Merge pull request #266 from loriab/docs1

pydantic >= 1.8.2

README.md

@@ -52,7 +52,7 @@ Physical constants can be acquired directly from the [NIST CODATA](https://physi
 >>> qcel.constants.get('hartree ENERGY in ev')
 27.21138602
 >>> pc = qcel.constants.get('hartree ENERGY in ev', return_tuple=True)
->>> pc.lbl
+>>> pc.label
 'Hartree energy in eV'
 >>> pc.data
 Decimal('27.21138602')

devtools/conda-envs/README.md

@@ -11,7 +11,8 @@ more common `conda create` (the commands are slightly different as of writing,
 circa Conda 4.3), so note the difference in commands.
 
 * `base.yaml` is environment specification for general use.
-* `minimal_pins.yaml` is primarily for CI canary testing. It specifies
+* `base-cf.yaml` is the conda-forge-only version of `base.yaml`.
+* `minimal.yaml` is primarily for CI canary testing. It specifies
   minimal dependency set and pins to what we think are the minimal versions.
 
 ## Requirements to use Environments

devtools/conda-envs/base-cf.yaml

@@ -7,7 +7,7 @@ dependencies:
   - nomkl
   - python
   - pint>=0.10.0
-  - pydantic>=1.5.0,!=1.6.0,!=1.8.0
+  - pydantic>=1.8.2
 
     # Optional depends
   - msgpack-python

devtools/conda-envs/base.yaml

@@ -8,8 +8,8 @@ dependencies:
   - nomkl
   - python
   - pint>=0.10.0
-  - pydantic>=1.5.0,!=1.6.0,!=1.8.0
-  - dataclasses 
+  - pydantic>=1.8.2
+  - dataclasses  # only for py36 and only b/c default channel pydantic missing the conditional dep
 
     # Optional depends
   - msgpack-python

devtools/conda-envs/minimal.yaml

@@ -8,7 +8,8 @@ dependencies:
   - nomkl
   - python
   - pint=0.10.0  # technically, qcel has no lower bound for pint version for py36,37 but needs 0.10 for 38
-  - pydantic=1.5.0
+  - pydantic=1.8.2
+  - dataclasses  # until drop py36
 
     # Testing
   - pytest=4.6.4  # technically, qcel works with 4.0.0 but c-f doesn't have py38 builds for it

docs/source/changelog.rst

@@ -14,6 +14,23 @@ Changelog
 .. +++++++++
 
 
+0.21.0 / 2021-MM-DD
+-------------------
+
+New Features
+++++++++++++
+- (:pr:`xxx`) Serialization learned msgpack mode that, in contrast to msgpack-ext, *doesn't* embed NumPy objects.
+
+Enhancements
+++++++++++++
+- (:pr:`266`) Testing function ``compare_values()`` learned to print RMS and MAX statistics for arrays.
+
+Bug Fixes
++++++++++
+- (:pr:`265`) Fix search path construction. @sheepforce
+- (:pr:`266`) Bump minimum pydantic to 1.8.2 to avoid security hole -- https://github.com/samuelcolvin/pydantic/security/advisories/GHSA-5jqp-qgf6-3pvh .
+
+
 0.20.0 / 2021-05-16
 -------------------
 

qcelemental/testing.py

@@ -166,13 +166,18 @@ def compare_values(
             diff[isclose] = 0.0
             diff_str = np.array_str(diff, max_line_width=120, precision=12, suppress_small=False)
             diff_str = "\n".join("    " + ln for ln in diff_str.splitlines())
+            digits_str += f" (o-e: RMS {_rms(cptd) - _rms(xptd):.1e}, MAX {np.amax(np.absolute(diff)):.1e})"
             message = """\t{}: computed value does not match {}.\n  Expected:\n{}\n  Observed:\n{}\n  Difference (passed elements are zeroed):\n{}\n""".format(
                 label, digits_str, xptd_str, cptd_str, diff_str
             )
 
     return return_handler(allclose, label, message, return_message, quiet)
 
 
+def _rms(arr: np.ndarray) -> float:
+    return np.sqrt(np.mean(np.square(arr)))
+
+
 def compare(
     expected: Union[int, bool, str, List[int], np.ndarray],
     computed: Union[int, bool, str, List[int], np.ndarray],

qcelemental/tests/test_testing.py

@@ -79,7 +79,7 @@
             False,
             (
                 None,
-                """test_compare_values: computed value does not match to atol=0.1.
+                """test_compare_values: computed value does not match to atol=0.1 (o-e: RMS -1.2e-02, MAX 6.0e+00).
   Expected:
     [0. 1. 2. 3.]
   Observed:
@@ -104,7 +104,7 @@
             False,
             (
                 None,
-                """test_compare_values: computed value does not match to atol=0.01.
+                """test_compare_values: computed value does not match to atol=0.01 (o-e: RMS 1.2e-02, MAX 2.0e-02).
   Expected:
     [0. 1. 2. 3.]
   Observed:
@@ -122,7 +122,7 @@
             False,
             (
                 None,
-                """test_compare_values: computed value does not match to atol=0.01.
+                """test_compare_values: computed value does not match to atol=0.01 (o-e: RMS 1.2e-02, MAX 2.0e-02).
   Expected:
     [[0. 1.]
      [2. 3.]]

setup.py

@@ -31,7 +31,7 @@
         package_data={'': [os.path.join('qcelemental', 'data', '*.json')]},
         setup_requires=[] + pytest_runner,
         python_requires='>=3.6',
-        install_requires=["numpy >= 1.12.0", "pint >= 0.10.0", "pydantic >=1.5.0,!=1.6.0,!=1.8.0"],
+        install_requires=["numpy >= 1.12.0", "pint >= 0.10.0", "pydantic >=1.8.2"],
         extras_require={
             'docs': [
                 'numpydoc',