From 2ce1b5330ebf30d4fd58b1982106e5dfe45ea783 Mon Sep 17 00:00:00 2001 From: __sp__ Date: Sun, 6 Dec 2015 09:08:07 -0800 Subject: [PATCH] Update dev docs Former-commit-id: 351e42fd6ccbb8e4ea4dce80f98b0ee7173e4f15 [formerly b51be3119b10815588ac514753de7b71d2417683] Former-commit-id: 712e49138cf91710d7dc760bd41d076519811898 --- CHANGES.rst | 9 +++++++++ README.rst | 9 ++------- docs/change_log.rst | 9 +++++++++ docs/installation.rst | 35 +++++++++++++++++++++-------------- docs/latest_changes.rst | 8 ++++++-- docs/pymatgen.io.rst | 16 ++++++++++++++++ pymatgen/__init__.py | 4 ++-- setup.py | 6 +++--- 8 files changed, 68 insertions(+), 28 deletions(-) diff --git a/CHANGES.rst b/CHANGES.rst index b2b8f229a86..6e2123a59e6 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -1,6 +1,15 @@ Change log ========== +v3.2.8 +------ + +* Make pyhull optional. +* Sulfur correction added to MaterialsProjectCompatibility for more accurate + sulfide formation energies. +* ADF io support. (Xin Chen) +* Bug fixes for spacegroup subgroup testing. + v3.2.7 ------ * Add warning for limited subgroup testing functionality in Spacegroup. diff --git a/README.rst b/README.rst index f7af6bfd128..482e8f2931b 100644 --- a/README.rst +++ b/README.rst @@ -30,13 +30,8 @@ Python 3.x support ================== With effect from version 3.0, pymatgen now supports both Python 2.7 as well -as Python 3.x. All underlying core dependencies (numpy, -pyhull and the spglib library) have been made Python 3 compatible, -and a completely rewritten CIF parser module (courtesy of William Davidson -Richards) has removed the dependency on PyCIFRW. We will support Python >= 3.3 -(ignoring v3.1 and v3.2). With the release of a new major version, -we also took the opportunity to streamline and cleanup some of the code, -which introduces a few backward incompatibilities. +as Python 3.x. All developers must ensure that their code passes the +unittests on both Py2.7 and 3.x. Why use pymatgen? ================= diff --git a/docs/change_log.rst b/docs/change_log.rst index b2b8f229a86..6e2123a59e6 100644 --- a/docs/change_log.rst +++ b/docs/change_log.rst @@ -1,6 +1,15 @@ Change log ========== +v3.2.8 +------ + +* Make pyhull optional. +* Sulfur correction added to MaterialsProjectCompatibility for more accurate + sulfide formation energies. +* ADF io support. (Xin Chen) +* Bug fixes for spacegroup subgroup testing. + v3.2.7 ------ * Add warning for limited subgroup testing functionality in Spacegroup. diff --git a/docs/installation.rst b/docs/installation.rst index fe37e66cf49..e494c3e3fa0 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -8,34 +8,41 @@ be available on `PyPI `_. 1. Python 2.7-3.x supported. All critical dependencies of pymatgen already have Python 3.x support. Only a few optional dependencies (VTK and ASE) do not. If you do not need those features, you can choose to work with Python 3. -2. numpy: For array, matrix and other numerical manipulations. Used extensively - by all core modules. -3. pyhull 1.5.2+: For generation of phase diagrams. -4. requests 2.0+: For the high-level interface to the Materials API. -5. monty 0.4.2+: For some common complementary functions, - design patterns (e.g., singleton) and decorators to the Python - standard library. +2. numpy>=1.9 +3. scipy>0.14 +4. monty>=0.7.0 +5. requests 2.0+ +6. pybtex +7. pyyaml +8. tabulate +9. six + +Most of these are fairly easy to install. The well-established numpy and scipy +should have ready-made installation packages for all platforms. The rest are +pure/semi-pure Python packages that installs without any issues with pip and +easy_install. Optional dependencies --------------------- -Optional libraries that are required if you need certain features: +Optional libraries that are required if you need certain features. -1. scipy 0.10+ (highly recommended): For use in Gaussian smearing and faster - Phase Diagrams. +1. pyhull 1.5.2+ (highly recommended): For electronic structure, generation of + Pourbaix diagrams. 2. matplotlib 1.1+ (highly recommended): For plotting (e.g., Phase Diagrams). -3. VTK with Python bindings 5.8+ (http://www.vtk.org/): For visualization of +3. sympy (highly recommended): For defect generation and analysis. +4. VTK with Python bindings 5.8+ (http://www.vtk.org/): For visualization of crystal structures using the pymatgen.vis package. Note that the VTK package is incompatible with Python 3.x at the moment. -4. Atomistic Simulation Environment or ASE 3.6+: Required for the usage of the +5. Atomistic Simulation Environment or ASE 3.6+: Required for the usage of the adapters in pymatgen.io.aseio between pymatgen's core Structure object and the Atoms object used by ASE. Get it at https://wiki.fysik.dtu.dk/ase/. Note that the ASE package is incompatible with Python 3.x at the moment. -5. OpenBabel with Python bindings (http://openbabel.org): Required for the +6. OpenBabel with Python bindings (http://openbabel.org): Required for the usage of the adapters in pymatgen.io.babelio between pymatgen's Molecule and OpenBabel's OBMol. Opens up input and output support for the very large number of input and output formats supported by OpenBabel. -6. nose - For unittesting. Not optional for developers. +7. nose - For unittesting. Not optional for developers. Optional non-Python programs ---------------------------- diff --git a/docs/latest_changes.rst b/docs/latest_changes.rst index 2d3401bbf47..21c0bb34949 100644 --- a/docs/latest_changes.rst +++ b/docs/latest_changes.rst @@ -1,6 +1,10 @@ Change log ========== -v3.2.7 +v3.2.8 ------ -* Add warning for limited subgroup testing functionality in Spacegroup. +* Make pyhull optional. +* Sulfur correction added to MaterialsProjectCompatibility for more accurate + sulfide formation energies. +* ADF io support. (Xin Chen) +* Bug fixes for spacegroup subgroup testing. diff --git a/docs/pymatgen.io.rst b/docs/pymatgen.io.rst index d3ee899bac4..40e4ad0467a 100644 --- a/docs/pymatgen.io.rst +++ b/docs/pymatgen.io.rst @@ -14,6 +14,14 @@ Subpackages Submodules ---------- +pymatgen.io.adf module +---------------------- + +.. automodule:: pymatgen.io.adf + :members: + :undoc-members: + :show-inheritance: + pymatgen.io.aiida module ------------------------ @@ -102,6 +110,14 @@ pymatgen.io.feffio_set module :undoc-members: :show-inheritance: +pymatgen.io.fiesta module +------------------------- + +.. automodule:: pymatgen.io.fiesta + :members: + :undoc-members: + :show-inheritance: + pymatgen.io.gaussian module --------------------------- diff --git a/pymatgen/__init__.py b/pymatgen/__init__.py index 7f5f8380462..28e4764ceb4 100644 --- a/pymatgen/__init__.py +++ b/pymatgen/__init__.py @@ -4,8 +4,8 @@ __email__ ="pymatgen@googlegroups.com" __maintainer__ = "Shyue Ping Ong" __maintainer_email__ ="shyuep@gmail.com" -__date__ = "Nov 19 2015" -__version__ = "3.2.7" +__date__ = "Dec 6 2015" +__version__ = "3.2.8" # Useful aliases for commonly used objects and modules. diff --git a/setup.py b/setup.py index d196a5d6905..b30e6cdb7fd 100644 --- a/setup.py +++ b/setup.py @@ -51,9 +51,9 @@ def get_spglib_ext(): setup( name="pymatgen", packages=find_packages(), - version="3.2.7", - install_requires=["numpy>=1.8", "six", "atomicfile", "requests", - "pybtex", "pyyaml", "monty>=0.7.0", "scipy>=0.10", + version="3.2.8", + install_requires=["numpy>=1.9", "six", "atomicfile", "requests", + "pybtex", "pyyaml", "monty>=0.7.0", "scipy>=0.14", "tabulate"], extras_require={"plotting": ["matplotlib>=1.1", "prettyplotlib"], "pourbaix diagrams, bandstructure": ["pyhull>=1.5.3"],