Merge branch 'main' into Fix-pDOS-issue-959

.github/workflows/cd.yml

@@ -16,10 +16,10 @@ jobs:
         -   name: Checkout source
             uses: actions/checkout@v2
 
-        -   name: Set up Python 3.8
+        -   name: Set up Python 3.9
             uses: actions/setup-python@v2
             with:
-                python-version: '3.8'
+                python-version: '3.9'
 
         -   name: Validate the tag version against the package version
             run: python .github/workflows/validate_release_tag.py $GITHUB_REF
@@ -43,7 +43,7 @@ jobs:
         -   name: Set up Python
             uses: actions/setup-python@v2
             with:
-                python-version: '3.8'
+                python-version: '3.9'
 
         -   name: Install Python dependencies
             run: pip install -e .[pre-commit,tests]
@@ -58,7 +58,7 @@ jobs:
 
         strategy:
             matrix:
-                python-version: ['3.8', '3.9', '3.10', '3.11']
+                python-version: ['3.9', '3.10', '3.11', '3.12']
 
         services:
             postgres:
@@ -100,10 +100,10 @@ jobs:
         -   name: Checkout source
             uses: actions/checkout@v2
 
-        -   name: Set up Python 3.8
+        -   name: Set up Python 3.9
             uses: actions/setup-python@v2
             with:
-                python-version: '3.8'
+                python-version: '3.9'
 
         -   name: Install flit
             run: pip install flit~=3.4

.github/workflows/ci.yml

@@ -22,7 +22,7 @@ jobs:
         -   name: Set up Python
             uses: actions/setup-python@v2
             with:
-                python-version: '3.8'
+                python-version: '3.9'
 
         -   name: Install Python dependencies
             run: pip install -e .[pre-commit,tests]
@@ -36,7 +36,7 @@ jobs:
 
         strategy:
             matrix:
-                python-version: ['3.8', '3.9', '3.10', '3.11']
+                python-version: ['3.9', '3.10', '3.11', '3.12']
 
         services:
             postgres:

.github/workflows/nightly.yml

@@ -20,7 +20,7 @@ jobs:
 
         strategy:
             matrix:
-                python-version: ['3.9', '3.10', '3.11']
+                python-version: ['3.9', '3.10', '3.11', '3.12']
 
         services:
             postgres:

.readthedocs.yml

@@ -15,4 +15,5 @@ python:
 # Let the build fail if there are any warnings
 sphinx:
     builder: html
+    configuration: docs/source/conf.py
     fail_on_warning: true

CHANGELOG.md

@@ -1,3 +1,24 @@
+## v4.8.0
+
+### ✨ New features
+
+* `Hubbard`: add useful utility functions  [[41f196b](https://github.com/aiidateam/aiida-quantumespresso/commit/41f196b2b46022c179bdce0dcd44ab338d956551)]
+* `PwParser`: Add XML schema for Quantum ESPRESSO v7.4 [[75808a9](https://github.com/aiidateam/aiida-quantumespresso/commit/75808a918075b7ef0ac3b82557b5325330ba0fdc)]
+
+### 👌 Improvements
+
+* `PhParser`: allow for pattern initialization  [[74a18bc](https://github.com/aiidateam/aiida-quantumespresso/commit/74a18bc59beafd62082b24f809bfba29a402489d)]
+* `PwBaseWorkChain`: Always do full restart for `ERROR_OUT_OF_WALLTIME` [[fcb8da9](https://github.com/aiidateam/aiida-quantumespresso/commit/fcb8da9a165fc4f6e94c29a6e4f1d29305da4548)]
+
+### 📚 Documentation
+
+* `README.md`: Correct `aiida-core` compatibility [[1c8a804](https://github.com/aiidateam/aiida-quantumespresso/commit/1c8a8049c005e791300b7d2ca7c4beae32257dc9)]
+
+### 🔧 Maintenance
+
+* Devops: Add explicit sphinx.configuration key to RTD conf  [[733c43f](https://github.com/aiidateam/aiida-quantumespresso/commit/733c43ff6b690c19eacb108154038ca93082d145)]
+* Update Python support: drop v3.8 and add v3.12 [[172540b](https://github.com/aiidateam/aiida-quantumespresso/commit/172540be5078e77d58b6a8cc1b28cbae2c6e70b9)]
+
 ## v4.7.0
 
 ### ✨ New features

docs/source/conf.py

@@ -48,9 +48,10 @@
 
 # Setting the intersphinx mapping to other readthedocs
 intersphinx_mapping = {
-    'python': ('https://docs.python.org/3.8', None),
+    'python': ('https://docs.python.org/3.9', None),
     'aiida': ('https://aiida.readthedocs.io/projects/aiida-core/en/latest/', None),
     'aiida_pseudo': ('http://aiida-pseudo.readthedocs.io/en/latest/', None),
+    'pymatgen': ('https://pymatgen.org/', None),
 }
 
 # Settings for the `autoapi.extenstion` automatically generating API docs
@@ -170,6 +171,7 @@
     (r'.*', r'Tuple.*'),
 ]
 nitpick_ignore = [
+    ('py:class', 'numpy.typing.ArrayLike'),
     ('py:class', 'AttributeDict'),
     ('py:class', 'ExitCode'),
     ('py:class', 'StructureData'),

pyproject.toml

@@ -14,13 +14,13 @@ classifiers = [
     'Framework :: AiiDA',
     'License :: OSI Approved :: MIT License',
     'Programming Language :: Python',
-    'Programming Language :: Python :: 3.8',
     'Programming Language :: Python :: 3.9',
     'Programming Language :: Python :: 3.10',
     'Programming Language :: Python :: 3.11',
+    'Programming Language :: Python :: 3.12',
 ]
 keywords = ['aiida', 'workflows']
-requires-python = '>=3.8'
+requires-python = '>=3.9'
 dependencies = [
     'aiida_core[atomic_tools]~=2.3',
     'aiida-pseudo~=1.1',

src/aiida_quantumespresso/__init__.py

@@ -1,3 +1,3 @@
 # -*- coding: utf-8 -*-
 """The official AiiDA plugin for Quantum ESPRESSO."""
-__version__ = '4.7.0'
+__version__ = '4.8.0'

src/aiida_quantumespresso/calculations/projwfc.py

@@ -31,12 +31,11 @@ class ProjwfcCalculation(NamelistsCalculation):
 
     xml_path = Path(NamelistsCalculation._default_parent_output_folder
                     ).joinpath(f'{NamelistsCalculation._PREFIX}.save', 'data-file-schema.xml')
-    _internal_retrieve_list = [
-        NamelistsCalculation._PREFIX + '.pdos*',
-    ]
+
     # The XML file is added to the temporary retrieve list since it is required for parsing, but already in the
     # repository of a an ancestor calculation.
     _retrieve_temporary_list = [
+        NamelistsCalculation._PREFIX + '.pdos*',
         xml_path.as_posix(),
     ]
 
@@ -60,8 +59,16 @@ def define(cls, spec):
         spec.default_output_node = 'output_parameters'
         spec.exit_code(301, 'ERROR_NO_RETRIEVED_TEMPORARY_FOLDER',
             message='The retrieved temporary folder could not be accessed.')
+        spec.exit_code(302, 'ERROR_OUTPUT_STDOUT_MISSING',
+            message='The retrieved folder did not contain the required stdout output file.')
         spec.exit_code(303, 'ERROR_OUTPUT_XML_MISSING',
             message='The retrieved folder did not contain the required XML file.')
+        spec.exit_code(310, 'ERROR_OUTPUT_STDOUT_READ',
+            message='The stdout output file could not be read.')
+        spec.exit_code(311, 'ERROR_OUTPUT_STDOUT_PARSE',
+            message='The stdout output file could not be parsed.')
+        spec.exit_code(312, 'ERROR_OUTPUT_STDOUT_INCOMPLETE',
+            message='The stdout output file was incomplete probably because the calculation got interrupted.')
         spec.exit_code(320, 'ERROR_OUTPUT_XML_READ',
             message='The XML output file could not be read.')
         spec.exit_code(321, 'ERROR_OUTPUT_XML_PARSE',
@@ -72,4 +79,6 @@ def define(cls, spec):
             message='The pdos_tot file could not be read from the retrieved folder.')
         spec.exit_code(340, 'ERROR_PARSING_PROJECTIONS',
             message='An exception was raised parsing bands and projections.')
+        spec.exit_code(350, 'ERROR_UNEXPECTED_PARSER_EXCEPTION',
+            message='The parser raised an unexpected exception: {exception}')
         # yapf: enable

src/aiida_quantumespresso/data/hubbard_structure.py

@@ -133,9 +133,11 @@ def append_hubbard_parameter(
         parameters = HubbardParameters.from_tuple(hp_tuple)
         hubbard = self.hubbard
 
-        if parameters not in hubbard.parameters:
-            hubbard.parameters.append(parameters)
-            self.hubbard = hubbard
+        if parameters in hubbard.parameters:
+            hubbard.parameters.remove(parameters)
+
+        hubbard.parameters.append(parameters)
+        self.hubbard = hubbard
 
     def pop_hubbard_parameters(self, index: int):
         """Pop Hubbard parameters in the list.

src/aiida_quantumespresso/parsers/parse_raw/ph.py

@@ -4,6 +4,8 @@
 The function that needs to be called from outside is parse_raw_ph_output(). Ideally, the functions should work even
 without aiida and will return a dictionary with parsed keys.
 """
+from __future__ import annotations
+
 import numpy
 from qe_tools import CONSTANTS
 
@@ -438,3 +440,47 @@ def parse_ph_dynmat(data, logs, lattice_parameter=None, also_eigenvectors=False,
         parsed_data['eigenvectors'] = eigenvectors
 
     return parsed_data
+
+
+def parse_initialization_qpoints(stdout: str) -> dict:
+    """Return the number of q-points from an initialization run.
+
+    Here, the initialization run refers to the one performed by specifying
+    `start_irr` and `last_irr` to 0 in the inputs.
+
+    :return: parsed dictionary
+
+    :raise: `RuntimeError` if the number of q-points cannot be parsed or it
+        differs from the number of q-points in the stdout list.
+    """
+    import re
+
+    parameters = {}
+
+    # Regular expression to match `N` in `(  N q-points)`
+    pattern = r'\(\s*(\d+)\s*q-points\)'
+    match = re.search(pattern, stdout)
+    if match:
+        parameters.update({'number_of_qpoints': int(match.group(1))})
+    else:
+        raise RuntimeError('the number of q-points cannot be parsed')
+
+    # Regular expression pattern to match the q-points section
+    pattern = r'\(\s*\d+\s*q-points\):\s*\n\s*N\s*xq\(1\)\s*xq\(2\)\s*xq\(3\)\s*\n((?:\s*\d+\s*[\d\.\-\s]+\n?)*)'
+    match = re.search(pattern, stdout)
+
+    if match:
+        q_points_block = match.group(1)
+
+        # Regular expression to match each line of coordinates
+        coord_pattern = r'\s*\d+\s*([\d\.\-]+)\s*([\d\.\-]+)\s*([\d\.\-]+)'
+
+        coords = re.findall(coord_pattern, q_points_block) # Find all coordinates in the block
+        q_points = [list(map(float, coord)) for coord in coords]
+    else:
+        raise RuntimeError('the list of q-points cannot be parsed')
+
+    if parameters['number_of_qpoints'] != len(q_points):
+        raise RuntimeError('the number of q-points do not coincde with the number of listed q-points')
+
+    return parameters