Merge branch 'main' into update/docker-container

Author: yakutovicha

.github/workflows/ci.yml

@@ -52,33 +52,12 @@ jobs:
         docker exec --tty --user aiida $DOCKERID /bin/bash -l -c 'cd /home/aiida/aiida-cp2k/ && py.test --cov aiida_cp2k --cov-append .'
 
 
-  pre-commit:
-    runs-on: ubuntu-latest
-    timeout-minutes: 10
-    strategy:
-      matrix:
-        python-version: [3.8]
-    steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install python dependencies
-      run: |
-        pip install --upgrade pip
-        pip install -e .[dev,docs]
-    - name: Run pre-commit
-      run: |
-        pre-commit install
-        pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
-
   docs:
     runs-on: ubuntu-latest
     timeout-minutes: 10
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.11]
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python ${{ matrix.python-version }}

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
 
         - id: check-json
@@ -19,7 +19,7 @@ repos:
           exclude: *exclude_pre_commit_hooks
 
   - repo: https://github.com/psf/black
-    rev: 23.9.1
+    rev: 23.12.1
     hooks:
         - id: black
           language_version: python3 # Should be a command that runs python3.6+
@@ -32,19 +32,19 @@ repos:
           args: [--count, --show-source, --statistics]
 
   - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
         - id: isort
           args: [--profile, black, --filter-files]
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.14.0
+    rev: v3.15.0
     hooks:
         - id: pyupgrade
           args: [--py37-plus]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.5.1
+    rev: v1.8.0
     hooks:
         - id: mypy
           additional_dependencies:

aiida_cp2k/__init__.py

@@ -6,6 +6,6 @@
 ###############################################################################
 """The official AiiDA plugin for CP2K."""
 
-__version__ = "2.0.0"
+__version__ = "2.1.0b1"
 
 # EOF

aiida_cp2k/parsers/__init__.py

@@ -6,6 +6,8 @@
 ###############################################################################
 """AiiDA-CP2K output parser."""
 
+import re
+
 import ase
 import numpy as np
 from aiida import common, engine, orm, parsers, plugins
@@ -128,7 +130,7 @@ def _read_stdout(self):
     def _parse_trajectory(self, structure):
         """CP2K trajectory parser."""
 
-        symbols = [str(site.kind_name) for site in structure.sites]
+        symbols = [re.sub(r"\d+", "", str(site.kind_name)) for site in structure.sites]
 
         # Handle the positions trajectory
         xyz_traj_fname = self.node.process_class._DEFAULT_TRAJECT_XYZ_FILE_NAME

aiida_cp2k/workchains/base.py

@@ -65,7 +65,7 @@ def results(self):
         trajectories = self._collect_all_trajetories()
         if trajectories:
             self.report("Work chain completed successfully, collecting all trajectories")
-            if self.ctx.inputs.parameters.get("GLOBAL", {}).get("RUN_TYPE") == "GEO_OPT":
+            if self.ctx.inputs.parameters.get_dict().get("GLOBAL", {}).get("RUN_TYPE") == "GEO_OPT":
                 output_trajectory = utils.merge_trajectory_data_non_unique(*trajectories)
             else:
                 output_trajectory = utils.merge_trajectory_data_unique(*trajectories)

docs/source/conf.py

@@ -15,13 +15,9 @@
 import time
 from typing import Dict
 
-from aiida.manage.configuration import load_documentation_profile
+from aiida.manage.configuration import Profile, load_profile
 
-# -- AiiDA-related setup --------------------------------------------------
-
-# Load the dummy profile even if we are running locally, this way the documentation will succeed even if the current
-# default profile of the AiiDA installation does not use a Django backend.
-load_documentation_profile()
+load_profile(Profile("docs", {"process_control": {}, "storage": {}}))
 
 # If we are not on READTHEDOCS load the Sphinx theme manually
 if not os.environ.get("READTHEDOCS", None):

pyproject.toml

@@ -18,7 +18,7 @@ classifiers = [
     "Operating System :: MacOS :: MacOS X",
     "Programming Language :: Python :: 3",
 ]
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 dependencies = [
     "aiida-core>=2.0.0,<3.0.0",
     "aiida-gaussian-datatypes",
@@ -40,7 +40,7 @@ dev = [
     "pytest~=6.0",
     "pytest-cov~=2.11.1",
     "coverage",
-    "pre-commit~=2.19",
+    "pre-commit~=3.6",
 ]
 docs = [
     "sphinx",
@@ -74,7 +74,7 @@ filterwarnings = [
 ]
 
 [tool.bumpver]
-current_version = "v2.0.0"
+current_version = "v2.1.0b1"
 version_pattern = "vMAJOR.MINOR.PATCH[PYTAGNUM]"
 commit_message = "Bump version {old_version} -> {new_version}."
 commit = true