Junit5 by johnmay · Pull Request #901 · cdk/cdk

johnmay · 2022-09-10T21:49:09Z

WIP - but almost done.
Some things to double check as per commit.

…g in the assertThrows and assertTimeout. Odd failures, probably due to the method order: CtxReaderTest:testClose() CDKOWLReader:testClose() CrystClustReader:testClose() ModelBuilder3DTest:testModelBuilder3D_reserpine() SlowTest was failing - needs more attention. MayGen Parameterised JUnit4 test left in place for now.

johnmay · 2022-09-11T12:50:16Z

Doing a before/after on the log - some tests have gone missing (probably missing annotations):

[john@sentinel:cdk]% diff main.log.norm after.log.norm
55c55
< [INFO] Tests run: 50, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.MappingTest
---
> [INFO] Tests run: 49, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.MappingTest
66c66
< [INFO] Tests run: 4425, Failures: 0, Errors: 0, Skipped: 0
---
> [INFO] Tests run: 4424, Failures: 0, Errors: 0, Skipped: 0
97c97
< [INFO] Tests run: 50, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.silent.MappingTest
---
> [INFO] Tests run: 49, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.silent.MappingTest
107c107
< [INFO] Tests run: 4192, Failures: 0, Errors: 0, Skipped: 0
---
> [INFO] Tests run: 4191, Failures: 0, Errors: 0, Skipped: 0
124c124
< [INFO] Tests run: 50, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.debug.DebugMappingTest
---
> [INFO] Tests run: 49, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.debug.DebugMappingTest
161c161
< [INFO] Tests run: 3980, Failures: 0, Errors: 0, Skipped: 0
---
> [INFO] Tests run: 3979, Failures: 0, Errors: 0, Skipped: 0
191,197d190
< [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.cml.CMLStackTest
< [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.cml.JumboTest
< [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.cml.JChemPaintTest
< [INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.cml.CMLFragmentsTest
< [INFO] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.cml.CML23FragmentsTest
< [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.cml.CML25FragmentsTest
< [INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.cml.Jumbo46CMLFragmentsTest
224c217
< [INFO] Tests run: 494, Failures: 0, Errors: 0, Skipped: 0
---
> [INFO] Tests run: 406, Failures: 0, Errors: 0, Skipped: 0

johnmay · 2022-09-11T13:01:09Z

un: 18, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.HINReaderTe	[INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.HINReaderTe
[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.cml.CMLFrag	[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.cml.CMLFrag
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.cml.CML25Fra	[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.cml.CML25Fra
[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.cml.CMLStack	[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.cml.CMLStack
[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.cml.JmolTest	[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.cml.JmolTest
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.cml.JChemPai	[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.cml.JChemPai
[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.cml.JumboTes	[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.cml.JumboTes
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.cml.CMLModul	[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.cml.CMLModul
[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.cml.Jumbo46	[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.cml.Jumbo46
[INFO] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.cml.CML23Fr	[INFO] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.cml.CML23Fr
[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.cml.CMLStack   <
[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.cml.JumboTes   <
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.cml.JChemPai   <
[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.cml.CMLFrag   <
[INFO] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.cml.CML23Fr   <
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.cml.CML25Fra   <
[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.cml.Jumbo46   <

johnmay · 2022-09-11T13:01:39Z

Fixed the missing annotations and the CML ones were previously run twice.

egonw · 2022-09-11T13:11:17Z

I vaguely remember thinking about running the CML tests more than once, with different XML parsing libraries. (But would not worry about it now anymore)

johnmay · 2022-09-11T13:12:59Z

Useful command to test the before/after log:

mvn clean verify | grep -F 'Tests run' | sed 's/, Time elapsed: [^ ]* s//' > before.log

johnmay · 2022-09-11T13:19:38Z

BINGO! Final "vintage" engine remove flagged it up

*/ @RunWith(value = Suite.class) @SuiteClasses(value = {CMLStackTest.class, JumboTest.class, JChemPaintTest.class, CMLFragmentsTest.class, CML23FragmentsTest.class, CML25FragmentsTest.class, Jumbo46CMLFragmentsTest.class}) public class CMLIOTests { }

…ally led to classes being run twice.

johnmay · 2022-09-11T13:39:45Z

testModelBuilder3D_reserpine() (SlowTest) is failing on master so once those checks complete I think this is good to go.

sonarqubecloud · 2022-09-11T13:55:10Z

Kudos, SonarCloud Quality Gate passed!

0 Bugs
0 Vulnerabilities
0 Security Hotspots
812 Code Smells

0.4% Coverage
0.4% Duplication

johnmay · 2022-09-11T15:00:23Z

[john@sentinel:cdk]% diff main.log.norm after2.log
55c55
< [INFO] Tests run: 50, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.MappingTest
---
> [INFO] Tests run: 54, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.MappingTest
66c66
< [INFO] Tests run: 4425, Failures: 0, Errors: 0, Skipped: 0
---
> [INFO] Tests run: 4429, Failures: 0, Errors: 0, Skipped: 0
97c97
< [INFO] Tests run: 50, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.silent.MappingTest
---
> [INFO] Tests run: 54, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.silent.MappingTest
107c107
< [INFO] Tests run: 4192, Failures: 0, Errors: 0, Skipped: 0
---
> [INFO] Tests run: 4196, Failures: 0, Errors: 0, Skipped: 0
124c124
< [INFO] Tests run: 50, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.debug.DebugMappingTest
---
> [INFO] Tests run: 54, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.debug.DebugMappingTest
161c161
< [INFO] Tests run: 3980, Failures: 0, Errors: 0, Skipped: 0
---
> [INFO] Tests run: 3984, Failures: 0, Errors: 0, Skipped: 0
191,197d190
< [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.cml.CMLStackTest
< [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.cml.JumboTest
< [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.cml.JChemPaintTest
< [INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.cml.CMLFragmentsTest
< [INFO] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.cml.CML23FragmentsTest
< [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.cml.CML25FragmentsTest
< [INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0 - in org.openscience.cdk.io.cml.Jumbo46CMLFragmentsTest
224c217
< [INFO] Tests run: 494, Failures: 0, Errors: 0, Skipped: 0
---
> [INFO] Tests run: 406, Failures: 0, Errors: 0, Skipped: 0

johnmay marked this pull request as draft September 10, 2022 21:49

johnmay added 6 commits September 11, 2022 06:20

As far as I can tell these specific exclusions are no longer needed.

779aaec

Move to Junit5 engine

d6fc4d5

IntelliJ "replace Junit4 assertion with Junit5 assertion"

1b0bd6c

Removed unused imports

7d5d73e

Rebase on master

ffd8058

johnmay force-pushed the junit5 branch from 880d805 to ffd8058 Compare September 11, 2022 05:22

johnmay added 9 commits September 11, 2022 06:26

Final uses of Junit4 Assert.

dbd663a

Junit5 parameterized tests - all uses of org.junit.Test updated.

c9034fb

Increase timeout

c160d8a

Replace SlowTest category annotation with JUnit5 tag

d687251

Remove the vintage engine dependency. All tests fully ported to JUnit5

5f207be

SonarCloud "bugs"

7755086

Make all the timeouts longer here

c8404d9

Fix missing test annotation

ca1bec3

These methods don't need to be public, as noted by SonarCloud

9633cab

Some missing test annotations

f31c896

Final removal of Junit4, these "Suites" are no longer needed and actu…

af1524d

…ally led to classes being run twice.

johnmay marked this pull request as ready for review September 11, 2022 13:39

egonw self-requested a review September 11, 2022 13:56

egonw self-assigned this Sep 11, 2022

egonw reviewed Sep 11, 2022

View reviewed changes

Comment thread base/test/src/main/java/org/openscience/cdk/test/interfaces/AbstractMappingTest.java

egonw assigned johnmay and unassigned egonw Sep 11, 2022

egonw merged commit daba2d4 into master Sep 11, 2022

johnmay deleted the junit5 branch September 12, 2022 11:42

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