Separate test files from main module and add CI

This also now ships all test data that you need to run tests, so you
don't need to download the file from hl7 again.

.github/workflows/ci.yaml

@@ -0,0 +1,52 @@
+name: CI
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+
+# The goal here is to cancel older workflows when a PR is updated (because it's pointless work)
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.ref_name }}
+  cancel-in-progress: true
+
+jobs:
+  unittest:
+    name: unit tests
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+          pip install pytest pytest-cov
+
+      - name: Test with pytest
+        run: |
+          python -m pytest --cov=fhirclient --cov-report=xml
+
+      - name: Log missing coverage
+        run: |
+          coverage report -m --skip-covered
+
+      - name: Check coverage report
+        if: github.ref != 'refs/heads/main'
+        uses: orgoro/[email protected]
+        with:
+          coverageFile: coverage.xml
+          token: ${{ secrets.GITHUB_TOKEN }}
+          thresholdAll: .70
+          thresholdNew: 1
+          thresholdModified: 1

.gitignore

@@ -1,6 +1,9 @@
 *.pyc
 __pycache__
 session_data
+/build/
+/dist/
+/*.egg-info/
 
 # docs
 /docs

fhir-parser-resources/settings.py

@@ -21,8 +21,7 @@
 
 # unit tests
 write_unittests = True
-tpl_unittest_target = '../fhirclient/models'    # target directory to write the generated unit test files to
-tpl_unittest_target_ptrn = '{}_tests.py'        # TODO: remove in future when we re-organize tests
+tpl_unittest_target = '../tests/models'         # target directory to write the generated unit test files to
 
 
 # all these files should be copied to dirname(`tpl_resource_target_ptrn`): tuples of (path/to/file, module, array-of-class-names)

fhir-parser-resources/template-unittest.py

@@ -1,21 +1,16 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-#
-#  Generated from FHIR {{ info.version }} on {{ info.date }}.
-#  {{ info.year }}, SMART Health IT.
-
+#  Generated from FHIR {{ info.version }}, SMART Health IT.
 
 import os
 import io
 import unittest
 import json
-from . import {{ class.module }}
-from .fhirdate import FHIRDate
+from fhirclient.models import {{ class.module }}
+from fhirclient.models.fhirdate import FHIRDate
 
 
 class {{ class.name }}Tests(unittest.TestCase):
     def instantiate_from(self, filename):
-        datadir = os.environ.get('FHIR_UNITTEST_DATADIR') or ''
+        datadir = os.path.join(os.path.dirname(__file__), '..', 'data', 'examples')
         with io.open(os.path.join(datadir, filename), 'r', encoding='utf-8') as handle:
             js = json.load(handle)
             self.assertEqual("{{ class.name }}", js["resourceType"])
@@ -36,7 +31,7 @@ def test{{ class.name }}{{ loop.index }}(self):
     def impl{{ class.name }}{{ loop.index }}(self, inst):
     {%- for onetest in tcase.tests %}
     {%- if "str" == onetest.klass.name %}
-        self.assertEqual(inst.{{ onetest.path }}, "{{ onetest.value|replace('\\n', '\\\\n')|replace('"', '\\"') }}")
+        self.assertEqual(inst.{{ onetest.path }}, "{{ onetest.value|replace('\\', '\\\\')|replace('"', '\\"') }}")
     {%- else %}{% if "int" == onetest.klass.name or "float" == onetest.klass.name or "NSDecimalNumber" == onetest.klass.name %}
         self.assertEqual(inst.{{ onetest.path }}, {{ onetest.value }})
     {%- else %}{% if "bool" == onetest.klass.name %}

setup.cfg

@@ -1,6 +1,5 @@
 [tool:pytest]
 minversion = 2.5
-python_files = *_tests.py
 
 [wheel]
 # Since we're a pure Python package, we can mark our wheels as universal.

setup.py

@@ -36,7 +36,7 @@ def find_version(*file_paths):
     license="APACHE2",
     author="SMART Platforms Team",
     author_email='[email protected]',
-    packages=find_packages(exclude=['test*', '*_tests.py']),
+    packages=find_packages(exclude=['tests*']),
     install_requires=['requests', 'isodate'],
     classifiers=[
         'Development Status :: 4 - Beta',

tests/README.md

@@ -0,0 +1,9 @@
+This folder holds test code and data.
+
+To re-generate the test models, run `./generate_models.py` from the project root.
+
+To re-generate the example test data, after re-generating the models,
+run:
+- `git rm tests/data/examples/*`
+- `cp fhir-parser/downloads/*example*.json tests/data/examples/`
+- `git add tests/data/examples/*`

tests/data/examples/account-example-with-guarantor.json

@@ -0,0 +1,76 @@
+{
+  "resourceType": "Account",
+  "id": "ewg",
+  "text": {
+    "status": "generated",
+    "div": "\u003cdiv xmlns\u003d\"http://www.w3.org/1999/xhtml\"\u003eInpatient Admission for Peter James Chalmers Account\u003c/div\u003e"
+  },
+  "identifier": [
+    {
+      "system": "urn:oid:0.1.2.3.4.5.6.7",
+      "value": "654321"
+    }
+  ],
+  "status": "active",
+  "type": {
+    "coding": [
+      {
+        "system": "http://terminology.hl7.org/CodeSystem/v3-ActCode",
+        "code": "PBILLACCT",
+        "display": "patient billing account"
+      }
+    ],
+    "text": "patient"
+  },
+  "name": "Inpatient: Peter James Chalmers",
+  "subject": [
+    {
+      "reference": "Patient/example",
+      "display": "Peter James Chalmers"
+    }
+  ],
+  "servicePeriod": {
+    "start": "2016-01-01",
+    "end": "2016-06-30"
+  },
+  "coverage": [
+    {
+      "coverage": {
+        "reference": "Coverage/9876B1"
+      },
+      "priority": 1
+    },
+    {
+      "coverage": {
+        "reference": "Coverage/7546D"
+      },
+      "priority": 2
+    }
+  ],
+  "owner": {
+    "reference": "Organization/f001",
+    "display": "Burgers University Medical Center"
+  },
+  "description": "Hospital charges",
+  "guarantor": [
+    {
+      "party": {
+        "reference": "RelatedPerson/benedicte",
+        "display": "Bénédicte du Marché"
+      },
+      "onHold": false,
+      "period": {
+        "start": "2016-01-01"
+      }
+    }
+  ],
+  "meta": {
+    "tag": [
+      {
+        "system": "http://terminology.hl7.org/CodeSystem/v3-ActReason",
+        "code": "HTEST",
+        "display": "test health data"
+      }
+    ]
+  }
+}

tests/data/examples/account-example.json

@@ -0,0 +1,57 @@
+{
+  "resourceType": "Account",
+  "id": "example",
+  "text": {
+    "status": "generated",
+    "div": "\u003cdiv xmlns\u003d\"http://www.w3.org/1999/xhtml\"\u003eHACC Funded Billing for Peter James Chalmers\u003c/div\u003e"
+  },
+  "identifier": [
+    {
+      "system": "urn:oid:0.1.2.3.4.5.6.7",
+      "value": "654321"
+    }
+  ],
+  "status": "active",
+  "type": {
+    "coding": [
+      {
+        "system": "http://terminology.hl7.org/CodeSystem/v3-ActCode",
+        "code": "PBILLACCT",
+        "display": "patient billing account"
+      }
+    ],
+    "text": "patient"
+  },
+  "name": "HACC Funded Billing for Peter James Chalmers",
+  "subject": [
+    {
+      "reference": "Patient/example",
+      "display": "Peter James Chalmers"
+    }
+  ],
+  "servicePeriod": {
+    "start": "2016-01-01",
+    "end": "2016-06-30"
+  },
+  "coverage": [
+    {
+      "coverage": {
+        "reference": "Coverage/7546D"
+      },
+      "priority": 1
+    }
+  ],
+  "owner": {
+    "reference": "Organization/hl7"
+  },
+  "description": "Hospital charges",
+  "meta": {
+    "tag": [
+      {
+        "system": "http://terminology.hl7.org/CodeSystem/v3-ActReason",
+        "code": "HTEST",
+        "display": "test health data"
+      }
+    ]
+  }
+}