diff --git a/MANIFEST b/MANIFEST index 3526d3255..7bcf7db43 100644 --- a/MANIFEST +++ b/MANIFEST @@ -1,4 +1,4 @@ -ac.bds.bps +.cirrus_disabled.yml bin/Biodiverse_icon.ico bin/BiodiverseGUI.pl bin/load_and_randomise.pl @@ -37,6 +37,7 @@ biodiverse.iml Biodiverse_extensions.txt BiodiverseGUI.bat cpanfile +csvcheck.pl data/coastline_lamberts.dbf data/coastline_lamberts.prj data/coastline_lamberts.sbn @@ -83,6 +84,7 @@ example_scripts/run_many_clusters_and_export_to_nexus.pl example_scripts/run_num_labels.pl example_scripts/use_label_ranges_as_spatial_conditions.pl extent_test.tif +goocanvas2_test.pl Installation.txt lib/App/Biodiverse.pm lib/Biodiverse/BaseData.pm @@ -94,6 +96,7 @@ lib/Biodiverse/BaseStruct/Export.pm lib/Biodiverse/Cluster.pm lib/Biodiverse/Common.pm lib/Biodiverse/Config.pm +lib/Biodiverse/Config/PARModules.pm lib/Biodiverse/ElementProperties.pm lib/Biodiverse/Exception.pm lib/Biodiverse/GUI/BasedataImport.pm @@ -259,6 +262,9 @@ t/AED_data.xlsx t/data/años.txt t/data/años_mx.txt t/data/años_mx_sparse.txt +t/data/años.txt +t/data/años_mx.txt +t/data/años_mx_sparse.txt 't/data/polygon data.CPG' 't/data/polygon data.dbf' 't/data/polygon data.prj' @@ -291,6 +297,11 @@ t/data/polygon_data_single_partx.shx 't/data/polyline data.shx' t/data/rast_nodata_is_nan.tfw t/data/rast_nodata_is_nan.tif +t/data/test_spreadsheet_import.ods +t/data/test_spreadsheet_import.xls +t/data/test_spreadsheet_import.xlsx +t/data/test_spreadsheet_import_dms_coords.xlsx +t/data/test_spreadsheet_import_matrix_form.xlsx t/dms_latlon.dbf t/dms_latlon.shp t/dms_latlon.shx @@ -314,11 +325,6 @@ t/ex_rasters/example_small.bds t/lib/Biodiverse/TestHelpers.pm t/lib/Utils.pm t/README.txt -t/test_spreadsheet_import.ods -t/test_spreadsheet_import.xls -t/test_spreadsheet_import.xlsx -t/test_spreadsheet_import_dms_coords.xlsx -t/test_spreadsheet_import_matrix_form.xlsx xt/.perlcritic-history xt/00-roundtrip-self-referential-structure.t xt/01-has-versions.t diff --git a/MANIFEST.bak b/MANIFEST.bak index 9365a88c4..df9ea2693 100644 --- a/MANIFEST.bak +++ b/MANIFEST.bak @@ -1,3 +1,4 @@ +.cirrus_disabled.yml bin/Biodiverse_icon.ico bin/BiodiverseGUI.pl bin/load_and_randomise.pl @@ -32,9 +33,11 @@ bin/ui/vboxRandomisePage.ui bin/ui/wndCellPopup.ui bin/ui/wndMain.ui bin/ui/wndOverlays.ui +biodiverse.iml Biodiverse_extensions.txt BiodiverseGUI.bat cpanfile +csvcheck.pl data/coastline_lamberts.dbf data/coastline_lamberts.prj data/coastline_lamberts.sbn @@ -90,6 +93,7 @@ lib/Biodiverse/BaseStruct/Export.pm lib/Biodiverse/Cluster.pm lib/Biodiverse/Common.pm lib/Biodiverse/Config.pm +lib/Biodiverse/Config/PARModules.pm lib/Biodiverse/ElementProperties.pm lib/Biodiverse/Exception.pm lib/Biodiverse/GUI/BasedataImport.pm @@ -177,66 +181,66 @@ lib/BiodiverseX/Indices/IEI.pm lib/BiodiverseX/Indices/Phylogenetic.pm LICENSE Makefile.PL -MANIFEST This list of files +MANIFEST MANIFEST.SKIP README.md +run_yath.sh t/00-load.t -t/01-clone_save_reload.t -t/01-csv_guesswork.t +t/01-clone-save-reload.t +t/01-csv-guesswork.t t/02-unicode-file-names.t t/10-ElementProperties.t +t/11-BaseData-exclusions.t +t/11-BaseData-group-props-from-raster.t t/11-BaseData-import-feature-data.t t/11-BaseData-import-spreadsheet.t t/11-BaseData-reintegrate-after-rand.t +t/11-BaseData-reorder-axes.t t/11-BaseData.t -t/11-BaseData_exclusions.t -t/11-BaseData_group_props_from_raster.t -t/11-BaseData_reorder_axes.t t/12-BaseStruct-export.t t/12-BaseStruct.t t/13-BootstrapBlock.t t/13-Tree.t -t/20-Biodiverse_Statistics-descr.t -t/20-Biodiverse_Statistics.t +t/20-Biodiverse-Statistics-descr.t +t/20-Biodiverse-Statistics.t t/21-ReadNexus.t +t/22-SpatialConditions-block-select.t +t/22-SpatialConditions-main.t +t/22-SpatialConditions-metadata.t +t/22-SpatialConditions-rectangle.t +t/22-SpatialConditions-side-in-line.t +t/22-SpatialConditions-side-left.t +t/22-SpatialConditions-side-right.t +t/22-SpatialConditions-sp-output-list-value.t +t/22-SpatialConditions-sp-points-in-clusters.t t/22-SpatialConditions2.t t/22-SpatialConditions3.t t/22-SpatialConditions4.t t/22-SpatialConditions5.t -t/22-SpatialConditions_block_select.t -t/22-SpatialConditions_main.t -t/22-SpatialConditions_metadata.t -t/22-SpatialConditions_rectangle.t -t/22-SpatialConditions_side_in_line.t -t/22-SpatialConditions_side_left.t -t/22-SpatialConditions_side_right.t -t/22-SpatialConditions_sp_output_list_value.t -t/22-SpatialConditions_sp_points_in_clusters.t t/23-Indices.t -t/24-Indices_element-properties-group.t -t/24-Indices_element-properties-label.t -t/24-Indices_element-properties-label_gistar_range_wtd.t -t/24-Indices_endemism.t -t/24-Indices_hierarchical-labels.t -t/24-Indices_inter-event-interval-statistics.t -t/24-Indices_lists-and-counts.t -t/24-Indices_lists_and_counts_rank_relative_abundances.t -t/24-Indices_matrix.t -t/24-Indices_numeric-labels.t -t/24-Indices_phylocom.results -t/24-Indices_phylocom.t -t/24-Indices_phylocom_nri_nti.t -t/24-Indices_phylogenetic-pd-endemism.t -t/24-Indices_phylogenetic.t -t/24-Indices_phylogenetic_local_PD.t -t/24-Indices_phylogenetic_relative.t -t/24-Indices_phylogenetic_turnover.t -t/24-Indices_rarity.t -t/24-Indices_richness_estimators.t -t/24-Indices_RW_turnover.t -t/24-Indices_taxonomic-dissimilarity-and-comparison.t -t/24-Indices_taxonomic_distinctness.t -t/24-Indices_turnover_with_empty_groups.t +t/24-Indices-element-properties-group.t +t/24-Indices-element-properties-label-gistar-range-wtd.t +t/24-Indices-element-properties-label.t +t/24-Indices-endemism.t +t/24-Indices-hierarchical-labels.t +t/24-Indices-inter-event-interval-statistics.t +t/24-Indices-lists-and-counts-rank-relative-abundances.t +t/24-Indices-lists-and-counts.t +t/24-Indices-matrix.t +t/24-Indices-numeric-labels.t +t/24-Indices-phylocom-nri-nti.t +t/24-Indices-phylocom.t +t/24-Indices-phylogenetic-local-PD.t +t/24-Indices-phylogenetic-pd-endemism.t +t/24-Indices-phylogenetic-relative.t +t/24-Indices-phylogenetic-turnover.t +t/24-Indices-phylogenetic.t +t/24-Indices-rarity.t +t/24-Indices-richness-estimators.t +t/24-Indices-RW-turnover.t +t/24-Indices-taxonomic-dissimilarity-and-comparison.t +t/24-Indices-taxonomic-distinctness.t +t/24-Indices-turnover-with-empty-groups.t t/25-Matrix.t t/26-Cluster.t t/26-Cluster2.t @@ -244,6 +248,7 @@ t/26-RegionGrower.t t/27-Spatial.t t/28-Randomisation.t t/28-Randomisation2.t +t/29-CANAPE.t t/30-Progress.t t/31-Remap.t t/31-RemapGuesser.t @@ -251,6 +256,9 @@ t/aed.bps t/aed.nwk t/AED_data.csv t/AED_data.xlsx +t/data/años.txt +t/data/años_mx.txt +t/data/años_mx_sparse.txt t/data/años.txt t/data/años_mx.txt t/data/años_mx_sparse.txt @@ -284,6 +292,13 @@ t/data/polygon_data_single_partx.shx 't/data/polyline data.shp' 't/data/polyline data.shp.xml' 't/data/polyline data.shx' +t/data/rast_nodata_is_nan.tfw +t/data/rast_nodata_is_nan.tif +t/data/test_spreadsheet_import.ods +t/data/test_spreadsheet_import.xls +t/data/test_spreadsheet_import.xlsx +t/data/test_spreadsheet_import_dms_coords.xlsx +t/data/test_spreadsheet_import_matrix_form.xlsx t/dms_latlon.dbf t/dms_latlon.shp t/dms_latlon.shx @@ -307,20 +322,15 @@ t/ex_rasters/example_small.bds t/lib/Biodiverse/TestHelpers.pm t/lib/Utils.pm t/README.txt -t/test_spreadsheet_import.ods -t/test_spreadsheet_import.xls -t/test_spreadsheet_import.xlsx -t/test_spreadsheet_import_dms_coords.xlsx -t/test_spreadsheet_import_matrix_form.xlsx xt/.perlcritic-history -xt/00-roundtrip_self_referential_structure.t -xt/01-has_versions.t -xt/02-versions_all_same.t -xt/03-has_pod.t +xt/00-roundtrip-self-referential-structure.t +xt/01-has-versions.t +xt/02-versions-all-same.t +xt/03-has-pod.t xt/04-pod-coverage.t xt/05-manifest.t xt/06-critic.t xt/07-notabs.t -xt/09-use_strict.t -xt/changes_format.t +xt/09-use-strict.t +xt/changes-format.t xt/README.txt diff --git a/xt/05-manifest.t b/xt/05-manifest.t index dcd352038..f113ff72b 100644 --- a/xt/05-manifest.t +++ b/xt/05-manifest.t @@ -3,9 +3,11 @@ use warnings; use Test::CheckManifest; use Test::More; -plan skip_all => q{We don't have a manufest yet, and need to move the gtk stuff out of the way or add to the ignore list}; +# plan skip_all => q{We don't have a manifest yet, and need to move the gtk stuff out of the way or add to the ignore list}; TODO: { - local $TODO = q{We don't have a manufest yet, and need to move the gtk stuff out of the way or add to the ignore list}; + local $TODO = q{Manifest test does not handle unicode file names on Windows}; ok_manifest(); }; + +done_testing(); \ No newline at end of file