File Changes for max

v1.2.15 to HEAD (2025-05-22 to 2025-11-12) review

• .readthedocs.yaml
  • lines changed 3, context: html, text, full: html, text
    fb985506637f048677f0a7da8f7cc19b581ce1ca Wed Oct 8 06:16:01 2025 -0700
    another fix
• .readthedocs.yml
  • lines changed 35, context: html, text, full: html, text
    75e645eb282fa8f81516cac8ce92b31d21ece726 Wed Oct 8 06:09:16 2025 -0700
    trying to fix rtd build fail
  • lines changed 35, context: html, text, full: html, text
    fb985506637f048677f0a7da8f7cc19b581ce1ca Wed Oct 8 06:16:01 2025 -0700
    another fix
• README.rst
  • lines changed 11, context: html, text, full: html, text
    3e78b320f1bd83e1a2fe2dc23fd660d34e186bf6 Fri Sep 26 09:31:19 2025 -0700
    adding examples
• build/doPush.sh
  • lines changed 1, context: html, text, full: html, text
    93f3e054ae5c36a657f964ad89b4bb246f15119b Fri Jun 20 06:28:03 2025 -0700
    I think there is a git pull missing in the push script
• docs/conf.py
  • lines changed 2, context: html, text, full: html, text
    18dd6ea0ae6c64a5ded831b520e046eabe389cbf Wed Oct 8 06:13:10 2025 -0700
    next try
• docs/howto.rst
  • lines changed 5, context: html, text, full: html, text
    d352dbd221f92bc4008d1f7c91fbf5cc98f36908 Thu Jul 31 07:21:29 2025 -0700
    adding atac docs for marc
• src/cbPyLib/cellbrowser/R/cellbrowser.R
  • lines changed 9, context: html, text, full: html, text
    44611123e060cd2efeb765ae05ac3b3369acb81b Thu Nov 6 06:20:34 2025 -0800
    addressing Visium V2 format, woodchuck liver dataset
  • lines changed 1, context: html, text, full: html, text
    93af16066536a5673ae5cc0f357748348340c96a Thu Nov 6 06:26:34 2025 -0800
    typo
  • lines changed 1, context: html, text, full: html, text
    1208c3efdace82a9243b4770520c8ca34a40d1aa Thu Nov 6 06:28:11 2025 -0800
    typo
  • lines changed 1, context: html, text, full: html, text
    ce9a3ef198cf80041f596e00943bcc775806d429 Thu Nov 6 06:33:09 2025 -0800
    flipping x and y for seurat
• src/cbPyLib/cellbrowser/cbWeb/js/cbData.js
  • lines changed 5, context: html, text, full: html, text
    39ba4769f6e0a2bf60e6641ce966062d23ce2d2b Fri Jun 20 10:39:10 2025 -0700
    do not sum values if not needed
  • lines changed 35, context: html, text, full: html, text
    b31323ed684da8a9f11edf81aba1e4ed6f20037a Thu Oct 23 09:16:04 2025 -0700
    handle NAN values betterthan before, important for the cortex-psi dataset
• src/cbPyLib/cellbrowser/cbWeb/js/cellBrowser.js
  • lines changed 1, context: html, text, full: html, text
    b58e484115835ff0480319007cc5af16a3d0a5bc Fri May 23 07:43:05 2025 -0700
    tiny change
  • lines changed 113, context: html, text, full: html, text
    1e682bf4a5e1776f9752d67e8becb2092926b5d5 Sat Jul 12 02:46:18 2025 -0700
    moving over Nan code, but knowing that there is a problem with the psi dataset
  • lines changed 112, context: html, text, full: html, text
    8d551f7d3103d3972b7314e27caa2b32d7aa8df8 Thu Oct 23 09:17:05 2025 -0700
    dont show color pickers when the field has too many values, small perf improvement, for dev-whole-brain-hqm&meta=Initial_Class_markers_level_2, brittney
  • lines changed 2, context: html, text, full: html, text
    92c89c6d39a97d00850b67a6e32677ce6aff094d Fri Nov 7 09:13:01 2025 -0800
    changing dataset when a dataset is open and the 2nd dataset has a diff label field breaks the dataset loading, fix that now
  • lines changed 6, context: html, text, full: html, text
    ea4850e19c7c50def3d53fee49c63d46a8f6a62d Fri Nov 7 10:30:45 2025 -0800
    fix for dataset flipping, refs #36661
• src/cbPyLib/cellbrowser/cbWeb/js/maxPlot.js
  • lines changed 1, context: html, text, full: html, text
    1e682bf4a5e1776f9752d67e8becb2092926b5d5 Sat Jul 12 02:46:18 2025 -0700
    moving over Nan code, but knowing that there is a problem with the psi dataset
• src/cbPyLib/cellbrowser/cellbrowser.py
  • lines changed 5, context: html, text, full: html, text
    f790971244c8ed7efc550cf5c86228ca5b242e4c Fri May 23 07:50:30 2025 -0700
    updating tabUniq
  • lines changed 6, context: html, text, full: html, text
    1e50fb3d3ab1219c45a6519d07b7b89fabc96ae8 Fri May 23 08:25:38 2025 -0700
    only sorting at top level, brittney
  • lines changed 4, context: html, text, full: html, text
    14e691e38eb579109dbc1df7b7077a3e2ec5d272 Fri Jun 6 08:42:22 2025 -0700
    suppressing perf warnings in numpy
  • lines changed 1, context: html, text, full: html, text
    854ccd1e70e59625464ba58d45d5818bbb1e46db Fri Jun 6 08:48:47 2025 -0700
    error msg
  • lines changed 1, context: html, text, full: html, text
    c9790a5fbf8797f8a36430682c51cc68009899bf Fri Jun 6 09:00:45 2025 -0700
    fixing bug where marker parsing used the wrong field for geneId, ds tm-cb/scrna
  • lines changed 27, context: html, text, full: html, text
    2d251af86fb82dbd404bea6f26525429afb7358b Thu Jun 19 10:16:13 2025 -0700
    add featDesc to conf file for PSI dataset
  • lines changed 1, context: html, text, full: html, text
    6a353cb29c2c5e7a4a8ef0089c3ac0083ffa781d Fri Jun 20 06:27:24 2025 -0700
    typo fix
  • lines changed 5, context: html, text, full: html, text
    2d2280e95cbe331ebb8411fcb9ec600ac8200898 Fri Jun 20 10:35:37 2025 -0700
    comments
  • lines changed 4, context: html, text, full: html, text
    ea8777d868c3941788a164aba71ade478cb1c8e9 Wed Jun 25 02:55:18 2025 -0700
    no output anymore if quickgenes is read and we have no symbol map, refs #29459
  • lines changed 8, context: html, text, full: html, text
    20d541d28092f1324307a0d34a1e65d145be6446 Thu Jun 26 04:46:08 2025 -0700
    removing config filename checks, refs #32013
  • lines changed 183, context: html, text, full: html, text
    a3e5065af17b8da62cf1fe1b310877c60fef13a8 Wed Jul 2 11:05:57 2025 -0700
    fixing int/float nan value replacement, refs #26440
  • lines changed 5, context: html, text, full: html, text
    f77821fea322cfbd8e982a7cc584e81f629f20e7 Thu Jul 3 08:25:35 2025 -0700
    prefer syms from matrix
  • lines changed 5, context: html, text, full: html, text
    b7c8d4de3cc60aea8cae6463077c4af70d6867ed Wed Jul 16 15:08:23 2025 -0700
    skipping quickgenes if markers not found
  • lines changed 16, context: html, text, full: html, text
    595ae73a63776a07d8d47fad24b2f3a4cf23f040 Mon Jul 21 13:26:47 2025 -0700
    allowing 8-digit hex color codes, mouse-dev-cardiac-spatial, marc
  • lines changed 5, context: html, text, full: html, text
    06d4b659f1ff4f3eae2346f9ebbe9ac4d0dfcb74 Thu Jul 31 07:18:04 2025 -0700
    fixing webcolors a little more, brittney
  • lines changed 30, context: html, text, full: html, text
    a83d99d31bc55dcad6f349b43ca2ebeac4dcb870 Thu Oct 23 07:00:13 2025 -0700
    handling the case uint32 matrix and Nans with numpy > 2, cortical-lineage-perturb-44tf/lr-clone-level, Marc
  • lines changed 3, context: html, text, full: html, text
    753e3019347b4bd90eb8caf4cfc25d851256a254 Thu Oct 23 09:17:31 2025 -0700
    remove dead code
  • lines changed 2, context: html, text, full: html, text
    71ed0396fa7e2e1f9c0a5254beaace62f95ede06 Thu Oct 30 08:24:47 2025 -0700
    fixing INTNAN bug, woodchuck-liver/healthy-liver-pbmc/, marc
• src/cbPyLib/cellbrowser/convert.py
  • lines changed 8, context: html, text, full: html, text
    c1bdbd09670416fb6efd05466977c45e2e9c9d95 Fri May 23 08:54:09 2025 -0700
    adding cbtools quickgenes command
  • lines changed 1, context: html, text, full: html, text
    906e4de349d22e0200d2baad80966ad2489da5d9 Fri May 23 08:55:10 2025 -0700
    small fix for prev commit
  • lines changed 1, context: html, text, full: html, text
    e8014694d55a343085e9fc661555398e003a7a96 Fri May 23 09:07:19 2025 -0700
    typo
  • lines changed 1, context: html, text, full: html, text
    a21a083f8efa63c9e50707291ea65fb49ea05a11 Fri May 23 09:09:06 2025 -0700
    typo again...
• src/cbPyLib/cellbrowser/genes.py
  • lines changed 16, context: html, text, full: html, text
    7a556d297a7e4cc0871f7189c2235d7422b30656 Thu Jul 31 07:17:27 2025 -0700
    adding the json command to cbGenes
  • lines changed 8, context: html, text, full: html, text
    f5fa2ebc9c1b54033cc804cd249bf6e807757c54 Thu Aug 14 06:42:16 2025 -0700
    allowing gene files for non-human atac seq datasets, for elegans-emb-multiome-atlas, Marc
• ucsc/datasetDiffs
  • lines changed 7, context: html, text, full: html, text
    9f13a83c45f20774ba2f749cc0ce25ba9c64aa73 Fri Jun 27 08:20:16 2025 -0700
    removing temp file after ucscDataset diffs run, because of perms problems
  • lines changed 2, context: html, text, full: html, text
    df34d48d0a831687d74c3ab4d1b7e65e4b484045 Fri Jun 27 08:34:09 2025 -0700
    fix for last commit
  • lines changed 1, context: html, text, full: html, text
    5eb777c509c66ea5b34de83c2283e9bf88214525 Fri Jun 27 08:34:25 2025 -0700
    fix for last commit
• ucsc/tabUniq
  • lines changed 1, context: html, text, full: html, text
    f790971244c8ed7efc550cf5c86228ca5b242e4c Fri May 23 07:50:30 2025 -0700
    updating tabUniq
• ucsc/updateNewsSec
  • lines changed 20, context: html, text, full: html, text
    232df494c4ee8f9e36fbd496b94e46f08a140628 Fri Jun 13 08:13:47 2025 -0700
    always make a new combined.html