v1.1.0

Changes to CLI interface

• Add subcommand annotate-barriers to modle_tools

What's Changed

• Improve text file parsing by @robomics in #107
• Add modle_tools annotate-barriers by @robomics in #109
• Bump deps by @robomics in #113 #114

Bugfix

• Bugfix by @robomics in #115
• Fix logic used to generate MoDLE version string from git metadata by @robomics in #111

Full Changelog: v1.0.1...v1.1.0

Docker images

• GHCR: ghcr.io/paulsengroup/modle:1.1.0
• DockerHub: paulsengroup/modle:1.1.0

Checksums (SHA256)

52da81d4365ef7889945f863743c177b8d2f41c3dcbfcd8f1f4c19a9cbccf52a  modle-1.1.0-x86_64-linux.tar.xz
fc96ec3f6c494b0de2bd6936d61ee87a364e3932fe2476cd94739ebb4c4f4567  modle-1.1.0.zip
f1bfd2c98ff131d555bc1504fab5c86f35521e51da87d5f66435c145e11a26e3  modle-1.1.0.tar.gz

v1.0.1 - Maintenance release

Maintenance release

Changes to CLI interface

• New option: --genomic-intervals (replaces --chrom-subranges)
• New option: --verbose
• Option --track-1d-lef-position is now true by default

What's Changed

• Bump deps by @robomics in #88 #92 #96 #98
• Migrate to Conan v2 by @robomics in #90
• Build Docker images for platform=linux/arm64 by @robomics in #89 #97
• Add CI for macos-13 by @robomics in #99
• Improvements to simulation scheduling by @robomics in #95
• Make formatting of log/error messages more consistent by @robomics in #101
• Update CLI by @robomics in #100
• Update parser for BED and .chrom.sizes files to support files enclosing strings using quotes by @robomics in #106

Bugfix

• Fix incorrect handling of --target-number-of-epochs by @robomics in #91

Full Changelog: v1.0.0...v1.0.1

Docker images

• GHCR: ghcr.io/paulsengroup/modle:1.0.1
• DockerHub: paulsengroup/modle:1.0.1

Checksums (SHA256)

ca752f97ebf184701cf683dbd148988ad33815303e9ea4c36fb281e4aba4a592  modle-1.0.1-x86_64-linux.tar.xz
ec665ad19576c045fff445aa8cfac2a2bd4a6b7f2f022c0d617231d6dad09388  modle-1.0.1.zip
66135d77127abac89fae1309346decd179a96ba512ded58dbdc3a8c802ca87f7  modle-1.0.1.tar.gz

v1.0.0 - First stable release!

First stable release! 🥳 🥳

This version of MoDLE is very similar to the one presented in MoDLE's paper: link.
This is mostly a maintenance release with some minor changes to the CLI interface, improvements to automated tests and CI and a couple of bug fixes.
Enjoy!

Changes to CLI interface

• New flag: --assembly-name
• Remove two hidden (and unsupported) subcommands: modle perturbate and modle replay

What's Changed

• Bump dependencies by @robomics in #50 #61 #62 #67
• Update Dockerfile by @robomics in #51
• Update CI by @robomics in #53 #54 #59 #60 #68 #69
• Add GHA workflow to build portable Linux binaries by @robomics in #55
• Fix bugs in modle_tools (#46, #47) by @robomics in #56
• Remove unused subcommands by @robomics in #57
• Use coolerpp for Cooler IO by @robomics in #58
• Update test suites by @robomics in #64
• Enable LTO by default by @robomics in #65
• Remove support for -DBUILD_SHARED_LIBS=ON by @robomics in #66
• Update test dataset by @robomics in #71
• Update integration test scripts by @robomics in #74
• Fix generated-by attr by @robomics in #79
• Fix broken error message by @robomics in #80
• Add --assembly-name CLI option to modle by @robomics in #81
• Add missing SPDX headers [no ci] by @robomics in #84
• Update README by @robomics in #85

Full Changelog: v1.0.0-rc.7...v1.0.0

Docker images

• GHCR: ghcr.io/paulsengroup/modle:1.0.0
• DockerHub: paulsengroup/modle:1.0.0

Checksums (SHA256)

df4a73d60a8b8518a6189cc164103cea139c4f6c828f7f1393acc6ff06836b3f  modle-1.0.0-x86_64-linux.tar.xz
5ac837be47c28c027a5a5c05ab7b365ae86c9080ca562ac910aabaab0d08ec0a  modle-1.0.0.zip
dd9ea8c08f3c5c7acc00996b8dde96bd321805f8a3f070f9a22f5be9d7240e5b  modle-1.0.0.tar.gz

v1.0.0-rc.7

Changes to CLI interface

• New flag: --interpret-extrusion-barrier-name-as-not-bound-stp
• New flag: --track-1d-lef-position

What's Changed

• Various changes to CI and unit tests by @robomics in #31
• Bump dependencies. Let Conan manage thread-pool and xoshiro by @robomics in #34
• Various small bugfixes by @robomics in #35
• Extend contact matrix class by @robomics in #33
• Update README by @robomics in #39
• Update integration test by @robomics in #38
• Bugfix for modle_tools by @robomics in #41
• Bump dependencies by @robomics in #42
• Update bigwig-related code by @robomics in #43
• Make puu tunable for each individual barrier by @robomics in #45
• Track LEF positions in 1D space by @robomics in #44

Full Changelog: v1.0.0-rc.6...v1.0.0-rc.7

Docker images

• GHCR: ghcr.io/paulsengroup/modle:1.0.0-rc.7
• DockerHub: paulsengroup/modle:1.0.0-rc.7

v1.0.0-rc.6

Important

The output produced by MoDLE v1.0.0-rc.6 differs from that of previous versions due to changes to the burn-in phase.

What's Changed

There are relatively few changes compared to the previous RC.
The main purpose of this RC is that of fixing a bug that could cause the burn-in phase to never end.

Full Changelog: v1.0.0-rc.5...v1.0.0-rc.6

Docker images

• GHCR: ghcr.io/paulsengroup/modle:1.0.0-rc.6
• DockerHub: paulsengroup/modle:1.0.0-rc.6

v1.0.0-rc.5

Important

The output produced by MoDLE v1.0.0-rc.5 differs from that of previous versions due to changes to the contact sampling logic.

Changes to CLI interface

• New option: --min-burnin-epochs
• New option: --probability-normalization-factor
• New option: --contact-sampling-interval
• --bin-size has been replaced by --resolution
• --num-loop-contacts-per-sampling-event and --num-tad-ontacts-per-sampling-event have been replaced by --tad-to-loop-contact-ratio
• --ctcf-occupied-probability-of-transition-to-self has been replaced with --extrusion-barrier-bound-stp
• --ctcf-not-occupied-probability-of-transition-to-self has been replaced with --extrusion-barrier-not-bound-stp
• --lef-fraction-for-contact-sampling has been removed. Use --contact-sampling-interval to control the contact sampling rate.

CLI options representing genomic distances now support common suffixes.

Example: --resolution=1kbp, --resolution=1kb and --resolution=1k.

What's Changed

• Various improvements to CLI by @robomics in #12
• Bump dependencies by @robomics in #13
• Bugfix in CLI validation by @robomics in #14
• Various small bugfix and improvements by @robomics in #15
• Make Lef and ExtrusionBarrier (mostly) constexpr by @robomics in #16
• Rework contact sampling by @robomics in #17
• Remove support for using Mersenne Twister as PRNG by @robomics in #19
• Update datasets for unit and integration test by @robomics in #20
• Rework extrusion barriers by @robomics in #18
• Various small bugfixes by @robomics in #27
• Add CI for macOS by @robomics in #28

Full Changelog: v1.0.0-rc.4...v1.0.0-rc.5

Docker images

• GHCR: ghcr.io/paulsengroup/modle:1.0.0-rc.5
• DockerHub: paulsengroup/modle:1.0.0-rc.5

v1.0.0-rc.4

What's Changed

• Hide experimental subcommands by @robomics
• Update Ubuntu CI by @robomics in #11
• Fix clang-8 and gcc-8 builds by @robomics
• Bump CLI11 by @robomics
• Update Dockerfile to run integration tests when using Buildkit by @robomics
• Use Ubuntu 22.04 as base image for the official Docker images by @robomics

Full Changelog: v1.0.0-rc.3...v1.0.0-rc.4

Docker images

• GHCR: ghcr.io/paulsengroup/modle:1.0.0-rc.4
• DockerHub: paulsengroup/modle:1.0.0-rc.4

v1.0.0-rc.3

What's Changed

• Fix build on AppleClang 12 and update README by @robomics in #6
• Bugfix contact registration by @robomics in #7
• Bump dependencies by @robomics in #8
• Add CITATION.cff by @robomics in #9
• Update CI pipeline by @robomics in #10

Full Changelog: v1.0.0-rc.2...v1.0.0-rc.3

Docker images

• GHCR: ghcr.io/paulsengroup/modle:1.0.0-rc.3
• DockerHub: paulsengroup/modle:1.0.0-rc.3

v1.0.0-rc.2

What's Changed

• Fix segfault introduced by 3425928

Full Changelog: v1.0.0-rc.1...v1.0.0-rc.2

Docker images

• GHCR: ghcr.io/paulsengroup/modle:1.0.0-rc.2
• DockerHub: paulsengroup/modle:1.0.0-rc.2

1.0.0-rc.1

First release candidate! 🎉

Docker images

• GHCR: ghcr.io/paulsengroup/modle:1.0.0-rc.1
• DockerHub: paulsengroup/modle:1.0.0-rc.1