Migrate new functionality froim 2022.

materialsproject · Mar 9, 2021 · 998a4f8 · 998a4f8
1 parent c1268d3
commit 998a4f8
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Showing 23 changed files with 116 additions and 10,100 deletions.
diff --git a/pymatgen/__init__.py b/pymatgen/__init__.py
@@ -11,12 +11,13 @@
 __email__ = "pymatgen@googlegroups.com"
 __maintainer__ = "Shyue Ping Ong"
 __maintainer_email__ = "shyuep@gmail.com"
-__version__ = "2021.3.5"
+__version__ = "2021.3.9"
 
 # Useful aliases for commonly used objects and modules.
 # Allows from pymatgen import <class> for quick usage.
 # Note that these have to come after the SETTINGS have been loaded. Otherwise, import does not work.
 
+from .core import SETTINGS, SETTINGS_FILE  # noqa
 from .core.composition import Composition  # noqa
 from .core.lattice import Lattice  # noqa
 from .core.operations import SymmOp  # noqa

diff --git a/pymatgen/alchemy/tests/test_materials.py b/pymatgen/alchemy/tests/test_materials.py
@@ -7,7 +7,7 @@
 import unittest
 import warnings
 
-from pymatgen.settings import SETTINGS
+from pymatgen.core import SETTINGS
 from pymatgen.alchemy.filters import ContainsSpecieFilter
 from pymatgen.alchemy.materials import TransformedStructure
 from pymatgen.core.structure import Structure

diff --git a/pymatgen/analysis/chemenv/utils/chemenv_config.py b/pymatgen/analysis/chemenv/utils/chemenv_config.py
@@ -10,7 +10,7 @@
 from os import makedirs
 from os.path import exists, expanduser
 
-from pymatgen.settings import SETTINGS
+from pymatgen.core import SETTINGS
 from pymatgen.analysis.chemenv.utils.scripts_utils import strategies_class_lookup
 
 

diff --git a/pymatgen/analysis/chemenv/utils/tests/test_chemenv_config.py b/pymatgen/analysis/chemenv/utils/tests/test_chemenv_config.py
@@ -9,7 +9,7 @@
 
 from monty.tempfile import ScratchDir
 
-from pymatgen.settings import SETTINGS
+from pymatgen.core import SETTINGS
 from pymatgen.analysis.chemenv.utils.chemenv_config import ChemEnvConfig
 
 config_file_dir = os.path.join(

diff --git a/pymatgen/analysis/diffusion_analyzer.py b/pymatgen/analysis/diffusion_analyzer.py
@@ -42,6 +42,13 @@
 __status__ = "Beta"
 __date__ = "5/2/13"
 
+warnings.warn(
+    "All code in pymatgen.analysis.diffusion_analyzer has been moved to the separate add-on package"
+    "pymatgen-diffusion, which also includes a lot more functionality for analyzing diffusion"
+    "calculations. This module here is retained for backwards compatibility. It will be removed from"
+    "2022.1.1."
+)
+
 
 class DiffusionAnalyzer(MSONable):
     """

diff --git a/pymatgen/analysis/tests/test_cost.py b/pymatgen/analysis/tests/test_cost.py
@@ -5,16 +5,14 @@
 import os
 import unittest
 
-import pymatgen
+from pymatgen.util.testing import PymatgenTest
 from pymatgen.analysis.cost import CostAnalyzer, CostDBCSV, CostDBElements
 
-module_dir = os.path.join(os.path.dirname(pymatgen.__file__), "..", "test_files")
-
 
 class CostAnalyzerTest(unittest.TestCase):
     def setUp(self):
-        self.ca1 = CostAnalyzer(CostDBCSV(os.path.join(module_dir, "costdb_1.csv")))
-        self.ca2 = CostAnalyzer(CostDBCSV(os.path.join(module_dir, "costdb_2.csv")))
+        self.ca1 = CostAnalyzer(CostDBCSV(os.path.join(PymatgenTest.TEST_FILES_DIR, "costdb_1.csv")))
+        self.ca2 = CostAnalyzer(CostDBCSV(os.path.join(PymatgenTest.TEST_FILES_DIR, "costdb_2.csv")))
 
     def test_cost_per_kg(self):
         self.assertAlmostEqual(self.ca1.get_cost_per_kg("Ag"), 3, 3)

diff --git a/pymatgen/analysis/tests/test_pourbaix_diagram.py b/pymatgen/analysis/tests/test_pourbaix_diagram.py
@@ -12,7 +12,7 @@
 import numpy as np
 from monty.serialization import loadfn
 
-from pymatgen.settings import SETTINGS
+from pymatgen.core import SETTINGS
 from pymatgen.analysis.pourbaix_diagram import (
     IonEntry,
     MultiEntry,

diff --git a/pymatgen/cli/pmg.py b/pymatgen/cli/pmg.py
@@ -13,7 +13,7 @@
 
 from tabulate import tabulate, tabulate_formats
 
-from pymatgen.settings import SETTINGS
+from pymatgen.core import SETTINGS
 from pymatgen.core.structure import Structure
 from pymatgen.cli.pmg_analyze import analyze
 from pymatgen.cli.pmg_config import configure_pmg

diff --git a/pymatgen/cli/pmg_config.py b/pymatgen/cli/pmg_config.py
@@ -17,7 +17,7 @@
 
 from monty.serialization import dumpfn, loadfn
 
-from pymatgen.settings import SETTINGS_FILE
+from pymatgen.core import SETTINGS_FILE
 
 
 def setup_potcars(args):

diff --git a/pymatgen/core/__init__.py b/pymatgen/core/__init__.py
@@ -7,10 +7,49 @@
 operations on them.
 """
 
+import os
+
+try:
+    import ruamel.yaml as yaml
+except ImportError:
+    try:
+        import ruamel_yaml as yaml  # type: ignore  # noqa
+    except ImportError:
+        import yaml  # type: ignore # noqa
+
 from .composition import Composition  # noqa
 from .lattice import Lattice  # noqa
 from .operations import SymmOp  # noqa
 from .periodic_table import DummySpecies, Element, Species  # noqa
 from .sites import PeriodicSite, Site  # noqa
 from .structure import IMolecule, IStructure, Molecule, Structure  # noqa
 from .units import ArrayWithUnit, FloatWithUnit, Unit  # noqa
+
+
+__author__ = "Pymatgen Development Team"
+__email__ = "pymatgen@googlegroups.com"
+__maintainer__ = "Shyue Ping Ong"
+__maintainer_email__ = "shyuep@gmail.com"
+__version__ = "2022.0.4"
+SETTINGS_FILE = os.path.join(os.path.expanduser("~"), ".pmgrc.yaml")
+
+
+def _load_pmg_settings():
+    try:
+        with open(SETTINGS_FILE, "rt") as f:
+            d = yaml.safe_load(f)
+    except IOError:
+        # If there are any errors, default to using environment variables
+        # if present.
+        d = {}
+        for k, v in os.environ.items():
+            if k.startswith("PMG_"):
+                d[k] = v
+            elif k in ["VASP_PSP_DIR", "MAPI_KEY", "DEFAULT_FUNCTIONAL"]:
+                d["PMG_" + k] = v
+    d = d or {}
+    return dict(d)
+
+
+SETTINGS = _load_pmg_settings()
+locals().update(SETTINGS)