Merge pull request #472 from lldelisle/remove_setup_py

change setup.py to project.toml

Author: Lucille Delisle

MANIFEST.in

@@ -0,0 +1 @@
+prune pygenometracks/tests

README.md

@@ -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
 ----------------

azure-pipelines.yml

@@ -54,7 +54,7 @@ stages:
           cat requirements_CI.txt | awk -v v=$(matplotlib.version) -v vp=$(python.version) 'BEGIN{print "python =="vp}{if($0~/matplotlib/){$0="matplotlib =="v}; print}' > requirements_CI_updated.txt
           conda create -n pygenometracks --yes -c conda-forge -c bioconda --file requirements_CI_updated.txt
           source activate pygenometracks
-          python setup.py install
+          python -m pip install .
         displayName: installing dependencies
       - script: |
           source activate pygenometracks
@@ -91,7 +91,7 @@ stages:
           conda info -a
           cat requirements_CI.txt | awk -v v=$(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 setup.py install
+          python -m pip install .
         displayName: installing dependencies
       - script: |
           source activate pygenometracks
@@ -109,7 +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:

bin/make_tracks_file

@@ -1,10 +1,9 @@
 import argparse
 import os
 import sys
+from importlib.metadata import version
 from pygenometracks.tracksClass import PlotTracks
 
-from pygenometracks._version import __version__
-
 
 def parse_arguments(args=None):
 
@@ -29,7 +28,7 @@ def parse_arguments(args=None):
                         required=True)
 
     parser.add_argument('--version', action='version',
-                        version=f'%(prog)s {__version__}')
+                        version=version('pyGenomeTracks'))
 
     return parser
 

bin/pgt

@@ -146,8 +146,9 @@
 import argparse
 import warnings
 
+from importlib.metadata import version
+
 from pygenometracks.tracksClass import PlotTracks
-from pygenometracks._version import __version__
 from .utilities import InputError, get_region
 import matplotlib.pyplot as plt
 
@@ -241,7 +242,7 @@ def parse_arguments(args=None):
                         action='store_true')
 
     parser.add_argument('--version', action='version',
-                        version=f'%(prog)s {__version__}')
+                        version=version('pyGenomeTracks'))
 
     return parser