[0KRunning with gitlab-runner 15.4.0 (43b2dc3d)[0;m
[0K on node2102 _xvqTFEz[0;m
section_start:1663873160:resolve_secrets
[0K[0K[36;1mResolving secrets[0;m[0;m
section_end:1663873160:resolve_secrets
[0Ksection_start:1663873160:prepare_executor
[0K[0K[36;1mPreparing the "docker" executor[0;m[0;m
[0KUsing Docker executor with image python:3.9 ...[0;m
[0;33mWARNING: Container based cache volumes creation is disabled. Will not create volume for "/cache"[0;m
[0KPulling docker image python:3.9 ...[0;m
[0KUsing docker image sha256:2bdff85784189a7edcf33da67029e6b3117398579ef0d7d6a7ca53af80cfb3c7 for python:3.9 with digest python@sha256:cfcc9ef77b6cf87f57327aacc6f9b50c7cdb4d7dd93662a36549f05b7403cd47 ...[0;m
section_end:1663873161:prepare_executor
[0Ksection_start:1663873161:prepare_script
[0K[0K[36;1mPreparing environment[0;m[0;m
Running on runner-xvqtfez-project-2317-concurrent-0 via node2102...
section_end:1663873162:prepare_script
[0Ksection_start:1663873162:get_sources
[0K[0K[36;1mGetting source from Git repository[0;m[0;m
[32;1mFetching changes...[0;m
Initialized empty Git repository in /builds/lscsoft/p-astro/.git/
[32;1mCreated fresh repository.[0;m
[32;1mChecking out 33eb0d21 as master...[0;m
[32;1mSkipping Git submodules setup[0;m
section_end:1663873168:get_sources
[0Ksection_start:1663873168:restore_cache
[0K[0K[36;1mRestoring cache[0;m[0;m
[32;1mChecking cache for test:python3.9-protected...[0;m
No URL provided, cache will not be downloaded from shared cache server. Instead a local version of cache will be extracted.[0;m
[32;1mSuccessfully extracted cache[0;m
section_end:1663873168:restore_cache
[0Ksection_start:1663873168:download_artifacts
[0K[0K[36;1mDownloading artifacts[0;m[0;m
[32;1mDownloading artifacts for tarball (2242665)...[0;m
Downloading artifacts from coordinator... ok [0;m id[0;m=2242665 responseStatus[0;m=200 OK token[0;m=e4aGyCX5
section_end:1663873170:download_artifacts
[0Ksection_start:1663873170:step_script
[0K[0K[36;1mExecuting "step_script" stage of the job script[0;m[0;m
[0KUsing docker image sha256:2bdff85784189a7edcf33da67029e6b3117398579ef0d7d6a7ca53af80cfb3c7 for python:3.9 with digest python@sha256:cfcc9ef77b6cf87f57327aacc6f9b50c7cdb4d7dd93662a36549f05b7403cd47 ...[0;m
[32;1m$ if $(grep -q debian /etc/os-release); then apt-get -yqq install findutils; elif $(grep -q rhel /etc/os-release); then yum -y -q install findutils; fi[0;m
[32;1m$ ${PYTHON:="python"} -m pip install ${PIP_OPTIONS} ${INSTALL_TARGET:="."}[0;m
Processing /builds/lscsoft/p-astro
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting astropy
Downloading astropy-5.1-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (11.0 MB)
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Collecting lalsuite
Downloading lalsuite-7.8-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (48.4 MB)
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Collecting numpy
Downloading numpy-1.23.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.1 MB)
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Collecting python-ligo-lw
Downloading python-ligo-lw-1.8.3.tar.gz (2.3 MB)
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Preparing metadata (setup.py): started
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Collecting scipy
Downloading scipy-1.9.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (43.9 MB)
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Collecting h5py
Downloading h5py-3.7.0-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (4.5 MB)
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Collecting pyerfa>=2.0
Downloading pyerfa-2.0.0.1-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (742 kB)
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Collecting PyYAML>=3.13
Downloading PyYAML-6.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (661 kB)
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Collecting packaging>=19.0
Downloading packaging-21.3-py3-none-any.whl (40 kB)
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Collecting ligo-segments
Downloading ligo-segments-1.4.0.tar.gz (51 kB)
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Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting matplotlib
Downloading matplotlib-3.6.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.8 MB)
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Collecting lscsoft-glue
Downloading lscsoft-glue-3.0.1.tar.gz (1.4 MB)
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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 python-dateutil
Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
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Collecting six
Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting tqdm
Downloading tqdm-4.64.1-py2.py3-none-any.whl (78 kB)
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Collecting pyparsing!=3.0.5,>=2.0.2
Downloading pyparsing-3.0.9-py3-none-any.whl (98 kB)
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Collecting pyRXP
Downloading pyRXP-3.0.1-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (297 kB)
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Collecting pyOpenSSL
Downloading pyOpenSSL-22.0.0-py2.py3-none-any.whl (55 kB)
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Collecting fonttools>=4.22.0
Downloading fonttools-4.37.3-py3-none-any.whl (959 kB)
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Collecting cycler>=0.10
Downloading cycler-0.11.0-py3-none-any.whl (6.4 kB)
Collecting pillow>=6.2.0
Downloading Pillow-9.2.0-cp39-cp39-manylinux_2_28_x86_64.whl (3.2 MB)
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Collecting kiwisolver>=1.0.1
Downloading kiwisolver-1.4.4-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (1.6 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 69.5 MB/s eta 0:00:00
Collecting contourpy>=1.0.1
Downloading contourpy-1.0.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (296 kB)
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Collecting cryptography>=35.0
Downloading cryptography-38.0.1-cp36-abi3-manylinux_2_28_x86_64.whl (4.2 MB)
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Collecting cffi>=1.12
Downloading cffi-1.15.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (441 kB)
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Collecting pycparser
Downloading pycparser-2.21-py2.py3-none-any.whl (118 kB)
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Building wheels for collected packages: p-astro, python-ligo-lw, ligo-segments, lscsoft-glue
Building wheel for p-astro (setup.py): started
Building wheel for p-astro (setup.py): finished with status 'done'
Created wheel for p-astro: filename=p_astro-1.0.0-py3-none-any.whl size=318290 sha256=5d55b218538877b9d6a8927659225d7efffcf94b6f65be5004401381f36363b9
Stored in directory: /builds/lscsoft/p-astro/.cache/pip/wheels/70/70/8d/5cb448e4635ee84e7ea0b97481678b89267f5f744976cc2522
Building wheel for python-ligo-lw (setup.py): started
Building wheel for python-ligo-lw (setup.py): finished with status 'done'
Created wheel for python-ligo-lw: filename=python_ligo_lw-1.8.3-cp39-cp39-linux_x86_64.whl size=152771 sha256=9a912357fbb9c6e34163f2b48fca69e6ea4f038dcde7c148d49086bb03abbf28
Stored in directory: /builds/lscsoft/p-astro/.cache/pip/wheels/24/4a/01/2b07c68ddef2b4de5051b79a49fb1f9a80a93b075cbf6f3269
Building wheel for ligo-segments (setup.py): started
Building wheel for ligo-segments (setup.py): finished with status 'done'
Created wheel for ligo-segments: filename=ligo_segments-1.4.0-cp39-cp39-linux_x86_64.whl size=104509 sha256=41b894f2eb7a28f7b5d2d7b3b690434da7abb2803ddcd418aecdb81874d972e2
Stored in directory: /builds/lscsoft/p-astro/.cache/pip/wheels/bf/48/4b/3b25ac327f65168ccf3ca1f7321bb533db6de5123847f9c6f7
Building wheel for lscsoft-glue (pyproject.toml): started
Building wheel for lscsoft-glue (pyproject.toml): finished with status 'done'
Created wheel for lscsoft-glue: filename=lscsoft_glue-3.0.1-cp39-cp39-linux_x86_64.whl size=244012 sha256=10ddfac54cd039dbae411388b98a9d1ed797fe5d3af03f22925d5ac483ee57a8
Stored in directory: /builds/lscsoft/p-astro/.cache/pip/wheels/49/14/fb/7969947b8a18347925a86d2f70e7f600512ed7857bc5cfe9b0
Successfully built p-astro python-ligo-lw ligo-segments lscsoft-glue
Installing collected packages: tqdm, six, PyYAML, pyRXP, pyparsing, pycparser, pillow, numpy, kiwisolver, fonttools, cycler, scipy, python-dateutil, pyerfa, packaging, ligo-segments, h5py, contourpy, cffi, matplotlib, cryptography, astropy, pyOpenSSL, lscsoft-glue, python-ligo-lw, lalsuite, p-astro
Successfully installed PyYAML-6.0 astropy-5.1 cffi-1.15.1 contourpy-1.0.5 cryptography-38.0.1 cycler-0.11.0 fonttools-4.37.3 h5py-3.7.0 kiwisolver-1.4.4 lalsuite-7.8 ligo-segments-1.4.0 lscsoft-glue-3.0.1 matplotlib-3.6.0 numpy-1.23.3 p-astro-1.0.0 packaging-21.3 pillow-9.2.0 pyOpenSSL-22.0.0 pyRXP-3.0.1 pycparser-2.21 pyerfa-2.0.0.1 pyparsing-3.0.9 python-dateutil-2.8.2 python-ligo-lw-1.8.3 scipy-1.9.1 six-1.16.0 tqdm-4.64.1
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
WARNING: You are using pip version 22.0.4; however, version 22.2.2 is available.
You should consider upgrading via the '/usr/local/bin/python -m pip install --upgrade pip' command.
[32;1m$ ${PYTHON} -m pip install ${PIP_OPTIONS} pytest pytest-cov ${TESTS_REQUIRE}[0;m
Collecting pytest
Downloading pytest-7.1.3-py3-none-any.whl (298 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 298.2/298.2 KB 12.1 MB/s eta 0:00:00
Collecting pytest-cov
Downloading pytest_cov-3.0.0-py3-none-any.whl (20 kB)
Collecting attrs>=19.2.0
Downloading attrs-22.1.0-py2.py3-none-any.whl (58 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 58.8/58.8 KB 15.3 MB/s eta 0:00:00
Collecting py>=1.8.2
Downloading py-1.11.0-py2.py3-none-any.whl (98 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 98.7/98.7 KB 16.3 MB/s eta 0:00:00
Collecting pluggy<2.0,>=0.12
Downloading pluggy-1.0.0-py2.py3-none-any.whl (13 kB)
Requirement already satisfied: packaging in /usr/local/lib/python3.9/site-packages (from pytest) (21.3)
Collecting iniconfig
Downloading iniconfig-1.1.1-py2.py3-none-any.whl (5.0 kB)
Collecting tomli>=1.0.0
Downloading tomli-2.0.1-py3-none-any.whl (12 kB)
Collecting coverage[toml]>=5.2.1
Downloading coverage-6.4.4-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (212 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 212.1/212.1 KB 39.3 MB/s eta 0:00:00
Requirement already satisfied: pyparsing!=3.0.5,>=2.0.2 in /usr/local/lib/python3.9/site-packages (from packaging->pytest) (3.0.9)
Installing collected packages: iniconfig, tomli, py, pluggy, coverage, attrs, pytest, pytest-cov
Successfully installed attrs-22.1.0 coverage-6.4.4 iniconfig-1.1.1 pluggy-1.0.0 py-1.11.0 pytest-7.1.3 pytest-cov-3.0.0 tomli-2.0.1
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
WARNING: You are using pip version 22.0.4; however, version 22.2.2 is available.
You should consider upgrading via the '/usr/local/bin/python -m pip install --upgrade pip' command.
[32;1m$ ${PYTHON} -m pip list installed[0;m
Package Version
--------------- -------
astropy 5.1
attrs 22.1.0
cffi 1.15.1
contourpy 1.0.5
coverage 6.4.4
cryptography 38.0.1
cycler 0.11.0
fonttools 4.37.3
h5py 3.7.0
iniconfig 1.1.1
kiwisolver 1.4.4
lalsuite 7.8
ligo-segments 1.4.0
lscsoft-glue 3.0.1
matplotlib 3.6.0
numpy 1.23.3
p-astro 1.0.0
packaging 21.3
Pillow 9.2.0
pip 22.0.4
pluggy 1.0.0
py 1.11.0
pycparser 2.21
pyerfa 2.0.0.1
pyOpenSSL 22.0.0
pyparsing 3.0.9
pyRXP 3.0.1
pytest 7.1.3
pytest-cov 3.0.0
python-dateutil 2.8.2
python-ligo-lw 1.8.3
PyYAML 6.0
scipy 1.9.1
setuptools 58.1.0
six 1.16.0
tomli 2.0.1
tqdm 4.64.1
wheel 0.37.1
WARNING: You are using pip version 22.0.4; however, version 22.2.2 is available.
You should consider upgrading via the '/usr/local/bin/python -m pip install --upgrade pip' command.
[32;1m$ python setup.py test[0;m
running pytest
running egg_info
writing p_astro.egg-info/PKG-INFO
writing dependency_links to p_astro.egg-info/dependency_links.txt
writing entry points to p_astro.egg-info/entry_points.txt
writing namespace_packages to p_astro.egg-info/namespace_packages.txt
writing requirements to p_astro.egg-info/requires.txt
writing top-level names to p_astro.egg-info/top_level.txt
reading manifest file 'p_astro.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE'
writing manifest file 'p_astro.egg-info/SOURCES.txt'
running build_ext
============================= test session starts ==============================
platform linux -- Python 3.9.14, pytest-7.1.3, pluggy-1.0.0
rootdir: /builds/lscsoft/p-astro
plugins: cov-3.0.0
collected 23 items
ligo/tests/test_p_astro.py . [ 4%]
ligo/tests/test_p_astro_computation.py .................. [ 82%]
ligo/tests/test_p_astro_gstlal.py .... [100%]
=============================== warnings summary ===============================
ligo/p_astro.py:264
/builds/lscsoft/p-astro/ligo/p_astro.py:264: DeprecationWarning: invalid escape sequence \i
'''
ligo/p_astro.py:743
/builds/lscsoft/p-astro/ligo/p_astro.py:743: DeprecationWarning: invalid escape sequence \s
'''
ligo/p_astro.py:777
/builds/lscsoft/p-astro/ligo/p_astro.py:777: DeprecationWarning: invalid escape sequence \L
'''
ligo/p_astro.py:840
/builds/lscsoft/p-astro/ligo/p_astro.py:840: DeprecationWarning: invalid escape sequence \L
'''
../../../usr/local/lib/python3.9/site-packages/glue/ligolw/__init__.py:102
/usr/local/lib/python3.9/site-packages/glue/ligolw/__init__.py:102: DeprecationWarning: glue.ligolw has been deprecated and is not being updated, please migrate your workflow to use the updated LIGO_LW XML format and interface supported by python-ligo-lw
warnings.warn(
ligo/tests/test_p_astro_gstlal.py: 122 warnings
/usr/local/lib/python3.9/site-packages/glue/ligolw/table.py:446: DeprecationWarning: PY_SSIZE_T_CLEAN will be required for '#' formats
for row in self._rowbuilder.append(self._tokenizer.append(content)):
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
====================== 23 passed, 127 warnings in 13.16s =======================
[32;1m$ entrypoints=$(python -c "import pkg_resources; print('\n'.join(e.name for e in pkg_resources.iter_entry_points('console_scripts') if 'p-astro' in e.dist.project_name))")[0;m
[32;1m$ for entrypoint in ${entrypoints}; do python -m coverage run --append --source=${COVERAGE_TARGET} $(which ${entrypoint}) --help ; done[0;m
/usr/local/lib/python3.9/site-packages/coverage/control.py:794: CoverageWarning: No data was collected. (no-data-collected)
self._warn("No data was collected.", slug="no-data-collected")
usage: Compute mean on Poisson count [-h] -i INPUT -r RANKING_DATA -c CONFIG
-o OUTPUT -s TRIGGER_DB [-f DATA_HISTORY]
optional arguments:
-h, --help show this help message and exit
-i INPUT, --input INPUT
Astropy table storing activation counts per source
category
-r RANKING_DATA, --ranking-data RANKING_DATA
Ranking stat pdf XML file to be used for f/b
-c CONFIG, --config CONFIG
Config file for extra parameters
-o OUTPUT, --output OUTPUT
Output file to store mean and covariance values in
JSON format
-s TRIGGER_DB, --trigger-db TRIGGER_DB
Gstlal trigger sqlite database
-f DATA_HISTORY, --data-history DATA_HISTORY
The FGMC data history as astropy table, possibly from
previous runs
/usr/local/lib/python3.9/site-packages/coverage/control.py:794: CoverageWarning: No data was collected. (no-data-collected)
self._warn("No data was collected.", slug="no-data-collected")
usage: p_astro_histogram_by_bin [-h] [-i INPUT] [-o OUTPUT] -c CONFIG
Executable to histogram triggers by SVD bin number
optional arguments:
-h, --help show this help message and exit
-i INPUT, --input INPUT
Astropy table containing data extracted from injection
database
-o OUTPUT, --output OUTPUT
Text file to store activation counts per bin and
source category
-c CONFIG, --config CONFIG
Config file with additional parameters
section_end:1663873247:step_script
[0Ksection_start:1663873247:after_script
[0K[0K[36;1mRunning after_script[0;m[0;m
[32;1mRunning after script...[0;m
[32;1m$ ${PYTHON} -m coverage report[0;m
No data to report.
section_end:1663873248:after_script
[0Ksection_start:1663873248:archive_cache
[0K[0K[36;1mSaving cache for successful job[0;m[0;m
[32;1mCreating cache test:python3.9-protected...[0;m
.cache/pip: found 402 matching files and directories[0;m
No URL provided, cache will not be uploaded to shared cache server. Cache will be stored only locally.[0;m
[32;1mCreated cache[0;m
section_end:1663873256:archive_cache
[0Ksection_start:1663873256:upload_artifacts_on_success
[0K[0K[36;1mUploading artifacts for successful job[0;m[0;m
[32;1mUploading artifacts...[0;m
[0;33mWARNING: junit*.xml: no matching files. Ensure that the artifact path is relative to the working directory[0;m
[31;1mERROR: No files to upload [0;m
[32;1mUploading artifacts...[0;m
[0;33mWARNING: coverage*.xml: no matching files. Ensure that the artifact path is relative to the working directory[0;m
[31;1mERROR: No files to upload [0;m
section_end:1663873257:upload_artifacts_on_success
[0Ksection_start:1663873257:cleanup_file_variables
[0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m
section_end:1663873258:cleanup_file_variables
[0K[32;1mJob succeeded[0;m