Initializing

MANIFEST.in

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+include README.md requirements.in requirements.txt

README.md

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+LogReader: A logreader function to read your files!
+===================================================
+
+![Python](https://img.shields.io/badge/python-3.6-blue.svg)
+[![PEP8](https://img.shields.io/badge/code%20style-pep8-orange.svg)](https://www.python.org/dev/peps/pep-0008/)
+
+
+Announcements
+=============
+
+-   Work has began! Dec 4th
+
+Installation 
+============
+
+LogReader is going to be distribute via PyPi and as the content store grows we can expand it to other pieces of software
+making it accessible to all regardless of what you use. Alternatively, you could have a glance at the source code and copy/paste
+it yourself.
+
+
+Structure of LogReader
+=======================
+
+Currently, the main subpackages are:
+
+- **logreader**: logreader main class. 
+
+
+Genesis
+=======
+
+LogReader was created because I noticed I was using the same variable across multiple scripts and figure it would be useful
+for folk to have.
+
+- Lead Developer [Suliman sharif](http://sulstice.github.io/)
+
+
+* * * * *
+
+External links
+==============
+
+

logreader/__init__.py

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+
+#!/usr/bin/env python3
+#
+# Intialization of the package
+#
+# ----------------------------
+
+from logreader.logreader import LogReader
+
+name='LogReader'

logreader/logreader.py

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+# Authentication to Apollo
+
+class LogReader(object):
+
+    __version__ = '0.0.1'
+
+    def __init__(self, target_directory, target_log):
+
+        '''
+
+        Initialize to find the target logs and readers
+
+        '''
+        self.user, self.hostname = self._read_authentication()
+
+        self.target_directory = target_directory
+        self.target_log = target_log
+        self.timings = {}
+        self._read_loggers()
+
+
+    def _read_authentication(self):
+
+
+        """
+
+        Read in the authentication file into apollo
+
+
+        """
+
+        from ruamel.yaml import YAML
+        yaml = YAML()
+
+        import os
+
+        cwd = os.path.dirname(os.path.abspath(__file__))
+
+        with open(os.path.join(cwd, 'auth_apollo.yml')) as auth_file:
+
+            try:
+                auth_info = yaml.load(auth_file)
+            except Exception as exc:
+                print('Problems handling in reading in the authentication file')
+
+
+        user = auth_info['username']
+        hostname = auth_info['host']
+
+        return user, hostname
+
+    def _read_loggers(self):
+
+        """
+
+        Read the log files for GROMACS software to get step values
+
+
+        """
+
+        from fabric.connection import Connection
+
+        with Connection(self.hostname, self.user) as portal:
+
+            # Find the file paths
+            file_paths_stream = portal.run('find ' + self.target_directory + ' -type f -name "' + self.target_log + '"', hide=True)
+            file_paths = file_paths_stream.stdout.strip().split('\n')
+
+            # Grep the logs
+            for file_path in file_paths:
+
+                stdout_stream = portal.run('tail -n 13 ' + file_path + '', hide=True)
+                stdout = stdout_stream.stdout.strip().split('\n')[0].split('vol')[0].strip().split(' ')[-1]
+                self.timings[file_path] = stdout
+
+    def generate_table(self):
+
+        '''
+
+        Generate a stdout of table values
+
+        '''
+
+        from beautifultable import BeautifulTable
+
+        table = BeautifulTable()
+
+        table.column_headers = ["--- File Path ---", "Step", "Time (ns)"]
+
+        for key, value in self.timings.items():
+
+            row = []
+            row.append(key.replace(self.target_log, ''))
+            row.append(value)
+            row.append(float(value) / 500000)
+
+            table.append_row(row)
+
+        print(table)

requirements.txt

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+ruamel.yaml==0.16.5
+fabric==2.5.0
+beautifultable==1.0.0

setup.py

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+
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+# package setup
+#
+# ------------------------------------------------
+
+# imports
+# -------
+import os
+
+# config
+# ------
+try:
+    from setuptools import setup, find_packages
+except ImportError:
+    from distutils.core import setup, find_packages
+
+# requirements
+# ------------
+with open('requirements.txt') as f:
+    REQUIREMENTS = f.read().strip().split('\n')
+
+if os.path.exists('README.md'):
+    long_description = open('README.md').read()
+else:
+    long_description = 'LogReader- A quick utility tool for reading log files'
+
+TEST_REQUIREMENTS = [
+    'pytest',
+    'pytest-runner'
+]
+
+# exec
+# ----
+setup(
+    name="logreader",
+    version="0.0.1",
+    packages=['logreader'],
+    license='MIT',
+    author="Suliman Sharif",
+    author_email="sharifsuliman1@gmail.com",
+    url="https://github.com/Shen-Group/LogReader",
+    install_requires=REQUIREMENTS,
+    long_description=long_description,
+    long_description_content_type='text/markdown',
+    zip_safe=False,
+    keywords='logreader logs GROMACS',
+    classifiers=[
+        'Development Status :: 4 - Beta',
+        'Natural Language :: English',
+        'License :: OSI Approved :: MIT License',
+        'Intended Audience :: Developers',
+        'Programming Language :: Python :: 3',
+        'Programming Language :: Python :: 3.3',
+        'Programming Language :: Python :: 3.4',
+        'Programming Language :: Python :: 3.5',
+        'Programming Language :: Python :: 3.6',
+        'Programming Language :: Python :: 3.7',
+    ],
+    test_suite='tests',
+    tests_require=TEST_REQUIREMENTS,
+)