Merge pull request #137 from JuDFTteam/release-0.9.0

🚀 Release `0.9.0`

.github/workflows/cd.yml

@@ -27,7 +27,7 @@ jobs:
       uses: actions/cache@v1
       with:
         path: ~/.cache/pip
-        key: pip-docs-${{ hashFiles('**/setup.json') }}
+        key: pip-docs-${{ hashFiles('**/pyproject.toml') }}
         restore-keys: |
           pip-docs-
 
@@ -71,7 +71,7 @@ jobs:
       uses: actions/cache@v1
       with:
         path: ~/.cache/pip
-        key: pip-pre-commit-${{ hashFiles('**/setup.json') }}
+        key: pip-pre-commit-${{ hashFiles('**/pyproject.toml') }}
         restore-keys: |
           pip-pre-commit-
 
@@ -97,6 +97,7 @@ jobs:
     strategy:
       matrix:
         python-version: ['3.10','3.9', '3.8', '3.7']
+      fail-fast: false
 
     steps:
     - uses: actions/checkout@v2
@@ -106,7 +107,7 @@ jobs:
       uses: actions/cache@v1
       with:
         path: ~/.cache/pip
-        key: pip-${{ matrix.python-version }}-tests-${{ hashFiles('**/setup.json') }}
+        key: pip-${{ matrix.python-version }}-tests-${{ hashFiles('**/pyproject.toml') }}
         restore-keys: |
           pip-${{ matrix.python-version }}-tests
 
@@ -129,10 +130,10 @@ jobs:
         codecov
 
     - uses: actions/upload-artifact@v2
+      if: failure()
       with:
-        name: Matplotlib comparison
-        path: mpl-results/fig_comparison.html
-        if-no-files-found: ignore
+        name: matplotlib-comparison-${{ matrix.python-version }}
+        path: mpl-results
 
   publish:
     name: Publish to PyPi

.github/workflows/ci.yml

@@ -21,7 +21,7 @@ jobs:
       uses: actions/cache@v1
       with:
         path: ~/.cache/pip
-        key: pip-docs-${{ hashFiles('**/setup.json') }}
+        key: pip-docs-${{ hashFiles('**/pyproject.toml') }}
         restore-keys: |
           pip-docs-
 
@@ -65,7 +65,7 @@ jobs:
       uses: actions/cache@v1
       with:
         path: ~/.cache/pip
-        key: pip-pre-commit-${{ hashFiles('**/setup.json') }}
+        key: pip-pre-commit-${{ hashFiles('**/pyproject.toml') }}
         restore-keys: |
           pip-pre-commit-
 
@@ -93,6 +93,7 @@ jobs:
       matrix:
         python-version: ['3.10','3.9', '3.8', '3.7']
         experimental: [false]
+      fail-fast: false
 
     name: tests-python-${{ matrix.python-version }}
     continue-on-error: ${{ matrix.experimental }}
@@ -105,7 +106,7 @@ jobs:
       uses: actions/cache@v1
       with:
         path: ~/.cache/pip
-        key: pip-${{ matrix.python-version }}-tests-${{ hashFiles('**/setup.json') }}
+        key: pip-${{ matrix.python-version }}-tests-${{ hashFiles('**/pyproject.toml') }}
         restore-keys: |
           pip-${{ matrix.python-version }}-tests
 
@@ -128,7 +129,7 @@ jobs:
         codecov
 
     - uses: actions/upload-artifact@v2
+      if: failure()
       with:
-        name: Matplotlib comparison
-        path: mpl-results/fig_comparison.html
-        if-no-files-found: ignore
+        name: matplotlib-comparison-${{ matrix.python-version }}
+        path: mpl-results

.pre-commit-config.yaml

@@ -19,7 +19,7 @@ repos:
     - id: check-added-large-files
     - id: forbid-new-submodules
 
-- repo: git://github.com/pre-commit/mirrors-yapf
+- repo: https://github.com/pre-commit/mirrors-yapf
   rev: v0.32.0
   hooks:
   - id: yapf

CHANGELOG.md

@@ -1,6 +1,39 @@
 # Changelog
 
-# v.0.8.0
+## v.0.9.0
+[full changelog](https://github.com/JuDFTteam/masci-tools/compare/v0.8.0...v0.9.0)
+
+### Added
+- New `bokeh` plot routine for matrix plot of rectangle patches with added texts [[#124]](https://github.com/JuDFTteam/masci-tools/pull/124)
+- Added TS contribution to free energy to output of `outxml_parser`
+
+### Improvements
+- Several arguments in XML setter functions were renamed for more consistent signatures.
+  The main changes are 
+   - `attributedict`/`change_dict` -> `changes`
+   - `attributename`/`attribv` -> `name`/`value`
+   - `add_number` -> `number_to_add`
+
+  The old signatures are still supported with deprecations if called via the `FleurXMLModifier` [[#118]](https://github.com/JuDFTteam/masci-tools/pull/118)
+- Remove constraint on `bokeh` version (previously `<=1.4.0`) [[#122]](https://github.com/JuDFTteam/masci-tools/pull/122)
+- Add `only_spin` option and calculate complete non-spinpolarized DOS for `spinpol=False` in `plot_fleur_dos` [[#125]](https://github.com/JuDFTteam/masci-tools/pull/125)
+- Refactored `CFCalculation`, i.e. naming of attributes handling of cutoffs. Added classmethod to construct instance directly from numpy arrays [[#127]](https://github.com/JuDFTteam/masci-tools/pull/127)
+- Refactored plotting methods for `CFCalculation` to allow the same parameter freedom as for the other matplolib routines [[#127]](https://github.com/JuDFTteam/masci-tools/pull/127)
+- Improvement to labels and legends in DOS/bandstructure plots. Matplotlib plots now put the legend centered below the plot and added latex labels to axis and ticks in bokeh (version `2.4.0` needed) [[#133]](https://github.com/JuDFTteam/masci-tools/pull/133)
+- `io_nmmpmat`: Allow negative indices in `read_nmmpmat_block` and raise error for invalid index
+### Bugfixes
+- Fix for signatures of `set_text`/`set_first_text`. These contained names of attribute setting functions [[#118]](https://github.com/JuDFTteam/masci-tools/pull/118)
+- Fix for validating arguments in `FleurXMLModifier` not accepting an argument named `name` when passed by keyword. [[#118]](https://github.com/JuDFTteam/masci-tools/pull/118)
+- Fixed problems in `masci_tools.testing.bokeh` when adding files for new bokeh versions [[#122]](https://github.com/JuDFTteam/masci-tools/pull/122)
+- Several fixes for `plot_fleur_dos`. Using the `area_plot` or specifying `color` explicitely could mess up the color order [[#132]](https://github.com/JuDFTteam/masci-tools/pull/132)
+- Fixed bug in `validate_nmmpmat` and consequently `FleurXMLModifier` not correctly validating denisty matrix files with certain off-diagonal elements being negative [[#135]](https://github.com/JuDFTteam/masci-tools/pull/135)
+- Fix for `HDF5Reader` for compatibility for file handles in `aiida-core` 2.0. The file handles coming from the file repository have no directly attached extension so the check if the file is a hdf file cannot be performed
+
+### For developers
+- Fixed upload of pytest-mpl results artifacts to include the whole directory with images and not just the HTML file [[#117]](https://github.com/JuDFTteam/masci-tools/pull/117)
+- Updated typing to newer version of `lxml-stubs` (`0.4.0`) [[#123]](https://github.com/JuDFTteam/masci-tools/pull/123)
+
+## v.0.8.0
 [full changelog](https://github.com/JuDFTteam/masci-tools/compare/v0.7.2...v0.8.0)
 
 ### Added
@@ -29,13 +62,13 @@
 - Reorganized visualization tests, making the regeneration of baseline images with `pytest-mpl` easier [[#101]](https://github.com/JuDFTteam/masci-tools/pull/101)
 - Switched build system from `setuptools` to `flit`, since this way all the configuration can be specified in the `pyproject.toml` and a lot of duplication of information is avoided (e.g. version numbers) [[#102]](https://github.com/JuDFTteam/masci-tools/pull/102)
 
-# v.0.7.2
+## v.0.7.2
 [full changelog](https://github.com/JuDFTteam/masci-tools/compare/v0.7.1...v0.7.2)
 
 ### Bugfixes
 - Fixed regression in ``set_atomgroup_label`` and ``set_species_label``. These functions could be used in previous versions with atom labels, that do not exist. This is not possible in ``v.0.7.1``. Since some parts of the ``aiida-fleur`` plugin relied on this the behaviour has to be kept.
 
-# v.0.7.1
+## v.0.7.1
 [full changelog](https://github.com/JuDFTteam/masci-tools/compare/v0.7.0...v0.7.1)
 
 ### Added
@@ -190,7 +223,7 @@ This release contains bugifxes for the visualization routines
 - Tool to analyze/work with greensfunctions calculated by Fleur `masci_tools.tools.greensfunction`
 ### Improvements
 - Several improvements of KKR parsers/parameters [[#13]](https://github.com/JuDFTteam/masci-tools/pull/13)
-- Introduced patching functions for the schema dictionaries to manually correct ambiguities (#48)
+- Introduced patching functions for the schema dictionaries to manually correct ambiguities [[#48]](https://github.com/JuDFTteam/masci-tools/pull/48)
 - Improvements of the `HDF5Reader` and  recipes for Fleur DOS/bandstructure calculation
 - For devs:
    - pylint warnings are no longer fatal for the CI jobs

docs/source/conf.py

@@ -27,7 +27,8 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ['sphinx.ext.autodoc',
+extensions = ['myst_parser',
+              'sphinx.ext.autodoc',
               'sphinx.ext.doctest',
               'sphinx.ext.todo',
               'sphinx.ext.coverage',
@@ -45,14 +46,13 @@
                        'lxml': ('https://lxml.de/apidoc/',None),
                        'h5py': ('https://docs.h5py.org/en/latest/', None)}
 
+myst_enable_extensions = []
+
 todo_include_todos = True
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 
-# The suffix of source filenames.
-source_suffix = '.rst'
-
 # The encoding of source files.
 #source_encoding = 'utf-8-sig'
 
@@ -395,15 +395,15 @@
     ('py:obj', 'bool'),
     ('py:obj', 'Mapping'),
     ('py:obj', 'plum'),
-    ('py:class', 'etree._xpath'),
-    ('py:class', 'etree._DictAnyStr'),
     ('py:class', 'etree._XPathObject'),
-    ('py:class', 'etree._XPathEvaluatorBase'),
     ('py:class', 'h5py._hl.group.Group'),
     ('py:class', 'etree._Element'),
+    ('py:class', 'etree.XPath'),
     ('py:class', 'TypeAlias'),
     ('py:class', 'Logger'),
     ('py:class', 'FilterType'),
+    ('py:class', 'XMLLike'),
+    ('py:class', 'etree.XPathElementEvaluator'),
 ]
 
 

docs/source/index.rst

@@ -76,7 +76,14 @@ Module reference (API)
    :maxdepth: 4
 
    module_guide/mg_index
-
+
+Reference
+##########
+
+.. toctree::
+   :maxdepth: 2
+
+   reference/index
 
 
 Indices and tables

docs/source/reference/_changelog.md

@@ -0,0 +1,4 @@
+```{include} ../../../CHANGELOG.md
+:relative-docs: docs/
+:relative-images:
+```

docs/source/reference/index.rst

@@ -0,0 +1,7 @@
+Reference
+==========
+
+.. toctree::
+    :maxdepth: 2
+
+    _changelog.md

masci_tools/__init__.py

@@ -21,7 +21,7 @@
 __copyright__ = ('Copyright (c), Forschungszentrum Jülich GmbH, IAS-1/PGI-1, Germany. '
                  'All rights reserved.')
 __license__ = 'MIT license, see LICENSE.txt file.'
-__version__ = '0.8.0'
+__version__ = '0.9.0'
 __authors__ = 'The JuDFT team. Also see AUTHORS.txt file.'
 
 logging.getLogger(__name__).addHandler(logging.NullHandler())

masci_tools/cmdline/commands/fleur_schema.py

@@ -98,7 +98,7 @@ def add_fleur_schema(schema_file, test_xml_file, overwrite, branch, api_key, fro
             project.files.raw(file_path=f'io/xml/{file_name}', ref=branch, streamed=True, action=f.write)
         echo.echo_success('Download successful')
 
-    xmlschema = etree.parse(os.fspath(schema_file))
+    xmlschema = etree.parse(schema_file)
     xmlschema, _ = clear_xml(xmlschema)
 
     namespaces = {'xsd': 'http://www.w3.org/2001/XMLSchema'}

masci_tools/io/common_functions.py

@@ -16,10 +16,11 @@
 from __future__ import annotations
 
 import io
-from typing import IO, Any, Generator, Iterable, NamedTuple, TypeVar
-try:
-    from typing import TypeAlias  #type:ignore
-except ImportError:
+from typing import IO, Any, Generator, Iterable, NamedTuple, TypeVar, Union, Tuple, List
+import sys
+if sys.version_info >= (3, 10):
+    from typing import TypeAlias
+else:
     from typing_extensions import TypeAlias
 import numpy as np
 from collections.abc import Sequence
@@ -47,9 +48,9 @@ def open_general(filename_or_handle: FileLike, iomode: str | None = None) -> IO[
     if reopen_file:
         if iomode is None:
             iomode = 'r'
-        f = open(filename_or_handle, iomode, encoding='utf8')
+        f = open(filename_or_handle, iomode, encoding='utf8')  #type:ignore[arg-type]
     else:
-        f = filename_or_handle
+        f = filename_or_handle  #type:ignore[assignment]
         if f.closed:  # reopen file if it was closed before
             if iomode is None:
                 f = open(f.name, f.mode, encoding='utf8')
@@ -446,9 +447,9 @@ def is_sequence(arg: Any) -> bool:
     return isinstance(arg, Sequence) and not isinstance(arg, str)
 
 
-_TVectorType = TypeVar('_TVectorType', 'tuple[float, float, float]', 'list[float]', np.ndarray)
+VectorType: TypeAlias = Union[Tuple[float, float, float], List[float], np.ndarray]
+_TVectorType = TypeVar('_TVectorType', bound=VectorType)
 """Generic type variable for atom position types"""
-VectorType: TypeAlias = 'tuple[float, float, float] | list[float] |  np.ndarray'
 
 
 def abs_to_rel(vector: _TVectorType, cell: list[list[float]] | np.ndarray) -> _TVectorType:
@@ -476,7 +477,7 @@ def abs_to_rel(vector: _TVectorType, cell: list[list[float]] | np.ndarray) -> _T
         return relative_vector.tolist()
     if isinstance(vector, tuple):
         return tuple(relative_vector)  #type:ignore
-    return relative_vector
+    return relative_vector  #type:ignore[return-value]
 
 
 def abs_to_rel_f(vector: _TVectorType, cell: list[list[float]] | np.ndarray, pbc: tuple[bool, bool,
@@ -514,7 +515,7 @@ def abs_to_rel_f(vector: _TVectorType, cell: list[list[float]] | np.ndarray, pbc
         return relative_vector.tolist()
     if isinstance(vector, tuple):
         return tuple(relative_vector)  #type:ignore
-    return relative_vector
+    return relative_vector  #type:ignore[return-value]
 
 
 def rel_to_abs(vector: _TVectorType, cell: list[list[float]] | np.ndarray) -> _TVectorType:
@@ -572,7 +573,7 @@ def rel_to_abs_f(vector: _TVectorType, cell: list[list[float]] | np.ndarray) ->
         return absolute_vector.tolist()
     if isinstance(vector, tuple):
         return tuple(absolute_vector)  #type:ignore
-    return absolute_vector
+    return absolute_vector  #type:ignore[return-value]
 
 
 def find_symmetry_relation(from_pos: VectorType,

masci_tools/io/fleur_inpgen.py

@@ -374,7 +374,7 @@ def write_inpgen_file(cell: np.ndarray | list[list[float]],
         if isinstance(file, io.IOBase):
             file.write(inpgen_file_content_str)
         else:
-            with open(file, 'w', encoding='utf-8') as inpfile:
+            with open(file, 'w', encoding='utf-8') as inpfile:  #type:ignore[arg-type]
                 inpfile.write(inpgen_file_content_str)
 
     return inpgen_file_content_str
@@ -493,8 +493,8 @@ def read_inpgen_file(
     if isinstance(file, io.IOBase):
         contents = file.read()
     else:
-        if os.path.exists(file):
-            with open(file, encoding='utf-8') as f:
+        if os.path.exists(file):  #type:ignore[arg-type]
+            with open(file, encoding='utf-8') as f:  #type:ignore[arg-type]
                 contents = f.read()
         else:
             contents = file