Merge pull request #4 from 3dem/devel

version 0.0.7

.gitignore

@@ -1,3 +1,16 @@
-*pyc
+#### Eclipse and so on
+.project
+.cproject
+.pydevproject
+.classpath
 .idea
 
+#### Python
+build/
+dist/
+*.egg-info/
+*.egg
+*.py[cod]
+__pycache__/
+*.so
+*~

CHANGES.txt

@@ -0,0 +1,2 @@
+0.0.7: exported Column via Table class
+0.0.6: first version for pip

MANIFEST.in

@@ -0,0 +1,3 @@
+include *.rst
+include LICENSE
+include *.txt

README.rst

@@ -0,0 +1,5 @@
+=======
+emtable
+=======
+
+Simple module to deal with EM tabular data (aka metadata)

emtable/__init__.py

@@ -0,0 +1,26 @@
+# **************************************************************************
+# *
+# * Authors:  J. M. de la Rosa Trevin ([email protected])
+# * Authors:  Grigory Sharov ([email protected])
+# *
+# * This program is free software; you can redistribute it and/or modify
+# * it under the terms of the GNU General Public License as published by
+# * the Free Software Foundation; either version 3 of the License, or
+# * (at your option) any later version.
+# *
+# * This program is distributed in the hope that it will be useful,
+# * but WITHOUT ANY WARRANTY; without even the implied warranty of
+# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# * GNU General Public License for more details.
+# *
+# * You should have received a copy of the GNU General Public License
+# * along with this program; if not, write to the Free Software
+# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
+# * 02111-1307  USA
+# *
+# *  All comments concerning this program package may be sent to the
+# *  e-mail address '[email protected]'
+# *
+# **************************************************************************
+
+from .metadata import *

metadata.py → emtable/metadata.py

@@ -19,7 +19,7 @@
 # *
 # **************************************************************************
 
-__version__ = '0.0.6'
+__version__ = '0.0.7'
 __author__ = 'Jose Miguel de la Rosa Trevin'
 
 
@@ -29,7 +29,7 @@
 from collections import OrderedDict, namedtuple
 
 
-class Column:
+class _Column:
     def __init__(self, name, type=None):
         self._name = name
         # Get the type from the LABELS dict, assume str by default
@@ -93,7 +93,7 @@ def _createColumns(self, columnList, line=None, guessType=False):
         """
         self._columns.clear()
 
-        if isinstance(columnList[0], Column):
+        if isinstance(columnList[0], _Column):
             for col in columnList:
                 self._columns[col.getName()] = col
         else:
@@ -103,7 +103,7 @@ def _createColumns(self, columnList, line=None, guessType=False):
                 typeList = [str] * len(columnList)
 
             for colName, colType in zip(columnList, typeList):
-                self._columns[colName] = Column(colName, colType)
+                self._columns[colName] = _Column(colName, colType)
 
         self._createRowClass()
 
@@ -298,6 +298,7 @@ class Table(_ColumnsList):
     """
     Reader = _Reader
     Writer = _Writer
+    Column = _Column
 
     def __init__(self, **kwargs):
         _ColumnsList.__init__(self)
@@ -412,7 +413,7 @@ def addColumns(self, *args):
                 map[colName] = value
                 constSet.add(value)
 
-            newCols[colName] = Column(colName, colType)
+            newCols[colName] = _Column(colName, colType)
 
         # Update columns and create new Row class
         self._columns.update(newCols)

tests/strings_star_relion.py → emtable/tests/strings_star_relion.py

@@ -1,7 +1,31 @@
+# **************************************************************************
+# *
+# * Authors:  J. M. de la Rosa Trevin ([email protected])
+# *
+# * This program is free software; you can redistribute it and/or modify
+# * it under the terms of the GNU General Public License as published by
+# * the Free Software Foundation; either version 3 of the License, or
+# * (at your option) any later version.
+# *
+# * This program is distributed in the hope that it will be useful,
+# * but WITHOUT ANY WARRANTY; without even the implied warranty of
+# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# * GNU General Public License for more details.
+# *
+# * You should have received a copy of the GNU General Public License
+# * along with this program; if not, write to the Free Software
+# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
+# * 02111-1307  USA
+# *
+# *  All comments concerning this program package may be sent to the
+# *  e-mail address '[email protected]'
+# *
+# **************************************************************************
+
 try:
-    from StringIO import StringIO ## for Python 2
+    from StringIO import StringIO  # for Python 2
 except ImportError:
-    from io import StringIO ## for Python 3
+    from io import StringIO  # for Python 3
 
 import unittest
 from metadata import Table

tests/test_basic.py → emtable/tests/test_basic.py

@@ -1,16 +1,39 @@
+# **************************************************************************
+# *
+# * Authors:  J. M. de la Rosa Trevin ([email protected])
+# *
+# * This program is free software; you can redistribute it and/or modify
+# * it under the terms of the GNU General Public License as published by
+# * the Free Software Foundation; either version 3 of the License, or
+# * (at your option) any later version.
+# *
+# * This program is distributed in the hope that it will be useful,
+# * but WITHOUT ANY WARRANTY; without even the implied warranty of
+# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# * GNU General Public License for more details.
+# *
+# * You should have received a copy of the GNU General Public License
+# * along with this program; if not, write to the Free Software
+# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
+# * 02111-1307  USA
+# *
+# *  All comments concerning this program package may be sent to the
+# *  e-mail address '[email protected]'
+# *
+# **************************************************************************
 
 import sys
 import os
 import psutil
 
 try:
-    from StringIO import StringIO ## for Python 2
+    from StringIO import StringIO  # for Python 2
 except ImportError:
-    from io import StringIO ## for Python 3
+    from io import StringIO  # for Python 3
 import unittest
 
 from metadata import Table
-from strings_star_relion import particles_3d_classify, one_micrograph_mc
+from .strings_star_relion import particles_3d_classify, one_micrograph_mc
 
 here = os.path.abspath(os.path.dirname(__file__))
 
@@ -301,4 +324,3 @@ def read_emcore():
     unittest.main()
     #read_metadata()
     #read_emcore()
-

setup.py

@@ -0,0 +1,66 @@
+# **************************************************************************
+# *
+# * Authors:  J. M. de la Rosa Trevin ([email protected])
+# * Authors:  Grigory Sharov ([email protected])
+# *
+# * This program is free software; you can redistribute it and/or modify
+# * it under the terms of the GNU General Public License as published by
+# * the Free Software Foundation; either version 3 of the License, or
+# * (at your option) any later version.
+# *
+# * This program is distributed in the hope that it will be useful,
+# * but WITHOUT ANY WARRANTY; without even the implied warranty of
+# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# * GNU General Public License for more details.
+# *
+# * You should have received a copy of the GNU General Public License
+# * along with this program; if not, write to the Free Software
+# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
+# * 02111-1307  USA
+# *
+# *  All comments concerning this program package may be sent to the
+# *  e-mail address '[email protected]'
+# *
+# **************************************************************************
+
+"""A setuptools based setup module.
+See:
+https://packaging.python.org/en/latest/distributing.html
+https://github.com/pypa/sampleproject
+"""
+
+# Always prefer setuptools over distutils
+from setuptools import setup, find_packages
+# To use a consistent encoding
+from codecs import open
+from os import path
+
+here = path.abspath(path.dirname(__file__))
+
+# Get the long description from the README file
+with open(path.join(here, 'README.rst'), encoding='utf-8') as f:
+    long_description = f.read()
+
+# Arguments marked as "Required" below must be included for upload to PyPI.
+# Fields marked as "Optional" may be commented out.
+
+setup(
+    name='emtable',  # Required
+    version='0.0.7',  # Required
+    description='Simple module to deal with EM tabular data (aka metadata)',  # Required
+    long_description=long_description,  # Optional
+    url='https://github.com/delarosatrevin/emtable',  # Optional
+    author='J.M. De la Rosa Trevin',  # Optional
+    author_email='[email protected]',  # Optional
+    classifiers=[  # Optional
+        'Development Status :: 4 - Beta',
+        'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
+        'Programming Language :: Python :: 3'
+    ],
+    keywords='electron-microscopy cryo-em structural-biology image-processing',  # Optional
+    packages=find_packages(),
+    project_urls={  # Optional
+        'Bug Reports': 'https://github.com/delarosatrevin/emtable/issues',
+        'Source': 'https://github.com/delarosatrevin/emtable',
+    },
+)