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Dev 3.0 #109

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  • 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
update IHMValidation software name
6ebc750
@aozalevsky
update PDB-IHM banner
0dca449
@aozalevsky
do not apply formatting if pdbid is empty
29607fa
@aozalevsky
improve formatting of crosslinking-MS data quality in summary table
f54dabb
@aozalevsky
update validation help pages
7608b7d
@aozalevsky
update IHMValidation name on the help page
9e2bf5b
@aozalevsky
Update docs
321a715
@aozalevsky
Update help links
95a032a
@aozalevsky
add help links to wwPDB xray validation report
12e3687
@aozalevsky
fix help 3dem help link
9c06f12
@aozalevsky
Fix Model details hierarchy
7c9ba03
@aozalevsky
Fix Overview hierarchy
f9b4106
@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
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