Merge pull request #789 from Zhuoying/fix-ld-wf

Initiate rebased branch for lattice dynamics

.github/workflows/test.yml

@@ -34,6 +34,10 @@ jobs:
           sudo apt-get install libopenbabel-dev
           # https://github.com/openbabel/openbabel/issues/2408#issuecomment-1014466193
           sudo ln -s /usr/include/openbabel3 /usr/local/include/openbabel3
+      
+      - name: Install phono3py
+        run: |
+          conda install -c conda-forge phono3py
 
       - name: Install dependencies
         run: |

atomate/common/firetasks/tests/test_parse_outputs.py

@@ -14,7 +14,8 @@
 
 
 class TestDrone(AbstractDrone):
-    def __init__(self):
+    @classmethod
+    def setUpClass(cls):
         pass
 
     def assimilate(self, path):

atomate/utils/tests/test_database.py

@@ -3,10 +3,9 @@
 """
 import os
 import unittest
-
 import boto3
 from maggma.stores import MemoryStore
-from moto import mock_s3
+from moto import mock_aws
 
 __author__ = "Jimmy Shen <[email protected]>"
 
@@ -19,7 +18,15 @@
 logger = get_logger(__name__)
 
 
+
+
 class TestToDb(CalcDb):
+    def setup_method(self,method):
+        self.reset()
+
+    def teardown_method(self,method):
+        pass
+
     def build_indexes(self, indexes=None, background=True):
         pass
 
@@ -37,7 +44,7 @@ def tearDownClass(cls):
         cls.testdb.connection.drop_database(cls.testdb.db_name)
 
     def test_s3_valid(self):
-        with mock_s3():
+        with mock_aws():
             conn = boto3.resource("s3", region_name="us-east-1")
             conn.create_bucket(Bucket="test_bucket")
             index_store = MemoryStore()
@@ -50,7 +57,7 @@ def test_s3_valid(self):
             self.assertEqual(res["data"], "111111111110111111")
 
     def test_s3_not_valid(self):
-        with mock_s3():
+        with mock_aws():
             conn = boto3.resource("s3", region_name="us-east-1")
             conn.create_bucket(Bucket="test_bucket_2")
             index_store = MemoryStore()
@@ -61,7 +68,7 @@ def test_s3_not_valid(self):
                 store.connect()
 
     def test_maggma_store_names(self):
-        with mock_s3():
+        with mock_aws():
             conn = boto3.resource("s3", region_name="us-east-1")
             conn.create_bucket(Bucket="test_bucket")
             index_store = MemoryStore()
@@ -84,7 +91,7 @@ def test_uri(self):
         calc_db.collection.insert_one({"task_id": "mp-1", "data": "12345"})
         self.assertEqual(calc_db.collection.find_one()["data"], "12345")
 
-        with mock_s3():
+        with mock_aws():
             conn = boto3.resource("s3", region_name="us-east-1")
             conn.create_bucket(Bucket="test_bucket")
             uri_db = TestToDb.from_db_file(db_dir + "/db_aws_uri.json")