Fix some bugs (#14)

* collection.update is removed in PyMongo 4+

collection.update is removed
https://pymongo.readthedocs.io/en/stable/migrate-to-pymongo4.html#collection-update-is-removed

* Update setup.py

The files in dfttk/analysis/database is required. It should included into package_data

dfttk/utils.py

@@ -519,9 +519,9 @@ def mark_adopted_TF(tag, db_file, adpoted, phonon=False):
         t_file = loadfn(config_to_dict()["FWORKER_LOC"])["env"]["db_file"]
         vasp_db = VaspCalcDb.from_db_file(t_file, admin=True)
     if vasp_db:
-        vasp_db.collection.update({'metadata.tag': tag}, {'$set': {'adopted': adpoted}}, upsert = True, multi = True)
+        vasp_db.collection.update_many({'metadata.tag': tag}, {'$set': {'adopted': adpoted}}, upsert = True)
         if phonon:
-            vasp_db.db['phonon'].update({'metadata.tag': tag}, {'$set': {'adopted': adpoted}}, upsert = True, multi = True)
+            vasp_db.db['phonon'].update_many({'metadata.tag': tag}, {'$set': {'adopted': adpoted}}, upsert = True)
 
 
 def mark_adopted(tag, db_file, volumes, phonon=False):
@@ -533,11 +533,11 @@ def mark_adopted(tag, db_file, volumes, phonon=False):
         t_file = loadfn(config_to_dict()["FWORKER_LOC"])["env"]["db_file"]
         vasp_db = VaspCalcDb.from_db_file(t_file, admin=True)
     for volume in volumes:
-        vasp_db.collection.update({'$and':[ {'metadata.tag': tag}, {'output.structure.lattice.volume': volume} ]},
-                                  {'$set': {'adopted': True}}, upsert = True, multi = False)            # Mark only one
+        vasp_db.collection.update_one({'$and':[ {'metadata.tag': tag}, {'output.structure.lattice.volume': volume} ]},
+                                  {'$set': {'adopted': True}}, upsert = True)            # Mark only one
         if phonon:
-            vasp_db.db['phonon'].update({'$and':[ {'metadata.tag': tag}, {'volume': volume} ]},
-                                        {'$set': {'adopted': True}}, upsert = True, multi = False)
+            vasp_db.db['phonon'].update_one({'$and':[ {'metadata.tag': tag}, {'volume': volume} ]},
+                                        {'$set': {'adopted': True}}, upsert = True)
 
 
 def consistent_check_db(db_file, tag):

setup.py

@@ -15,7 +15,8 @@ def readme():
     version=versioneer.get_version(),
     cmdclass=versioneer.get_cmdclass(),
     packages=find_packages(exclude=["*.tests", "*.tests.*", "tests.*", "tests"]),
-    package_data = {'dfttk.structure_builders' : ["prototype_anrl.all", "aflow_prototype_db.json"]},
+    package_data = {'dfttk.structure_builders' : ["prototype_anrl.all", "aflow_prototype_db.json"],
+                    'dfttk.analysis' : ['database/*']},
     description='Density functional theory workflows for finite temperature thermodynamics based on atomate workflows. Created by the Phases Research Lab',
     long_description=readme(),
     install_requires=['atomate>=0.9.4', 'tinydb', 'phonopy', 'ase', 'pymatgen', 'numpy>=1.20.1'],