multiqc: init at 1.25.1 #364029
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multiqc: init at 1.25.1 #364029
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I messed up trying to rebase my last commits. I decided to delete my branch and recreate it. Sorry about that! |
ofborg
bot
added
8.has: package (new)
apraga
reviewed
Jan 4, 2025
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Also, tests fails to run :
last 25 log lines:
> custom_content | some_science: Found 1 sample (image)
> ------------------------------ Captured log call -------------------------------
> INFO multiqc.core.file_search:file_search.py:56 Search path: /build/multiqc/test-data/data/custom_content
> INFO multiqc.core.file_search:file_search.py:56 Search path: /build/multiqc
> INFO multiqc.core.file_search:file_search.py:76 Only using modules: custom_content
> ERROR multiqc.report:report.py:365 Error: MultiQC is running in source code directory! /build/multiqc
> WARNING multiqc.report:report.py:366 Please see the docs for how to use MultiQC: https://docs.seqera.io/multiqc/#running-multiqc
> WARNING multiqc.modules.custom_content.custom_content:custom_content.py:238 Not able to parse custom data in box_single_sample_mqc.txt
> WARNING multiqc.modules.custom_content.custom_content:custom_content.py:238 Not able to parse custom data in linegraph_multiple_samples_mqc.txt
> WARNING multiqc.modules.custom_content.custom_content:custom_content.py:707 Inconsistent number of columns found in table_data_mqc.out! Skipping..
> WARNING multiqc.modules.custom_content.custom_content:custom_content.py:238 Not able to parse custom data in table_data_mqc.out
> WARNING multiqc.modules.custom_content.custom_content:custom_content.py:707 Inconsistent number of columns found in with_parent_id_table_mqc.txt! Skipping..
> WARNING multiqc.modules.custom_content.custom_content:custom_content.py:238 Not able to parse custom data in with_parent_id_table_mqc.txt
> WARNING multiqc.modules.custom_content.custom_content:custom_content.py:238 Not able to parse custom data in general_stats_txt_mqc.tsv
> WARNING multiqc.modules.custom_content.custom_content:custom_content.py:707 Inconsistent number of columns found in table_txt_mqc.txt! Skipping..
> WARNING multiqc.modules.custom_content.custom_content:custom_content.py:238 Not able to parse custom data in table_txt_mqc.txt
> WARNING multiqc.modules.custom_content.custom_content:custom_content.py:537 Image plot type found with more than one dataset in Test-Mire2
> INFO multiqc.modules.custom_content.custom_content:custom_content.py:351 Test-Mire2: Found 1 sample (image)
> WARNING multiqc.modules.custom_content.custom_content:custom_content.py:537 Image plot type found with more than one dataset in dupRadar_plot
> INFO multiqc.modules.custom_content.custom_content:custom_content.py:351 dupRadar_plot: Found 1 sample (image)
> WARNING multiqc.modules.custom_content.custom_content:custom_content.py:537 Image plot type found with more than one dataset in some_science
> INFO multiqc.modules.custom_content.custom_content:custom_content.py:351 some_science: Found 1 sample (image)
> =========================== short test summary info ============================
> FAILED tests/test_custom_content.py::test_on_all_example_files - pydantic_core._pydantic_core.ValidationError: 9 validation errors for InputRow
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| owner = "ewels"; | ||
| repo = "MultiQC_TestData"; | ||
| rev = "bfecc7365746caba6fd80f20df9cd630db1c6f60"; | ||
| sha256 = "sha256-HPgPgeWf0K5jCVPcQj5ecsMWZixs3Nw5riwD4M1dr9E="; |
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Is there a reason not to use https://github.com/MultiQC/test-data ? In my PR packaging 1.21, I managed to get it working
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| src = fetchFromGitHub { | ||
| owner = "jsvine"; | ||
| repo = "spectra"; | ||
| rev = "refs/tags/v${version}"; | ||
| sha256 = "sha256-4A2TWTxYqckJ3DX5cd2KN3KXcmO/lQdXmOEnGi76RsA="; | ||
| }; | ||
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| dependencies = [ colormath ]; | ||
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| build-system = [ setuptools ]; | ||
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| postInstall = "install -Dm755 $src/spectra/grapefruit.py $out/bin/grapefruit.py"; |
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Maybe fetchPypi would be better ? See my PR for inspiration.
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PyPI source releases often have tests stripped, which isn't ideal. I personally would recommend using source repos if possible
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| doCheck = false; # tests require nose. An outdated python library. | ||
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| # pytestFlagsArray = [ "-W 'ignore:pkg_resources is deprecated as an API:DeprecationWarning'" ]; |
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