Add new functions/methods to featurize module

.github/workflows/python-package.yml

@@ -37,7 +37,7 @@ jobs:
       fail-fast: false
       matrix:
         python-version: ["3.10", "3.11", "3.12"]
-        split: [1, 2, 3, 4, 5, 6]
+        split: [1, 2, 3, 4, 5]
 
 
     steps:
@@ -67,7 +67,7 @@ jobs:
         MPLBACKEND: Agg  # non-interactive backend for matplotlib
       run: |
         micromamba activate lobpy
-        pytest --cov=lobsterpy --cov-report term-missing --cov-append --splits 6 --group ${{ matrix.split }} -vv --durations-path ./tests/test_data/.pytest-split-durations
+        pytest --cov=lobsterpy --cov-report term-missing --cov-append --splits 5 --group ${{ matrix.split }} -vv --durations-path ./tests/test_data/.pytest-split-durations
 
     - name: Upload coverage
       if: matrix.python-version == '3.10'

.pre-commit-config.yaml

@@ -1,4 +1,4 @@
-exclude: ^(docs|examples|tests|.github)
+exclude: ^(docs|examples|.github|tests/test_data)
 
 ci:
   autoupdate_schedule: monthly

docs/tutorial/commandlineinterface.rst

@@ -15,7 +15,7 @@ Creating input files
 
 
 With LobsterPy, these intricate details are handled with a single command. We need the standard VASP input files, i.e. 
-``INCAR, KPOINTS, POTCAR and POSCAR`` in the calculation directory. Once you have these files, one needs to run the following command:
+``INCAR, KPOINTS, POTCAR and CONTCAR`` in the calculation directory. Once you have these files, one needs to run the following command:
 
 ``lobsterpy create-inputs``
 

docs/tutorial/tutorial.ipynb

@@ -92,7 +92,7 @@
    "source": [
     "# Initialize Analysis object\n",
     "analyse = Analysis(\n",
-    "    path_to_poscar=directory / \"POSCAR.gz\",\n",
+    "    path_to_poscar=directory / \"CONTCAR.gz\",\n",
     "    path_to_icohplist=directory / \"ICOHPLIST.lobster.gz\",\n",
     "    path_to_cohpcar=directory / \"COHPCAR.lobster.gz\",\n",
     "    path_to_charge=directory / \"CHARGE.lobster.gz\",\n",
@@ -195,7 +195,7 @@
     "\n",
     "```python\n",
     "analyse = Analysis(\n",
-    "    path_to_poscar=directory / \"POSCAR.gz\",\n",
+    "    path_to_poscar=directory / \"CONTCAR.gz\",\n",
     "    path_to_icohplist=directory / \"ICOBILIST.lobster.gz\",\n",
     "    path_to_cohpcar=directory / \"COBICAR.lobster.gz\",\n",
     "    path_to_charge=directory / \"CHARGE.lobster.gz\",\n",
@@ -232,7 +232,7 @@
    "outputs": [],
    "source": [
     "analyse = Analysis(\n",
-    "    path_to_poscar=directory / \"POSCAR.gz\",\n",
+    "    path_to_poscar=directory / \"CONTCAR.gz\",\n",
     "    path_to_icohplist=directory / \"ICOHPLIST.lobster.gz\",\n",
     "    path_to_cohpcar=directory / \"COHPCAR.lobster.gz\",\n",
     "    path_to_charge=directory / \"CHARGE.lobster.gz\",\n",
@@ -358,7 +358,7 @@
    "source": [
     "# Get calculation quality summary dict\n",
     "calc_quality_K3Sb = Analysis.get_lobster_calc_quality_summary(\n",
-    "            path_to_poscar=directory / \"POSCAR.gz\",\n",
+    "            path_to_poscar=directory / \"CONTCAR.gz\",\n",
     "            path_to_charge=directory / \"CHARGE.lobster.gz\",\n",
     "            path_to_lobsterin=directory / \"lobsterin.gz\",\n",
     "            path_to_lobsterout=directory / \"lobsterout.gz\",\n",
@@ -557,7 +557,7 @@
     "# Load Lobster DOS\n",
     "directory = Path(\".\") / \"..\" / \"..\" / \"tests\" / \"test_data\" / \"NaCl_comp_range\"\n",
     "dos = Doscar(doscar=directory / 'DOSCAR.lobster.gz',\n",
-    "             structure_file=directory / 'POSCAR.gz')"
+    "             structure_file=directory / 'CONTCAR.gz')"
    ]
   },
   {
@@ -569,7 +569,7 @@
     "# Load Lobster DOS (Change this cell block type to Code when executing locally)\n",
     "directory = Path(\"LobsterPy\") / \"tests\" / \"test_data\" / \"NaCl_comp_range\"\n",
     "dos = Doscar(doscar=directory / 'DOSCAR.lobster.gz',\n",
-    "             structure_file=directory / 'POSCAR.gz')\n",
+    "             structure_file=directory / 'CONTCAR.gz')\n",
     "```"
    ]
   },
@@ -585,9 +585,7 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "a271f2f0",
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "style.use('default') # Complete reset the matplotlib figure style\n",
@@ -658,7 +656,7 @@
    "outputs": [],
    "source": [
     "graph_NaCl_all = LobsterGraph(\n",
-    "    path_to_poscar=directory / \"POSCAR.gz\",\n",
+    "    path_to_poscar=directory / \"CONTCAR.gz\",\n",
     "    path_to_charge=directory / \"CHARGE.lobster.gz\",\n",
     "    path_to_cohpcar=directory / \"COHPCAR.lobster.gz\",\n",
     "    path_to_icohplist=directory / \"ICOHPLIST.lobster.gz\",\n",
@@ -679,7 +677,7 @@
     "```python\n",
     "#### (Change this cell block type to Code or copy it from here when executing locally)\n",
     "graph_NaCl_all = LobsterGraph(\n",
-    "    path_to_poscar=directory / \"POSCAR.gz\",\n",
+    "    path_to_poscar=directory / \"CONTCAR.gz\",\n",
     "    path_to_charge=directory / \"CHARGE.lobster.gz\",\n",
     "    path_to_cohpcar=directory / \"COHPCAR.lobster.gz\",\n",
     "    path_to_icohplist=directory / \"ICOHPLIST.lobster.gz\",\n",
@@ -1067,7 +1065,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.4"
+   "version": "3.10.14"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {

examples/example_script_NaCl.py

@@ -7,7 +7,7 @@
 
 # Setup analysis dict
 analyse = Analysis(
-    path_to_poscar=os.path.join(directory, "POSCAR"),
+    path_to_poscar=os.path.join(directory, "CONTCAR"),
     path_to_icohplist=os.path.join(directory, "ICOHPLIST.lobster"),
     path_to_cohpcar=os.path.join(directory, "COHPCAR.lobster"),
     path_to_charge=os.path.join(directory, "CHARGE.lobster"),

examples/example_script_NaCl_Structure_graph.py

@@ -1,7 +1,7 @@
 from lobsterpy.structuregraph.graph import LobsterGraph
 
 graph_NaCl_all = LobsterGraph(
-    path_to_poscar="./NaCl_comp_range/POSCAR.gz",
+    path_to_poscar="./NaCl_comp_range/CONTCAR.gz",
     path_to_charge="./NaCl_comp_range/CHARGE.lobster.gz",
     path_to_cohpcar="./NaCl_comp_range/COHPCAR.lobster.gz",
     path_to_icohplist="./NaCl_comp_range/ICOHPLIST.lobster.gz",

examples/example_script_NaCl_all.py

@@ -7,7 +7,7 @@
 
 # Setup analysis dict
 analyse = Analysis(
-    path_to_poscar=os.path.join(directory, "POSCAR"),
+    path_to_poscar=os.path.join(directory, "CONTCAR"),
     path_to_icohplist=os.path.join(directory, "ICOHPLIST.lobster"),
     path_to_cohpcar=os.path.join(directory, "COHPCAR.lobster"),
     path_to_charge=os.path.join(directory, "CHARGE.lobster"),

examples/example_script_NaCl_orbitalwise.py

@@ -7,7 +7,7 @@
 
 # Setup analysis dict
 analyse = Analysis(
-    path_to_poscar=os.path.join(directory, "POSCAR"),
+    path_to_poscar=os.path.join(directory, "CONTCAR"),
     path_to_icohplist=os.path.join(directory, "ICOHPLIST.lobster"),
     path_to_cohpcar=os.path.join(directory, "COHPCAR.lobster"),
     path_to_charge=os.path.join(directory, "CHARGE.lobster"),

pyproject.toml

@@ -128,7 +128,7 @@ ignore = [
   "RUF012",  # Disable checks for mutable class args. This is a non-problem.
   "SIM105",  # Use contextlib.suppress(OSError) instead of try-except-pass
   "SIM114",  # Combine `if` branches using logical `or` operator
-  "TCH002",  # Move third-party import into a type-checking block
+  "TC002",  # Move third-party import into a type-checking block
 ]
 pydocstyle.convention = "google"
 

src/lobsterpy/cli.py

@@ -63,10 +63,10 @@ def get_parser() -> argparse.ArgumentParser:
     structure_file.add_argument(
         "-fstruct",
         "--file-structure",
-        default="POSCAR",
+        default="CONTCAR",
         dest="structure",
         type=Path,
-        help='path to structure file. Default is "POSCAR". '
+        help='path to structure file. Default is "CONTCAR". '
         'Can also read "POSCAR.lobster" file or any '
         'suitable file format supported by pymatgen "Structure.from_file" method.',
     )
@@ -561,7 +561,7 @@ def get_parser() -> argparse.ArgumentParser:
         ],
         help=(
             "Deliver a text description of the LOBSTER calc quality analysis. "
-            "Mandatory required files: POSCAR, POTCAR, lobsterout, lobsterin. "
+            "Mandatory required files: CONTCAR, POTCAR, lobsterout, lobsterin. "
             "Optional files (BVA comparison): CHARGE.lobster, "
             "(DOS comparison): DOSCAR.lobster/ DOSCAR.LSO.lobster, Vasprun.xml."
         ),
@@ -874,14 +874,14 @@ def run(args):
             )
             options = {"are_cobis": False, "are_coops": False}
 
-        struture_filename = get_file_paths(path_to_lobster_calc=Path(os.getcwd()), requested_files=["structure"]).get(
+        structure_filename = get_file_paths(path_to_lobster_calc=Path(os.getcwd()), requested_files=["structure"]).get(
             "structure"
         )
 
         completecohp = CompleteCohp.from_file(
             fmt="LOBSTER",
             filename=filename,
-            structure_file=struture_filename,
+            structure_file=structure_filename,
             **options,
         )
         if args.multi_cobis:
@@ -963,7 +963,7 @@ def run(args):
 
         # Check for .gz files exist for default values and update accordingly
         default_files = {
-            "structure": "POSCAR",
+            "structure": "CONTCAR",
             "potcar": "POTCAR",
             "incar": "INCAR",
         }

src/lobsterpy/featurize/__init__.py

@@ -3,4 +3,4 @@
 
 """This package provides the modules for featurzing Lobster data ready for ML studies."""
 
-from .utils import get_file_paths, get_structure_path
+from .utils import get_electronegativities, get_file_paths, get_reduced_mass, get_structure_path, sort_dict_by_value