Merge pull request #237 from loriab/schemalint13

QCSchema coordination, testing, and export

.github/workflows/CI.yml

@@ -1,20 +1,29 @@
 name: CI
 
-on: [push, pull_request]
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
 
 jobs:
   build:
 
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-latest
     strategy:
       matrix:
         cfg:
           - conda-env: minimal
             python-version: 3.6
+            label: mindep
           - conda-env: base
             python-version: 3.6
+            label: minpy
           - conda-env: base
-            python-version: 3.8
+            python-version: 3.9
+            label: full
     env:
       PYVER: ${{ matrix.cfg.python-version }}
       CONDA_ENV: ${{ matrix.cfg.conda-env }}
@@ -54,5 +63,12 @@ jobs:
         eval "$(conda shell.bash hook)" && conda activate test
         pytest -rws -v --cov=qcelemental --color=yes --cov-report=xml qcelemental/
 
+    - name: PyTest Validate
+      shell: bash
+      if: matrix.cfg.label == 'full'
+      run: |
+        eval "$(conda shell.bash hook)" && conda activate test
+        pytest -rws -v --color=yes --validate qcelemental/
+
     - name: CodeCov  
       uses: codecov/codecov-action@v1

.github/workflows/QCSchema.yml_wip

@@ -0,0 +1,90 @@
+name: QCSchema
+
+on: [pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        conda-env: [base]
+        python-version: [3.7]
+    env:
+      PYVER: ${{ matrix.python-version }}
+      CONDA_ENV: ${{ matrix.conda-env }}
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v2
+      with:
+        path: qcel
+
+    - name: Checkout schema repo
+      uses: actions/checkout@v2
+      with:
+        repository: MolSSI/QCSchema
+        path: qcsk
+        ref: qcsk_export_2
+        #ref: master
+        persist-credentials: true
+        fetch-depth: 0
+        token: ${{ secrets.qcschema_from_qcelemental }}
+
+    - name: Python Setup
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Create Environment
+      shell: bash
+      working-directory: ./qcel
+      run: |
+        eval "$(conda shell.bash hook)" && conda activate
+        python devtools/scripts/create_conda_env.py -n=test -p=$PYVER devtools/conda-envs/$CONDA_ENV.yaml
+
+    - name: Install
+      shell: bash
+      working-directory: ./qcel
+      run: |
+        eval "$(conda shell.bash hook)" && conda activate test
+        python -m pip install . --no-deps
+
+    - name: Environment Information
+      shell: bash
+      run: |
+        eval "$(conda shell.bash hook)" && conda activate test
+        conda list --show-channel-urls
+
+    - name: QCSchema from QCElemental
+      shell: bash
+      working-directory: ./qcel
+      run: |
+        eval "$(conda shell.bash hook)" && conda activate test
+        make qcschema
+        ls -l qcschema
+        cp -p qcschema/* ../qcsk/qcschema/data/vdev/
+        mv ../qcsk/qcschema/data/vdev/QCSchema.schema ../qcsk/qcschema/dev/
+
+    - name: Compare Schemas (generated vs. community)
+      shell: bash
+      working-directory: ./qcsk
+      run: |
+        git diff --color-words
+        pull_number=$(jq --raw-output .pull_request.number "$GITHUB_EVENT_PATH")
+        branch=qcel-${pull_number}
+        git checkout -b ${branch}
+        git remote -v
+        git config --local user.email "[email protected]"
+        git config --local user.name "GitHub Action"
+        git add -A
+        git commit -m "auto-generated from QCElemental"
+        echo "::set-env name=prbranch::${branch}"
+
+    - name: Propose changes
+      uses: ad-m/github-push-action@master
+      with:
+        directory: ./qcsk
+        repository: MolSSI/QCSchema
+        branch: ${{ env.prbranch }}
+        github_token: ${{ secrets.qcschema_from_qcelemental }}
+        force: true

.gitignore

@@ -119,3 +119,7 @@ runinfo/*
 # VSCode
 .vscode/
 raw_data/**/*_blob.py
+
+# autogen
+qcschema/*.schema
+qcelemental/tests/qcschema_instances/*/*.json

Makefile

@@ -43,6 +43,12 @@ data: cpu_data
 cpu_data:
 	(cd raw_data/cpu_data; python build_cpu_data.py; mv cpu_data_blob.py ../../qcelemental/info/data/)
 
+.PHONY: qcschema
+qcschema:
+	mkdir -p qcschema
+	python -c "exec(\"import pathlib, qcelemental\nfor md in qcelemental.models.qcschema_models():\n\tmfile = (pathlib.Path('qcschema') / md.__name__).with_suffix('.schema')\n\twith open(mfile, 'w') as fp:\n\t\tfp.write(md.schema_json(indent=None))\")"
+	python -c "exec(\"import json, pathlib, pydantic, qcelemental\nwith open((pathlib.Path('qcschema') / 'QCSchema').with_suffix('.schema'), 'w') as fp:\n\tjson.dump(pydantic.schema.schema(qcelemental.models.qcschema_models(), title='QCSchema'), fp, indent=4)\")"
+
 .PHONY: clean
 clean:
 	rm -rf `find . -name __pycache__`

devtools/conda-envs/base.yaml

@@ -8,7 +8,7 @@ dependencies:
   - nomkl
   - python
   - pint>=0.10.0
-  - pydantic>=1.0.0
+  - pydantic>=1.5.0,!=1.6.0
 
     # Optional depends
   - msgpack-python
@@ -20,3 +20,4 @@ dependencies:
   - pytest-cov
   - codecov
   - scipy  # tests an aspect of a helper fn not used by qcel functionality
+  - jsonschema

devtools/conda-envs/minimal.yaml

@@ -8,9 +8,10 @@ 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=1.2.0  # technically, qcel works with 1.0.0 but c-f doesn't have py38 builds for it
+  - pydantic=1.5.0
 
     # Testing
   - pytest=4.6.4  # technically, qcel works with 4.0.0 but c-f doesn't have py38 builds for it
   - pytest-cov
   - codecov
+  - jsonschema

docs/source/changelog.rst

@@ -19,15 +19,22 @@ Changelog
 
 New Features
 ++++++++++++
+- (:pr:`247`) Exports models to JSON Schema with ``make schema``.
+- (:pr:`247`) Build bank of JSON examples from Pydantic models defined in tests. Test that bank against exported schema with ``pytest --validate qcelemental/``.
+- (:pr:`247`) Many model descriptions edited, dimensions added to array properties, ``AtomicInput.model.basis`` now takes
+  ``BasisSet`` object not just string, several properties added to match QCSchema, several limitations on number and
+  uniqueness imposed.
 
 Enhancements
 ++++++++++++
+- (:pr:`247`) Improve mypy conformance including dynamic provenance. Necessitates Pydantic >=1.5.
+- (:pr:`247`) ``a0`` without underscore added as computable pint unit.
 - (: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.
+- (:pr:`249`) Fixes web tests that weren't marked.
 
 
 0.17.0 / 2020-10-01

qcelemental/conftest.py

@@ -0,0 +1,40 @@
+from pathlib import Path
+
+import pytest
+
+
+def pytest_addoption(parser):
+    parser.addoption(
+        "--validate", action="store_true", help="validate JSON from previous test run against exported schema"
+    )
+
+
+@pytest.fixture(scope="session", autouse=True)
+def set_up_overall(request):
+    # in all pytest runs except --validate (which uses the files), clear away the JSON examples and generate fresh
+    if not request.config.getoption("--validate", default=False):
+        _data_path = Path(__file__).parent.resolve() / "tests" / "qcschema_instances"
+        for fl in _data_path.rglob("*.json"):
+            fl.unlink()
+
+
+def pytest_runtest_setup(item):
+    # there's a bug where can only set options if specify path in call, so needs to be ``pytest qcelemental/ --validate``
+
+    # skip     the validate-generated-instances-against-exported-schema tests on most ``pytest`` runs.
+    # run only the validate-generated-instances-against-exported-schema tests on ``pytest --validate`` runs.
+    if not item.config.getoption("--validate", default=False) and item.name.startswith("test_qcschema"):
+        pytest.skip("can't run with --validate option")
+    elif item.config.getoption("--validate", default=False) and not item.name.startswith("test_qcschema"):
+        pytest.skip("need --validate option to run")
+
+
+# Uncomment below to probe for tests needing `@using_web`
+
+# import socket
+#
+# class block_network(socket.socket):
+#    def __init__(self, *args, **kwargs):
+#        raise Exception("Network call blocked")
+#
+# socket.socket = block_network

qcelemental/models/__init__.py

@@ -12,5 +12,18 @@
 from .basis import BasisSet
 from .common_models import ComputeError, DriverEnum, FailedOperation, Provenance
 from .molecule import Molecule
-from .procedures import Optimization, OptimizationInput, OptimizationResult
-from .results import AtomicInput, AtomicResult, AtomicResultProperties, Result, ResultInput, ResultProperties
+from .procedures import OptimizationInput, OptimizationResult
+from .procedures import Optimization  # scheduled for removal
+from .results import AtomicInput, AtomicResult, AtomicResultProperties
+from .results import Result, ResultInput, ResultProperties  # scheduled for removal
+
+
+def qcschema_models():
+    return [
+        AtomicInput,
+        AtomicResult,
+        AtomicResultProperties,
+        BasisSet,
+        Molecule,
+        Provenance,
+    ]

qcelemental/models/basemodels.py

@@ -125,6 +125,8 @@ def serialize(
         include: Optional[Set[str]] = None,
         exclude: Optional[Set[str]] = None,
         exclude_unset: Optional[bool] = None,
+        exclude_defaults: Optional[bool] = None,
+        exclude_none: Optional[bool] = None,
     ) -> Union[bytes, str]:
         """Generates a serialized representation of the model
 
@@ -138,6 +140,10 @@ def serialize(
             Fields to be excluded in the serialization.
         exclude_unset : Optional[bool], optional
             If True, skips fields that have default values provided.
+        exclude_defaults: Optional[bool], optional
+            If True, skips fields that have set or defaulted values equal to the default.
+        exclude_none: Optional[bool], optional
+            If True, skips fields that have value ``None``.
 
         Returns
         -------
@@ -152,6 +158,10 @@ def serialize(
             kwargs["exclude"] = exclude
         if exclude_unset:
             kwargs["exclude_unset"] = exclude_unset
+        if exclude_defaults:
+            kwargs["exclude_defaults"] = exclude_defaults
+        if exclude_none:
+            kwargs["exclude_none"] = exclude_none
 
         data = self.dict(**kwargs)
 
@@ -182,3 +192,6 @@ def compare(self, other: Union["ProtoModel", BaseModel], **kwargs) -> bool:
 class AutodocBaseSettings(BaseSettings):
     def __init_subclass__(cls) -> None:
         cls.__doc__ = AutoPydanticDocGenerator(cls, always_apply=True)
+
+
+qcschema_draft = "http://json-schema.org/draft-04/schema#"