Merge pull request #56 from mxochicale/54-pytest

54 - created pytest path, tidies scripts and READMEs and updates eVE.yaml #54

pyVEs/bareVE.yml

@@ -4,6 +4,7 @@
 ## INSTALL MAMBA EV: mamba env create -f *VE.yml
 ## ACTIVATE MAMBA ENV: mamba activate *VE
 ## REMOVE MAMBA ENV: mamba remove -n *VE --all
+## mamba env update --prune -n bareVE -f bareVE.yaml
 
 name: bareVE
 channels:
@@ -24,7 +25,6 @@ dependencies:
      - vtk>=9.3.0
      ### VERSIONS of opencv-contrib-python-headless  https://pypi.org/project/opencv-contrib-python-headless/#history
      - opencv-contrib-python-headless>=4.7.0.68
-     #
      - h5py
      #- pyvista #https://pypi.org/project/pyvista/#history #https://github.com/pyvista/pyvista/tags
      #- qimage2ndarray

pyVEs/eVE.yml

@@ -5,24 +5,39 @@
 ## UPDATE MAMBA ENV: mamba env update -f *VE.yml --prune
 ## ACTIVATE MAMBA ENV: mamba activate *VE
 ## REMOVE MAMBA ENV: mamba remove -n *VE --all
+## mamba env update --prune -n eVE -f eVE.yaml
 
 name: eVE # experimental and light Virtual Environmnet
 channels:
-  - conda-forge #pyside6
+  - conda-forge
 dependencies:
-  - python=3.11
   #- python=3.8
+  #- python=3.9
+  #- python=3.10
+  - python=3.11
   - pip
   - pip:
-     - pyside6 #https://pypi.org/project/PySide6/#history
-     - matplotlib
-     - opencv-python
-     - scikit-learn
-     - notebook
-     - pandas
-     - seaborn
-     #- opencv-contrib-python-headless #https://pypi.org/project/opencv-contrib-python-headless/#history
-     - araviq6
+     - pytest
+     - pytest-mock
+     - pyyaml
+     - requests
+     ### VERSIONS of pyside6: https://pypi.org/project/PySide6/#history
+     #- pyside6>=6.4.2
+     ### VERSIONS of VTK https://gitlab.kitware.com/vtk/vtk/-/tags
+     #- vtk>=9.0.3
+     #- vtk>=9.2.0
+     #- vtk>=9.2.5
+     #- vtk>=9.3.0
+     ### VERSIONS of opencv-contrib-python-headless  https://pypi.org/project/opencv-contrib-python-headless/#history
+     #- opencv-contrib-python-headless>=4.7.0.68     
+     #- opencv-contrib-python-headless
+     #- opencv-python
+     #- matplotlib
+     #- scikit-learn
+     #- notebook
+     #- pandas
+     #- seaborn
+     #- araviq6
      #- civiq6
      #- cv2PySide6
      #- qimage2ndarray

pytest/README.md

@@ -0,0 +1,22 @@
+# Python Testing with Pytest
+
+## Unit testing
+The typical testing workflow is showing below ([py-pkgs-testing](https://py-pkgs.org/05-testing.html)).     
+<img src="fig-testing-workflows.png" height="200">
+
+```
+mamba activate eVE
+pytest -sv tests/yaml_files/test_simple.yaml 
+```
+* Options
+```
+#-s option. All print statements -v it's a short --verbose
+-m?
+-k?
+```
+
+## References 
+* https://github.com/jashburn8020/python-testing-with-pytest 
+* https://docs.python.org/dev/library/unittest.mock.html
+* https://pypi.org/project/pytest-mock/
+

python/pytest/unittest_mock/examples/patch_examples/example00.py → pytest/tests/test_mocker_sums.py

@@ -1,5 +1,5 @@
 import pytest
-from mock import call
+from mock import call #pip install pytest-mock
 
 # References
 # https://stackoverflow.com/questions/53434986/using-mocker-to-patch-with-pytest

pytest/tests/test_my_class.py

@@ -0,0 +1,33 @@
+from unittest.mock import patch
+# https://kimsereylam.com/python/2021/03/19/how-to-use-patch-in-python-unittest.html
+
+class MyClass:
+    my_class_attribute = 1
+
+    def __init__(self):
+        self.instance_attribute_value = 2
+
+    def method_do_something(self):
+        return f"hello {self.instance_attribute_value}"
+
+
+def test_instance_attribute_value():
+    o = MyClass()
+    with patch.object(o, "instance_attribute_value", return_value=33):
+        print(f"PRINT o.instance_attribute_value: {o.instance_attribute_value()}")
+        assert o.instance_attribute_value() is 33
+
+def test_path_my_class_attribute():
+    o = MyClass()
+    with patch.object(o, "my_class_attribute", return_value=3):
+        print(f"PRINT o.my_class_attribute: {o.my_class_attribute()}")
+        assert o.my_class_attribute() is 3
+
+def test_patch_method_do_sth():
+    o = MyClass()
+    with patch.object(o, "method_do_something", return_value="hello"):
+        print(f"PRINT: o.method_do_something(): {o.method_do_something()}")
+        assert o.method_do_something() is "hello"
+
+
+

pytest/tests/week05-testing/README.md

@@ -0,0 +1,49 @@
+# week05-testing
+
+## issues
+```
+
+pytest test_times.py 
+=============================================================== test session starts ================================================================
+platform linux -- Python 3.11.7, pytest-7.4.3, pluggy-1.3.0
+rootdir: /home/mxochicale/repositories/mxochicale/code/pytest/tests/week05-testing
+plugins: mock-3.12.0
+collected 7 items                                                                                                                                  
+
+test_times.py ......F                                                                                                                        [100%]
+
+===================================================================== FAILURES =====================================================================
+_________________________________________________________________ test_iss_passes __________________________________________________________________
+
+    def test_iss_passes():
+        with mock.patch("requests.get", new=mock.MagicMock(return_value=ISS_response())) as mymock:
+>           iss_over_London = iss_passes(51.5074, -0.1278)
+
+test_times.py:61: 
+_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
+times.py:35: in iss_passes
+    return [(datetime.datetime.fromtimestamp(x['risetime']).strftime("%Y-%m-%d %H:%M:%S"),
+_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
+
+.0 = <dict_keyiterator object at 0x7f32b1822390>
+
+>   return [(datetime.datetime.fromtimestamp(x['risetime']).strftime("%Y-%m-%d %H:%M:%S"),
+             (datetime.datetime.fromtimestamp(x['risetime'] + x['duration'])).strftime("%Y-%m-%d %H:%M:%S"))
+            for x in response]
+E   TypeError: string indices must be integers, not 'str'
+
+times.py:35: TypeError
+--------------------------------------------------------------- Captured stdout call ---------------------------------------------------------------
+200
+{'message': 'success', 'request': {'altitude': 10.0, 'datetime': 1703321064.740006, 'latitude': 51.5074, 'longitude': -0.1278, 'passes': 5}, 'response': [{'duration': 446, 'risetime': 1703409497.740006}, {'duration': 628, 'risetime': 1703415159.740006}, {'duration': 656, 'risetime': 1703420935.740006}, {'duration': 655, 'risetime': 1703426740.740006}, {'duration': 632, 'risetime': 1703432544.740006}]}
+============================================================= short test summary info ==============================================================
+FAILED test_times.py::test_iss_passes - TypeError: string indices must be integers, not 'str'
+=========================================================== 1 failed, 6 passed in 0.14s =================================
+
+```
+
+## References
+* https://github.com/UCL-COMP0233-22-23/times-tests
+* https://github.com/UCL-MPHY0021-21-22/RSE-Classwork/issues/16
+* https://gist.github.com/alessandrofelder/8fb8e34f29970cd8e05c4c18d30f98f5
+`

python/pytest/unittest_mock/examples/week05-testing/times.py → pytest/tests/week05-testing/times.py

@@ -1,11 +1,6 @@
 import datetime
 import requests
 
-#References
-# https://github.com/UCL-COMP0233-22-23/times-tests
-# https://github.com/UCL-MPHY0021-21-22/RSE-Classwork/issues/16
-# https://gist.github.com/alessandrofelder/8fb8e34f29970cd8e05c4c18d30f98f5
-
 def time_range(start_time, end_time, number_of_intervals=1, gap_between_intervals_s=0):
     start_time_s = datetime.datetime.strptime(start_time, "%Y-%m-%d %H:%M:%S")
     end_time_s = datetime.datetime.strptime(end_time, "%Y-%m-%d %H:%M:%S")
@@ -22,15 +17,21 @@ def iss_passes(lat, lon, n=5):
     Returns a time_range-like output for intervals of time when the International Space Station
     passes at a given location and for a number of days from today.
     """
-    iss_request = requests.get("http://api.open-notify.org/iss-pass.json",
+    #http://open-notify.org/Open-Notify-API/
+    #iss_request = requests.get("http://api.open-notify.org/iss-pass.json") #404
+    #iss_request = requests.get("http://api.open-notify.org/iss-pass.json",
+    iss_request = requests.get("http://api.open-notify.org/iss-now.json",
                                params={
                                    "lat": lat,
                                    "lon": lon,
-                                   "n": n})    
+                                   "n": n})   
+    print(iss_request.status_code)
     if iss_request.status_code != 200:
         # if the request failed for some reason
         return []
-    response = iss_request.json()['response']
+    #response = iss_request.json()['response']
+    response = iss_request.json()
+    print(response)
     return [(datetime.datetime.fromtimestamp(x['risetime']).strftime("%Y-%m-%d %H:%M:%S"),
              (datetime.datetime.fromtimestamp(x['risetime'] + x['duration'])).strftime("%Y-%m-%d %H:%M:%S"))
             for x in response]

pytest/tests/yaml_files/conftest.py

@@ -0,0 +1,59 @@
+# content of conftest.py
+import pytest
+
+def pytest_collect_file(parent, file_path):
+    print(f"\n")
+    print(f'PRINT pytest_collect_file > parent: {parent}')
+    print(f'PRINT pytest_collect_fiel > file_path: {file_path}')
+    if file_path.suffix == ".yaml" and file_path.name.startswith("test"):
+        return YamlFile.from_parent(parent, path=file_path)
+
+
+class YamlFile(pytest.File):
+    def collect(self):
+        # We need a yaml parser, e.g. PyYAML.
+        import yaml
+
+        print(f'PRINT YamlFile > pytest.File: {pytest.File}')
+        print(f'PRINT YamlFile > self: {self}')
+
+        raw = yaml.safe_load(self.path.open())
+        print(f'PRINT YamlFile > raw: {raw}')
+        for name, spec in sorted(raw.items()):
+            print(f'  PRINT YamlFile > name: {name}')
+            print(f'  PRINT YamlFile > spec: {spec}')
+            yield YamlItem.from_parent(self, name=name, spec=spec)
+
+
+class YamlItem(pytest.Item):
+    def __init__(self, *, spec, **kwargs):
+        super().__init__(**kwargs)
+        self.spec = spec
+        #print(f'PRINT2 YamlItem > self.spec: {self.spec}')
+
+    def runtest(self):
+        for name, value in sorted(self.spec.items()):
+            # Some custom test execution (dumb example follows).
+            print(f"\n")
+            print(f'PRINT2 YamlItem::runtest() > name: {name}')
+            print(f'PRINT2 YamlItem::runtest() > value: {value}')
+            if name != value:
+                raise YamlException(self, name, value)
+
+    def repr_failure(self, excinfo):
+        """Called when self.runtest() raises an exception."""
+        if isinstance(excinfo.value, YamlException):
+            return "\n".join(
+                [
+                    "usecase execution failed",
+                    "   spec failed: {1!r}: {2!r}".format(*excinfo.value.args),
+                    "   no further details known at this point.",
+                ]
+            )
+
+    def reportinfo(self):
+        return self.path, 0, f"usecase: {self.name}"
+
+
+class YamlException(Exception):
+    """Custom exception for error reporting."""

pytest/tests/yaml_files/test_simple.yaml

@@ -0,0 +1,8 @@
+# test_simple.yaml
+ok:
+    sub1: sub1
+
+hello:
+    world: world1
+    some: some
+