Merge pull request #763 from jmmshn/ci_fix

Fix various CI issues

Author: Zhuoying

atomate/vasp/firetasks/electrode_tasks.py

@@ -10,15 +10,7 @@
 from atomate.vasp.database import VaspCalcDb
 from atomate.vasp.firetasks import pass_vasp_result
 from atomate.vasp.fireworks.core import OptimizeFW, StaticFW
-
-try:
-    from pymatgen.analysis.defects import ChargeInsertionAnalyzer
-except ImportError:
-    print(
-        "Failed to import ChargeInsertionAnalyzer. This is likely due to converting the pymatgen defects module "
-        "to a namespace package. See https://github.com/materialsproject/pymatgen/pull/2582#issuecomment-1198318101 "
-        "for updates."
-    )
+from pymatgen.analysis.defects.utils import ChargeInsertionAnalyzer
 
 __author__ = "Jimmy Shen"
 __email__ = "[email protected]"

atomate/vasp/firetasks/write_inputs.py

@@ -630,7 +630,6 @@ def run_task(self, fw_spec):
             t_cls = None
             for m in [
                 "advanced_transformations",
-                "defect_transformations",
                 "site_transformations",
                 "standard_transformations",
             ]:

atomate/vasp/test_files/setup_test/POSCAR

@@ -1,10 +1,10 @@
 Si2
 1.0
-3.840198 0.000000 0.000000
-1.920099 3.325710 0.000000
-0.000000 -2.217138 3.135509
+   3.8401979336999998    0.0000000000000000    0.0000000000000000
+   1.9200989667999999    3.3257101909000002    0.0000000000000000
+   0.0000000000000000   -2.2171384942999999    3.1355090603000000
 Si
 2
 direct
-0.000000 0.000000 0.000000 Si
-0.750000 0.500000 0.750000 Si
+   0.0000000000000000    0.0000000000000000    0.0000000000000000 Si
+   0.7500000000000000    0.5000000000000000    0.7500000000000000 Si

atomate/vasp/tests/test_setup.py

@@ -1,4 +1,5 @@
 import os
+from turtle import pos
 import unittest
 
 from pymatgen.core import IStructure, Lattice

requirements-ci.txt

@@ -1,5 +1,5 @@
-boto3==1.17.97
+Flask==2.1.3
 coverage==5.5
-moto==2.0.10
+moto==3.1.18
 pytest-cov==2.12.1
 pytest==6.2.4

requirements.txt

@@ -1,16 +1,16 @@
 custodian==2022.5.26
 FireWorks==2.0.3
-maggma==0.44.0
-monty==2021.6.10
-networkx==2.5.1
-numpy
-pandas==1.2.5
-paramiko==2.10.1
-pydash==5.0.0
-pymatgen-analysis-diffusion
-pymatgen
-pymongo
-pyyaml==5.4.1
-ruamel.yaml==0.17.9
-scipy==1.7.2
-tqdm==4.61.1
+maggma==0.48.1
+monty==2022.9.9
+networkx==2.8.6
+numpy==1.23.3
+pandas==1.4.4
+paramiko==2.11.0
+pydash==5.1.0
+pymatgen-analysis-diffusion==2022.7.21
+pymatgen-analysis-defects==2022.9.14
+pymatgen==2022.9.8
+pymongo==4.2.0
+ruamel.yaml==0.17.21
+scipy==1.9.1
+tqdm==4.64.1

setup.py

@@ -33,6 +33,7 @@
             "paramiko",
             "pydash>=4.1.0",
             "pymatgen-analysis-diffusion",
+            "pymatgen-analysis-defects>=2022.9.14",
             "pymatgen",
             "pymongo",
             "pyyaml>=5.1.2",