pkgsrc/biology
ryoon 0e65e0d997 gnome-chemistry-utils: Update to 0.14.16
Changelog:
Version 0.14.16:
	GChemPaint:
		* Do not show buttons for non yet implemented tools.

Version 0.14.15:
	GCCV library:
		* Don't use the abs() function on unsigned numbers.
	Other:
		* Updated appdata files.

Version 0.14.14:
	Mozilla plugin:
	* Fix build.

Version 0.14.13:
	GChemPaint:
		* Optional use of Lasem to display maths.
		* Fix rendering with gtk+ >= 3.20.
		* Fix crash with atom charges larger than 1.
		* Fix crash when deleting a bond outside a molecule. [#48256]
	Gnumeric plugin:
		* Add monoisotopicmass function in gnumeric and more.
	Databases:
		* Update names for elements 113, 115, 117 and 118.

Version 0.14.12:
	GChemPaint:
		* Enhanced Chemdraw formats support. [sr #108952]
		* Optional use of Lasem to display maths.
		* Fix rendering with gtk+ >= 3.20.
	GChemCalc:
		* Don't crash on "Ac" string. [#47366]

Version 0.14.11:
	GChemPaint:
		* Fix an infinite loop condition in retrosyntheses alignment.
		* Don't crash when importing an invalid string. [Redhat bug #1285154]
		* Fix drawing when zoomed.
		* Fix various runtime errors.
		* Fix crash when creating a reaction with no product.
		* Enhanced Chemdraw formats support.
		* Fix embedding of a whole molecule inside brackets. [#47224]
	GChemTable:
		* Don't crash when showing an already existing chart.
		[Redhat bug #1302135]
	GCrystal:
		* Fix build with gcc-6. [Redhat bug #1307546]
	GCrystal and GChem3D:
		* Don't crash when rendering to memory (images and print). [#47169]
	Other:
		* Added keywords to desktop files.
		* Updated appdata files.

Version 0.14.10:
	GChemPaint:
		* Fix an object bounds issue.
	Mozilla plugin:
		* Supports the npapi-sdk package as requirement.
	Other:
		* Fixed typos in appdata files.

Version 0.14.9:
	GChemPaint:
		* Ensure that the document size is always updated. [#43091]
	3d viewer and GCrystal:
		* Fix rotation. [#42977] (patch from Toni Andjelkovic)
	All applications:
		* Add appdata files.

Version 0.14.8
	GChemPaint:
		* Fix drawing with Gtk+ >= 3.10.

Version 0.14.7
	GCrystal:
		* Fix crash in dialogs with recent Gtk+.
	Mozilla plugin:
		* Fix crashers for 2D and 3D molecules.

Version 0.14.6
	3d viewer:
		* Avoid empty entries in recent list.
	CGchemPaint:
		* Restore .mol files support.
		* Fix CML import (also affected 3d viewer and >GCrystal).
		* Fix BMP export.
	GCrystal:
		* Fix test order in lines code. [#41261]
	GSpectrum:
		* Fix access to uninitialized data.
		* Don' double free a string.
	GOffice component:
		* Don't crash when editing after saving a GChemPaint object.
	Mozilla plugin:
		* Fix supported mime-types list. (see Debian bug #716961)
	Other:
		* Fix build on FreeBSD (Koop Mast). [#41256]

Version 0.14.5
	GChemPaint:
		* Make adding template work again.

Version 0.14.4
	GChemPaint:
		* Do not use a NULL atom properties. [#40194]

Version 0.14.3
	GChemPaint:
		* Really close the window on delete event.
		* Don't crash when aligning ungrouped objects.
	GChemTable:
		* Fix crash when using masses in a graph.
		* Fix graph behavior after edition.
	All:
		* Make sure to not create a C++ locale from a NULL string.

Version 0.14.2
	GChemPaint:
		* Fix crash when loading some molecules (was introduced in 0.14.1).

Version 0.14.1
	GChemPaint:
		* Do not allow a mesomery destruction when inside a reaction.
		* Fix molecule deletion inside a mesomery.
		* Fix reactant deletion inside a reaction.
		* Don't crash when a mesomery inside a reaction is destroyed.
		* Check molecule consistency when loading, avoids a stack overflow.
		* Enhanced representaion of chiral molecules imported from CML and other
		formats.
		* Fix crash when deleting a cyclic bond.
	GCrystal:
		* Fix row selection operations order in grids.

Version 0.14.0
	GChemPaint:
		* Fix reaction construction.
		* Fix non bonding electron pairs.

Version 0.13.99
	GChemPaint:
		* Fix squiggle bonds period.
		* Allow brackets around a mesomery.
		* Allow a mesomery inside a reaction.
		* Fixed some meomory access issues.
		* Fixed crash when loading a group.
		* Fixed mesomery construction.
		* Fixed crash when ungrouping.

Version 0.13.98
	GChemPaint:
		* Don't freeze after an aborted molecules merge.
		* Initialize the bond order for the Newman projection tool.
		* Don't crash when adding brackets around a fragment.
		* Fix undoing a molecule partial flip.
		* Fix bracket stoichiometry index position after a transform.
		* Fix explicit lone pairs count evaluation.

Version 0.13.92
	GChemCalc
		* Updated the documentation.
	GChemPaint:
		* Fix View::BuildSVG() and View::BuildEPS() which were missing the
		trailing 0.
		* Fix misleading error message while saving.
		* Fix loading of arrows inside a group. [#27032]
	GCrystal:
		* Apply element change to all slected atoms.
		* Updated the documentation.
	GSpectrum:
		* Add "Response factor" as supported unit.
		* Fixed widgets spacing.
		* Updated the documentation.
	GChemTable:
		* Updated the documentation.

Version 0.13.91
	3d viewer:
		* Show all menu items when a molecule is loaded from the command line.
		* Updated user documentation.
	GChemPaint:
		* Don't crash on startup.
	All:
		* Fix localization issues.
		* Fixed modal message boxes behavior.

Version 0.13.90
	3d viewer:
		* Fix import from pdb files. [#36582]
	GCrystal:
		* Fix infinite loop condition. [#36583]
		* Fix atomic radius change issue.
	GChemTable:
		* Fix languages translation.

Version 0.13.7
	GChemPaint:
		* Fixed crash when selecting the alignment item inside a mechanism
		step. [#35626]
	GCrystal:
		* Fixed loading CIF files using uptodate space groups descriptions.
	Other:
		* License is now GPL version 3 (except for the OpenBabel related code).
		* Fix build on big endian machines (Dan Horak). [#36175]
		* Updated API documentation.

Version 0.13.6
	GChemPaint:
		* fixed text position serialization. [#34947]
		* add some support for Newman projections.
		* accept some multisteps reactions.
	Goffice component:
		* Add support for 3D molecular structures.
	Other:
		* Fixed pixmaps installation directory. [#35272]
		* fixed build with ->l,--no-undefined. [patch #7677]

Version 0.13.5
	3d viewer:
		* Import from InChI or SMILES.
		* Export to GChemPaint and GChemCalc.
		* Generates InChI, InChiKey and SMILES.
		* Add access to databases.
	GChemPaint:
		* Brackets inside a molecule accept a stoichiometry coefficient.
	GCrystal:
		* Use multiple selection in atoms and lines dialogs.
	GSpectrum:
		* Allow markup in combo boxes and axes titles.
	Goffice component:
		* Add support for crystal structures.
	Other:
		* Fixed one more OpenGL related crasher.

Version 0.13.4
	All:
		* Ported to Gtk+-3.0.
	GCrystal:
		* Use the new GcrGrid item in atoms, lines and cleavages dialogs.
		* Make these and size dialogs instant apply.
	GChemTable:
		* Use a more complete tip window for elements.

Version 0.13.3
	GChemPaint:
		* Fixed build with gcc-4.6. [#32363]
		* Allow colored atomic symbols on a per-document basis.
		* Brackets tool now working, not perfectly though.
	Other:
		* Don't use POLLRDHUP when not defined. [#32768]
		* Split libgcu so that libgcu itself never calls gtk+ directly.

Version 0.13.2
	GChemPaint:
		* Do not allow document changes using keyboard while
		dragging the mouse. [#31812]
		* Don't add new molecules when undoing a mechanism arrow deletion.
		[#32433]
		* Removed the Wikipedia tool which was obsolete.
		* Reorganized molecule contextual menu with new 3D options
		and databases access.
	Other:
		* OpenBabel support has been moved to a separate process and greatly
		enhanced, specially for 3D export from gchempaint.
		* A lot of bugs have been fixed.

Version 0.13.1
	GSpectrum:
		* Loads NUTS files.
		* Transforms FID to spectrum.

Version 0.13.0
	GChemPaint:
		* New "lasso" tool to allow partial selections.
		* New "brackets" tool (doesn't work yet).
	Other:
		* libgcr: new library for GCrystal.
		* Fixed all bugs discovered in the 0.12 banch.
2020-06-29 13:04:48 +00:00
..
arka biology/arka: document 2 instances of char as array index 2020-05-03 14:58:18 +00:00
azara *: recursive bump for libffi 2020-03-08 16:47:24 +00:00
bcftools all: migrate several HOMEPAGEs to https 2020-01-18 23:30:05 +00:00
bioperl biology: align variable assignments 2019-11-02 22:09:00 +00:00
bodr Revbump for icu 2020-06-02 08:22:31 +00:00
bwa all: migrate some SourceForge homepage URLs back from https to http 2020-01-26 05:26:08 +00:00
canu biology/canu: fix build on NetBSD-8.0-x86_64 2020-05-16 19:50:21 +00:00
cdhit Bump PKGREVISIONs for perl 5.30.0 2019-08-11 13:17:48 +00:00
chemical-mime-data chemical-mime-data: comment out dead sites 2017-12-24 09:42:12 +00:00
chemtool librsvg: update bl3.mk to remove libcroco in rust case 2020-03-10 22:08:37 +00:00
clustalw Comment out some dead HOMEPAGEs. 2017-08-01 17:40:08 +00:00
coalesce Comment out some dead HOMEPAGEs. 2017-08-01 17:40:08 +00:00
fastDNAml
fastp biology/fastp: document possible array[char] bug 2020-05-25 05:18:35 +00:00
fluctuate Comment out some dead HOMEPAGEs. 2017-08-01 17:40:08 +00:00
gabedit librsvg: update bl3.mk to remove libcroco in rust case 2020-03-10 22:08:37 +00:00
genesplicer
glimmer Sort PLIST files. 2018-01-01 22:29:15 +00:00
gnome-chemistry-utils gnome-chemistry-utils: Update to 0.14.16 2020-06-29 13:04:48 +00:00
gp all: migrate homepages from http to https 2020-01-26 17:30:40 +00:00
gromacs Revbump for icu 2020-06-02 08:22:31 +00:00
hisat2 Bump PKGREVISIONs for perl 5.30.0 2019-08-11 13:17:48 +00:00
hmmer Convert all occurrences (353 by my count) of 2017-01-19 18:52:01 +00:00
htslib revbump after updating security/nettle 2020-05-22 10:55:42 +00:00
kallisto biology/kallisto: Switch from archivers/szip to archivers/libaec 2019-05-01 12:38:54 +00:00
lucy mark packages that fail with -Werror=char-subscripts 2020-05-20 06:09:03 +00:00
mopac
mpqc biology: align variable assignments 2019-11-02 22:09:00 +00:00
mummer all: migrate some SourceForge homepage URLs back from https to http 2020-01-26 05:26:08 +00:00
ncbi-blast+ Revbump for icu 2020-06-02 08:22:31 +00:00
nut all: migrate some SourceForge homepage URLs back from https to http 2020-01-26 05:26:08 +00:00
openbabel openbabel: Fix PLIST 2020-06-29 12:40:02 +00:00
p5-Bio-ASN1-EntrezGene Bump PKGREVISIONs for perl 5.30.0 2019-08-11 13:17:48 +00:00
pdbalign
phylip biology: align variable assignments 2019-11-02 22:09:00 +00:00
plink Multiple packages: Replace obsolete maintainer email 2019-01-13 22:06:42 +00:00
plinkseq Multiple packages: Replace obsolete maintainer email 2019-01-13 22:06:42 +00:00
primer3 *: Convert broken sourceforge HOMEPAGEs back to http 2020-03-20 11:57:22 +00:00
profit Moved documentation to share/doc/${PKGBASE}. Bumped PKGREVISION. 2016-07-24 21:11:52 +00:00
puzzle biology: align variable assignments 2019-11-02 22:09:00 +00:00
py-biopython all: migrate homepages from http to https 2020-01-26 17:30:40 +00:00
py-mol py-mol: use buildlink for py-numpy 2020-04-27 18:33:18 +00:00
py-pydicom py-pydicom: Update to 1.3.0 2019-10-01 14:45:29 +00:00
rasmol
samtools all: migrate homepages from http to https 2020-01-26 17:30:40 +00:00
sewer Sort PLIST files. 2018-01-01 22:29:15 +00:00
stacks Bump PKGREVISIONs for perl 5.30.0 2019-08-11 13:17:48 +00:00
stride Comment out dead sites. 2017-09-04 18:00:49 +00:00
trimmomatic biology/trimmomatic: import Trimmomatic-0.38 2018-07-25 15:14:32 +00:00
vsearch Fix portability 2020-03-26 02:37:38 +00:00
xylem all: migrate homepages from http to https 2020-01-26 17:30:40 +00:00
Makefile py-biopython: initial commit 2019-08-09 21:52:34 +00:00