[0KRunning with gitlab-runner 14.6.0 (5316d4ac)[0;m
[0K on zavolan-group-ci-shared-runner 2xM8DJPt[0;m
section_start:1691653921:prepare_executor
[0K[0K[36;1mPreparing the "docker" executor[0;m[0;m
[0KUsing Docker executor with image python:3.10-slim-buster ...[0;m
[0KPulling docker image python:3.10-slim-buster ...[0;m
[0KUsing docker image sha256:93b9055430ce944e6316e724e814427c9ad63c3fb9d87577f7e8436b9aa594c3 for python:3.10-slim-buster with digest python@sha256:37aa274c2d001f09b14828450d903c55f821c90f225fdfdd80c5180fcca77b3f ...[0;m
section_end:1691653922:prepare_executor
[0Ksection_start:1691653922:prepare_script
[0K[0K[36;1mPreparing environment[0;m[0;m
Running on runner-2xm8djpt-project-2339-concurrent-0 via zavolan-ci.scicore.unibas.ch...
section_end:1691653923:prepare_script
[0Ksection_start:1691653923:get_sources
[0K[0K[36;1mGetting source from Git repository[0;m[0;m
[32;1mFetching changes with git depth set to 20...[0;m
Reinitialized existing Git repository in /builds/zavolan_group/tools/terminal-fragment-selector/.git/
[32;1mChecking out acd2a084 as main...[0;m
Removing terminal_fragment_selector.egg-info/
[32;1mSkipping Git submodules setup[0;m
section_end:1691653923:get_sources
[0Ksection_start:1691653923:step_script
[0K[0K[36;1mExecuting "step_script" stage of the job script[0;m[0;m
[0KUsing docker image sha256:93b9055430ce944e6316e724e814427c9ad63c3fb9d87577f7e8436b9aa594c3 for python:3.10-slim-buster with digest python@sha256:37aa274c2d001f09b14828450d903c55f821c90f225fdfdd80c5180fcca77b3f ...[0;m
[32;1m$ pip install -r requirements.txt[0;m
Collecting argparse
Downloading argparse-1.4.0-py2.py3-none-any.whl (23 kB)
Collecting biopython
Downloading biopython-1.81-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 59.7 MB/s eta 0:00:00
Collecting numpy>=1.23.3
Downloading numpy-1.25.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (18.2 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 18.2/18.2 MB 108.4 MB/s eta 0:00:00
Collecting pandas>=1.4.4
Downloading pandas-2.0.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.3 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.3/12.3 MB 130.6 MB/s eta 0:00:00
Collecting tzdata>=2022.1
Downloading tzdata-2023.3-py2.py3-none-any.whl (341 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 341.8/341.8 kB 54.3 MB/s eta 0:00:00
Collecting pytz>=2020.1
Downloading pytz-2023.3-py2.py3-none-any.whl (502 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 502.3/502.3 kB 68.0 MB/s eta 0:00:00
Collecting python-dateutil>=2.8.2
Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 247.7/247.7 kB 58.2 MB/s eta 0:00:00
Collecting six>=1.5
Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
Installing collected packages: pytz, argparse, tzdata, six, numpy, python-dateutil, biopython, pandas
Successfully installed argparse-1.4.0 biopython-1.81 numpy-1.25.2 pandas-2.0.3 python-dateutil-2.8.2 pytz-2023.3 six-1.16.0 tzdata-2023.3
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
[notice] A new release of pip is available: 23.0.1 -> 23.2.1
[notice] To update, run: pip install --upgrade pip
[32;1m$ pip install -r requirements_dev.txt[0;m
Collecting pytest
Downloading pytest-7.4.0-py3-none-any.whl (323 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 323.6/323.6 kB 8.0 MB/s eta 0:00:00
Collecting coverage
Downloading coverage-7.2.7-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (228 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 228.7/228.7 kB 52.3 MB/s eta 0:00:00
Collecting flake8
Downloading flake8-6.1.0-py2.py3-none-any.whl (58 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 58.3/58.3 kB 22.0 MB/s eta 0:00:00
Collecting flake8-docstrings
Downloading flake8_docstrings-1.7.0-py2.py3-none-any.whl (5.0 kB)
Collecting mypy
Downloading mypy-1.4.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.0 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.0/12.0 MB 90.6 MB/s eta 0:00:00
Collecting pylint
Downloading pylint-2.17.5-py3-none-any.whl (536 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 536.7/536.7 kB 37.0 MB/s eta 0:00:00
Collecting tomli>=1.0.0
Downloading tomli-2.0.1-py3-none-any.whl (12 kB)
Collecting exceptiongroup>=1.0.0rc8
Downloading exceptiongroup-1.1.2-py3-none-any.whl (14 kB)
Collecting iniconfig
Downloading iniconfig-2.0.0-py3-none-any.whl (5.9 kB)
Collecting packaging
Downloading packaging-23.1-py3-none-any.whl (48 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 48.9/48.9 kB 19.4 MB/s eta 0:00:00
Collecting pluggy<2.0,>=0.12
Downloading pluggy-1.2.0-py3-none-any.whl (17 kB)
Collecting pycodestyle<2.12.0,>=2.11.0
Downloading pycodestyle-2.11.0-py2.py3-none-any.whl (31 kB)
Collecting mccabe<0.8.0,>=0.7.0
Downloading mccabe-0.7.0-py2.py3-none-any.whl (7.3 kB)
Collecting pyflakes<3.2.0,>=3.1.0
Downloading pyflakes-3.1.0-py2.py3-none-any.whl (62 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.6/62.6 kB 26.2 MB/s eta 0:00:00
Collecting pydocstyle>=2.1
Downloading pydocstyle-6.3.0-py3-none-any.whl (38 kB)
Collecting typing-extensions>=4.1.0
Downloading typing_extensions-4.7.1-py3-none-any.whl (33 kB)
Collecting mypy-extensions>=1.0.0
Downloading mypy_extensions-1.0.0-py3-none-any.whl (4.7 kB)
Collecting tomlkit>=0.10.1
Downloading tomlkit-0.12.1-py3-none-any.whl (37 kB)
Collecting dill>=0.2
Downloading dill-0.3.7-py3-none-any.whl (115 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 115.3/115.3 kB 41.2 MB/s eta 0:00:00
Collecting astroid<=2.17.0-dev0,>=2.15.6
Downloading astroid-2.15.6-py3-none-any.whl (278 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 278.3/278.3 kB 63.8 MB/s eta 0:00:00
Collecting platformdirs>=2.2.0
Downloading platformdirs-3.10.0-py3-none-any.whl (17 kB)
Collecting isort<6,>=4.2.5
Downloading isort-5.12.0-py3-none-any.whl (91 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 91.2/91.2 kB 27.2 MB/s eta 0:00:00
Collecting wrapt<2,>=1.11
Downloading wrapt-1.15.0-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (78 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.4/78.4 kB 25.0 MB/s eta 0:00:00
Collecting lazy-object-proxy>=1.4.0
Downloading lazy_object_proxy-1.9.0-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (63 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 63.3/63.3 kB 21.4 MB/s eta 0:00:00
Collecting snowballstemmer>=2.2.0
Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 93.0/93.0 kB 30.4 MB/s eta 0:00:00
Installing collected packages: snowballstemmer, wrapt, typing-extensions, tomlkit, tomli, pyflakes, pydocstyle, pycodestyle, pluggy, platformdirs, packaging, mypy-extensions, mccabe, lazy-object-proxy, isort, iniconfig, exceptiongroup, dill, coverage, pytest, mypy, flake8, astroid, pylint, flake8-docstrings
Successfully installed astroid-2.15.6 coverage-7.2.7 dill-0.3.7 exceptiongroup-1.1.2 flake8-6.1.0 flake8-docstrings-1.7.0 iniconfig-2.0.0 isort-5.12.0 lazy-object-proxy-1.9.0 mccabe-0.7.0 mypy-1.4.1 mypy-extensions-1.0.0 packaging-23.1 platformdirs-3.10.0 pluggy-1.2.0 pycodestyle-2.11.0 pydocstyle-6.3.0 pyflakes-3.1.0 pylint-2.17.5 pytest-7.4.0 snowballstemmer-2.2.0 tomli-2.0.1 tomlkit-0.12.1 typing-extensions-4.7.1 wrapt-1.15.0
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
[notice] A new release of pip is available: 23.0.1 -> 23.2.1
[notice] To update, run: pip install --upgrade pip
[32;1m$ pip install -e .[0;m
Obtaining file:///builds/zavolan_group/tools/terminal-fragment-selector
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting argparse
Using cached argparse-1.4.0-py2.py3-none-any.whl (23 kB)
Requirement already satisfied: biopython in /usr/local/lib/python3.10/site-packages (from terminal-fragment-selector==0.1.1) (1.81)
Requirement already satisfied: numpy>=1.23.3 in /usr/local/lib/python3.10/site-packages (from terminal-fragment-selector==0.1.1) (1.25.2)
Requirement already satisfied: pandas>=1.4.4 in /usr/local/lib/python3.10/site-packages (from terminal-fragment-selector==0.1.1) (2.0.3)
Requirement already satisfied: python-dateutil>=2.8.2 in /usr/local/lib/python3.10/site-packages (from pandas>=1.4.4->terminal-fragment-selector==0.1.1) (2.8.2)
Requirement already satisfied: pytz>=2020.1 in /usr/local/lib/python3.10/site-packages (from pandas>=1.4.4->terminal-fragment-selector==0.1.1) (2023.3)
Requirement already satisfied: tzdata>=2022.1 in /usr/local/lib/python3.10/site-packages (from pandas>=1.4.4->terminal-fragment-selector==0.1.1) (2023.3)
Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.10/site-packages (from python-dateutil>=2.8.2->pandas>=1.4.4->terminal-fragment-selector==0.1.1) (1.16.0)
Installing collected packages: argparse, terminal-fragment-selector
Running setup.py develop for terminal-fragment-selector
Successfully installed argparse-1.4.0 terminal-fragment-selector-0.1.1
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
[notice] A new release of pip is available: 23.0.1 -> 23.2.1
[notice] To update, run: pip install --upgrade pip
[32;1m$ coverage run --source term_frag_sel -m pytest[0;m
============================= test session starts ==============================
platform linux -- Python 3.10.12, pytest-7.4.0, pluggy-1.2.0
rootdir: /builds/zavolan_group/tools/terminal-fragment-selector
collected 4 items
tests/test_cli.py .. [ 50%]
tests/test_frag.py . [ 75%]
tests/test_utils.py . [100%]
============================== 4 passed in 0.92s ===============================
[32;1m$ coverage report -m[0;m
Name Stmts Miss Cover Missing
--------------------------------------------------------------
term_frag_sel/__init__.py 0 0 100%
term_frag_sel/cli.py 61 21 66% 30-53, 129, 133-139
term_frag_sel/fragmentation.py 26 0 100%
term_frag_sel/utils.py 9 0 100%
--------------------------------------------------------------
TOTAL 96 21 78%
section_end:1691653941:step_script
[0Ksection_start:1691653941:cleanup_file_variables
[0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m
section_end:1691653942:cleanup_file_variables
[0K[32;1mJob succeeded[0;m