From f6002d29e879b27d46699fc7f2b6f037458b07f7 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Sat, 14 Dec 2024 15:07:50 +0100 Subject: [PATCH] add linter exceptions --- chemicaltoolbox/PaDEL/.lint_skip | 2 ++ chemicaltoolbox/autodock_vina/docking/.lint_skip | 3 +++ chemicaltoolbox/autodock_vina/prepare_box/.lint_skip | 1 + chemicaltoolbox/autodock_vina/prepare_ligand/.lint_skip | 1 + .../autodock_vina/prepare_receptor/.lint_skip | 1 + chemicaltoolbox/chembl/.lint_skip | 3 +++ chemicaltoolbox/chemfp/.lint_skip | 1 + chemicaltoolbox/confab/.lint_skip | 1 + chemicaltoolbox/data_source/get_online_data/.lint_skip | 1 + chemicaltoolbox/data_source/get_pubchem/.lint_skip | 3 +++ chemicaltoolbox/fpocket/.lint_skip | 3 +++ chemicaltoolbox/im-pipelines/.lint_skip | 3 +++ chemicaltoolbox/mordred/.lint_skip | 1 + chemicaltoolbox/natural_product_likeness/.lint_skip | 3 +++ chemicaltoolbox/openbabel/.lint_skip | 2 ++ chemicaltoolbox/openduck/.lint_skip | 1 + chemicaltoolbox/rdkit/.lint_skip | 2 ++ chemicaltoolbox/rdock/.lint_skip | 1 + chemicaltoolbox/rxdock/.lint_skip | 2 ++ chemicaltoolbox/silicos-it/align-it/.lint_skip | 1 + chemicaltoolbox/silicos-it/qed/.lint_skip | 1 + chemicaltoolbox/silicos-it/shape-it/.lint_skip | 3 +++ chemicaltoolbox/simsearch/.lint_skip | 1 + .../.lint_skip | 1 + tools/GraphClust/AggregateAlignments/.lint_skip | 1 + tools/GraphClust/AlignCluster/.lint_skip | 5 +++++ tools/GraphClust/CMFinder/.lint_skip | 3 +++ tools/GraphClust/CollectResults/.lint_skip | 3 +++ tools/GraphClust/CollectResultsNoAlign/.lint_skip | 2 ++ tools/GraphClust/GSPAN/.lint_skip | 3 +++ tools/GraphClust/LocARNAGraphClust/.lint_skip | 4 ++++ tools/GraphClust/NSPDK/.lint_skip | 4 ++++ tools/GraphClust/Plotting/.lint_skip | 2 ++ tools/GraphClust/PrepareForMlocarna/.lint_skip | 1 + tools/GraphClust/Preprocessing/.lint_skip | 1 + tools/GraphClust/Structure_GSPAN/.lint_skip | 5 +++++ tools/agat/.lint_skip | 1 + tools/antismash/.lint_skip | 2 ++ tools/atactk_trim_adapters/.lint_skip | 1 + tools/bamhash/.lint_skip | 3 +++ tools/barcode_collapse/.lint_skip | 1 + tools/bismark/.lint_skip | 5 +++++ tools/blobtoolkit/.lint_skip | 2 ++ tools/canu/.lint_skip | 1 + tools/cellpose/.lint_skip | 2 ++ tools/cellprofiler/.lint_skip | 5 +++++ tools/chatgpt/.lint_skip | 2 ++ tools/chipseeker/.lint_skip | 1 + tools/circexplorer/.lint_skip | 1 + tools/combine_metaphlan_humann/.lint_skip | 1 + tools/compare_humann2_output/.lint_skip | 1 + tools/edta/.lint_skip | 5 +++++ tools/epicseg/.lint_skip | 2 ++ tools/file_manipulation/.lint_skip | 3 +++ tools/find_subsequences/.lint_skip | 2 ++ tools/flexynesis/.lint_skip | 1 + tools/flux/.lint_skip | 1 + tools/footprint/.lint_skip | 3 +++ tools/format_cd_hit_output/.lint_skip | 3 +++ tools/format_metaphlan2_output/.lint_skip | 2 ++ tools/gotohscan/.lint_skip | 4 ++++ tools/hclust2/.lint_skip | 5 +++++ tools/hictk/.lint_skip | 1 + tools/hicup/.lint_skip | 2 ++ tools/image_processing/bia-ftplinks/.lint_skip | 1 + tools/image_processing/graphicsmagick/.lint_skip | 1 + tools/image_processing/imagej2/.lint_skip | 1 + tools/instagraal/.lint_skip | 1 + tools/itsx/.lint_skip | 1 + tools/jbrowse2/.lint_skip | 3 +++ tools/lighter/.lint_skip | 1 + tools/mafft/.lint_skip | 1 + tools/methyldackel/.lint_skip | 1 + tools/methylkit/.lint_skip | 2 ++ tools/mgnify_seqprep/.lint_skip | 1 + tools/minced/.lint_skip | 2 ++ tools/minipolish/.lint_skip | 1 + tools/mitohifi/.lint_skip | 2 ++ tools/motus/.lint_skip | 1 + tools/music_deconvolution/.lint_skip | 2 ++ tools/nanopolish/.lint_skip | 2 ++ tools/netboxr/.lint_skip | 1 + tools/nextdenovo/.lint_skip | 3 +++ tools/openms/.lint_skip | 9 +++++++++ tools/pandas_rolling_window/.lint_skip | 3 +++ tools/pg_tools/.lint_skip | 1 + tools/pharmcat/.lint_skip | 3 +++ tools/piranha/.lint_skip | 3 +++ tools/plotly_parallel_coordinates_plot/.lint_skip | 1 + tools/plotly_regression_performance_plots/.lint_skip | 1 + tools/protease_prediction/.lint_skip | 5 +++++ tools/replaceColumn/.lint_skip | 1 + tools/rna_tools/antarna/.lint_skip | 2 ++ tools/rna_tools/aresite2/.lint_skip | 3 +++ tools/rna_tools/blockclust/.lint_skip | 3 +++ tools/rna_tools/cmsearch_deoverlap/.lint_skip | 1 + tools/rna_tools/cmv/.lint_skip | 3 +++ tools/rna_tools/cofold/.lint_skip | 3 +++ tools/rna_tools/dewseq/.lint_skip | 2 ++ tools/rna_tools/exparna/.lint_skip | 4 ++++ tools/rna_tools/graphprot/.lint_skip | 1 + tools/rna_tools/htseq-clip/.lint_skip | 2 ++ tools/rna_tools/infernal/.lint_skip | 4 ++++ tools/rna_tools/intarna/.lint_skip | 1 + tools/rna_tools/locarna/.lint_skip | 3 +++ tools/rna_tools/mea/.lint_skip | 3 +++ tools/rna_tools/miRDeep2/miRDeep2/.lint_skip | 2 ++ tools/rna_tools/miRDeep2/miRDeep2_mapper/.lint_skip | 3 +++ tools/rna_tools/mqc/.lint_skip | 1 + tools/rna_tools/paralyzer/.lint_skip | 2 ++ tools/rna_tools/pipmir/.lint_skip | 1 + tools/rna_tools/rbpbench/.lint_skip | 2 ++ tools/rna_tools/rcas/.lint_skip | 6 ++++++ tools/rna_tools/ribotaper/.lint_skip | 2 ++ tools/rna_tools/rna_shapes/.lint_skip | 2 ++ tools/rna_tools/rnacode/.lint_skip | 4 ++++ tools/rna_tools/rnaformer/.lint_skip | 1 + tools/rna_tools/rnalien/.lint_skip | 2 ++ tools/rna_tools/rnaz/.lint_skip | 4 ++++ tools/rna_tools/sshmm/.lint_skip | 2 ++ tools/rna_tools/targetfinder/.lint_skip | 1 + tools/rna_tools/trna_prediction/.lint_skip | 3 +++ tools/rna_tools/vienna_rna/.lint_skip | 9 +++++++++ tools/sailfish/.lint_skip | 2 ++ tools/salmon/.lint_skip | 3 +++ tools/sed/.lint_skip | 6 ++++++ tools/segemehl/.lint_skip | 3 +++ tools/sklearn/.lint_skip | 4 ++++ tools/splitfasta/.lint_skip | 1 + tools/statistics/.lint_skip | 3 +++ tools/stress_ng/.lint_skip | 3 +++ tools/text_processing/add_line_to_file/.lint_skip | 1 + .../text_processing/column_arrange_by_header/.lint_skip | 1 + .../join_files_on_column_fuzzy/.lint_skip | 3 +++ .../text_processing/split_file_to_collection/.lint_skip | 1 + tools/text_processing/text_processing/.lint_skip | 2 ++ tools/tgsgapcloser/.lint_skip | 2 ++ tools/tiara/.lint_skip | 1 + tools/tool_recommendation_model/.lint_skip | 1 + tools/trim_galore/.lint_skip | 2 ++ tools/uniprot_rest_interface/.lint_skip | 1 + tools/vt/.lint_skip | 2 ++ tools/wtdbg/.lint_skip | 3 +++ 143 files changed, 321 insertions(+) create mode 100644 chemicaltoolbox/PaDEL/.lint_skip create mode 100644 chemicaltoolbox/autodock_vina/docking/.lint_skip create mode 100644 chemicaltoolbox/autodock_vina/prepare_box/.lint_skip create mode 100644 chemicaltoolbox/autodock_vina/prepare_ligand/.lint_skip create mode 100644 chemicaltoolbox/autodock_vina/prepare_receptor/.lint_skip create mode 100644 chemicaltoolbox/chembl/.lint_skip create mode 100644 chemicaltoolbox/chemfp/.lint_skip create mode 100644 chemicaltoolbox/confab/.lint_skip create mode 100644 chemicaltoolbox/data_source/get_online_data/.lint_skip create mode 100644 chemicaltoolbox/data_source/get_pubchem/.lint_skip create mode 100644 chemicaltoolbox/fpocket/.lint_skip create mode 100644 chemicaltoolbox/im-pipelines/.lint_skip create mode 100644 chemicaltoolbox/mordred/.lint_skip create mode 100644 chemicaltoolbox/natural_product_likeness/.lint_skip create mode 100644 chemicaltoolbox/openbabel/.lint_skip create mode 100644 chemicaltoolbox/openduck/.lint_skip create mode 100644 chemicaltoolbox/rdkit/.lint_skip create mode 100644 chemicaltoolbox/rdock/.lint_skip create mode 100644 chemicaltoolbox/rxdock/.lint_skip create mode 100644 chemicaltoolbox/silicos-it/align-it/.lint_skip create mode 100644 chemicaltoolbox/silicos-it/qed/.lint_skip create mode 100644 chemicaltoolbox/silicos-it/shape-it/.lint_skip create mode 100644 chemicaltoolbox/simsearch/.lint_skip create mode 100644 data_managers/data_manager_sortmerna_database_downloader/.lint_skip create mode 100644 tools/GraphClust/AggregateAlignments/.lint_skip create mode 100644 tools/GraphClust/AlignCluster/.lint_skip create mode 100644 tools/GraphClust/CMFinder/.lint_skip create mode 100644 tools/GraphClust/CollectResults/.lint_skip create mode 100644 tools/GraphClust/CollectResultsNoAlign/.lint_skip create mode 100644 tools/GraphClust/GSPAN/.lint_skip create mode 100644 tools/GraphClust/LocARNAGraphClust/.lint_skip create mode 100644 tools/GraphClust/NSPDK/.lint_skip create mode 100644 tools/GraphClust/Plotting/.lint_skip create mode 100644 tools/GraphClust/PrepareForMlocarna/.lint_skip create mode 100644 tools/GraphClust/Preprocessing/.lint_skip create mode 100644 tools/GraphClust/Structure_GSPAN/.lint_skip create mode 100644 tools/agat/.lint_skip create mode 100644 tools/antismash/.lint_skip create mode 100644 tools/atactk_trim_adapters/.lint_skip create mode 100644 tools/bamhash/.lint_skip create mode 100644 tools/barcode_collapse/.lint_skip create mode 100644 tools/bismark/.lint_skip create mode 100644 tools/blobtoolkit/.lint_skip create mode 100644 tools/canu/.lint_skip create mode 100644 tools/cellpose/.lint_skip create mode 100644 tools/cellprofiler/.lint_skip create mode 100644 tools/chatgpt/.lint_skip create mode 100644 tools/chipseeker/.lint_skip create mode 100644 tools/circexplorer/.lint_skip create mode 100644 tools/combine_metaphlan_humann/.lint_skip create mode 100644 tools/compare_humann2_output/.lint_skip create mode 100644 tools/edta/.lint_skip create mode 100644 tools/epicseg/.lint_skip create mode 100644 tools/file_manipulation/.lint_skip create mode 100644 tools/find_subsequences/.lint_skip create mode 100644 tools/flexynesis/.lint_skip create mode 100644 tools/flux/.lint_skip create mode 100644 tools/footprint/.lint_skip create mode 100644 tools/format_cd_hit_output/.lint_skip create mode 100644 tools/format_metaphlan2_output/.lint_skip create mode 100644 tools/gotohscan/.lint_skip create mode 100644 tools/hclust2/.lint_skip create mode 100644 tools/hictk/.lint_skip create mode 100644 tools/hicup/.lint_skip create mode 100644 tools/image_processing/bia-ftplinks/.lint_skip create mode 100644 tools/image_processing/graphicsmagick/.lint_skip create mode 100644 tools/image_processing/imagej2/.lint_skip create mode 100644 tools/instagraal/.lint_skip create mode 100644 tools/itsx/.lint_skip create mode 100644 tools/jbrowse2/.lint_skip create mode 100644 tools/lighter/.lint_skip create mode 100644 tools/mafft/.lint_skip create mode 100644 tools/methyldackel/.lint_skip create mode 100644 tools/methylkit/.lint_skip create mode 100644 tools/mgnify_seqprep/.lint_skip create mode 100644 tools/minced/.lint_skip create mode 100644 tools/minipolish/.lint_skip create mode 100644 tools/mitohifi/.lint_skip create mode 100644 tools/motus/.lint_skip create mode 100644 tools/music_deconvolution/.lint_skip create mode 100644 tools/nanopolish/.lint_skip create mode 100644 tools/netboxr/.lint_skip create mode 100644 tools/nextdenovo/.lint_skip create mode 100644 tools/openms/.lint_skip create mode 100644 tools/pandas_rolling_window/.lint_skip create mode 100644 tools/pg_tools/.lint_skip create mode 100644 tools/pharmcat/.lint_skip create mode 100644 tools/piranha/.lint_skip create mode 100644 tools/plotly_parallel_coordinates_plot/.lint_skip create mode 100644 tools/plotly_regression_performance_plots/.lint_skip create mode 100644 tools/protease_prediction/.lint_skip create mode 100644 tools/replaceColumn/.lint_skip create mode 100644 tools/rna_tools/antarna/.lint_skip create mode 100644 tools/rna_tools/aresite2/.lint_skip create mode 100644 tools/rna_tools/blockclust/.lint_skip create mode 100644 tools/rna_tools/cmsearch_deoverlap/.lint_skip create mode 100644 tools/rna_tools/cmv/.lint_skip create mode 100644 tools/rna_tools/cofold/.lint_skip create mode 100644 tools/rna_tools/dewseq/.lint_skip create mode 100644 tools/rna_tools/exparna/.lint_skip create mode 100644 tools/rna_tools/graphprot/.lint_skip create mode 100644 tools/rna_tools/htseq-clip/.lint_skip create mode 100644 tools/rna_tools/infernal/.lint_skip create mode 100644 tools/rna_tools/intarna/.lint_skip create mode 100644 tools/rna_tools/locarna/.lint_skip create mode 100644 tools/rna_tools/mea/.lint_skip create mode 100644 tools/rna_tools/miRDeep2/miRDeep2/.lint_skip create mode 100644 tools/rna_tools/miRDeep2/miRDeep2_mapper/.lint_skip create mode 100644 tools/rna_tools/mqc/.lint_skip create mode 100644 tools/rna_tools/paralyzer/.lint_skip create mode 100644 tools/rna_tools/pipmir/.lint_skip create mode 100644 tools/rna_tools/rbpbench/.lint_skip create mode 100644 tools/rna_tools/rcas/.lint_skip create mode 100644 tools/rna_tools/ribotaper/.lint_skip create mode 100644 tools/rna_tools/rna_shapes/.lint_skip create mode 100644 tools/rna_tools/rnacode/.lint_skip create mode 100644 tools/rna_tools/rnaformer/.lint_skip create mode 100644 tools/rna_tools/rnalien/.lint_skip create mode 100644 tools/rna_tools/rnaz/.lint_skip create mode 100644 tools/rna_tools/sshmm/.lint_skip create mode 100644 tools/rna_tools/targetfinder/.lint_skip create mode 100644 tools/rna_tools/trna_prediction/.lint_skip create mode 100644 tools/rna_tools/vienna_rna/.lint_skip create mode 100644 tools/sailfish/.lint_skip create mode 100644 tools/salmon/.lint_skip create mode 100644 tools/sed/.lint_skip create mode 100644 tools/segemehl/.lint_skip create mode 100644 tools/sklearn/.lint_skip create mode 100644 tools/splitfasta/.lint_skip create mode 100644 tools/statistics/.lint_skip create mode 100644 tools/stress_ng/.lint_skip create mode 100644 tools/text_processing/add_line_to_file/.lint_skip create mode 100644 tools/text_processing/column_arrange_by_header/.lint_skip create mode 100644 tools/text_processing/join_files_on_column_fuzzy/.lint_skip create mode 100644 tools/text_processing/split_file_to_collection/.lint_skip create mode 100644 tools/text_processing/text_processing/.lint_skip create mode 100644 tools/tgsgapcloser/.lint_skip create mode 100644 tools/tiara/.lint_skip create mode 100644 tools/tool_recommendation_model/.lint_skip create mode 100644 tools/trim_galore/.lint_skip create mode 100644 tools/uniprot_rest_interface/.lint_skip create mode 100644 tools/vt/.lint_skip create mode 100644 tools/wtdbg/.lint_skip diff --git a/chemicaltoolbox/PaDEL/.lint_skip b/chemicaltoolbox/PaDEL/.lint_skip new file mode 100644 index 0000000000..f530e93cdd --- /dev/null +++ b/chemicaltoolbox/PaDEL/.lint_skip @@ -0,0 +1,2 @@ +TestsCaseValidation +TestsParamInInputs diff --git a/chemicaltoolbox/autodock_vina/docking/.lint_skip b/chemicaltoolbox/autodock_vina/docking/.lint_skip new file mode 100644 index 0000000000..62b87ca483 --- /dev/null +++ b/chemicaltoolbox/autodock_vina/docking/.lint_skip @@ -0,0 +1,3 @@ +ConditionalParamTypeBool +TestsCaseValidation +TestsExpectNumOutputs diff --git a/chemicaltoolbox/autodock_vina/prepare_box/.lint_skip b/chemicaltoolbox/autodock_vina/prepare_box/.lint_skip new file mode 100644 index 0000000000..a68d017209 --- /dev/null +++ b/chemicaltoolbox/autodock_vina/prepare_box/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/chemicaltoolbox/autodock_vina/prepare_ligand/.lint_skip b/chemicaltoolbox/autodock_vina/prepare_ligand/.lint_skip new file mode 100644 index 0000000000..a68d017209 --- /dev/null +++ b/chemicaltoolbox/autodock_vina/prepare_ligand/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/chemicaltoolbox/autodock_vina/prepare_receptor/.lint_skip b/chemicaltoolbox/autodock_vina/prepare_receptor/.lint_skip new file mode 100644 index 0000000000..a68d017209 --- /dev/null +++ b/chemicaltoolbox/autodock_vina/prepare_receptor/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/chemicaltoolbox/chembl/.lint_skip b/chemicaltoolbox/chembl/.lint_skip new file mode 100644 index 0000000000..cb1c08eecc --- /dev/null +++ b/chemicaltoolbox/chembl/.lint_skip @@ -0,0 +1,3 @@ +InputsNameRedundantArgument +TestsCaseValidation +ValidDatatypes diff --git a/chemicaltoolbox/chemfp/.lint_skip b/chemicaltoolbox/chemfp/.lint_skip new file mode 100644 index 0000000000..8b0ac00d7f --- /dev/null +++ b/chemicaltoolbox/chemfp/.lint_skip @@ -0,0 +1 @@ +ValidDatatypes diff --git a/chemicaltoolbox/confab/.lint_skip b/chemicaltoolbox/confab/.lint_skip new file mode 100644 index 0000000000..a68d017209 --- /dev/null +++ b/chemicaltoolbox/confab/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/chemicaltoolbox/data_source/get_online_data/.lint_skip b/chemicaltoolbox/data_source/get_online_data/.lint_skip new file mode 100644 index 0000000000..f98c941cb6 --- /dev/null +++ b/chemicaltoolbox/data_source/get_online_data/.lint_skip @@ -0,0 +1 @@ +CitationsNoValid diff --git a/chemicaltoolbox/data_source/get_pubchem/.lint_skip b/chemicaltoolbox/data_source/get_pubchem/.lint_skip new file mode 100644 index 0000000000..2be791776c --- /dev/null +++ b/chemicaltoolbox/data_source/get_pubchem/.lint_skip @@ -0,0 +1,3 @@ +CitationsMissing +InputsMissing +TestsMissing diff --git a/chemicaltoolbox/fpocket/.lint_skip b/chemicaltoolbox/fpocket/.lint_skip new file mode 100644 index 0000000000..ccee25d931 --- /dev/null +++ b/chemicaltoolbox/fpocket/.lint_skip @@ -0,0 +1,3 @@ +TestsCaseValidation +TestsExpectNumOutputs +TestsParamInInputs diff --git a/chemicaltoolbox/im-pipelines/.lint_skip b/chemicaltoolbox/im-pipelines/.lint_skip new file mode 100644 index 0000000000..62b87ca483 --- /dev/null +++ b/chemicaltoolbox/im-pipelines/.lint_skip @@ -0,0 +1,3 @@ +ConditionalParamTypeBool +TestsCaseValidation +TestsExpectNumOutputs diff --git a/chemicaltoolbox/mordred/.lint_skip b/chemicaltoolbox/mordred/.lint_skip new file mode 100644 index 0000000000..a68d017209 --- /dev/null +++ b/chemicaltoolbox/mordred/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/chemicaltoolbox/natural_product_likeness/.lint_skip b/chemicaltoolbox/natural_product_likeness/.lint_skip new file mode 100644 index 0000000000..98828d337c --- /dev/null +++ b/chemicaltoolbox/natural_product_likeness/.lint_skip @@ -0,0 +1,3 @@ +InputsBoolDistinctValues +OutputsLabelDuplicatedFilter +TestsExpectNumOutputs diff --git a/chemicaltoolbox/openbabel/.lint_skip b/chemicaltoolbox/openbabel/.lint_skip new file mode 100644 index 0000000000..1517e90027 --- /dev/null +++ b/chemicaltoolbox/openbabel/.lint_skip @@ -0,0 +1,2 @@ +TestsCaseValidation +ValidDatatypes diff --git a/chemicaltoolbox/openduck/.lint_skip b/chemicaltoolbox/openduck/.lint_skip new file mode 100644 index 0000000000..2092d1d0d6 --- /dev/null +++ b/chemicaltoolbox/openduck/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/chemicaltoolbox/rdkit/.lint_skip b/chemicaltoolbox/rdkit/.lint_skip new file mode 100644 index 0000000000..1f78d73fa8 --- /dev/null +++ b/chemicaltoolbox/rdkit/.lint_skip @@ -0,0 +1,2 @@ +TestsCaseValidation +XMLOrder diff --git a/chemicaltoolbox/rdock/.lint_skip b/chemicaltoolbox/rdock/.lint_skip new file mode 100644 index 0000000000..2092d1d0d6 --- /dev/null +++ b/chemicaltoolbox/rdock/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/chemicaltoolbox/rxdock/.lint_skip b/chemicaltoolbox/rxdock/.lint_skip new file mode 100644 index 0000000000..db84bbeb2f --- /dev/null +++ b/chemicaltoolbox/rxdock/.lint_skip @@ -0,0 +1,2 @@ +TestsCaseValidation +ToolVersionPEP404 diff --git a/chemicaltoolbox/silicos-it/align-it/.lint_skip b/chemicaltoolbox/silicos-it/align-it/.lint_skip new file mode 100644 index 0000000000..8b0ac00d7f --- /dev/null +++ b/chemicaltoolbox/silicos-it/align-it/.lint_skip @@ -0,0 +1 @@ +ValidDatatypes diff --git a/chemicaltoolbox/silicos-it/qed/.lint_skip b/chemicaltoolbox/silicos-it/qed/.lint_skip new file mode 100644 index 0000000000..a68d017209 --- /dev/null +++ b/chemicaltoolbox/silicos-it/qed/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/chemicaltoolbox/silicos-it/shape-it/.lint_skip b/chemicaltoolbox/silicos-it/shape-it/.lint_skip new file mode 100644 index 0000000000..a683753347 --- /dev/null +++ b/chemicaltoolbox/silicos-it/shape-it/.lint_skip @@ -0,0 +1,3 @@ +OutputsLabelDuplicatedFilter +TestsExpectNumOutputs +ValidDatatypes diff --git a/chemicaltoolbox/simsearch/.lint_skip b/chemicaltoolbox/simsearch/.lint_skip new file mode 100644 index 0000000000..2092d1d0d6 --- /dev/null +++ b/chemicaltoolbox/simsearch/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/data_managers/data_manager_sortmerna_database_downloader/.lint_skip b/data_managers/data_manager_sortmerna_database_downloader/.lint_skip new file mode 100644 index 0000000000..2a25b72db6 --- /dev/null +++ b/data_managers/data_manager_sortmerna_database_downloader/.lint_skip @@ -0,0 +1 @@ +InputsMissing diff --git a/tools/GraphClust/AggregateAlignments/.lint_skip b/tools/GraphClust/AggregateAlignments/.lint_skip new file mode 100644 index 0000000000..a68d017209 --- /dev/null +++ b/tools/GraphClust/AggregateAlignments/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/GraphClust/AlignCluster/.lint_skip b/tools/GraphClust/AlignCluster/.lint_skip new file mode 100644 index 0000000000..4b7373aa71 --- /dev/null +++ b/tools/GraphClust/AlignCluster/.lint_skip @@ -0,0 +1,5 @@ +InputsNameRedundantArgument +TestsCaseValidation +ToolNameWhitespace +XMLOrder +XSD diff --git a/tools/GraphClust/CMFinder/.lint_skip b/tools/GraphClust/CMFinder/.lint_skip new file mode 100644 index 0000000000..c85c54905b --- /dev/null +++ b/tools/GraphClust/CMFinder/.lint_skip @@ -0,0 +1,3 @@ +TestsCaseValidation +TestsParamInInputs +XMLOrder diff --git a/tools/GraphClust/CollectResults/.lint_skip b/tools/GraphClust/CollectResults/.lint_skip new file mode 100644 index 0000000000..507c521a19 --- /dev/null +++ b/tools/GraphClust/CollectResults/.lint_skip @@ -0,0 +1,3 @@ +ConditionalParamTypeBool +InputsNameRedundantArgument +OutputsFormat diff --git a/tools/GraphClust/CollectResultsNoAlign/.lint_skip b/tools/GraphClust/CollectResultsNoAlign/.lint_skip new file mode 100644 index 0000000000..54df30a96e --- /dev/null +++ b/tools/GraphClust/CollectResultsNoAlign/.lint_skip @@ -0,0 +1,2 @@ +ConditionalParamTypeBool +OutputsFormat diff --git 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index 0000000000..319d7dc3a9 --- /dev/null +++ b/tools/rna_tools/trna_prediction/.lint_skip @@ -0,0 +1,3 @@ +OutputsLabelDuplicatedFilter +TestsCaseValidation +TestsExpectNumOutputs diff --git a/tools/rna_tools/vienna_rna/.lint_skip b/tools/rna_tools/vienna_rna/.lint_skip new file mode 100644 index 0000000000..2255233d56 --- /dev/null +++ b/tools/rna_tools/vienna_rna/.lint_skip @@ -0,0 +1,9 @@ +ConditionalWhenMissing +InputsNameDuplicate +InputsNameRedundantArgument +OutputsLabelDuplicatedFilter +OutputsLabelDuplicatedNoFilter +TestsCaseValidation +TestsExpectNumOutputs +TestsOutputDefined +ValidDatatypes diff --git a/tools/sailfish/.lint_skip b/tools/sailfish/.lint_skip new file mode 100644 index 0000000000..9a302b9948 --- /dev/null +++ b/tools/sailfish/.lint_skip @@ -0,0 +1,2 @@ +TestsCaseValidation +TestsExpectNumOutputs diff --git a/tools/salmon/.lint_skip b/tools/salmon/.lint_skip new file mode 100644 index 0000000000..1832c43ccb --- /dev/null +++ b/tools/salmon/.lint_skip @@ -0,0 +1,3 @@ +TestsCaseValidation +TestsParamInInputs +ValidDatatypes diff --git a/tools/sed/.lint_skip b/tools/sed/.lint_skip new file mode 100644 index 0000000000..99c412df31 --- /dev/null +++ b/tools/sed/.lint_skip @@ -0,0 +1,6 @@ +CitationsMissing +OutputsFormatInput +TestsMissing +ValidDatatypes +XMLOrder +XSD diff --git a/tools/segemehl/.lint_skip b/tools/segemehl/.lint_skip new file mode 100644 index 0000000000..ccee25d931 --- /dev/null +++ b/tools/segemehl/.lint_skip @@ -0,0 +1,3 @@ +TestsCaseValidation +TestsExpectNumOutputs +TestsParamInInputs diff --git a/tools/sklearn/.lint_skip b/tools/sklearn/.lint_skip new file mode 100644 index 0000000000..760a7d14d8 --- /dev/null +++ b/tools/sklearn/.lint_skip @@ -0,0 +1,4 @@ +OutputsLabelDuplicatedFilter +TestsCaseValidation +TestsExpectNumOutputs +TestsParamInInputs diff --git a/tools/splitfasta/.lint_skip b/tools/splitfasta/.lint_skip new file mode 100644 index 0000000000..2092d1d0d6 --- /dev/null +++ b/tools/splitfasta/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/statistics/.lint_skip b/tools/statistics/.lint_skip new file mode 100644 index 0000000000..a1dfd5c897 --- /dev/null +++ b/tools/statistics/.lint_skip @@ -0,0 +1,3 @@ +CitationsMissing +InputsNameDuplicate +TestsCaseValidation diff --git a/tools/stress_ng/.lint_skip b/tools/stress_ng/.lint_skip new file mode 100644 index 0000000000..626940c397 --- /dev/null +++ b/tools/stress_ng/.lint_skip @@ -0,0 +1,3 @@ +CitationsMissing +TestsCaseValidation +TestsParamInInputs diff --git a/tools/text_processing/add_line_to_file/.lint_skip b/tools/text_processing/add_line_to_file/.lint_skip new file mode 100644 index 0000000000..f98c941cb6 --- /dev/null +++ b/tools/text_processing/add_line_to_file/.lint_skip @@ -0,0 +1 @@ +CitationsNoValid diff --git a/tools/text_processing/column_arrange_by_header/.lint_skip b/tools/text_processing/column_arrange_by_header/.lint_skip new file mode 100644 index 0000000000..1c8564f34b --- /dev/null +++ b/tools/text_processing/column_arrange_by_header/.lint_skip @@ -0,0 +1 @@ +CommandInterpreterDeprecated diff --git a/tools/text_processing/join_files_on_column_fuzzy/.lint_skip b/tools/text_processing/join_files_on_column_fuzzy/.lint_skip new file mode 100644 index 0000000000..4a005be6b5 --- /dev/null +++ b/tools/text_processing/join_files_on_column_fuzzy/.lint_skip @@ -0,0 +1,3 @@ +CitationsNoValid +TestsCaseValidation +TestsParamInInputs diff --git a/tools/text_processing/split_file_to_collection/.lint_skip b/tools/text_processing/split_file_to_collection/.lint_skip new file mode 100644 index 0000000000..2092d1d0d6 --- /dev/null +++ b/tools/text_processing/split_file_to_collection/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/text_processing/text_processing/.lint_skip b/tools/text_processing/text_processing/.lint_skip new file mode 100644 index 0000000000..4835fb975a --- /dev/null +++ b/tools/text_processing/text_processing/.lint_skip @@ -0,0 +1,2 @@ +OutputsFilterExpression +TestsCaseValidation diff --git a/tools/tgsgapcloser/.lint_skip b/tools/tgsgapcloser/.lint_skip new file mode 100644 index 0000000000..1f78d73fa8 --- /dev/null +++ b/tools/tgsgapcloser/.lint_skip @@ -0,0 +1,2 @@ +TestsCaseValidation +XMLOrder diff --git a/tools/tiara/.lint_skip b/tools/tiara/.lint_skip new file mode 100644 index 0000000000..273da24a36 --- /dev/null +++ b/tools/tiara/.lint_skip @@ -0,0 +1 @@ +XSD diff --git a/tools/tool_recommendation_model/.lint_skip b/tools/tool_recommendation_model/.lint_skip new file mode 100644 index 0000000000..2092d1d0d6 --- /dev/null +++ b/tools/tool_recommendation_model/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/trim_galore/.lint_skip b/tools/trim_galore/.lint_skip new file mode 100644 index 0000000000..1f78d73fa8 --- /dev/null +++ b/tools/trim_galore/.lint_skip @@ -0,0 +1,2 @@ +TestsCaseValidation +XMLOrder diff --git a/tools/uniprot_rest_interface/.lint_skip b/tools/uniprot_rest_interface/.lint_skip new file mode 100644 index 0000000000..2092d1d0d6 --- /dev/null +++ b/tools/uniprot_rest_interface/.lint_skip @@ -0,0 +1 @@ +TestsCaseValidation diff --git a/tools/vt/.lint_skip b/tools/vt/.lint_skip new file mode 100644 index 0000000000..8b79cd50f6 --- /dev/null +++ b/tools/vt/.lint_skip @@ -0,0 +1,2 @@ +TestsCaseValidation +XSD diff --git a/tools/wtdbg/.lint_skip b/tools/wtdbg/.lint_skip new file mode 100644 index 0000000000..c85c54905b --- /dev/null +++ b/tools/wtdbg/.lint_skip @@ -0,0 +1,3 @@ +TestsCaseValidation +TestsParamInInputs +XMLOrder