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Merge pull request #424 from deeptools/develop
Release 3.8
2 parents 2085e04 + 9115792 commit b8918d4

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‎README.md

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

‎azure-pipelines.yml

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

‎docs/content/all_default_properties.csv

Lines changed: 74 additions & 73 deletions
Original file line numberDiff line numberDiff line change
@@ -1,73 +1,74 @@
1-
parameter,x_axis,epilogos,links,domains,bed,gtf,narrow_peak,bigwig,bedgraph,bedgraph_matrix,hlines,hic_matrix,hic_matrix_square,maf,scalebar
2-
overlay_previous,no,no,no,no,no,no,no,no,no,no,no,no,no,no,no
3-
where,bottom,,,,,,,,,,,,,,left
4-
fontsize,15,,,,12,12,,,,,,,,,12
5-
categories_file,,not set,,,,,,,,,,,,,
6-
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,
7-
links_type,,,arcs,,,,,,,,,,,,
8-
line_width,,,not set,0.5,0.5,0.5,1,,,,0.5,,,0.5,0.5
9-
line_style,,,solid,,,,,,,,solid,,,,
10-
color,,,blue,#1f78b4,#1f78b4,#1f78b4,#FF000080,#33a02c,#a6cee3,,black,,,,black
11-
alpha,,,0.8,,,,,1,1,,1,,,,1
12-
max_value,,,not set,not set,not set,,not set,not set,not set,not set,not set,not set,not set,,
13-
min_value,,,not set,not set,not set,,,not set,not set,not set,not set,not set,not set,,
14-
ylim,,,not set,,,,,,,,,,,,
15-
compact_arcs_level,,,0,,,,,,,,,,,,
16-
use_middle,,,false,,,,,,false,,,,,,
17-
region2,,,not set,,,,,,,,,,not set,,
18-
border_color,,,,black,black,black,,,,,,,,,
19-
prefered_name,,,,transcript_name,transcript_name,transcript_name,,,,,,,,,
20-
merge_transcripts,,,,false,false,false,,,,,,,,,
21-
labels,,,,,true,true,,,,,,,,,
22-
style,,,,,flybase,flybase,,,,,,,,,
23-
display,,,,,stacked,stacked,,,,,,,,,
24-
max_labels,,,,,60,60,,,,,,,,,
25-
merge_overlapping_exons,,,,,false,false,,,,,,,,,
26-
global_max_row,,,,,false,false,,,,,,,,,
27-
gene_rows,,,,,not set,not set,,,,,,,,,
28-
arrow_interval,,,,,2,2,,,,,,,,,
29-
arrowhead_included,,,,,false,false,,,,,,,,,
30-
arrowhead_fraction,,,,,0.004,0.004,,,,,,,,,
31-
color_utr,,,,,grey,grey,,,,,,,,,
32-
color_backbone,,,,,black,black,,,,,,,,,
33-
height_utr,,,,,1,1,,,,,,,,,
34-
arrow_length,,,,,not set,not set,,,,,,,,,
35-
all_labels_inside,,,,,false,false,,,,,,,,,
36-
labels_in_margin,,,,,false,false,,,,,,,,,
37-
fontstyle,,,,,normal,normal,,,,,,,,,
38-
show_data_range,,,,,,,true,true,true,true,true,,,,
39-
show_labels,,,,,,,true,,,,,,,,
40-
use_summit,,,,,,,true,,,,,,,,
41-
width_adjust,,,,,,,1.5,,,,,,,,
42-
type,,,,,,,peak,fill,fill,matrix,,,,,
43-
negative_color,,,,,,,,not set,not set,,,,,,
44-
nans_to_zeros,,,,,,,,false,false,,,,,,
45-
summary_method,,,,,,,,mean,not set,,,,,,
46-
number_of_bins,,,,,,,,700,700,,,,,,
47-
transform,,,,,,,,no,no,,,no,no,,
48-
log_pseudocount,,,,,,,,0,0,,,,,,
49-
y_axis_values,,,,,,,,transformed,transformed,,,,,,
50-
second_file*,,,,,,,,not set,not set,,,,,,
51-
operation*,,,,,,,,file,file,,,,,,
52-
grid,,,,,,,,false,false,,,,,,
53-
rasterize,,,,,,,,,false,true,,true,true,,
54-
pos_score_in_bin,,,,,,,,,,center,,,,,
55-
plot_horizontal_lines,,,,,,,,,,false,,,,,
56-
colormap,,,,,,,,,,viridis,,RdYlBu_r,RdYlBu_r,,
57-
individual_color,,,,,,,,,,grey,,,,,
58-
summary_color,,,,,,,,,,#1f77b4,,,,,
59-
depth,,,,,,,,,,,,100000,,,
60-
show_masked_bins,,,,,,,,,,,,false,false,,
61-
scale_factor,,,,,,,,,,,,1,1,,
62-
file_index,,,,,,,,,,,,,,not set,
63-
color_identical,,,,,,,,,,,,,,black,
64-
color_mismatch,,,,,,,,,,,,,,grey,
65-
color_gap,,,,,,,,,,,,,,lightgrey,
66-
species_order,,,,,,,,,,,,,,not set,
67-
species_labels,,,,,,,,,,,,,,not set,
68-
species_order_only,,,,,,,,,,,,,,false,
69-
display_ref_seq,,,,,,,,,,,,,,false,
70-
x_center,,,,,,,,,,,,,,,not set
71-
size,,,,,,,,,,,,,,,not set
72-
scalebar_start_position,,,,,,,,,,,,,,,not set
73-
scalebar_end_position,,,,,,,,,,,,,,,not set
1+
parameter,x_axis,epilogos,links,domains,bed,gtf,narrow_peak,bigwig,bedgraph,bedgraph_matrix,hlines,hic_matrix,hic_matrix_square,maf,scalebar,vlines,vhighlight
2+
overlay_previous,no,no,no,no,no,no,no,no,no,no,no,no,no,no,no,,
3+
where,bottom,,,,,,,,,,,,,,left,,
4+
fontsize,15,,,,12,12,,,,,,,,,12,,
5+
categories_file,,not set,,,,,,,,,,,,,,,
6+
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,,,
7+
links_type,,,arcs,,,,,,,,,,,,,,
8+
line_width,,,not set,0.5,0.5,0.5,1,,,,0.5,,,0.5,0.5,0.5,0.5
9+
line_style,,,solid,,,,,,,,solid,,,,,dashed,
10+
color,,,blue,#1f78b4,#1f78b4,#1f78b4,#FF000080,#33a02c,#a6cee3,,black,,,,black,black,yellow
11+
alpha,,,0.8,,,,,1,1,,1,,,,1,0.7,0.5
12+
max_value,,,not set,not set,not set,,not set,not set,not set,not set,not set,not set,not set,,,,
13+
min_value,,,not set,not set,not set,,,not set,not set,not set,not set,not set,not set,,,,
14+
ylim,,,not set,,,,,,,,,,,,,,
15+
compact_arcs_level,,,0,,,,,,,,,,,,,,
16+
use_middle,,,false,,,,,,false,,,,,,,,
17+
region2,,,not set,,,,,,,,,,not set,,,,
18+
border_color,,,,black,black,black,,,,,,,,,,,none
19+
prefered_name,,,,transcript_name,transcript_name,transcript_name,,,,,,,,,,,
20+
merge_transcripts,,,,false,false,false,,,,,,,,,,,
21+
labels,,,,,true,true,,,,,,,,,,,
22+
style,,,,,flybase,flybase,,,,,,,,,,,
23+
display,,,,,stacked,stacked,,,,,,,,,,,
24+
max_labels,,,,,60,60,,,,,,,,,,,
25+
merge_overlapping_exons,,,,,false,false,,,,,,,,,,,
26+
global_max_row,,,,,false,false,,,,,,,,,,,
27+
gene_rows,,,,,not set,not set,,,,,,,,,,,
28+
arrow_interval,,,,,2,2,,,,,,,,,,,
29+
arrowhead_included,,,,,false,false,,,,,,,,,,,
30+
arrowhead_fraction,,,,,0.004,0.004,,,,,,,,,,,
31+
color_utr,,,,,grey,grey,,,,,,,,,,,
32+
color_backbone,,,,,black,black,,,,,,,,,,,
33+
height_utr,,,,,1,1,,,,,,,,,,,
34+
arrow_length,,,,,not set,not set,,,,,,,,,,,
35+
all_labels_inside,,,,,false,false,,,,,,,,,,,
36+
labels_in_margin,,,,,false,false,,,,,,,,,,,
37+
fontstyle,,,,,normal,normal,,,,,,,,,,,
38+
show_data_range,,,,,,,true,true,true,true,true,,,,,,
39+
show_labels,,,,,,,true,,,,,,,,,,
40+
use_summit,,,,,,,true,,,,,,,,,,
41+
width_adjust,,,,,,,1.5,,,,,,,,,,
42+
type,,,,,,,peak,fill,fill,matrix,,,,,,,
43+
negative_color,,,,,,,,not set,not set,,,,,,,,
44+
nans_to_zeros,,,,,,,,false,false,,,,,,,,
45+
summary_method,,,,,,,,mean,not set,,,,,,,,
46+
number_of_bins,,,,,,,,700,700,,,,,,,,
47+
transform,,,,,,,,no,no,,,no,no,,,,
48+
log_pseudocount,,,,,,,,0,0,,,,,,,,
49+
y_axis_values,,,,,,,,transformed,transformed,,,,,,,,
50+
second_file*,,,,,,,,not set,not set,,,,,,,,
51+
operation*,,,,,,,,file,file,,,,,,,,
52+
grid,,,,,,,,false,false,,,,,,,,
53+
rasterize,,,,,,,,,false,true,,true,true,,,,
54+
pos_score_in_bin,,,,,,,,,,center,,,,,,,
55+
plot_horizontal_lines,,,,,,,,,,false,,,,,,,
56+
colormap,,,,,,,,,,viridis,,RdYlBu_r,RdYlBu_r,,,,
57+
individual_color,,,,,,,,,,grey,,,,,,,
58+
summary_color,,,,,,,,,,#1f77b4,,,,,,,
59+
depth,,,,,,,,,,,,100000,,,,,
60+
show_masked_bins,,,,,,,,,,,,false,false,,,,
61+
scale_factor,,,,,,,,,,,,1,1,,,,
62+
file_index,,,,,,,,,,,,,,not set,,,
63+
color_identical,,,,,,,,,,,,,,black,,,
64+
color_mismatch,,,,,,,,,,,,,,grey,,,
65+
color_gap,,,,,,,,,,,,,,lightgrey,,,
66+
species_order,,,,,,,,,,,,,,not set,,,
67+
species_labels,,,,,,,,,,,,,,not set,,,
68+
species_order_only,,,,,,,,,,,,,,false,,,
69+
display_ref_seq,,,,,,,,,,,,,,false,,,
70+
x_center,,,,,,,,,,,,,,,not set,,
71+
size,,,,,,,,,,,,,,,not set,,
72+
scalebar_start_position,,,,,,,,,,,,,,,not set,,
73+
scalebar_end_position,,,,,,,,,,,,,,,not set,,
74+
zorder,,,,,,,,,,,,,,,,10,-100

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