Merge pull request #216 from JuDFTteam/release-0.14.0

🚀 Release `0.14.0`

.github/workflows/cd.yml

@@ -31,13 +31,13 @@ jobs:
     - uses: actions/checkout@v3
 
     - name: Set up Python 3.10
-      uses: actions/setup-python@v4.2.0
+      uses: actions/setup-python@v4.3.0
       with:
         python-version: '3.10'
 
     - name: Cache python dependencies
       id: cache-pip
-      uses: actions/cache@v3.0.6
+      uses: actions/cache@v3.0.9
       with:
         path: ~/.cache/pip
         key: pip-docs-${{ hashFiles('**/pyproject.toml') }}
@@ -82,15 +82,15 @@ jobs:
 
     - name: Cache python dependencies
       id: cache-pip
-      uses: actions/cache@v3.0.6
+      uses: actions/cache@v3.0.9
       with:
         path: ~/.cache/pip
         key: pip-pre-commit-${{ hashFiles('**/pyproject.toml') }}
         restore-keys: |
           pip-pre-commit-
 
     - name: Set up Python 3.8
-      uses: actions/setup-python@v4.2.0
+      uses: actions/setup-python@v4.3.0
       with:
         python-version: 3.8
 
@@ -112,10 +112,12 @@ jobs:
       matrix:
         python-version: ['3.10','3.9', '3.8']
         experimental: [false]
+        extra-dependencies: ['testing,bokeh-plots,cmdline-extras']
         pytest-cmdline: ['']
         include:
           - python-version: '3.7'
             experimental: false
+            extra-dependencies: 'testing,bokeh-plots'
             pytest-cmdline: '-o addopts="--cov=masci_tools --cov=tests --cov-report xml"'
         # include:
         #   - python-version: '3.11-dev'
@@ -130,22 +132,22 @@ jobs:
 
     - name: Cache python dependencies
       id: cache-pip
-      uses: actions/cache@v3.0.6
+      uses: actions/cache@v3.0.9
       with:
         path: ~/.cache/pip
         key: pip-${{ matrix.python-version }}-tests-${{ hashFiles('**/pyproject.toml') }}
         restore-keys: |
           pip-${{ matrix.python-version }}-tests
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4.2.0
+      uses: actions/setup-python@v4.3.0
       with:
         python-version: ${{ matrix.python-version }}
 
 
     - name: Install python dependencies
       run: |
-        pip install -e .[testing,bokeh-plots]
+        pip install -e .[${{ matrix.extra-dependencies }}]
         pip install pyhull
 
     - name: Run pytest
@@ -170,7 +172,7 @@ jobs:
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python 3.7
-        uses: actions/setup-python@v4.2.0
+        uses: actions/setup-python@v4.3.0
         with:
           python-version: 3.7
       - name: Install flit

.github/workflows/ci.yml

@@ -25,13 +25,13 @@ jobs:
     - uses: actions/checkout@v3
 
     - name: Set up Python 3.10
-      uses: actions/setup-python@v4.2.0
+      uses: actions/setup-python@v4.3.0
       with:
         python-version: '3.10'
 
     - name: Cache python dependencies
       id: cache-pip
-      uses: actions/cache@v3.0.6
+      uses: actions/cache@v3.0.9
       with:
         path: ~/.cache/pip
         key: pip-docs-${{ hashFiles('**/pyproject.toml') }}
@@ -76,15 +76,15 @@ jobs:
 
     - name: Cache python dependencies
       id: cache-pip
-      uses: actions/cache@v3.0.6
+      uses: actions/cache@v3.0.9
       with:
         path: ~/.cache/pip
         key: pip-pre-commit-${{ hashFiles('**/pyproject.toml') }}
         restore-keys: |
           pip-pre-commit-
 
     - name: Set up Python 3.8
-      uses: actions/setup-python@v4.2.0
+      uses: actions/setup-python@v4.3.0
       with:
         python-version: 3.8
 
@@ -107,10 +107,12 @@ jobs:
       matrix:
         python-version: ['3.10','3.9', '3.8']
         experimental: [false]
+        extra-dependencies: ['testing,bokeh-plots,cmdline-extras']
         pytest-cmdline: [""]
         include:
           - python-version: '3.7'
             experimental: false
+            extra-dependencies: 'testing,bokeh-plots'
             pytest-cmdline: '-o addopts="--cov=masci_tools --cov=tests --cov-report xml"'
           #- python-version: '3.11.0-rc.2'
           #  experimental: true
@@ -125,15 +127,15 @@ jobs:
 
     - name: Cache python dependencies
       id: cache-pip
-      uses: actions/cache@v3.0.6
+      uses: actions/cache@v3.0.9
       with:
         path: ~/.cache/pip
         key: pip-${{ matrix.python-version }}-tests-${{ hashFiles('**/pyproject.toml') }}
         restore-keys: |
           pip-${{ matrix.python-version }}-tests
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4.2.0
+      uses: actions/setup-python@v4.3.0
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -148,7 +150,7 @@ jobs:
 
     - name: Install python dependencies
       run: |
-        pip install -e .[testing,bokeh-plots]
+        pip install -e .[${{ matrix.extra-dependencies }}]
         pip install pyhull
 
     - name: Run pytest

.github/workflows/fleur-release.yml

@@ -14,7 +14,7 @@ jobs:
     - uses: actions/checkout@v3
 
     - name: Set up Python 3.8
-      uses: actions/setup-python@v4.2.0
+      uses: actions/setup-python@v4.3.0
       with:
         python-version: 3.8
 
@@ -40,7 +40,7 @@ jobs:
       run: exit 1
 
     - name: Create Pull Request
-      uses: peter-evans/create-pull-request@v4.0.4
+      uses: peter-evans/create-pull-request@v4.1.3
       with:
         commit-message: "[fleur release] Fleur schema update"
         branch: fleur-release/schema

.pre-commit-config.yaml

@@ -5,7 +5,7 @@ ci:
 
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v4.4.0
     hooks:
     - id: double-quote-string-fixer
       types: [python]
@@ -33,7 +33,7 @@ repos:
     additional_dependencies: ['toml']
 
 - repo: https://github.com/ikamensh/flynt/
-  rev: '0.76'
+  rev: '0.77'
   hooks:
   -   id: flynt
       args: [
@@ -42,7 +42,7 @@ repos:
       ]
 
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v2.37.3
+    rev: v3.3.0
     hooks:
     -   id: pyupgrade
         args: [

CHANGELOG.md

@@ -1,10 +1,29 @@
 # Changelog
 
 ## latest
-[full changelog](https://github.com/JuDFTteam/masci-tools/compare/v0.13.0...develop)
+[full changelog](https://github.com/JuDFTteam/masci-tools/compare/v0.14.0...develop)
 
 Nothing here yet
 
+## v.0.14.0
+[full changelog](https://github.com/JuDFTteam/masci-tools/compare/v0.13.0...v0.14.0)
+
+### Added
+- Command `masci-tools convert-inpgen` to transform common structure formats, e.g. `cif` into inpgen files. Uses `ase` or `pymatgen` with the corresponding fleur plugins `ase-fleur` and `pymatgen-io-fleur` (install additional dependencies `cmdline-extras`)[[#215]](https://github.com/JuDFTteam/masci-tools/pull/215)
+- Functions `get_inpgen_comments` and `readd_inpgen_comments` to keep the comments of the inp.xml file containing the inpgen commandline and file content through functions using `clear_xml`
+
+### Improvements
+- `write/read_fleur_inpgen` now supports the magnetic moment definitions in the inpgen input file introduced in MaX-6.1 (also the `scf` namelist) [[#213]](https://github.com/JuDFTteam/masci-tools/pull/213)
+- `get_structuredata` also reads out the magnetic moments [[#213]](https://github.com/JuDFTteam/masci-tools/pull/213)
+- `FleurXMLModifier.modify_xmlfile` now keeps the inpgen comments by default (controlled by option `keep_inpgen_comments`)
+
+### Bugfixes
+- Serveral fixes for Fleur DOS plots [[#212]](https://github.com/JuDFTteam/masci-tools/pull/212):
+  - Fixed wrong summation of atom weights for files containing 10 or more atomtypes
+  - Fixed crashes using a custom weight not conforming to the naming scheme of weights in the `banddos.hdf`
+  - Fixed specification of parameters by DOS label not working if the spin suffix is omitted
+
+
 ## v.0.13.0
 [full changelog](https://github.com/JuDFTteam/masci-tools/compare/v0.12.0...v0.13.0)
 

codecov.yml

@@ -26,5 +26,5 @@ comment:
   require_changes: no
 
 ignore:
-  - "masci_tools/util/kkr_rms_tracker.py"
-  - "masci_tools/util/modifypotential.py"
+  - "masci_tools/tools/kkr_rms_tracker.py"
+  - "masci_tools/tools/modifypotential.py"

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__ = '0.13.0'
+__version__ = '0.14.0'
 __authors__ = 'The JuDFT team. Also see AUTHORS.txt file.'
 
 logging.getLogger(__name__).addHandler(logging.NullHandler())

masci_tools/cmdline/commands/__init__.py

@@ -1,4 +1,4 @@
 """
 Import all the command groups to include in the cli
 """
-from . import (fleur_schema, parse, plot, tools)
+from . import (convert_inpgen, fleur_schema, parse, plot, tools)

masci_tools/cmdline/commands/convert_inpgen.py

@@ -0,0 +1,51 @@
+"""
+CLI commands for converting common structure definition formats to fleur inpgen files
+"""
+from .root import cli
+import click
+
+from pathlib import Path
+import os
+
+from masci_tools.cmdline.utils import echo
+
+try:
+    import pymatgen
+    from pymatgen.core import Structure
+except ImportError:
+    pymatgen = None
+
+try:
+    import ase
+    from ase.io import read, write
+except ImportError:
+    ase = None
+
+
+@cli.command('convert-inpgen')
+@click.argument('input-file', type=click.Path(exists=True, path_type=Path, resolve_path=True))
+@click.argument('output-file', type=click.Path(path_type=Path, resolve_path=True))
+@click.option('-c',
+              '--converter',
+              type=click.Choice(['ase', 'pymatgen']),
+              help='Which library is used to read in the given file format',
+              default='pymatgen')
+def convert_inpgen(input_file, output_file, converter):
+    """Convert the given file to an fleur inpgen file
+    """
+
+    input_file = os.fspath(input_file)
+    output_file = os.fspath(output_file)
+
+    if converter == 'ase':
+        if ase is None:
+            echo.echo_critical('ase is not installed. Please install the packages ase and ase-fleur')
+
+        atoms = read(input_file)
+        write(output_file, atoms, format='fleur-inpgen')
+    elif converter == 'pymatgen':
+        if pymatgen is None:
+            echo.echo_critical('pymatgen is not installed. Please install the packages pymatgen and pymatgen-io-fleur')
+
+        struc = Structure.from_file(os.fspath(input_file))
+        struc.to(output_file, fmt='fleur-inpgen')

masci_tools/io/cif2inp_ase.py

@@ -14,6 +14,11 @@
 Independent utility script to convert cif file formats to input for the inpgen code
 Usage: `python cif2inp_ase.py <filename.cif>`
 """
+import warnings
+
+warnings.warn(
+    'The cif2inp_ase.py script is deprecated. Use the command'
+    'masci-tools convert-inpgen <filename.cif> <out-filename> --converter ase', DeprecationWarning)
 
 import sys
 import ase.io

masci_tools/io/common_functions.py

@@ -22,10 +22,10 @@
     from typing import TypeAlias
 else:
     from typing_extensions import TypeAlias
-try:
+if sys.version_info >= (3, 8):
     from typing import Literal
-except ImportError:
-    from typing_extensions import Literal  #type:ignore[misc]
+else:
+    from typing_extensions import Literal
 import numpy as np
 from collections.abc import Sequence
 from masci_tools.util.typing import FileLike
@@ -652,6 +652,7 @@ class AtomSiteProperties(NamedTuple):
     position: list[float]  #TODO could be made generic with VectorType
     symbol: str
     kind: str
+    magnetic_moment: Literal['up', 'down'] | float | list[float] | None = None
 
 
 def get_wigner_matrix(l: int, alpha: float, beta: float, gamma: float = 0.0, inverse: bool = False) -> np.ndarray: