fix: allow ccd residues with missing coords #735
You are viewing an older attempt in the history of this workflow run.
View latest attempt.
davegraystest_and_deploy.yml
on: pull_request
Build CCD and wheel for reusing it in several CI jobs
4m 54s
Generate wheels matrix
12s
Check code style
12s
Build source distribution
32s
Test interfaces to databases and applications
3m 18s
Test interface to Muscle 5
26s
Matrix: Build & Test
Upload documentation to GitHub Releases and documentation website
0s
Upload package to GitHub Releases & PyPI
0s
Annotations
1 error and 21 warnings
|
Test interface to Muscle 5
The process '/home/runner/miniconda3/condabin/mamba' failed with exit code 1
|
|
Generate wheels matrix
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
|
Check code style
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
|
Build CCD and wheel for reusing it in several CI jobs
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
|
Upload CCD to GitHub Releases
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
|
Test interface to Muscle 5
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
|
Test interface to Muscle 5
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
|
|
Test interface to Muscle 5
error libmamba Error when extracting package: Could not chdir info/git
|
|
Test interface to Muscle 5
Found incorrect download: _libgcc_mutex. Aborting
|
|
Test interface to Muscle 5
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/home/runner/miniconda3/lib/python3.12/site-packages/conda/exception_handler.py", line 18, in __call__
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/home/runner/miniconda3/lib/python3.12/site-packages/mamba/mamba.py", line 960, in exception_converter
raise e
File "/home/runner/miniconda3/lib/python3.12/site-packages/mamba/mamba.py", line 953, in exception_converter
exit_code = _wrapped_main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/runner/miniconda3/lib/python3.12/site-packages/mamba/mamba.py", line 899, in _wrapped_main
result = do_call(parsed_args, p)
^^^^^^^^^^^^^^^^^^^^^^^
File "/home/runner/miniconda3/lib/python3.12/site-packages/mamba/mamba.py", line 768, in do_call
exit_code = create(args, parser)
^^^^^^^^^^^^^^^^^^^^
File "/home/runner/miniconda3/lib/python3.12/site-packages/mamba/mamba.py", line 603, in create
return install(args, parser, "create")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/runner/miniconda3/lib/python3.12/site-packages/mamba/mamba.py", line 559, in install
transaction.fetch_extract_packages()
RuntimeError: Found incorrect download: _libgcc_mutex. Aborting
`$ /home/runner/miniconda3/condabin/mamba create --name biotite-dev python=3.11`
environment variables:
CIO_TEST=<not set>
CONDA=/home/runner/miniconda3
CONDA_ROOT=/home/runner/miniconda3
CURL_CA_BUNDLE=<not set>
DEPLOYMENT_BASEPATH=/opt/runner
GITHUB_EVENT_PATH=/home/runner/work/_temp/_github_workflow/event.json
GITHUB_PATH=/home/runner/work/_temp/_runner_file_commands/add_path_5f12120f-41a7-
44d0-beb7-240acea5dda2
LD_PRELOAD=<not set>
PATH=/home/runner/miniconda3/condabin:/snap/bin:/home/runner/.local/bin:/op
t/pipx_bin:/home/runner/.cargo/bin:/home/runner/.config/composer/vendo
r/bin:/usr/local/.ghcup/bin:/home/runner/.dotnet/tools:/usr/local/sbin
:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/ga
mes:/snap/bin
REQUESTS_CA_BUNDLE=<not set>
SELENIUM_JAR_PATH=/usr/share/java/selenium-server.jar
SSL_CERT_FILE=<not set>
SWIFT_PATH=/usr/share/swift/usr/bin
active environment : None
user config file : /home/runner/.condarc
populated config files : /home/runner/miniconda3/.condarc
/home/runner/.condarc
conda version : 24.11.2
conda-build version : not installed
python version : 3.12.8.final.0
solver : libmamba (default)
virtual packages : __archspec=1=zen2
__conda=24.11.2=0
__glibc=2.35=0
__linux=6.5.0=0
__unix=0=0
base environment : /home/runner/miniconda3 (writable)
conda av data dir : /home/runner/miniconda3/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
package cache : /home/runner/conda_pkgs_dir
envs directories : /home/runner/miniconda3/envs
/home/runner/.conda/envs
platform : linux-64
user-agent : conda/24.11.2 requests/2.32.3 CPython/3.12.8 Linux/6.5.0-1025-azure ubuntu/22.04.5 glibc/2.35 solver/libmamba conda-libmamba-solver/24.9.0 libmambapy/1.5.12
UID:GID : 1001:128
netrc file : None
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
If you suspect this error is being caused by a malfunctioning plugin,
consid
|
|
Build source distribution
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
|
Test interfaces to databases and applications
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
|
Test interfaces to databases and applications
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:201: FutureWarning: Adding 'defaults' to channel list implicitly is deprecated and will be removed in 25.3.
To remove this warning, please choose a default channel explicitly with conda's regular configuration system, e.g. by adding 'defaults' to the list of channels:
conda config --add channels defaults
For more information see https://docs.conda.io/projects/conda/en/stable/user-guide/configuration/use-condarc.html
deprecated.topic(
|
|
Test interfaces to databases and applications
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
|
|
Build documentation
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
|
Build documentation
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:201: FutureWarning: Adding 'defaults' to channel list implicitly is deprecated and will be removed in 25.3.
To remove this warning, please choose a default channel explicitly with conda's regular configuration system, e.g. by adding 'defaults' to the list of channels:
conda config --add channels defaults
For more information see https://docs.conda.io/projects/conda/en/stable/user-guide/configuration/use-condarc.html
deprecated.topic(
|
|
Build documentation
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
|
|
Run benchmarks
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
|
Build & Test (cp311-manylinux_x86_64, ubuntu-latest)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
|
Build & Test (cp312-manylinux_x86_64, ubuntu-latest)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
|
Build & Test (cp313-manylinux_x86_64, ubuntu-latest)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
|
Build & Test (cp310-manylinux_x86_64, ubuntu-latest)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
Artifacts
Produced during runtime
| Name | Size | |
|---|---|---|
|
ccd
|
33.3 MB |
|
|
documentation
|
74.4 MB |
|
|
internal-build
|
49.8 MB |
|
|
release-cp310-macosx_arm64
|
36.7 MB |
|
|
release-cp310-macosx_x86_64
|
36.9 MB |
|
|
release-cp310-manylinux_x86_64
|
49.5 MB |
|
|
release-cp310-win_amd64
|
36.7 MB |
|
|
release-cp311-macosx_arm64
|
36.7 MB |
|
|
release-cp311-macosx_x86_64
|
36.9 MB |
|
|
release-cp311-manylinux_x86_64
|
50.5 MB |
|
|
release-cp311-win_amd64
|
36.7 MB |
|
|
release-cp312-macosx_arm64
|
36.7 MB |
|
|
release-cp312-macosx_x86_64
|
36.9 MB |
|
|
release-cp312-manylinux_x86_64
|
52.2 MB |
|
|
release-cp312-win_amd64
|
36.6 MB |
|
|
release-cp313-macosx_arm64
|
36.7 MB |
|
|
release-cp313-macosx_x86_64
|
36.9 MB |
|
|
release-cp313-manylinux_x86_64
|
52 MB |
|
|
release-cp313-win_amd64
|
36.6 MB |
|
|
release-sdist
|
33.8 MB |
|