Test

CHANGELOG.md

@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - `gc_clamp` property
 - `single_runs` property
 ### Changed
+- Test system modified
 ### Removed
 - `property` deleter & setter
 ## [0.1] - 2024-11-27

autopep8.bat

@@ -1,3 +1,4 @@
 python -m autopep8 opr --recursive --aggressive --aggressive --in-place --pep8-passes 2000 --max-line-length 120 --verbose --ignore=E721
 python -m autopep8 otherfiles --recursive --aggressive --aggressive --in-place --pep8-passes 2000 --max-line-length 120 --verbose --ignore=E721
+python -m autopep8 tests --recursive --aggressive --aggressive --in-place --pep8-passes 2000 --max-line-length 120 --verbose --ignore=E721
 python -m autopep8 setup.py --recursive --aggressive --aggressive --in-place --pep8-passes 2000 --max-line-length 120 --verbose

autopep8.sh

@@ -1,4 +1,5 @@
 #!/bin/sh
 python -m autopep8 opr --recursive --aggressive --aggressive --in-place --pep8-passes 2000 --max-line-length 120 --verbose --ignore=E721
 python -m autopep8 otherfiles --recursive --aggressive --aggressive --in-place --pep8-passes 2000 --max-line-length 120 --verbose --ignore=E721
+python -m autopep8 tests --recursive --aggressive --aggressive --in-place --pep8-passes 2000 --max-line-length 120 --verbose --ignore=E721
 python -m autopep8 setup.py --recursive --aggressive --aggressive --in-place --pep8-passes 2000 --max-line-length 120 --verbose

tests/test_cache.py

@@ -0,0 +1,34 @@
+from opr import Primer, MeltingTemperature
+
+TEST_CASE_NAME = "Cache tests"
+
+
+def test_mwc():
+    oprimer = Primer("ATCGATCGATCGATCGAT")
+    molecular_weight = oprimer.molecular_weight
+    assert round(oprimer.molecular_weight, 1) == round(molecular_weight, 1)
+
+
+def test_gc_content():
+    oprimer = Primer("ATTCG")
+    gc_content = oprimer.gc_content
+    assert oprimer.gc_content == gc_content
+
+
+def test_gc_clamp():
+    oprimer = Primer("ATCGATCGATCGATCGGTCG")
+    gc_clamp = oprimer.gc_clamp
+    assert oprimer.gc_clamp == gc_clamp
+
+
+def test_melt_temp():
+    oprimer = Primer("ATCGATCGATCGATCGATCG")
+    basic_melt_temp = oprimer.melting_temperature(MeltingTemperature.BASIC)
+    assert round(oprimer.melting_temperature(MeltingTemperature.BASIC), 1) == round(basic_melt_temp, 1)
+
+
+def test_single_runs():
+    oprimer = Primer("AAAAATTCGGGGATCCCCG")
+    runs = oprimer.single_runs
+    assert oprimer.single_runs['A'] == runs['A'] and oprimer.single_runs['T'] == runs[
+        'T'] and oprimer.single_runs['C'] == runs['C'] and oprimer.single_runs['G'] == runs['G']

tests/test_calculations.py

@@ -1,57 +1,68 @@
-from opr import Primer
-from opr.primer import MeltingTemperature
+from opr import Primer, MeltingTemperature
 
 TEST_CASE_NAME = "Calculations tests"
 
+
 def test_mwc():
     oprimer = Primer("ATCGATCGATCGATCGAT")
     assert round(oprimer.molecular_weight, 1) == 5498.7
 
-def test_gc_content_1(): #Reference: https://jamiemcgowan.ie/bioinf/gc_content.html
+
+def test_gc_content_1():  # Reference: https://jamiemcgowan.ie/bioinf/gc_content.html
     oprimer = Primer("ATCG")
     assert oprimer.gc_content == 0.5
 
-def test_gc_content_2(): #Reference: https://jamiemcgowan.ie/bioinf/gc_content.html
+
+def test_gc_content_2():  # Reference: https://jamiemcgowan.ie/bioinf/gc_content.html
     oprimer = Primer("ATTCG")
     assert oprimer.gc_content == 0.4
 
-def test_gc_content_3(): #Reference: https://jamiemcgowan.ie/bioinf/gc_content.html
+
+def test_gc_content_3():  # Reference: https://jamiemcgowan.ie/bioinf/gc_content.html
     oprimer = Primer("ATTTTTT")
     assert oprimer.gc_content == 0
 
-def test_gc_clamp_1(): #Reference: https://www.bioinformatics.org/sms2/pcr_primer_stats.html
+
+def test_gc_clamp_1():  # Reference: https://www.bioinformatics.org/sms2/pcr_primer_stats.html
     oprimer = Primer("ATCGATCGATCGATCGGTCG")
     assert oprimer.gc_clamp == 4
 
-def test_gc_clamp_2(): #Reference: https://www.bioinformatics.org/sms2/pcr_primer_stats.html
+
+def test_gc_clamp_2():  # Reference: https://www.bioinformatics.org/sms2/pcr_primer_stats.html
     oprimer = Primer("ATCG")
     assert oprimer.gc_clamp == 0
 
-def test_gc_clamp_3(): #Reference: https://www.bioinformatics.org/sms2/pcr_primer_stats.html
+
+def test_gc_clamp_3():  # Reference: https://www.bioinformatics.org/sms2/pcr_primer_stats.html
     oprimer = Primer("ACTTA")
     assert oprimer.gc_clamp == 1
 
-def test_melt_temp_1(): #Reference: http://biotools.nubic.northwestern.edu/OligoCalc.html
+
+def test_melt_temp_1():  # Reference: http://biotools.nubic.northwestern.edu/OligoCalc.html
     oprimer = Primer("ATCGATCGATCGATCGATCG")
     basic_melt_temp = oprimer.melting_temperature(MeltingTemperature.BASIC)
-    assert round(basic_melt_temp,1) == 51.8
+    assert round(basic_melt_temp, 1) == 51.8
+
 
-def test_melt_temp_2(): #Reference: http://biotools.nubic.northwestern.edu/OligoCalc.html
+def test_melt_temp_2():  # Reference: http://biotools.nubic.northwestern.edu/OligoCalc.html
     oprimer = Primer("ATCG")
     basic_melt_temp = oprimer.melting_temperature(method=MeltingTemperature.BASIC)
-    assert round(basic_melt_temp,1) == 12
+    assert round(basic_melt_temp, 1) == 12
 
-def test_single_runs_1(): #Reference: https://www.oligoevaluator.com/OligoCalcServlet
+
+def test_single_runs_1():  # Reference: https://www.oligoevaluator.com/OligoCalcServlet
     oprimer = Primer("ATCGATCG")
     runs = oprimer.single_runs
     assert runs['A'] == 0 and runs['T'] == 0 and runs['C'] == 0 and runs['G'] == 0
 
-def test_single_runs_2(): #Reference: https://www.oligoevaluator.com/OligoCalcServlet
+
+def test_single_runs_2():  # Reference: https://www.oligoevaluator.com/OligoCalcServlet
     oprimer = Primer("ATTCGATCCCCG")
     runs = oprimer.single_runs
     assert runs['A'] == 0 and runs['T'] == 2 and runs['C'] == 4 and runs['G'] == 0
 
-def test_single_runs_3(): #Reference: https://www.oligoevaluator.com/OligoCalcServlet
+
+def test_single_runs_3():  # Reference: https://www.oligoevaluator.com/OligoCalcServlet
     oprimer = Primer("AAAAATTCGGGGATCCCCG")
     runs = oprimer.single_runs
     assert runs['A'] == 5 and runs['T'] == 2 and runs['C'] == 4 and runs['G'] == 4

tests/test_errors.py

@@ -0,0 +1,32 @@
+import pytest
+from opr import Primer, MeltingTemperature, OPRBaseError
+
+TEST_CASE_NAME = "Errors tests"
+
+
+def test_addition():
+    oprimer = Primer("ATCGATCGATCGATCGAT")
+    with pytest.raises(OPRBaseError, match=r"You can only add two Primer objects."):
+        oprimer + 2
+
+
+def test_multiply():
+    oprimer = Primer("ATCGATCGATCGATCGAT")
+    with pytest.raises(OPRBaseError, match=r"The primer sequence can only be multiplied by an integer."):
+        oprimer * "2"
+
+
+def test_validate_primer_1():
+    with pytest.raises(OPRBaseError, match=r"Primer sequence should be a string variable."):
+        oprimer = Primer(222)
+
+
+def test_validate_primer_2():
+    with pytest.raises(OPRBaseError, match=r"Primer sequence should only contain the nucleotide bases A, T, C, and G."):
+        oprimer = Primer("ATCGATCGATCGATCGAF")
+
+
+def test_melting_temperature():
+    oprimer = Primer("ATCGATCGATCGATCGAT")
+    with pytest.raises(NotImplementedError, match=r"This method for calculating melting temperature has not been implemented."):
+        oprimer.melting_temperature(method=MeltingTemperature.NEAREST_NEIGHBOR)

tests/test_operations.py

@@ -1,66 +1,76 @@
 from opr import Primer
 
-TEST_CASE_NAME = "operations testcase"
+TEST_CASE_NAME = "Operations tests"
 
-def test_reverse_1(): #Reference: https://www.qiagen.com/us/applications/enzymes/tools-and-calculators/reverse-complement-converter
+
+def test_reverse_1():  # Reference: https://www.qiagen.com/us/applications/enzymes/tools-and-calculators/reverse-complement-converter
     oprimer = Primer("ATCGATCGATCGATCGAT")
     oprimer_reversed = oprimer.reverse(inplace=False)
     assert oprimer_reversed.sequence == "TAGCTAGCTAGCTAGCTA"
 
-def test_reverse_2(): #Reference: https://www.qiagen.com/us/applications/enzymes/tools-and-calculators/reverse-complement-converter
+
+def test_reverse_2():  # Reference: https://www.qiagen.com/us/applications/enzymes/tools-and-calculators/reverse-complement-converter
     oprimer = Primer("ATCGATCGATCGATCGAT")
     oprimer_reversed = oprimer.reverse()
     assert oprimer_reversed.sequence == "TAGCTAGCTAGCTAGCTA"
 
-def test_reverse_3(): #Reference: https://www.qiagen.com/us/applications/enzymes/tools-and-calculators/reverse-complement-converter
+
+def test_reverse_3():  # Reference: https://www.qiagen.com/us/applications/enzymes/tools-and-calculators/reverse-complement-converter
     oprimer = Primer("ATCGATCGATCGATCGAT")
     oprimer.reverse(inplace=True)
     assert oprimer.sequence == "TAGCTAGCTAGCTAGCTA"
 
 
-def test_complement_1(): #Reference: https://www.qiagen.com/us/applications/enzymes/tools-and-calculators/reverse-complement-converter
+def test_complement_1():  # Reference: https://www.qiagen.com/us/applications/enzymes/tools-and-calculators/reverse-complement-converter
     oprimer = Primer("ATCGGCTAAATCGGCTAA")
     oprimer_complemented = oprimer.complement(inplace=False)
     assert oprimer_complemented.sequence == "TAGCCGATTTAGCCGATT"
 
-def test_complement_2(): #Reference: https://www.qiagen.com/us/applications/enzymes/tools-and-calculators/reverse-complement-converter
+
+def test_complement_2():  # Reference: https://www.qiagen.com/us/applications/enzymes/tools-and-calculators/reverse-complement-converter
     oprimer = Primer("ATCGGCTAAATCGGCTAA")
     oprimer_complemented = oprimer.complement()
     assert oprimer_complemented.sequence == "TAGCCGATTTAGCCGATT"
 
-def test_complement_3(): #Reference: https://www.qiagen.com/us/applications/enzymes/tools-and-calculators/reverse-complement-converter
+
+def test_complement_3():  # Reference: https://www.qiagen.com/us/applications/enzymes/tools-and-calculators/reverse-complement-converter
     oprimer = Primer("ATCGGCTAAATCGGCTAA")
     oprimer.complement(inplace=True)
     assert oprimer.sequence == "TAGCCGATTTAGCCGATT"
 
+
 def test_length():
     oprimer = Primer("ATCGGCTAAATCGGCTAA")
     assert len(oprimer) == 18
 
+
 def test_addition():
     oprimer_1 = Primer("ATCG")
     oprimer_2 = Primer("GATC")
     oprimer_concat = oprimer_1 + oprimer_2
     assert oprimer_concat.sequence == "ATCGGATC"
 
+
 def test_multiply():
     oprimer_1 = Primer("ATCG")
     oprimer_concat = oprimer_1 * 4
     assert oprimer_concat.sequence == "ATCGATCGATCGATCG"
 
+
 def test_equality1():
     oprimer_1 = Primer("ATCG")
     oprimer_2 = Primer("ATCG")
     assert oprimer_1 == oprimer_2
 
+
 def test_equality2():
     oprimer_1 = Primer("ATCG")
     oprimer_2 = Primer("ATCGC")
     assert oprimer_1 != oprimer_2
 
+
 def test_str():
     oprimer_1 = Primer("ATCG")
     oprimer_2 = Primer("ATCGC")
     oprimer_concat = oprimer_1 + oprimer_2
     assert str(oprimer_1) + str(oprimer_2) == oprimer_concat.sequence
-