132 uncertainty improvements - #158

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dimalvovs wants to merge 216 commits into

132-uncertainty-improvements

Commits on Sep 30, 2024

init Sasha's approach to tests
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c603316
add lost files
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46f56be
update testthat linkingg
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48180f4
configure.ac fixed; test are enabled by default
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0fd0f18
added REQUIRE
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fd3fd90
testthat-tweak.h is in ..
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5fe4d2c
tag \[vector\] added to vector test
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c46dc69

Commits on Oct 1, 2024

testthat provides catch.h
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850ef88
we added the sparce vector test to what we can run
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7d00008
trying to add testConcurrentAtomicDomain.cpp, build error
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2b058fc

Commits on Oct 2, 2024

commented nonworking test
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889c8c0
modified headers in tests to new version
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1ff64c6
update cpp test doc
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cc2922b

Commits on Dec 5, 2024

additional pmax param
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daf2cd9
two arguments and backcompat
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eb767c3
save debug into a branch
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2dd5e18
Merge branch '85-cpp-tests' into 132-debug
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941281d

Commits on Dec 13, 2024

added random.h and changed AtomicDomain to ConcurrentAtomicDomain; now, we can compile it
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84dfc65
Revived matrix tests
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f93c35d
Added tags to matrix test
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e365a26

Commits on Dec 15, 2024

Startted pad test
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7ab11b3
pad test added, compiled and failed
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3f79e2e

Commits on Dec 16, 2024

Added pad+sum test to vector and it failed
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bae0dc0
vector/matrix pad fixed
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88fc63e

Commits on Dec 17, 2024

added copy assign test
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d758b07
New uncertainity for dense model compiled
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3efffbc
rm chisq test for now
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d5578e6
update version for functional tests
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0054cd8

Commits on Dec 18, 2024

Commits on Dec 19, 2024

one more debug line
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dea3ae6
operator = is not necessary for Matrix, sorry
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b0eae5e

Commits on Dec 20, 2024

added pmax test
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d97d05b
shorten names
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return created; conxt Vector in patams of pmax
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return created; conxt Vector in patams of pmax
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d8590ef
fixing errors
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bd11860
it compiles
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b27dc16
pmax test fails
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16a9755
min and max search were inited with 0; fixed, now init with first elememt
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db47de2
min and max search were inited with 0; fixed, now init with first elememt
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5741cfc
use std::max and std::min instead of gaps::
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be8541f
added tests for 2ar - min and max and for a nondiaginal matrix value after pmax. All OK, so we found the bug in matrix and vector gaps::min
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dc27053

Commits on Dec 21, 2024

rm fgsea temporarily
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rm fgsea temporarily
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ba38dd5
Merge branch '132-uncertainty-improvements' of github.com:FertigLab/CoGAPS into 132-uncertainty-improvements
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fcf3a4d

Commits on Dec 24, 2024

fgsea returned
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54755b5

Commits on Dec 29, 2024

Dockerfile: we are not to install BiocManager; BiocManager installs fgsea before dependecies; ask=FALSE fo the BiocManager::install run
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7733bb2

Commits on Dec 30, 2024

Commits on Jan 2, 2025

started starse matrix check
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009c168

Commits on Jan 3, 2025

typo in filename fixed
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4bdd04a
sparsematrix cpp test
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1903dc1

Commits on Jan 4, 2025

removed temp dwbug output
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18ce2e5
Remove matrix debug lines
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0332198

Commits on Jan 5, 2025

test for A and P columns to be nonzero
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4f0fae3
editing the test title, and no more global vars
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f883fe8

Commits on Jan 6, 2025

parameters test implemented
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849daa2

Commits on Jan 9, 2025

THe params objects in the metafata of the results objects were of old structure and their loading from data caused warnings. Fixed.
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daa2de7

Commits on Jan 10, 2025

added dense sampler cpp test seed
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b0888ee
Added gist matrix part, going on
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12e7c53
Update README.md -- added multiple tag calls
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0578ec2
Added sampler updates, going on
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cc8e8e3

Commits on Jan 12, 2025

Commits on Jan 13, 2025

tests for A and P matrix added
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9d6709e

Commits on Jan 14, 2025

added more comments
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0058a9e
tiny matrix multiplication test
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4fb2a2d

Commits on Jan 15, 2025

Now, we also print the matrices in tiny_matrix test
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9027397
addedi tiny matrix multiplication test for P sampler
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d66a0bb
swapped A-AP and P-AP outputw
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641dca3

Commits on Jan 17, 2025

Commits on Jan 20, 2025

Started dev notes here
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2d9e72d
A(P) sampler notes started
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06b26f6
eq test
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eq test goes on
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76f1c5e
eq test goes on
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note goes on
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1c70a27
typo in \times
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note goes oni, matrix sizes are there
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note goes oni, P matrix sizes are there
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note goes oni, P matrix name is there
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bc451f5

Commits on Jan 21, 2025

A(P) sampler note is written.
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1fbbaa2

Commits on Apr 3, 2025

Update AtomicDomain.h
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03a9095
Update AtomicDomain.cpp
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6209b84
Update AtomicDomain.cpp
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91a1a1c
Update AtomicDomain.h
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e90d3c4
Update AtomicDomain.h
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f229b19

Commits on Apr 4, 2025

Atom.h
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9647391
Converting all index types to size_t, looks like completed.
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653c2b6
Converting all index types to size_t, random32 -> random64, get error on run on dense test
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fdfcd37

Commits on Apr 5, 2025

Commits on Apr 6, 2025

Commits on Apr 7, 2025

erase rewritten
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3ebef56
output pos() in erase test
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58c71d8
separated case for random atom
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919e121
Started to test GapsRng
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70112ca
comments
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15513f3
added random atom index get
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c0915a4
size_t tests
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dc82d4f

Commits on Apr 8, 2025

more saparate tests
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084bfd3
Added GAPS_ASSERT size()gt 0
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feca8ce
stepwize test randomatom
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12af14a
better way to make asserts prototyped
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e802c6c
Fix of section name, fro, -> from
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37edc1f

Commits on Apr 9, 2025

commented the ConcurrentDomain, hope, temporary
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815a160
asserts returned to the life
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896aade
added asserts to Random*
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27c6d55
Added REQUIRE_THROWS
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ce96ebf
Added assert to check wheter lower boundary is actually lower
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6006c12
Added (0,2) test
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b849fbd
MutableMap is unsafe; we omit now
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d2300f3
Added REQUIRE_THROWS, now can run all atomic tests by the common test tag
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3b4e932
Removed MutableMap; made the erase consistent; edited assert
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9dadfc3
Comments
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6b7b4c6
added const access to atomic storage and to map
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fc70ec6
moved const methods to public
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39acd9e
test structure on 4 atoms
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b52b86b

Commits on Apr 10, 2025

Commits on May 1, 2025

Commits on May 2, 2025

Commits on May 5, 2025

test for platform, old mac clang loose correct value when voverting double to uint64_t for the values really close to uint64_t maximal value.
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ac8a2e1

Commits on May 6, 2025

added <limits>
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abcacab

Commits on May 7, 2025

test is more verbose ans easy to understand
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ec5b7b6

Commits on Jun 23, 2026

configure version changed
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f5bff5e
Fix SIMD NaN in alphaParameters on Mac Intel (SSE4/AVX)

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bfd5e09

Commits on Jun 26, 2026

context for branch 132
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92e9647

Commits on Jun 27, 2026

Fix SIMD_PAD to prevent compiler auto-vectorization OOB on ARM

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60f9406

Commits on Jun 28, 2026

issue with 8 added
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b4beed4
Reformat non-compiled test files to match active test format

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ffa4770

Commits on Jul 1, 2026

Fix grammar
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5b18bda
Added fileparser, sorted
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83e85a5
4.6.1
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Math.h instead of math.h
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Fix testFileParsers: remove duplicate includes, use system.file() for self-contained paths

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a2ed06b
Add pull_request trigger to build-push-container workflow
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172a3d1

Commits on Jul 2, 2026

fixed
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HashSets
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Merge branch '132-uncertainty-improvements' of github.com:FertigLab/CoGAPS into 132-uncertainty-improvements
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593401e
minor edit in case name
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Hybrid added
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908bdf8

Commits on Jul 3, 2026

Fix stale iterator in AtomicDomain::move()

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aa2495c

Commits on Jul 4, 2026

Prepare documantation for next steps
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e32ce54
english version of tsklist to remove async
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8145ef9

Commits on Jul 5, 2026

Fix gaps::min/max(SparseVector) segfault on empty sparse vector

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dab57f2

Commits on Jul 6, 2026

Enable more C++ unit tests in the build

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989db34
Remove the asynchronous (OpenMP) Gibbs sampler

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0b599b3

Commits on Jul 7, 2026

Add post-async-removal test-coverage & suspicious-code audit

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551add5
Fix checkpoint deserialization of SingleThreadedGibbsSampler (>> not <<)

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3a4a293
Guard gaps::nonZeroMean against an all-zero matrix (0/0 = NaN)

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581e8b5
Guard dense/hybrid gaps::min/max/whichMax against empty containers

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f9af5f4

Commits on Jul 8, 2026

Fill C++ serialization unit tests; fix SparseVector deserialization

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f4c06f8
Remove vestigial maxThreads/asynchronousUpdates fields from GapsParameters

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Add --enable-checkpoints configure toggle (off by default)

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Plans updated: testthet added
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Revive the disabled testRandom distribution tests

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29fb0df

Commits on Jul 10, 2026

Make sparseOptimization consistent with the dense sampler (uncertainty floor)

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bbd36a5

Commits on Jul 11, 2026

Revive AtomicDomain serialization test; drop superseded GibbsSampler stub

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Revive testSparseIterator edge-case tests; drop white-box testSparseVector block

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c3b7094

Commits on Jul 12, 2026

Exercise update() in the sampler tests and assert chiSq decreases

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c209456

Commits on Jul 13, 2026

Guard SparseNormalModel::chiSq() against pre-sync() NULL deref (issue #18)

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Floor the uncertainty in SparseNormalModel::chiSq(); unify via invSSq() (issue #19)

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Document the dense vs. sparse uncertainty model

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dddeb39
Remove empty SparseNegativeBinomialModel.{h,cpp} placeholder files

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Make test_cpp.R actually gate on the C++ unit tests (Phase 4)

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Implement the chi-square consistency test (Phase 4)

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Clean up .Rbuildignore: exclude planning dir, use .o catch-all (Phase 4)

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Document the annotation-weighted subset sampling issue

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079e39e

Commits on Jul 14, 2026

Drop dead nThreads/asynchronousUpdates entries from allParams (Phase 4)

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Silence distributed-mode warnings in test_output_across_modes (Phase 4)

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b094f6d

Commits on Aug 2, 2026

Merge branch 'master' into 132-uncertainty-improvements
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2b14871
Stop tracking the local VS Code C/C++ config
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Recompress the packaged datasets with xz
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Tidy the branch notes; move the static_cast reproducer out of src/
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Add a NEWS entry for the async removal and the uncertainty fixes
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Add CLAUDE.md
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Commits on Aug 4, 2026

Fix scCoGAPS()/GWCoGAPS(), broken by nPatterns becoming mandatory
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Match the lp vectors in test_patternMarkers.R to nPatterns
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Update the DESCRIPTION date
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Silence the R CMD check NOTEs and the last two test warnings
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Fix binaryA(), fromCSV() and show(CogapsParams); cover them with tests
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Add cpp tests for elementSq, dot_diff, mean and sparsity
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Regenerate configure from configure.ac; document the aclocal step
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Report each C++ test case as its own testthat expectation
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Record the inherited master defects in the branch notes
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Document machine setup; note that commit permission does not carry over
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dee76c1

Commits on Aug 9, 2026

Add an index of the branch notes

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Commits on Aug 10, 2026

Move the developer notes to dev-notes/

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Fold AGENTS.md into CLAUDE.md; move the Russian rules to dev-notes/rus/

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Commits on Aug 11, 2026

Cover issue 20 in the uncertainty write-up; refresh its code map

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Unhide the Russian rules file

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Record the next three tasks in dev-notes/rus/plan-rus.md

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Document the non-R prerequisites in the setup section

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Record the one-pattern stitchTogether crash as inherited defect 6

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Keep the stitched matrices two-dimensional when there is one pattern

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Note the zero meanChiSq of distributed runs next to the chi-square task

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Commits on Aug 12, 2026

Revert changes back to state of 76ce2a25, no 161-distributed-fails-fix story here yet.
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