All File Changes

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

• .readthedocs.yaml
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    fb985506637f048677f0a7da8f7cc19b581ce1ca Wed Oct 8 06:16:01 2025 -0700
    another fix
• .readthedocs.yml
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    75e645eb282fa8f81516cac8ce92b31d21ece726 Wed Oct 8 06:09:16 2025 -0700
    trying to fix rtd build fail
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    fb985506637f048677f0a7da8f7cc19b581ce1ca Wed Oct 8 06:16:01 2025 -0700
    another fix
• README.rst
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    3e78b320f1bd83e1a2fe2dc23fd660d34e186bf6 Fri Sep 26 09:31:19 2025 -0700
    adding examples
• build/buildEnv.sh
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    f0b34443de1f1bef77765a285120f867f7678660 Wed Nov 12 13:14:39 2025 -0800
    CB software release v1.2.16
• build/doPush.sh
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    93f3e054ae5c36a657f964ad89b4bb246f15119b Fri Jun 20 06:28:03 2025 -0700
    I think there is a git pull missing in the push script
• contributing.md
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    fb1865d70fd03332e9776bc85771cc1c8a37463c Sun Sep 14 12:01:21 2025 -0700
    moving to python3 for default script stubs and adding a note to contributing.md
• docs/conf.py
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    18dd6ea0ae6c64a5ded831b520e046eabe389cbf Wed Oct 8 06:13:10 2025 -0700
    next try
• docs/howto.rst
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    d352dbd221f92bc4008d1f7c91fbf5cc98f36908 Thu Jul 31 07:21:29 2025 -0700
    adding atac docs for marc
• src/cbBuild
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    fb1865d70fd03332e9776bc85771cc1c8a37463c Sun Sep 14 12:01:21 2025 -0700
    moving to python3 for default script stubs and adding a note to contributing.md
• src/cbGenes
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    fb1865d70fd03332e9776bc85771cc1c8a37463c Sun Sep 14 12:01:21 2025 -0700
    moving to python3 for default script stubs and adding a note to contributing.md
• src/cbGet
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    fb1865d70fd03332e9776bc85771cc1c8a37463c Sun Sep 14 12:01:21 2025 -0700
    moving to python3 for default script stubs and adding a note to contributing.md
• src/cbHub
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    fb1865d70fd03332e9776bc85771cc1c8a37463c Sun Sep 14 12:01:21 2025 -0700
    moving to python3 for default script stubs and adding a note to contributing.md
• src/cbImportCellranger
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    fb1865d70fd03332e9776bc85771cc1c8a37463c Sun Sep 14 12:01:21 2025 -0700
    moving to python3 for default script stubs and adding a note to contributing.md
• src/cbImportScanpy
  • lines changed 1, context: html, text, full: html, text
    fb1865d70fd03332e9776bc85771cc1c8a37463c Sun Sep 14 12:01:21 2025 -0700
    moving to python3 for default script stubs and adding a note to contributing.md
• src/cbImportSeurat
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    fb1865d70fd03332e9776bc85771cc1c8a37463c Sun Sep 14 12:01:21 2025 -0700
    moving to python3 for default script stubs and adding a note to contributing.md
• src/cbMarkerAnnotate
  • lines changed 1, context: html, text, full: html, text
    fb1865d70fd03332e9776bc85771cc1c8a37463c Sun Sep 14 12:01:21 2025 -0700
    moving to python3 for default script stubs and adding a note to contributing.md
• 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
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    93af16066536a5673ae5cc0f357748348340c96a Thu Nov 6 06:26:34 2025 -0800
    typo
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    1208c3efdace82a9243b4770520c8ca34a40d1aa Thu Nov 6 06:28:11 2025 -0800
    typo
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    ce9a3ef198cf80041f596e00943bcc775806d429 Thu Nov 6 06:33:09 2025 -0800
    flipping x and y for seurat
• src/cbPyLib/cellbrowser/cbWeb/css/cellBrowser.css
  • lines changed 8, context: html, text, full: html, text
    1cb6101966fb67d99d92a26ac82e8f12f8307909 Thu May 22 13:25:14 2025 -0700
    Adding css for legend buttons.
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    19e8f78e2e7f3f5fa9f8b7d19d8f5ed20301d174 Fri May 23 08:41:59 2025 -0700
    Making legend buttons more uniform.
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    2210699f461f50a127c54c147c79f2733ec8b22d Fri May 23 10:57:28 2025 -0700
    More changes to legend buttons and styling.
• 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
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    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 4, context: html, text, full: html, text
    3e733747dcb442b0b8c52993cefd7a62033c0f05 Thu May 22 13:17:42 2025 -0700
    Removing legend button class.
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    b58e484115835ff0480319007cc5af16a3d0a5bc Fri May 23 07:43:05 2025 -0700
    tiny change
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    2210699f461f50a127c54c147c79f2733ec8b22d Fri May 23 10:57:28 2025 -0700
    More changes to legend buttons and styling.
  • lines changed 1, context: html, text, full: html, text
    fa48f53c418532878d233ce6f8539dcbbb0bc0bf Fri May 23 11:05:41 2025 -0700
    Added margin to 'Apply' button in 'Layout' tab.
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    5be5ace9656a05f4571cbf57bef9a7815fd4e621 Fri Jun 6 08:43:26 2025 -0700
    Adding Cell Annotation Platform url.
  • 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
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    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
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    1e50fb3d3ab1219c45a6519d07b7b89fabc96ae8 Fri May 23 08:25:38 2025 -0700
    only sorting at top level, brittney
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    297f415cbd369921895e0adb7143202e5cc489f4 Fri May 23 09:16:54 2025 -0700
    Changed cellbrowser.conf template to remove 'body_parts' tag.
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    4f7059f9f4121d2dd19c685b3b144838ef8b0c19 Wed Jun 4 13:53:40 2025 -0700
    cbImportScanpy now removes metadata fields that have '*_ontology_term_id'.
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    db3ab1719978e0691cd9401a5c3e164e5ec29d93 Wed Jun 4 13:58:19 2025 -0700
    Fixing atachSearch typo.
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    14e691e38eb579109dbc1df7b7077a3e2ec5d272 Fri Jun 6 08:42:22 2025 -0700
    suppressing perf warnings in numpy
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    854ccd1e70e59625464ba58d45d5818bbb1e46db Fri Jun 6 08:48:47 2025 -0700
    error msg
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    c9790a5fbf8797f8a36430682c51cc68009899bf Fri Jun 6 09:00:45 2025 -0700
    fixing bug where marker parsing used the wrong field for geneId, ds tm-cb/scrna
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    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
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    2d2280e95cbe331ebb8411fcb9ec600ac8200898 Fri Jun 20 10:35:37 2025 -0700
    comments
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    ea8777d868c3941788a164aba71ade478cb1c8e9 Wed Jun 25 02:55:18 2025 -0700
    no output anymore if quickgenes is read and we have no symbol map, refs #29459
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    20d541d28092f1324307a0d34a1e65d145be6446 Thu Jun 26 04:46:08 2025 -0700
    removing config filename checks, refs #32013
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    a3e5065af17b8da62cf1fe1b310877c60fef13a8 Wed Jul 2 11:05:57 2025 -0700
    fixing int/float nan value replacement, refs #26440
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    f77821fea322cfbd8e982a7cc584e81f629f20e7 Thu Jul 3 08:25:35 2025 -0700
    prefer syms from matrix
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    b7c8d4de3cc60aea8cae6463077c4af70d6867ed Wed Jul 16 15:08:23 2025 -0700
    skipping quickgenes if markers not found
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    595ae73a63776a07d8d47fad24b2f3a4cf23f040 Mon Jul 21 13:26:47 2025 -0700
    allowing 8-digit hex color codes, mouse-dev-cardiac-spatial, marc
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    d03a89dc413d8f529778e5ad23b3e296dd2e99b2 Tue Jul 29 09:03:31 2025 -0700
    fixing issue with cbScanpy not properly getting inMeta declared in scanpy.conf
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    06d4b659f1ff4f3eae2346f9ebbe9ac4d0dfcb74 Thu Jul 31 07:18:04 2025 -0700
    fixing webcolors a little more, brittney
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    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
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    753e3019347b4bd90eb8caf4cfc25d851256a254 Thu Oct 23 09:17:31 2025 -0700
    remove dead code
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    71ed0396fa7e2e1f9c0a5254beaace62f95ede06 Thu Oct 30 08:24:47 2025 -0700
    fixing INTNAN bug, woodchuck-liver/healthy-liver-pbmc/, marc
• src/cbPyLib/cellbrowser/convert.py
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    c1bdbd09670416fb6efd05466977c45e2e9c9d95 Fri May 23 08:54:09 2025 -0700
    adding cbtools quickgenes command
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    906e4de349d22e0200d2baad80966ad2489da5d9 Fri May 23 08:55:10 2025 -0700
    small fix for prev commit
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    e8014694d55a343085e9fc661555398e003a7a96 Fri May 23 09:07:19 2025 -0700
    typo
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    a21a083f8efa63c9e50707291ea65fb49ea05a11 Fri May 23 09:09:06 2025 -0700
    typo again...
• src/cbPyLib/cellbrowser/geneinfo.py
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    b7f624b1913a3b14792339272310d378db114886 Fri Jul 11 09:01:49 2025 -0700
    making changes so that cbMarkerAnnotate works on seurat marker files and outputs annotated seurat marker files that work with cbBuild
• src/cbPyLib/cellbrowser/genes.py
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    d17cf65947b999bfaf88af1fc6eaaff2c1f1080a Wed Jun 25 10:54:12 2025 -0700
    changing hgdownload urls from cse -> gi
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    7a556d297a7e4cc0871f7189c2235d7422b30656 Thu Jul 31 07:17:27 2025 -0700
    adding the json command to cbGenes
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    f5fa2ebc9c1b54033cc804cd249bf6e807757c54 Thu Aug 14 06:42:16 2025 -0700
    allowing gene files for non-human atac seq datasets, for elegans-emb-multiome-atlas, Marc
• src/cbPyLib/cellbrowser/hubmaker.py
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    175c26e8907957b668222471a3b33ee0a13b602c Fri Jul 18 09:04:53 2025 -0700
    fixing cbHub to output same number of barChartColors as there are clusters
• ucsc/cbMove
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    6f3bf289f143c60b78ca17898f374b35121ee908 Mon Jun 23 15:30:41 2025 -0700
    Adding cbMove script that moves uploaded files to CB dataset directory.
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    7ad9dbbdd91a8af353c35fcc239110e7644ca854 Tue Jul 1 12:05:26 2025 -0700
    Added new options to cbMove script.
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    3ca204528035c798f2ac4d46958721df4659310f Tue Jul 1 12:35:17 2025 -0700
    Small change, changed time format to allow HH:MM
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    dd626c7ec6ba839b0f51d3ef0f30f91bc5f23d80 Wed Oct 29 15:10:48 2025 -0700
    Adding in new code to also copy config files from cb-submit directory
• ucsc/datasetDiffs
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    9f13a83c45f20774ba2f749cc0ce25ba9c64aa73 Fri Jun 27 08:20:16 2025 -0700
    removing temp file after ucscDataset diffs run, because of perms problems
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    df34d48d0a831687d74c3ab4d1b7e65e4b484045 Fri Jun 27 08:34:09 2025 -0700
    fix for last commit
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    5eb777c509c66ea5b34de83c2283e9bf88214525 Fri Jun 27 08:34:25 2025 -0700
    fix for last commit
• ucsc/processMarkers
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    d409dc301e4bda2d1fa29a795224e0e8b6abf7b0 Thu Sep 25 19:34:34 2025 -0700
    adding script to process markers from CellMarker, PanglaoDb, and singleCellBase, outputs json files for human and mouse marker genes from these files, refs #24611
• ucsc/tabUniq
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    f790971244c8ed7efc550cf5c86228ca5b242e4c Fri May 23 07:50:30 2025 -0700
    updating tabUniq
• ucsc/updateNewsSec
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    232df494c4ee8f9e36fbd496b94e46f08a140628 Fri Jun 13 08:13:47 2025 -0700
    always make a new combined.html
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    1468e11700d139e452a7e77f9e30b4f87f9f38ec Fri Jun 13 15:30:58 2025 -0700
    Fixing script so that only one entry per date is added to combined.html,added several options to script to control output directories for the various files which is mostly useful for debugging

• lines changed: 1309
• files changed: 78