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Fixing Ensemble Compara option to be consistent with other options #40

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merged 2 commits into from
Aug 6, 2024

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@bergsalex bergsalex commented Aug 6, 2024

This PR changes the name of option --algorithm 'Ensembl Compara' to --algorithm EnsemblCompara, removing the need for quotes, and making command usage consistent across Windows and MacOS.

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github-actions bot commented Aug 6, 2024

Test Coverage Report

---------- coverage: platform linux, python 3.11.9-final-0 -----------
Name                                                                     Stmts   Miss  Cover
--------------------------------------------------------------------------------------------
src/geneweaver/client/__init__.py                                            2      0   100%
src/geneweaver/client/api/__init__.py                                        0      0   100%
src/geneweaver/client/api/aon.py                                            32     12    62%
src/geneweaver/client/api/exc.py                                             3      0   100%
src/geneweaver/client/api/genes.py                                           8      0   100%
src/geneweaver/client/api/genesets.py                                       22      2    91%
src/geneweaver/client/api/graph.py                                          50     30    40%
src/geneweaver/client/api/utils.py                                          21      0   100%
src/geneweaver/client/auth.py                                               76     13    83%
src/geneweaver/client/batch/__init__.py                                      0      0   100%
src/geneweaver/client/cli/__init__.py                                        0      0   100%
src/geneweaver/client/cli/beta/__init__.py                                   5      0   100%
src/geneweaver/client/cli/beta/auth.py                                      22      0   100%
src/geneweaver/client/cli/main.py                                           14      0   100%
src/geneweaver/client/core/__init__.py                                       1      0   100%
src/geneweaver/client/core/app_dir.py                                       22     13    41%
src/geneweaver/client/core/config.py                                         2      0   100%
src/geneweaver/client/core/config_class.py                                  26      0   100%
src/geneweaver/client/datasets/__init__.py                                   1      0   100%
src/geneweaver/client/datasets/base.py                                      30      0   100%
src/geneweaver/client/datasets/nci60/__init__.py                             1      0   100%
src/geneweaver/client/datasets/nci60/dna_combined_acgh_gene_summary.py      26     10    62%
src/geneweaver/client/exceptions.py                                          1      0   100%
src/geneweaver/client/gedb.py                                              174     51    71%
src/geneweaver/client/parser/__init__.py                                     1      0   100%
src/geneweaver/client/parser/batch.py                                       61     51    16%
src/geneweaver/client/parser/general.py                                     42     12    71%
src/geneweaver/client/render/__init__.py                                     0      0   100%
src/geneweaver/client/user_config.py                                        20     20     0%
src/geneweaver/client/utils/__init__.py                                      0      0   100%
src/geneweaver/client/utils/aon.py                                          15      0   100%
src/geneweaver/client/utils/cli/__init__.py                                  0      0   100%
src/geneweaver/client/utils/cli/decorators/__init__.py                       0      0   100%
src/geneweaver/client/utils/cli/decorators/errors.py                        12      2    83%
src/geneweaver/client/utils/cli/decorators/options.py                       21     21     0%
src/geneweaver/client/utils/cli/print/__init__.py                            0      0   100%
src/geneweaver/client/utils/cli/print/csv.py                                12      8    33%
src/geneweaver/client/utils/cli/print/file_info.py                          10      0   100%
src/geneweaver/client/utils/cli/print/tables.py                             10      0   100%
src/geneweaver/client/utils/cli/prompt/__init__.py                           0      0   100%
src/geneweaver/client/utils/cli/prompt/bool.py                              10      0   100%
src/geneweaver/client/utils/cli/prompt/enum.py                              49     25    49%
src/geneweaver/client/utils/cli/prompt/generic.py                           33     13    61%
src/geneweaver/client/utils/cli/prompt/list.py                              26      4    85%
src/geneweaver/client/utils/cli/prompt/none.py                              15      3    80%
src/geneweaver/client/utils/cli/prompt/pydantic.py                          41      0   100%
--------------------------------------------------------------------------------------------
TOTAL                                                                      917    290    68%
Coverage HTML written to dir htmlcov

FAIL Required test coverage of 70% not reached. Total coverage: 68.38%
================= 6221 passed, 8 skipped, 4 warnings in 22.41s =================

@bergsalex bergsalex marked this pull request as ready for review August 6, 2024 13:41
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@gerring gerring left a comment

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Thanks for giving me the easy ones...

@bergsalex bergsalex merged commit fe49e6f into main Aug 6, 2024
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2 participants