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gwyddion: Update to 2.69
Module Name: pkgsrc-wip
Committed By: Atsushi Toyokura <asteria.at%gmail.com@localhost>
Pushed By: steleto
Date: Sat Nov 1 16:12:47 2025 +0900
Changeset: 66d11ee954809b3592a8fe7f2d71f12147b0f93e
Modified Files:
gwyddion/Makefile
gwyddion/PLIST
gwyddion/distinfo
Log Message:
gwyddion: Update to 2.69
Version 2.69 (Released: 28 July 2025)
Application
- Translations updated: Czech, Russian.
- File menu: Image stack import was added.
Libraries
- libgwyapp: Workaround for data browser drag'n'drop dropping wrong
data in KDE Plasma in Wayland was improved to catch non-image data
types.
- libgwyapp: Default curve map and volume data previews attemp to
filter out outliers and a filtering option was also added to the
explicit preview creation.
- libgwyapp: Curve length was added as a possible curve map preview.
- libgwyapp: New high-level function for loading an image stack.
Modules
- Talos (new): Imports ThemoFisher Talos TEM images.
- RMI TMD (new): Imports RMI TrueMap Data v2.0 files.
- Curve map ASCII export (new): Simple export of curve maps to text
with one curve per line.
- Curve map ASCII import (new): Read back the curve map text export
format.
- Curve Map Cut to Segments: Invert option was added for
- Approach-Retract splitting using curves where the split point is at
the maximum, not minimum.
- Igor: Mismatched channel titles in exported IBW files were
corrected.
- HDF5: Invalid/missing values in DATX are handled correctly now (by
masking and interpolating).
- Nanoscope: Files with explicit Slow Axis Size do not have the
vertical size corrected twice any more, which resulted in wrong
physical dimensions.
- DME file: Possible crash in MS Windows upon file import was fixed.
- JPK scan: Force curve map import attempts to avoid placeholder pause
segments, which previously caused a non-uniform channels error.
- MFM Current Line and Parallel Field: Memory handling bugs were fixed.
Version 2.68 (Released: 24 March 2025)
Application
- Translations updated: Czech.
Libraries
- libgwyprocess: Functions for angularly averaged 2D PSDF were added.
- libgwyprocess: Fixed brick transposition not updating the real
dimensions correctly.
- libgwyapp: Row levelling in file open preview was changed to median,
avoiding the global tilt sometimes added by median difference.
- libgwyapp: GwyParamTable reset is actually handled for range-from
and range-to type controls.
- libgwyapp: Items in metadata browser can be filtered by name.
Modules
- Volume clustering (new): Volume data clustering, replacing volume
k-means and k-medians and adding new methods, such as DBSCAN.
- Zyvex (new): Imports ZyVector Scanz data files.
- Accurion ellipsometry (new): Imports ASCII data maps exported from
Accurion ellipsometers.
- K-means, K-medians: Removed (replaced with Volume clustering).
- HDF5 and a dozen other file modules: Import is now corectly recorded
in the log.
- 2D ACF, 2D PSDF: Wrong sensitivity of target graph selector was fixed.
- 2D PSDF: The output curves are just sections of the 2D PSDF and have
the same units as 2D PSDF.
- Statistical functions: Angularly averaged PSDF was added.
- Wave synthesis: Incorrect phase and amplitude outputs for cosh waves
were corrected. Complementary displacement wave output was
added. Underflow is handled better, allowing farther sources with
decay.
- Coerce: Skew parameter of skew-normal distribution can be negative.
- Curve Map Find Position: Fixed possible crash when working with
individual curve segments.
- Frequency split: Spectral density plot not displaying with wide and
flat images was corrected.
Others
- Compilation: Python detection on python3-only systems was fixed,
making build scripts actually work there.
Version 2.67 (Released: 11 November 2024)
Application
- Translations updated: Czech, Russian.
Libraries
- libgwyddion: ACF and PSDF fitting preset initial guesses were improved.
- libgwyddion: Function for checking for a regular lattice was added,
able to handle rotation and some moderate defects.
- libgwyddion: gwy_raw_data_size() was updated for the new types added
since 2.65 and gwy_raw_data_size_bits() was added, useful for
fractional sizes.
- libgwyddion: gwy_convert_raw_data() can handle 10byte x86
‘extended’ floating point numbers.
- libgwyddion: Functions for filling an array with arithmetic
progression and accumulation/rewind of array of counts were added.
- libgwyprocess: Function for the entire facet levelling procedure was
added.
- libgwyprocess: Function for facet distribution computation was added.
- libgwyprocess: Function for polynomial scan line levelling was added.
- libgwyapp: Workaround was added for data browser drag'n'drop
dropping wrong data in KDE Plasma in Wayland (and possibly other
environments).
- libgwyapp: Log message handling can be modified using a new function.
Modules
- Curve map fit (new): Fits general functions to curve map curves.
- Curve map volumize (new): Converts regular curve map data to volume
data.
- XYZ Reduce (new): Reduces number of points in a XYZ data array.
- XYZ 1D FFT filter (new): Performs FFT filtering in the XYZ data
array, treating it as time series of equidistant values.
- PFM (new): Performs processing of vector Piezoresponse Force
Microscopy data consisting of measurements in two perpendicular
directions.
- Periodic translate (new): Translate image in the XY plane, treating
it as periodic.
- Residue synthesis (new): Simulates surfaces resembling film residue
after partial dissolution.
- HDF5: Support for Nanosurf NHF file format was added. Missing data
units in EPFL files were corrected.
- Keyence: Wrong physical data scales and metadata in imported VK3
files were corrected.
- Nanoscope: Uses FV Lines for the number of scan lines in force
volume data.
- Image export: Fonts with attributes like ‘Bold’ or ‘Italics’ are
correctly loaded back from settings (instead of the font being reset
to default). Round interpolation should make images in exported SVGs
pixelated and masks should always be pixelated in SVG (as they are in
PDF).
- Correlation length tool: Rewritten using the new self-consistent ACF
paper. It also displays ACF and PSDF plots and lots of other
imaprovements.
- Volume equiplane, Z-pos level: Crash for data with Z-calibration was
fixed.
- Volume Crop: Missing coordinate units were corrected.
- Mutual Crop: Has a preview, can create new images and allows method
selection.
- Statistical functions tool: Radial ACF subtracts the mean value
automatically. Result not being always updated upon masking mode
changes was fixed.
- Volume slice: Clear selection button was added. Fixed previews not
correctly updating according to changing selection in some cases.
- Volume plane level: Zero mean value function was added.
- Lattice synthesis: Incorrect lattice scaling was fixed.
- Volume facet level: The progress bar actually works and the
computation is cancellable.
- Fit terraces (image and graph) and volume and graph ASCII export:
Output files are written with native EOLs, not always Unix.
- Facet analysis: Manual rotation of points works correctly again.
- Frequency split: A PSDF and filter shape plot was added.
- Grain filter: It now actually reads the ranges file with remembered
ranges the for various quantities when run non-interactively.
Others
- Compilation: configure now aborts when basic C99 maths functions
like cbrt(), hypot() or erf() are not available. Gwyddion code has
been using erf() unconditionally for many years so the change just
makes it manifest.
- Compilation: Various auxiliary Python build scripts, generally used
in builds from subversion, work with any Python version (2.7 or
3.x). Python checks were split into pygwy and interpreter for the
scripts. Pygwy compiler and linker variables are now prefixed PYTHON2_
instead of PYTHON_.
- Plug-in proxy: Configuring with --disable-plugin-proxy now also
prevents the installation of all plug-in support files.
- Python: Standalone Python module gwy initialises GTK+ more
carefully, making it work at least to some degree without a display.
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=66d11ee954809b3592a8fe7f2d71f12147b0f93e
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
gwyddion/Makefile | 2 +-
gwyddion/PLIST | 18 ++++++++++++++----
gwyddion/distinfo | 6 +++---
3 files changed, 18 insertions(+), 8 deletions(-)
diffs:
diff --git a/gwyddion/Makefile b/gwyddion/Makefile
index f9e60e354e..bf3825f621 100644
--- a/gwyddion/Makefile
+++ b/gwyddion/Makefile
@@ -1,6 +1,6 @@
# $NetBSD: Makefile,v 1.5 2014/05/09 07:38:43 thomasklausner Exp $
-DISTNAME= gwyddion-2.66
+DISTNAME= gwyddion-2.69
CATEGORIES= graphics #science
MASTER_SITES= ${MASTER_SITE_SOURCEFORGE:=gwyddion/}
EXTRACT_SUFX= .tar.xz
diff --git a/gwyddion/PLIST b/gwyddion/PLIST
index 20489e6fc2..3aae53c443 100644
--- a/gwyddion/PLIST
+++ b/gwyddion/PLIST
@@ -187,11 +187,12 @@ lib/gwyddion/modules/file/pixmap.la
lib/gwyddion/modules/file/rhk-sm4.la
lib/gwyddion/modules/file/spml.la
lib/gwyddion/modules/file/surffile.la
+lib/gwyddion/modules/file/zyvex.la
lib/gwyddion/modules/graph/graph.la
lib/gwyddion/modules/layer/layer.la
lib/gwyddion/modules/plugin-proxy.la
lib/gwyddion/modules/process/process.la
-${PLIST.pygwy}lib/gwyddion/modules/pygwy.la
+lib/gwyddion/modules/pygwy.la
lib/gwyddion/modules/tool/tools.la
lib/gwyddion/modules/volume/volume.la
lib/gwyddion/modules/xyz/xyz.la
@@ -210,7 +211,7 @@ lib/libgwydraw2.la
lib/libgwymodule2.la
lib/libgwyprocess2.la
lib/pkgconfig/gwyddion.pc
-${PLIST.pygwy}${PYSITELIB}/gwy.la
+${PYSITELIB}/gwy.la
man/man1/gwyddion-thumbnailer.1
man/man1/gwyddion.1
man/man3/Gwyddion::dump.3pm
@@ -274,6 +275,8 @@ share/gtk-doc/html/libgwyapp/api-index-2-61.html
share/gtk-doc/html/libgwyapp/api-index-2-62.html
share/gtk-doc/html/libgwyapp/api-index-2-63.html
share/gtk-doc/html/libgwyapp/api-index-2-64.html
+share/gtk-doc/html/libgwyapp/api-index-2-67.html
+share/gtk-doc/html/libgwyapp/api-index-2-69.html
share/gtk-doc/html/libgwyapp/api-index-2-7.html
share/gtk-doc/html/libgwyapp/api-index-2-9.html
share/gtk-doc/html/libgwyapp/api-index-all.html
@@ -352,6 +355,7 @@ share/gtk-doc/html/libgwyddion/api-index-2-61.html
share/gtk-doc/html/libgwyddion/api-index-2-62.html
share/gtk-doc/html/libgwyddion/api-index-2-63.html
share/gtk-doc/html/libgwyddion/api-index-2-64.html
+share/gtk-doc/html/libgwyddion/api-index-2-67.html
share/gtk-doc/html/libgwyddion/api-index-2-7.html
share/gtk-doc/html/libgwyddion/api-index-2-8.html
share/gtk-doc/html/libgwyddion/api-index-2-9.html
@@ -462,6 +466,7 @@ share/gtk-doc/html/libgwydgets/api-index-2-61.html
share/gtk-doc/html/libgwydgets/api-index-2-62.html
share/gtk-doc/html/libgwydgets/api-index-2-63.html
share/gtk-doc/html/libgwydgets/api-index-2-64.html
+share/gtk-doc/html/libgwydgets/api-index-2-67.html
share/gtk-doc/html/libgwydgets/api-index-2-7.html
share/gtk-doc/html/libgwydgets/api-index-2-8.html
share/gtk-doc/html/libgwydgets/api-index-all.html
@@ -703,6 +708,7 @@ share/gtk-doc/html/libgwydgets/gwy_tip_lateral_force-24.png
share/gtk-doc/html/libgwydgets/gwy_tip_map-24.png
share/gtk-doc/html/libgwydgets/gwy_tip_model-24.png
share/gtk-doc/html/libgwydgets/gwy_tip_pid-24.png
+share/gtk-doc/html/libgwydgets/gwy_translate_periodically-24.png
share/gtk-doc/html/libgwydgets/gwy_unrotate-24.png
share/gtk-doc/html/libgwydgets/gwy_value_invert-24.png
share/gtk-doc/html/libgwydgets/gwy_volume-24.png
@@ -883,6 +889,8 @@ share/gtk-doc/html/libgwyprocess/api-index-2-62.html
share/gtk-doc/html/libgwyprocess/api-index-2-63.html
share/gtk-doc/html/libgwyprocess/api-index-2-64.html
share/gtk-doc/html/libgwyprocess/api-index-2-66.html
+share/gtk-doc/html/libgwyprocess/api-index-2-67.html
+share/gtk-doc/html/libgwyprocess/api-index-2-68.html
share/gtk-doc/html/libgwyprocess/api-index-2-7.html
share/gtk-doc/html/libgwyprocess/api-index-2-8.html
share/gtk-doc/html/libgwyprocess/api-index-all.html
@@ -921,7 +929,7 @@ share/gtk-doc/html/libgwyprocess/right.png
share/gtk-doc/html/libgwyprocess/style.css
share/gtk-doc/html/libgwyprocess/up-insensitive.png
share/gtk-doc/html/libgwyprocess/up.png
-${PLIST.pygwy}share/gtksourceview-2.0/language-specs/pygwy.lang
+share/gtksourceview-2.0/language-specs/pygwy.lang
share/gwyddion/glmaterials/Alien-Alloy
share/gwyddion/glmaterials/Black-Plastic
share/gwyddion/glmaterials/Black-Rubber
@@ -964,6 +972,7 @@ share/gwyddion/gradients/Blue-Violet
share/gwyddion/gradients/Blue-Yellow
share/gwyddion/gradients/Body
share/gwyddion/gradients/Caribbean
+share/gwyddion/gradients/Clusters
share/gwyddion/gradients/Code-V
share/gwyddion/gradients/Cold
share/gwyddion/gradients/DFit
@@ -1251,6 +1260,7 @@ share/gwyddion/pixmaps/gwy_tip_lateral_force-24.png
share/gwyddion/pixmaps/gwy_tip_map-24.png
share/gwyddion/pixmaps/gwy_tip_model-24.png
share/gwyddion/pixmaps/gwy_tip_pid-24.png
+share/gwyddion/pixmaps/gwy_translate_periodically-24.png
share/gwyddion/pixmaps/gwy_unrotate-24.png
share/gwyddion/pixmaps/gwy_value_invert-24.png
share/gwyddion/pixmaps/gwy_volume-24.png
@@ -1279,7 +1289,7 @@ share/gwyddion/pixmaps/gwy_zoom_in-24.png
share/gwyddion/pixmaps/gwy_zoom_out-24.png
share/gwyddion/pixmaps/gwyddion.ico
share/gwyddion/pixmaps/splash.png
-${PLIST.pygwy}share/gwyddion/pygwy/gwyutils.py
+share/gwyddion/pygwy/gwyutils.py
share/gwyddion/ui/toolbox.xml
share/gwyddion/user-guide-modules
share/icons/hicolor/48x48/apps/gwyddion.png
diff --git a/gwyddion/distinfo b/gwyddion/distinfo
index 44de3dfad1..f0145f244b 100644
--- a/gwyddion/distinfo
+++ b/gwyddion/distinfo
@@ -1,5 +1,5 @@
$NetBSD: distinfo,v 1.1.1.1 2011/09/20 00:00:37 jihbed Exp $
-BLAKE2s (gwyddion-2.66.tar.xz) = a53396ceb0f8d5fc44e2930e978efaf74830b33de6bf2027a6b4033d261aef54
-SHA512 (gwyddion-2.66.tar.xz) = 0f0952c5bcf61c79349f6a99e188a5a83fd0527554adaaf82bc29fd2574e5f1602921d5e0490b0bb7e7f5ab4dd517d42807c6e8878d585a67f0910d84d5ea188
-Size (gwyddion-2.66.tar.xz) = 5390884 bytes
+BLAKE2s (gwyddion-2.69.tar.xz) = b4c2e229904e8019787534db177097fa8c3cd0acf0faffdac03e1a6e7b009278
+SHA512 (gwyddion-2.69.tar.xz) = c11a2e7c1eb533800c97695c50227da6f58865bea002bcc9fd050d3f86e9f4aa80e426d610e9b27fde8167ced5b762f2d6f3d02106dab11348ba2af3a1812261
+Size (gwyddion-2.69.tar.xz) = 5476852 bytes
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