Merge refactored branch into main - #9

Merged

pjhop merged 78 commits into

mainfrom

Mar 31, 2026

Commits on Sep 30, 2025

refactoring core gdb methods/functions + >90% coverage
pjhop
committed
553366c

Commits on Oct 20, 2025

varSet refactoring
pjhop
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4bdb033
refactored varSet unit tests (>90% coverage)
pjhop
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a50297d
genoMatrix refactoring
pjhop
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a1fda07
genoMatrix unit test refactoring (>90%)
pjhop
committed
9d74812
refactoring summariseGeno
pjhop
committed
90ed689
add asserts
pjhop
committed
526e65c
replace aggregateFile and associated methods with aggDb
pjhop
committed
94b9d59
refactored gdb-aggregate method (using aggDb)
pjhop
committed
ce5482c
assocTest refactoring
pjhop
committed
d025cdd
refactor assocTest_gdb
pjhop
committed
67cf889
replace assoctest_aggregateFile with assoctest_aggdb + refactor
pjhop
committed
eb0f2d4
refactor rvatResult
pjhop
committed
2a1b1e3
update nullmodelGSA to aggdb
pjhop
committed
24ee3a1
update internal data
pjhop
committed
6d6bb79
update cli
pjhop
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3700348
minor fixes in geneSetAssoc tests
pjhop
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51aed93
replace aggregateFile tests with aggdb tests
pjhop
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4343ffa
minor updates cli tests
pjhop
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5eaa201
add test helper functions
pjhop
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0435360
minor updates unit tests
pjhop
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79d3d00
updates DESCRIPTION/NAMESPACE and documentation
pjhop
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761d2aa
small fix unit tests
pjhop
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b17f17e
add test data
pjhop
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cdf19f6
small fix in unit tests
pjhop
committed
39dea48
minor fixes
pjhop
committed
d88c383

Commits on Oct 26, 2025

refactor genoMatrix unit tests (>90% coverage)
pjhop
committed
3508f50

Commits on Nov 2, 2025

refactor summariseGeno unit tests (>90% coverage)
pjhop
committed
6994358

Commits on Nov 16, 2025

minor updates aggdb + updated unit tests aggdb and related methods (>90% coverage)
pjhop
committed
977e3c0

Commits on Dec 10, 2025

minor updates assocTest + refactoring assocTest unit tests
pjhop
committed
7f7730f
refactoring of rvatResult unit tests
pjhop
committed
0b19300
reformat mapToCDS.R
pjhop
committed
abe7d83

Commits on Dec 17, 2025

refactor mapToCDS
pjhop
committed
2a122dd
reformat vcfUtils.R
pjhop
committed
925c015
linting mapToCDS
pjhop
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a974c0e
vcfUtils: reformatting
pjhop
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9c8bb40
spatialClust.R: reformat
pjhop
committed
764ef17
spatialClust linting
pjhop
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678320f
refactoring of spatialClust
pjhop
committed
603fab7
reformat geneSetAssoc.R
pjhop
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c5183bf
move geneSet functions and methods to separate file
pjhop
committed
8a9748a

Commits on Dec 18, 2025

geneSet.R linting
pjhop
committed
456d86b

Commits on Dec 21, 2025

geneSet.R refactoring
pjhop
committed
2737ad6
reformat geneSet unit tests
pjhop
committed
af21f12

Commits on Dec 23, 2025

update geneSet unit tests
pjhop
committed
8814c27

Commits on Dec 28, 2025

format geneSetAssoc unit tests
pjhop
committed
13c84aa

Commits on Dec 29, 2025

reorganize geneSetAssoc unit tests
pjhop
committed
d6ebb33

Commits on Dec 31, 2025

geneSetAssoc: linting
pjhop
committed
15a8502

Commits on Jan 3, 2026

refactor geneSetAssoc unit tests + bump to >80% coverage
pjhop
committed
cfa229c

Commits on Jan 6, 2026

geneSetAssoc: refactoring
pjhop
committed
befde00

Commits on Jan 10, 2026

geneSetAssoc: refactor core GSA parts
pjhop
committed
b06799f
geneSetAssoc: refactor conditional GSA and cell-type enrichments
pjhop
committed
9169557

Commits on Jan 12, 2026

geneSetAssoc: minor updates refactoring + cleanup
pjhop
committed
aa5b528
remove rvatViewer code (will me moved to separate package)
pjhop
committed
33c9b3a
fix aggdb documentation/examples
pjhop
committed
7d34802

Commits on Jan 17, 2026

update documentation + move examples to separate files
pjhop
committed
b0442ad

Commits on Feb 8, 2026

Commits on Feb 16, 2026

minor fix gdb and related methods
pjhop
committed
338eb3b

Commits on Feb 18, 2026

minor fixes + file renamings
pjhop
committed
d21b34d

Commits on Feb 19, 2026

minor fixes documentation
pjhop
committed
81efb14
fix data paths in unit tests
pjhop
committed
39ee4f6
version bump + format DESCRIPTION
pjhop
committed
98ceee4
minor fixes unit tests
pjhop
committed
27a0829

Commits on Feb 20, 2026

minor fixes
pjhop
committed
a8d8dee

Commits on Feb 24, 2026

update air formatting
pjhop
committed
27b595b

Commits on Feb 25, 2026

update man
pjhop
committed
653e516

Commits on Mar 10, 2026

remaining formatting
pjhop
committed
672a75b

Commits on Mar 13, 2026

minor fixes
pjhop
committed
26f034f

Commits on Mar 26, 2026

add snapshots + R CMD check workflow
pjhop
committed
fd013ee
avoid opening all aggdb connections simultaneously in aggdbList
pjhop
committed
3b6fa0d

Commits on Mar 29, 2026

minor update
pjhop
committed
a62427d
add rvatData to remotes in DESCRIPTION
pjhop
committed
d9ca5db
minor unit test fix
pjhop
committed
a8df225

Commits on Mar 30, 2026

add v.0.4.0 to changelog
pjhop
committed
5c8eb74
couple of minor fixes
pjhop
committed
eee1e68