Releases: macs3-project/MACS
MACS3 v3.0.1
What's Changed
- fix labels for signal files from
hmmratac
by @philippadoherty in #611 - remove cython from setup.py requirements by @taoliu in #612
- documentation with Sphinx by @taoliu in #618
- Jaccard Index method to test similarity of outputs by @taoliu in #619
- patch hmmlearn, fix dependencies by @taoliu in #620
Full Changelog: https://github.com/macs3-project/MACS/blob/release/macs3/3.0.1/ChangeLog
MACS3 v3.0.0
First release of MACS3 (v3.0.0). Compared with the previous v3.0.0b3, changes are:
- Cython 3 support #579
- BEDPE support in hmmratac #580
- correct libm support #587
- removal of the requirement of pip and wheel #589
- rewritten and reorganized documentation #597
Check other updates in MACS3 so far in previous beta/alpha releases and the ChangeLog file.
v3.0.0 beta 3 release
The third beta version of MACS3, addressing the Cython issue and adding more HMMRATAC options.
- New features from beta2:
-
HMMRATAC module
--modelonly option: only generate HMM model and quit
-t or --training: customized training regions can be provided through this option.
--min-frag-p: exclude fragments with abnormal fragment length while generating four signal tracks. #577 Check
macs3 hmmratac -h
. -
testing for Mac OS12 is added.
-
We require Cython 0.29.*. The new Cython3 will break our codes. We will adopt Cython3 later. #574
MACS2 v2.2.9.1
Since Cython has a major upgrade to 3.0, previous MACS2 can't be automatically installed through pip. Now we changed some requirements for dependencies: Python: 3.7 to 3.11, Cython 0.29.*, and Numpy >=0.19. The MACS3 setup.py script has been borrowed into MACS2 codes. Also, we tested MACS2 on Mac OS12 through Github Actions as well.
(overwrite the previous v2.2.9 since I forgot to include some changes to the documentation.)
v3.0.0 beta 2 release
MACS3 beta 2 release includes some improvements on hmmratac
command. We've added the cutoff-analysis
feature as in callpeak
subcommand to hmmratac
. It will provide help for users to decide the correct cutoff for training HMM. We also add the memory usage display to the runtime message. Also, we brought back GitHub Action testing for s390x, power64le, and armv7. We will work on rest of the documentation for the next release.
MACS2 v2.2.8
Now support Python 3.6-3.11, and newer numpy and cython, tested on x86 and ARM. Please note that .c files from cython pyx files have been removed from the package. They should be regenerated during installation so Cython is required.
v3.0.0 beta 1 release
MACS3 beta 1 release includes the new hmmratac
command. We rewrote the HMMRATAC (Tarbell 2019) idea in Python. Now all the functions for MACS3 release is ready. We plan to do some optimization and tweaking on hmmratac
feature in the next beta release and finish the documentation.
v3.0.0 Alpha 7 release
v3.0.0 Alpha 6 release
v3.0.0 Alpha 5 release
The fifth alpha release fixed an issue to correctly set CFLAG for older gcc compiler. Also, now it will use simde-no-test
instead of simde
as sub-module. The setup.py
script has been cleaned up.