8 py312h66e93f0_0 conda-forge

+ tqdm 4.67.1 pyhd8ed1ab_1 conda-forge

+ zstandard 0.23.0 py312hef9b889_1 conda-forge

+ conda-package-streaming 0.11.0 pyhd8ed1ab_0 conda-forge

+ urllib3 2.3.0 pyhd8ed1ab_0 conda-forge

+ conda-package-handling 2.4.0 pyha770c72_1 conda-forge

+ requests 2.32.3 pyhd8ed1ab_1 conda-forge

+ conda 24.11.2 py312h7900ff3_1 conda-forge

+ conda-libmamba-solver 24.9.0 pyhd8ed1ab_0 conda-forge

+ mamba 1.5.12 py312h9460a1c_0 conda-forge

Summary:

Install: 84 packages

Total download: 0 B

Transaction starting

Transaction finished

To activate this environment, use:

micromamba activate /home/runner/sct_7.2.dev0/python

micromamba activate /scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/python

Or to execute a single command in this environment, use:

micromamba run -p /home/runner/sct_7.2.dev0/python mycommand

micromamba run -p /scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/python mycommand

installation finished.

Creating conda environment...

Channels:

- defaults

- conda-forge

- nodefaults

Platform: linux-64

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

Solving environment: ...working... done

==> WARNING: A newer version of conda exists. <==

current version: 24.11.2

latest version: 25.9.1

Please update conda by running

$ conda update -n base -c conda-forge conda

## Package Plan ##

environment location: /home/runner/sct_7.2.dev0/python/envs/venv_sct

environment location: /scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/python/envs/venv_sct

added / updated specs:

- python=3.10

The following packages will be downloaded:

package | build

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

bzip2-1.0.8 | hda65f42_8 254 KB conda-forge

_libgcc_mutex-0.1 | main 3 KB

ca-certificates-2025.10.5 | hbd8a1cb_0 152 KB conda-forge

_openmp_mutex-5.1 | 1_gnu 21 KB

ld_impl_linux-64-2.44 | ha97dd6f_2 730 KB conda-forge

bzip2-1.0.8 | h5eee18b_6 262 KB

libexpat-2.7.1 | hecca717_0 73 KB conda-forge

ca-certificates-2025.9.9 | h06a4308_0 127 KB

libffi-3.5.2 | h9ec8514_0 56 KB conda-forge

expat-2.7.1 | h6a678d5_0 182 KB

libgcc-15.2.0 | h767d61c_7 803 KB conda-forge

ld_impl_linux-64-2.44 | h153f514_2 672 KB

libgcc-ng-15.2.0 | h69a702a_7 29 KB conda-forge

libffi-3.4.4 | h6a678d5_1 141 KB

libgomp-15.2.0 | h767d61c_7 437 KB conda-forge

libgcc-ng-11.2.0 | h1234567_1 5.3 MB

liblzma-5.8.1 | hb9d3cd8_2 110 KB conda-forge

libgomp-11.2.0 | h1234567_1 474 KB

libnsl-2.0.1 | hb9d3cd8_1 33 KB conda-forge

libstdcxx-ng-11.2.0 | h1234567_1 4.7 MB

libsqlite-3.50.4 | h0c1763c_0 911 KB conda-forge

libuuid-1.41.5 | h5eee18b_0 27 KB

libuuid-2.41.2 | he9a06e4_0 36 KB conda-forge

libxcb-1.17.0 | h9b100fa_0 430 KB

ncurses-6.5 | h2d0b736_3 871 KB conda-forge

libzlib-1.3.1 | hb25bd0a_0 59 KB

openssl-3.5.4 | h26f9b46_0 3.0 MB conda-forge

ncurses-6.5 | h7934f7d_0 1.1 MB

pip-25.2 | pyh8b19718_0 1.1 MB conda-forge

openssl-3.0.18 | hd6dcaed_0 4.5 MB

python-3.10.19 |hd994cfb_1_cpython 24.2 MB conda-forge

pip-25.2 | pyhc872135_0 1.2 MB

readline-8.2 | h8c095d6_2 276 KB conda-forge

pthread-stubs-0.3 | h0ce48e5_1 5 KB

setuptools-80.9.0 | pyhff2d567_0 731 KB conda-forge

python-3.10.18 | h1a3bd86_0 26.5 MB

tk-8.6.13 |noxft_hd72426e_102 3.1 MB conda-forge

readline-8.3 | hc2a1206_0 471 KB

tzdata-2025b | h78e105d_0 120 KB conda-forge

setuptools-80.9.0 | py310h06a4308_0 1.4 MB

sqlite-3.50.2 | hb25bd0a_1 1.1 MB

tk-8.6.15 | h54e0aa7_0 3.4 MB

tzdata-2025b | h04d1e81_0 116 KB

wheel-0.45.1 | py310h06a4308_0 115 KB

xorg-libx11-1.8.12 | h9b100fa_1 895 KB

xorg-libxau-1.0.12 | h9b100fa_0 13 KB

xorg-libxdmcp-1.1.5 | h9b100fa_0 19 KB

xorg-xorgproto-2024.1 | h5eee18b_1 580 KB

xz-5.6.4 | h5eee18b_1 567 KB

zlib-1.3.1 | hb25bd0a_0 96 KB

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

Total: 36.9 MB

Total: 54.5 MB

The following NEW packages will be INSTALLED:

_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge

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

_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu

_openmp_mutex pkgs/main/linux-64::_openmp_mutex-5.1-1_gnu

bzip2 conda-forge/linux-64::bzip2-1.0.8-hda65f42_8

bzip2 pkgs/main/linux-64::bzip2-1.0.8-h5eee18b_6

ca-certificates conda-forge/noarch::ca-certificates-2025.10.5-hbd8a1cb_0

ca-certificates pkgs/main/linux-64::ca-certifica

ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.44-ha97dd6f_2

libexpat conda-forge/linux-64::libexpat-2.7.1-hecca717_0

libffi conda-forge/linux-64::libffi-3.5.2-h9ec8514_0

libgcc conda-forge/linux-64::libgcc-15.2.0-h767d61c_7

libgcc-ng conda-forge/linux-64::libg

Saved diffs

Original text

Open file

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

Checking OS type and version...

Linux runnervmnfq8z 6.8.0-1036-azure #42~22.04.1-Ubuntu SMP Fri Sep 12 00:09:41 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux

Checking requirements...

OK!

Source files not present. Downloading source files (@ master) to /tmp/tmp.zRQSjifCZQ/spinalcordtoolbox.
Cloning into '/tmp/tmp.zRQSjifCZQ/spinalcordtoolbox'...

SCT version ......... 7.2.dev0
Installation type ... package
Operating system .... linux (unknown)
Shell config ........ /home/runner/.bashrc

Checking permissions on required file /home/runner/.bashrc:
  - File exists: True
  - File ownership: True
  - Read permissions: True
  - Write permissions: True

SCT will be installed here: [/home/runner/sct_7.2.dev0]

Copying source files from /tmp/tmp.zRQSjifCZQ/spinalcordtoolbox to /home/runner/sct_7.2.dev0

wget -nv -O /tmp/tmp.zRQSjifCZQ/miniforge.sh https://github.com/conda-forge/miniforge/releases/download/24.11.2-1/Miniforge3-Linux-x86_64.sh

Installing Miniforge...

bash /tmp/tmp.zRQSjifCZQ/miniforge.sh -p /home/runner/sct_7.2.dev0/python -b -f

PREFIX=/home/runner/sct_7.2.dev0/python
Unpacking payload ...
Extracting _libgcc_mutex-0.1-conda_forge.tar.bz2
Extracting ca-certificates-2024.12.14-hbcca054_0.conda
Extracting ld_impl_linux-64-2.43-h712a8e2_2.conda
Extracting pybind11-abi-4-hd8ed1ab_3.tar.bz2
Extracting python_abi-3.12-5_cp312.conda
Extracting tzdata-2024b-hc8b5060_0.conda
Extracting libgomp-14.2.0-h77fa898_1.conda
Extracting _openmp_mutex-4.5-2_gnu.tar.bz2
Extracting libgcc-14.2.0-h77fa898_1.conda
Extracting c-ares-1.34.4-hb9d3cd8_0.conda
Extracting libexpat-2.6.4-h5888daf_0.conda
Extracting libgcc-ng-14.2.0-h69a702a_1.conda
Extracting liblzma-5.6.3-hb9d3cd8_1.conda
Extracting libstdcxx-14.2.0-hc0a3c3a_1.conda
Extracting libzlib-1.3.1-hb9d3cd8_2.conda
Extracting openssl-3.4.0-hb9d3cd8_0.conda
Extracting reproc-14.2.5.post0-hb9d3cd8_0.conda
Extracting bzip2-1.0.8-h4bc722e_7.conda
Extracting keyutils-1.6.1-h166bdaf_0.tar.bz2
Extracting libev-4.33-hd590300_2.conda
Extracting libffi-3.4.2-h7f98852_5.tar.bz2
Extracting libiconv-1.17-hd590300_2.conda
Extracting libnsl-2.0.1-hd590300_0.conda
Extracting libsqlite-3.47.2-hee588c1_0.conda
Extracting libssh2-1.11.1-hf672d98_0.conda
Extracting libstdcxx-ng-14.2.0-h4852527_1.conda
Extracting libuuid-2.38.1-h0b41bf4_0.conda
Extracting libxcrypt-4.4.36-hd590300_1.conda
Extracting lz4-c-1.10.0-h5888daf_1.conda
Extracting lzo-2.10-hd590300_1001.conda
Extracting ncurses-6.5-he02047a_1.conda
Extracting reproc-cpp-14.2.5.post0-h5888daf_0.conda
Extracting tk-8.6.13-noxft_h4845f30_101.conda
Extracting fmt-11.0.2-h434a139_0.conda
Extracting libedit-3.1.20191231-he28a2e2_2.tar.bz2
Extracting libnghttp2-1.64.0-h161d5f1_0.conda
Extracting libsolv-0.7.30-h3509ff9_0.conda
Extracting libxml2-2.13.5-h0d44e9d_1.conda
Extracting readline-8.2-h8228510_1.conda
Extracting yaml-cpp-0.8.0-h59595ed_0.conda
Extracting zstd-1.5.6-ha6fb4c9_0.conda
Extracting krb5-1.21.3-h659f571_0.conda
Extracting libarchive-3.7.7-h4585015_3.conda
Extracting python-3.12.8-h9e4cc4f_1_cpython.conda
Extracting libcurl-8.11.1-h332b0f4_0.conda
Extracting menuinst-2.2.0-py312h7900ff3_0.conda
Extracting archspec-0.2.3-pyhd8ed1ab_0.conda
Extracting boltons-24.0.0-pyhd8ed1ab_1.conda
Extracting brotli-python-1.1.0-py312h2ec8cdc_2.conda
Extracting certifi-2024.12.14-pyhd8ed1ab_0.conda
Extracting charset-normalizer-3.4.1-pyhd8ed1ab_0.conda
Extracting colorama-0.4.6-pyhd8ed1ab_1.conda
Extracting distro-1.9.0-pyhd8ed1ab_1.conda
Extracting frozendict-2.4.6-py312h66e93f0_0.conda
Extracting hpack-4.0.0-pyhd8ed1ab_1.conda
Extracting hyperframe-6.0.1-pyhd8ed1ab_1.conda
Extracting idna-3.10-pyhd8ed1ab_1.conda
Extracting jsonpointer-3.0.0-py312h7900ff3_1.conda
Extracting libmamba-1.5.12-h49b8a8d_0.conda
Extracting packaging-24.2-pyhd8ed1ab_2.conda
Extracting platformdirs-4.3.6-pyhd8ed1ab_1.conda
Extracting pluggy-1.5.0-pyhd8ed1ab_1.conda
Extracting pycosat-0.6.6-py312h66e93f0_2.conda
Extracting pycparser-2.22-pyh29332c3_1.conda
Extracting pysocks-1.7.1-pyha55dd90_7.conda
Extracting ruamel.yaml.clib-0.2.8-py312h66e93f0_1.conda
Extracting setuptools-75.6.0-pyhff2d567_1.conda
Extracting truststore-0.10.0-pyhd8ed1ab_0.conda
Extracting wheel-0.45.1-pyhd8ed1ab_1.conda
Extracting cffi-1.17.1-py312h06ac9bb_0.conda
Extracting h2-4.1.0-pyhd8ed1ab_1.conda
Extracting jsonpatch-1.33-pyhd8ed1ab_1.conda
Extracting libmambapy-1.5.12-py312hbaee817_0.conda
Extracting pip-24.3.1-pyh8b19718_2.conda
Extracting ruamel.yaml-0.18.8-py312h66e93f0_0.conda
Extracting tqdm-4.67.1-pyhd8ed1ab_1.conda
Extracting zstandard-0.23.0-py312hef9b889_1.conda
Extracting conda-package-streaming-0.11.0-pyhd8ed1ab_0.conda
Extracting urllib3-2.3.0-pyhd8ed1ab_0.conda
Extracting conda-package-handling-2.4.0-pyha770c72_1.conda
Extracting requests-2.32.3-pyhd8ed1ab_1.conda
Extracting conda-24.11.2-py312h7900ff3_1.conda
Extracting conda-libmamba-solver-24.9.0-pyhd8ed1ab_0.conda
Extracting mamba-1.5.12-py312h9460a1c_0.conda

Installing base environment...

Transaction

Prefix: /home/runner/sct_7.2.dev0/python

Updating specs:

- conda-forge/linux-64::_libgcc_mutex==0.1=conda_forge[md5=d7c89558ba9fa0495403155b64376d81]
   - conda-forge/linux-64::ca-certificates==2024.12.14=hbcca054_0[md5=720523eb0d6a9b0f6120c16b2aa4e7de]
   - conda-forge/linux-64::ld_impl_linux-64==2.43=h712a8e2_2[md5=048b02e3962f066da18efe3a21b77672]
   - conda-forge/noarch::pybind11-abi==4=hd8ed1ab_3[md5=878f923dd6acc8aeb47a75da6c4098be]
   - conda-forge/linux-64::python_abi==3.12=5_cp312[md5=0424ae29b104430108f5218a66db7260]
   - conda-forge/noarch::tzdata==2024b=hc8b5060_0[md5=8ac3367aafb1cc0a068483c580af8015]
   - conda-forge/linux-64::libgomp==14.2.0=h77fa898_1[md5=cc3573974587f12dda90d96e3e55a702]
   - conda-forge/linux-64::_openmp_mutex==4.5=2_gnu[md5=73aaf86a425cc6e73fcf236a5a46396d]
   - conda-forge/linux-64::libgcc==14.2.0=h77fa898_1[md5=3cb76c3f10d3bc7f1105b2fc9db984df]
   - conda-forge/linux-64::c-ares==1.34.4=hb9d3cd8_0[md5=e2775acf57efd5af15b8e3d1d74d72d3]
   - conda-forge/linux-64::libexpat==2.6.4=h5888daf_0[md5=db833e03127376d461e1e13e76f09b6c]
   - conda-forge/linux-64::libgcc-ng==14.2.0=h69a702a_1[md5=e39480b9ca41323497b05492a63bc35b]
   - conda-forge/linux-64::liblzma==5.6.3=hb9d3cd8_1[md5=2ecf2f1c7e4e21fcfe6423a51a992d84]
   - conda-forge/linux-64::libstdcxx==14.2.0=hc0a3c3a_1[md5=234a5554c53625688d51062645337328]
   - conda-forge/linux-64::libzlib==1.3.1=hb9d3cd8_2[md5=edb0dca6bc32e4f4789199455a1dbeb8]
   - conda-forge/linux-64::openssl==3.4.0=hb9d3cd8_0[md5=23cc74f77eb99315c0360ec3533147a9]
   - conda-forge/linux-64::reproc==14.2.5.post0=hb9d3cd8_0[md5=69fbc0a9e42eb5fe6733d2d60d818822]
   - conda-forge/linux-64::bzip2==1.0.8=h4bc722e_7[md5=62ee74e96c5ebb0af99386de58cf9553]
   - conda-forge/linux-64::keyutils==1.6.1=h166bdaf_0[md5=30186d27e2c9fa62b45fb1476b7200e3]
   - conda-forge/linux-64::libev==4.33=hd590300_2[md5=172bf1cd1ff8629f2b1179945ed45055]
   - conda-forge/linux-64::libffi==3.4.2=h7f98852_5[md5=d645c6d2ac96843a2bfaccd2d62b3ac3]
   - conda-forge/linux-64::libiconv==1.17=hd590300_2[md5=d66573916ffcf376178462f1b61c941e]
   - conda-forge/linux-64::libnsl==2.0.1=hd590300_0[md5=30fd6e37fe21f86f4bd26d6ee73eeec7]
   - conda-forge/linux-64::libsqlite==3.47.2=hee588c1_0[md5=b58da17db24b6e08bcbf8fed2fb8c915]
   - conda-forge/linux-64::libssh2==1.11.1=hf672d98_0[md5=be2de152d8073ef1c01b7728475f2fe7]
   - conda-forge/linux-64::libstdcxx-ng==14.2.0=h4852527_1[md5=8371ac6457591af2cf6159439c1fd051]
   - conda-forge/linux-64::libuuid==2.38.1=h0b41bf4_0[md5=40b61aab5c7ba9ff276c41cfffe6b80b]
   - conda-forge/linux-64::libxcrypt==4.4.36=hd590300_1[md5=5aa797f8787fe7a17d1b0821485b5adc]
   - conda-forge/linux-64::lz4-c==1.10.0=h5888daf_1[md5=9de5350a85c4a20c685259b889aa6393]
   - conda-forge/linux-64::lzo==2.10=hd590300_1001[md5=ec7398d21e2651e0dcb0044d03b9a339]
   - conda-forge/linux-64::ncurses==6.5=he02047a_1[md5=70caf8bb6cf39a0b6b7efc885f51c0fe]
   - conda-forge/linux-64::reproc-cpp==14.2.5.post0=h5888daf_0[md5=828302fca535f9cfeb598d5f7c204323]
   - conda-forge/linux-64::tk==8.6.13=noxft_h4845f30_101[md5=d453b98d9c83e71da0741bb0ff4d76bc]
   - conda-forge/linux-64::fmt==11.0.2=h434a139_0[md5=995f7e13598497691c1dc476d889bc04]
   - conda-forge/linux-64::libedit==3.1.20191231=he28a2e2_2[md5=4d331e44109e3f0e19b4cb8f9b82f3e1]
   - conda-forge/linux-64::libnghttp2==1.64.0=h161d5f1_0[md5=19e57602824042dfd0446292ef90488b]
   - conda-forge/linux-64::libsolv==0.7.30=h3509ff9_0[md5=02539b77d25aa4f65b20246549e256c3]
   - conda-forge/linux-64::libxml2==2.13.5=h0d44e9d_1[md5=f5b05674697ae7d2c5932766695945e1]
   - conda-forge/linux-64::readline==8.2=h8228510_1[md5=47d31b792659ce70f470b5c82fdfb7a4]
   - conda-forge/linux-64::yaml-cpp==0.8.0=h59595ed_0[md5=965eaacd7c18eb8361fd12bb9e7a57d7]
   - conda-forge/linux-64::zstd==1.5.6=ha6fb4c9_0[md5=4d056880988120e29d75bfff282e0f45]
   - conda-forge/linux-64::krb5==1.21.3=h659f571_0[md5=3f43953b7d3fb3aaa1d0d0723d91e368]
   - conda-forge/linux-64::libarchive==3.7.7=h4585015_3[md5=a28808eae584c7f519943719b2a2b386]
   - conda-forge/linux-64::python==3.12.8=h9e4cc4f_1_cpython[md5=7fd2fd79436d9b473812f14e86746844]
   - conda-forge/linux-64::libcurl==8.11.1=h332b0f4_0[md5=2b3e0081006dc21e8bf53a91c83a055c]
   - conda-forge/linux-64::menuinst==2.2.0=py312h7900ff3_0[md5=f22f8e77b36e67297feffe03eefd5375]
   - conda-forge/noarch::archspec==0.2.3=pyhd8ed1ab_0[md5=192278292e20704f663b9c766909d67b]
   - conda-forge/noarch::boltons==24.0.0=pyhd8ed1ab_1[md5=d88c38e66d85ecc9c7e2c4110676bbf4]
   - conda-forge/linux-64::brotli-python==1.1.0=py312h2ec8cdc_2[md5=b0b867af6fc74b2a0aa206da29c0f3cf]
   - conda-forge/noarch::certifi==2024.12.14=pyhd8ed1ab_0[md5=6feb87357ecd66733be3279f16a8c400]
   - conda-forge/noarch::charset-normalizer==3.4.1=pyhd8ed1ab_0[md5=e83a31202d1c0a000fce3e9cf3825875]
   - conda-forge/noarch::colorama==0.4.6=pyhd8ed1ab_1[md5=962b9857ee8e7018c22f2776ffa0b2d7]
   - conda-forge/noarch::distro==1.9.0=pyhd8ed1ab_1[md5=0a2014fd9860f8b1eaa0b1f3d3771a08]
   - conda-forge/linux-64::frozendict==2.4.6=py312h66e93f0_0[md5=9fa8408745a0621314b7751d11fecc18]
   - conda-forge/noarch::hpack==4.0.0=pyhd8ed1ab_1[md5=2aa5ff7fa34a81b9196532c84c10d865]
   - conda-forge/noarch::hyperframe==6.0.1=pyhd8ed1ab_1[md5=566e75c90c1d0c8c459eb0ad9833dc7a]
   - conda-forge/noarch::idna==3.10=pyhd8ed1ab_1[md5=39a4f67be3286c86d696df570b1201b7]
   - conda-forge/linux-64::jsonpointer==3.0.0=py312h7900ff3_1[md5=6b51f7459ea4073eeb5057207e2e1e3d]
   - conda-forge/linux-64::libmamba==1.5.12=h49b8a8d_0[md5=d6aec145c4f2473c09c2699d74f6dfc0]
   - conda-forge/noarch::packaging==24.2=pyhd8ed1ab_2[md5=3bfed7e6228ebf2f7b9eaa47f1b4e2aa]
   - conda-forge/noarch::platformdirs==4.3.6=pyhd8ed1ab_1[md5=577852c7e53901ddccc7e6a9959ddebe]
   - conda-forge/noarch::pluggy==1.5.0=pyhd8ed1ab_1[md5=e9dcbce5f45f9ee500e728ae58b605b6]
   - conda-forge/linux-64::pycosat==0.6.6=py312h66e93f0_2[md5=08223e6a73e0bca5ade16ec4cebebf23]
   - conda-forge/noarch::pycparser==2.22=pyh29332c3_1[md5=12c566707c80111f9799308d9e265aef]
   - conda-forge/noarch::pysocks==1.7.1=pyha55dd90_7[md5=461219d1a5bd61342293efa2c0c90eac]
   - conda-forge/linux-64::ruamel.yaml.clib==0.2.8=py312h66e93f0_1[md5=532c3e5d0280be4fea52396ec1fa7d5d]
   - conda-forge/noarch::setuptools==75.6.0=pyhff2d567_1[md5=fc80f7995e396cbaeabd23cf46c413dc]
   - conda-forge/noarch::truststore==0.10.0=pyhd8ed1ab_0[md5=ad1c20cd193e3044bcf17798c33b9d67]
   - conda-forge/noarch::wheel==0.45.1=pyhd8ed1ab_1[md5=75cb7132eb58d97896e173ef12ac9986]
   - conda-forge/linux-64::cffi==1.17.1=py312h06ac9bb_0[md5=a861504bbea4161a9170b85d4d2be840]
   - conda-forge/noarch::h2==4.1.0=pyhd8ed1ab_1[md5=825927dc7b0f287ef8d4d0011bb113b1]
   - conda-forge/noarch::jsonpatch==1.33=pyhd8ed1ab_1[md5=cb60ae9cf02b9fcb8004dec4089e5691]
   - conda-forge/linux-64::libmambapy==1.5.12=py312hbaee817_0[md5=88dd983e44c86cdde2817ecfa7d84d5a]
   - conda-forge/noarch::pip==24.3.1=pyh8b19718_2[md5=04e691b9fadd93a8a9fad87a81d4fd8f]
   - conda-forge/linux-64::ruamel.yaml==0.18.8=py312h66e93f0_0[md5=b77952bccd6b8d5c46e2f54354b4296b]
   - conda-forge/noarch::tqdm==4.67.1=pyhd8ed1ab_1[md5=9efbfdc37242619130ea42b1cc4ed861]
   - conda-forge/linux-64::zstandard==0.23.0=py312hef9b889_1[md5=8b7069e9792ee4e5b4919a7a306d2e67]
   - conda-forge/noarch::conda-package-streaming==0.11.0=pyhd8ed1ab_0[md5=bc9533d8616a97551ed144789bf9c1cd]
   - conda-forge/noarch::urllib3==2.3.0=pyhd8ed1ab_0[md5=32674f8dbfb7b26410ed580dd3c10a29]
   - conda-forge/noarch::conda-package-handling==2.4.0=pyha770c72_1[md5=28b86d110bda4ef40e680d1afa9ddb1d]
   - conda-forge/noarch::requests==2.32.3=pyhd8ed1ab_1[md5=a9b9368f3701a417eac9edbcae7cb737]
   - conda-forge/linux-64::conda==24.11.2=py312h7900ff3_1[md5=2dff8a88fb65b9c99f6c28aad1126c66]
   - conda-forge/noarch::conda-libmamba-solver==24.9.0=pyhd8ed1ab_0[md5=45378d089c5f72c9c0d63d58414c645d]
   - conda-forge/linux-64::mamba==1.5.12=py312h9460a1c_0[md5=59a9360536caad98732fdfdc320e41dc]

Package                         Version  Build               Channel         Size
─────────────────────────────────────────────────────────────────────────────────────
  Install:
─────────────────────────────────────────────────────────────────────────────────────

+ _libgcc_mutex                     0.1  conda_forge         conda-forge         
  + ca-certificates            2024.12.14  hbcca054_0          conda-forge         
  + ld_impl_linux-64                 2.43  h712a8e2_2          conda-forge         
  + pybind11-abi                        4  hd8ed1ab_3          conda-forge         
  + python_abi                       3.12  5_cp312             conda-forge         
  + tzdata                          2024b  hc8b5060_0          conda-forge         
  + libgomp                        14.2.0  h77fa898_1          conda-forge         
  + _openmp_mutex                     4.5  2_gnu               conda-forge         
  + libgcc                         14.2.0  h77fa898_1          conda-forge         
  + c-ares                         1.34.4  hb9d3cd8_0          conda-forge         
  + libexpat                        2.6.4  h5888daf_0          conda-forge         
  + libgcc-ng                      14.2.0  h69a702a_1          conda-forge         
  + liblzma                         5.6.3  hb9d3cd8_1          conda-forge         
  + libstdcxx                      14.2.0  hc0a3c3a_1          conda-forge         
  + libzlib                         1.3.1  hb9d3cd8_2          conda-forge         
  + openssl                         3.4.0  hb9d3cd8_0          conda-forge         
  + reproc                   14.2.5.post0  hb9d3cd8_0          conda-forge         
  + bzip2                           1.0.8  h4bc722e_7          conda-forge         
  + keyutils                        1.6.1  h166bdaf_0          conda-forge         
  + libev                            4.33  hd590300_2          conda-forge         
  + libffi                          3.4.2  h7f98852_5          conda-forge         
  + libiconv                         1.17  hd590300_2          conda-forge         
  + libnsl                          2.0.1  hd590300_0          conda-forge         
  + libsqlite                      3.47.2  hee588c1_0          conda-forge         
  + libssh2                        1.11.1  hf672d98_0          conda-forge         
  + libstdcxx-ng                   14.2.0  h4852527_1          conda-forge         
  + libuuid                        2.38.1  h0b41bf4_0          conda-forge         
  + libxcrypt                      4.4.36  hd590300_1          conda-forge         
  + lz4-c                          1.10.0  h5888daf_1          conda-forge         
  + lzo                              2.10  hd590300_1001       conda-forge         
  + ncurses                           6.5  he02047a_1          conda-forge         
  + reproc-cpp               14.2.5.post0  h5888daf_0          conda-forge         
  + tk                             8.6.13  noxft_h4845f30_101  conda-forge         
  + fmt                            11.0.2  h434a139_0          conda-forge         
  + libedit                  3.1.20191231  he28a2e2_2          conda-forge         
  + libnghttp2                     1.64.0  h161d5f1_0          conda-forge         
  + libsolv                        0.7.30  h3509ff9_0          conda-forge         
  + libxml2                        2.13.5  h0d44e9d_1          conda-forge         
  + readline                          8.2  h8228510_1          conda-forge         
  + yaml-cpp                        0.8.0  h59595ed_0          conda-forge         
  + zstd                            1.5.6  ha6fb4c9_0          conda-forge         
  + krb5                           1.21.3  h659f571_0          conda-forge         
  + libarchive                      3.7.7  h4585015_3          conda-forge         
  + python                         3.12.8  h9e4cc4f_1_cpython  conda-forge         
  + libcurl                        8.11.1  h332b0f4_0          conda-forge         
  + menuinst                        2.2.0  py312h7900ff3_0     conda-forge         
  + archspec                        0.2.3  pyhd8ed1ab_0        conda-forge         
  + boltons                        24.0.0  pyhd8ed1ab_1        conda-forge         
  + brotli-python                   1.1.0  py312h2ec8cdc_2     conda-forge         
  + certifi                    2024.12.14  pyhd8ed1ab_0        conda-forge         
  + charset-normalizer              3.4.1  pyhd8ed1ab_0        conda-forge         
  + colorama                        0.4.6  pyhd8ed1ab_1        conda-forge         
  + distro                          1.9.0  pyhd8ed1ab_1        conda-forge         
  + frozendict                      2.4.6  py312h66e93f0_0     conda-forge         
  + hpack                           4.0.0  pyhd8ed1ab_1        conda-forge         
  + hyperframe                      6.0.1  pyhd8ed1ab_1        conda-forge         
  + idna                             3.10  pyhd8ed1ab_1        conda-forge         
  + jsonpointer                     3.0.0  py312h7900ff3_1     conda-forge         
  + libmamba                       1.5.12  h49b8a8d_0          conda-forge         
  + packaging                        24.2  pyhd8ed1ab_2        conda-forge         
  + platformdirs                    4.3.6  pyhd8ed1ab_1        conda-forge         
  + pluggy                          1.5.0  pyhd8ed1ab_1        conda-forge         
  + pycosat                         0.6.6  py312h66e93f0_2     conda-forge         
  + pycparser                        2.22  pyh29332c3_1        conda-forge         
  + pysocks                         1.7.1  pyha55dd90_7        conda-forge         
  + ruamel.yaml.clib                0.2.8  py312h66e93f0_1     conda-forge         
  + setuptools                     75.6.0  pyhff2d567_1        conda-forge         
  + truststore                     0.10.0  pyhd8ed1ab_0        conda-forge         
  + wheel                          0.45.1  pyhd8ed1ab_1        conda-forge         
  + cffi                           1.17.1  py312h06ac9bb_0     conda-forge         
  + h2                              4.1.0  pyhd8ed1ab_1        conda-forge         
  + jsonpatch                        1.33  pyhd8ed1ab_1        conda-forge         
  + libmambapy                     1.5.12  py312hbaee817_0     conda-forge         
  + pip                            24.3.1  pyh8b19718_2        conda-forge         
  + ruamel.yaml                    0.18.8  py312h66e93f0_0     conda-forge         
  + tqdm                           4.67.1  pyhd8ed1ab_1        conda-forge         
  + zstandard                      0.23.0  py312hef9b889_1     conda-forge         
  + conda-package-streaming        0.11.0  pyhd8ed1ab_0        conda-forge         
  + urllib3                         2.3.0  pyhd8ed1ab_0        conda-forge         
  + conda-package-handling          2.4.0  pyha770c72_1        conda-forge         
  + requests                       2.32.3  pyhd8ed1ab_1        conda-forge         
  + conda                         24.11.2  py312h7900ff3_1     conda-forge         
  + conda-libmamba-solver          24.9.0  pyhd8ed1ab_0        conda-forge         
  + mamba                          1.5.12  py312h9460a1c_0     conda-forge

Summary:

Install: 84 packages

Total download: 0 B

Transaction starting

Transaction finished

To activate this environment, use:

micromamba activate /home/runner/sct_7.2.dev0/python

Or to execute a single command in this environment, use:

micromamba run -p /home/runner/sct_7.2.dev0/python mycommand

installation finished.

Creating conda environment...

Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

==> WARNING: A newer version of conda exists. <==
    current version: 24.11.2
    latest version: 25.9.1

Please update conda by running

$ conda update -n base -c conda-forge conda

## Package Plan ##

environment location: /home/runner/sct_7.2.dev0/python/envs/venv_sct

added / updated specs:
    - python=3.10

The following packages will be downloaded:

package                    |            build
    ---------------------------|-----------------
    bzip2-1.0.8                |       hda65f42_8         254 KB  conda-forge
    ca-certificates-2025.10.5  |       hbd8a1cb_0         152 KB  conda-forge
    ld_impl_linux-64-2.44      |       ha97dd6f_2         730 KB  conda-forge
    libexpat-2.7.1             |       hecca717_0          73 KB  conda-forge
    libffi-3.5.2               |       h9ec8514_0          56 KB  conda-forge
    libgcc-15.2.0              |       h767d61c_7         803 KB  conda-forge
    libgcc-ng-15.2.0           |       h69a702a_7          29 KB  conda-forge
    libgomp-15.2.0             |       h767d61c_7         437 KB  conda-forge
    liblzma-5.8.1              |       hb9d3cd8_2         110 KB  conda-forge
    libnsl-2.0.1               |       hb9d3cd8_1          33 KB  conda-forge
    libsqlite-3.50.4           |       h0c1763c_0         911 KB  conda-forge
    libuuid-2.41.2             |       he9a06e4_0          36 KB  conda-forge
    ncurses-6.5                |       h2d0b736_3         871 KB  conda-forge
    openssl-3.5.4              |       h26f9b46_0         3.0 MB  conda-forge
    pip-25.2                   |     pyh8b19718_0         1.1 MB  conda-forge
    python-3.10.19             |hd994cfb_1_cpython        24.2 MB  conda-forge
    readline-8.2               |       h8c095d6_2         276 KB  conda-forge
    setuptools-80.9.0          |     pyhff2d567_0         731 KB  conda-forge
    tk-8.6.13                  |noxft_hd72426e_102         3.1 MB  conda-forge
    tzdata-2025b               |       h78e105d_0         120 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        36.9 MB

The following NEW packages will be INSTALLED:

_libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge 
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-2_gnu 
  bzip2              conda-forge/linux-64::bzip2-1.0.8-hda65f42_8 
  ca-certificates    conda-forge/noarch::ca-certificates-2025.10.5-hbd8a1cb_0 
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.44-ha97dd6f_2 
  libexpat           conda-forge/linux-64::libexpat-2.7.1-hecca717_0 
  libffi             conda-forge/linux-64::libffi-3.5.2-h9ec8514_0 
  libgcc             conda-forge/linux-64::libgcc-15.2.0-h767d61c_7 
  libgcc-ng          conda-forge/linux-64::libgcc-ng-15.2.0-h69a702a_7 
  libgomp            conda-forge/linux-64::libgomp-15.2.0-h767d61c_7 
  liblzma            conda-forge/linux-64::liblzma-5.8.1-hb9d3cd8_2 
  libnsl             conda-forge/linux-64::libnsl-2.0.1-hb9d3cd8_1 
  libsqlite          conda-forge/linux-64::libsqlite-3.50.4-h0c1763c_0 
  libuuid            conda-forge/linux-64::libuuid-2.41.2-he9a06e4_0 
  libxcrypt          conda-forge/linux-64::libxcrypt-4.4.36-hd590300_1 
  libzlib            conda-forge/linux-64::libzlib-1.3.1-hb9d3cd8_2 
  ncurses            conda-forge/linux-64::ncurses-6.5-h2d0b736_3 
  openssl            conda-forge/linux-64::openssl-3.5.4-h26f9b46_0 
  pip                conda-forge/noarch::pip-25.2-pyh8b19718_0 
  python             conda-forge/linux-64::python-3.10.19-hd994cfb_1_cpython 
  readline           conda-forge/linux-64::readline-8.2-h8c095d6_2 
  setuptools         conda-forge/noarch::setuptools-80.9.0-pyhff2d567_0 
  tk                 conda-forge/linux-64::tk-8.6.13-noxft_hd72426e_102 
  tzdata             conda-forge/noarch::tzdata-2025b-h78e105d_0 
  wheel              conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_1

Downloading and Extracting Packages: ...working...
python-3.10.19       | 24.2 MB   |            |   0%

tk-8.6.13            | 3.1 MB    |            |   0%

openssl-3.5.4        | 3.0 MB    |            |   0%

pip-25.2             | 1.1 MB    |            |   0%

libsqlite-3.50.4     | 911 KB    |            |   0%

ncurses-6.5          | 871 KB    |            |   0%

libgcc-15.2.0        | 803 KB    |            |   0%

setuptools-80.9.0    | 731 KB    |            |   0%

ld_impl_linux-64-2.4 | 730 KB    |            |   0%

libgomp-15.2.0       | 437 KB    |            |   0%

readline-8.2         | 276 KB    |            |   0%

bzip2-1.0.8          | 254 KB    |            |   0%

ca-certificates-2025 | 152 KB    |            |   0%

tzdata-2025b         | 120 KB    |            |   0%

liblzma-5.8.1        | 110 KB    |            |   0%

libexpat-2.7.1       | 73 KB     |            |   0%

libffi-3.5.2         | 56 KB     |            |   0%

libuuid-2.41.2       | 36 KB     |            |   0%

libnsl-2.0.1         | 33 KB     |            |   0%

... (more hidden) ...

pip-25.2             | 1.1 MB    | ########## | 100% 
python-3.10.19       | 24.2 MB   | #          |  11%

tk-8.6.13            | 3.1 MB    |            |   1%

openssl-3.5.4        | 3.0 MB    | ######1    |  61%

libsqlite-3.50.4     | 911 KB    | ########## | 100%

ncurses-6.5          | 871 KB    | 1          |   2%

libgcc-15.2.0        | 803 KB    | 1          |   2%

ncurses-6.5          | 871 KB    | ########## | 100% 
python-3.10.19       | 24.2 MB   | ##3        |  24%

libgcc-15.2.0        | 803 KB    | ########## | 100%

openssl-3.5.4        | 3.0 MB    | ########## | 100%

setuptools-80.9.0    | 731 KB    | 2          |   2%

libsqlite-3.50.4     | 911 KB    | ########## | 100%

ld_impl_linux-64-2.4 | 730 KB    | 2          |   2%

setuptools-80.9.0    | 731 KB    | ########## | 100%

libgomp-15.2.0       | 437 KB    | 3          |   4%

tk-8.6.13            | 3.1 MB    | ########## | 100%

ld_impl_linux-64-2.4 | 730 KB    | ########## | 100% 
python-3.10.19       | 24.2 MB   | ###6       |  37%

libgomp-15.2.0       | 437 KB    | ########## | 100%

readline-8.2         | 276 KB    | 5          |   6%

readline-8.2         | 276 KB    | ########## | 100%

ca-certificates-2025 | 152 KB    | #          |  11%

bzip2-1.0.8          | 254 KB    | 6          |   6%

ca-certificates-2025 | 152 KB    | ########## | 100%

tzdata-2025b         | 120 KB    | #3         |  13%

liblzma-5.8.1        | 110 KB    | #4         |  15%

bzip2-1.0.8          | 254 KB    | ########## | 100%

tzdata-2025b         | 120 KB    | ########## | 100%

liblzma-5.8.1        | 110 KB    | ########## | 100%

libexpat-2.7.1       | 73 KB     | ##1        |  22%

libexpat-2.7.1       | 73 KB     | ########## | 100%

libnsl-2.0.1         | 33 KB     | ####8      |  49% 
python-3.10.19       | 24.2 MB   | #####1     |  51%

libnsl-2.0.1         | 33 KB     | ########## | 100%

libffi-3.5.2         | 56 KB     | ##8        |  28%

libffi-3.5.2         | 56 KB     | ########## | 100%

... (more hidden) ...

libuuid-2.41.2       | 36 KB     | ####4      |  44%

libuuid-2.41.2       | 36 KB     | ########## | 100%

libgcc-15.2.0        | 803 KB    | ########## | 100%

libgcc-15.2.0        | 803 KB    | ########## | 100% 
python-3.10.19       | 24.2 MB   | ######8    |  68% 
python-3.10.19       | 24.2 MB   | ########9  |  89%

openssl-3.5.4        | 3.0 MB    | ########## | 100%

pip-25.2             | 1.1 MB    | ########## | 100%

pip-25.2             | 1.1 MB    | ########## | 100% 
python-3.10.19       | 24.2 MB   | ########## | 100%

setuptools-80.9.0    | 731 KB    | ########## | 100%

ld_impl_linux-64-2.4 | 730 KB    | ########## | 100%

tk-8.6.13            | 3.1 MB    | ########## | 100%

libgomp-15.2.0       | 437 KB    | ########## | 100%

ca-certificates-2025 | 152 KB    | ########## | 100%

readline-8.2         | 276 KB    | ########## | 100%

bzip2-1.0.8          | 254 KB    | ########## | 100%

liblzma-5.8.1        | 110 KB    | ########## | 100%

libexpat-2.7.1       | 73 KB     | ########## | 100%

libnsl-2.0.1         | 33 KB     | ########## | 100%

libffi-3.5.2         | 56 KB     | ########## | 100%

... (more hidden) ...

libuuid-2.41.2       | 36 KB     | ########## | 100%

tzdata-2025b         | 120 KB    | ########## | 100%

ncurses-6.5          | 871 KB    | ########## | 100%

ncurses-6.5          | 871 KB    | ########## | 100% 
python-3.10.19       | 24.2 MB   | ########## | 100%

done
Preparing transaction: - \ done
Verifying transaction: / - \ | / - \ | / done
Executing transaction: \ | / - \ | / - \ | / - \ | / - \ | / - \ done
#
# To activate this environment, use
#
#     $ conda activate /home/runner/sct_7.2.dev0/python/envs/venv_sct
#
# To deactivate an active environment, use
#
#     $ conda deactivate

Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

==> WARNING: A newer version of conda exists. <==
    current version: 24.11.2
    latest version: 25.9.1

Please update conda by running

$ conda update -n base -c conda-forge conda

## Package Plan ##

environment location: /home/runner/sct_7.2.dev0/python/envs/venv_sct

added / updated specs:
    - libstdcxx-ng

The following packages will be downloaded:

package                    |            build
    ---------------------------|-----------------
    libstdcxx-15.2.0           |       h8f9b012_7         3.7 MB  conda-forge
    libstdcxx-ng-15.2.0        |       h4852527_7          29 KB  conda-forge
    ------------------------------------------------------------
                                           Total:         3.7 MB

The following NEW packages will be INSTALLED:

libstdcxx          conda-forge/linux-64::libstdcxx-15.2.0-h8f9b012_7 
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-15.2.0-h4852527_7

Downloading and Extracting Packages: ...working...
libstdcxx-15.2.0     | 3.7 MB    |            |   0%

libstdcxx-ng-15.2.0  | 29 KB     |            |   0%

libstdcxx-ng-15.2.0  | 29 KB     | ########## | 100%

libstdcxx-ng-15.2.0  | 29 KB     | ########## | 100% 
libstdcxx-15.2.0     | 3.7 MB    | ########4  |  84% 
libstdcxx-15.2.0     | 3.7 MB    | ########## | 100% 
libstdcxx-15.2.0     | 3.7 MB    | ########## | 100%

done
Preparing transaction: - done
Verifying transaction: | done
Executing transaction: - done
Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

==> WARNING: A newer version of conda exists. <==
    current version: 24.11.2
    latest version: 25.9.1

Please update conda by running

$ conda update -n base -c conda-forge conda

# All requested packages already installed.

Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

==> WARNING: A newer version of conda exists. <==
    current version: 24.11.2
    latest version: 25.9.1

Please update conda by running

$ conda update -n base -c conda-forge conda

## Package Plan ##

environment location: /home/runner/sct_7.2.dev0/python/envs/venv_sct

added / updated specs:
    - xorg-libxinerama

The following packages will be downloaded:

package                    |            build
    ---------------------------|-----------------
    libxcb-1.17.0              |       h8a09558_0         387 KB  conda-forge
    pthread-stubs-0.4          |    hb9d3cd8_1002           8 KB  conda-forge
    xorg-libx11-1.8.12         |       h4f16b4b_0         816 KB  conda-forge
    xorg-libxau-1.0.12         |       hb9d3cd8_0          14 KB  conda-forge
    xorg-libxdmcp-1.1.5        |       hb9d3cd8_0          19 KB  conda-forge
    xorg-libxext-1.3.6         |       hb9d3cd8_0          49 KB  conda-forge
    xorg-libxinerama-1.1.5     |       h5888daf_1          14 KB  conda-forge
    ------------------------------------------------------------
                                           Total:         1.3 MB

The following NEW packages will be INSTALLED:

libxcb             conda-forge/linux-64::libxcb-1.17.0-h8a09558_0 
  pthread-stubs      conda-forge/linux-64::pthread-stubs-0.4-hb9d3cd8_1002 
  xorg-libx11        conda-forge/linux-64::xorg-libx11-1.8.12-h4f16b4b_0 
  xorg-libxau        conda-forge/linux-64::xorg-libxau-1.0.12-hb9d3cd8_0 
  xorg-libxdmcp      conda-forge/linux-64::xorg-libxdmcp-1.1.5-hb9d3cd8_0 
  xorg-libxext       conda-forge/linux-64::xorg-libxext-1.3.6-hb9d3cd8_0 
  xorg-libxinerama   conda-forge/linux-64::xorg-libxinerama-1.1.5-h5888daf_1

Downloading and Extracting Packages: ...working...
xorg-libx11-1.8.12   | 816 KB    |            |   0%

libxcb-1.17.0        | 387 KB    |            |   0%

xorg-libxext-1.3.6   | 49 KB     |            |   0%

xorg-libxdmcp-1.1.5  | 19 KB     |            |   0%

xorg-libxau-1.0.12   | 14 KB     |            |   0%

xorg-libxinerama-1.1 | 14 KB     |            |   0%

pthread-stubs-0.4    | 8 KB      |            |   0%

xorg-libxau-1.0.12   | 14 KB     | ########## | 100%

xorg-libxext-1.3.6   | 49 KB     | ########## | 100%

libxcb-1.17.0        | 387 KB    | ########## | 100%

xorg-libxdmcp-1.1.5  | 19 KB     | ########## | 100% 
xorg-libx11-1.8.12   | 816 KB    | ########## | 100% 
xorg-libx11-1.8.12   | 816 KB    | ########## | 100%

xorg-libxau-1.0.12   | 14 KB     | ########## | 100%

xorg-libxinerama-1.1 | 14 KB     | ########## | 100%

pthread-stubs-0.4    | 8 KB      | ########## | 100%

xorg-libxext-1.3.6   | 49 KB     | ########## | 100%

xorg-libxdmcp-1.1.5  | 19 KB     | ########## | 100%

xorg-libxinerama-1.1 | 14 KB     | ########## | 100%

pthread-stubs-0.4    | 8 KB      | ########## | 100%

libxcb-1.17.0        | 387 KB    | ########## | 100%

libxcb-1.17.0        | 387 KB    | ########## | 100% 
xorg-libx11-1.8.12   | 816 KB    | ########## | 100%

done
Preparing transaction: - done
Verifying transaction: | / done
Executing transaction: \ done
Requirement already satisfied: pip!=21.2.* in ./python/envs/venv_sct/lib/python3.10/site-packages (25.2)

Installing Python dependencies...

Using requirements.txt (git installation)

Looking in indexes: https://pypi.org/simple, https://download.pytorch.org/whl/cpu
Ignoring msvc-runtime: markers 'sys_platform == "win32"' don't match your environment
Collecting certifi
  Downloading certifi-2025.10.5-py3-none-any.whl.metadata (2.5 kB)
Collecting acvl_utils!=0.2.1 (from -r requirements.txt (line 7))
  Downloading acvl_utils-0.2.5.tar.gz (29 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting blosc2!=3.9.0 (from -r requirements.txt (line 12))
  Downloading blosc2-3.10.2-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (7.1 kB)
Collecting dipy==1.8.0 (from -r requirements.txt (line 14))
  Downloading dipy-1.8.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (8.6 kB)
Collecting h5py!=3.15.0 (from -r requirements.txt (line 16))
  Downloading h5py-3.15.1-cp310-cp310-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (3.0 kB)
Collecting ivadomed (from -r requirements.txt (line 20))
  Downloading ivadomed-2.9.10-py3-none-any.whl.metadata (6.4 kB)
Collecting matplotlib (from -r requirements.txt (line 21))
  Downloading matplotlib-3.10.7-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (11 kB)
Collecting matplotlib-inline (from -r requirements.txt (line 26))
  Downloading matplotlib_inline-0.1.7-py3-none-any.whl.metadata (3.9 kB)
Collecting nibabel (from -r requirements.txt (line 34))
  Downloading nibabel-5.3.2-py3-none-any.whl.metadata (9.1 kB)
Collecting nilearn (from -r requirements.txt (line 35))
  Downloading nilearn-0.12.1-py3-none-any.whl.metadata (9.9 kB)
Collecting nnunetv2!=2.4.*,<2.6,>2.3.0 (from -r requirements.txt (line 42))
  Downloading nnunetv2-2.5.2.tar.gz (200 kB)
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Collecting numpy<2 (from -r requirements.txt (line 44))
  Downloading numpy-1.26.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB)
Collecting numexpr!=2.14.0 (from -r requirements.txt (line 47))
  Downloading numexpr-2.14.1-cp310-cp310-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB)
Collecting onnxruntime!=1.16.0,<1.22.0,>=1.7.0 (from -r requirements.txt (line 53))
  Downloading onnxruntime-1.21.1-cp310-cp310-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (4.5 kB)
Collecting onnx<1.16.2 (from -r requirements.txt (line 56))
  Downloading onnx-1.16.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (16 kB)
Collecting pandas (from -r requirements.txt (line 57))
  Downloading pandas-2.3.3-cp310-cp310-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (91 kB)
Collecting portalocker (from -r requirements.txt (line 58))
  Downloading portalocker-3.2.0-py3-none-any.whl.metadata (8.7 kB)
Collecting psutil (from -r requirements.txt (line 59))
  Downloading psutil-7.1.1-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (23 kB)
Collecting pyqt5>=5.15.0 (from -r requirements.txt (line 62))
  Downloading PyQt5-5.15.11-cp38-abi3-manylinux_2_17_x86_64.whl.metadata (2.1 kB)
Collecting PyQt5-Qt5==5.15.2 (from -r requirements.txt (line 67))
  Downloading PyQt5_Qt5-5.15.2-py3-none-manylinux2014_x86_64.whl.metadata (535 bytes)
Collecting pystrum>=0.3 (from -r requirements.txt (line 70))
  Downloading pystrum-0.4.tar.gz (17 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting pytest (from -r requirements.txt (line 71))
  Downloading pytest-8.4.2-py3-none-any.whl.metadata (7.7 kB)
Collecting pytest-cov (from -r requirements.txt (line 72))
  Downloading pytest_cov-7.0.0-py3-none-any.whl.metadata (31 kB)
Collecting requests (from -r requirements.txt (line 73))
  Downloading requests-2.32.5-py3-none-any.whl.metadata (4.9 kB)
Collecting requirements-parser (from -r requirements.txt (line 74))
  Downloading requirements_parser-0.13.0-py3-none-any.whl.metadata (4.7 kB)
Collecting scipy (from -r requirements.txt (line 75))
  Downloading scipy-1.15.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB)
Collecting scikit-image (from -r requirements.txt (line 76))
  Downloading scikit_image-0.25.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (14 kB)
Collecting scikit-learn (from -r requirements.txt (line 77))
  Downloading scikit_learn-1.7.2-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (11 kB)
Collecting totalspineseg (from -r requirements.txt (line 78))
  Downloading totalspineseg-20250709-py3-none-any.whl.metadata (17 kB)
Collecting xlwt (from -r requirements.txt (line 79))
  Downloading xlwt-1.3.0-py2.py3-none-any.whl.metadata (3.5 kB)
Collecting torch<2.3 (from -r requirements.txt (line 91))
  Downloading https://download.pytorch.org/whl/cpu/torch-2.2.2%2Bcpu-cp310-cp310-linux_x86_64.whl (186.8 MB)
Collecting tqdm (from -r requirements.txt (line 92))
  Downloading tqdm-4.67.1-py3-none-any.whl.metadata (57 kB)
Collecting transforms3d (from -r requirements.txt (line 93))
  Downloading transforms3d-0.4.2-py3-none-any.whl.metadata (2.8 kB)
Collecting urllib3 (from -r requirements.txt (line 94))
  Downloading urllib3-2.5.0-py3-none-any.whl.metadata (6.5 kB)
Collecting pytest_console_scripts (from -r requirements.txt (line 95))
  Downloading pytest_console_scripts-1.4.1-py3-none-any.whl.metadata (11 kB)
Collecting pyyaml (from -r requirements.txt (line 96))
  Downloading pyyaml-6.0.3-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (2.4 kB)
Collecting voxelmorph (from -r requirements.txt (line 97))
  Downloading voxelmorph-0.2-py3-none-any.whl.metadata (660 bytes)
Collecting wquantiles (from -r requirements.txt (line 98))
  Downloading wquantiles-0.6-py3-none-any.whl.metadata (1.1 kB)
Collecting xlsxwriter (from -r requirements.txt (line 101))
  Downloading xlsxwriter-3.2.9-py3-none-any.whl.metadata (2.7 kB)
Collecting monai[nibabel] (from -r requirements.txt (line 27))
  Downloading monai-1.5.1-py3-none-any.whl.metadata (13 kB)
Collecting cython!=0.29.29,>=0.29.24 (from dipy==1.8.0->-r requirements.txt (line 14))
  Downloading cython-3.1.5-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (4.3 kB)
Collecting packaging>=21 (from dipy==1.8.0->-r requirements.txt (line 14))
  Downloading packaging-25.0-py3-none-any.whl.metadata (3.3 kB)
Collecting trx-python>=0.2.9 (from dipy==1.8.0->-r requirements.txt (line 14))
  Downloading trx_python-0.3-py3-none-any.whl.metadata (2.7 kB)
Collecting dynamic-network-architectures<0.4,>=0.3.1 (from nnunetv2!=2.4.*,<2.6,>2.3.0->-r requirements.txt (line 42))
  Downloading dynamic_network_architectures-0.3.1.tar.gz (20 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting dicom2nifti (from nnunetv2!=2.4.*,<2.6,>2.3.0->-r requirements.txt (line 42))
  Downloading dicom2nifti-2.6.2-py3-none-any.whl.metadata (1.5 kB)
Collecting batchgenerators>=0.25 (from nnunetv2!=2.4.*,<2.6,>2.3.0->-r requirements.txt (line 42))
  Downloading batchgenerators-0.25.1.tar.gz (76 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting SimpleITK>=2.2.1 (from nnunetv2!=2.4.*,<2.6,>2.3.0->-r requirements.txt (line 42))
  Downloading simpleitk-2.5.2-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (7.2 kB)
Collecting graphviz (from nnunetv2!=2.4.*,<2.6,>2.3.0->-r requirements.txt (line 42))
  Downloading graphviz-0.21-py3-none-any.whl.metadata (12 kB)
Collecting tifffile (from nnunetv2!=2.4.*,<2.6,>2.3.0->-r requirements.txt (line 42))
  Downloading tifffile-2025.5.10-py3-none-any.whl.metadata (31 kB)
Collecting seaborn (from nnunetv2!=2.4.*,<2.6,>2.3.0->-r requirements.txt (line 42))
  Downloading seaborn-0.13.2-py3-none-any.whl.metadata (5.4 kB)
Collecting imagecodecs (from nnunetv2!=2.4.*,<2.6,>2.3.0->-r requirements.txt (line 42))
  Downloading imagecodecs-2025.3.30-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (20 kB)
Collecting yacs (from nnunetv2!=2.4.*,<2.6,>2.3.0->-r requirements.txt (line 42))
  Downloading yacs-0.1.8-py3-none-any.whl.metadata (639 bytes)
Collecting batchgeneratorsv2>=0.2 (from nnunetv2!=2.4.*,<2.6,>2.3.0->-r requirements.txt (line 42))
  Downloading batchgeneratorsv2-0.3.0.tar.gz (44 kB)
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Collecting einops (from nnunetv2!=2.4.*,<2.6,>2.3.0->-r requirements.txt (line 42))
  Downloading einops-0.8.1-py3-none-any.whl.metadata (13 kB)
Collecting connected-components-3d (from acvl_utils!=0.2.1->-r requirements.txt (line 7))
  Downloading connected_components_3d-3.26.0-cp310-cp310-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (32 kB)
Collecting coloredlogs (from onnxruntime!=1.16.0,<1.22.0,>=1.7.0->-r requirements.txt (line 53))
  Downloading coloredlogs-15.0.1-py2.py3-none-any.whl.metadata (12 kB)
Collecting flatbuffers (from onnxruntime!=1.16.0,<1.22.0,>=1.7.0->-r requirements.txt (line 53))
  Downloading flatbuffers-25.9.23-py2.py3-none-any.whl.metadata (875 bytes)
Collecting protobuf (from onnxruntime!=1.16.0,<1.22.0,>=1.7.0->-r requirements.txt (line 53))
  Downloading protobuf-6.33.0-cp39-abi3-manylinux2014_x86_64.whl.metadata (593 bytes)
Collecting sympy (from onnxruntime!=1.16.0,<1.22.0,>=1.7.0->-r requirements.txt (line 53))
  Downloading https://download.pytorch.org/whl/sympy-1.14.0-py3-none-any.whl.metadata (12 kB)
Collecting filelock (from torch<2.3->-r requirements.txt (line 91))
  Downloading filelock-3.20.0-py3-none-any.whl.metadata (2.1 kB)
Collecting typing-extensions>=4.8.0 (from torch<2.3->-r requirements.txt (line 91))
  Downloading https://download.pytorch.org/whl/typing_extensions-4.15.0-py3-none-any.whl.metadata (3.3 kB)
Collecting networkx (from torch<2.3->-r requirements.txt (line 91))
  Downloading https://download.pytorch.org/whl/networkx-3.5-py3-none-any.whl.metadata (6.3 kB)
Collecting jinja2 (from torch<2.3->-r requirements.txt (line 91))
  Downloading https://download.pytorch.org/whl/jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB)
Collecting fsspec (from torch<2.3->-r requirements.txt (line 91))
  Downloading https://download.pytorch.org/whl/fsspec-2025.9.0-py3-none-any.whl.metadata (10 kB)
Collecting ndindex (from blosc2!=3.9.0->-r requirements.txt (line 12))
  Downloading ndindex-1.10.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.6 kB)
Collecting msgpack (from blosc2!=3.9.0->-r requirements.txt (line 12))
  Downloading msgpack-1.1.2-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (8.1 kB)
Collecting platformdirs (from blosc2!=3.9.0->-r requirements.txt (line 12))
  Downloading platformdirs-4.5.0-py3-none-any.whl.metadata (12 kB)
Collecting py-cpuinfo (from blosc2!=3.9.0->-r requirements.txt (line 12))
  Downloading py_cpuinfo-9.0.0-py3-none-any.whl.metadata (794 bytes)
Collecting csv-diff>=1.0 (from ivadomed->-r requirements.txt (line 20))
  Downloading csv_diff-1.2-py3-none-any.whl.metadata (5.3 kB)
Collecting loguru~=0.5 (from ivadomed->-r requirements.txt (line 20))
  Downloading loguru-0.7.3-py3-none-any.whl.metadata (22 kB)
Collecting imageio>=2.31.4 (from ivadomed->-r requirements.txt (line 20))
  Downloading imageio-2.37.0-py3-none-any.whl.metadata (5.2 kB)
Collecting joblib~=1.0 (from ivadomed->-r requirements.txt (line 20))
  Downloading joblib-1.5.2-py3-none-any.whl.metadata (5.6 kB)
Collecting pandas (from -r requirements.txt (line 57))
  Downloading pandas-1.5.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB)
Collecting pybids<0.15.6,>=0.14.0 (from ivadomed->-r requirements.txt (line 20))
  Downloading pybids-0.15.5-py3-none-any.whl.metadata (3.2 kB)
Collecting tensorboard>=1.15.0 (from ivadomed->-r requirements.txt (line 20))
  Downloading tensorboard-2.20.0-py3-none-any.whl.metadata (1.8 kB)
Collecting torchio>=0.18.68 (from ivadomed->-r requirements.txt (line 20))
  Downloading torchio-0.20.23-py3-none-any.whl.metadata (52 kB)
Collecting torchvision>=0.9.1 (from ivadomed->-r requirements.txt (line 20))
  Downloading https://download.pytorch.org/whl/cpu/torchvision-0.24.0%2Bcpu-cp310-cp310-manylinux_2_28_x86_64.whl.metadata (5.9 kB)
Collecting wandb>=0.12.11 (from ivadomed->-r requirements.txt (line 20))
  Downloading wandb-0.22.2-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (10 kB)
Collecting importlib-resources>=5.12 (from nibabel->-r requirements.txt (line 34))
  Downloading importlib_resources-6.5.2-py3-none-any.whl.metadata (3.9 kB)
Collecting python-dateutil>=2.8.1 (from pandas->-r requirements.txt (line 57))
  Downloading python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
Collecting pytz>=2020.1 (from pandas->-r requirements.txt (line 57))
  Downloading pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB)
Collecting pillow>=10.1 (from scikit-image->-r requirements.txt (line 76))
  Downloading pillow-12.0.0-cp310-cp310-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (8.8 kB)
Collecting lazy-loader>=0.4 (from scikit-image->-r requirements.txt (line 76))
  Downloading lazy_loader-0.4-py3-none-any.whl.metadata (7.6 kB)
Collecting formulaic<0.4,>=0.2.4 (from pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 20))
  Downloading formulaic-0.3.4-py3-none-any.whl.metadata (5.6 kB)
Collecting sqlalchemy<1.4.0.dev0 (from pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 20))
  Downloading SQLAlchemy-1.3.24.tar.gz (6.4 MB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting bids-validator (from pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 20))
  Downloading bids_validator-1.14.7.post0-py3-none-any.whl.metadata (39 kB)
Collecting num2words (from pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 20))
  Downloading num2words-0.5.14-py3-none-any.whl.metadata (13 kB)
Collecting click>=8.0 (from pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 20))
  Downloading click-8.3.0-py3-none-any.whl.metadata (2.6 kB)
Collecting astor>=0.8 (from formulaic<0.4,>=0.2.4->pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 20))
  Downloading astor-0.8.1-py2.py3-none-any.whl.metadata (4.2 kB)
Collecting interface-meta<2.0.0,>=1.2.0 (from formulaic<0.4,>=0.2.4->pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 20))
  Downloading interface_meta-1.3.0-py3-none-any.whl.metadata (6.7 kB)
Collecting wrapt>=1.0 (from formulaic<0.4,>=0.2.4->pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 20))
  Downloading wrapt-2.0.0-cp310-cp310-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl.metadata (8.8 kB)
Collecting contourpy>=1.0.1 (from matplotlib->-r requirements.txt (line 21))
  Downloading contourpy-1.3.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.5 kB)
Collecting cycler>=0.10 (from matplotlib->-r requirements.txt (line 21))
  Downloading cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB)
Collecting fonttools>=4.22.0 (from matplotlib->-r requirements.txt (line 21))
  Downloading fonttools-4.60.1-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (112 kB)
Collecting kiwisolver>=1.3.1 (from matplotlib->-r requirements.txt (line 21))
  Downloading kiwisolver-1.4.9-cp310-cp310-manylinux_2_12_x86_64.manylinux2010_x86_64.whl.metadata (6.3 kB)
Collecting pyparsing>=3 (from matplotlib->-r requirements.txt (line 21))
  Downloading pyparsing-3.2.5-py3-none-any.whl.metadata (5.0 kB)
Collecting traitlets (from matplotlib-inline->-r requirements.txt (line 26))
  Downloading traitlets-5.14.3-py3-none-any.whl.metadata (10 kB)
INFO: pip is looking at multiple versions of monai[nibabel] to determine which version is compatible with other requirements. This could take a while.
Collecting monai[nibabel] (from -r requirements.txt (line 27))
  Downloading monai-1.5.0-py3-none-any.whl.metadata (13 kB)
  Downloading monai-1.4.0-py3-none-any.whl.metadata (11 kB)
Collecting lxml (from nilearn->-r requirements.txt (line 35))
  Downloading lxml-6.0.2-cp310-cp310-manylinux_2_26_x86_64.manylinux_2_28_x86_64.whl.metadata (3.6 kB)
INFO: pip is looking at multiple versions of nilearn to determine which version is compatible with other requirements. This could take a while.
Collecting nilearn (from -r requirements.txt (line 35))
  Downloading nilearn-0.12.0-py3-none-any.whl.metadata (9.9 kB)
  Downloading nilearn-0.11.1-py3-none-any.whl.metadata (9.3 kB)
  Downloading nilearn-0.11.0-py3-none-any.whl.metadata (8.8 kB)
  Downloading nilearn-0.10.4-py3-none-any.whl.metadata (7.8 kB)
Collecting PyQt5-sip<13,>=12.15 (from pyqt5>=5.15.0->-r requirements.txt (line 62))
  Downloading pyqt5_sip-12.17.1-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.whl.metadata (494 bytes)
Collecting six (from pystrum>=0.3->-r requirements.txt (line 70))
  Downloading six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
Collecting exceptiongroup>=1 (from pytest->-r requirements.txt (line 71))
  Downloading exceptiongroup-1.3.0-py3-none-any.whl.metadata (6.7 kB)
Collecting iniconfig>=1 (from pytest->-r requirements.txt (line 71))
  Downloading iniconfig-2.3.0-py3-none-any.whl.metadata (2.5 kB)
Collecting pluggy<2,>=1.5 (from pytest->-r requirements.txt (line 71))
  Downloading pluggy-1.6.0-py3-none-any.whl.metadata (4.8 kB)
Collecting pygments>=2.7.2 (from pytest->-r requirements.txt (line 71))
  Downloading pygments-2.19.2-py3-none-any.whl.metadata (2.5 kB)
Collecting tomli>=1 (from pytest->-r requirements.txt (line 71))
  Downloading tomli-2.3.0-py3-none-any.whl.metadata (10 kB)
Collecting coverage>=7.10.6 (from coverage[toml]>=7.10.6->pytest-cov->-r requirements.txt (line 72))
  Downloading coverage-7.11.0-cp310-cp310-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl.metadata (9.0 kB)
Collecting charset_normalizer<4,>=2 (from requests->-r requirements.txt (line 73))
  Downloading charset_normalizer-3.4.4-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (37 kB)
Collecting idna<4,>=2.5 (from requests->-r requirements.txt (line 73))
  Downloading idna-3.11-py3-none-any.whl.metadata (8.4 kB)
Collecting threadpoolctl>=3.1.0 (from scikit-learn->-r requirements.txt (line 77))
  Downloading threadpoolctl-3.6.0-py3-none-any.whl.metadata (13 kB)
Collecting gryds (from totalspineseg->-r requirements.txt (line 78))
  Downloading gryds-0.0.9-py3-none-any.whl.metadata (1.0 kB)
Collecting neurite>=0.2 (from voxelmorph->-r requirements.txt (line 97))
  Downloading neurite-0.2-py3-none-any.whl.metadata (653 bytes)
Collecting future (from batchgenerators>=0.25->nnunetv2!=2.4.*,<2.6,>2.3.0->-r requirements.txt (line 42))
  Downloading future-1.0.0-py3-none-any.whl.metadata (4.0 kB)
Collecting unittest2 (from batchgenerators>=0.25->nnunetv2!=2.4.*,<2.6,>2.3.0->-r requirements.txt (line 42))
  Downloading unittest2-1.1.0-py2.py3-none-any.whl.metadata (15 kB)
Collecting fft-conv-pytorch (from batchgeneratorsv2>=0.2->nnunetv2!=2.4.*,<2.6,>2.3.0->-r requirements.txt (line 42))
  Downloading fft_conv_pytorch-1.2.0-py3-none-any.whl.metadata (2.8 kB)
Collecting dictdiffer (from csv-diff>=1.0->ivadomed->-r requirements.txt (line 20))
  Downloading dictdiffer-0.9.0-py2.py3-none-any.whl.metadata (4.8 kB)
INFO: pip is looking at multiple versions of networkx to determine which version is compatible with other requirements. This could take a while.
Collecting networkx (from torch<2.3->-r requirements.txt (line 91))
  Downloading networkx-3.4.2-py3-none-any.whl.metadata (6.3 kB)
Collecting absl-py>=0.4 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 20))
  Downloading absl_py-2.3.1-py3-none-any.whl.metadata (3.3 kB)
Collecting grpcio>=1.48.2 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 20))
  Downloading grpcio-1.75.1-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (3.7 kB)
Collecting markdown>=2.6.8 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 20))
  Downloading markdown-3.9-py3-none-any.whl.metadata (5.1 kB)
Collecting setuptools>=41.0.0 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 20))
  Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Collecting tensorboard-data-server<0.8.0,>=0.7.0 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 20))
  Downloading tensorboard_data_server-0.7.2-py3-none-manylinux_2_31_x86_64.whl.metadata (1.1 kB)
Collecting werkzeug>=1.0.1 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 20))
  Downloading werkzeug-3.1.3-py3-none-any.whl.metadata (3.7 kB)
Collecting deprecated>=1.2 (from torchio>=0.18.68->ivadomed->-r requirements.txt (line 20))
  Downloading Deprecated-1.2.18-py2.py3-none-any.whl.metadata (5.7 kB)
Collecting humanize>=0.1 (from torchio>=0.18.68->ivadomed->-r requirements.txt (line 20))
  Downloading humanize-4.14.0-py3-none-any.whl.metadata (7.8 kB)
Collecting rich>=10 (from torchio>=0.18.68->ivadomed->-r requirements.txt (line 20))
  Downloading rich-14.2.0-py3-none-any.whl.metadata (18 kB)
Collecting typer>=0.1 (from torchio>=0.18.68->ivadomed->-r requirements.txt (line 20))
  Downloading typer-0.19.2-py3-none-any.whl.metadata (16 kB)
Collecting wrapt>=1.0 (from formulaic<0.4,>=0.2.4->pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 20))
  Downloading wrapt-1.17.3-cp310-cp310-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl.metadata (6.4 kB)
Collecting markdown-it-py>=2.2.0 (from rich>=10->torchio>=0.18.68->ivadomed->-r requirements.txt (line 20))
  Downloading markdown_it_py-4.0.0-py3-none-any.whl.metadata (7.3 kB)
Collecting mdurl~=0.1 (from markdown-it-py>=2.2.0->rich>=10->torchio>=0.18.68->ivadomed->-r requirements.txt (line 20))
  Downloading mdurl-0.1.2-py3-none-any.whl.metadata (1.6 kB)
INFO: pip is looking at multiple versions of torchvision to determine which version is compatible with other requirements. This could take a while.
Collecting torchvision>=0.9.1 (from ivadomed->-r requirements.txt (line 20))
  Downloading torchvision-0.24.0-cp310-cp310-manylinux_2_28_x86_64.whl.metadata (5.9 kB)
  Downloading https://download.pytorch.org/whl/cpu/torchvision-0.23.0%2Bcpu-cp310-cp310-manylinux_2_28_x86_64.whl.metadata (6.1 kB)
  Downloading torchvision-0.23.0-cp310-cp310-manylinux_2_28_x86_64.whl.metadata (6.1 kB)
  Downloading https://download.pytorch.org/whl/cpu/torchvision-0.22.1%2Bcpu-cp310-cp310-manylinux_2_28_x86_64.whl.metadata (6.1 kB)
  Downloading torchvision-0.22.1-cp310-cp310-manylinux_2_28_x86_64.whl.metadata (6.1 kB)
  Downloading https://download.pytorch.org/whl/cpu/torchvision-0.22.0%2Bcpu-cp310-cp310-manylinux_2_28_x86_64.whl.metadata (6.1 kB)
  Downloading torchvision-0.22.0-cp310-cp310-manylinux_2_28_x86_64.whl.metadata (6.1 kB)
INFO: pip is still looking at multiple versions of torchvision to determine which version is compatible with other requirements. This could take a while.
  Downloading https://download.pytorch.org/whl/cpu/torchvision-0.21.0%2Bcpu-cp310-cp310-linux_x86_64.whl.metadata (6.1 kB)
  Downloading torchvision-0.21.0-cp310-cp310-manylinux1_x86_64.whl.metadata (6.1 kB)
  Downloading https://download.pytorch.org/whl/cpu/torchvision-0.20.1%2Bcpu-cp310-cp310-linux_x86_64.whl (1.8 MB)
  Downloading torchvision-0.20.1-cp310-cp310-manylinux1_x86_64.whl.metadata (6.1 kB)
  Downloading https://download.pytorch.org/whl/cpu/torchvision-0.20.0%2Bcpu-cp310-cp310-linux_x86_64.whl (1.8 MB)
INFO: This is taking longer than usual. You might need to provide the dependency resolver with stricter constraints to reduce runtime. See https://pip.pypa.io/warnings/backtracking for guidance. If you want to abort this run, press Ctrl + C.
  Downloading torchvision-0.20.0-cp310-cp310-manylinux1_x86_64.whl.metadata (6.1 kB)
  Downloading https://download.pytorch.org/whl/cpu/torchvision-0.19.1%2Bcpu-cp310-cp310-linux_x86_64.whl (1.6 MB)
  Downloading torchvision-0.19.1-cp310-cp310-manylinux1_x86_64.whl.metadata (6.0 kB)
  Downloading https://download.pytorch.org/whl/cpu/torchvision-0.19.0%2Bcpu-cp310-cp310-linux_x86_64.whl (1.6 MB)
  Downloading torchvision-0.19.0-cp310-cp310-manylinux1_x86_64.whl.metadata (6.0 kB)
  Downloading https://download.pytorch.org/whl/cpu/torchvision-0.18.1%2Bcpu-cp310-cp310-linux_x86_64.whl (1.6 MB)
  Downloading torchvision-0.18.1-cp310-cp310-manylinux1_x86_64.whl.metadata (6.6 kB)
  Downloading https://download.pytorch.org/whl/cpu/torchvision-0.18.0%2Bcpu-cp310-cp310-linux_x86_64.whl (1.6 MB)
  Downloading torchvision-0.18.0-cp310-cp310-manylinux1_x86_64.whl.metadata (6.6 kB)
  Downloading https://download.pytorch.org/whl/cpu/torchvision-0.17.2%2Bcpu-cp310-cp310-linux_x86_64.whl (1.6 MB)
Collecting setuptools-scm (from trx-python>=0.2.9->dipy==1.8.0->-r requirements.txt (line 14))
  Downloading setuptools_scm-9.2.2-py3-none-any.whl.metadata (7.7 kB)
Collecting deepdiff (from trx-python>=0.2.9->dipy==1.8.0->-r requirements.txt (line 14))
  Downloading deepdiff-8.6.1-py3-none-any.whl.metadata (8.6 kB)
Collecting shellingham>=1.3.0 (from typer>=0.1->torchio>=0.18.68->ivadomed->-r requirements.txt (line 20))
  Downloading shellingham-1.5.4-py2.py3-none-any.whl.metadata (3.5 kB)
Collecting gitpython!=3.1.29,>=1.0.0 (from wandb>=0.12.11->ivadomed->-r requirements.txt (line 20))
  Downloading gitpython-3.1.45-py3-none-any.whl.metadata (13 kB)
Collecting pydantic<3 (from wandb>=0.12.11->ivadomed->-r requirements.txt (line 20))
  Downloading pydantic-2.12.3-py3-none-any.whl.metadata (87 kB)
Collecting sentry-sdk>=2.0.0 (from wandb>=0.12.11->ivadomed->-r requirements.txt (line 20))
  Downloading sentry_sdk-2.42.0-py2.py3-none-any.whl.metadata (10 kB)
Collecting annotated-types>=0.6.0 (from pydantic<3->wandb>=0.12.11->ivadomed->-r requirements.txt (line 20))
  Downloading annotated_types-0.7.0-py3-none-any.whl.metadata (15 kB)
Collecting pydantic-core==2.41.4 (from pydantic<3->wandb>=0.12.11->ivadomed->-r requirements.txt (line 20))
  Downloading pydantic_core-2.41.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (7.3 kB)
Collecting typing-inspection>=0.4.2 (from pydantic<3->wandb>=0.12.11->ivadomed->-r requirements.txt (line 20))
  Downloading typing_inspection-0.4.2-py3-none-any.whl.metadata (2.6 kB)
Collecting gitdb<5,>=4.0.1 (from gitpython!=3.1.29,>=1.0.0->wandb>=0.12.11->ivadomed->-r requirements.txt (line 20))
  Downloading gitdb-4.0.12-py3-none-any.whl.metadata (1.2 kB)
Collecting smmap<6,>=3.0.1 (from gitdb<5,>=4.0.1->gitpython!=3.1.29,>=1.0.0->wandb>=0.12.11->ivadomed->-r requirements.txt (line 20))
  Downloading smmap-5.0.2-py3-none-any.whl.metadata (4.3 kB)
Collecting MarkupSafe>=2.1.1 (from werkzeug>=1.0.1->tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 20))
  Downloading markupsafe-3.0.3-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (2.7 kB)
Collecting bidsschematools>=0.10 (from bids-validator->pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 20))
  Downloading bidsschematools-1.1.0-py3-none-any.whl.metadata (3.2 kB)
Collecting acres (from bidsschematools>=0.10->bids-validator->pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 20))
  Downloading acres-0.5.0-py3-none-any.whl.metadata (6.2 kB)
Collecting humanfriendly>=9.1 (from coloredlogs->onnxruntime!=1.16.0,<1.22.0,>=1.7.0->-r requirements.txt (line 53))
  Downloading humanfriendly-10.0-py2.py3-none-any.whl.metadata (9.2 kB)
Collecting orderly-set<6,>=5.4.1 (from deepdiff->trx-python>=0.2.9->dipy==1.8.0->-r requirements.txt (line 14))
  Downloading orderly_set-5.5.0-py3-none-any.whl.metadata (6.6 kB)
Collecting pydicom>=3.0.0 (from dicom2nifti->nnunetv2!=2.4.*,<2.6,>2.3.0->-r requirements.txt (line 42))
  Downloading pydicom-3.0.1-py3-none-any.whl.metadata (9.4 kB)
Collecting python-gdcm (from dicom2nifti->nnunetv2!=2.4.*,<2.6,>2.3.0->-r requirements.txt (line 42))
  Downloading python_gdcm-3.2.2-cp310-cp310-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (3.8 kB)
Collecting docopt>=0.6.2 (from num2words->pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 20))
  Downloading docopt-0.6.2.tar.gz (25 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting mpmath<1.4,>=1.1.0 (from sympy->onnxruntime!=1.16.0,<1.22.0,>=1.7.0->-r requirements.txt (line 53))
  Downloading https://download.pytorch.org/whl/mpmath-1.3.0-py3-none-any.whl (536 kB)
Collecting argparse (from unittest2->batchgenerators>=0.25->nnunetv2!=2.4.*,<2.6,>2.3.0->-r requirements.txt (line 42))
  Downloading argparse-1.4.0-py2.py3-none-any.whl.metadata (2.8 kB)
Collecting traceback2 (from unittest2->batchgenerators>=0.25->nnunetv2!=2.4.*,<2.6,>2.3.0->-r requirements.txt (line 42))
  Downloading traceback2-1.4.0-py2.py3-none-any.whl.metadata (1.5 kB)
Collecting linecache2 (from traceback2->unittest2->batchgenerators>=0.25->nnunetv2!=2.4.*,<2.6,>2.3.0->-r requirements.txt (line 42))
  Downloading linecache2-1.0.0-py2.py3-none-any.whl.metadata (1000 bytes)
Downloading dipy-1.8.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (8.9 MB)
Downloading PyQt5_Qt5-5.15.2-py3-none-manylinux2014_x86_64.whl (59.9 MB)
Downloading numpy-1.26.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (18.2 MB)
Downloading onnxruntime-1.21.1-cp310-cp310-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (16.0 MB)
Downloading onnx-1.16.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (15.9 MB)
Downloading certifi-2025.10.5-py3-none-any.whl (163 kB)
Downloading blosc2-3.10.2-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (4.5 MB)
Downloading h5py-3.15.1-cp310-cp310-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (4.7 MB)
Downloading ivadomed-2.9.10-py3-none-any.whl (240 kB)
Downloading nibabel-5.3.2-py3-none-any.whl (3.3 MB)
Downloading pandas-1.5.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.1 MB)
Downloading scikit_image-0.25.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (14.8 MB)
Downloading joblib-1.5.2-py3-none-any.whl (308 kB)
Downloading loguru-0.7.3-py3-none-any.whl (61 kB)
Downloading pybids-0.15.5-py3-none-any.whl (14.9 MB)
Downloading formulaic-0.3.4-py3-none-any.whl (68 kB)
Downloading interface_meta-1.3.0-py3-none-any.whl (14 kB)
Downloading seaborn-0.13.2-py3-none-any.whl (294 kB)
Downloading matplotlib-3.10.7-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (8.7 MB)
Downloading matplotlib_inline-0.1.7-py3-none-any.whl (9.9 kB)
Downloading monai-1.4.0-py3-none-any.whl (1.5 MB)
Downloading nilearn-0.10.4-py3-none-any.whl (10.4 MB)
Downloading numexpr-2.14.1-cp310-cp310-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (440 kB)
Downloading portalocker-3.2.0-py3-none-any.whl (22 kB)
Downloading psutil-7.1.1-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (290 kB)
Downloading PyQt5-5.15.11-cp38-abi3-manylinux_2_17_x86_64.whl (8.2 MB)
Downloading pyqt5_sip-12.17.1-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.whl (271 kB)
Downloading pytest-8.4.2-py3-none-any.whl (365 kB)
Downloading pluggy-1.6.0-py3-none-any.whl (20 kB)
Downloading pytest_cov-7.0.0-py3-none-any.whl (22 kB)
Downloading requests-2.32.5-py3-none-any.whl (64 kB)
Downloading urllib3-2.5.0-py3-none-any.whl (129 kB)
Downloading charset_normalizer-3.4.4-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (153 kB)
Downloading idna-3.11-py3-none-any.whl (71 kB)
Downloading requirements_parser-0.13.0-py3-none-any.whl (14 kB)
Downloading scipy-1.15.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (37.7 MB)
Downloading scikit_learn-1.7.2-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (9.7 MB)
Downloading totalspineseg-20250709-py3-none-any.whl (79 kB)
Downloading xlwt-1.3.0-py2.py3-none-any.whl (99 kB)
Downloading tqdm-4.67.1-py3-none-any.whl (78 kB)
Downloading transforms3d-0.4.2-py3-none-any.whl (1.4 MB)
Downloading pytest_console_scripts-1.4.1-py3-none-any.whl (10 kB)
Downloading pyyaml-6.0.3-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (770 kB)
Downloading voxelmorph-0.2-py3-none-any.whl (54 kB)
Downloading wquantiles-0.6-py3-none-any.whl (3.3 kB)
Downloading xlsxwriter-3.2.9-py3-none-any.whl (175 kB)
Downloading astor-0.8.1-py2.py3-none-any.whl (27 kB)
Downloading click-8.3.0-py3-none-any.whl (107 kB)
Downloading contourpy-1.3.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (325 kB)
Downloading coverage-7.11.0-cp310-cp310-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl (244 kB)
Downloading csv_diff-1.2-py3-none-any.whl (13 kB)
Downloading cycler-0.12.1-py3-none-any.whl (8.3 kB)
Downloading cython-3.1.5-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (3.4 MB)
Downloading exceptiongroup-1.3.0-py3-none-any.whl (16 kB)
Downloading fonttools-4.60.1-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (4.8 MB)
Downloading imageio-2.37.0-py3-none-any.whl (315 kB)
Downloading importlib_resources-6.5.2-py3-none-any.whl (37 kB)
Downloading iniconfig-2.3.0-py3-none-any.whl (7.5 kB)
Downloading kiwisolver-1.4.9-cp310-cp310-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (1.6 MB)
Downloading lazy_loader-0.4-py3-none-any.whl (12 kB)
Downloading networkx-3.4.2-py3-none-any.whl (1.7 MB)
Downloading neurite-0.2-py3-none-any.whl (108 kB)
Downloading packaging-25.0-py3-none-any.whl (66 kB)
Downloading pillow-12.0.0-cp310-cp310-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (7.0 MB)
Downloading protobuf-6.33.0-cp39-abi3-manylinux2014_x86_64.whl (323 kB)
Downloading pygments-2.19.2-py3-none-any.whl (1.2 MB)
Downloading pyparsing-3.2.5-py3-none-any.whl (113 kB)
Downloading python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
Downloading pytz-2025.2-py2.py3-none-any.whl (509 kB)
Downloading simpleitk-2.5.2-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (52.6 MB)
Downloading six-1.17.0-py2.py3-none-any.whl (11 kB)
Downloading tensorboard-2.20.0-py3-none-any.whl (5.5 MB)
Downloading tensorboard_data_server-0.7.2-py3-none-manylinux_2_31_x86_64.whl (6.6 MB)
Downloading absl_py-2.3.1-py3-none-any.whl (135 kB)
Downloading grpcio-1.75.1-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (6.5 MB)
Downloading https://download.pytorch.org/whl/typing_extensions-4.15.0-py3-none-any.whl (44 kB)
Downloading markdown-3.9-py3-none-any.whl (107 kB)
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Downloading threadpoolctl-3.6.0-py3-none-any.whl (18 kB)
Downloading tifffile-2025.5.10-py3-none-any.whl (226 kB)
Downloading tomli-2.3.0-py3-none-any.whl (14 kB)
Downloading torchio-0.20.23-py3-none-any.whl (194 kB)
Downloading Deprecated-1.2.18-py2.py3-none-any.whl (10.0 kB)
Downloading wrapt-1.17.3-cp310-cp310-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl (81 kB)
Downloading einops-0.8.1-py3-none-any.whl (64 kB)
Downloading humanize-4.14.0-py3-none-any.whl (132 kB)
Downloading rich-14.2.0-py3-none-any.whl (243 kB)
Downloading markdown_it_py-4.0.0-py3-none-any.whl (87 kB)
Downloading mdurl-0.1.2-py3-none-any.whl (10.0 kB)
Downloading trx_python-0.3-py3-none-any.whl (45 kB)
Downloading typer-0.19.2-py3-none-any.whl (46 kB)
Downloading shellingham-1.5.4-py2.py3-none-any.whl (9.8 kB)
Downloading wandb-0.22.2-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (19.9 MB)
Downloading pydantic-2.12.3-py3-none-any.whl (462 kB)
Downloading pydantic_core-2.41.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.1 MB)
Downloading annotated_types-0.7.0-py3-none-any.whl (13 kB)
Downloading gitpython-3.1.45-py3-none-any.whl (208 kB)
Downloading gitdb-4.0.12-py3-none-any.whl (62 kB)
Downloading smmap-5.0.2-py3-none-any.whl (24 kB)
Downloading sentry_sdk-2.42.0-py2.py3-none-any.whl (379 kB)
Downloading typing_inspection-0.4.2-py3-none-any.whl (14 kB)
Downloading werkzeug-3.1.3-py3-none-any.whl (224 kB)
Downloading markupsafe-3.0.3-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (20 kB)
Downloading bids_validator-1.14.7.post0-py3-none-any.whl (23 kB)
Downloading bidsschematools-1.1.0-py3-none-any.whl (179 kB)
Downloading acres-0.5.0-py3-none-any.whl (12 kB)
Downloading coloredlogs-15.0.1-py2.py3-none-any.whl (46 kB)
Downloading humanfriendly-10.0-py2.py3-none-any.whl (86 kB)
Downloading connected_components_3d-3.26.0-cp310-cp310-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (4.6 MB)
Downloading deepdiff-8.6.1-py3-none-any.whl (91 kB)
Downloading orderly_set-5.5.0-py3-none-any.whl (13 kB)
Downloading dicom2nifti-2.6.2-py3-none-any.whl (43 kB)
Downloading pydicom-3.0.1-py3-none-any.whl (2.4 MB)
Downloading dictdiffer-0.9.0-py2.py3-none-any.whl (16 kB)
Downloading fft_conv_pytorch-1.2.0-py3-none-any.whl (6.8 kB)
Downloading filelock-3.20.0-py3-none-any.whl (16 kB)
Downloading flatbuffers-25.9.23-py2.py3-none-any.whl (30 kB)
Downloading https://download.pytorch.org/whl/fsspec-2025.9.0-py3-none-any.whl (199 kB)
Downloading future-1.0.0-py3-none-any.whl (491 kB)
Downloading graphviz-0.21-py3-none-any.whl (47 kB)
Downloading gryds-0.0.9-py3-none-any.whl (31 kB)
Downloading imagecodecs-2025.3.30-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (43.4 MB)
Downloading https://download.pytorch.org/whl/jinja2-3.1.6-py3-none-any.whl (134 kB)
Downloading lxml-6.0.2-cp310-cp310-manylinux_2_26_x86_64.manylinux_2_28_x86_64.whl (5.3 MB)
Downloading msgpack-1.1.2-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (406 kB)
Downloading ndindex-1.10.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (501 kB)
Downloading num2words-0.5.14-py3-none-any.whl (163 kB)
Downloading platformdirs-4.5.0-py3-none-any.whl (18 kB)
Downloading py_cpuinfo-9.0.0-py3-none-any.whl (22 kB)
Downloading python_gdcm-3.2.2-cp310-cp310-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (13.3 MB)
Downloading setuptools_scm-9.2.2-py3-none-any.whl (62 kB)
Downloading https://download.pytorch.org/whl/sympy-1.14.0-py3-none-any.whl (6.3 MB)
Downloading traitlets-5.14.3-py3-none-any.whl (85 kB)
Downloading unittest2-1.1.0-py2.py3-none-any.whl (96 kB)
Downloading argparse-1.4.0-py2.py3-none-any.whl (23 kB)
Downloading traceback2-1.4.0-py2.py3-none-any.whl (16 kB)
Downloading linecache2-1.0.0-py2.py3-none-any.whl (12 kB)
Downloading yacs-0.1.8-py3-none-any.whl (14 kB)
Building wheels for collected packages: nnunetv2, acvl_utils, dynamic-network-architectures, sqlalchemy, pystrum, batchgenerators, batchgeneratorsv2, docopt
  Building wheel for nnunetv2 (pyproject.toml): started
  Building wheel for nnunetv2 (pyproject.toml): finished with status 'done'
  Created wheel for nnunetv2: filename=nnunetv2-2.5.2-py3-none-any.whl size=270734 sha256=0f899771e1c1a82645adfad6fe00151156a168aecea685f6b1ab3a98a8fe8429
  Stored in directory: /home/runner/.cache/pip/wheels/61/b4/d9/5916f251c9378926a472f89e11ebc0dde9d0b7de41826f1c12
  DEPRECATION: Building 'acvl_utils' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'acvl_utils'. Discussion can be found at https://github.com/pypa/pip/issues/6334
  Building wheel for acvl_utils (setup.py): started
  Building wheel for acvl_utils (setup.py): finished with status 'done'
  Created wheel for acvl_utils: filename=acvl_utils-0.2.5-py3-none-any.whl size=27243 sha256=34d494f1757147c5495116a1d508999249d3532cb5ffe4b394ce4669c20140c7
  Stored in directory: /home/runner/.cache/pip/wheels/11/68/32/42aed9ef6a7c3ff868f84b243120481ef8a19d0ddbc2551133
  DEPRECATION: Building 'dynamic-network-architectures' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'dynamic-network-architectures'. Discussion can be found at https://github.com/pypa/pip/issues/6334
  Building wheel for dynamic-network-architectures (setup.py): started
  Building wheel for dynamic-network-architectures (setup.py): finished with status 'done'
  Created wheel for dynamic-network-architectures: filename=dynamic_network_architectures-0.3.1-py3-none-any.whl size=30108 sha256=fca1a384d5564e376760e28e100f281cbf48eb147dfc9586f5430e28edb2feaf
  Stored in directory: /home/runner/.cache/pip/wheels/55/1b/13/a6419c8dbf998b9343710355ec3edc5c8e24d9b7b22eec95fb
  DEPRECATION: Building 'sqlalchemy' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'sqlalchemy'. Discussion can be found at https://github.com/pypa/pip/issues/6334
  Building wheel for sqlalchemy (setup.py): started
  Building wheel for sqlalchemy (setup.py): finished with status 'done'
  Created wheel for sqlalchemy: filename=sqlalchemy-1.3.24-cp310-cp310-linux_x86_64.whl size=1220404 sha256=3d0e64f66ab469d744dac72962aab8821252a0dfef82037ba9ffd75d8f6f3563
  Stored in directory: /home/runner/.cache/pip/wheels/27/51/b3/3481e88d5a5ba95dd4aafedc9316774d941c4ba61cfb93add8
  DEPRECATION: Building 'pystrum' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'pystrum'. Discussion can be found at https://github.com/pypa/pip/issues/6334
  Building wheel for pystrum (setup.py): started
  Building wheel for pystrum (setup.py): finished with status 'done'
  Created wheel for pystrum: filename=pystrum-0.4-py3-none-any.whl size=19569 sha256=20a30f7c388f30d177f58bb986d82781b4b476c4e41bab6320de3bdc16d30ca3
  Stored in directory: /home/runner/.cache/pip/wheels/aa/08/d0/914025beb5a12a855b8aafd22eeedc547198684a3f4409f66c
  DEPRECATION: Building 'batchgenerators' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'batchgenerators'. Discussion can be found at https://github.com/pypa/pip/issues/6334
  Building wheel for batchgenerators (setup.py): started
  Building wheel for batchgenerators (setup.py): finished with status 'done'
  Created wheel for batchgenerators: filename=batchgenerators-0.25.1-py3-none-any.whl size=93163 sha256=1a287f5c5e2c77501170609bf7238465fabd22f9e8780510d39b71bbfc2c55b7
  Stored in directory: /home/runner/.cache/pip/wheels/be/1b/30/b3f066999ad01855fc903fe7c93c25682333dd5645d5c75434
  Building wheel for batchgeneratorsv2 (pyproject.toml): started
  Building wheel for batchgeneratorsv2 (pyproject.toml): finished with status 'done'
  Created wheel for batchgeneratorsv2: filename=batchgeneratorsv2-0.3.0-py3-none-any.whl size=65215 sha256=65df84e02f7c82d7c2cd5f181cce535082803d1b383b8cd8c7c4e20b9cf2eab1
  Stored in directory: /home/runner/.cache/pip/wheels/85/91/18/f246cf6cecb275d0e293271390794a0c090621cfc1ab1501c7
  DEPRECATION: Building 'docopt' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'docopt'. Discussion can be found at https://github.com/pypa/pip/issues/6334
  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=13783 sha256=80d5b11012d68e5f292dbc4b9c532c4b04a87bb20968ce582db0a7ea1dece35b
  Stored in directory: /home/runner/.cache/pip/wheels/fc/ab/d4/5da2067ac95b36618c629a5f93f809425700506f72c9732fac
Successfully built nnunetv2 acvl_utils dynamic-network-architectures sqlalchemy pystrum batchgenerators batchgeneratorsv2 docopt
Installing collected packages: xlwt, SimpleITK, pytz, PyQt5-Qt5, py-cpuinfo, mpmath, linecache2, flatbuffers, docopt, dictdiffer, argparse, xlsxwriter, wrapt, urllib3, typing-extensions, traitlets, traceback2, tqdm, tomli, threadpoolctl, tensorboard-data-server, sympy, sqlalchemy, smmap, six, shellingham, setuptools, pyyaml, python-gdcm, PyQt5-sip, pyparsing, pygments, pydicom, psutil, protobuf, portalocker, pluggy, platformdirs, pillow, packaging, orderly-set, numpy, num2words, networkx, ndindex, msgpack, mdurl, MarkupSafe, markdown, lxml, loguru, kiwisolver, joblib, interface-meta, iniconfig, importlib-resources, idna, humanize, humanfriendly, graphviz, future, fsspec, fonttools, filelock, einops, cython, cycler, coverage, click, charset_normalizer, certifi, astor, annotated-types, acres, absl-py, yacs, wquantiles, werkzeug, unittest2, typing-inspection, transforms3d, tifffile, setuptools-scm, sentry-sdk, scipy, requirements-parser, requests, python-dateutil, pyqt5, pydantic-core, onnx, numexpr, nibabel, matplotlib-inline, markdown-it-py, lazy-loader, jinja2, imageio, imagecodecs, h5py, grpcio, gitdb, exceptiongroup, deprecated, deepdiff, csv-diff, contourpy, connected-components-3d, coloredlogs, bidsschematools, trx-python, torch, tensorboard, scikit-learn, scikit-image, rich, pytest, pydantic, pandas, onnxruntime, matplotlib, gryds, gitpython, dicom2nifti, blosc2, bids-validator, wandb, typer, torchvision, seaborn, pytest-cov, pytest_console_scripts, pystrum, nilearn, monai, formulaic, fft-conv-pytorch, dynamic-network-architectures, dipy, batchgenerators, torchio, pybids, neurite, batchgeneratorsv2, acvl_utils, voxelmorph, nnunetv2, ivadomed, totalspineseg
Successfully installed MarkupSafe-3.0.3 PyQt5-Qt5-5.15.2 PyQt5-sip-12.17.1 SimpleITK-2.5.2 absl-py-2.3.1 acres-0.5.0 acvl_utils-0.2.5 annotated-types-0.7.0 argparse-1.4.0 astor-0.8.1 batchgenerators-0.25.1 batchgeneratorsv2-0.3.0 bids-validator-1.14.7.post0 bidsschematools-1.1.0 blosc2-3.10.2 certifi-2025.10.5 charset_normalizer-3.4.4 click-8.3.0 coloredlogs-15.0.1 connected-components-3d-3.26.0 contourpy-1.3.2 coverage-7.11.0 csv-diff-1.2 cycler-0.12.1 cython-3.1.5 deepdiff-8.6.1 deprecated-1.2.18 dicom2nifti-2.6.2 dictdiffer-0.9.0 dipy-1.8.0 docopt-0.6.2 dynamic-network-architectures-0.3.1 einops-0.8.1 exceptiongroup-1.3.0 fft-conv-pytorch-1.2.0 filelock-3.20.0 flatbuffers-25.9.23 fonttools-4.60.1 formulaic-0.3.4 fsspec-2025.9.0 future-1.0.0 gitdb-4.0.12 gitpython-3.1.45 graphviz-0.21 grpcio-1.75.1 gryds-0.0.9 h5py-3.15.1 humanfriendly-10.0 humanize-4.14.0 idna-3.11 imagecodecs-2025.3.30 imageio-2.37.0 importlib-resources-6.5.2 iniconfig-2.3.0 interface-meta-1.3.0 ivadomed-2.9.10 jinja2-3.1.6 joblib-1.5.2 kiwisolver-1.4.9 lazy-loader-0.4 linecache2-1.0.0 loguru-0.7.3 lxml-6.0.2 markdown-3.9 markdown-it-py-4.0.0 matplotlib-3.10.7 matplotlib-inline-0.1.7 mdurl-0.1.2 monai-1.4.0 mpmath-1.3.0 msgpack-1.1.2 ndindex-1.10.0 networkx-3.4.2 neurite-0.2 nibabel-5.3.2 nilearn-0.10.4 nnunetv2-2.5.2 num2words-0.5.14 numexpr-2.14.1 numpy-1.26.4 onnx-1.16.1 onnxruntime-1.21.1 orderly-set-5.5.0 packaging-25.0 pandas-1.5.3 pillow-12.0.0 platformdirs-4.5.0 pluggy-1.6.0 portalocker-3.2.0 protobuf-6.33.0 psutil-7.1.1 py-cpuinfo-9.0.0 pybids-0.15.5 pydantic-2.12.3 pydantic-core-2.41.4 pydicom-3.0.1 pygments-2.19.2 pyparsing-3.2.5 pyqt5-5.15.11 pystrum-0.4 pytest-8.4.2 pytest-cov-7.0.0 pytest_console_scripts-1.4.1 python-dateutil-2.9.0.post0 python-gdcm-3.2.2 pytz-2025.2 pyyaml-6.0.3 requests-2.32.5 requirements-parser-0.13.0 rich-14.2.0 scikit-image-0.25.2 scikit-learn-1.7.2 scipy-1.15.3 seaborn-0.13.2 sentry-sdk-2.42.0 setuptools-80.9.0 setuptools-scm-9.2.2 shellingham-1.5.4 six-1.17.0 smmap-5.0.2 sqlalchemy-1.3.24 sympy-1.14.0 tensorboard-2.20.0 tensorboard-data-server-0.7.2 threadpoolctl-3.6.0 tifffile-2025.5.10 tomli-2.3.0 torch-2.2.2+cpu torchio-0.20.23 torchvision-0.17.2+cpu totalspineseg-20250709 tqdm-4.67.1 traceback2-1.4.0 traitlets-5.14.3 transforms3d-0.4.2 trx-python-0.3 typer-0.19.2 typing-extensions-4.15.0 typing-inspection-0.4.2 unittest2-1.1.0 urllib3-2.5.0 voxelmorph-0.2 wandb-0.22.2 werkzeug-3.1.3 wquantiles-0.6 wrapt-1.17.3 xlsxwriter-3.2.9 xlwt-1.3.0 yacs-0.1.8

Installing spinalcordtoolbox...

Obtaining file:///home/runner/sct_7.2.dev0
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Checking if build backend supports build_editable: started
  Checking if build backend supports build_editable: finished with status 'done'
  Getting requirements to build editable: started
  Getting requirements to build editable: finished with status 'done'
  Preparing editable metadata (pyproject.toml): started
  Preparing editable metadata (pyproject.toml): finished with status 'done'
Building wheels for collected packages: spinalcordtoolbox
  Building editable for spinalcordtoolbox (pyproject.toml): started
  Building editable for spinalcordtoolbox (pyproject.toml): finished with status 'done'
  Created wheel for spinalcordtoolbox: filename=spinalcordtoolbox-7.2.dev0-0.editable-py3-none-any.whl size=9857 sha256=12cd1cafc61c7a9a2a2cdf17b753e9dff188a37fb41ef83498e656458a7d08ee
  Stored in directory: /tmp/pip-ephem-wheel-cache-8x_luzj5/wheels/29/26/62/cf9910ce78d28f5231ab6a31eafe946f8ca65cb20b62bea290
Successfully built spinalcordtoolbox
Installing collected packages: spinalcordtoolbox
Successfully installed spinalcordtoolbox-7.2.dev0

Creating launchers for Python scripts...

Installing binaries...

sct_download_data -d binaries_linux -k

--
Spinal Cord Toolbox (7.2.dev0)

sct_download_data -d binaries_linux -k
--

Trying URL: https://github.com/spinalcordtoolbox/spinalcordtoolbox-binaries/releases/download/r20221109/spinalcordtoolbox-binaries_linux.tar.gz
Downloading: spinalcordtoolbox-binaries_linux.tar.gz
Creating temporary folder (/tmp/sct_2025-10-20_11-05-11_install-data_na9d631e)
Unzip data to: /tmp/sct_2025-10-20_11-05-11_install-data_na9d631e
Copying data to: /home/runner/sct_7.2.dev0/bin
Removing temporary folders...
Done!

Total runtime; 2.572 seconds.

All requirements installed!

Installing data...

mkdir -p /home/runner/sct_7.2.dev0/data

sct_download_data -d default -k

--
Spinal Cord Toolbox (7.2.dev0)

sct_download_data -d default -k
--

Trying URL: https://github.com/spinalcordtoolbox/PAM50/releases/download/r20250730/PAM50-r20250730.zip
Downloading: PAM50-r20250730.zip
Creating temporary folder (/tmp/sct_2025-10-20_11-05-14_install-data_c8gs39ju)
Unzip data to: /tmp/sct_2025-10-20_11-05-14_install-data_c8gs39ju
Copying data to: /home/runner/sct_7.2.dev0/data/PAM50
Removing temporary folders...
Trying URL: https://github.com/spinalcordtoolbox/deepseg_gm_models/releases/download/r20180205/20220325_deepseg_gm_models_onnx.zip
Downloading: 20220325_deepseg_gm_models_onnx.zip
Creating temporary folder (/tmp/sct_2025-10-20_11-05-14_install-data_q_xbc2rr)
Unzip data to: /tmp/sct_2025-10-20_11-05-14_install-data_q_xbc2rr
Copying data to: /home/runner/sct_7.2.dev0/data/deepseg_gm_models
Removing temporary folders...
Trying URL: https://github.com/spinalcordtoolbox/deepseg_sc_models/releases/download/r20180610/20220325_deepseg_sc_models_onnx.zip
Downloading: 20220325_deepseg_sc_models_onnx.zip
Creating temporary folder (/tmp/sct_2025-10-20_11-05-14_install-data_vo4q18ox)
Unzip data to: /tmp/sct_2025-10-20_11-05-14_install-data_vo4q18ox
Copying data to: /home/runner/sct_7.2.dev0/data/deepseg_sc_models
Removing temporary folders...
Trying URL: https://github.com/spinalcordtoolbox/deepseg_lesion_models/releases/download/r20180613/20220325_deepseg_lesion_models_onnx.zip
Downloading: 20220325_deepseg_lesion_models_onnx.zip
Creating temporary folder (/tmp/sct_2025-10-20_11-05-15_install-data_u2xoo84_)
Unzip data to: /tmp/sct_2025-10-20_11-05-15_install-data_u2xoo84_
Copying data to: /home/runner/sct_7.2.dev0/data/deepseg_lesion_models
Removing temporary folders...
Trying URL: https://github.com/ivadomed/multimodal-registration/releases/download/r20220512/models.zip
Downloading: models.zip
Creating temporary folder (/tmp/sct_2025-10-20_11-05-16_install-data_9hz5ogru)
Unzip data to: /tmp/sct_2025-10-20_11-05-16_install-data_9hz5ogru
Copying data to: /home/runner/sct_7.2.dev0/data/deepreg_models
Removing temporary folders...
Trying URL: https://github.com/spinalcordtoolbox/PAM50-normalized-metrics/archive/refs/tags/r20250321.zip
Downloading: PAM50-normalized-metrics-r20250321.zip
Creating temporary folder (/tmp/sct_2025-10-20_11-05-19_install-data_hzi_raq9)
Unzip data to: /tmp/sct_2025-10-20_11-05-19_install-data_hzi_raq9
Copying data to: /home/runner/sct_7.2.dev0/data/PAM50_normalized_metrics
Removing temporary folders...
Done!

Total runtime; 6.184 seconds.

WARNING: no checks will be run (installation will not be validated)

Installation finished successfully!

Changed text

Open file

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

Checking OS type and version...

Linux imaging-gpu-05 5.15.0-153-generic #163-Ubuntu SMP Thu Aug 7 16:37:18 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux

Checking requirements...

OK!

SCT version ......... 7.2.dev0
Installation type ... in-place
Operating system .... linux (unknown)
Shell config ........ /home/lchauvin/.bashrc

Checking permissions on required file /home/lchauvin/.bashrc:
  - File exists: True
  - File ownership: True
  - Read permissions: True
  - Write permissions: True

WARNING: Directory already exists. Files will be overwritten.

SCT will be installed here: [/scratch/02/lchauvin/workspace/projects/spinalcordtoolbox]

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

Downloading Miniforge...

wget -nv -O /tmp/tmp.fRYleHJK6d/miniforge.sh https://github.com/conda-forge/miniforge/releases/download/24.11.2-1/Miniforge3-Linux-x86_64.sh

Installing Miniforge...

bash /tmp/tmp.fRYleHJK6d/miniforge.sh -p /scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/python -b -f

PREFIX=/scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/python
Unpacking payload ...
Extracting _libgcc_mutex-0.1-conda_forge.tar.bz2
Extracting ca-certificates-2024.12.14-hbcca054_0.conda
Extracting ld_impl_linux-64-2.43-h712a8e2_2.conda
Extracting pybind11-abi-4-hd8ed1ab_3.tar.bz2
Extracting python_abi-3.12-5_cp312.conda
Extracting tzdata-2024b-hc8b5060_0.conda
Extracting libgomp-14.2.0-h77fa898_1.conda
Extracting _openmp_mutex-4.5-2_gnu.tar.bz2
Extracting libgcc-14.2.0-h77fa898_1.conda
Extracting c-ares-1.34.4-hb9d3cd8_0.conda
Extracting libexpat-2.6.4-h5888daf_0.conda
Extracting libgcc-ng-14.2.0-h69a702a_1.conda
Extracting liblzma-5.6.3-hb9d3cd8_1.conda
Extracting libstdcxx-14.2.0-hc0a3c3a_1.conda
Extracting libzlib-1.3.1-hb9d3cd8_2.conda
Extracting openssl-3.4.0-hb9d3cd8_0.conda
Extracting reproc-14.2.5.post0-hb9d3cd8_0.conda
Extracting bzip2-1.0.8-h4bc722e_7.conda
Extracting keyutils-1.6.1-h166bdaf_0.tar.bz2
Extracting libev-4.33-hd590300_2.conda
Extracting libffi-3.4.2-h7f98852_5.tar.bz2
Extracting libiconv-1.17-hd590300_2.conda
Extracting libnsl-2.0.1-hd590300_0.conda
Extracting libsqlite-3.47.2-hee588c1_0.conda
Extracting libssh2-1.11.1-hf672d98_0.conda
Extracting libstdcxx-ng-14.2.0-h4852527_1.conda
Extracting libuuid-2.38.1-h0b41bf4_0.conda
Extracting libxcrypt-4.4.36-hd590300_1.conda
Extracting lz4-c-1.10.0-h5888daf_1.conda
Extracting lzo-2.10-hd590300_1001.conda
Extracting ncurses-6.5-he02047a_1.conda
Extracting reproc-cpp-14.2.5.post0-h5888daf_0.conda
Extracting tk-8.6.13-noxft_h4845f30_101.conda
Extracting fmt-11.0.2-h434a139_0.conda
Extracting libedit-3.1.20191231-he28a2e2_2.tar.bz2
Extracting libnghttp2-1.64.0-h161d5f1_0.conda
Extracting libsolv-0.7.30-h3509ff9_0.conda
Extracting libxml2-2.13.5-h0d44e9d_1.conda
Extracting readline-8.2-h8228510_1.conda
Extracting yaml-cpp-0.8.0-h59595ed_0.conda
Extracting zstd-1.5.6-ha6fb4c9_0.conda
Extracting krb5-1.21.3-h659f571_0.conda
Extracting libarchive-3.7.7-h4585015_3.conda
Extracting python-3.12.8-h9e4cc4f_1_cpython.conda
Extracting libcurl-8.11.1-h332b0f4_0.conda
Extracting menuinst-2.2.0-py312h7900ff3_0.conda
Extracting archspec-0.2.3-pyhd8ed1ab_0.conda
Extracting boltons-24.0.0-pyhd8ed1ab_1.conda
Extracting brotli-python-1.1.0-py312h2ec8cdc_2.conda
Extracting certifi-2024.12.14-pyhd8ed1ab_0.conda
Extracting charset-normalizer-3.4.1-pyhd8ed1ab_0.conda
Extracting colorama-0.4.6-pyhd8ed1ab_1.conda
Extracting distro-1.9.0-pyhd8ed1ab_1.conda
Extracting frozendict-2.4.6-py312h66e93f0_0.conda
Extracting hpack-4.0.0-pyhd8ed1ab_1.conda
Extracting hyperframe-6.0.1-pyhd8ed1ab_1.conda
Extracting idna-3.10-pyhd8ed1ab_1.conda
Extracting jsonpointer-3.0.0-py312h7900ff3_1.conda
Extracting libmamba-1.5.12-h49b8a8d_0.conda
Extracting packaging-24.2-pyhd8ed1ab_2.conda
Extracting platformdirs-4.3.6-pyhd8ed1ab_1.conda
Extracting pluggy-1.5.0-pyhd8ed1ab_1.conda
Extracting pycosat-0.6.6-py312h66e93f0_2.conda
Extracting pycparser-2.22-pyh29332c3_1.conda
Extracting pysocks-1.7.1-pyha55dd90_7.conda
Extracting ruamel.yaml.clib-0.2.8-py312h66e93f0_1.conda
Extracting setuptools-75.6.0-pyhff2d567_1.conda
Extracting truststore-0.10.0-pyhd8ed1ab_0.conda
Extracting wheel-0.45.1-pyhd8ed1ab_1.conda
Extracting cffi-1.17.1-py312h06ac9bb_0.conda
Extracting h2-4.1.0-pyhd8ed1ab_1.conda
Extracting jsonpatch-1.33-pyhd8ed1ab_1.conda
Extracting libmambapy-1.5.12-py312hbaee817_0.conda
Extracting pip-24.3.1-pyh8b19718_2.conda
Extracting ruamel.yaml-0.18.8-py312h66e93f0_0.conda
Extracting tqdm-4.67.1-pyhd8ed1ab_1.conda
Extracting zstandard-0.23.0-py312hef9b889_1.conda
Extracting conda-package-streaming-0.11.0-pyhd8ed1ab_0.conda
Extracting urllib3-2.3.0-pyhd8ed1ab_0.conda
Extracting conda-package-handling-2.4.0-pyha770c72_1.conda
Extracting requests-2.32.3-pyhd8ed1ab_1.conda
Extracting conda-24.11.2-py312h7900ff3_1.conda
Extracting conda-libmamba-solver-24.9.0-pyhd8ed1ab_0.conda
Extracting mamba-1.5.12-py312h9460a1c_0.conda

Installing base environment...

Transaction

Prefix: /scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/python

Updating specs:

Summary:

Install: 84 packages

Total download: 0 B

Transaction starting

Transaction finished

To activate this environment, use:

micromamba activate /scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/python

Or to execute a single command in this environment, use:

micromamba run -p /scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/python mycommand

installation finished.

Creating conda environment...

Channels:
 - defaults
 - conda-forge
 - nodefaults
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

==> WARNING: A newer version of conda exists. <==
    current version: 24.11.2
    latest version: 25.9.1

Please update conda by running

$ conda update -n base -c conda-forge conda

## Package Plan ##

environment location: /scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/python/envs/venv_sct

added / updated specs:
    - python=3.10

The following packages will be downloaded:

package                    |            build
    ---------------------------|-----------------
    _libgcc_mutex-0.1          |             main           3 KB
    _openmp_mutex-5.1          |            1_gnu          21 KB
    bzip2-1.0.8                |       h5eee18b_6         262 KB
    ca-certificates-2025.9.9   |       h06a4308_0         127 KB
    expat-2.7.1                |       h6a678d5_0         182 KB
    ld_impl_linux-64-2.44      |       h153f514_2         672 KB
    libffi-3.4.4               |       h6a678d5_1         141 KB
    libgcc-ng-11.2.0           |       h1234567_1         5.3 MB
    libgomp-11.2.0             |       h1234567_1         474 KB
    libstdcxx-ng-11.2.0        |       h1234567_1         4.7 MB
    libuuid-1.41.5             |       h5eee18b_0          27 KB
    libxcb-1.17.0              |       h9b100fa_0         430 KB
    libzlib-1.3.1              |       hb25bd0a_0          59 KB
    ncurses-6.5                |       h7934f7d_0         1.1 MB
    openssl-3.0.18             |       hd6dcaed_0         4.5 MB
    pip-25.2                   |     pyhc872135_0         1.2 MB
    pthread-stubs-0.3          |       h0ce48e5_1           5 KB
    python-3.10.18             |       h1a3bd86_0        26.5 MB
    readline-8.3               |       hc2a1206_0         471 KB
    setuptools-80.9.0          |  py310h06a4308_0         1.4 MB
    sqlite-3.50.2              |       hb25bd0a_1         1.1 MB
    tk-8.6.15                  |       h54e0aa7_0         3.4 MB
    tzdata-2025b               |       h04d1e81_0         116 KB
    wheel-0.45.1               |  py310h06a4308_0         115 KB
    xorg-libx11-1.8.12         |       h9b100fa_1         895 KB
    xorg-libxau-1.0.12         |       h9b100fa_0          13 KB
    xorg-libxdmcp-1.1.5        |       h9b100fa_0          19 KB
    xorg-xorgproto-2024.1      |       h5eee18b_1         580 KB
    xz-5.6.4                   |       h5eee18b_1         567 KB
    zlib-1.3.1                 |       hb25bd0a_0          96 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-5.1-1_gnu 
  bzip2              pkgs/main/linux-64::bzip2-1.0.8-h5eee18b_6 
  ca-certificates    pkgs/main/linux-64::ca-certificates-2025.9.9-h06a4308_0 
  expat              pkgs/main/linux-64::expat-2.7.1-h6a678d5_0 
  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.44-h153f514_2 
  libffi             pkgs/main/linux-64::libffi-3.4.4-h6a678d5_1 
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-11.2.0-h1234567_1 
  libgomp            pkgs/main/linux-64::libgomp-11.2.0-h1234567_1 
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-11.2.0-h1234567_1 
  libuuid            pkgs/main/linux-64::libuuid-1.41.5-h5eee18b_0 
  libxcb             pkgs/main/linux-64::libxcb-1.17.0-h9b100fa_0 
  libzlib            pkgs/main/linux-64::libzlib-1.3.1-hb25bd0a_0 
  ncurses            pkgs/main/linux-64::ncurses-6.5-h7934f7d_0 
  openssl            pkgs/main/linux-64::openssl-3.0.18-hd6dcaed_0 
  pip                pkgs/main/noarch::pip-25.2-pyhc872135_0 
  pthread-stubs      pkgs/main/linux-64::pthread-stubs-0.3-h0ce48e5_1 
  python             pkgs/main/linux-64::python-3.10.18-h1a3bd86_0 
  readline           pkgs/main/linux-64::readline-8.3-hc2a1206_0 
  setuptools         pkgs/main/linux-64::setuptools-80.9.0-py310h06a4308_0 
  sqlite             pkgs/main/linux-64::sqlite-3.50.2-hb25bd0a_1 
  tk                 pkgs/main/linux-64::tk-8.6.15-h54e0aa7_0 
  tzdata             pkgs/main/noarch::tzdata-2025b-h04d1e81_0 
  wheel              pkgs/main/linux-64::wheel-0.45.1-py310h06a4308_0 
  xorg-libx11        pkgs/main/linux-64::xorg-libx11-1.8.12-h9b100fa_1 
  xorg-libxau        pkgs/main/linux-64::xorg-libxau-1.0.12-h9b100fa_0 
  xorg-libxdmcp      pkgs/main/linux-64::xorg-libxdmcp-1.1.5-h9b100fa_0 
  xorg-xorgproto     pkgs/main/linux-64::xorg-xorgproto-2024.1-h5eee18b_1 
  xz                 pkgs/main/linux-64::xz-5.6.4-h5eee18b_1 
  zlib               pkgs/main/linux-64::zlib-1.3.1-hb25bd0a_0

Downloading and Extracting Packages: ...working...
python-3.10.18       | 26.5 MB   |            |   0%

libgcc-ng-11.2.0     | 5.3 MB    |            |   0%

libstdcxx-ng-11.2.0  | 4.7 MB    |            |   0%

openssl-3.0.18       | 4.5 MB    |            |   0%

tk-8.6.15            | 3.4 MB    |            |   0%

setuptools-80.9.0    | 1.4 MB    |            |   0%

pip-25.2             | 1.2 MB    |            |   0%

sqlite-3.50.2        | 1.1 MB    |            |   0%

ncurses-6.5          | 1.1 MB    |            |   0%

xorg-libx11-1.8.12   | 895 KB    |            |   0%

ld_impl_linux-64-2.4 | 672 KB    |            |   0%

xorg-xorgproto-2024. | 580 KB    |            |   0%

xz-5.6.4             | 567 KB    |            |   0%

libgomp-11.2.0       | 474 KB    |            |   0%

readline-8.3         | 471 KB    |            |   0%

libxcb-1.17.0        | 430 KB    |            |   0%

bzip2-1.0.8          | 262 KB    |            |   0%

expat-2.7.1          | 182 KB    |            |   0%

libffi-3.4.4         | 141 KB    |            |   0%

... (more hidden) ...
python-3.10.18       | 26.5 MB   |            |   0%

libgcc-ng-11.2.0     | 5.3 MB    |            |   0%

libstdcxx-ng-11.2.0  | 4.7 MB    |            |   0%

tk-8.6.15            | 3.4 MB    |            |   0%

openssl-3.0.18       | 4.5 MB    |            |   0% 
python-3.10.18       | 26.5 MB   | 4          |   5%

libstdcxx-ng-11.2.0  | 4.7 MB    | #          |  11%

libgcc-ng-11.2.0     | 5.3 MB    | ##1        |  21%

tk-8.6.15            | 3.4 MB    | #1         |  12%

openssl-3.0.18       | 4.5 MB    | 5          |   5% 
python-3.10.18       | 26.5 MB   | #8         |  19%

tk-8.6.15            | 3.4 MB    | ####7      |  47%

libgcc-ng-11.2.0     | 5.3 MB    | ########## | 100%

openssl-3.0.18       | 4.5 MB    | ##8        |  28%

libstdcxx-ng-11.2.0  | 4.7 MB    | ########## | 100%

libstdcxx-ng-11.2.0  | 4.7 MB    | ########## | 100% 
python-3.10.18       | 26.5 MB   | ###6       |  36%

tk-8.6.15            | 3.4 MB    | #########3 |  93%

pip-25.2             | 1.2 MB    | 1          |   1%

openssl-3.0.18       | 4.5 MB    | #####      |  50%

setuptools-80.9.0    | 1.4 MB    | 1          |   1% 
python-3.10.18       | 26.5 MB   | #####      |  51%

pip-25.2             | 1.2 MB    | ########## | 100%

tk-8.6.15            | 3.4 MB    | ########## | 100%

openssl-3.0.18       | 4.5 MB    | #########3 |  93%

setuptools-80.9.0    | 1.4 MB    | ########## | 100%

setuptools-80.9.0    | 1.4 MB    | ########## | 100% 
python-3.10.18       | 26.5 MB   | ######6    |  66%

sqlite-3.50.2        | 1.1 MB    | 1          |   1%

xorg-libx11-1.8.12   | 895 KB    | 1          |   2%

openssl-3.0.18       | 4.5 MB    | ########## | 100%

ncurses-6.5          | 1.1 MB    | 1          |   1%

sqlite-3.50.2        | 1.1 MB    | ########## | 100% 
python-3.10.18       | 26.5 MB   | ########   |  81%

xorg-libx11-1.8.12   | 895 KB    | ########## | 100%

ncurses-6.5          | 1.1 MB    | ########## | 100%

ld_impl_linux-64-2.4 | 672 KB    | 2          |   2%

xz-5.6.4             | 567 KB    | 2          |   3%

xorg-xorgproto-2024. | 580 KB    | 2          |   3% 
python-3.10.18       | 26.5 MB   | #########8 |  98%

ld_impl_linux-64-2.4 | 672 KB    | ########## | 100%

libstdcxx-ng-11.2.0  | 4.7 MB    | ########## | 100%

xz-5.6.4             | 567 KB    | ########## | 100%

libgomp-11.2.0       | 474 KB    | 3          |   3%

xorg-xorgproto-2024. | 580 KB    | ########## | 100%

libgomp-11.2.0       | 474 KB    | ########## | 100%

libxcb-1.17.0        | 430 KB    | 3          |   4%

libgcc-ng-11.2.0     | 5.3 MB    | ########## | 100%

readline-8.3         | 471 KB    | 3          |   3%

expat-2.7.1          | 182 KB    | 8          |   9%

bzip2-1.0.8          | 262 KB    | 6          |   6%

libxcb-1.17.0        | 430 KB    | ########## | 100%

expat-2.7.1          | 182 KB    | ########## | 100%

bzip2-1.0.8          | 262 KB    | ########## | 100%

readline-8.3         | 471 KB    | ########## | 100%

libffi-3.4.4         | 141 KB    | #1         |  11%

libffi-3.4.4         | 141 KB    | ########## | 100%

... (more hidden) ...

pip-25.2             | 1.2 MB    | ########## | 100%

pip-25.2             | 1.2 MB    | ########## | 100% 
python-3.10.18       | 26.5 MB   | ########## | 100%

tk-8.6.15            | 3.4 MB    | ########## | 100%

sqlite-3.50.2        | 1.1 MB    | ########## | 100%

openssl-3.0.18       | 4.5 MB    | ########## | 100%

xorg-libx11-1.8.12   | 895 KB    | ########## | 100%

setuptools-80.9.0    | 1.4 MB    | ########## | 100%

ld_impl_linux-64-2.4 | 672 KB    | ########## | 100%

xz-5.6.4             | 567 KB    | ########## | 100%

libgomp-11.2.0       | 474 KB    | ########## | 100%

xorg-xorgproto-2024. | 580 KB    | ########## | 100%

expat-2.7.1          | 182 KB    | ########## | 100%

libxcb-1.17.0        | 430 KB    | ########## | 100%

bzip2-1.0.8          | 262 KB    | ########## | 100%

readline-8.3         | 471 KB    | ########## | 100%

libffi-3.4.4         | 141 KB    | ########## | 100%

... (more hidden) ...

ncurses-6.5          | 1.1 MB    | ########## | 100%

ncurses-6.5          | 1.1 MB    | ########## | 100% 
python-3.10.18       | 26.5 MB   | ########## | 100%

done
Preparing transaction: - \ done
Verifying transaction: / - \ | / - \ | / - \ | done
Executing transaction: - \ | / - \ | / - \ | / - done
#
# To activate this environment, use
#
#     $ conda activate /scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/python/envs/venv_sct
#
# To deactivate an active environment, use
#
#     $ conda deactivate

Channels:
 - conda-forge
 - defaults
 - nodefaults
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

==> WARNING: A newer version of conda exists. <==
    current version: 24.11.2
    latest version: 25.9.1

Please update conda by running

$ conda update -n base -c conda-forge conda

## Package Plan ##

environment location: /scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/python/envs/venv_sct

added / updated specs:
    - libstdcxx-ng

The following packages will be downloaded:

package                    |            build
    ---------------------------|-----------------
    ca-certificates-2025.10.5  |       hbd8a1cb_0         152 KB  conda-forge
    libgcc-15.2.0              |       h767d61c_7         803 KB  conda-forge
    libgcc-ng-15.2.0           |       h69a702a_7          29 KB  conda-forge
    libgomp-15.2.0             |       h767d61c_7         437 KB  conda-forge
    libstdcxx-15.2.0           |       h8f9b012_7         3.7 MB  conda-forge
    libstdcxx-ng-15.2.0        |       h4852527_7          29 KB  conda-forge
    openssl-3.5.4              |       h26f9b46_0         3.0 MB  conda-forge
    ------------------------------------------------------------
                                           Total:         8.1 MB

The following NEW packages will be INSTALLED:

libgcc             conda-forge/linux-64::libgcc-15.2.0-h767d61c_7 
  libstdcxx          conda-forge/linux-64::libstdcxx-15.2.0-h8f9b012_7

The following packages will be UPDATED:

ca-certificates    pkgs/main/linux-64::ca-certificates-2~ --> conda-forge/noarch::ca-certificates-2025.10.5-hbd8a1cb_0 
  libgcc-ng          pkgs/main::libgcc-ng-11.2.0-h1234567_1 --> conda-forge::libgcc-ng-15.2.0-h69a702a_7 
  libgomp              pkgs/main::libgomp-11.2.0-h1234567_1 --> conda-forge::libgomp-15.2.0-h767d61c_7 
  libstdcxx-ng       pkgs/main::libstdcxx-ng-11.2.0-h12345~ --> conda-forge::libstdcxx-ng-15.2.0-h4852527_7 
  openssl              pkgs/main::openssl-3.0.18-hd6dcaed_0 --> conda-forge::openssl-3.5.4-h26f9b46_0

Downloading and Extracting Packages: ...working...
libstdcxx-15.2.0     | 3.7 MB    |            |   0%

openssl-3.5.4        | 3.0 MB    |            |   0%

libgcc-15.2.0        | 803 KB    |            |   0%

libgomp-15.2.0       | 437 KB    |            |   0%

ca-certificates-2025 | 152 KB    |            |   0%

libstdcxx-ng-15.2.0  | 29 KB     |            |   0%

libgcc-ng-15.2.0     | 29 KB     |            |   0%

libgomp-15.2.0       | 437 KB    | 3          |   4%

libgcc-15.2.0        | 803 KB    | 1          |   2%

openssl-3.5.4        | 3.0 MB    |            |   1%

ca-certificates-2025 | 152 KB    | #          |  11% 
libstdcxx-15.2.0     | 3.7 MB    |            |   0%

ca-certificates-2025 | 152 KB    | ########## | 100%

libgomp-15.2.0       | 437 KB    | ########## | 100%

libgcc-15.2.0        | 803 KB    | ########## | 100%

ca-certificates-2025 | 152 KB    | ########## | 100%

openssl-3.5.4        | 3.0 MB    | #####8     |  59%

libgcc-ng-15.2.0     | 29 KB     | #####5     |  56%

libgcc-ng-15.2.0     | 29 KB     | ########## | 100%

libstdcxx-ng-15.2.0  | 29 KB     | #####5     |  56%

libstdcxx-ng-15.2.0  | 29 KB     | ########## | 100% 
libstdcxx-15.2.0     | 3.7 MB    | ####1      |  42%

libgomp-15.2.0       | 437 KB    | ########## | 100%

openssl-3.5.4        | 3.0 MB    | ########## | 100%

libgcc-ng-15.2.0     | 29 KB     | ########## | 100%

libgcc-ng-15.2.0     | 29 KB     | ########## | 100% 
libstdcxx-15.2.0     | 3.7 MB    | ########2  |  83%

libgcc-15.2.0        | 803 KB    | ########## | 100%

libstdcxx-ng-15.2.0  | 29 KB     | ########## | 100%

libgcc-15.2.0        | 803 KB    | ########## | 100%

libstdcxx-ng-15.2.0  | 29 KB     | ########## | 100% 
libstdcxx-15.2.0     | 3.7 MB    | ########## | 100%

openssl-3.5.4        | 3.0 MB    | ########## | 100% 
libstdcxx-15.2.0     | 3.7 MB    | ########## | 100%

done
Preparing transaction: - done
Verifying transaction: | / done
Executing transaction: \ done
Channels:
 - conda-forge
 - defaults
 - nodefaults
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

==> WARNING: A newer version of conda exists. <==
    current version: 24.11.2
    latest version: 25.9.1

Please update conda by running

$ conda update -n base -c conda-forge conda

## Package Plan ##

environment location: /scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/python/envs/venv_sct

added / updated specs:
    - libffi

The following packages will be downloaded:

package                    |            build
    ---------------------------|-----------------
    c-ares-1.34.5              |       hb9d3cd8_0         202 KB  conda-forge
    curl-8.14.1                |       h332b0f4_0         176 KB  conda-forge
    graalpy-23.0.0             | 0_graalvm_native       326.8 MB  conda-forge
    keyutils-1.6.3             |       hb9d3cd8_0         131 KB  conda-forge
    libcurl-8.14.1             |       h332b0f4_0         439 KB  conda-forge
    libedit-3.1.20250104       | pl5321h7949ede_0         132 KB  conda-forge
    libffi-3.5.2               |       h9ec8514_0          56 KB  conda-forge
    libnghttp2-1.67.0          |       had1ee68_0         651 KB  conda-forge
    libssh2-1.11.1             |       hcf80075_0         298 KB  conda-forge
    patch-2.8                  |    hb03c661_1002         114 KB  conda-forge
    python-3.10.8              |0_native230_graalpy          88 KB  conda-forge
    python_abi-3.10            |8_graalpy230_310_native           7 KB  conda-forge
    zstd-1.5.7                 |       hb8e6e7a_2         554 KB  conda-forge
    ------------------------------------------------------------
                                           Total:       329.6 MB

The following NEW packages will be INSTALLED:

c-ares             conda-forge/linux-64::c-ares-1.34.5-hb9d3cd8_0 
  curl               conda-forge/linux-64::curl-8.14.1-h332b0f4_0 
  graalpy            conda-forge/linux-64::graalpy-23.0.0-0_graalvm_native 
  keyutils           conda-forge/linux-64::keyutils-1.6.3-hb9d3cd8_0 
  krb5               conda-forge/linux-64::krb5-1.21.3-h659f571_0 
  libcurl            conda-forge/linux-64::libcurl-8.14.1-h332b0f4_0 
  libedit            conda-forge/linux-64::libedit-3.1.20250104-pl5321h7949ede_0 
  libev              conda-forge/linux-64::libev-4.33-hd590300_2 
  libnghttp2         conda-forge/linux-64::libnghttp2-1.67.0-had1ee68_0 
  libssh2            conda-forge/linux-64::libssh2-1.11.1-hcf80075_0 
  patch              conda-forge/linux-64::patch-2.8-hb03c661_1002 
  python_abi         conda-forge/noarch::python_abi-3.10-8_graalpy230_310_native 
  zstd               conda-forge/linux-64::zstd-1.5.7-hb8e6e7a_2

The following packages will be UPDATED:

libffi                 pkgs/main::libffi-3.4.4-h6a678d5_1 --> conda-forge::libffi-3.5.2-h9ec8514_0

The following packages will be SUPERSEDED by a higher-priority channel:

python               pkgs/main::python-3.10.18-h1a3bd86_0 --> conda-forge::python-3.10.8-0_native230_graalpy

Downloading and Extracting Packages: ...working...
graalpy-23.0.0       | 326.8 MB  |            |   0%

libnghttp2-1.67.0    | 651 KB    |            |   0%

zstd-1.5.7           | 554 KB    |            |   0%

libcurl-8.14.1       | 439 KB    |            |   0%

libssh2-1.11.1       | 298 KB    |            |   0%

c-ares-1.34.5        | 202 KB    |            |   0%

curl-8.14.1          | 176 KB    |            |   0%

libedit-3.1.20250104 | 132 KB    |            |   0%

keyutils-1.6.3       | 131 KB    |            |   0%

patch-2.8            | 114 KB    |            |   0%

python-3.10.8        | 88 KB     |            |   0%

libffi-3.5.2         | 56 KB     |            |   0%

python_abi-3.10      | 7 KB      |            |   0%

libcurl-8.14.1       | 439 KB    | 3          |   4%

libnghttp2-1.67.0    | 651 KB    | 2          |   2%

libssh2-1.11.1       | 298 KB    | 5          |   5%

libcurl-8.14.1       | 439 KB    | ########## | 100%

libnghttp2-1.67.0    | 651 KB    | ########## | 100%

libcurl-8.14.1       | 439 KB    | ########## | 100%

zstd-1.5.7           | 554 KB    | 2          |   3%

libssh2-1.11.1       | 298 KB    | ########## | 100%

c-ares-1.34.5        | 202 KB    | 7          |   8%

libnghttp2-1.67.0    | 651 KB    | ########## | 100%

c-ares-1.34.5        | 202 KB    | ########## | 100%

keyutils-1.6.3       | 131 KB    | #2         |  12%

keyutils-1.6.3       | 131 KB    | ########## | 100%

curl-8.14.1          | 176 KB    | 9          |   9%

zstd-1.5.7           | 554 KB    | ########## | 100%

curl-8.14.1          | 176 KB    | ########## | 100%

patch-2.8            | 114 KB    | #3         |  14%

libffi-3.5.2         | 56 KB     | ##8        |  28%

libffi-3.5.2         | 56 KB     | ########## | 100%

patch-2.8            | 114 KB    | ########## | 100% 
graalpy-23.0.0       | 326.8 MB  |            |   0%

libedit-3.1.20250104 | 132 KB    | #2         |  12%

keyutils-1.6.3       | 131 KB    | ########## | 100%

libedit-3.1.20250104 | 132 KB    | ########## | 100%

python-3.10.8        | 88 KB     | #8         |  18%

python-3.10.8        | 88 KB     | ########## | 100%

python_abi-3.10      | 7 KB      | ########## | 100%

c-ares-1.34.5        | 202 KB    | ########## | 100%

c-ares-1.34.5        | 202 KB    | ########## | 100% 
graalpy-23.0.0       | 326.8 MB  |            |   1%

curl-8.14.1          | 176 KB    | ########## | 100%

zstd-1.5.7           | 554 KB    | ########## | 100%

libssh2-1.11.1       | 298 KB    | ########## | 100%

libffi-3.5.2         | 56 KB     | ########## | 100%

patch-2.8            | 114 KB    | ########## | 100%

libedit-3.1.20250104 | 132 KB    | ########## | 100%

python_abi-3.10      | 7 KB      | ########## | 100%

python-3.10.8        | 88 KB     | ########## | 100%

python-3.10.8        | 88 KB     | ########## | 100% 
graalpy-23.0.0       | 326.8 MB  | 1          |   1% 
graalpy-23.0.0       | 326.8 MB  | 2          |   2% 
graalpy-23.0.0       | 326.8 MB  | 3          |   3% 
graalpy-23.0.0       | 326.8 MB  | 4          |   4% 
graalpy-23.0.0       | 326.8 MB  | 5          |   5% 
graalpy-23.0.0       | 326.8 MB  | 6          |   6% 
graalpy-23.0.0       | 326.8 MB  | 6          |   7% 
graalpy-23.0.0       | 326.8 MB  | 7          |   8% 
graalpy-23.0.0       | 326.8 MB  | 8          |   8% 
graalpy-23.0.0       | 326.8 MB  | 9          |   9% 
graalpy-23.0.0       | 326.8 MB  | 9          |  10% 
graalpy-23.0.0       | 326.8 MB  | #          |  10% 
graalpy-23.0.0       | 326.8 MB  | #1         |  12% 
graalpy-23.0.0       | 326.8 MB  | #3         |  14% 
graalpy-23.0.0       | 326.8 MB  | #5         |  15% 
graalpy-23.0.0       | 326.8 MB  | #6         |  17% 
graalpy-23.0.0       | 326.8 MB  | #8         |  19% 
graalpy-23.0.0       | 326.8 MB  | ##         |  20% 
graalpy-23.0.0       | 326.8 MB  | ##1        |  22% 
graalpy-23.0.0       | 326.8 MB  | ##4        |  24% 
graalpy-23.0.0       | 326.8 MB  | ##5        |  26% 
graalpy-23.0.0       | 326.8 MB  | ##8        |  28% 
graalpy-23.0.0       | 326.8 MB  | ###        |  30% 
graalpy-23.0.0       | 326.8 MB  | ###2       |  32% 
graalpy-23.0.0       | 326.8 MB  | ###4       |  34% 
graalpy-23.0.0       | 326.8 MB  | ###6       |  36% 
graalpy-23.0.0       | 326.8 MB  | ###8       |  38% 
graalpy-23.0.0       | 326.8 MB  | ####       |  41% 
graalpy-23.0.0       | 326.8 MB  | ####2      |  43% 
graalpy-23.0.0       | 326.8 MB  | ####4      |  45% 
graalpy-23.0.0       | 326.8 MB  | ####6      |  47% 
graalpy-23.0.0       | 326.8 MB  | ####8      |  49% 
graalpy-23.0.0       | 326.8 MB  | #####      |  51% 
graalpy-23.0.0       | 326.8 MB  | #####2     |  53% 
graalpy-23.0.0       | 326.8 MB  | #####4     |  55% 
graalpy-23.0.0       | 326.8 MB  | #####7     |  57% 
graalpy-23.0.0       | 326.8 MB  | #####9     |  60% 
graalpy-23.0.0       | 326.8 MB  | ######1    |  62% 
graalpy-23.0.0       | 326.8 MB  | ######3    |  64% 
graalpy-23.0.0       | 326.8 MB  | ######5    |  66% 
graalpy-23.0.0       | 326.8 MB  | ######7    |  68% 
graalpy-23.0.0       | 326.8 MB  | ######9    |  69% 
graalpy-23.0.0       | 326.8 MB  | #######1   |  72% 
graalpy-23.0.0       | 326.8 MB  | #######3   |  74% 
graalpy-23.0.0       | 326.8 MB  | #######6   |  77% 
graalpy-23.0.0       | 326.8 MB  | #######9   |  79% 
graalpy-23.0.0       | 326.8 MB  | ########1  |  82% 
graalpy-23.0.0       | 326.8 MB  | ########4  |  85% 
graalpy-23.0.0       | 326.8 MB  | ########7  |  88% 
graalpy-23.0.0       | 326.8 MB  | #########  |  90% 
graalpy-23.0.0       | 326.8 MB  | #########2 |  93% 
graalpy-23.0.0       | 326.8 MB  | #########5 |  95% 
graalpy-23.0.0       | 326.8 MB  | #########8 |  98% 
graalpy-23.0.0       | 326.8 MB  | ########## | 100% 
graalpy-23.0.0       | 326.8 MB  | ########## | 100%

done
Preparing transaction: - \ done
Verifying transaction: / - \ | done
Executing transaction: - \ | / done
Channels:
 - conda-forge
 - defaults
 - nodefaults
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

==> WARNING: A newer version of conda exists. <==
    current version: 24.11.2
    latest version: 25.9.1

Please update conda by running

$ conda update -n base -c conda-forge conda

## Package Plan ##

environment location: /scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/python/envs/venv_sct

added / updated specs:
    - xorg-libxinerama

The following packages will be downloaded:

package                    |            build
    ---------------------------|-----------------
    xorg-libxext-1.3.6         |       hb9d3cd8_0          49 KB  conda-forge
    xorg-libxinerama-1.1.5     |       h5888daf_1          14 KB  conda-forge
    ------------------------------------------------------------
                                           Total:          62 KB

The following NEW packages will be INSTALLED:

xorg-libxext       conda-forge/linux-64::xorg-libxext-1.3.6-hb9d3cd8_0 
  xorg-libxinerama   conda-forge/linux-64::xorg-libxinerama-1.1.5-h5888daf_1

Downloading and Extracting Packages: ...working...
xorg-libxext-1.3.6   | 49 KB     |            |   0%

xorg-libxinerama-1.1 | 14 KB     |            |   0% 
xorg-libxext-1.3.6   | 49 KB     | ###2       |  33% 
xorg-libxext-1.3.6   | 49 KB     | ########## | 100% 
xorg-libxext-1.3.6   | 49 KB     | ########## | 100%

xorg-libxinerama-1.1 | 14 KB     | ########## | 100%

==> WARNING: A newer version of conda exists. <==
    current version: 24.11.2
    latest version: 25.9.1

Please update conda by running

$ conda update -n base -c conda-forge conda

## Package Plan ##

environment location: /scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/python/envs/venv_sct

added / updated specs:
    - git

The following packages will be downloaded:

package                    |            build
    ---------------------------|-----------------
    git-2.51.0                 | pl5321h8305f47_1        10.7 MB  conda-forge
    libexpat-2.7.1             |       hecca717_0          73 KB  conda-forge
    libiconv-1.18              |       h3b78370_2         772 KB  conda-forge
    pcre2-10.46                |       h1321c63_0         1.2 MB  conda-forge
    perl-5.32.1                | 7_hd590300_perl5        12.7 MB  conda-forge
    ------------------------------------------------------------
                                           Total:        25.4 MB

The following NEW packages will be INSTALLED:

git                conda-forge/linux-64::git-2.51.0-pl5321h8305f47_1 
  libexpat           conda-forge/linux-64::libexpat-2.7.1-hecca717_0 
  libiconv           conda-forge/linux-64::libiconv-1.18-h3b78370_2 
  libxcrypt          conda-forge/linux-64::libxcrypt-4.4.36-hd590300_1 
  pcre2              conda-forge/linux-64::pcre2-10.46-h1321c63_0 
  perl               conda-forge/linux-64::perl-5.32.1-7_hd590300_perl5

Downloading and Extracting Packages: ...working...
perl-5.32.1          | 12.7 MB   |            |   0%

git-2.51.0           | 10.7 MB   |            |   0%

pcre2-10.46          | 1.2 MB    |            |   0%

libiconv-1.18        | 772 KB    |            |   0%

libexpat-2.7.1       | 73 KB     |            |   0%

libexpat-2.7.1       | 73 KB     | ##1        |  22%

libexpat-2.7.1       | 73 KB     | ########## | 100%

pcre2-10.46          | 1.2 MB    | 1          |   1%

libexpat-2.7.1       | 73 KB     | ########## | 100% 
perl-5.32.1          | 12.7 MB   |            |   0%

libiconv-1.18        | 772 KB    | 2          |   2%

git-2.51.0           | 10.7 MB   |            |   0%

pcre2-10.46          | 1.2 MB    | ########## | 100%

pcre2-10.46          | 1.2 MB    | ########## | 100% 
perl-5.32.1          | 12.7 MB   | #7         |  18%

libiconv-1.18        | 772 KB    | ########## | 100%

git-2.51.0           | 10.7 MB   | #3         |  13% 
perl-5.32.1          | 12.7 MB   | ######5    |  65%

libiconv-1.18        | 772 KB    | ########## | 100%

git-2.51.0           | 10.7 MB   | ####9      |  50% 
perl-5.32.1          | 12.7 MB   | ########## | 100% 
perl-5.32.1          | 12.7 MB   | ########## | 100%

pcre2-10.46          | 1.2 MB    | ########## | 100%

git-2.51.0           | 10.7 MB   | ########## | 100%

git-2.51.0           | 10.7 MB   | ########## | 100% 
perl-5.32.1          | 12.7 MB   | ########## | 100%

done
Preparing transaction: - done
Verifying transaction: | / - \ | / - \ done
Executing transaction: / - \ done
<frozen graalpy.pip_hook>:48: RuntimeWarning: You are using an untested version of pip. GraalPy provides patches and workarounds for a number of packages when used with compatible pip versions. We recommend to stick with the pip version that ships with this version of GraalPy.
WARNING: Disabling truststore because platform isn't supported
Requirement already satisfied: pip!=21.2.* in ./python/envs/venv_sct/lib/python3.10/site-packages (25.2)

Installing Python dependencies...

Using requirements.txt (git installation)

<frozen graalpy.pip_hook>:48: RuntimeWarning: You are using an untested version of pip. GraalPy provides patches and workarounds for a number of packages when used with compatible pip versions. We recommend to stick with the pip version that ships with this version of GraalPy.
WARNING: Disabling truststore because platform isn't supported
Looking in indexes: https://pypi.org/simple, https://download.pytorch.org/whl/cpu
Ignoring msvc-runtime: markers 'sys_platform == "win32"' don't match your environment
Collecting certifi
  Using cached certifi-2025.10.5-py3-none-any.whl.metadata (2.5 kB)
Collecting acvl_utils!=0.2.1 (from -r requirements.txt (line 7))
  Using cached acvl_utils-0.2.5.tar.gz (29 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting blosc2<3.9.0 (from -r requirements.txt (line 10))
  Using cached blosc2-3.8.0.tar.gz (3.8 MB)
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Installing backend dependencies: started
  Installing backend dependencies: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Collecting dipy==1.8.0 (from -r requirements.txt (line 12))
  Using cached dipy-1.8.0.tar.gz (6.5 MB)
  Installing build dependencies: started
  Installing build dependencies: still running...
  Installing build dependencies: still running...
  Installing build dependencies: still running...
  Installing build dependencies: still running...
  Installing build dependencies: still running...
  Installing build dependencies: still running...
  Installing build dependencies: still running...
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Installing backend dependencies: started
  Installing backend dependencies: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): still running...
  Preparing metadata (pyproject.toml): finished with status 'error'
  error: subprocess-exited-with-error
  
  × Preparing metadata (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [53 lines of output]
      + meson setup /tmp/pip-install-gn9aomip/dipy_e68bd84e8a5f4aafb5171c94b41f5756 /tmp/pip-install-gn9aomip/dipy_e68bd84e8a5f4aafb5171c94b41f5756/.mesonpy-187uu8c7 -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md --native-file=/tmp/pip-install-gn9aomip/dipy_e68bd84e8a5f4aafb5171c94b41f5756/.mesonpy-187uu8c7/meson-python-native-file.ini
      The Meson build system
      Version: 1.9.1
      Source dir: /tmp/pip-install-gn9aomip/dipy_e68bd84e8a5f4aafb5171c94b41f5756
      Build dir: /tmp/pip-install-gn9aomip/dipy_e68bd84e8a5f4aafb5171c94b41f5756/.mesonpy-187uu8c7
      Build type: native build
      Project name: dipy
      Project version: 1.8.0
      C compiler for the host machine: cc (gcc 11.4.0 "cc (Ubuntu 11.4.0-1ubuntu1~22.04.2) 11.4.0")
      C linker for the host machine: cc ld.bfd 2.38
      C++ compiler for the host machine: c++ (gcc 11.4.0 "c++ (Ubuntu 11.4.0-1ubuntu1~22.04.2) 11.4.0")
      C++ linker for the host machine: c++ ld.bfd 2.38
      Cython compiler for the host machine: cython (cython 3.1.4)
      Host machine cpu family: x86_64
      Host machine cpu: x86_64
      Program python found: YES (/scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/python/envs/venv_sct/bin/python3.10)
      Run-time dependency python found: YES 3.10
      Program cython found: YES (/tmp/pip-build-env-iti1pbxp/overlay/bin/cython)
      Library m found: YES
      Compiler for C supports arguments -Wno-maybe-uninitialized: YES
      Compiler for C supports arguments -Wno-discarded-qualifiers: YES
      Compiler for C supports arguments -Wno-empty-body: YES
      Compiler for C supports arguments -Wno-implicit-function-declaration: YES
      Compiler for C supports arguments -Wno-parentheses: YES
      Compiler for C supports arguments -Wno-switch: YES
      Compiler for C supports arguments -Wno-unused-label: YES
      Compiler for C supports arguments -Wno-unused-variable: YES
      Compiler for C++ supports arguments -Wno-cpp: YES
      Compiler for C++ supports arguments -Wno-deprecated-declarations: YES
      Compiler for C++ supports arguments -Wno-class-memaccess: YES
      Compiler for C++ supports arguments -Wno-format-truncation: YES
      Compiler for C++ supports arguments -Wno-format-extra-args: YES
      Compiler for C++ supports arguments -Wno-format: YES
      Compiler for C++ supports arguments -Wno-non-virtual-dtor: YES
      Compiler for C++ supports arguments -Wno-sign-compare: YES
      Compiler for C++ supports arguments -Wno-switch: YES
      Compiler for C++ supports arguments -Wno-terminate: YES
      Compiler for C++ supports arguments -Wno-unused-but-set-variable: YES
      Compiler for C++ supports arguments -Wno-unused-function: YES
      Compiler for C++ supports arguments -Wno-unused-local-typedefs: YES
      Compiler for C++ supports arguments -Wno-unused-variable: YES
      Compiler for C++ supports arguments -Wno-int-in-bool-context: YES
      
      ../dipy/meson.build:106:17: ERROR: Command `/scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/python/envs/venv_sct/bin/python3.10 -c '
      import numpy as np
      try:
        incdir = os.path.relpath(np.get_include())
      except Exception:
        incdir = np.get_include()
      print(incdir)
        '` failed with status -6.
      
      A full log can be found at /tmp/pip-install-gn9aomip/dipy_e68bd84e8a5f4aafb5171c94b41f5756/.mesonpy-187uu8c7/meson-logs/meson-log.txt
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

Failed running pip install: 1

Installation failed!

Please find the file "/scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/install_sct_log.txt",
then upload it as a .txt attachment in a new topic on SCT's forum:
--> https://forum.spinalcordmri.org/c/sct