All File Changes

v431_preview to v431_preview2 (2022-05-02 to 2022-05-09) v431

• confs/asia.hg.conf
  • lines changed 16, context: html, text, full: html, text
    70bc62197a794d87bd537faf9a9503dab93f8f35 Sun May 8 01:11:45 2022 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 16, context: html, text, full: html, text
    70bc62197a794d87bd537faf9a9503dab93f8f35 Sun May 8 01:11:45 2022 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwbeta.hg.conf
  • lines changed 12, context: html, text, full: html, text
    70bc62197a794d87bd537faf9a9503dab93f8f35 Sun May 8 01:11:45 2022 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 16, context: html, text, full: html, text
    70bc62197a794d87bd537faf9a9503dab93f8f35 Sun May 8 01:11:45 2022 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgSession/hgSession.c
  • lines changed 7, context: html, text, full: html, text
    b092bd3c370e60f403178e881a268a3d8b4c400f Thu May 5 14:50:43 2022 -0700
    Shouldn't be able to make a session with no name, refs #29373
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 4, context: html, text, full: html, text
    1c6bf09a81d042f648d6526dba88d3ba3904e12a Sat May 7 08:05:22 2022 -0700
    Adding a link to bigBed blog on bigDetail entry in FAQ
  • lines changed 1, context: html, text, full: html, text
    a10f1ce41547c142261ab3b3d71f8c487fa1f202 Sat May 7 08:12:23 2022 -0700
    rephrasing sentence pointing to bigBed blog
• src/hg/htdocs/FAQ/FAQlink.html
  • lines changed 8, context: html, text, full: html, text
    d79b7484867eab1499cb2dc2d107f13d8cd42617 Fri May 6 13:39:49 2022 -0700
    Adding link to blog on sharing URLs to new FAQlink.html#trackHubLoading entry refs #24314
  • lines changed 2, context: html, text, full: html, text
    6ad770e5335065436319be1bc1d0b44201d6ad2f Fri May 6 13:43:53 2022 -0700
    Adding missing comma refs #24314
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 3, context: html, text, full: html, text
    877e21d910787f83dc6f437c5fa778bc958a576b Mon May 2 10:41:14 2022 -0700
    Code review changes refs #29326
• src/hg/htdocs/goldenPath/help/bigMaf.html
  • lines changed 5, context: html, text, full: html, text
    bd4a2b6d4fa1c37037bad56c4639d56b706803e4 Tue May 3 12:46:28 2022 -0700
    Cleaning up headers in bigMaf as working on doc bigRmsk refs #29356
  • lines changed 61, context: html, text, full: html, text
    478ca956c630cc79efc533d1cc19f765faea38e1 Wed May 4 14:19:47 2022 -0700
    Improving the bigMaf page to have hints about the frames and summary options, and the autoSql about those files (inspired by doc work on bigRmsk). refs #29372
  • lines changed 1, context: html, text, full: html, text
    f485654f4d659e942229c0af82a1d78339f29362 Thu May 5 10:04:13 2022 -0700
    Adding an anchor to bigMaf.html about frames summary supporting files. refs #29372
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 10, context: html, text, full: html, text
    77b3375e4c19ea49971bc9f301c8ee13b401f974 Wed May 4 10:08:24 2022 -0700
    Adding a link to blog post about sharing URLs in custom tracks user guide, refs #24314
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 8, context: html, text, full: html, text
    64333950e1969f11dc45b318865bccf51eb0245e Tue May 3 16:00:26 2022 -0700
    Adding documentation for the hicDistanceMin and hicDistanceMax trackDb settings, refs #29280
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
  • lines changed 6, context: html, text, full: html, text
    64333950e1969f11dc45b318865bccf51eb0245e Tue May 3 16:00:26 2022 -0700
    Adding documentation for the hicDistanceMin and hicDistanceMax trackDb settings, refs #29280
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 4, context: html, text, full: html, text
    877e21d910787f83dc6f437c5fa778bc958a576b Mon May 2 10:41:14 2022 -0700
    Code review changes refs #29326
  • lines changed 22, context: html, text, full: html, text
    64333950e1969f11dc45b318865bccf51eb0245e Tue May 3 16:00:26 2022 -0700
    Adding documentation for the hicDistanceMin and hicDistanceMax trackDb settings, refs #29280
  • lines changed 4, context: html, text, full: html, text
    94346959c7ba753c9adc354a8f0f2a1a022d0af5 Thu May 5 10:01:30 2022 -0700
    Adding links to bigMaf help page with frames and summary info. refs #29372
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 11, context: html, text, full: html, text
    775dc94f2a27a50f782ee886a0dddddff41d0065 Mon May 2 17:09:38 2022 -0700
    Pushing and announcing gnomAD Mut constraint #29026
  • lines changed 3, context: html, text, full: html, text
    319fba7ba20ec5769939efc9237b6c3cd2dd1f76 Tue May 3 16:07:48 2022 -0700
    Typo fix #29206
• src/hg/htdocs/gtex.html
  • lines changed 1, context: html, text, full: html, text
    dfd20baf681696d022a58efdad86db4f0ca3b849 Tue May 3 13:40:13 2022 -0700
    Sqashing old icon, no RM
• src/hg/htdocs/indexNews.html
  • lines changed 11, context: html, text, full: html, text
    775dc94f2a27a50f782ee886a0dddddff41d0065 Mon May 2 17:09:38 2022 -0700
    Pushing and announcing gnomAD Mut constraint #29026
  • lines changed 1, context: html, text, full: html, text
    ec4db382b4afb041231c1d457ad7f6042e9cf714 Tue May 3 15:24:43 2022 -0700
    fixing typo refs #29206
• src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
  • lines changed 12, context: html, text, full: html, text
    e587fbd14b501a1fec7b8d6a10b7c4a08c81f47d Mon May 2 14:19:07 2022 -0700
    adding repeatMasker.version.txt file and alert to missing fa.gz or 2bit.bpt files no redmine
• src/hg/makeDb/doc/evaSnp3.txt
  • lines changed 453, context: html, text, full: html, text
    754be93f931254dfaf897d382a7b6847a2bbaa39 Tue May 3 14:50:47 2022 -0700
    Adding the updated evaSnp3 pipeline which now includes canFam3 and has better handling of multi-allelic variants. Refs #29031
• src/hg/makeDb/doc/hg19.txt
  • lines changed 4, context: html, text, full: html, text
    fb75f30bb5d7fc58874d8765f209d13934c96276 Fri May 6 02:59:50 2022 -0700
    fixing up HMC track, refs #29153, spent waaaay to much time with this track
• src/hg/makeDb/doc/hg38/gnomad.txt
  • lines changed 3, context: html, text, full: html, text
    6f3383011d3d8aa64883b9437baec9440052046f Fri May 6 08:05:10 2022 -0700
    adding chrX scores to gnomad constraints on hg38, refs #29026
• src/hg/makeDb/doc/hg38/hmc.txt
  • lines changed 4, context: html, text, full: html, text
    fb75f30bb5d7fc58874d8765f209d13934c96276 Fri May 6 02:59:50 2022 -0700
    fixing up HMC track, refs #29153, spent waaaay to much time with this track
• src/hg/makeDb/doc/hg38/jarvis.txt
  • lines changed 8, context: html, text, full: html, text
    27fd1e0b2d3b1df5be807a9405db92fe1479192b Mon May 9 05:43:38 2022 -0700
    fixing up makedoc for jarvis, refs #29154
• src/hg/makeDb/doc/wuhCor1/variantMuts.txt
  • lines changed 20, context: html, text, full: html, text
    cadea00489bd3ae3b295f3237ef9eab3dbf65f10 Wed May 4 07:23:58 2022 -0700
    adding ba.4 and ba.5 tracks to wuhcor1, refs #29375
• src/hg/makeDb/scripts/hmc/hmcToWig.py
  • lines changed 87, context: html, text, full: html, text
    bd24865e9b1f065a61e8069a5eb056cf91dd7fc8 Thu May 5 09:34:46 2022 -0700
    adding hmc make script, refs #29153
  • lines changed 35, context: html, text, full: html, text
    fb75f30bb5d7fc58874d8765f209d13934c96276 Fri May 6 02:59:50 2022 -0700
    fixing up HMC track, refs #29153, spent waaaay to much time with this track
• src/hg/makeDb/trackDb/human/avada.html
  • lines changed 3, context: html, text, full: html, text
    0412170f60a10832c07489dd5fadf5656ae8e148 Thu May 5 07:55:04 2022 -0700
    forgot once more than probesets are usually on hg19, not hg38, adding a note for myself to the docs page. Also adding a note that avada has been lifted to hg38. no redmines.
• src/hg/makeDb/trackDb/human/constraint.ra
  • lines changed 1, context: html, text, full: html, text
    d498335adfefc70cbf9673f489688bd34503d521 Thu May 5 09:50:40 2022 -0700
    more polishing up of the constraint scores super track, refs #29153 and refs #29154
  • lines changed 14, context: html, text, full: html, text
    fb75f30bb5d7fc58874d8765f209d13934c96276 Fri May 6 02:59:50 2022 -0700
    fixing up HMC track, refs #29153, spent waaaay to much time with this track
• src/hg/makeDb/trackDb/human/constraintSuper.html
  • lines changed 57, context: html, text, full: html, text
    c09a7a320420ebbd4262d6611b244a07b009336b Thu May 5 08:54:17 2022 -0700
    starting docs for HMC and Jarvis, refs #29153 and refs #29154
  • lines changed 13, context: html, text, full: html, text
    d498335adfefc70cbf9673f489688bd34503d521 Thu May 5 09:50:40 2022 -0700
    more polishing up of the constraint scores super track, refs #29153 and refs #29154
  • lines changed 17, context: html, text, full: html, text
    fb75f30bb5d7fc58874d8765f209d13934c96276 Fri May 6 02:59:50 2022 -0700
    fixing up HMC track, refs #29153, spent waaaay to much time with this track
  • lines changed 22, context: html, text, full: html, text
    26d42ebd36016677dac1a3b49695e2b6768d6ba1 Fri May 6 05:48:11 2022 -0700
    small addition to hmc docs page, refs #
• src/hg/makeDb/trackDb/human/constraintSuper.ra
  • lines changed 14, context: html, text, full: html, text
    fb75f30bb5d7fc58874d8765f209d13934c96276 Fri May 6 02:59:50 2022 -0700
    fixing up HMC track, refs #29153, spent waaaay to much time with this track
• src/hg/makeDb/trackDb/human/exomeProbesets.html
  • lines changed 8, context: html, text, full: html, text
    0412170f60a10832c07489dd5fadf5656ae8e148 Thu May 5 07:55:04 2022 -0700
    forgot once more than probesets are usually on hg19, not hg38, adding a note for myself to the docs page. Also adding a note that avada has been lifted to hg38. no redmines.
• src/hg/makeDb/trackDb/human/gtexCov.ra
  • lines changed 54, context: html, text, full: html, text
    f72a53450af8d83fabb7ec7273d641453e168876 Wed May 4 18:03:28 2022 -0700
    fixed filenames on gtex coverage track, refs #29381
• src/hg/makeDb/trackDb/human/hg19/affyArchive.ra
  • lines changed 1, context: html, text, full: html, text
    b7a0329dfe82a5f49c4b324627a52871fce5d036 Wed May 4 08:11:21 2022 -0700
    Squashing old pennantIcons, no RM
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    b7a0329dfe82a5f49c4b324627a52871fce5d036 Wed May 4 08:11:21 2022 -0700
    Squashing old pennantIcons, no RM
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV39lift37.ra
  • lines changed 1, context: html, text, full: html, text
    b7a0329dfe82a5f49c4b324627a52871fce5d036 Wed May 4 08:11:21 2022 -0700
    Squashing old pennantIcons, no RM
• src/hg/makeDb/trackDb/human/hg38/cons241way.html
  • lines changed 10, context: html, text, full: html, text
    b1961e97b318909051fc9070837ab17494d5da67 Fri May 6 05:45:59 2022 -0700
    documenting bug in cons241 cactus track on the docs page, emails with Hiram, Markd, Braney, no redmine
• src/hg/makeDb/trackDb/human/hg38/gnomad.html
  • lines changed 2, context: html, text, full: html, text
    36e6f34cedb100600d85f1ceaeb830666d5eda81 Fri May 6 08:08:42 2022 -0700
    doc'ing gnomad chrX scores.
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 2, context: html, text, full: html, text
    775dc94f2a27a50f782ee886a0dddddff41d0065 Mon May 2 17:09:38 2022 -0700
    Pushing and announcing gnomAD Mut constraint #29026
  • lines changed 1, context: html, text, full: html, text
    36e6f34cedb100600d85f1ceaeb830666d5eda81 Fri May 6 08:08:42 2022 -0700
    doc'ing gnomad chrX scores.
• src/hg/makeDb/trackDb/human/hg38/gnomadV3_1_1.html
  • lines changed 10, context: html, text, full: html, text
    775dc94f2a27a50f782ee886a0dddddff41d0065 Mon May 2 17:09:38 2022 -0700
    Pushing and announcing gnomAD Mut constraint #29026
  • lines changed 1, context: html, text, full: html, text
    1adcec8795007009c447b5225d52c4eb29382cd3 Tue May 3 11:02:37 2022 -0700
    Slight word modification for #29206
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    bae16bda6f8e30866d951ecf1a60b4b9c7fd8cc9 Fri May 6 16:21:16 2022 -0700
    Adding note about mutation contraint chrX data refs #29206
• src/hg/makeDb/trackDb/human/hg38/kidneyStewart.ra
  • lines changed 1, context: html, text, full: html, text
    b7a0329dfe82a5f49c4b324627a52871fce5d036 Wed May 4 08:11:21 2022 -0700
    Squashing old pennantIcons, no RM
• src/hg/makeDb/trackDb/human/hg38/mane.html
  • lines changed 3, context: html, text, full: html, text
    153ee6d59e873299185856043a9b4fcd469a95b9 Wed May 4 10:41:35 2022 -0700
    Generalizing the MANE name to now just say Select, and adding a sentence that the track includes the clinical transcripts, no RM. Refs Max,Anna.
• src/hg/makeDb/trackDb/human/hg38/mane.ra
  • lines changed 1, context: html, text, full: html, text
    b7a0329dfe82a5f49c4b324627a52871fce5d036 Wed May 4 08:11:21 2022 -0700
    Squashing old pennantIcons, no RM
  • lines changed 2, context: html, text, full: html, text
    153ee6d59e873299185856043a9b4fcd469a95b9 Wed May 4 10:41:35 2022 -0700
    Generalizing the MANE name to now just say Select, and adding a sentence that the track includes the clinical transcripts, no RM. Refs Max,Anna.
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    b7a0329dfe82a5f49c4b324627a52871fce5d036 Wed May 4 08:11:21 2022 -0700
    Squashing old pennantIcons, no RM
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV39.ra
  • lines changed 1, context: html, text, full: html, text
    b7a0329dfe82a5f49c4b324627a52871fce5d036 Wed May 4 08:11:21 2022 -0700
    Squashing old pennantIcons, no RM
• src/hg/makeDb/trackDb/human/hmc.ra
  • lines changed 1, context: html, text, full: html, text
    d498335adfefc70cbf9673f489688bd34503d521 Thu May 5 09:50:40 2022 -0700
    more polishing up of the constraint scores super track, refs #29153 and refs #29154
  • lines changed 46, context: html, text, full: html, text
    fb75f30bb5d7fc58874d8765f209d13934c96276 Fri May 6 02:59:50 2022 -0700
    fixing up HMC track, refs #29153, spent waaaay to much time with this track
  • lines changed 2, context: html, text, full: html, text
    dfc9b0299bec4bfa134663c775ef1d9d70e32bdd Fri May 6 03:06:41 2022 -0700
    small tweaks to constraint tracks, refs #29153
• src/hg/makeDb/trackDb/human/jarvis.ra
  • lines changed 1, context: html, text, full: html, text
    d498335adfefc70cbf9673f489688bd34503d521 Thu May 5 09:50:40 2022 -0700
    more polishing up of the constraint scores super track, refs #29153 and refs #29154
  • lines changed 1, context: html, text, full: html, text
    fb75f30bb5d7fc58874d8765f209d13934c96276 Fri May 6 02:59:50 2022 -0700
    fixing up HMC track, refs #29153, spent waaaay to much time with this track
  • lines changed 1, context: html, text, full: html, text
    dfc9b0299bec4bfa134663c775ef1d9d70e32bdd Fri May 6 03:06:41 2022 -0700
    small tweaks to constraint tracks, refs #29153
• src/hg/makeDb/trackDb/human/jaspar.ra
  • lines changed 1, context: html, text, full: html, text
    b7a0329dfe82a5f49c4b324627a52871fce5d036 Wed May 4 08:11:21 2022 -0700
    Squashing old pennantIcons, no RM
• src/hg/makeDb/trackDb/human/refSeqComposite.html
  • lines changed 295, context: html, text, full: html, text
    c71281301ba035188bb402d91d6940aad6b0c12a Mon May 2 15:21:44 2022 -0700
    Updating the html for the non-human ncbiRefSeq tracks, refs #29127
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    b7a0329dfe82a5f49c4b324627a52871fce5d036 Wed May 4 08:11:21 2022 -0700
    Squashing old pennantIcons, no RM
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    28283c6fd389638ee667a24fb7e938c2222a4535 Wed May 4 18:13:51 2022 -0700
    correctly use $D in bigDataUrl path names so the track only shows up on the correct browser no redmine
  • lines changed 1, context: html, text, full: html, text
    fb75f30bb5d7fc58874d8765f209d13934c96276 Fri May 6 02:59:50 2022 -0700
    fixing up HMC track, refs #29153, spent waaaay to much time with this track
• src/hg/makeDb/trackDb/mouse/jaspar.ra
  • lines changed 1, context: html, text, full: html, text
    b7a0329dfe82a5f49c4b324627a52871fce5d036 Wed May 4 08:11:21 2022 -0700
    Squashing old pennantIcons, no RM
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    b7a0329dfe82a5f49c4b324627a52871fce5d036 Wed May 4 08:11:21 2022 -0700
    Squashing old pennantIcons, no RM
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM28.ra
  • lines changed 1, context: html, text, full: html, text
    b7a0329dfe82a5f49c4b324627a52871fce5d036 Wed May 4 08:11:21 2022 -0700
    Squashing old pennantIcons, no RM
• src/hg/makeDb/trackDb/refSeqComposite.html
  • lines changed 23, context: html, text, full: html, text
    c71281301ba035188bb402d91d6940aad6b0c12a Mon May 2 15:21:44 2022 -0700
    Updating the html for the non-human ncbiRefSeq tracks, refs #29127
• src/hg/makeDb/trackDb/virus/wuhCor1/resist.html
  • lines changed 7, context: html, text, full: html, text
    b3c5b5d39e924c9632c6456e1638d971184deadb Tue May 3 14:59:09 2022 -0700
    Minor changes for drug resistance track update refs #28889
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    b3c5b5d39e924c9632c6456e1638d971184deadb Tue May 3 14:59:09 2022 -0700
    Minor changes for drug resistance track update refs #28889
  • lines changed 1, context: html, text, full: html, text
    cadea00489bd3ae3b295f3237ef9eab3dbf65f10 Wed May 4 07:23:58 2022 -0700
    adding ba.4 and ba.5 tracks to wuhcor1, refs #29375
  • lines changed 1, context: html, text, full: html, text
    b7a0329dfe82a5f49c4b324627a52871fce5d036 Wed May 4 08:11:21 2022 -0700
    Squashing old pennantIcons, no RM
• src/hg/makeDb/trackDb/virus/wuhCor1/variantMuts.ra
  • lines changed 60, context: html, text, full: html, text
    cadea00489bd3ae3b295f3237ef9eab3dbf65f10 Wed May 4 07:23:58 2022 -0700
    adding ba.4 and ba.5 tracks to wuhcor1, refs #29375
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    2671a45e23726cd9b102520f02df27e24c2661d0 Wed May 4 17:54:04 2022 -0700
    fix wrong filename for aa strains wuhcor1 track, refs #29375
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    7db8713edd386c7393b9eed2855389071dcd258e Thu May 5 15:28:56 2022 -0700
    Adding pennantIcon to updated VoC track refs #29375
• src/hg/makeDb/trackDbToTxt/makefile
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    4d281833c93fd7df59076b28710e3c5483501f97 Sun May 8 13:06:27 2022 -0700
    first cut of utility to convert trackDb tables into hub trackDb.txt files
• src/hg/makeDb/trackDbToTxt/trackDbToTxt.c
  • lines changed 145, context: html, text, full: html, text
    4d281833c93fd7df59076b28710e3c5483501f97 Sun May 8 13:06:27 2022 -0700
    first cut of utility to convert trackDb tables into hub trackDb.txt files
• src/hg/utils/automation/asmHubTrackDb.sh
  • lines changed 6, context: html, text, full: html, text
    e3c90a0c1514cc8f4e0bf17618fd2d2d06e235ef Mon May 2 10:16:21 2022 -0700
    clean up loose ends no redmine
• src/hg/utils/automation/doAssemblyHub.pl
  • lines changed 3, context: html, text, full: html, text
    e3c90a0c1514cc8f4e0bf17618fd2d2d06e235ef Mon May 2 10:16:21 2022 -0700
    clean up loose ends no redmine
• src/hg/utils/automation/doAugustus.pl
  • lines changed 1, context: html, text, full: html, text
    e3c90a0c1514cc8f4e0bf17618fd2d2d06e235ef Mon May 2 10:16:21 2022 -0700
    clean up loose ends no redmine
• src/hg/utils/automation/doXenoRefGene.pl
  • lines changed 2, context: html, text, full: html, text
    e3c90a0c1514cc8f4e0bf17618fd2d2d06e235ef Mon May 2 10:16:21 2022 -0700
    clean up loose ends no redmine
• src/product/installer/browserSetup.sh
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    61b3317ed3251ea30b5222f9e47aad8cc59745db Tue May 3 02:09:37 2022 -0700
    finally, add RNAplot and dot_static to GBIC, not redmine, email between Jorge and QA. I planned to do this in 2017, but then forgot
• src/utils/qa/checkHTTPS
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    a0219de08f640590679fc1467d50170733fae6d6 Sat May 7 10:53:37 2022 -0700
    Adding CIRM sites to the certificate renewal check, per Clay's request
• src/utils/qa/weeklybld/buildEnv.csh
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    10efbcc831902cbc7aab3e38f9aa831eae5bad00 Mon May 9 10:00:55 2022 -0700
    v431 preview2, refs #29357

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• files changed: 90