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4.0.0 - #1452

Merged

WardDeb merged 397 commits into

masterfrom

4.0.0

Sep 5, 2026

Merged

4.0.0#1452
WardDeb merged 397 commits into
masterfrom
4.0.0

This pull request is big! We're only showing the most recent 250 commits

Commits on Jan 31, 2025
- Merge branch '4.0.0' of github.com:deeptools/deepTools into bamComp_fix
  WardDeb
  committed
  e2e975c
- proper coalesce bamcompare, make tempzip struct global
  WardDeb
  committed
  d669a3a
- Merge pull request #1378 from deeptools/bamComp_fix
  WardDeb
  authored
  d1afa73
- Merge branch '4.0.0' of github.com:deeptools/deepTools into 4.0.0
  Mohit Navandar
  committed
  7222691
- cm.py removed
  Mohit Navandar
  committed
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- cm.py removal
  Mohit Navandar
  committed
  a9ea6bc
Commits on Feb 3, 2025
- suppress / fix compiler warnings
  WardDeb
  committed
  30d71cb
- properly set test mod in lib
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  committed
  fd315d7
- proper blacklist filtering
  WardDeb
  committed
  47052b0
- include basic linux builds again
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  committed
  c79aa04
- linux builds cache
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  committed
  8a0270e
- drop the sscache for now
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  committed
  b30f28d
- Merge pull request #1379 from deeptools/refinement
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  authored
  141f6fb
- rollback to default
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  committed
  32d08b1
- include openssl in the crate
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  committed
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- try the openssl workaround
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  committed
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- typo build actino
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  bb1b48e
- include clang in prereqs for building
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  88f8b34
- take a step back
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- higher manylinux
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  4d9aef1
- drop the update, running blind here.
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- sudo then ?
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- go root then
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  committed
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- and an update
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  committed
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- revert manylinux vers
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- and 2014 ?
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- 2014 -> 2_28
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- almost full circle now
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Commits on Feb 4, 2025
- multilib include in apt ?
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  committed
  f40afd3
- boost manylinux to 2_28
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  committed
  9958ee4
- combine all filtering options in 1 struct, remove ignoreDups as an option
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  committed
  e44a49a
- try maturin builds based on cramjam template
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  a26b325
Commits on Feb 5, 2025
- wip rewrite filtering machinery
  WardDeb
  committed
  3004cf4
- fix arg order with blacklist
  WardDeb
  committed
  7866c7a
- Merge pull request #1380 from deeptools/verbose_flag
  WardDeb
  authored
  96de717
- test simpler build action
  WardDeb
  committed
  84cdddf
- trigger build on push
  WardDeb
  committed
  70a3246
- ssh access for debugging with my key
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- added libssl-dev system dependency
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  9f25a51
- oh doble checkout mybadd.
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  50ca3f0
- button not appearing, probably github being github. let's get debug session regardless of how it was triggered.
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  committed
  cec937b
- go
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  f61d8cc
- go
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- go
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- added workflow_dispatch everywhere but pypi
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- go
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- go
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- go
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- go
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  fb8cdac
- move blacklist into filteringomit region pileups to test for bs1 ?
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  committed
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- go
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Commits on Feb 6, 2025
- go
  adRn-s
  committed
  fcfad13
- go
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  committed
  9decd23
- go
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  committed
  ec75b1a
- go
  adRn-s
  committed
  3671867
- test
  adRn-s
  committed
  2a6900d
- Merge branch 'builds' of github.com:deeptools/deepTools into builds
  adRn-s
  committed
  acb512f
- test
  adRn-s
  committed
  8dbdd29
- ok
  adRn-s
  committed
  8453e84
- go
  adRn-s
  committed
  6741f89
- re-enable manylinux
  adRn-s
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  36f9311
- manylinux at its oldest, 2010
  adRn-s
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  febe75c
- manylinux 2014\?
  adRn-s
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  711f00a
- manylinux at its oldest, 2010. retry bc it was my bad apparently.
  adRn-s
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  14fa221
- manylinux: 2010
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  d8c2a04
- manylinux: 2014
  adRn-s
  committed
  d33aa46
- manylinux: 2_24 => Debian 9 (Stretch)
  adRn-s
  committed
  f09afc9
- https://github.com/PyO3/maturin-action/issues/249
  adRn-s
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  ec64810
- https://github.com/PyO3/maturin-action/issues/249
  adRn-s
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- before-script-linux with all bells and whistles
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  6967a5c
- go
  adRn-s
  committed
  81d20bc
- should've kept it vendored maybe
  adRn-s
  committed
  c3bb8a1
- debian 9 repos needs fixin coz EOL
  adRn-s
  committed
  c7a0bbf
- manylinux: 2_28
  adRn-s
  committed
  7bcc76f
- manylinux: 2_34 // Debian 12
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  76f351f
- manylinux: 2_28 // Debian 10
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  f3582e4
- manylinux: 2_28 // Debian 10
  adRn-s
  committed
  9142af2
- manylinux: 2_28 // AlmaLinux 8
  adRn-s
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  01e7280
- enabling other linux cpu architectures
  adRn-s
  committed
  0822d2f
- macos
  adRn-s
  committed
  3bed4bc
- LGTM?
  adRn-s
  committed
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- windows?
  adRn-s
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  fdc2426
- static/ musl was removed.
  adRn-s
  committed
  389f02f
- windows?
  adRn-s
  committed
  37e2ce5
- windows?
  adRn-s
  committed
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- windows?
  adRn-s
  committed
  9fbb9df
- ok or what
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- ok or what
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Commits on Feb 7, 2025
- drop bs1 - pileups in favor of records, to allow same filter strategy everywhere. Chunk big parts of chromosomes to keep memory within limits
  WardDeb
  committed
  63f12ee
Commits on Feb 11, 2025
- ARMv8 support for Linux
  adRn-s
  committed
  c33f8fa
- skip this when building for ARMv8
  adRn-s
  committed
  22121b6
- what OS is this?
  adRn-s
  committed
  34cd7ec
- dev-mode
  adRn-s
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  aa36568
- headers for compiling under jammy
  adRn-s
  committed
  f466261
- ouch.
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  4d64c4a
- huh?
  adRn-s
  committed
  bdee3ce
- same error is expected now
  adRn-s
  committed
  f320576
- this should do it
  adRn-s
  committed
  fea1bcd
- or not
  adRn-s
  committed
  87d6254
- how about vendoring
  adRn-s
  committed
  8bc363b
- maybe
  adRn-s
  committed
  17602af
- hack that (dependency) tree!
  adRn-s
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  46a97d9
- how about windows?
  adRn-s
  committed
  53c3fb6
- not agaaain..
  adRn-s
  committed
  dd27488
- disable sccache for the time being
  adRn-s
  committed
  59206d8
- static compiling, maybe later
  adRn-s
  committed
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- almost somewhere but where??
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  40af734
- disable sccache
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  committed
  19b0080
Commits on Feb 12, 2025
- the return of the dependencies
  adRn-s
  committed
  e39119b
- aarch64 dependencies into ubuntu jammy
  adRn-s
  committed
  c666492
- incoming static binary
  adRn-s
  committed
  b837f35
- windows support
  adRn-s
  committed
  182d945
- another try
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  committed
  8df63ce
- windows' poor DX
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  committed
  c20da6e
Commits on Feb 17, 2025
- fix args conflict in bc2
  WardDeb
  committed
  ba95267
Commits on Feb 26, 2025
- deps update (remove plotly, upgrades)
  Juan Caballero
  committed
  fe4686e
- removing plotly
  Juan Caballero
  committed
  0ff93d9
Commits on Feb 27, 2025
- adding new options, removing plotly
  Juan Caballero
  committed
  86ff1e1
- adding debug steps
  Juan Caballero
  committed
  8eb30f5
- updating PCA plotting
  Juan Caballero
  committed
  59fef08
Commits on Feb 28, 2025
- pca updates
  Juan Caballero
  committed
  e977578
- removing plotly and updates on correlation plots
  Juan Caballero
  committed
  371bf5c
- updating plotting
  Juan Caballero
  committed
  a63e449
Commits on Mar 3, 2025
- normalize name to avoid warning emails after upload of wheels
  adRn-s
  committed
  7d34958
- normalize name to avoid warning emails after upload of wheels
  adRn-s
  committed
  19effc5
- this is the oldest that setup-python GH-Action has available
  adRn-s
  committed
  4fa919b
- drop print statements
  WardDeb
  committed
  eee4ced
- CI: Maturin Builds Wheels for Linux and OSX, both x86 and aarch64
  adRn-s
  authored
  1570949
Commits on Mar 5, 2025
- Merge branch '4.0.0' of github.com:deeptools/deepTools into filtering
  WardDeb
  committed
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Commits on Mar 6, 2025
- 4 changes to changelog in docs
  WardDeb
  committed
  1a48153
- drop length metric collection in mbs mode
  WardDeb
  committed
  aba9bbe
Commits on Mar 7, 2025
- updating scree plot
  Juan Caballero
  committed
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Commits on Mar 18, 2025
- Corrected visual aesthetics, removed the label extensions like .filtered.bam / .bed, and removed plotly
  Mohit Navandar
  committed
  e6d28f1
- updated heatmap, profile and enrichment plot
  Mohit Navandar
  committed
  35ac8e2
Commits on Mar 20, 2025
- changing deps version to minimal for python 3.9
  Juan Caballero
  committed
  38c3d2c
- separate filtering functionality into a separate mod. Simplify part of the covcalc
  WardDeb
  committed
  a6af11e
Commits on Mar 21, 2025
- removing plotly
  Juan Caballero
  committed
  752478d
- remove numpy ignore warnings
  Juan Caballero
  committed
  215f06a
- removing plotly, using ggplot style
  Juan Caballero
  committed
  cbf3707
- updating test plot
  Juan Caballero
  committed
  48df9ec
- updating test plot
  Juan Caballero
  committed
  05e597d
Commits on Mar 24, 2025
- modified the plot index: enabled for single sample
  Mohit Navandar
  committed
  8adeaf0
- modified the plot index: enabled for single sample
  Mohit Navandar
  committed
  fa91875
- x lables: retained only sample names
  Mohit Navandar
  committed
  c34c70c
- test: plotHeatmap, plotEnrichment, plotProfile
  Mohit Navandar
  committed
  62f9eb3
- Merge branch '4.0.0_viz' of github.com:deeptools/deepTools into 4.0.0_viz
  Mohit Navandar
  committed
  aff1435
- changes: plotHeatmap, plotProfile, plotEnrichment
  Mohit Navandar
  committed
  4a665fe
- ggplot args
  Mohit Navandar
  committed
  41e1dd1
- ggplot args
  Mohit Navandar
  committed
  bb9756a
- ggplot args
  Mohit Navandar
  committed
  736d124
- ggplot args
  Mohit Navandar
  committed
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Commits on Mar 28, 2025
- removing plotly option (deprecated)
  Juan Caballero
  committed
  ad11ac0
- adding ggplot flag
  Juan Caballero
  committed
  dff9257
- using ggplot theme as parameter
  Juan Caballero
  committed
  042410e
- plotPCA unit test
  Juan Caballero
  committed
  c35e297
- setting ggplot as optional param
  Juan Caballero
  committed
  c78632f
- unit test for plotFingerprint
  Juan Caballero
  committed
  5489956
- setting ggplot as an optional param
  Juan Caballero
  committed
  a2553c1
- updated plot
  Juan Caballero
  committed
  164bf3e
- setting ggplot as an optional param
  Juan Caballero
  committed
  85df741
- updated plot
  Juan Caballero
  committed
  e80c670
- Merge branch '4.0.0_viz' of github.com:deeptools/deepTools into 4.0.0_viz
  Juan Caballero
  committed
  0aba595
- updating test plot
  Juan Caballero
  committed
  643d900
- updating test plot
  Juan Caballero
  committed
  ec82c0a
- updating test plot
  Juan Caballero
  committed
  1e48b9c
- test data for plotPCA
  Juan Caballero
  committed
  36a43bf
- increased tolerance in image comparison
  Juan Caballero
  committed
  0c3c370
- fixing typo
  Juan Caballero
  committed
  026ea8b
- testing only the plot
  Juan Caballero
  committed
  f1717e6
- method update
  Juan Caballero
  committed
  35a22ce
- docs updates for viz
  Juan Caballero
  committed
  3deb1f6
- removed plotly link
  Juan Caballero
  committed
  358b31c
Commits on Mar 31, 2025
- fixing labels for plotFingerprint test
  Juan Caballero
  committed
  13a07ac
- proper offset implementation, non offsets encoded as (0,0)
  WardDeb
  committed
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Commits on Apr 1, 2025
- Merge pull request #1387 from deeptools/4.0.0_viz
  WardDeb
  authored
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Commits on Apr 2, 2025
- split up extendreads & extendreadslen
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  committed
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Commits on Apr 3, 2025
- filtering options finalized
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  committed
  b6b5846
- Merge branch '4.0.0' of github.com:deeptools/deepTools into filtering
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  committed
  dd6be5d
- Merge pull request #1389 from deeptools/filtering
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  authored
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- drop the python signal to allow killing rust
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  committed
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- Merge pull request #1391 from deeptools/ctrl_c
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  authored
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Commits on Apr 4, 2025
- ctrl-c in computematrix too
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  committed
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Commits on Apr 16, 2025
- bugfixes and alignment to tests
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  committed
  6260e6b
- drop exactscaling, ignoreDuplicates from arguments, workaround for old python code
  WardDeb
  committed
  4d663bf
- deal with different pseudocount / scalefactor options on CLI
  WardDeb
  committed
  b0df173
- drop ignoreduplicates from parser
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  committed
  48c0e2a
- reflect changes in changelog
  WardDeb
  committed
  c419875
- update pytests bamCoverage, bamCompare
  WardDeb
  committed
  a0935c3
- drop ignoreDups from plotter functions
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  committed
  c907ec8
- test updates
  WardDeb
  committed
  4a910c1
- properly parse bed6 (score & strand)
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  committed
  49c1fc0
Commits on Apr 17, 2025
- pytest under rust venv with maturin install
  WardDeb
  committed
  43c2c83
- drop venv from test action
  WardDeb
  committed
  4919387
- regroup test actions into build / test / wheel names
  WardDeb
  committed
  c402c36
- typo venv
  WardDeb
  committed
  c1a3c6e
- round of all floats to 2 decimal places
  WardDeb
  committed
  ee929a1
- update test to accomodate rounded floats
  WardDeb
  committed
  b186712
Commits on Apr 22, 2025
- update computeMatrix expected test files
  WardDeb
  committed
  75f9aef
- computematrix testing with rust version
  WardDeb
  committed
  1411bee
- weed out last computematrix bugs in negative stranded bed/gtf
  WardDeb
  committed
  1b42a04
- reflect matrix changes in changelog
  WardDeb
  committed
  9eb0c88
Commits on Apr 23, 2025
- Merge pull request #1395 from deeptools/pytest_updates
  WardDeb
  authored
  3df381c
- planemo tests bamCoverage, bamCompare. Fix Offset processing in arg parsing bamCov
  WardDeb
  committed
  3bd7572
- update plotcorrelation, pca and profiler to new version
  WardDeb
  committed
  221fa42
- rollback the offset2 -> pos0 1 to 0
  WardDeb
  committed
  ab9f82b
- alsieve for now the old version
  WardDeb
  committed
  6dcacb2
- Merge pull request #1396 from deeptools/planemo_tests
  WardDeb
  authored
  4414609
Commits on Apr 24, 2025
- rename gh action files
  WardDeb
  committed
  4439fbd
- move rest tests into folder, set up mod
  WardDeb
  committed
  1f99fbf
- Merge pull request #1397 from deeptools/rust_tests
  WardDeb
  authored
  6282ee7
Commits on Jun 23, 2026
- 4.0.0 installation (#1429)
  WardDeb
  authored
  f2d36a6
Commits on Jun 24, 2026
- 4.0.0 planemo (#1430)
  WardDeb
  authored
  045a821
Commits on Jul 8, 2026
- towards multiple routes: pixi, uv or pipx.
  adRn-s
  committed
  9e13ea7
- Add pytests for plotCorrelation (salvage of #1370) (#1432)
  
  adRn-s
  and
  SaimMomin12
  authored
  ee0a7c4
- Add pytest for r_computematrix (Rust computeMatrix) (#1433)
  
  authored
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Commits on Jul 9, 2026
- Add data-output tests for plotPCA and plotFingerprint (#1435)
  
  adRn-s
  and
  claude
  authored
  b4dbdfe
- Add tests for bamCoverage RPKM/scaleFactor and alignmentSieve fragment/strand filtering (#1434)
  
  adRn-s
  and
  claude
  authored
  ed84627
Commits on Jul 13, 2026
- feat: lightweight PCA backend (scipy/numpy SVD) (#1431)
  
  adRn-s
  and
  claude
  authored
  663cc47
- Make plotPCA data-output test robust to BLAS near-zero noise
  adRn-s
  committed
  bc6ba7f
Commits on Jul 23, 2026
- Alsieve implementation (#1438)
  
  WardDeb
  and
  NavandarM
  authored
  3b7f189
Commits on Jul 24, 2026
- drop ignoredups old mbs for comparison purposes (#1439)
  WardDeb
  authored
  f8f06ef
Commits on Jul 29, 2026
- Optimization (#1442)
  WardDeb
  authored
  207aa80
Commits on Aug 3, 2026
- ci: add zizmor pre-commit hook and harden workflows (#1437)
  adRn-s
  authored
  ef0fab8
Commits on Aug 7, 2026
- deeptools tests and matplotlib version issue fixed (#1444)
  NavandarM
  authored
  c8696fd
Commits on Aug 12, 2026
- test: Exhaustive testing (#1443)
  WardDeb
  authored
  4aa0a34
Commits on Aug 13, 2026
- feat: gz support (#1446)
  WardDeb
  authored
  bc98e6e
Commits on Aug 16, 2026
- feat: drop hashmap for dense vec+indexing (computematrix memory footprint)
  WardDeb
  authored
  0f07abf
Commits on Sep 2, 2026
- more cargo tests (#1448)
  WardDeb
  authored
  821c4a1
Commits on Sep 4, 2026
- 4.0.0 cleanup (#1450)
  WardDeb
  authored
  4db9d81

Commits

Commits on Jan 31, 2025

Commits on Feb 3, 2025

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