Merge pull request #386 from deeptools/develop

Release 3.7

Author: Lucille Delisle

.readthedocs.yml

@@ -1,5 +1,5 @@
 # yaml file to configure readthedocs build
 python:
-   version: 3.6
+   version: 3.7
    setup_py_install: true
    pip_install: False

.travis.yml

@@ -1,10 +1,9 @@
 [![PyPI Version](https://img.shields.io/pypi/v/pyGenomeTracks.svg?style=plastic)](https://pypi.org/project/pyGenomeTracks/) [![bioconda-badge](https://img.shields.io/conda/vn/bioconda/pyGenomeTracks.svg?style=plastic)](https://anaconda.org/bioconda/pygenometracks)
 [![bioconda-badge](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=plastic)](http://bioconda.github.io)
-[![Build Status](https://travis-ci.org/deeptools/pyGenomeTracks.svg?branch=master)](https://travis-ci.org/deeptools/pyGenomeTracks)
+[![Build Status on Azure](https://dev.azure.com/wolffj/pyGenomeTracks/_apis/build/status/deeptools.pyGenomeTracks?branchName=master)](https://dev.azure.com/wolffj/pyGenomeTracks/_build/latest?definitionId=2&branchName=master)
 ![Coverage](./docs/coverage.svg)
 [![European Galaxy server](https://img.shields.io/badge/usegalaxy-.eu-brightgreen?logo=data:image/png;base64,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)](https://usegalaxy.eu/root?tool_id=pygenomeTracks)
 
-
 pyGenomeTracks
 ==============
 
@@ -17,10 +16,13 @@ are highly customizable. Currently, it is possible to plot:
  * bigwig
  * bed/gtf (many options)
  * bedgraph
+ * bedgraph matrices (like TAD-separation scores)
  * epilogos
  * narrow peaks
- * links (represented as arcs)
- * Hi-C matrices
+ * links (represented as arcs, triangles or squares)
+ * Hi-C matrices (as triangle or squares)
+ * fasta
+ * maf (multiple alignment format)
 
 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)):
 
@@ -33,60 +35,76 @@ pyGenomeTracks from [Ramírez et al. 2017](https://www.nature.com/articles/s4146
 
 Table of content
 ----------------
-  * [Installation](#installation)
-  * [Usage](#usage)
-  * [Citation](#citation)
-  * [Documentation](#documentation)
-  * [External users](#external-users)
-
 
+* [Installation](#installation)
+* [Usage](#usage)
+* [Citation](#citation)
+* [Documentation](#documentation)
+* [External users](#external-users)
 
 Installation
 ------------
-pyGenomeTracks works with python >=3.6.
+
+pyGenomeTracks works with python >=3.7.
 
 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 python=3.7
 ```
+
 To get a specific version, one can specify it. For example:
 
 ```bash
-$ conda create -n pygenometracks -c bioconda -c conda-forge pygenometracks=3.5 python=3.7
+conda create -n pygenometracks -c bioconda -c conda-forge pygenometracks=3.5 python=3.7
 ```
 
-Also, pyGenomeTracks can be installed using pip
+However, we noticed that conda installation can be quite slow so using mamba can help.
+You first need to create the environment and install mamba:
 
 ```bash
-$ pip install pyGenomeTracks
+conda create -n pygenometracks -c bioconda -c conda-forge mamba python=3.7
 ```
 
-Since version 3.5, pyGenomeTracks uses BEDTools, don't forget to install it or load it into your environment
+Then activate the environment and install pygenometracks with mamba:
 
+```bash
+conda activate pygenometracks
+mamba install -c defaults -c bioconda -c conda-forge pygenometracks
+```
 
-If the latest version wants to be installed use:
+or if you want a specific version:
 
 ```bash
-$ pip install  git+https://github.com/deeptools/pyGenomeTracks.git
+conda create -n pygenometracks -c bioconda -c conda-forge mamba python=3.7
+conda activate pygenometracks
+mamba install -c defaults -c bioconda -c conda-forge pygenometracks=3.5
 ```
 
+Also, pyGenomeTracks can be installed using pip
+
+```bash
+pip install pyGenomeTracks
+```
+
+Since version 3.5, pyGenomeTracks uses BEDTools, don't forget to install it or load it into your environment.
 
 Usage
 -----
+
 To run pyGenomeTracks a configuration file describing the tracks is required. The easiest way to create this file is using the program `make_tracks_file` which creates a configuration file with
 defaults that can be easily changed. The format is:
 
 ```bash
-$ make_tracks_file --trackFiles <file1.bed> <file2.bw> ... -o tracks.ini
+make_tracks_file --trackFiles <file1.bed> <file2.bw> ... -o tracks.ini
 ```
 
 `make_tracks_file` uses the file ending to guess the file type.
 
 Then, a region can be plotted using:
 
 ```bash
-$ pyGenomeTracks --tracks tracks.ini --region chr2:10,000,000-11,000,000 --outFileName nice_image.pdf
+pyGenomeTracks --tracks tracks.ini --region chr2:10,000,000-11,000,000 --outFileName nice_image.pdf
 ```
 
 The ending `--outFileName` defines the image format. If `.pdf` is used, then the resulting image is a pdf. The options are pdf, png and svg.
@@ -102,8 +120,9 @@ optional arguments:
   --region REGION       Region to plot, the format is chr:start-end
   --BED BED             Instead of a region, a file containing the regions to
                         plot, in BED format, can be given. If this is the
-                        case, multiple files will be created using a prefix
-                        the value of --outFileName
+                        case, multiple files will be created. It will use the
+                        value of --outFileName as a template and put the
+                        coordinates between the file name and the extension.
   --width WIDTH         figure width in centimeters (default is 40)
   --plotWidth PLOTWIDTH
                         width in centimeters of the plotting (central) part
@@ -136,14 +155,14 @@ optional arguments:
 <!--- End of possible arguments of pgt -->
 
 Citation
----------
+--------
+
 If you use pyGenomeTracks in your analysis, you can cite the following papers:
 
 Fidel Ramírez, Vivek Bhardwaj, Laura Arrigoni, Kin Chung Lam, Björn A. Grüning, José Villaveces, Bianca Habermann, Asifa Akhtar & Thomas Manke. High-resolution TADs reveal DNA sequences underlying genome organization in flies. Nature Communications (2018) [doi:10.1038/s41467-017-02525-w](https://www.nature.com/articles/s41467-017-02525-w)
 
 Lopez-Delisle L, Rabbani L, Wolff J, Bhardwaj V, Backofen R, Grüning B, Ramírez F, Manke T. pyGenomeTracks: reproducible plots for multivariate genomic data sets. Bioinformatics. 2020 Aug 3:btaa692. [doi: 10.1093/bioinformatics/btaa692](https://doi.org/10.1093/bioinformatics/btaa692). Epub ahead of print. PMID: 32745185.
 
-
 Documentation
 -------------
 

README.md

@@ -0,0 +1,118 @@
+pr:
+  autoCancel: true
+
+stages:
+- stage: test
+  jobs:
+    - job: Linux
+      timeoutInMinutes: 0
+      pool:
+        vmImage: 'ubuntu-latest'
+      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'
+          Python38HighMatplotlib:
+            python.version: '3.8'
+            matplotlib.version: '3.5.1'
+          Python39HighMatplotlib:
+            python.version: '3.9'
+            matplotlib.version: '3.5.1'
+
+      steps:
+      - bash: |
+          echo "##vso[task.prependpath]$CONDA/bin"
+          hash -r
+        displayName: Add conda to PATH
+      - bash: |
+          conda config --set always_yes yes --set changeps1 no
+          conda info -a
+          cat requirements_CI.txt | awk -v v=$(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 defaults -c conda-forge -c bioconda --file requirements_CI_updated.txt
+          python setup.py install
+        displayName: installing dependencies
+      - script: |
+          source activate pygenometracks
+          flake8 . --exclude=.venv,.build,build --ignore=E501,F403,E402,F999,F405,E712,W503
+        displayName: linting
+      - script: |
+          source activate pygenometracks
+          py.test pygenometracks --doctest-modules -n 4
+        displayName: pytest
+
+    - job: OSX
+      timeoutInMinutes: 0
+      pool:
+        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'
+          Python38HighMatplotlib:
+            python.version: '3.8'
+            matplotlib.version: '3.5.1'
+          Python39HighMatplotlib:
+            python.version: '3.9'
+            matplotlib.version: '3.5.1'
+
+      steps:
+      - bash: |
+          echo "##vso[task.prependpath]$CONDA/bin"
+          hash -r
+        displayName: Add conda to PATH
+      # On Hosted macOS, the agent user doesn't have ownership of Miniconda's installation directory/
+      # We need to take ownership if we want to update conda or install packages globally
+      - bash: sudo chown -R $USER $CONDA
+        displayName: Take ownership of conda installation
+      - bash: |
+          conda config --set always_yes yes --set changeps1 no
+          conda info -a
+          cat requirements_CI.txt | awk -v v=$(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 defaults -c conda-forge -c bioconda --file requirements_CI_updated.txt
+          python setup.py install
+        displayName: installing dependencies
+      - script: |
+          source activate pygenometracks
+          flake8 . --exclude=.venv,.build,build --ignore=E501,F403,E402,F999,F405,E712,W503
+        displayName: linting
+      - script: |
+          source activate pygenometracks
+          py.test pygenometracks --doctest-modules -n 4
+        displayName: pytest
+
+- ${{ if eq(variables['Build.SourceBranch'], 'refs/heads/master') }}:
+  - stage: Deploy
+    dependsOn: [test]
+    condition: succeeded()
+    jobs:
+    - job: pypi
+      pool:
+        vmImage: 'Ubuntu-latest'
+      container: python:3.8
+      steps:
+      - script: |
+          python setup.py sdist bdist_wheel
+          python -m pip install --user --upgrade twine
+          python -m twine upload -r pypi dist/*
+        env:
+          TWINE_USERNAME: lldelisle
+          TWINE_PASSWORD: $(TWINE_LUCILLE_PASSWORD)
+        displayName: 'Push to Python Package Index'

azure-pipelines.yml

@@ -26,9 +26,12 @@
 MOCK_MODULES = ['pygenometracks.tracksClass',  # (required for both)
                 # For plotTracks in plotTracks
                 'matplotlib',
+                'matplotlib.pyplot',
                 # For plotTracks in utilities
+                'matplotlib.ticker',
                 'numpy',
                 'tqdm',
+                'pyfaidx',
                 'intervaltree',
                 'pybedtools']
 
@@ -70,7 +73,7 @@ def get_version():
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ['sphinxarg.ext']
+extensions = ['sphinx_rtd_theme', 'sphinxarg.ext']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']