Merge pull request #167 from JuDFTteam/release-1.3.1

🚀 Release 1.3.1

.zenodo.json

@@ -1,7 +1,7 @@
 {
  "upload_type": "software",
  "language": "eng", 
- "title": "JuDFTteam/aiida-fleur: AiiDA-FLEUR release v1.2.1", 
+ "title": "JuDFTteam/aiida-fleur: AiiDA-FLEUR", 
  "license": {
  "id": "MIT"
  }, 
@@ -75,5 +75,5 @@
  "identifier": "https://www.wikidata.org/wiki/Q6786605"
  }
  ], 
- "description": "<p><strong> This software contains a plugin that enables the usage of the all-electron DFT FLEUR program with the AiiDA framework.</strong></p>\n\n<p>Feel free to contribute.</p>\n\nThe code is hosted on GitHub at: https://github.com/JuDFTteam/aiida-fleur</p>\n\n<p>The documentation is hosted on https://aiida-fleur.readthedocs.io.</p>\n\n<p>Most functionality and workflows was developed for the use with the DFT program FLEUR developed at the Forschungszentrum J&uuml;lich (see http://judft.de, https://flapw.de for further information on the codes) and in the context of the AiiDA framework (https://aiida.net).</p>\n\n<p><strong>Installation</strong></p>\n\n<blockquote>\n<p><br>\npip install aiida-core<br>\n&nbsp;</p>\n</blockquote>\n\n<p><strong>Dependencies</strong></p>\n\n<p>These python packages are needed:</p>\n\n<ul>\n\t<li>`aiida-core[atomic_tools]`</li>\n\t<li>`masci-tools`</li>\n\t<li>`lxml`</li>\n\t<li>`pyhull` &nbsp;</li>\n\t<li>`sympy`</li>\n\t<li>`numpy`</li>\n\t<li>`future`</li>\n\t<li>`pyhull`</li>\n\t<li>`sqlalchemy<1.4`</li>\n</ul>\n\n<p><strong>Layout of aiida-fleur</strong></p>\n\n<ul>\n\t<li>&nbsp;`calculation`: Contains AiiDA job calculation plugins for the inpgen code and the FLEUR code.\n\t<ul>\n\t<li>`cmdline`: Contains files for the commandline interface.</li>\n\t</ul>\n\t</li>\n\t<li>`tests`: auto tests of `aiida-fleur` functions</li>\n\t<li>`common`: Contains base classes and constants which are used throughout the package.</li>\n\t<li>`data`: Contains AiiDA data plugins specific to FLEUR.</li>\n\t<li>`parsers`: Contains parser AiiDA plugins for the job calculation plugins.</li>\n\t<li>`tools`: Contains basic utility and high level utility which is rather complete</li>\n\t<li>`workflows`: Contains a collection of AiiDA workchains (workflows) specific to FLEUR which have HPC and HTC capabilties with full provenance tracking. </li>\n</ul>\n\n<p><strong>License</strong>:<br>\naiida-fleur is distributed under the terms and conditions of the MIT license which is specified in the `LICENSE` file.</p>"
+ "description": "<p><strong> This software contains a plugin that enables the usage of the all-electron DFT FLEUR program with the AiiDA framework.</strong></p>\n\n<p>Feel free to contribute.</p>\n\nThe code is hosted on GitHub at: https://github.com/JuDFTteam/aiida-fleur</p>\n\n<p>The documentation is hosted on https://aiida-fleur.readthedocs.io.</p>\n\n<p>Most functionality and workflows was developed for the use with the DFT program FLEUR developed at the Forschungszentrum J&uuml;lich (see http://judft.de, https://flapw.de for further information on the codes) and in the context of the AiiDA framework (https://aiida.net).</p>\n\n<p><strong>Installation</strong></p>\n\n<blockquote>\n<p><br>\npip install aiida-fleur<br>\n&nbsp;</p>\n</blockquote>\n\n<p><strong>Dependencies</strong></p>\n\n<p>These python packages are needed:</p>\n\n<ul>\n\t<li>`aiida-core[atomic_tools]`</li>\n\t<li>`masci-tools`</li>\n\t<li>`lxml`</li>\n\t<li>`pyhull` &nbsp;</li>\n\t<li>`sympy`</li>\n\t<li>`numpy`</li>\n\t<li>`future`</li>\n\t<li>`pyhull`</li>\n\t<li>`sqlalchemy<1.4`</li>\n</ul>\n\n<p><strong>Layout of aiida-fleur</strong></p>\n\n<ul>\n\t<li>&nbsp;`calculation`: Contains AiiDA job calculation plugins for the inpgen code and the FLEUR code.\n\t<ul>\n\t<li>`cmdline`: Contains files for the commandline interface.</li>\n\t</ul>\n\t</li>\n\t<li>`tests`: auto tests of `aiida-fleur` functions</li>\n\t<li>`common`: Contains base classes and constants which are used throughout the package.</li>\n\t<li>`data`: Contains AiiDA data plugins specific to FLEUR.</li>\n\t<li>`parsers`: Contains parser AiiDA plugins for the job calculation plugins.</li>\n\t<li>`tools`: Contains basic utility and high level utility which is rather complete</li>\n\t<li>`workflows`: Contains a collection of AiiDA workchains (workflows) specific to FLEUR which have HPC and HTC capabilties with full provenance tracking. </li>\n</ul>\n\n<p><strong>License</strong>:<br>\naiida-fleur is distributed under the terms and conditions of the MIT license which is specified in the `LICENSE` file.</p>"
 }

CHANGELOG.md

@@ -1,5 +1,11 @@
 # Changelog
 
+## v.1.3.1
+### release compatible with AiiDA-core 1.3.0+
+- Fix for masci-tools dependency constraint. The constraint would previously reject the next minor version of masci-tools (i.e `0.10.0`)
+- Small fixes in zenodo metadata
+- Added `convert_inpxml` method to `FleurinpData` to convert to different file versions
+
 ## v.1.3.0
 ### release compatible with AiiDA-core 1.3.0+
 - Guraranteed support for Fleur versions up to Max6

README.md

@@ -7,7 +7,7 @@
 [![Build status](https://github.com/JuDFTteam/aiida-fleur/workflows/aiida-fleur/badge.svg?branch=develop&event=push)](https://github.com/JuDFTteam/aiida-fleur/actions)
 [![Documentation Status](https://readthedocs.org/projects/aiida-fleur/badge/?version=develop)](https://aiida-fleur.readthedocs.io/en/develop/?badge=develop)
 [![codecov](https://codecov.io/gh/JuDFTteam/aiida-fleur/branch/develop/graph/badge.svg)](https://codecov.io/gh/JuDFTteam/aiida-fleur)
-
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5531549.svg)](https://doi.org/10.5281/zenodo.5531549)
 
 This software contains a plugin that enables the usage of the all-electron
 DFT [FLEUR code](http://www.flapw.de) with the [AiiDA framework](http://www.aiida.net).

aiida_fleur/__init__.py

@@ -11,4 +11,4 @@
 '''
 AiiDA-FLEUR
 '''
-__version__ = '1.3.0'
+__version__ = '1.3.1'

aiida_fleur/data/fleurinp.py

@@ -18,14 +18,14 @@
 # TODO: 2D cell get kpoints and get structure also be carefull with tria = T!!!
 # TODO : maybe save when get_structure or get_kpoints was executed on fleurinp,
 # because otherwise return this node instead of creating a new one!
-
 import os
 import io
 import re
 
 from lxml import etree
 import warnings
 
+from aiida import orm
 from aiida.orm import Data, Node, load_node, CalcJobNode, Bool
 from aiida.common.exceptions import InputValidationError, ValidationError
 from aiida.engine.processes.functions import calcfunction as cf
@@ -98,7 +98,7 @@ class FleurinpData(Data):
  FleurinpData that way and start a new calculation from it.
  """
 
- __version__ = '0.5.0'
+ __version__ = '0.6.0'
 
  def __init__(self, **kwargs):
  """
@@ -655,3 +655,49 @@ def get_tag(self, xpath):
  root = xmltree.getroot()
 
  return eval_xpath(root, xpath)
+
+ @cf
+ def convert_inpxml(self, to_version: orm.Str) -> 'FleurinpData':
+ """
+ Convert the fleurinp data node to a different inp.xml version
+ and return a clone of the node
+
+ .. note::
+ If the Fleurinp contains included xml trees the resulting
+ FleurinpData will contain only the combined inp.xml
+ """
+ return self.convert_inpxml_ncf(to_version.value)
+
+ def convert_inpxml_ncf(self, to_version: str) -> 'FleurinpData':
+ """
+ Convert the fleurinp data node to a different inp.xml version
+ and return a clone of the node
+
+ .. note::
+ If the Fleurinp contains included xml trees the resulting
+ FleurinpData will contain only the combined inp.xml
+ """
+ from masci_tools.tools.fleur_inpxml_converter import convert_inpxml
+ import tempfile
+ clone = self.clone()
+
+ xmltree, schema_dict = clone.load_inpxml(remove_blank_text=True)
+ try:
+ converted_tree = convert_inpxml(xmltree, schema_dict, to_version)
+ except FileNotFoundError as exc:
+ raise ValueError(
+ f"No conversion available from version {schema_dict['inp_version']} to {to_version}\n"
+ 'Please create the conversion by running\n'
+ f" masci-tools generate-conversion {schema_dict['inp_version']} {to_version}\n") from exc
+
+ clone.del_file('inp.xml')
+ with tempfile.TemporaryDirectory() as td:
+ inpxml_path = os.path.join(td, 'inp.xml')
+ converted_tree.write(inpxml_path, encoding='utf-8', pretty_print=True)
+ clone.set_file(inpxml_path, 'inp.xml')
+
+ # default label and description
+ clone.label = 'fleurinp_converted'
+ clone.description = f"Fleurinpdata converted from version {schema_dict['inp_version']} to {to_version}"
+
+ return clone

setup.json

@@ -1,5 +1,5 @@
 {
- "version": "1.3.0",
+ "version": "1.3.1",
  "name": "aiida-fleur",
  "url": "https://github.com/JuDFTteam/aiida-fleur",
  "license": "MIT License, see LICENSE.txt file.",
@@ -33,7 +33,7 @@
  "lxml~=4.8",
  "numpy~=1.16,>=1.16.4",
  "sympy",
- "masci-tools ~= 0.9.0,>=0.9.1",
+ "masci-tools~=0.9,>=0.9.1",
  "future",
  "pyhull",
  "more_itertools",

tests/conftest.py

@@ -705,7 +705,7 @@ def fleur_local_code(mock_code_factory, pytestconfig, request):
  entry_point='fleur.fleur',
  ignore_files=[
  '_aiidasubmit.sh', 'cdnc', 'out', 'FleurInputSchema.xsd', 'FleurOutputSchema.xsd',
- 'cdn.hdf', 'usage.json', 'cdn*', 'mixing_history.*', 'juDFT_times.json',
+ 'cdn.hdf', 'usage.json', 'cdn*', 'mixing_history*', 'juDFT_times.json',
  '*.config', '*.econfig', 'struct*.xsf', 'band.gnu'
  ])
 

tests/data/test_fleurinp.py

@@ -175,6 +175,23 @@ def test_get_tag(create_fleurinp, inpxmlfilepath):
  assert tag != []
 
 
+def test_fleurinp_convert_inpxml(create_fleurinp):
+ """
+ Test that the convert_inpxml method works correctly
+ """
+ inpxmlfilepath = os.path.abspath(os.path.join(inpxmlfilefolder, '../files/inpxml/FePt/31/inp.xml'))
+
+ fleurinp = create_fleurinp(inpxmlfilepath)
+
+ fleurinp_converted = fleurinp.convert_inpxml_ncf('0.34')
+
+ assert fleurinp_converted.files == ['inp.xml']
+ assert fleurinp_converted.inp_version == '0.34'
+
+ #Random check that the bzintegration tag has moved
+ assert 'bzIntegration' in fleurinp_converted.inp_dict['cell']
+
+
 folderlist = [
  os.path.abspath(os.path.join(inpxmlfilefolder, '../files/inpxml/Fe_1l_SOCXML/files')),
  os.path.abspath(os.path.join(inpxmlfilefolder, '../files/inpxml/FePt')),

tests/workflows/calculations/mock-fleur-1c30a846a65b8818922083f20fda9a73/JUDFT_WARN_ONLY

@@ -0,0 +1 @@
+/n