From 7342e01b24ccdad96b04a877bb58c1537dde0277 Mon Sep 17 00:00:00 2001 From: apregier Date: Mon, 1 Jul 2019 16:02:48 -0500 Subject: [PATCH 1/4] Get the last > char This should allow there to be > characters inside of a quoted Description field --- svtyper/parsers.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/svtyper/parsers.py b/svtyper/parsers.py index e17d234..1357b8c 100644 --- a/svtyper/parsers.py +++ b/svtyper/parsers.py @@ -53,15 +53,15 @@ def add_header(self, header): elif line.split('=')[0] == '##reference': self.reference = line.rstrip().split('=')[1] elif line.split('=')[0] == '##INFO': - a = line[line.find('<')+1:line.find('>')] + a = line[line.find('<')+1:line.rfind('>')] r = re.compile(r'(?:[^,\"]|\"[^\"]*\")+') self.add_info(*[b.split('=')[1] for b in r.findall(a)]) elif line.split('=')[0] == '##ALT': - a = line[line.find('<')+1:line.find('>')] + a = line[line.find('<')+1:line.rfind('>')] r = re.compile(r'(?:[^,\"]|\"[^\"]*\")+') self.add_alt(*[b.split('=')[1] for b in r.findall(a)]) elif line.split('=')[0] == '##FORMAT': - a = line[line.find('<')+1:line.find('>')] + a = line[line.find('<')+1:line.rfind('>')] r = re.compile(r'(?:[^,\"]|\"[^\"]*\")+') self.add_format(*[b.split('=')[1] for b in r.findall(a)]) elif line[0] == '#' and line[1] != '#': From a82ab3f76a62d12286ba094ec7217de48636146f Mon Sep 17 00:00:00 2001 From: apregier Date: Wed, 28 Aug 2019 14:27:15 -0500 Subject: [PATCH 2/4] Pin version to something compatible with 2.7 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 61687ad..51074c5 100644 --- a/setup.py +++ b/setup.py @@ -21,7 +21,7 @@ license=license, url='https://github.com/hall-lab/svtyper', setup_requires=['pytest-runner'], - tests_require=['pytest'], + tests_require=['pytest==4.6.4'], install_requires=[ 'pysam>=0.15.0', 'numpy', From a3a8cae3d1c0dfc10295f5622d57e4c692cf794f Mon Sep 17 00:00:00 2001 From: apregier Date: Wed, 28 Aug 2019 15:19:29 -0500 Subject: [PATCH 3/4] Update version --- svtyper/version.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/svtyper/version.py b/svtyper/version.py index 3e98833..6518ba0 100644 --- a/svtyper/version.py +++ b/svtyper/version.py @@ -1,2 +1,2 @@ __author__ = "Colby Chiang (colbychiang@wustl.edu)" -__version__ = "v0.7.0" +__version__ = "v0.7.1" From 8e728089b36128b3eebd64f63c75d101cf3e1740 Mon Sep 17 00:00:00 2001 From: apregier Date: Wed, 4 Sep 2019 15:30:28 -0500 Subject: [PATCH 4/4] New pypi just wants name of license in setup.py --- setup.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/setup.py b/setup.py index 51074c5..837133d 100644 --- a/setup.py +++ b/setup.py @@ -5,9 +5,6 @@ with open('README.md') as f: readme = f.read() -with open('LICENSE') as f: - license = f.read() - with open('svtyper/version.py') as f: exec(f.read()) @@ -16,9 +13,10 @@ version=__version__, description='Bayesian genotyper for structural variants', long_description=readme, + long_description_content_type='text/markdown', author=__author__, author_email='colbychiang@wustl.edu', - license=license, + license='MIT License', url='https://github.com/hall-lab/svtyper', setup_requires=['pytest-runner'], tests_require=['pytest==4.6.4'],