[0KRunning with gitlab-runner 14.6.0 (5316d4ac)[0;m
[0K on zavolan-group-ci-shared-runner 2xM8DJPt[0;m
section_start:1660738232:prepare_executor
[0K[0K[36;1mPreparing the "docker" executor[0;m[0;m
[0KUsing Docker executor with image python:3.9-slim-buster ...[0;m
[0KPulling docker image python:3.9-slim-buster ...[0;m
[0KUsing docker image sha256:83e74122cf8aaafa5a8b680afdd34ccffc788ebd156fa749bcee685c65af4790 for python:3.9-slim-buster with digest python@sha256:16679847af0311d2ff955210e80e45ebae29e5ff3638568e5220879dc96549bb ...[0;m
section_end:1660738233:prepare_executor
[0Ksection_start:1660738233:prepare_script
[0K[0K[36;1mPreparing environment[0;m[0;m
Running on runner-2xm8djpt-project-1932-concurrent-0 via zavolan-ci.scicore.unibas.ch...
section_end:1660738234:prepare_script
[0Ksection_start:1660738234:get_sources
[0K[0K[36;1mGetting source from Git repository[0;m[0;m
[32;1mFetching changes with git depth set to 50...[0;m
Reinitialized existing Git repository in /builds/zavolan_group/pipelines/scrna-seq-simulation/.git/
[32;1mChecking out 9e85bcbc as readme...[0;m
Removing .coverage
Removing .mypy_cache/
Removing .pytest_cache/
Removing src.egg-info/
Removing src/__pycache__/
Removing tests/__pycache__/
[32;1mSkipping Git submodules setup[0;m
section_end:1660738235:get_sources
[0Ksection_start:1660738235:step_script
[0K[0K[36;1mExecuting "step_script" stage of the job script[0;m[0;m
[0KUsing docker image sha256:83e74122cf8aaafa5a8b680afdd34ccffc788ebd156fa749bcee685c65af4790 for python:3.9-slim-buster with digest python@sha256:16679847af0311d2ff955210e80e45ebae29e5ff3638568e5220879dc96549bb ...[0;m
[32;1m$ pip install -r requirements.txt[0;m
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$ pip install -r requirements_dev.txt[0;m
Collecting coverage
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 10.7 MB/s eta 0:00:00
Collecting flake8
Downloading flake8-5.0.4-py2.py3-none-any.whl (61 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.9/61.9 KB 17.9 MB/s eta 0:00:00
Collecting flake8-docstrings
Downloading flake8_docstrings-1.6.0-py2.py3-none-any.whl (5.7 kB)
Collecting mypy
Downloading mypy-0.971-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (17.6 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 17.6/17.6 MB 94.5 MB/s eta 0:00:00
Collecting pandas
Downloading pandas-1.4.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.7 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.7/11.7 MB 102.5 MB/s eta 0:00:00
Collecting pytest
Downloading pytest-7.1.2-py3-none-any.whl (297 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 297.0/297.0 KB 58.0 MB/s eta 0:00:00
Collecting pyflakes<2.6.0,>=2.5.0
Downloading pyflakes-2.5.0-py2.py3-none-any.whl (66 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 66.1/66.1 KB 20.4 MB/s eta 0:00:00
Collecting pycodestyle<2.10.0,>=2.9.0
Downloading pycodestyle-2.9.1-py2.py3-none-any.whl (41 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 41.5/41.5 KB 13.0 MB/s eta 0:00:00
Collecting mccabe<0.8.0,>=0.7.0
Downloading mccabe-0.7.0-py2.py3-none-any.whl (7.3 kB)
Collecting pydocstyle>=2.1
Downloading pydocstyle-6.1.1-py3-none-any.whl (37 kB)
Collecting typing-extensions>=3.10
Downloading typing_extensions-4.3.0-py3-none-any.whl (25 kB)
Collecting tomli>=1.1.0
Downloading tomli-2.0.1-py3-none-any.whl (12 kB)
Collecting mypy-extensions>=0.4.3
Downloading mypy_extensions-0.4.3-py2.py3-none-any.whl (4.5 kB)
Collecting numpy>=1.18.5
Downloading numpy-1.23.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.1 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 17.1/17.1 MB 102.5 MB/s eta 0:00:00
Collecting python-dateutil>=2.8.1
Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 247.7/247.7 KB 51.4 MB/s eta 0:00:00
Collecting pytz>=2020.1
Downloading pytz-2022.2.1-py2.py3-none-any.whl (500 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 500.6/500.6 KB 72.7 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 24.7 MB/s eta 0:00:00
Collecting attrs>=19.2.0
Downloading attrs-22.1.0-py2.py3-none-any.whl (58 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 58.8/58.8 KB 20.7 MB/s eta 0:00:00
Collecting pluggy<2.0,>=0.12
Downloading pluggy-1.0.0-py2.py3-none-any.whl (13 kB)
Collecting packaging
Downloading packaging-21.3-py3-none-any.whl (40 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 40.8/40.8 KB 11.2 MB/s eta 0:00:00
Collecting iniconfig
Downloading iniconfig-1.1.1-py2.py3-none-any.whl (5.0 kB)
Collecting snowballstemmer
Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 93.0/93.0 KB 20.7 MB/s eta 0:00:00
Collecting six>=1.5
Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting pyparsing!=3.0.5,>=2.0.2
Downloading pyparsing-3.0.9-py3-none-any.whl (98 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 98.3/98.3 KB 31.3 MB/s eta 0:00:00
Installing collected packages: snowballstemmer, pytz, mypy-extensions, iniconfig, typing-extensions, tomli, six, pyparsing, pyflakes, pydocstyle, pycodestyle, py, pluggy, numpy, mccabe, coverage, attrs, python-dateutil, packaging, mypy, flake8, pytest, pandas, flake8-docstrings
Successfully installed attrs-22.1.0 coverage-6.4.4 flake8-5.0.4 flake8-docstrings-1.6.0 iniconfig-1.1.1 mccabe-0.7.0 mypy-0.971 mypy-extensions-0.4.3 numpy-1.23.2 packaging-21.3 pandas-1.4.3 pluggy-1.0.0 py-1.11.0 pycodestyle-2.9.1 pydocstyle-6.1.1 pyflakes-2.5.0 pyparsing-3.0.9 pytest-7.1.2 python-dateutil-2.8.2 pytz-2022.2.1 six-1.16.0 snowballstemmer-2.2.0 tomli-2.0.1 typing-extensions-4.3.0
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$ pip install -e .[0;m
Obtaining file:///builds/zavolan_group/pipelines/scrna-seq-simulation
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Installing collected packages: src
Running setup.py develop for src
Successfully installed src-0.0.0
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 pytest[0;m
============================= test session starts ==============================
platform linux -- Python 3.9.13, pytest-7.1.2, pluggy-1.0.0
rootdir: /builds/zavolan_group/pipelines/scrna-seq-simulation
collected 13 items
tests/test_parser.py . [ 7%]
tests/test_poly_a.py .......... [ 84%]
tests/test_root.py . [ 92%]
tests/test_sampleinput.py . [100%]
============================== 13 passed in 0.29s ==============================
section_end:1660738251:step_script
[0Ksection_start:1660738251:cleanup_file_variables
[0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m
section_end:1660738251:cleanup_file_variables
[0K[32;1mJob succeeded[0;m