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Merge pull request #474 from deeptools/develop
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Release 3.19
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@lldelisle
lldelisle authored May 6, 2024
2 parents b8918d4 + e588397 commit 8b0c96b
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1 change: 1 addition & 0 deletions MANIFEST.in
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prune pygenometracks/tests
12 changes: 6 additions & 6 deletions README.md
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Expand Up @@ -26,12 +26,12 @@ are highly customizable. Currently, it is possible to plot:

Here is a scheme which describe how pyGenomeTracks is working (graphical abstract of [Lopez-Delisle et al. 2020](https://doi.org/10.1093/bioinformatics/btaa692)):

![pyGenomeTracks](./docs/content/images/graphicalabstract.png)
![pyGenomeTracks](https://github.com/deeptools/pyGenomeTracks/blob/b8918d43b0bd1ca9dd2939fdd0d93a5a297d0453/docs/content/images/graphicalabstract.png)

pyGenomeTracks can make plots with or without Hi-C data. The following is an example output of
pyGenomeTracks from [Ramírez et al. 2017](https://www.nature.com/articles/s41467-017-02525-w)

![pyGenomeTracks example](./docs/content/images/hic_example_nat_comm_small.png)
![pyGenomeTracks example](https://github.com/deeptools/pyGenomeTracks/blob/b8918d43b0bd1ca9dd2939fdd0d93a5a297d0453/docs/content/images/hic_example_nat_comm_small.png)

Table of content
----------------
Expand All @@ -45,12 +45,12 @@ Table of content
Installation
------------

pyGenomeTracks works with python >=3.7.
pyGenomeTracks works with python >=3.8.

The recommended way to install pyGenomeTracks is via conda

```bash
conda create -n pygenometracks -c bioconda -c conda-forge pygenometracks python=3.7
conda create -n pygenometracks -c bioconda -c conda-forge pygenometracks
```

To get a specific version, one can specify it. For example:
Expand All @@ -63,7 +63,7 @@ However, we noticed that conda installation can be quite slow so using mamba can
You first need to create the environment and install mamba:

```bash
conda create -n pygenometracks -c bioconda -c conda-forge mamba python=3.7
conda create -n pygenometracks -c bioconda -c conda-forge mamba python=3.9
```

Then activate the environment and install pygenometracks with mamba:
Expand Down Expand Up @@ -112,7 +112,7 @@ The ending `--outFileName` defines the image format. If `.pdf` is used, then the
Description of other possible arguments:
<!--- Start of possible arguments of pgt -->
``` text
optional arguments:
options:
-h, --help show this help message and exit
--tracks TRACKS File containing the instructions to plot the tracks.
The tracks.ini file can be genarated using the
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38 changes: 14 additions & 24 deletions azure-pipelines.yml
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Expand Up @@ -30,21 +30,18 @@ stages:
vmImage: 'ubuntu-latest'
strategy:
matrix:
Python37LowMatplotlib:
python.version: '3.7'
matplotlib.version: '3.1.1'
Python37HighMatplotlib:
python.version: '3.7'
matplotlib.version: '3.5.3'
Python38LowMatplotlib:
python.version: '3.8'
matplotlib.version: '3.1.1'
Python38HighMatplotlib:
python.version: '3.8'
matplotlib.version: '3.6.2'
matplotlib.version: '3.6.0'
Python39HighMatplotlib:
python.version: '3.9'
matplotlib.version: '3.6.2'
matplotlib.version: '3.7.3'
Python310HighMatplotlib:
python.version: '3.10'
matplotlib.version: '3.8.4'

steps:
- bash: |
Expand All @@ -54,11 +51,10 @@ stages:
- bash: |
conda config --set always_yes yes --set changeps1 no
conda info -a
cat requirements_CI.txt | awk -v v=$(matplotlib.version) '{if($0~/matplotlib/){$0="matplotlib =="v}; print}' > requirements_CI_updated.txt
conda create -n pygenometracks --yes -c conda-forge -c bioconda python=$(python.version) mamba
cat requirements_CI.txt | awk -v v=$(matplotlib.version) -v vp=$(python.version) 'BEGIN{print "python =="vp}{if($0~/matplotlib/){$0="matplotlib =="v}; print}' > requirements_CI_updated.txt
conda create -n pygenometracks --yes -c conda-forge -c bioconda --file requirements_CI_updated.txt
source activate pygenometracks
mamba install --yes -c conda-forge -c bioconda --file requirements_CI_updated.txt
python setup.py install
python -m pip install .
displayName: installing dependencies
- script: |
source activate pygenometracks
Expand All @@ -71,12 +67,6 @@ stages:
vmImage: 'macOS-11'
strategy:
matrix:
Python37LowMatplotlib:
python.version: '3.7'
matplotlib.version: '3.1.1'
Python37HighMatplotlib:
python.version: '3.7'
matplotlib.version: '3.5.1'
Python38LowMatplotlib:
python.version: '3.8'
matplotlib.version: '3.1.1'
Expand All @@ -99,11 +89,9 @@ stages:
- bash: |
conda config --set always_yes yes --set changeps1 no
conda info -a
cat requirements_CI.txt | awk -v v=$(matplotlib.version) '{if($0~/matplotlib/){$0="matplotlib =="v}; print}' > requirements_CI_updated.txt
conda create -n pygenometracks --yes -c conda-forge -c bioconda python=$(python.version) mamba
source activate pygenometracks
mamba install --yes -c conda-forge -c bioconda --file requirements_CI_updated.txt
python setup.py install
cat requirements_CI.txt | awk -v v=$(matplotlib.version) -v vp=$(python.version) 'BEGIN{print "python =="vp}{if($0~/matplotlib/){$0="matplotlib =="v}; print}' > requirements_CI_updated.txt
conda create -n pygenometracks --yes -c conda-forge -c bioconda --file requirements_CI_updated.txt
python -m pip install .
displayName: installing dependencies
- script: |
source activate pygenometracks
Expand All @@ -121,7 +109,9 @@ stages:
container: python:3.8
steps:
- script: |
python setup.py sdist bdist_wheel
python -m pip install --upgrade pip
pip install build
python -m build
python -m pip install --user --upgrade twine
python -m twine upload -r pypi dist/*
env:
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7 changes: 0 additions & 7 deletions bin/make_tracks_file
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1 change: 0 additions & 1 deletion bin/pgt
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11 changes: 0 additions & 11 deletions bin/pyGenomeTracks
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4 changes: 3 additions & 1 deletion docs/content/all_default_properties.csv
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Expand Up @@ -32,9 +32,11 @@ color_utr,,,,,grey,grey,,,,,,,,,,,
color_backbone,,,,,black,black,,,,,,,,,,,
height_utr,,,,,1,1,,,,,,,,,,,
arrow_length,,,,,not set,not set,,,,,,,,,,,
height_intron,,,,,0.5,0.5,,,,,,,,,,,
all_labels_inside,,,,,false,false,,,,,,,,,,,
labels_in_margin,,,,,false,false,,,,,,,,,,,
fontstyle,,,,,normal,normal,,,,,,,,,,,
color_arrow,,,,,black,black,,,,,,,,,,,
show_data_range,,,,,,,true,true,true,true,true,,,,,,
show_labels,,,,,,,true,,,,,,,,,,
use_summit,,,,,,,true,,,,,,,,,,
Expand All @@ -50,7 +52,7 @@ y_axis_values,,,,,,,,transformed,transformed,,,,,,,,
second_file*,,,,,,,,not set,not set,,,,,,,,
operation*,,,,,,,,file,file,,,,,,,,
grid,,,,,,,,false,false,,,,,,,,
rasterize,,,,,,,,,false,true,,true,true,,,,
rasterize,,,,,,,,,false,true,,true,true,false,,,
pos_score_in_bin,,,,,,,,,,center,,,,,,,
plot_horizontal_lines,,,,,,,,,,false,,,,,,,
colormap,,,,,,,,,,viridis,,RdYlBu_r,RdYlBu_r,,,,
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4 changes: 3 additions & 1 deletion docs/content/all_default_properties_rst.txt
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Expand Up @@ -34,9 +34,11 @@ color_utr
color_backbone black black
height_utr 1 1
arrow_length not set not set
height_intron 0.5 0.5
all_labels_inside false false
labels_in_margin false false
fontstyle normal normal
color_arrow black black
show_data_range true true true true true
show_labels true
use_summit true
Expand All @@ -52,7 +54,7 @@ y_axis_values
second_file* not set not set
operation* file file
grid false false
rasterize false true true true
rasterize false true true true false
pos_score_in_bin center
plot_horizontal_lines false
colormap viridis RdYlBu_r RdYlBu_r
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10 changes: 4 additions & 6 deletions docs/content/all_possible_properties.txt
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- **overlay_previous**:

- for *x_axis, epilogos, links, domains, bed, gtf, narrow_peak, bigwig, bedgraph, bedgraph_matrix, hlines, hic_matrix, hic_matrix_square, maf, scalebar, fasta, spacer*: no, yes, share-y
- for *x_axis, epilogos, links, domains, bed, gtf, narrow_peak, bigwig, bedgraph, bedgraph_matrix, hlines, hic_matrix, hic_matrix_square, maf, scalebar, spacer, fasta*: no, yes, share-y

- **where**:

Expand Down Expand Up @@ -34,13 +34,11 @@

- **style**:

- for *bed, gtf*: flybase, UCSC, tssarrow
- for *bed, gtf*: flybase, UCSC, tssarrow, exonarrows

- **display**:

- for *bed*: collapsed, triangles, interleaved, stacked, squares

- for *gtf*: collapsed, triangles, interleaved, stacked
- for *bed, gtf*: collapsed, triangles, interleaved, stacked, squares, deletions, inversions

- **fontstyle**:

Expand Down Expand Up @@ -114,7 +112,7 @@

- **rasterize**:

- for *bedgraph, bedgraph_matrix, hic_matrix, hic_matrix_square*: true, false
- for *bedgraph, bedgraph_matrix, hic_matrix, hic_matrix_square, maf*: true, false

- **pos_score_in_bin**:

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