From cbbd28c171ad802f2e5d668c47c7a3c9297ea4e4 Mon Sep 17 00:00:00 2001 From: pbashyal-nmdp Date: Fri, 24 Jan 2020 12:56:06 -0600 Subject: [PATCH 1/6] Cleanup README --- README.rst | 21 ++++++++------------- pyard/pyard.py | 2 +- requirements.txt | 6 ------ 3 files changed, 9 insertions(+), 20 deletions(-) delete mode 100644 requirements.txt diff --git a/README.rst b/README.rst index 1e57502..d529ecd 100644 --- a/README.rst +++ b/README.rst @@ -1,5 +1,5 @@ =============================== -pyARD +py-ard =============================== @@ -20,16 +20,19 @@ ARD reduction for HLA with python Install ------- +# from source + .. code-block:: - # from source python3 -m venv venv source venv/bin/activate - pip install -r requirements.txt + python setup.py install - # from PyPi - pip install pyard +# from PyPi + +.. code-block:: + pip install py-ard Example @@ -61,11 +64,3 @@ Example # 'B*07:02:01G+B*07:02:01G^A*01:01:01G+A*02:01:01G/A*02:02' -Credits ---------- - -This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template. - -.. _Cookiecutter: https://github.com/audreyr/cookiecutter -.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage - diff --git a/pyard/pyard.py b/pyard/pyard.py index 7dfd3bf..3690525 100644 --- a/pyard/pyard.py +++ b/pyard/pyard.py @@ -435,7 +435,7 @@ def redux_gl(self, glstring: str, redux_type: str) -> str: def isvalid(self, allele: str) -> str: """ - Determines valididy of an allele + Determines validity of an allele :param allele: An HLA allele. :type: str diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index def159f..0000000 --- a/requirements.txt +++ /dev/null @@ -1,6 +0,0 @@ -numpy==1.14.0 -pandas==0.22.0 -python-dateutil==2.6.1 -pytz==2018.3 -six==1.11.0 -typing==3.6.4 From a6dc2a2ba24e5f7e925ff6b8bc820264c19da0d3 Mon Sep 17 00:00:00 2001 From: pbashyal-nmdp Date: Fri, 24 Jan 2020 12:57:56 -0600 Subject: [PATCH 2/6] Cleanup README --- README.rst | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/README.rst b/README.rst index d529ecd..319db70 100644 --- a/README.rst +++ b/README.rst @@ -17,10 +17,8 @@ ARD reduction for HLA with python * Documentation: https://pyard.readthedocs.io. -Install -------- - -# from source +Install from source +------------------- .. code-block:: @@ -29,7 +27,8 @@ Install python setup.py install -# from PyPi +Install from PyPi +----------------- .. code-block:: pip install py-ard From 66568c66751cba7ae48b358c0a4a68f6ef2e595b Mon Sep 17 00:00:00 2001 From: pbashyal-nmdp Date: Fri, 24 Jan 2020 12:58:25 -0600 Subject: [PATCH 3/6] Cleanup README --- README.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/README.rst b/README.rst index 319db70..d316384 100644 --- a/README.rst +++ b/README.rst @@ -31,6 +31,7 @@ Install from PyPi ----------------- .. code-block:: + pip install py-ard From 2ea2c315ad9582e3db39464b8cdc2aa4423bd46e Mon Sep 17 00:00:00 2001 From: pbashyal-nmdp Date: Fri, 24 Jan 2020 13:07:01 -0600 Subject: [PATCH 4/6] Update version to 0.0.12 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 889f91b..d1df2c4 100644 --- a/setup.py +++ b/setup.py @@ -42,7 +42,7 @@ setup( name='py-ard', - version='0.0.11', + version='0.0.12', description="ARD reduction for HLA with python", long_description=readme + '\n\n' + history, author="CIBMTR", From acd2406413eb8863b4bbb8e9f629b970cea44b71 Mon Sep 17 00:00:00 2001 From: pbashyal-nmdp Date: Fri, 27 Mar 2020 14:55:08 -0500 Subject: [PATCH 5/6] Update to version 0.0.13 --- pyard/__init__.py | 5 ++--- setup.cfg | 2 +- setup.py | 2 +- 3 files changed, 4 insertions(+), 5 deletions(-) diff --git a/pyard/__init__.py b/pyard/__init__.py index 680d1f7..8b8afcb 100644 --- a/pyard/__init__.py +++ b/pyard/__init__.py @@ -24,6 +24,5 @@ from __future__ import absolute_import from .pyard import ARD -__author__ = """Michael Halagan""" -__email__ = 'mhalagan@nmdp.org' -__version__ = '0.0.10' +__author__ = """NMDP Bioinformatics""" +__version__ = '0.0.13' diff --git a/setup.cfg b/setup.cfg index 2d0c840..a919b18 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.0.10 +current_version = 0.0.13 commit = True tag = True diff --git a/setup.py b/setup.py index 5cbfdc6..521826c 100644 --- a/setup.py +++ b/setup.py @@ -42,7 +42,7 @@ setup( name='py-ard', - version='0.0.12', + version='0.0.13', description="ARD reduction for HLA with python", long_description=readme + '\n\n' + history, author="CIBMTR", From f32ba238b2e1ab1d510600caf54a86b468600443 Mon Sep 17 00:00:00 2001 From: pbashyal-nmdp Date: Tue, 14 Apr 2020 15:07:09 -0500 Subject: [PATCH 6/6] Updated version to 0.0.14 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 521826c..6fd5fee 100644 --- a/setup.py +++ b/setup.py @@ -42,7 +42,7 @@ setup( name='py-ard', - version='0.0.13', + version='0.0.14', description="ARD reduction for HLA with python", long_description=readme + '\n\n' + history, author="CIBMTR",