Merge pull request #424 from deeptools/develop

Release 3.8

README.md

@@ -70,15 +70,15 @@ Then activate the environment and install pygenometracks with mamba:
 
 ```bash
 conda activate pygenometracks
-mamba install -c bioconda -c conda-forge pygenometracks
+mamba install -c conda-forge -c bioconda pygenometracks
 ```
 
 or if you want a specific version:
 
 ```bash
 conda create -n pygenometracks -c bioconda -c conda-forge mamba python=3.7
 conda activate pygenometracks
-mamba install -c bioconda -c conda-forge pygenometracks=3.5
+mamba install -c conda-forge -c bioconda pygenometracks=3.5
 ```
 
 Also, pyGenomeTracks can be installed using pip

azure-pipelines.yml

@@ -18,7 +18,7 @@ stages:
           python -m pip install --user --upgrade flake8
         displayName: install flake8
       - script:
-          flake8 . --exclude=.venv,.build,build --ignore=E501,F403,E402,F999,F405,E712,W503,E275
+          flake8 . --exclude=.venv,.build,build --ignore=E501,F403,E402,F999,F405,E712,W503
         displayName: linting
 - stage: test
   dependsOn: [lint]
@@ -35,16 +35,16 @@ stages:
             matplotlib.version: '3.1.1'
           Python37HighMatplotlib:
             python.version: '3.7'
-            matplotlib.version: '3.5.1'
+            matplotlib.version: '3.5.3'
           Python38LowMatplotlib:
             python.version: '3.8'
             matplotlib.version: '3.1.1'
           Python38HighMatplotlib:
             python.version: '3.8'
-            matplotlib.version: '3.5.1'
+            matplotlib.version: '3.6.2'
           Python39HighMatplotlib:
             python.version: '3.9'
-            matplotlib.version: '3.5.1'
+            matplotlib.version: '3.6.2'
 
       steps:
       - bash: |

docs/content/all_default_properties.csv

@@ -1,73 +1,74 @@
-parameter,x_axis,epilogos,links,domains,bed,gtf,narrow_peak,bigwig,bedgraph,bedgraph_matrix,hlines,hic_matrix,hic_matrix_square,maf,scalebar
-overlay_previous,no,no,no,no,no,no,no,no,no,no,no,no,no,no,no
-where,bottom,,,,,,,,,,,,,,left
-fontsize,15,,,,12,12,,,,,,,,,12
-categories_file,,not set,,,,,,,,,,,,,
-orientation,,not set,not set,not set,not set,not set,not set,not set,not set,not set,not set,not set,not set,not set,
-links_type,,,arcs,,,,,,,,,,,,
-line_width,,,not set,0.5,0.5,0.5,1,,,,0.5,,,0.5,0.5
-line_style,,,solid,,,,,,,,solid,,,,
-color,,,blue,#1f78b4,#1f78b4,#1f78b4,#FF000080,#33a02c,#a6cee3,,black,,,,black
-alpha,,,0.8,,,,,1,1,,1,,,,1
-max_value,,,not set,not set,not set,,not set,not set,not set,not set,not set,not set,not set,,
-min_value,,,not set,not set,not set,,,not set,not set,not set,not set,not set,not set,,
-ylim,,,not set,,,,,,,,,,,,
-compact_arcs_level,,,0,,,,,,,,,,,,
-use_middle,,,false,,,,,,false,,,,,,
-region2,,,not set,,,,,,,,,,not set,,
-border_color,,,,black,black,black,,,,,,,,,
-prefered_name,,,,transcript_name,transcript_name,transcript_name,,,,,,,,,
-merge_transcripts,,,,false,false,false,,,,,,,,,
-labels,,,,,true,true,,,,,,,,,
-style,,,,,flybase,flybase,,,,,,,,,
-display,,,,,stacked,stacked,,,,,,,,,
-max_labels,,,,,60,60,,,,,,,,,
-merge_overlapping_exons,,,,,false,false,,,,,,,,,
-global_max_row,,,,,false,false,,,,,,,,,
-gene_rows,,,,,not set,not set,,,,,,,,,
-arrow_interval,,,,,2,2,,,,,,,,,
-arrowhead_included,,,,,false,false,,,,,,,,,
-arrowhead_fraction,,,,,0.004,0.004,,,,,,,,,
-color_utr,,,,,grey,grey,,,,,,,,,
-color_backbone,,,,,black,black,,,,,,,,,
-height_utr,,,,,1,1,,,,,,,,,
-arrow_length,,,,,not set,not set,,,,,,,,,
-all_labels_inside,,,,,false,false,,,,,,,,,
-labels_in_margin,,,,,false,false,,,,,,,,,
-fontstyle,,,,,normal,normal,,,,,,,,,
-show_data_range,,,,,,,true,true,true,true,true,,,,
-show_labels,,,,,,,true,,,,,,,,
-use_summit,,,,,,,true,,,,,,,,
-width_adjust,,,,,,,1.5,,,,,,,,
-type,,,,,,,peak,fill,fill,matrix,,,,,
-negative_color,,,,,,,,not set,not set,,,,,,
-nans_to_zeros,,,,,,,,false,false,,,,,,
-summary_method,,,,,,,,mean,not set,,,,,,
-number_of_bins,,,,,,,,700,700,,,,,,
-transform,,,,,,,,no,no,,,no,no,,
-log_pseudocount,,,,,,,,0,0,,,,,,
-y_axis_values,,,,,,,,transformed,transformed,,,,,,
-second_file*,,,,,,,,not set,not set,,,,,,
-operation*,,,,,,,,file,file,,,,,,
-grid,,,,,,,,false,false,,,,,,
-rasterize,,,,,,,,,false,true,,true,true,,
-pos_score_in_bin,,,,,,,,,,center,,,,,
-plot_horizontal_lines,,,,,,,,,,false,,,,,
-colormap,,,,,,,,,,viridis,,RdYlBu_r,RdYlBu_r,,
-individual_color,,,,,,,,,,grey,,,,,
-summary_color,,,,,,,,,,#1f77b4,,,,,
-depth,,,,,,,,,,,,100000,,,
-show_masked_bins,,,,,,,,,,,,false,false,,
-scale_factor,,,,,,,,,,,,1,1,,
-file_index,,,,,,,,,,,,,,not set,
-color_identical,,,,,,,,,,,,,,black,
-color_mismatch,,,,,,,,,,,,,,grey,
-color_gap,,,,,,,,,,,,,,lightgrey,
-species_order,,,,,,,,,,,,,,not set,
-species_labels,,,,,,,,,,,,,,not set,
-species_order_only,,,,,,,,,,,,,,false,
-display_ref_seq,,,,,,,,,,,,,,false,
-x_center,,,,,,,,,,,,,,,not set
-size,,,,,,,,,,,,,,,not set
-scalebar_start_position,,,,,,,,,,,,,,,not set
-scalebar_end_position,,,,,,,,,,,,,,,not set
+parameter,x_axis,epilogos,links,domains,bed,gtf,narrow_peak,bigwig,bedgraph,bedgraph_matrix,hlines,hic_matrix,hic_matrix_square,maf,scalebar,vlines,vhighlight
+overlay_previous,no,no,no,no,no,no,no,no,no,no,no,no,no,no,no,,
+where,bottom,,,,,,,,,,,,,,left,,
+fontsize,15,,,,12,12,,,,,,,,,12,,
+categories_file,,not set,,,,,,,,,,,,,,,
+orientation,,not set,not set,not set,not set,not set,not set,not set,not set,not set,not set,not set,not set,not set,,,
+links_type,,,arcs,,,,,,,,,,,,,,
+line_width,,,not set,0.5,0.5,0.5,1,,,,0.5,,,0.5,0.5,0.5,0.5
+line_style,,,solid,,,,,,,,solid,,,,,dashed,
+color,,,blue,#1f78b4,#1f78b4,#1f78b4,#FF000080,#33a02c,#a6cee3,,black,,,,black,black,yellow
+alpha,,,0.8,,,,,1,1,,1,,,,1,0.7,0.5
+max_value,,,not set,not set,not set,,not set,not set,not set,not set,not set,not set,not set,,,,
+min_value,,,not set,not set,not set,,,not set,not set,not set,not set,not set,not set,,,,
+ylim,,,not set,,,,,,,,,,,,,,
+compact_arcs_level,,,0,,,,,,,,,,,,,,
+use_middle,,,false,,,,,,false,,,,,,,,
+region2,,,not set,,,,,,,,,,not set,,,,
+border_color,,,,black,black,black,,,,,,,,,,,none
+prefered_name,,,,transcript_name,transcript_name,transcript_name,,,,,,,,,,,
+merge_transcripts,,,,false,false,false,,,,,,,,,,,
+labels,,,,,true,true,,,,,,,,,,,
+style,,,,,flybase,flybase,,,,,,,,,,,
+display,,,,,stacked,stacked,,,,,,,,,,,
+max_labels,,,,,60,60,,,,,,,,,,,
+merge_overlapping_exons,,,,,false,false,,,,,,,,,,,
+global_max_row,,,,,false,false,,,,,,,,,,,
+gene_rows,,,,,not set,not set,,,,,,,,,,,
+arrow_interval,,,,,2,2,,,,,,,,,,,
+arrowhead_included,,,,,false,false,,,,,,,,,,,
+arrowhead_fraction,,,,,0.004,0.004,,,,,,,,,,,
+color_utr,,,,,grey,grey,,,,,,,,,,,
+color_backbone,,,,,black,black,,,,,,,,,,,
+height_utr,,,,,1,1,,,,,,,,,,,
+arrow_length,,,,,not set,not set,,,,,,,,,,,
+all_labels_inside,,,,,false,false,,,,,,,,,,,
+labels_in_margin,,,,,false,false,,,,,,,,,,,
+fontstyle,,,,,normal,normal,,,,,,,,,,,
+show_data_range,,,,,,,true,true,true,true,true,,,,,,
+show_labels,,,,,,,true,,,,,,,,,,
+use_summit,,,,,,,true,,,,,,,,,,
+width_adjust,,,,,,,1.5,,,,,,,,,,
+type,,,,,,,peak,fill,fill,matrix,,,,,,,
+negative_color,,,,,,,,not set,not set,,,,,,,,
+nans_to_zeros,,,,,,,,false,false,,,,,,,,
+summary_method,,,,,,,,mean,not set,,,,,,,,
+number_of_bins,,,,,,,,700,700,,,,,,,,
+transform,,,,,,,,no,no,,,no,no,,,,
+log_pseudocount,,,,,,,,0,0,,,,,,,,
+y_axis_values,,,,,,,,transformed,transformed,,,,,,,,
+second_file*,,,,,,,,not set,not set,,,,,,,,
+operation*,,,,,,,,file,file,,,,,,,,
+grid,,,,,,,,false,false,,,,,,,,
+rasterize,,,,,,,,,false,true,,true,true,,,,
+pos_score_in_bin,,,,,,,,,,center,,,,,,,
+plot_horizontal_lines,,,,,,,,,,false,,,,,,,
+colormap,,,,,,,,,,viridis,,RdYlBu_r,RdYlBu_r,,,,
+individual_color,,,,,,,,,,grey,,,,,,,
+summary_color,,,,,,,,,,#1f77b4,,,,,,,
+depth,,,,,,,,,,,,100000,,,,,
+show_masked_bins,,,,,,,,,,,,false,false,,,,
+scale_factor,,,,,,,,,,,,1,1,,,,
+file_index,,,,,,,,,,,,,,not set,,,
+color_identical,,,,,,,,,,,,,,black,,,
+color_mismatch,,,,,,,,,,,,,,grey,,,
+color_gap,,,,,,,,,,,,,,lightgrey,,,
+species_order,,,,,,,,,,,,,,not set,,,
+species_labels,,,,,,,,,,,,,,not set,,,
+species_order_only,,,,,,,,,,,,,,false,,,
+display_ref_seq,,,,,,,,,,,,,,false,,,
+x_center,,,,,,,,,,,,,,,not set,,
+size,,,,,,,,,,,,,,,not set,,
+scalebar_start_position,,,,,,,,,,,,,,,not set,,
+scalebar_end_position,,,,,,,,,,,,,,,not set,,
+zorder,,,,,,,,,,,,,,,,10,-100