Merge pull request #741 from janosh/fix-m1-install

Require minimum maggma version 0.39.0

Author: itsduowang

atomate/qchem/drones.py

@@ -4,7 +4,6 @@
 import json
 import os
 import traceback
-from collections import OrderedDict
 from fnmatch import fnmatch
 from itertools import chain
 
@@ -119,10 +118,10 @@ def filter_files(self, path, file_pattern):
             file_pattern (string): base files to be searched for
 
         Returns:
-            OrderedDict of the names of the files to be processed further.
-            The key is set from list of run types: self.runs
+            dict: names of the files to be processed further. The key is set from list
+                of run types: self.runs
         """
-        processed_files = OrderedDict()
+        processed_files = {}
         files = os.listdir(path)
         for r in self.runs:
             # try subfolder schema

atomate/utils/tests/test_utils.py

@@ -123,5 +123,6 @@ def test_get_database(self):
 
         db = get_database(os.path.join(MODULE_DIR, "db.json"))
         self.assertTrue(isinstance(db, Database))
-        self.assertEqual(db.client.address[0], "localhost")
         self.assertEqual(db.name, "atomate_unittest")
+        db.client.start_session()  # needed to start the connection and populate db.client.address
+        self.assertEqual(db.client.address, ("localhost", 27017))

atomate/vasp/drones.py

@@ -11,7 +11,6 @@
 import re
 import traceback
 import warnings
-from collections import OrderedDict
 from fnmatch import fnmatch
 
 import numpy as np
@@ -235,10 +234,10 @@ def filter_files(self, path, file_pattern="vasprun.xml"):
             file_pattern (string): files to be searched for
 
         Returns:
-            OrderedDict of the names of the files to be processed further.
-            The key is set from list of run types: self.runs
+            dict: names of the files to be processed further. The key is set from list
+                of run types: self.runs
         """
-        processed_files = OrderedDict()
+        processed_files = {}
         files = os.listdir(path)
         for r in self.runs:
             # try subfolder schema

atomate/vasp/firetasks/parse_outputs.py

@@ -1281,7 +1281,7 @@ def nested_copy(a):
         summaries.append(summary)
 
         mmdb.collection = mmdb.db["hubbard_hund_linresp"]
-        mmdb.collection.insert(summaries)
+        mmdb.collection.insert_many(summaries)
 
         logger.info("Hubbard-Hund linear response analysis is complete.")
 
@@ -1507,7 +1507,7 @@ def run_task(self, fw_spec):
             summaries.append(summary)
 
         mmdb.collection = mmdb.db["magnetic_orderings"]
-        mmdb.collection.insert(summaries)
+        mmdb.collection.insert_many(summaries)
 
         logger.info("Magnetic orderings calculation complete.")
 

atomate/vasp/firetasks/tests/test_polarization_to_db.py

@@ -34,9 +34,9 @@ def test_polarizationtodb(self):
 
         coll = bson.decode_all(coll_raw)
 
-        db = self.get_task_collection()
+        task_coll = self.get_task_collection()
         for c in coll:
-            db.insert(c)
+            task_coll.insert_one(c)
 
         new_fw_spec = {
             "_fw_env": {"db_file": os.path.join(db_dir, "db.json")},

atomate/vasp/submission_filter.py

@@ -7,20 +7,8 @@
 
 class SubmissionFilter(AbstractStructureFilter):
     NO_POTCARS = [
-        "Po",
-        "At",
-        "Rn",
-        "Fr",
-        "Ra",
-        "Am",
-        "Cm",
-        "Bk",
-        "Cf",
-        "Es",
-        "Fm",
-        "Md",
-        "No",
-        "Lr",
+        *["Po", "At", "Rn", "Fr", "Ra", "Am", "Cm"],
+        *["Bk", "Cf", "Es", "Fm", "Md", "No", "Lr"],
     ]
 
     def __init__(

requirements.txt

@@ -1,6 +1,6 @@
 custodian==2022.1.17
 FireWorks==1.9.7
-maggma==0.29.2
+maggma==0.39.0
 monty==2021.6.10
 networkx==2.5.1
 numpy
@@ -9,7 +9,7 @@ paramiko==2.7.2
 pydash==5.0.0
 pymatgen-analysis-diffusion
 pymatgen
-pymongo<4.0.0
+pymongo
 pyyaml==5.4.1
 ruamel.yaml==0.17.9
 scipy==1.7.0

scripts/atwf

@@ -14,8 +14,8 @@ from pymatgen.core import Lattice, Structure
 from pymatgen.ext.matproj import MPRester
 from pymatgen.util.testing import PymatgenTest
 
+from atomate.common.powerups import add_namefile, add_tags
 from atomate.utils.utils import get_wf_from_spec_dict, load_class
-from atomate.vasp.powerups import add_namefile, add_tags
 from atomate.vasp.workflows.presets import core
 
 default_yaml = """fireworks:

setup.py

@@ -24,7 +24,7 @@
         install_requires=[
             "custodian>=2019.8.24",
             "FireWorks>=1.4.0",
-            "maggma>=0.26.0",
+            "maggma>=0.39.0",
             "monty>=2.0.6",
             "networkx",
             "numpy",
@@ -33,7 +33,7 @@
             "pydash>=4.1.0",
             "pymatgen-analysis-diffusion",
             "pymatgen",
-            "pymongo<4.0.0",
+            "pymongo",
             "pyyaml>=5.1.2",
             "ruamel.yaml",
             "scipy",