[0KRunning with gitlab-runner 14.6.0 (5316d4ac)[0;m
[0K on zavolan-group-ci-shared-runner 2xM8DJPt[0;m
section_start:1695125030: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:1695125032:prepare_executor
[0Ksection_start:1695125032:prepare_script
[0K[0K[36;1mPreparing environment[0;m[0;m
Running on runner-2xm8djpt-project-2335-concurrent-0 via zavolan-ci.scicore.unibas.ch...
section_end:1695125032:prepare_script
[0Ksection_start:1695125032: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/transcript-structure-generator/.git/
[32;1mChecking out f18bac7e as dev...[0;m
Removing transcript_structure_generator.egg-info/
[32;1mSkipping Git submodules setup[0;m
section_end:1695125033:get_sources
[0Ksection_start:1695125033: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 matplotlib
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Collecting numpy<2,>=1.21
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Collecting contourpy>=1.0.1
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Installing collected packages: pytz, tzdata, six, pyparsing, pillow, packaging, numpy, kiwisolver, fonttools, cycler, python-dateutil, contourpy, pandas, matplotlib
Successfully installed contourpy-1.1.1 cycler-0.11.0 fonttools-4.42.1 kiwisolver-1.4.5 matplotlib-3.8.0 numpy-1.26.0 packaging-23.1 pandas-2.1.0 pillow-10.0.1 pyparsing-3.1.1 python-dateutil-2.8.2 pytz-2023.3.post1 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
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Collecting mypy
Downloading mypy-1.5.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.1 MB)
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Collecting coverage
Downloading coverage-7.3.1-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (229 kB)
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Collecting tomli>=1.1.0
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Collecting wrapt<2,>=1.11
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Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.10/site-packages (from python-dateutil>=2.7->matplotlib->-r requirements_dev.txt (line 1)) (1.16.0)
Installing collected packages: snowballstemmer, wrapt, typing-extensions, tomlkit, tomli, pyflakes, pydocstyle, pycodestyle, pluggy, platformdirs, 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-7.3.1 dill-0.3.7 exceptiongroup-1.1.3 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-1.5.1 mypy-extensions-1.0.0 platformdirs-3.10.0 pluggy-1.3.0 pycodestyle-2.11.0 pydocstyle-6.3.0 pyflakes-3.1.0 pylint-2.17.5 pytest-7.4.2 snowballstemmer-2.2.0 tomli-2.0.1 tomlkit-0.12.1 typing-extensions-4.8.0 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/transcript-structure-generator
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Requirement already satisfied: matplotlib in /usr/local/lib/python3.10/site-packages (from transcript-structure-generator==0.2.0) (3.8.0)
Requirement already satisfied: pandas in /usr/local/lib/python3.10/site-packages (from transcript-structure-generator==0.2.0) (2.1.0)
Requirement already satisfied: numpy<2,>=1.21 in /usr/local/lib/python3.10/site-packages (from matplotlib->transcript-structure-generator==0.2.0) (1.26.0)
Requirement already satisfied: python-dateutil>=2.7 in /usr/local/lib/python3.10/site-packages (from matplotlib->transcript-structure-generator==0.2.0) (2.8.2)
Requirement already satisfied: kiwisolver>=1.0.1 in /usr/local/lib/python3.10/site-packages (from matplotlib->transcript-structure-generator==0.2.0) (1.4.5)
Requirement already satisfied: fonttools>=4.22.0 in /usr/local/lib/python3.10/site-packages (from matplotlib->transcript-structure-generator==0.2.0) (4.42.1)
Requirement already satisfied: pyparsing>=2.3.1 in /usr/local/lib/python3.10/site-packages (from matplotlib->transcript-structure-generator==0.2.0) (3.1.1)
Requirement already satisfied: pillow>=6.2.0 in /usr/local/lib/python3.10/site-packages (from matplotlib->transcript-structure-generator==0.2.0) (10.0.1)
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Requirement already satisfied: contourpy>=1.0.1 in /usr/local/lib/python3.10/site-packages (from matplotlib->transcript-structure-generator==0.2.0) (1.1.1)
Requirement already satisfied: packaging>=20.0 in /usr/local/lib/python3.10/site-packages (from matplotlib->transcript-structure-generator==0.2.0) (23.1)
Requirement already satisfied: tzdata>=2022.1 in /usr/local/lib/python3.10/site-packages (from pandas->transcript-structure-generator==0.2.0) (2023.3)
Requirement already satisfied: pytz>=2020.1 in /usr/local/lib/python3.10/site-packages (from pandas->transcript-structure-generator==0.2.0) (2023.3.post1)
Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.10/site-packages (from python-dateutil>=2.7->matplotlib->transcript-structure-generator==0.2.0) (1.16.0)
Installing collected packages: transcript-structure-generator
Running setup.py develop for transcript-structure-generator
Successfully installed transcript-structure-generator-0.2.0
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$ coverage run --source tsg -m pytest[0;m
============================= test session starts ==============================
platform linux -- Python 3.10.12, pytest-7.4.2, pluggy-1.3.0
rootdir: /builds/zavolan_group/tools/transcript-structure-generator
collected 8 items
tests/test_main.py ........ [100%]
=============================== warnings summary ===============================
tests/test_main.py::TestGtf::test_parsed
/builds/zavolan_group/tools/transcript-structure-generator/tsg/main.py:271: FutureWarning: Returning a DataFrame from Series.apply when the supplied function returns a Series is deprecated and will be removed in a future version.
).apply(pd.Series)
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
========================= 8 passed, 1 warning in 0.35s =========================
[32;1m$ coverage report -m[0;m
Name Stmts Miss Cover Missing
-----------------------------------------------
tsg/__init__.py 4 0 100%
tsg/__main__.py 3 3 0% 2-5
tsg/cli.py 37 37 0% 2-134
tsg/main.py 150 69 54% 23-28, 55, 61, 136-144, 157-159, 177-178, 225, 252-257, 290-301, 305, 322-326, 328-333, 368-369, 397, 427-428, 452-455, 468-477, 504-537
-----------------------------------------------
TOTAL 194 109 44%
section_end:1695125053:step_script
[0Ksection_start:1695125053:cleanup_file_variables
[0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m
section_end:1695125054:cleanup_file_variables
[0K[32;1mJob succeeded[0;m