V2-samplesheet-maker

Coverage Report

============================= test session starts ==============================
platform linux -- Python 3.10.13, pytest-8.0.1, pluggy-1.4.0
rootdir: /home/runner/work/v2-samplesheet-maker/v2-samplesheet-maker
plugins: cov-4.1.0
collected 29 items

tests/v2_samplesheet_maker/classes/test_samplesheet.py ...
tests/v2_samplesheet_maker/classes/test_sections.py ................
tests/v2_samplesheet_maker/utils/test_cli.py ..........

=============================== warnings summary ===============================
src/v2_samplesheet_maker/classes/samplesheet.py:10
/home/runner/work/v2-samplesheet-maker/v2-samplesheet-maker/src/v2_samplesheet_maker/classes/samplesheet.py:10: DeprecationWarning:
Pyarrow will become a required dependency of pandas in the next major release of pandas (pandas 3.0),
(to allow more performant data types, such as the Arrow string type, and better interoperability with other libraries)
but was not found to be installed on your system.
If this would cause problems for you,
please provide us feedback at https://github.com/pandas-dev/pandas/issues/54466

import pandas as pd

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html

---------- coverage: platform linux, python 3.10.13-final-0 ----------
Name Stmts Miss Cover
--------------------------------------------------------------------------------------
src/v2_samplesheet_maker/__init__.py 0 0 100%
src/v2_samplesheet_maker/classes/__init__.py 0 0 100%
src/v2_samplesheet_maker/classes/samplesheet.py 141 37 74%
src/v2_samplesheet_maker/classes/super_sections.py 130 27 79%
src/v2_samplesheet_maker/enums.py 10 0 100%
src/v2_samplesheet_maker/globals.py 0 0 100%
src/v2_samplesheet_maker/models/__init__.py 0 0 100%
src/v2_samplesheet_maker/models/bcl_convert_sections.py 56 2 96%
src/v2_samplesheet_maker/models/cloud_section.py 36 10 72%
src/v2_samplesheet_maker/models/run_info_sections.py 36 2 94%
src/v2_samplesheet_maker/models/samplesheet.py 13 13 0%
src/v2_samplesheet_maker/models/tso500l_sections.py 43 6 86%
src/v2_samplesheet_maker/run/__init__.py 0 0 100%
src/v2_samplesheet_maker/run/v2_samplesheet_reader.py 16 16 0%
src/v2_samplesheet_maker/run/v2_samplesheet_writer.py 14 14 0%
src/v2_samplesheet_maker/section_classes/bcl_convert_sections.py 16 2 88%
src/v2_samplesheet_maker/section_classes/cloud_sections.py 30 6 80%
src/v2_samplesheet_maker/section_classes/run_info_sections.py 12 0 100%
src/v2_samplesheet_maker/section_classes/tso500l_sections.py 20 2 90%
src/v2_samplesheet_maker/utils/__init__.py 25 3 88%
src/v2_samplesheet_maker/utils/cli.py 52 3 94%
src/v2_samplesheet_maker/utils/docopt_docs.py 4 4 0%
src/v2_samplesheet_maker/utils/logger.py 37 8 78%
--------------------------------------------------------------------------------------
TOTAL 691 155 78%

======================== 29 passed, 1 warning in 0.89s =========================

Coverage Report

============================= test session starts ==============================
platform linux -- Python 3.10.13, pytest-8.0.0, pluggy-1.4.0
rootdir: /home/runner/work/v2-samplesheet-maker/v2-samplesheet-maker
plugins: cov-4.1.0
collected 22 items

tests/v2_samplesheet_maker/classes/test_samplesheet.py .
tests/v2_samplesheet_maker/classes/test_sections.py ................
tests/v2_samplesheet_maker/utils/test_cli.py .....

=============================== warnings summary ===============================
src/v2_samplesheet_maker/classes/super_sections.py:4
/home/runner/work/v2-samplesheet-maker/v2-samplesheet-maker/src/v2_samplesheet_maker/classes/super_sections.py:4: DeprecationWarning:
Pyarrow will become a required dependency of pandas in the next major release of pandas (pandas 3.0),
(to allow more performant data types, such as the Arrow string type, and better interoperability with other libraries)
but was not found to be installed on your system.
If this would cause problems for you,
please provide us feedback at https://github.com/pandas-dev/pandas/issues/54466

import pandas as pd

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html

---------- coverage: platform linux, python 3.10.13-final-0 ----------
Name Stmts Miss Cover
--------------------------------------------------------------------------------------
src/v2_samplesheet_maker/__init__.py 0 0 100%
src/v2_samplesheet_maker/classes/__init__.py 0 0 100%
src/v2_samplesheet_maker/classes/samplesheet.py 75 20 73%
src/v2_samplesheet_maker/classes/super_sections.py 111 23 79%
src/v2_samplesheet_maker/enums.py 10 0 100%
src/v2_samplesheet_maker/globals.py 0 0 100%
src/v2_samplesheet_maker/models/__init__.py 0 0 100%
src/v2_samplesheet_maker/models/bcl_convert_sections.py 52 2 96%
src/v2_samplesheet_maker/models/cloud_section.py 28 6 79%
src/v2_samplesheet_maker/models/run_info_sections.py 30 1 97%
src/v2_samplesheet_maker/models/samplesheet.py 13 13 0%
src/v2_samplesheet_maker/models/tso500l_sections.py 39 4 90%
src/v2_samplesheet_maker/run/__init__.py 0 0 100%
src/v2_samplesheet_maker/run/v2_samplesheet_writer.py 14 14 0%
src/v2_samplesheet_maker/section_classes/bcl_convert_sections.py 16 2 88%
src/v2_samplesheet_maker/section_classes/cloud_sections.py 29 13 55%
src/v2_samplesheet_maker/section_classes/run_info_sections.py 12 0 100%
src/v2_samplesheet_maker/section_classes/tso500l_sections.py 20 2 90%
src/v2_samplesheet_maker/utils/__init__.py 0 0 100%
src/v2_samplesheet_maker/utils/cli.py 33 3 91%
src/v2_samplesheet_maker/utils/docopt_docs.py 2 2 0%
src/v2_samplesheet_maker/utils/logger.py 37 8 78%
--------------------------------------------------------------------------------------
TOTAL 521 113 78%

======================== 22 passed, 1 warning in 0.80s =========================

Coverage Report

============================= test session starts ==============================
platform linux -- Python 3.10.13, pytest-7.4.4, pluggy-1.3.0
rootdir: /home/runner/work/v2-samplesheet-maker/v2-samplesheet-maker
plugins: cov-4.1.0
collected 22 items

tests/v2_samplesheet_maker/classes/test_samplesheet.py .
tests/v2_samplesheet_maker/classes/test_sections.py ................
tests/v2_samplesheet_maker/utils/test_cli.py .....

---------- coverage: platform linux, python 3.10.13-final-0 ----------
Name Stmts Miss Cover
--------------------------------------------------------------------------------------
src/v2_samplesheet_maker/__init__.py 0 0 100%
src/v2_samplesheet_maker/classes/__init__.py 0 0 100%
src/v2_samplesheet_maker/classes/samplesheet.py 75 20 73%
src/v2_samplesheet_maker/classes/super_sections.py 111 23 79%
src/v2_samplesheet_maker/enums.py 10 0 100%
src/v2_samplesheet_maker/globals.py 0 0 100%
src/v2_samplesheet_maker/models/__init__.py 0 0 100%
src/v2_samplesheet_maker/models/bcl_convert_sections.py 52 2 96%
src/v2_samplesheet_maker/models/cloud_section.py 28 6 79%
src/v2_samplesheet_maker/models/run_info_sections.py 30 1 97%
src/v2_samplesheet_maker/models/samplesheet.py 13 13 0%
src/v2_samplesheet_maker/models/tso500l_sections.py 30 4 87%
src/v2_samplesheet_maker/run/__init__.py 0 0 100%
src/v2_samplesheet_maker/run/v2_samplesheet_writer.py 14 14 0%
src/v2_samplesheet_maker/section_classes/bcl_convert_sections.py 16 2 88%
src/v2_samplesheet_maker/section_classes/cloud_sections.py 29 13 55%
src/v2_samplesheet_maker/section_classes/run_info_sections.py 12 0 100%
src/v2_samplesheet_maker/section_classes/tso500l_sections.py 20 2 90%
src/v2_samplesheet_maker/utils/__init__.py 0 0 100%
src/v2_samplesheet_maker/utils/cli.py 33 3 91%
src/v2_samplesheet_maker/utils/docopt_docs.py 2 2 0%
src/v2_samplesheet_maker/utils/logger.py 37 8 78%
--------------------------------------------------------------------------------------
TOTAL 512 113 78%


============================== 22 passed in 0.77s ==============================

Coverage Report

============================= test session starts ==============================
platform linux -- Python 3.10.13, pytest-7.4.4, pluggy-1.3.0
rootdir: /home/runner/work/v2-samplesheet-maker/v2-samplesheet-maker
plugins: cov-4.1.0
collected 22 items

tests/v2_samplesheet_maker/classes/test_samplesheet.py .
tests/v2_samplesheet_maker/classes/test_sections.py ..........F..FF.
tests/v2_samplesheet_maker/utils/test_cli.py .....

=================================== FAILURES ===================================
_______ TestBCLConvertDataRow.test_bclconvert_data_row_with_extra_params _______

self = <test_sections.TestBCLConvertDataRow object at 0x7f2b02ea9ab0>

def test_bclconvert_data_row_with_extra_params(self):
try:
BCLConvertDataRow(**self.bclconvert_data_row_with_extra_params)
> assert False
E assert False

tests/v2_samplesheet_maker/classes/test_sections.py:190: AssertionError
------------------------------ Captured log call -------------------------------
WARNING <module>:super_sections.py:30 Keyword argument 'foo=bar' was not used
____________ TestBCLConvertDataSection.test_bclconvert_data_section ____________

self = <test_sections.TestBCLConvertDataSection object at 0x7f2b02ea97b0>

def test_bclconvert_data_section(self):
Get valid standard data
> BCLConvertDataSection.get_bclconvert_datarows_from_list(self.valid_bclconvert_data)
E AttributeError: type object 'BCLConvertDataSection' has no attribute 'get_bclconvert_datarows_from_list'

tests/v2_samplesheet_maker/classes/test_sections.py:250: AttributeError
___ TestBCLConvertDataSection.test_bclconvert_data_section_with_extra_params ___

self = <test_sections.TestBCLConvertDataSection object at 0x7f2b02ea9780>

def test_bclconvert_data_section_with_extra_params(self):
Get valid data with settings input
> BCLConvertDataSection.get_bclconvert_datarows_from_list(self.valid_bclconvert_data_with_settings)
E AttributeError: type object 'BCLConvertDataSection' has no attribute 'get_bclconvert_datarows_from_list'

tests/v2_samplesheet_maker/classes/test_sections.py:254: AttributeError

---------- coverage: platform linux, python 3.10.13-final-0 ----------
Name Stmts Miss Cover
--------------------------------------------------------------------------------------
src/v2_samplesheet_maker/__init__.py 0 0 100%
src/v2_samplesheet_maker/classes/__init__.py 0 0 100%
src/v2_samplesheet_maker/classes/samplesheet.py 44 13 70%
src/v2_samplesheet_maker/classes/super_sections.py 96 18 81%
src/v2_samplesheet_maker/enums.py 10 0 100%
src/v2_samplesheet_maker/globals.py 0 0 100%
src/v2_samplesheet_maker/models/__init__.py 0 0 100%
src/v2_samplesheet_maker/models/bcl_convert_sections.py 46 0 100%
src/v2_samplesheet_maker/models/cloud_section.py 27 6 78%
src/v2_samplesheet_maker/models/run_info_sections.py 30 1 97%
src/v2_samplesheet_maker/models/samplesheet.py 13 13 0%
src/v2_samplesheet_maker/models/tso500l_sections.py 25 25 0%
src/v2_samplesheet_maker/run/__init__.py 0 0 100%
src/v2_samplesheet_maker/run/v2_samplesheet_writer.py 14 14 0%
src/v2_samplesheet_maker/section_classes/bcl_convert_sections.py 12 0 100%
src/v2_samplesheet_maker/section_classes/cloud_sections.py 20 6 70%
src/v2_samplesheet_maker/section_classes/run_info_sections.py 12 0 100%
src/v2_samplesheet_maker/utils/__init__.py 0 0 100%
src/v2_samplesheet_maker/utils/cli.py 32 3 91%
src/v2_samplesheet_maker/utils/docopt_docs.py 2 2 0%
src/v2_samplesheet_maker/utils/logger.py 33 15 55%
--------------------------------------------------------------------------------------
TOTAL 416 116 72%

=========================== short test summary info ============================
FAILED tests/v2_samplesheet_maker/classes/test_sections.py::TestBCLConvertDataRow::test_bclconvert_data_row_with_extra_params - assert False
FAILED tests/v2_samplesheet_maker/classes/test_sections.py::TestBCLConvertDataSection::test_bclconvert_data_section - AttributeError: type object 'BCLConvertDataSection' has no attribute 'get_bclconvert_datarows_from_list'
FAILED tests/v2_samplesheet_maker/classes/test_sections.py::TestBCLConvertDataSection::test_bclconvert_data_section_with_extra_params - AttributeError: type object 'BCLConvertDataSection' has no attribute 'get_bclconvert_datarows_from_list'
========================= 3 failed, 19 passed in 0.75s =========================

Coverage Report

============================= test session starts ==============================
platform linux -- Python 3.10.13, pytest-7.4.3, pluggy-1.3.0
rootdir: /home/runner/work/v2-samplesheet-maker/v2-samplesheet-maker
plugins: cov-4.1.0
collected 22 items

tests/v2_samplesheet_maker/classes/test_samplesheet.py .
tests/v2_samplesheet_maker/classes/test_sections.py ................
tests/v2_samplesheet_maker/utils/test_cli.py .....

---------- coverage: platform linux, python 3.10.13-final-0 ----------
Name Stmts Miss Cover
---------------------------------------------------------------------------
src/v2_samplesheet_maker/__init__.py 0 0 100%
src/v2_samplesheet_maker/classes/__init__.py 0 0 100%
src/v2_samplesheet_maker/classes/samplesheet.py 37 15 59%
src/v2_samplesheet_maker/classes/sections.py 121 1 99%
src/v2_samplesheet_maker/classes/super_sections.py 46 12 74%
src/v2_samplesheet_maker/enums.py 11 0 100%
src/v2_samplesheet_maker/globals.py 2 2 0%
src/v2_samplesheet_maker/models/__init__.py 0 0 100%
src/v2_samplesheet_maker/models/samplesheet.py 8 8 0%
src/v2_samplesheet_maker/models/sections.py 53 0 100%
src/v2_samplesheet_maker/run/__init__.py 0 0 100%
src/v2_samplesheet_maker/run/v2_samplesheet_writer.py 14 14 0%
src/v2_samplesheet_maker/utils/__init__.py 0 0 100%
src/v2_samplesheet_maker/utils/cli.py 32 3 91%
src/v2_samplesheet_maker/utils/docopt_docs.py 2 2 0%
src/v2_samplesheet_maker/utils/logger.py 33 15 55%
---------------------------------------------------------------------------
TOTAL 359 72 80%


============================== 22 passed in 0.82s ==============================

Coverage Report

============================= test session starts ==============================
platform linux -- Python 3.10.13, pytest-7.4.3, pluggy-1.3.0
rootdir: /home/runner/work/v2-samplesheet-maker/v2-samplesheet-maker
plugins: cov-4.1.0
collected 22 items

tests/v2_samplesheet_maker/classes/test_samplesheet.py .
tests/v2_samplesheet_maker/classes/test_sections.py ................
tests/v2_samplesheet_maker/utils/test_cli.py .....

---------- coverage: platform linux, python 3.10.13-final-0 ----------
Name Stmts Miss Cover
---------------------------------------------------------------------------
src/v2_samplesheet_maker/__init__.py 0 0 100%
src/v2_samplesheet_maker/classes/__init__.py 0 0 100%
src/v2_samplesheet_maker/classes/samplesheet.py 37 15 59%
src/v2_samplesheet_maker/classes/sections.py 115 1 99%
src/v2_samplesheet_maker/classes/super_sections.py 46 12 74%
src/v2_samplesheet_maker/enums.py 11 0 100%
src/v2_samplesheet_maker/globals.py 2 2 0%
src/v2_samplesheet_maker/models/__init__.py 0 0 100%
src/v2_samplesheet_maker/models/samplesheet.py 8 8 0%
src/v2_samplesheet_maker/models/sections.py 53 0 100%
src/v2_samplesheet_maker/run/__init__.py 0 0 100%
src/v2_samplesheet_maker/run/v2_samplesheet_writer.py 14 14 0%
src/v2_samplesheet_maker/utils/__init__.py 0 0 100%
src/v2_samplesheet_maker/utils/cli.py 32 3 91%
src/v2_samplesheet_maker/utils/docopt_docs.py 2 2 0%
src/v2_samplesheet_maker/utils/logger.py 33 15 55%
---------------------------------------------------------------------------
TOTAL 353 72 80%


============================== 22 passed in 0.79s ==============================