Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Addition of Unit Testing for all projects #30

Open
kMutagene opened this issue Nov 8, 2018 · 1 comment
Open

Addition of Unit Testing for all projects #30

kMutagene opened this issue Nov 8, 2018 · 1 comment
Labels
good first issue priority-medium project-all Issues regarding all projects up-for-grabs
Milestone
Backlog

Comments

@kMutagene
Copy link
Member

kMutagene commented Nov 8, 2018 •
edited
Loading

Description

None of the projects currently contain any unit tests. There are placeholder tests under the BioFSharp.Tests.NetCore project, which use Expecto.

How to design tests:
Basically, you can do what you want, as long as the test is as granular and self-contained as possible. Some inspiration can be taken from the current tests or this blog post:
https://stackify.com/unit-testing-basics-best-practices/ (ignore the C# code and setup instructions and focus on the concepts)

How to add tests:

How to run tests(from project root):

  • Windows: ./build.cmd -t runTestsAll
  • Linux: ./build.sh -t runTestsDotnet

Starting point resources

Expecto docs
This well written blog post
@kMutagene kMutagene added up-for-grabs priority-medium project-all Issues regarding all projects labels Nov 8, 2018
@kMutagene kMutagene pinned this issue Jul 25, 2019
@kMutagene
Copy link
Member Author

Example commit for addition of tests: 456b000

ZimmerD added a commit that referenced this issue Aug 1, 2019
@ZimmerD
#30: add unit tests for Element.fs
34f7c49
ZimmerD added a commit that referenced this issue Aug 1, 2019
@ZimmerD
#30: refactor existing unit tests
0a51f94
ZimmerD added a commit that referenced this issue Aug 1, 2019
@ZimmerD
#30: refactor tests using nested testlists
728091b
ZimmerD added a commit that referenced this issue Aug 1, 2019
@ZimmerD
#30: finished Unit testing Elements.fs
0204260
ZimmerD added a commit that referenced this issue Aug 2, 2019
@ZimmerD
#30: unit testing formula.fs
87344ef
ZimmerD added a commit that referenced this issue Aug 2, 2019
@ZimmerD
#30: refactor unit testing
23f7a3c
ZimmerD added a commit that referenced this issue Aug 2, 2019
@ZimmerD
#30: add unit tests for IBioItem.fs
87279e1
ZimmerD added a commit that referenced this issue Aug 2, 2019
@ZimmerD
#30: add unit testing TaggedSequence.fs
adc4108
ZimmerD added a commit that referenced this issue Aug 5, 2019
@ZimmerD
add Testing.fs
0472f29 
#30: add unit testing IsotopicDistribution.fs
@kMutagene kMutagene added this to the Backlog milestone Feb 19, 2020
kMutagene added a commit that referenced this issue Jun 22, 2020
@kMutagene
#30 Add unit tests for BioCollections functions
9ae84cc
ZimmerD added a commit to ZimmerD/BioFSharp that referenced this issue Jun 26, 2020
@ZimmerD
CSBiology#30: add unit tests for Digestion.isCuttingSide
6cea597
This was referenced Jul 17, 2020
Merged
Merged
kMutagene pushed a commit that referenced this issue Jul 21, 2020
@graemevissers
#30 : Add bio list tests (#103)
92060ff 
* Add testCase "isEqual" to BioList testList

* Add testCase "toString" to testList "BioList"

* Fix "toString" and add "toMonoisotopicMass" test

* Add testCase "toAverageMass"

* Add "toMonoisotopicMassWith"

* Add testCase "toAverageMassWith"

* Add testCase "toCompositionVector"

* Fix error message for "toCompositionVector"

* Change "BioList.ofBioArray" to "List.ofArray"
kMutagene referenced this issue Jul 21, 2020
@kMutagene
Add Amino Acid name and symbol tests
d1cf06b
@kMutagene kMutagene mentioned this issue Jul 29, 2020
Merged
1 task
kMutagene pushed a commit that referenced this issue Jul 29, 2020
@graemevissers
#30 : Add BioSeq tests (#106)
af6ef09 
* Add testCase "isEqual" to BioList testList

* Add testCase "toString" to testList "BioList"

* Fix "toString" and add "toMonoisotopicMass" test

* Add testCase "toAverageMass"

* Add "toMonoisotopicMassWith"

* Add testCase "toAverageMassWith"

* Add testCase "toCompositionVector"

* Fix error message for "toCompositionVector"

* Change "BioList.ofBioArray" to "List.ofArray"

* Change BioSeq.ofArray to Seq.ofArray

* Add "isEqual" to testList "BioSeq"

* Add testCase "toString"

* Add testCase "toMonoisotopicMass"

* Add testCase "toAverageMass"

* Add testCase "toMonoisotopicMassWith"

* Add testCase "toAverageMassWith"

* Add testList "toCompositionVector"
kMutagene pushed a commit that referenced this issue Aug 7, 2020
@graemevissers
#30: Add AminoAcids tests (#107)
acc78f9 
* Add "teset_rangePpm" to testList "BioFSharp.Mass"

* Add testCase "formula" to testList "AminoAcids"

* Add "formulaModifiedAA" to testList "AminoAcids"

* Fix "formulaModifiedAA" testCase

* Add "isTerminator" to testList "AminoAcids"

* Add "isGap" to testList "AminoAcids"

* Add "setModification" to testList "AminoAcids"

* Clean up tests

* Change error message for test "setModification"

* Add "setModifications" to "AminoAcids" testList

* Add "getModifications" to "AminoAcids" testList
kMutagene added a commit that referenced this issue Aug 21, 2020
@graemevissers @kMutagene
#30: Add amino acid tests (#108)
1f317ba 
* Add "teset_rangePpm" to testList "BioFSharp.Mass"

* Add testCase "formula" to testList "AminoAcids"

* Add "formulaModifiedAA" to testList "AminoAcids"

* Fix "formulaModifiedAA" testCase

* Add "isTerminator" to testList "AminoAcids"

* Add "isGap" to testList "AminoAcids"

* Add "setModification" to testList "AminoAcids"

* Clean up tests

* Change error message for test "setModification"

* Add "setModifications" to "AminoAcids" testList

* Add "getModifications" to "AminoAcids" testList

* Add testCase "getAminoAcidWithoutMod"

* Add test "tryGetModifications"

* Add test "tryGetModifications_withNone"

* Add test "isotopicLabelFunc"

* Add "isotopicLabelFunc_withUnmodifiedAAs"

* Add "charToParsedAminoAcidChar"

* Add test "aminoAcidSetStandard"

* Add test "aminoAcidSetProteinogenic"

* Add test "aminoAcidSetProteinogenicEucaryotes"

* Add test "aminoAcidSetAmbiguity"

* Add test "aminoAcidSetGapTer"

* Add test "aminoAcidSetPosCharged"

* Add test "aminoAcidSetNegCharged"

* Add test "aminoAcidSetPolarUncharged"

* Add test "aminoAcidSetHydrophobic"

* Add test "aminoAcidSetSpecialCases"

* Add test "isPolarUncharged"

* Add test "isModified_withUnmodAAs"

* Add test "isModified_withModAAs"

* Add test "getModifications_withUnmodAAs"

* Delete coverage.xml.637327725072680050L.exn

Seems like these are artifacts from your testing process, i cant reproduce these when starting the tests from your branch, so i would delete these and merge the PR afterwards

* Delete coverage.xml.637330276045185520L.exn

see previous commit

* Fix merge commit for aa tests

Co-authored-by: Kevin Schneider <[email protected]>
Co-authored-by: Kevin Schneider <[email protected]>
kMutagene pushed a commit that referenced this issue Aug 26, 2020
@graemevissers
#30: Add nucleotide tests (#109)
668753c 
* Add testCase "symbol"

* Add test "formula"

* Add test "isTerminator"

* Add test "isTerminator"

* Add test "isGap"

* Add test "name"

* Add NucleotideTests.fs to Main. Fix errors

* Add test "charToParsedNucleotideChar"

* Add test "complement"

* Add test "replaceTbyU"

* Add test "replaceUbyT"
graemevissers added a commit to graemevissers/BioFSharp that referenced this issue Aug 26, 2020
@graemevissers
Merge pull request #4 from CSBiology/developer
7f36eae 
CSBiology#30: Add nucleotide tests (CSBiology#109)
kMutagene added a commit that referenced this issue Sep 9, 2020
@graemevissers @kMutagene
#30: Add phyl tree tests (#110)
604a6cc 
* Add test "countLeafs"

* Add test "map"

* Add test "iter"

* Add test "fold"

* Add test "tryGetNodeBy"

* Delete coverage.xml.637344003428108790L.exn

Co-authored-by: Kevin Schneider <[email protected]>
HLWeil pushed a commit to HLWeil/BioFSharp that referenced this issue Sep 21, 2020
@graemevissers @HLWeil
CSBiology#30: Add AminoAcids tests (CSBiology#107)
075d5e9 
* Add "teset_rangePpm" to testList "BioFSharp.Mass"

* Add testCase "formula" to testList "AminoAcids"

* Add "formulaModifiedAA" to testList "AminoAcids"

* Fix "formulaModifiedAA" testCase

* Add "isTerminator" to testList "AminoAcids"

* Add "isGap" to testList "AminoAcids"

* Add "setModification" to testList "AminoAcids"

* Clean up tests

* Change error message for test "setModification"

* Add "setModifications" to "AminoAcids" testList

* Add "getModifications" to "AminoAcids" testList
HLWeil pushed a commit to HLWeil/BioFSharp that referenced this issue Sep 21, 2020
@graemevissers @kMutagene @HLWeil
CSBiology#30: Add amino acid tests (CSBiology#108)
b9baf82 
* Add "teset_rangePpm" to testList "BioFSharp.Mass"

* Add testCase "formula" to testList "AminoAcids"

* Add "formulaModifiedAA" to testList "AminoAcids"

* Fix "formulaModifiedAA" testCase

* Add "isTerminator" to testList "AminoAcids"

* Add "isGap" to testList "AminoAcids"

* Add "setModification" to testList "AminoAcids"

* Clean up tests

* Change error message for test "setModification"

* Add "setModifications" to "AminoAcids" testList

* Add "getModifications" to "AminoAcids" testList

* Add testCase "getAminoAcidWithoutMod"

* Add test "tryGetModifications"

* Add test "tryGetModifications_withNone"

* Add test "isotopicLabelFunc"

* Add "isotopicLabelFunc_withUnmodifiedAAs"

* Add "charToParsedAminoAcidChar"

* Add test "aminoAcidSetStandard"

* Add test "aminoAcidSetProteinogenic"

* Add test "aminoAcidSetProteinogenicEucaryotes"

* Add test "aminoAcidSetAmbiguity"

* Add test "aminoAcidSetGapTer"

* Add test "aminoAcidSetPosCharged"

* Add test "aminoAcidSetNegCharged"

* Add test "aminoAcidSetPolarUncharged"

* Add test "aminoAcidSetHydrophobic"

* Add test "aminoAcidSetSpecialCases"

* Add test "isPolarUncharged"

* Add test "isModified_withUnmodAAs"

* Add test "isModified_withModAAs"

* Add test "getModifications_withUnmodAAs"

* Delete coverage.xml.637327725072680050L.exn

Seems like these are artifacts from your testing process, i cant reproduce these when starting the tests from your branch, so i would delete these and merge the PR afterwards

* Delete coverage.xml.637330276045185520L.exn

see previous commit

* Fix merge commit for aa tests

Co-authored-by: Kevin Schneider <[email protected]>
Co-authored-by: Kevin Schneider <[email protected]>
HLWeil pushed a commit to HLWeil/BioFSharp that referenced this issue Sep 21, 2020
@graemevissers @HLWeil
CSBiology#30: Add nucleotide tests (CSBiology#109)
9fbd9ab 
* Add testCase "symbol"

* Add test "formula"

* Add test "isTerminator"

* Add test "isTerminator"

* Add test "isGap"

* Add test "name"

* Add NucleotideTests.fs to Main. Fix errors

* Add test "charToParsedNucleotideChar"

* Add test "complement"

* Add test "replaceTbyU"

* Add test "replaceUbyT"
HLWeil pushed a commit to HLWeil/BioFSharp that referenced this issue Sep 21, 2020
@graemevissers @kMutagene @HLWeil
CSBiology#30: Add phyl tree tests (CSBiology#110)
9a4910b 
* Add test "countLeafs"

* Add test "map"

* Add test "iter"

* Add test "fold"

* Add test "tryGetNodeBy"

* Delete coverage.xml.637344003428108790L.exn

Co-authored-by: Kevin Schneider <[email protected]>
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
good first issue priority-medium project-all Issues regarding all projects up-for-grabs
Projects
None yet
Milestone
Backlog
Development

No branches or pull requests
1 participant
@kMutagene