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materialsproject · Sep 12, 2014 · 8127526 · 8127526
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diff --git a/CHANGES.rst b/CHANGES.rst
@@ -1,6 +1,28 @@
 Change log
 ==========
 
+v3.0.0
+------
+* Pymatgen is now completely Python 2.7 and Python 3.x compatible!
+* Spglib and pyhull have been updated to support Python 3.x.
+* Completely rewritten pure python cifio module (courtesy of William Davidson
+  Richards) removed dependency on PyCIFRW, which has been causing many issues
+  with installation.
+* Structure and Molecule now supports a very convenient to() and from_str and
+  from_file functionality. Instead of trying to load the appropriate parser,
+  you can output and read from the appropriate formats directly. See example
+  usage.
+* ~50% speedup to LinearAssignment code.
+* Continuous integration and contribution guidelines now include Python 3.
+* **Backwards incompatible changes**
+* matgenie.py has now been renamed simply "pmg" for brevity.
+* All deprecated methods in pymatgen 2.x have been removed. E.g.,
+  pymatgen.core.structure_modifier is no longer available.
+* Pymatgen classes now uses the as_dict() method protocol implemented in the
+  Monty package. The to_dict property is now deprecated and will be removed
+  in pymatgen v3.1.
+* Update main docs page examples with the new Structure to, from formats.
+
 v2.10.6
 -------
 * Bug fix for np1.9 incompatibility. Now works.

diff --git a/docs/_static/Basic functionality.html b/docs/_static/Basic functionality.html
diff --git a/docs/_static/Molecule.html b/docs/_static/Molecule.html
diff --git a/docs/change_log.rst b/docs/change_log.rst
@@ -1,6 +1,28 @@
 Change log
 ==========
 
+v3.0.0
+------
+* Pymatgen is now completely Python 2.7 and Python 3.x compatible!
+* Spglib and pyhull have been updated to support Python 3.x.
+* Completely rewritten pure python cifio module (courtesy of William Davidson
+  Richards) removed dependency on PyCIFRW, which has been causing many issues
+  with installation.
+* Structure and Molecule now supports a very convenient to() and from_str and
+  from_file functionality. Instead of trying to load the appropriate parser,
+  you can output and read from the appropriate formats directly. See example
+  usage.
+* ~50% speedup to LinearAssignment code.
+* Continuous integration and contribution guidelines now include Python 3.
+* **Backwards incompatible changes**
+* matgenie.py has now been renamed simply "pmg" for brevity.
+* All deprecated methods in pymatgen 2.x have been removed. E.g.,
+  pymatgen.core.structure_modifier is no longer available.
+* Pymatgen classes now uses the as_dict() method protocol implemented in the
+  Monty package. The to_dict property is now deprecated and will be removed
+  in pymatgen v3.1.
+* Update main docs page examples with the new Structure to, from formats.
+
 v2.10.6
 -------
 * Bug fix for np1.9 incompatibility. Now works.

diff --git a/docs/contributing.rst b/docs/contributing.rst
@@ -92,12 +92,17 @@ following must be satisfied for your contributions to be accepted into pymatgen.
    We allow a few exceptions when they are well-justified (e.g., Element's
    atomic number is given a variable name of capital Z, in line with accepted
    scientific convention), but generally, PEP 8 must be observed.
-3. **Documentation** required for all modules, classes and methods. In
+3. **Python 3**. All code should seamless work with Python 2.7 and Python 3.x.
+   Please read Python's official guidelines on how to write Python 3.x
+   compatible code, including the usage of the "six" package. It is recommended
+   that you install the "python-modernize" package and run it before submitting
+   any pull requests.
+4. **Documentation** required for all modules, classes and methods. In
    particular, the method docstrings should make clear the arguments expected
    and the return values. For complex algorithms (e.g., an Ewald summation), a
    summary of the alogirthm should be provided, and preferably with a link to a
    publication outlining the method in detail.
-4. **IDE**. We highly recommend the use of Eclipse + PyDev or PyCharm. You
+5. **IDE**. We highly recommend the use of Eclipse + PyDev or PyCharm. You
    should also set up pylint and pep8 and turn those on within the Eclipse
    PyDev setup. This will warn of any issues with coding styles.
 

diff --git a/docs/index.rst b/docs/index.rst
@@ -337,8 +337,8 @@ API documentation
 For detailed documentation of all modules and classes, please refer to the
 :doc:`API docs </modules>`.
 
-matgenie.py - Command line tool
--------------------------------
+pmg - Command line tool
+-----------------------
 
 To demonstrate the capabilities of pymatgen and to make it easy for users to
 quickly use the functionality, pymatgen comes with a set of useful scripts
@@ -347,46 +347,46 @@ installed to your path by default when you install pymatgen through the
 typical installation routes.
 
 Here, we will discuss the most versatile of these scripts, known as
-matgenie.py. The typical usage of matgenie.py is::
+pmg. The typical usage of pmg is::
 
-    matgenie.py {analyze, plotdos, plotchgint, convert, symm, view, compare} additional_arguments
+    pmg {analyze, plotdos, plotchgint, convert, symm, view, compare} additional_arguments
 
-At any time, you can use ``"matgenie.py --help"`` or ``"matgenie.py subcommand
+At any time, you can use ``"pmg --help"`` or ``"pmg subcommand
 --help"`` to bring up a useful help message on how to use these subcommands.
 Here are a few examples of typical usages::
 
     #Parses all vasp runs in a directory and display the basic energy
     #information. Saves the data in a file called vasp_data.gz for subsequent
     #reuse.
 
-    matgenie.py analyze .
+    pmg analyze .
 
     #Plot the dos from the vasprun.xml file.
 
-    matgenie.py plotdos vasprun.xml
+    pmg plotdos vasprun.xml
 
     #Convert between file formats. The script attempts to intelligently
     #determine the file type. Input file types supported include CIF,
     #vasprun.xml, POSCAR, CSSR. You can force the script to assume certain file
-    #types by specifying additional arguments. See matgenie.py convert -h.
+    #types by specifying additional arguments. See pmg convert -h.
 
-    matgenie.py convert input_filename output_filename.
+    pmg convert input_filename output_filename.
 
     #Obtain spacegroup information.
 
-    matgenie.py symm -s filename1 filename2
+    pmg symm -s filename1 filename2
 
     #Visualize a structure. Requires VTK to be installed.
 
-    matgenie.py view filename
+    pmg view filename
 
     #Compare two structures for similarity
 
-    matgenie.py compare filename1 filename2
+    pmg compare filename1 filename2
 
     #Generate a POTCAR with symbols Li_sv O and the PBE functional
 
-    matgenie.py generate --potcar Li_sv O --functional PBE
+    pmg generate --potcar Li_sv O --functional PBE
 
 ipmg - A Custom ipython shell
 -----------------------------

diff --git a/docs/latest_changes.rst b/docs/latest_changes.rst
@@ -1,10 +1,24 @@
 Change log
 ==========
 
-v2.10.6
--------
-* Bug fix for np1.9 incompatibility. Now works.
-* Use wheel for pymatgen deployments.
-* matgenie.py is now renamed to pmg for faster CLI usage.
-* Improvements to KPOINTS automatic generation.
-* Simpler and faster Structure.get_all_neighbors
+v3.0.0
+------
+* Pymatgen is now completely Python 2.7 and Python 3.x compatible!
+* Spglib and pyhull have been updated to support Python 3.x.
+* Completely rewritten pure python cifio module (courtesy of William Davidson
+  Richards) removed dependency on PyCIFRW, which has been causing many issues
+  with installation.
+* Structure and Molecule now supports a very convenient to() and from_str and
+  from_file functionality. Instead of trying to load the appropriate parser,
+  you can output and read from the appropriate formats directly. See example
+  usage.
+* ~50% speedup to LinearAssignment code.
+* Continuous integration and contribution guidelines now include Python 3.
+* **Backwards incompatible changes**
+* matgenie.py has now been renamed simply "pmg" for brevity.
+* All deprecated methods in pymatgen 2.x have been removed. E.g.,
+  pymatgen.core.structure_modifier is no longer available.
+* Pymatgen classes now uses the as_dict() method protocol implemented in the
+  Monty package. The to_dict property is now deprecated and will be removed
+  in pymatgen v3.1.
+* Update main docs page examples with the new Structure to, from formats.
diff --git a/docs/pymatgen.analysis.pourbaix.rst b/docs/pymatgen.analysis.pourbaix.rst
@@ -1,6 +1,12 @@
 pymatgen.analysis.pourbaix package
 ==================================
 
+Subpackages
+-----------
+
+.. toctree::
+
+
 Submodules
 ----------
 

diff --git a/docs/pymatgen.core.rst b/docs/pymatgen.core.rst
@@ -90,14 +90,6 @@ pymatgen.core.structure module
     :undoc-members:
     :show-inheritance:
 
-pymatgen.core.structure_modifier module
----------------------------------------
-
-.. automodule:: pymatgen.core.structure_modifier
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
 pymatgen.core.surface module
 ----------------------------
 

diff --git a/pymatgen/__init__.py b/pymatgen/__init__.py
@@ -3,7 +3,7 @@
                         "Sai Jayaraman", "Michael Kocher", "Dan Gunter",
                         "Shreyas Cholia", "Vincent L Chevrier",
                         "Rickard Armiento"])
-__date__ = "Sep 10 2014"
+__date__ = "Sep 12 2014"
 __version__ = "3.0.0"
 
 #Useful aliases for commonly used objects and modules.