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Merged
aozalevsky merged 67 commits into from
Oct 14, 2025
Merged

Dev 3.0 #109

aozalevsky merged 67 commits into from
Oct 14, 2025

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@aozalevsky
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@aozalevsky aozalevsky commented Jul 10, 2025

  • 3DEM support
  • Refined table of contents in PDF
  • Various minor fixes and improvements

@aozalevsky aozalevsky added this to the v3.0 milestone Jul 10, 2025
@aozalevsky aozalevsky self-assigned this Jul 10, 2025
@aozalevsky aozalevsky marked this pull request as draft July 10, 2025 22:28
aozalevsky added 18 commits July 10, 2025 15:30
@aozalevsky
rename docker to singularity
0ed2e4b
@aozalevsky
Update wwPDB urls
e51857f
@aozalevsky
add --nogui cli option to chimera and chimerax version checks
52c5d00
@aozalevsky
update molprobity version check
83de1ec
@aozalevsky
update Singularity.def with cryo-em dependencies
2402079
@aozalevsky
enable 3dem by-default and improve switch behavior
3b5d5ac
@aozalevsky
improve detection of the software used to generate report
9a0023e
@aozalevsky
add specimen preparation details: vitrification vs staining
51d2e5b
@aozalevsky
fix emdb help links
749563a
@aozalevsky
update mapq and va names
0ed55f2
@aozalevsky
typos and uk/us english corrections
01583b2
@aozalevsky
sync method name, type, and description column names with full valida…
5462726 
…tion report
@aozalevsky
display extended pdb ids
7dc7555
@aozalevsky
update AFDB api
90fd7c7
@aozalevsky
update at a glance plots: unique colors for each data type; removed a…
a70581c 
…lpha
@aozalevsky
add datasets summary table; move summary section at the begging, befo…
5e38caa 
…re the overall quality
@aozalevsky
improve em navbar checks
232feed
@aozalevsky
remove IM from the PDB-IHM banner
3d98e0f
@aozalevsky
Replace help urls with macro
57add58
@aozalevsky
fix Overall quality hierarchy
513176f
@aozalevsky
change alignment to top
dc148bd
@aozalevsky
revert help links from beta to main
6d1fae7
@aozalevsky
Update numbering of sections in the docs
5504077
@aozalevsky
Update numbering of sections in the summary table
f3c914d
@aozalevsky
Update numbering of sections in the full pdf report
d925284
@aozalevsky
Update numbering of sections on the htlm pages
2a633c5
@aozalevsky
improve formatting of . and ? as Not available
128d496
@aozalevsky
sort datasets according their ids
7e6a789
@aozalevsky
update help page
698577a
@aozalevsky
reorder type checks
071b34f
@aozalevsky
Update SAS I(q) unit labels
25f005d
@aozalevsky
avoid None in case of missing atoms or data quality during crosslinki…
c5c3ad9 
…ng assesment
@aozalevsky
improve checking of 3DEM data for SUPRESSED EMDB entries
b619ea0
@aozalevsky
move parser and other init procedures under the __main__
a487d43
@aozalevsky
Update plot labels
8913480
@aozalevsky
update help pages and help notes
d72afa4
@aozalevsky
update AFDB file versions
c03eaf7
@aozalevsky
Add a note that model precision is provided by the depositor
3ab734d
@aozalevsky
fix typo in the about_validation.html
e97357c
@aozalevsky
setup readthedocs
519ad37
@aozalevsky
add readthedocs config
0b2d5a3
@aozalevsky
update READMEs
3ba348f
@aozalevsky
fix typos in the help
cd27652
@aozalevsky
Update license headers for py, html and j2 files
02860ee
@aozalevsky
update singularity docs
a10da41
@aozalevsky
update singularity README
63afef4
@aozalevsky aozalevsky marked this pull request as ready for review October 14, 2025 18:15
@aozalevsky aozalevsky merged commit 96cd112 into main Oct 14, 2025
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