Keep boto3 optional (#836)

* Keep boto3 optional

* Remove boto3 from setup

* Linting

* Fix legacy molecules

* Remove url extraction test

* Do not skip charge density test

* Fix es test

* Remove print

* Linting

* Temp exclude new molecules resters from generic tests

* Linting

mp_api/client/core/client.py

@@ -17,7 +17,6 @@
 from typing import Any, Dict, Generic, List, Optional, Tuple, TypeVar, Union
 from urllib.parse import quote, urljoin
 
-import boto3
 import requests
 from botocore import UNSIGNED
 from botocore.config import Config
@@ -32,6 +31,11 @@
 from mp_api.client.core.settings import MAPIClientSettings
 from mp_api.client.core.utils import api_sanitize, validate_ids
 
+try:
+    import boto3
+except ImportError:
+    boto3 = None
+
 try:
     from pymatgen.core import __version__ as pmg_version  # type: ignore
 except ImportError:  # pragma: no cover
@@ -132,6 +136,13 @@ def session(self) -> requests.Session:
 
     @property
     def s3_resource(self):
+        if boto3 is None:
+            raise MPRestError(
+                "boto3 not installed. To query charge density, "
+                "band structure, or density of states data first "
+                "install with: 'pip install boto3'"
+            )
+
         if not self._s3_resource:
             self._s3_resource = boto3.resource(
                 "s3", config=Config(signature_version=UNSIGNED)
@@ -329,6 +340,7 @@ def _query_open_data(self, bucket: str, prefix: str, key: str) -> dict:
         Returns:
             dict: MontyDecoded data
         """
+
         ref = self.s3_resource.Object(bucket, f"{prefix}/{key}.json.gz")  # type: ignore
         bytes = ref.get()["Body"]  # type: ignore
 

mp_api/client/mprester.py

@@ -24,7 +24,6 @@
 from mp_api.client.core.settings import MAPIClientSettings
 from mp_api.client.core.utils import validate_ids
 from mp_api.client.routes import GeneralStoreRester, MessagesRester, UserSettingsRester
-from mp_api.client.routes.legacy import LegacyMoleculesRester
 from mp_api.client.routes.materials import (
     AbsorptionRester,
     AlloysRester,
@@ -57,19 +56,7 @@
     ThermoRester,
     XASRester,
 )
-from mp_api.client.routes.molecules import (
-    AssociatedMoleculeRester,
-    MoleculeRester,
-    MoleculesBondRester,
-    MoleculesOrbitalsRester,
-    MoleculesPartialChargesRester,
-    MoleculesPartialSpinsRester,
-    MoleculesRedoxRester,
-    MoleculesSummaryRester,
-    MoleculesTaskRester,
-    MoleculesThermoRester,
-    MoleculesVibrationRester,
-)
+from mp_api.client.routes.molecules import MoleculeRester
 
 _DEPRECATION_WARNING = (
     "MPRester is being modernized. Please use the new method suggested and "
@@ -124,20 +111,7 @@ class MPRester:
     chemenv: ChemenvRester
 
     # Molecules
-    molecules_bonding: MoleculesBondRester
-    molecules_associated: AssociatedMoleculeRester
     molecules: MoleculeRester
-    molecules_orbital: MoleculesOrbitalsRester
-    molecules_partial_charges: MoleculesPartialChargesRester
-    molecules_partial_spins: MoleculesPartialSpinsRester
-    molecules_redox: MoleculesRedoxRester
-    molecules_summary: MoleculesSummaryRester
-    molecules_tasks: MoleculesTaskRester
-    molecules_thermo: MoleculesThermoRester
-    molecules_vibrations: MoleculesVibrationRester
-
-    # Legacy
-    legacy_jcesr: LegacyMoleculesRester
 
     # Generic
     doi: DOIRester

mp_api/client/routes/materials/__init__.py

@@ -15,7 +15,6 @@
 from .grain_boundary import GrainBoundaryRester
 from .magnetism import MagnetismRester
 from .materials import MaterialsRester
-from .molecules import MoleculesRester
 from .oxidation_states import OxidationStatesRester
 from .phonon import PhononRester
 from .piezo import PiezoRester

mp_api/client/routes/molecules/__init__.py

@@ -1,4 +1,5 @@
 from .bonds import MoleculesBondRester
+from .jcesr import JcesrMoleculesRester
 from .molecules import AssociatedMoleculeRester, MoleculeRester
 from .orbitals import MoleculesOrbitalsRester
 from .partial_charges import MoleculesPartialChargesRester

mp_api/client/routes/legacy/jcesr.py → mp_api/client/routes/molecules/jcesr.py

@@ -7,8 +7,8 @@
 from mp_api.client.core import BaseRester
 
 
-class LegacyMoleculesRester(BaseRester[MoleculesDoc]):
-    suffix = "legacy/jcesr"
+class JcesrMoleculesRester(BaseRester[MoleculesDoc]):
+    suffix = "molecules/jcesr"
     document_model = MoleculesDoc  # type: ignore
     primary_key = "task_id"
 

setup.py

@@ -30,7 +30,6 @@
         "requests>=2.23.0",
         "monty>=2021.3.12",
         "emmet-core>=0.54.0",
-        "boto3",
     ],
     extras_require={
         "all": ["emmet-core[all]>=0.54.0", "custodian", "mpcontribs-client", "boto3"],

tests/materials/test_charge_density.py

@@ -2,7 +2,6 @@
 import typing
 
 import pytest
-from emmet.core.charge_density import ChgcarDataDoc
 
 from mp_api.client.routes.materials.charge_density import ChargeDensityRester
 
@@ -98,24 +97,24 @@ def test_download_for_task_ids(tmpdir, rester):
     assert "mp-1791788.json.gz" in files
 
 
-def test_extract_s3_url_info(rester):
-    url_doc_dict = {
-        "task_id": "mp-1896591",
-        "url": "https://minio.materialsproject.org/phuck/atomate_chgcar_fs/6021584c12afbe14911d1b8e",
-        "s3_url_prefix": "https://mp-volumetric.s3.amazonaws.com/atomate_chgcar_fs/",
-        "fs_id": "6021584c12afbe14911d1b8e",
-        "requested_datetime": {"$date": {"$numberLong": "1650389943209"}},
-        "expiry_datetime": None,
-    }
+# def test_extract_s3_url_info(rester):
+#     url_doc_dict = {
+#         "task_id": "mp-1896591",
+#         "url": "https://minio.materialsproject.org/phuck/atomate_chgcar_fs/6021584c12afbe14911d1b8e",
+#         "s3_url_prefix": "https://mp-volumetric.s3.amazonaws.com/atomate_chgcar_fs/",
+#         "fs_id": "6021584c12afbe14911d1b8e",
+#         "requested_datetime": {"$date": {"$numberLong": "1650389943209"}},
+#         "expiry_datetime": None,
+#     }
 
-    url_doc = ChgcarDataDoc(**url_doc_dict)
+#     url_doc = ChgcarDataDoc(**url_doc_dict)
 
-    bucket, prefix = rester._extract_s3_url_info(url_doc)
+#     bucket, prefix = rester._extract_s3_url_info(url_doc)
 
-    assert bucket == "phuck"
-    assert prefix == "atomate_chgcar_fs"
+#     assert bucket == "phuck"
+#     assert prefix == "atomate_chgcar_fs"
 
-    bucket, prefix = rester._extract_s3_url_info(url_doc, use_minio=False)
+#     bucket, prefix = rester._extract_s3_url_info(url_doc, use_minio=False)
 
-    assert bucket == "mp-volumetric"
-    assert prefix == "atomate_chgcar_fs"
+#     assert bucket == "mp-volumetric"
+#     assert prefix == "atomate_chgcar_fs"

tests/materials/test_electronic_structure.py

@@ -58,7 +58,11 @@ def test_es_client(es_rester):
         for entry in param_tuples:
             param = entry[0]
             if param not in es_excluded_params:
-                param_type = entry[1].__args__[0]
+                try:
+                    param_type = entry[1].__args__[0]
+                except AttributeError:
+                    param_type = entry[1]
+
                 q = None
 
                 if param in es_custom_field_tests:

tests/legacy/test_jcesr.py → tests/molecules/test_jcesr.py

@@ -4,12 +4,12 @@
 import pytest
 from pymatgen.core.periodic_table import Element
 
-from mp_api.client.routes.legacy.jcesr import LegacyMoleculesRester
+from mp_api.client.routes.molecules.jcesr import JcesrMoleculesRester
 
 
 @pytest.fixture
 def rester():
-    rester = LegacyMoleculesRester()
+    rester = JcesrMoleculesRester()
     yield rester
     rester.session.close()
 

tests/test_client.py

@@ -37,22 +37,27 @@
     "materials_xas",
     "materials_elasticity",
     "materials_fermi",
-    "molecules_vibrations",
     # "alloys",
     # "summary",
 ]  # temp
 
 
 mpr = MPRester()
 
+# Temporarily ignore molecules resters while molecules query operators are changed
+resters_to_test = [
+    rester for rester in mpr._all_resters if "molecule" not in rester.suffix
+]
+
 
 @pytest.mark.skipif(
     os.environ.get("MP_API_KEY", None) is None, reason="No API key found."
 )
-@pytest.mark.parametrize("rester", mpr._all_resters)
+@pytest.mark.parametrize("rester", resters_to_test)
 def test_generic_get_methods(rester):
     # -- Test generic search and get_data_by_id methods
     name = rester.suffix.replace("/", "_")
+
     if name not in ignore_generic:
         if name not in key_only_resters:
             doc = rester._query_resource_data(

tests/test_mprester.py

@@ -298,7 +298,7 @@ def test_get_phonon_data_by_material_id(self, mpr):
         dos = mpr.get_phonon_dos_by_material_id("mp-2172")
         assert isinstance(dos, PhononDos)
 
-    @pytest.mark.skip(reason="Test needs fixing with ENV variables")
+    # @pytest.mark.skip(reason="Test needs fixing with ENV variables")
     def test_get_charge_density_data(self, mpr):
         chgcar = mpr.get_charge_density_from_material_id("mp-149")
         assert isinstance(chgcar, Chgcar)