Merge pull request #10 from chrisjsewell/add-pypi-build

Improve `structure_generate`

.gitignore

@@ -3,6 +3,8 @@
 *.swp
 ~*
 *~
+build/
+dist/
 .project
 *.egg*
 .DS_Store

.travis.yml

@@ -16,7 +16,7 @@ matrix:
     - python: 3.6
       env: TEST_TYPE="version"
     - python: 3.6
-      env: TEST_TYPE="pytest" TEST_AIIDA_BACKEND="django"
+      env: TEST_TYPE="pytest" TEST_AIIDA_BACKEND="django" PYPI_DEPLOY=true
     - python: 2.7
       env: TEST_TYPE="pytest" TEST_AIIDA_BACKEND="django"
     - python: 3.6 
@@ -81,3 +81,14 @@ script:
 
 # after_success:
 # - coveralls
+
+deploy:
+  - provider: pypi
+    distributions: "sdist bdist_wheel"
+    user: cjsewell
+    password:
+      secure: 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
+    on:
+      branch: master
+      tags: true
+      condition: $PYPI_DEPLOY = true

README.md

@@ -1,4 +1,5 @@
 [![Build Status](https://travis-ci.org/abelcarreras/aiida-lammps.svg?branch=master)](https://travis-ci.org/abelcarreras/aiida-lammps)
+[![PyPI](https://img.shields.io/pypi/v/aiida-lammps.svg)](https://pypi.python.org/pypi/aiida-lammps/)
 
 # AiiDA LAMMPS plugin
 
@@ -14,6 +15,7 @@ Note: `lammps.combinate` requires `aiida-phonopy` (https://github.com/abelcarrer
 plugin to work, DynaPhoPy can be found in: https://github.com/abelcarreras/aiida-phonopy
 
 - [AiiDA LAMMPS plugin](#AiiDA-LAMMPS-plugin)
+  - [Installation](#Installation)
   - [Built-in Potential Support](#Built-in-Potential-Support)
   - [Examples](#Examples)
     - [Code Setup](#Code-Setup)
@@ -23,6 +25,14 @@ plugin to work, DynaPhoPy can be found in: https://github.com/abelcarreras/aiida
     - [Optimisation Calculation](#Optimisation-Calculation)
     - [MD Calculation](#MD-Calculation)
 
+## Installation
+
+To install from pypi:
+
+```shell
+pip install aiida-lammps
+```
+
 ## Built-in Potential Support
 
 - EAM

aiida_lammps/__init__.py

@@ -1 +1 @@
-__version__ = "0.4.0b3"
+__version__ = "0.4.1b3"

aiida_lammps/calculations/lammps/__init__.py

@@ -110,7 +110,7 @@ class BaseLammpsCalculation(CalcJob):
     _DEFAULT_OUTPUT_INFO_FILE_NAME = "system_info.dump"
     _DEFAULT_OUTPUT_RESTART_FILE_NAME = 'lammps.restart'
 
-    _retrieve_list = ['log.lammps']
+    _retrieve_list = []
     _retrieve_temporary_list = []
     _cmdline_params = ['-in', _INPUT_FILE_NAME]
     _stdout_name = None
@@ -123,6 +123,8 @@ def define(cls, spec):
                    help='lammps potential')
         spec.input('parameters', valid_type=Dict,
                    help='the parameters', required=False)
+        spec.input('metadata.options.cell_transform_filename',
+                   valid_type=six.string_types, default="cell_transform.npy")
         spec.input('metadata.options.output_filename',
                    valid_type=six.string_types, default=cls._DEFAULT_OUTPUT_FILE_NAME)
         spec.input('metadata.options.trajectory_name',
@@ -199,8 +201,11 @@ def prepare_for_submission(self, tempfolder):
         potential_txt = self.inputs.potential.get_potential_file()
 
         # Setup structure
-        structure_txt = generate_lammps_structure(self.inputs.structure,
-                                                  self.inputs.potential.atom_style)
+        structure_txt, struct_transform = generate_lammps_structure(
+            self.inputs.structure, self.inputs.potential.atom_style)
+
+        with open(tempfolder.get_abs_path(self.options.cell_transform_filename), 'w+b') as handle:
+            np.save(handle, struct_transform)
 
         if "parameters" in self.inputs:
             parameters = self.inputs.parameters
@@ -255,7 +260,9 @@ def prepare_for_submission(self, tempfolder):
 
         calcinfo = CalcInfo()
         calcinfo.uuid = self.uuid
-        calcinfo.retrieve_list = self._retrieve_list
+        calcinfo.retrieve_list = self._retrieve_list + [
+            self.options.output_filename,
+            self.options.cell_transform_filename]
         calcinfo.retrieve_temporary_list = self._retrieve_temporary_list
         calcinfo.codes_info = [codeinfo]