Merge pull request #105 from andyfaff/test

TST: move tests into orsopy hierarchy

.github/workflows/pylint.yml

@@ -28,4 +28,3 @@ jobs:
       - name: Lint
         run: |
           flake8 --max-line-length=120 --ignore=F401,W503,E203 --count --show-source --statistics orsopy
-          flake8 --max-line-length=120 --ignore=F401,W503,E203 --count --show-source --statistics tests

.github/workflows/pytest.yml

@@ -31,7 +31,7 @@ jobs:
       
       - name: Test with pytest
         run: |
-          pytest
+          pytest --pyargs orsopy
 
       - name: Test with coverage
         run: |
@@ -68,4 +68,4 @@ jobs:
 
       - name: Test with pytest
         run: |
-          pytest
+          pytest --pyargs orsopy

tests/test_fileio/test_base.py → orsopy/fileio/tests/test_base.py

@@ -3,12 +3,11 @@
 """
 # pylint: disable=R0201
 
-import pathlib
+from pathlib import Path
 import unittest
 
 from datetime import datetime
 from math import log, sqrt
-from os.path import join as pjoin
 
 import pint
 import pytest
@@ -18,6 +17,9 @@
 from orsopy.fileio import base, orso
 
 
+pth = Path(__file__).absolute().parent
+
+
 class TestErrorValue(unittest.TestCase):
     """
     Testing the Value class.
@@ -501,21 +503,21 @@ def test_creation_for_existing_file(self):
         """
         Creation for a file that does exist with a given modified date.
         """
-        fname = pathlib.Path("README.rst")
+        fname = Path(pth / "not_orso.ort")
         value = base.File(str(fname.absolute()), datetime.fromtimestamp(fname.stat().st_mtime))
-        assert value.file == str(pathlib.Path().resolve().joinpath("README.rst"))
+        assert value.file == str(fname)
         assert value.timestamp == datetime.fromtimestamp(fname.stat().st_mtime)
 
     def test_to_yaml_for_existing_file(self):
         """
         Transformation to yaml a file that does exist with a given modified
         date.
         """
-        fname = pathlib.Path("README.rst")
+        fname = Path(pth / "not_orso.ort")
         value = base.File(str(fname.absolute()), datetime.fromtimestamp(fname.stat().st_mtime))
         assert (
             value.to_yaml()
-            == f'file: {str(pathlib.Path().resolve().joinpath("README.rst"))}\n'
+            == f'file: {str(fname)}\n'
             + "timestamp: "
             + f"{datetime.fromtimestamp(fname.stat().st_mtime).isoformat()}\n"
         )
@@ -525,27 +527,27 @@ def test_creation_for_existing_file_no_mod_time(self):
         Transformation to yaml a file that does exist without a given
         modified date.
         """
-        fname = pathlib.Path("AUTHORS.rst")
+        fname = Path(pth / "not_orso.ort")
         value = base.File(str(fname.absolute()), None)
-        assert value.file == str(pathlib.Path().resolve().joinpath("AUTHORS.rst"))
+        assert value.file == str(fname)
         assert value.timestamp == datetime.fromtimestamp(fname.stat().st_mtime)
 
     def test_to_yaml_for_existing_file_no_mod_time(self):
         """
         Transformation to yaml a file that does exist without a given
         modified date.
         """
-        fname = pathlib.Path("AUTHORS.rst")
+        fname = Path(pth / "not_orso.ort")
         value = base.File(str(fname.absolute()), None)
         assert (
             value.to_yaml()
             == "file: "
-            + f'{str(pathlib.Path().resolve().joinpath("AUTHORS.rst"))}\n'
+            + f'{str(fname)}\n'
             + "timestamp: "
             + f"{datetime.fromtimestamp(fname.stat().st_mtime).isoformat()}\n"
         )
 
 
 def test_not_orso():
     with pytest.raises(base.NotOrsoCompatibleFileError, match="First line does not appea"):
-        orso.load_orso(pjoin("tests", "not_orso.ort"))
+        orso.load_orso(pth / "not_orso.ort")

tests/test_fileio/test_data_source.py → orsopy/fileio/tests/test_data_source.py

@@ -2,14 +2,17 @@
 Tests for fileio.data_source module
 """
 
-import pathlib
+from pathlib import Path
 import unittest
 
 from datetime import datetime
 
 from orsopy.fileio import base, data_source
 
 
+pth = Path(__file__).absolute().parent
+
+
 class TestExperiment(unittest.TestCase):
     """
     Testing the Experiment class.
@@ -260,27 +263,29 @@ def test_creation(self):
         """
         Creation with minimal set.
         """
+        fname = pth / "not_orso.ort"
         value = data_source.Measurement(
             data_source.InstrumentSettings(base.Value(4.0, "deg"), base.ValueRange(2.0, 12.0, "angstrom"),),
-            [base.File(str(pathlib.Path().resolve().joinpath("README.rst")), None)],
+            [base.File(str(fname), None)],
         )
         assert value.instrument_settings.incident_angle.magnitude == 4.0
         assert value.instrument_settings.incident_angle.unit == "deg"
         assert value.instrument_settings.wavelength.min == 2.0
         assert value.instrument_settings.wavelength.max == 12.0
         assert value.instrument_settings.wavelength.unit == "angstrom"
-        assert value.data_files[0].file == str(pathlib.Path().resolve().joinpath("README.rst"))
-        assert value.data_files[0].timestamp == datetime.fromtimestamp(pathlib.Path("README.rst").stat().st_mtime)
+        assert value.data_files[0].file == str(pth / "not_orso.ort")
+        assert value.data_files[0].timestamp == datetime.fromtimestamp(fname.stat().st_mtime)
 
     def test_to_yaml(self):
         """
         Transform to yaml with minimal set.
         """
+        fname = pth / "not_orso.ort"
+
         value = data_source.Measurement(
             data_source.InstrumentSettings(base.Value(4.0, "deg"), base.ValueRange(2.0, 12.0, "angstrom"),),
-            [base.File(str(pathlib.Path().resolve().joinpath("README.rst")), None)],
+            [base.File(str(fname), None)],
         )
-        fname = pathlib.Path("README.rst")
         assert (
             value.to_yaml()
             == "instrument_settings:\n  incident_angle:"
@@ -294,44 +299,48 @@ def test_creation_optionals(self):
         """
         Creation with optionals.
         """
+        fname0 = pth / "not_orso.ort"
+        fname1 = pth / "test_base.py"
+
         value = data_source.Measurement(
             data_source.InstrumentSettings(base.Value(4.0, "deg"), base.ValueRange(2.0, 12.0, "angstrom"),),
-            [base.File(str(pathlib.Path().resolve().joinpath("README.rst")), None)],
-            [base.File(str(pathlib.Path().resolve().joinpath("AUTHORS.rst")), None)],
+            [base.File(str(fname0), None)],
+            [base.File(str(fname1), None)],
         )
         assert value.instrument_settings.incident_angle.magnitude == 4.0
         assert value.instrument_settings.incident_angle.unit == "deg"
         assert value.instrument_settings.wavelength.min == 2.0
         assert value.instrument_settings.wavelength.max == 12.0
         assert value.instrument_settings.wavelength.unit == "angstrom"
-        assert value.data_files[0].file == str(pathlib.Path().resolve().joinpath("README.rst"))
-        assert value.data_files[0].timestamp == datetime.fromtimestamp(pathlib.Path("README.rst").stat().st_mtime)
-        assert value.additional_files[0].file == str(pathlib.Path().resolve().joinpath("AUTHORS.rst"))
+        assert value.data_files[0].file == str(fname0)
+        assert value.data_files[0].timestamp == datetime.fromtimestamp(fname0.stat().st_mtime)
+        assert value.additional_files[0].file == str(fname1)
         assert value.additional_files[0].timestamp == datetime.fromtimestamp(
-            pathlib.Path("AUTHORS.rst").stat().st_mtime
+            fname1.stat().st_mtime
         )
 
     def test_to_yaml_optionals(self):
         """
         Transform to yaml with optionals.
         """
+        fname0 = pth / "not_orso.ort"
+        fname1 = pth / "test_base.py"
+
         value = data_source.Measurement(
             data_source.InstrumentSettings(base.Value(4.0, "deg"), base.ValueRange(2.0, 12.0, "angstrom"),),
-            [base.File(str(pathlib.Path().resolve().joinpath("README.rst")), None)],
-            [base.File(str(pathlib.Path().resolve().joinpath("AUTHORS.rst")), None)],
+            [base.File(str(fname0), None)],
+            [base.File(str(fname1), None)],
             "energy-dispersive",
         )
-        fname = pathlib.Path("README.rst")
-        gname = pathlib.Path("AUTHORS.rst")
         assert (
             value.to_yaml()
             == "instrument_settings:\n  incident_angle:"
             + " {magnitude: 4.0, unit: deg}\n  wavelength: {min: "
             + "2.0, max: 12.0, unit: angstrom}\ndata_files:\n- file: "
-            + f"{str(fname.absolute())}\n  timestamp: "
-            + f"{datetime.fromtimestamp(fname.stat().st_mtime).isoformat()}\n"
+            + f"{str(fname0.absolute())}\n  timestamp: "
+            + f"{datetime.fromtimestamp(fname0.stat().st_mtime).isoformat()}\n"
             + "additional_files:\n- file: "
-            + f"{str(gname.absolute())}\n  timestamp: "
-            + f"{datetime.fromtimestamp(gname.stat().st_mtime).isoformat()}\n"
+            + f"{str(fname1.absolute())}\n  timestamp: "
+            + f"{datetime.fromtimestamp(fname1.stat().st_mtime).isoformat()}\n"
             + "scheme: energy-dispersive\n"
         )

tests/test_fileio/test_model_language.py → orsopy/fileio/tests/test_model_language.py

@@ -3,7 +3,6 @@
 """
 # pylint: disable=R0201
 
-import pathlib
 import unittest
 
 from datetime import datetime

tests/test_fileio/test_orso.py → orsopy/fileio/tests/test_orso.py

@@ -2,7 +2,7 @@
 Tests for fileio module
 """
 
-import os.path
+from pathlib import Path
 import unittest
 
 from datetime import datetime
@@ -18,6 +18,9 @@
 from orsopy.fileio.reduction import Reduction, Software
 
 
+pth = Path(__file__).absolute().parent
+
+
 class TestOrso(unittest.TestCase):
     """
     Testing the Orso class.
@@ -226,7 +229,7 @@ def test_extra_elements(self):
         # if there are extra elements present in the ORT file they should still
         # be loadable. They won't be there as dataclass fields, but they'll be
         # visible as attributes.
-        datasets = fileio.load_orso(os.path.join("tests", "test_example.ort"))
+        datasets = fileio.load_orso(pth / "test_example.ort")
         info = datasets[0].info
         assert hasattr(info.data_source.measurement.instrument_settings.incident_angle, "resolution")
 

tests/test_fileio/test_schema.py → orsopy/fileio/tests/test_schema.py

@@ -1,5 +1,5 @@
 import json
-import os.path
+from pathlib import Path
 
 import jsonschema
 import numpy as np
@@ -8,15 +8,16 @@
 from orsopy import fileio
 from orsopy.fileio.base import _read_header_data, _validate_header_data
 
+pth = Path(__file__).absolute().parent
+
 
 class TestSchema:
     def test_example_ort(self):
-        pth = os.path.dirname(fileio.__file__)
-        schema_pth = os.path.join(pth, "schema", "refl_header.schema.json")
+        schema_pth = pth / ".." / "schema" / "refl_header.schema.json"
         with open(schema_pth, "r") as f:
             schema = json.load(f)
 
-        dct_list, data, version = _read_header_data(os.path.join("tests", "test_example.ort"), validate=True)
+        dct_list, data, version = _read_header_data(pth / "test_example.ort", validate=True)
         assert data[0].shape == (2, 4)
         assert version == "0.1"
 
@@ -29,7 +30,7 @@ def test_example_ort(self):
         _validate_header_data(dct_list)
 
         # try a 2 dataset file
-        dct_list, data, version = _read_header_data(os.path.join("tests", "test_example2.ort"), validate=True)
+        dct_list, data, version = _read_header_data(pth / "test_example2.ort", validate=True)
         assert len(dct_list) == 2
         assert dct_list[1]["data_set"] == "spin_down"
         assert data[1].shape == (4, 4)

setup.cfg

@@ -31,3 +31,4 @@ include_package_data = True
 [options.package_data]
 orsopy.slddb.element_table = nabs_geant4/*.npz
 orsopy.fileio = schema/*.*
+orsopy.fileio.tests = *.ort