Merge pull request #150 from smart-on-fhir/mikix/ci

Separate test files from main module and add CI

.coveragerc

@@ -0,0 +1,2 @@
+[run]
+omit = fhirclient/models/*

.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: .35
+          thresholdNew: 1
+          thresholdModified: 0

.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.sh` 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"
+      }
+    ]
+  }
+}