#Changes by release

[0.10.3.dev0] (2023-11-30) - Multifile support for `.star`

convert multiple .star files into a single EMDB-SFF file
new class sfftk.formats.star.RelionMultiStarSegmentation
however, only one mask/particle will be accepted for all, which is handy when displaying the particles with different colours on the same viz.

[0.10.2.dev1] (2023-11-20) - Remove print warning for OLS

[0.10.2.dev0] (2023-11-16) - Extra arguments for working with RELION `.star` files

--euler-angle-convention is now user-modifiable
--radians flag to treat angles as radians instead of degrees
adapt to changes in OLS
print warning for OLS bug which does not honour --start for search

[0.10.1.dev1] (2023-10-26) - Extension of previous bugfix

[0.10.1.dev0] (2023-10-26) - Improvements to display of search results

bugfix: when running sff notes search '<term>' --as-text, any multi-line labels are concatenated without spaces (FIXED)

[0.10.0.dev0] (2023-10-24) - Improvements to display of search results

display search results --as-text
select search results to save to file using the --filter-rows option
if concatenating search results to text file then option --no-header to only include results
new classes to sfftk.notes.find: CSVTable and CSVRow
associated unit tests with minor cleanup

[0.9.0.dev2] (2023-10-03) - Minor corrections and cleanup

[0.9.0.dev1] (2023-09-27) - Using shape_primitive_list for subtomogram averages

changed convert argument --particles to --subtomogram-average
required sfftk-rw>=0.8.1 to work

[0.9.0.dev0] (2023-09-20) - Handling RELION STAR files

basic working API
starreader documentation
skeleton implementation of star converter
test files
main entry point for starsplit and starcrop
display progres bar while reading RELION .star file
prep starsplit: split a .star file by image name; options to handle heterogeneity
prep starcrop: crop a .star file to a certain number of rows
unit tests for all the above
--image-name-field to specify field with image/tomogram

[0.8.5] (2023-06-22) - Now `sff view` on STL files displays the bounding box; fixed failing tests

[0.8.4] (2023-02-08) - Added `GlobalSimpleNote` to annotate a segmentation

[0.8.3] (2023-01-27) - Now merging annotations and optionally include colour

use --include-colour when merging annotations to include manually edited colours from a source EMDB-SFF file

[0.8.2] (2023-01-20) - Bugfix for reading MRC files

[0.8.1] (2023-01-19) - Stable merging of masks

new mergemask option --skip-assessment to go straight to merging and skip checking binary-ness
reinstated --allow-overlap flag; overlapping masks blocked by default; failure on the first detected overlap
fixed a bug which excluded some data from merged mrc headers
updated documentation to outline best practices when merging masks (only use merging for relatively small volumes otherwise convert large binary masks into STL meshes)
fixed bug when deleting fewer than the total number of external references
new tests to check mask merging

[0.8.0.dev1] (2022-11-29) - Merge masks

sff prep mergemask to merge multiple binary masks
updated documentation to reflect new feature

[0.7.4.post1] (2022-10-19) - v0.7.4.post1: Refinement of `sff notes search -R [emdb|empiar]` to display meaningful results

[0.7.4] (2022-10-17) - Tentative fix for search EMDB and EMPIAR search

not all search features remain e.g. --start is ignored, search results count unavailable

[0.7.3] (2022-10-17) - Trivial bugfix and documentation update for transforms

viewing transforms
inserting transforms from .map files
modifying transforms using the notes utility
fix typo in parser

[0.7.2] (2022-10-10) - Bugfixes for CI/CD and docbuild

fixes for Github workflow
removal of mock packages which prevented documentation build
requirements.txt for building documentation
remove all appearances of from __future__ import <foo>
remove most uses of python2-3 adaption functions
inclusion of missing image file to run test
now including explicit rtd configs (.readthedocs.yml)
added numpy as explicit dependency
removed source dependency for ahds

[0.7.1] (2022-10-07) - Bugfix for annotation

temporary file should exclude geometry: FIXED

[0.7.0] (2022-10-04) - Support for working with transforms

sff view --transform file.map now outputs the image-to-physical space transform; sff view file.map will still output
user may choose how to display the transform using sff view --transform [--print-array (default) | --print-csv | --print-ssv] file.map
sff convert now takes an option --image that takes an .map/.mrc/.rec file and extracts the transform to set as transform 0 ; excluding --image <file.map> produces a warning and possibly wrong transform 0
sff notes [add|edit|del] [-x/--transform-id <int>] [-X/--transform <12-floats>] file.sff to add/modify/delete transforms
sff notes show -H file.sff now displays the table of transforms
all formats now honour --image <file.map> to set the correct transform
sfftk.readers.mapreader.compute_transform('file.map') computes transform; when computing the transform from MAP file, only reads the header
all associated tests
correct spelling for ångström
minor cleanup and improvements
bugfixes for cases not caught by tests e.g. merge annotation does not interact with transform_list - must be done manually
for map file we will not write skew and translation matrices; assume rectilinear lattices
bugfix: sff notes add was always adding extra software
bugfix: display of transforms when empty
tests for edit and del of notes: OK
incomplete updates to documentation
including image used for testing transforms

[0.6.1.dev0] - 2022-09-06

improvements for reading SuRVoS files with additional attributes

[0.6.0.dev2] - 2022-09-02

Cleanup

removed all u"..." strings and other Python2 related code
run flake8 checks; considerable reformatting

[0.6.0.dev1] - 2022-09-02

Bugfixes

removed .travis.yml since we don't use them anymore
added ilastik.IlastikHeader class, which was implied but absent >:(
fixed github workflow by removing py27 and py35 and quote py3.10

[0.6.0.dev0] - 2022-09-01

dropped support for Python2.7; requires Python3.6+
fixed #22
now convert takes keywords; updated documentation to show keywords required

[0.5.5.dev1] - 2020-11-10

trivial

[0.5.5.dev0] - 2020-05-27

Completed (rudimentary) support for ilastik segmentations

convert ilastik .h5 simple segmentation to EMDB-SFF
disambiguate .h5 with menu or --subtype-index <int> option
unit tests for new reader/format

[0.5.4.dev0] - 2020-05-20

Bugfixes: correct handling of conversion with exclusion of geometry for JSON

added unit tests for the above
deleted test data files not required
trivial fix to dox for modreader.py
added type casting for segreader.py and survosreader.py from numpy types to Python types

[0.5.3.dev0] - 2020-05-15

Bugfixes: annotation issues

tests to handle adding external references when the current list has some with id collisions; fix implemented in sfftk-rw v0.6.5.dev0
fixed saving of annotations; fix implemented in sfftk-rw v0.6.6.dev0
updated test data for the above tests
Travis-CI configs: was failing with numpy; had fixed by locking numpy to 1.15.4; fix -> replaced python setup.py develop with pip install -e .

[0.5.2.dev3] - 2020-04-14

Updates to dependencies for Py27

pyparsing<3.0, kiwisolver<1.2.0 (Py27 deprecation)
fix for failing sfftk.unittests.test_core.TestCoreParserTests.test_multi_tool
simplified tool test in sfftk.core.parser

[0.5.2.dev1] - 2020-04-01

extended tests_parser from sfftk-rw

[0.5.2.dev0] - 2020-03-25

Bugfixes for faulty IMOD conversion
triangle indices for IMOD meshes were double: fixed by dividing index values by 2
extended tests to catch this for all mesh-types
added package URLs to setup.py; changed main URL to github.io one

[0.5.1.dev0] - 2020-03-23

Bugfixes for faulty conversions
fixed several formats that omitted important fields (am, map, seg, surf)
strengthened tests for formats
handle conversions for multifiles (stl, map)
sort coverage report by Cover(age)

[0.5.0.dev0] - 2020-03-20

Documentation cleanup (complete)

[0.4.0.dev0] - 2019-09-09

Python3 support

now depends on ahds v0.2.0.dev0 which is Python3 compatible

[0.3.1.dev5] - 2018-08-01

Documentation

shorted README.rst to render on pypi
replaced todo with note in toolkit.rst

[0.3.1.dev4] - 2018-08-01

Multi-file support for STL files

docs rebuild
map, stl: segment file basenames (not full path)
new multi-file tests for STL and MAP