From 8eb4e692e63384369aebf7333c96423f11cf9b86 Mon Sep 17 00:00:00 2001
From: "Gabriel A. Devenyi" <gdevenyi@gmail.com>
Date: Thu, 12 Mar 2020 09:07:08 -0400
Subject: [PATCH 1/4] Update version number

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index a753415..f020acc 100644
--- a/setup.py
+++ b/setup.py
@@ -12,7 +12,7 @@
 
 setup(
     name='qbatch',
-    version='2.1.5',
+    version='2.2',
     description='Execute shell command lines in parallel on Slurm, S(sun|on of) Grid Engine (SGE) and PBS/Torque clusters',
     author="Jon Pipitone, Gabriel A. Devenyi",
     author_email="jon@pipitone.ca, gdevenyi@gmail.com",

From 36d0cd840207ae624f4e14041c331922db60f110 Mon Sep 17 00:00:00 2001
From: "Gabriel A. Devenyi" <gdevenyi@gmail.com>
Date: Thu, 12 Mar 2020 09:17:17 -0400
Subject: [PATCH 2/4] Update setup.py to new markdown readme support for long
 description in PyPi

---
 setup.py | 43 ++++++++++++++++++++++---------------------
 1 file changed, 22 insertions(+), 21 deletions(-)

diff --git a/setup.py b/setup.py
index f020acc..7812de1 100644
--- a/setup.py
+++ b/setup.py
@@ -1,42 +1,43 @@
 #!/usr/bin/env python
 
 from setuptools import setup
+from io import open
 
-# pypi doesn't like markdown
-# https://github.com/pypa/packaging-problems/issues/46
-try:
-    import pypandoc
-    description = pypandoc.convert('README.md', 'rst')
-except (IOError, ImportError):
-    description = ''
+# read the contents of your README file
+from os import path
+this_directory = path.abspath(path.dirname(__file__))
+with open(path.join(this_directory, 'README.md'), encoding='utf-8') as f:
+    long_description = f.read()
 
 setup(
     name='qbatch',
     version='2.2',
-    description='Execute shell command lines in parallel on Slurm, S(sun|on of) Grid Engine (SGE) and PBS/Torque clusters',
+    description='Execute shell command lines in parallel on Slurm, '
+    'S(un|on of) Grid Engine (SGE) and PBS/Torque clusters',
     author="Jon Pipitone, Gabriel A. Devenyi",
     author_email="jon@pipitone.ca, gdevenyi@gmail.com",
     license='Unlicense',
     url="https://github.com/pipitone/qbatch",
-    long_description=description,
-    entry_points = {
+    long_description=long_description,
+    long_description_content_type='text/markdown',
+    entry_points={
         "console_scripts": [
             "qbatch=qbatch:qbatchParser",
         ]
     },
     packages=["qbatch"],
     classifiers=[
-       'Development Status :: 5 - Production/Stable',
-       'Environment :: Console',
-       'Intended Audience :: Science/Research',
-       'License :: Public Domain',
-       'Natural Language :: English',
-       'Operating System :: POSIX :: Linux',
-       'Programming Language :: Python :: 2',
-       'Programming Language :: Python :: 3',
-       'Topic :: System :: Clustering',
-       'Topic :: System :: Distributed Computing',
-       'Topic :: Utilities',
+        'Development Status :: 5 - Production/Stable',
+        'Environment :: Console',
+        'Intended Audience :: Science/Research',
+        'License :: Public Domain',
+        'Natural Language :: English',
+        'Operating System :: POSIX :: Linux',
+        'Programming Language :: Python :: 2',
+        'Programming Language :: Python :: 3',
+        'Topic :: System :: Clustering',
+        'Topic :: System :: Distributed Computing',
+        'Topic :: Utilities',
     ],
     install_requires=[
         "six",

From e9cbafdba355858769f627e2e16f77d0f7631b6d Mon Sep 17 00:00:00 2001
From: "Gabriel A. Devenyi" <gdevenyi@gmail.com>
Date: Thu, 12 Mar 2020 09:34:01 -0400
Subject: [PATCH 3/4] Add CITATION.cff file

---
 CITATION.cff | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 CITATION.cff

diff --git a/CITATION.cff b/CITATION.cff
new file mode 100644
index 0000000..f8ffc64
--- /dev/null
+++ b/CITATION.cff
@@ -0,0 +1,19 @@
+# YAML 1.2
+---
+cff-version: "1.1.0"
+abstract: |
+    "Execute shell command lines in parallel on Slurm, S(un|on of) Grid Engine (SGE) and PBS/Torque clusters"
+message: "If you use this software, please cite it as below."
+authors:
+  - 
+    family-names: Devenyi
+    given-names: "Gabriel Allan"
+    orcid: "https://orcid.org/0000-0002-7766-1187"
+  -
+    family-names: Pipitone
+    given-names: Jon
+    orcid: "https://orcid.org/0000-0001-6313-5701"
+title: qbatch
+repository-code: "https://github.com/pipitone/qbatch"
+version: "2.2"
+date-released: 2020-03-12

From a018702eba34a5f7104d0e65934eda9480f8f41c Mon Sep 17 00:00:00 2001
From: "Gabriel A. Devenyi" <gdevenyi@gmail.com>
Date: Thu, 12 Mar 2020 09:40:08 -0400
Subject: [PATCH 4/4] Switch from --chdir to -D to support older slurm
 instances where the long for option is different

---
 qbatch/qbatch.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/qbatch/qbatch.py b/qbatch/qbatch.py
index b1ab4af..e90d692 100755
--- a/qbatch/qbatch.py
+++ b/qbatch/qbatch.py
@@ -132,7 +132,7 @@ def _setupVars():
     #SBATCH --nodes={nodes}
     #SBATCH {ppj}
     #SBATCH {logfile}
-    #SBATCH --chdir={workdir}
+    #SBATCH -D {workdir}
     #SBATCH --job-name={job_name}
     #SBATCH {o_memopts}
     #SBATCH {o_queue}