Merge pull request #53 from JuDFTteam/release-0.4.8

Release 0.4.8

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.4.7
+current_version = 0.4.8
 commit = True
 tag = True
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?

.github/workflows/cd.yml

@@ -17,10 +17,10 @@ jobs:
     steps:
     - uses: actions/checkout@v2
 
-    - name: Set up Python 3.7
+    - name: Set up Python 3.8
       uses: actions/setup-python@v2
       with:
-        python-version: 3.7
+        python-version: 3.8
 
     - name: Cache python dependencies
       id: cache-pip
@@ -45,11 +45,23 @@ jobs:
       run: |
         SPHINXOPTS='-nW' make -C docs html
 
-
   pre-commit:
     runs-on: ubuntu-latest
     timeout-minutes: 30
 
+    strategy:
+      matrix:
+        include:
+          - name: pre-commit-errors
+            skip-hooks: pylint-warnings
+            strict: false
+          - name: pre-commit-warnings
+            skip-hooks: pylint-errors
+            strict: true
+
+    name: ${{ matrix.name }}
+    continue-on-error: ${{ matrix.strict }}
+
     steps:
     - uses: actions/checkout@v2
 
@@ -74,7 +86,7 @@ jobs:
 
     - name: Run pre-commit
       run: |
-        pre-commit run --all-files || (git status --short; git diff ; exit 1)
+        SKIP=${{ matrix.skip-hooks }} pre-commit run --all-files || (git status --short; git diff ; exit 1)
 
   tests:
 
@@ -109,7 +121,7 @@ jobs:
 
     - name: Run pytest
       run: |
-        cd masci_tools/tests/ && ./run_all_cov.sh
+        cd tests/ && ./run_all_cov.sh
 
     - name: Upload code coverage report
       run: |
@@ -118,7 +130,7 @@ jobs:
 
   publish:
     name: Publish to PyPi
-    needs: [docs, tests] # pre-commit is not yet ready (so we cannot depend on it)
+    needs: [docs, tests, pre-commit] #pylint-warnings could be added at some later point
     if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
     runs-on: ubuntu-latest
     steps:

.github/workflows/ci.yml

@@ -11,10 +11,10 @@ jobs:
     steps:
     - uses: actions/checkout@v2
 
-    - name: Set up Python 3.7
+    - name: Set up Python 3.8
       uses: actions/setup-python@v2
       with:
-        python-version: 3.7
+        python-version: 3.8
 
     - name: Cache python dependencies
       id: cache-pip
@@ -40,10 +40,22 @@ jobs:
         SPHINXOPTS='-nW' make -C docs html
 
   pre-commit:
-
     runs-on: ubuntu-latest
     timeout-minutes: 30
 
+    strategy:
+      matrix:
+        include:
+          - name: pre-commit-errors
+            skip-hooks: pylint-warnings
+            strict: false
+          - name: pre-commit-warnings
+            skip-hooks: pylint-errors
+            strict: true
+
+    name: ${{ matrix.name }}
+    continue-on-error: ${{ matrix.strict }}
+
     steps:
     - uses: actions/checkout@v2
 
@@ -56,10 +68,10 @@ jobs:
         restore-keys: |
           pip-pre-commit-
 
-    - name: Set up Python 3.7
+    - name: Set up Python 3.8
       uses: actions/setup-python@v2
       with:
-        python-version: 3.7
+        python-version: 3.8
 
     - name: Install python dependencies
       run: |
@@ -68,7 +80,8 @@ jobs:
 
     - name: Run pre-commit
       run: |
-        pre-commit run --all-files || (git status --short; git diff ; exit 1)
+        SKIP=${{ matrix.skip-hooks }} pre-commit run --all-files || (git status --short; git diff ; exit 1)
+
 
   tests:
 
@@ -103,7 +116,7 @@ jobs:
 
     - name: Run pytest
       run: |
-        cd masci_tools/tests/ && ./run_all_cov.sh
+        cd tests/ && ./run_all_cov.sh
 
     - name: Upload code coverage report
       run: |

.gitignore

@@ -21,6 +21,7 @@ publish_to_pypi.sh
 __pycache__/
 *.py[cod]
 *$py.class
+*.py.bak
 
 # C extensions
 *.so

.pre-commit-config.yaml

@@ -10,9 +10,12 @@ repos:
       types: [python]
     - id: trailing-whitespace
       types: [python]
+    - id: check-yaml
+    - id: check-added-large-files
+    - id: forbid-new-submodules
 
 - repo: git://github.com/pre-commit/mirrors-yapf
-  rev: v0.30.0
+  rev: v0.31.0
   hooks:
   - id: yapf
     name: yapf
@@ -23,12 +26,31 @@ repos:
         )$
     args: ['-i']
 
+- repo: https://github.com/ikamensh/flynt/
+  rev: '0.55'
+  hooks:
+  -   id: flynt
+      args: [
+          '--line-length=120',
+          '--fail-on-change',
+      ]
+
 - repo: local
   hooks:
 
-  - id: pylint
-    name: pylint
+  - id: pylint-errors
+    name: pylint-errors
+    entry: pylint
+    args: [-d, W, -d, R, -d, C]
+    verbose: true
+    types: [python]
+    language: system
+    exclude: '^(docs/)|(examples/)'
+
+  - id: pylint-warnings
+    name: pylint-warnings
     entry: pylint
+    verbose: true
     types: [python]
     language: system
     exclude: '^(docs/)|(examples/)'

.readthedocs.yml

@@ -5,7 +5,7 @@ formats:
   - pdf
 
 python:
-  version: 3.7
+  version: 3.8
   install:
     - method: pip
       path: .

docs/source/module_guide/code.rst

@@ -52,6 +52,9 @@ Calculation tools
 .. automodule:: masci_tools.tools.cf_calculation
    :members:
 
+.. automodule:: masci_tools.tools.greensfunction
+   :members:
+
 IO helper functions and file parsers
 +++++++++++++++++++++++++++++++++++++
 

docs/source/user_guide/fleurxmlmodifier.rst

@@ -81,7 +81,7 @@ On the other hand, there are shortcut methods that already know some paths:
     * :py:func:`~masci_tools.io.fleurxmlmodifier.FleurXMLModifier.set_attrib_value()`: user-friendly method for setting attributes in the xml file by specifying their name
     * :py:func:`~masci_tools.io.fleurxmlmodifier.FleurXMLModifier.set_first_attrib_value()`: user-friendly method for setting the first occurrence of an attribute in the xml file by specifying its name
     * :py:func:`~masci_tools.io.fleurxmlmodifier.FleurXMLModifier.add_number_to_attrib()`: user-friendly method for adding to or multiplying values of attributes in the xml file by specifying their name
-    * :py:func:`~masci_tools.io.fleurxmlmodifier.FleurXMLModifier.set_first_attrib_value()`: user-friendly method for adding to or multiplying values of the first occurrence of an attribute in the xml file by specifying its name
+    * :py:func:`~masci_tools.io.fleurxmlmodifier.FleurXMLModifier.add_number_to_first_attrib()`: user-friendly method for adding to or multiplying values of the first occurrence of the attribute in the xml file by specifying their name
     * :py:func:`~masci_tools.io.fleurxmlmodifier.FleurXMLModifier.set_text()`: user-friendly method for setting text on xml elements in the xml file by specifying their name
     * :py:func:`~masci_tools.io.fleurxmlmodifier.FleurXMLModifier.set_first_text()`: user-friendly method for setting the text on the first occurrence of an xml element in the xml file by specifying its name
     * :py:func:`~masci_tools.io.fleurxmlmodifier.FleurXMLModifier.set_simple_tag()`: user-friendly method for creating and setting attributes on simple xml elements (only attributes) in the xml file by specifying its name

masci_tools/__init__.py

@@ -13,6 +13,6 @@
 '''
 import logging
 
-__version__ = '0.4.7'
+__version__ = '0.4.8'
 
 logging.getLogger(__name__).addHandler(logging.NullHandler())

masci_tools/io/common_functions.py

@@ -353,8 +353,7 @@ def get_ef_from_potfile(potfile):
     """
     extract fermi energy from potfile
     """
-    f = open_general(potfile)
-    with f:
+    with open_general(potfile) as f:
         txt = f.readlines()
     ef = float(txt[3].split()[1])
     return ef
@@ -411,14 +410,14 @@ def convert_to_fortran(val, quote_strings=True):
         else:
             val_str = '.false.'
     elif isinstance(val, numbers.Integral):
-        val_str = '{:d}'.format(val)
+        val_str = f'{val:d}'
     elif isinstance(val, numbers.Real):
-        val_str = ('{:18.10e}'.format(val)).replace('e', 'd')
+        val_str = f'{val:18.10e}'.replace('e', 'd')
     elif isinstance(val, str):
         if quote_strings:
-            val_str = "'{!s}'".format(val)
+            val_str = f"'{val!s}'"
         else:
-            val_str = '{!s}'.format(val)
+            val_str = f'{val!s}'
     else:
         raise ValueError(f"Invalid value '{val}' of type '{type(val)}' passed, accepts only booleans, ints, "
                          'floats and strings')

masci_tools/io/fleurxmlmodifier.py

@@ -18,7 +18,7 @@
 """
 from collections import namedtuple
 from lxml import etree
-import copy
+
 from masci_tools.util.xml.collect_xml_setters import XPATH_SETTERS, SCHEMA_DICT_SETTERS, NMMPMAT_SETTERS
 #Enable warnings for missing docstrings
 #pylint: enable=missing-function-docstring
@@ -83,7 +83,6 @@ def __init__(self, validate_signatures=True):
         self._tasks = []
         self.validate_signatures = validate_signatures
 
-
     @classmethod
     def fromList(cls, task_list, *args, **kwargs):
         """
@@ -98,17 +97,25 @@ def fromList(cls, task_list, *args, **kwargs):
         """
 
         fm = cls(*args, **kwargs)
+        fm.add_task_list(task_list)
+        return fm
+
+    def add_task_list(self, task_list):
+        """
+        Add a list of tasks to be added
+
+        :param task_list: list of tuples first index is the name of the method
+                          second is defining the arguments by keyword in a dict
+        """
 
-        facade_methods = fm.get_avail_actions()
+        facade_methods = self.get_avail_actions()
 
         for name, kwargs in task_list:
             try:
                 facade_methods[name](**kwargs)
             except KeyError as exc:
                 raise ValueError(f"Unknown modification method '{name}'") from exc
 
-        return fm
-
     def _validate_signature(self, name, *args, **kwargs):
         """
         Validate that the given arguments to the registration
@@ -139,7 +146,7 @@ def _validate_signature(self, name, *args, **kwargs):
             except TypeError as exc:
                 raise TypeError(
                     f"The given arguments for the registration method '{name}' are not valid for the XML modifying function"
-                ) from exc
+                    f'The following error was raised: {exc}') from exc
 
     @classmethod
     def apply_modifications(cls, xmltree, nmmp_lines, modification_tasks, validate_changes=True):
@@ -180,10 +187,6 @@ def apply_modifications(cls, xmltree, nmmp_lines, modification_tasks, validate_c
                 action = cls.nmmpmat_functions[task.name]
                 nmmp_lines = action(xmltree, nmmp_lines, schema_dict, *task.args, **task.kwargs)
 
-            elif task.name in cls.no_xmltree_functions:
-                action = cls.nmmpmat_functions[task.name]
-                nmmp_lines = action(xmltree, nmmp_lines, schema_dict, *task.args, **task.kwargs)
-
             else:
                 raise ValueError(f'Unknown task {task.name}')