Merge pull request #249 from loriab/working18

add using_web and maintenance

LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2018-2020, The Molecular Sciences Software Institute
+Copyright (c) 2018-2021, The Molecular Sciences Software Institute
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

Makefile

@@ -1,5 +1,5 @@
 .DEFAULT_GOAL := all
-isort = isort -rc qcelemental
+isort = isort --float-to-top qcelemental
 black = black qcelemental
 autoflake = autoflake -ir --remove-all-unused-imports --ignore-init-module-imports --remove-unused-variables qcelemental
 

docs/source/changelog.rst

@@ -1,7 +1,7 @@
 Changelog
 =========
 
-.. X.Y.0 / 2020-MM-DD
+.. X.Y.0 / 2021-MM-DD
 .. -------------------
 ..
 .. New Features
@@ -14,6 +14,22 @@ Changelog
 .. +++++++++
 
 
+0.18.0 / 2021-MM-DD
+-------------------
+
+New Features
+++++++++++++
+
+Enhancements
+++++++++++++
+- (:pr:`246`) Removes types deprecated in NumPy v1.20.0.
+
+Bug Fixes
++++++++++
+- (:pr:`244`) Fixes where in code validation throws if ``center_data`` missing from ``BasisSet`` model.
+- (:pr:`1000`) Fixes web tests that weren't marked.
+
+
 0.17.0 / 2020-10-01
 -------------------
 

qcelemental/checkup_data/cfour_primary_masses.py

@@ -1,6 +1,7 @@
 # DATA ATMSS from ~line 150 of cfour/joda/pertable.f
 
 # fmt: off
+
 cfour_primary_masses = [
     1.007825035E+00,
     4.00260324E+00,

qcelemental/checkup_data/periodictable.py

@@ -7,6 +7,7 @@
 """
 
 # fmt: off
+
 _temp_element = [
     "GHOST", "HYDROGEN", "HELIUM", "LITHIUM", "BERYLLIUM", "BORON", "CARBON", "NITROGEN", "OXYGEN", "FLUORINE", "NEON",
     "SODIUM", "MAGNESIUM", "ALUMINUM", "SILICON", "PHOSPHORUS", "SULFUR", "CHLORINE", "ARGON", "POTASSIUM", "CALCIUM",

qcelemental/data/alvarez_2008_covalent_radii.py

@@ -5,6 +5,7 @@
 """
 
 # fmt: off
+
 alvarez_2008_covalent_radii = {
     'title':
     'Covalent radii revisited',

qcelemental/data/mantina_2009_vanderwaals_radii.py

@@ -9,6 +9,7 @@
 """
 
 # fmt: off
+
 mantina_2009_vanderwaals_radii = {
     'title':
     'Consistent van der Waals Radii for the Whole Main Group',

qcelemental/info/data/dft_data_blob.py

@@ -5,7 +5,6 @@
 File Authors: QCElemental Authors
 """
 
-
 data_blob = {
     "version": "1.4a2.dev215",
     "functionals": {

qcelemental/molparse/from_arrays.py

@@ -311,7 +311,7 @@ def from_arrays(
             geom = []
         else:
             raise ValidationError("""For domain 'qm', `geom` must be provided.""")
-    if domain == "efp" and (geom_hints is None or np.asarray(geom_hints).size == 0):
+    if domain == "efp" and (geom_hints is None or np.asarray(geom_hints, dtype=object).size == 0):
         if missing_enabled_return == "none":
             return {}
         elif missing_enabled_return == "minimal":

qcelemental/molparse/pubchem.py

@@ -36,9 +36,9 @@ def __str__(self):
 
     def get_sdf(self):
         """Function to return the SDF (structure-data file) of the PubChem object."""
-        from urllib.request import urlopen, Request
-        from urllib.parse import quote
         from urllib.error import URLError
+        from urllib.parse import quote
+        from urllib.request import Request, urlopen
 
         if len(self.dataSDF) == 0:
             url = "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/{}/SDF?record_type=3d".format(
@@ -125,9 +125,9 @@ def get_pubchem_results(name):
     input string. Builds a PubChemObj object if found.
 
     """
-    from urllib.request import urlopen
-    from urllib.parse import quote
     from urllib.error import URLError
+    from urllib.parse import quote
+    from urllib.request import urlopen
 
     if name.isdigit():
         print("\tSearching PubChem database for CID {}".format(name))

qcelemental/physical_constants/context.py

@@ -11,7 +11,7 @@
 from .ureg import build_units_registry
 
 if TYPE_CHECKING:
-    from pint import quantity, UnitRegistry  # lgtm: [py/unused-import]
+    from pint import UnitRegistry, quantity  # lgtm: [py/unused-import]
 
 
 class PhysicalConstantsContext:

qcelemental/physical_constants/ureg.py

@@ -3,6 +3,7 @@
 """
 
 # We only want the ureg builder exposed
+
 __all__ = ["build_units_registry"]
 
 

qcelemental/tests/test_molparse_pubchem.py

@@ -105,6 +105,7 @@ def test_pubchem_4c():
     assert compare_molrecs(fullans, final["qm"], tnm() + ": full")
 
 
+@using_web
 def test_pubchem_error_d():
     subject = """
     pubchem:-55
@@ -115,6 +116,7 @@ def test_pubchem_error_d():
             qcelemental.molparse.from_string(subject, return_processed=True)
 
 
+@using_web
 def test_pubchem_error_e():
     # no 3D structure available
     subject = """
@@ -127,6 +129,7 @@ def test_pubchem_error_e():
             qcelemental.molparse.from_string(subject)
 
 
+@using_web
 def test_pubchem_error_f():
     subject = """
     pubchem: 100000000000000

setup.py

@@ -67,6 +67,7 @@
             'Programming Language :: Python :: 3.6',
             'Programming Language :: Python :: 3.7',
             'Programming Language :: Python :: 3.8',
+            'Programming Language :: Python :: 3.9',
         ],
         zip_safe=False,
         long_description=long_description,