Recent Releases of modle
modle - v1.1.0
Changes to CLI interface
- Add subcommand
annotate-barrierstomodle_tools
What's Changed
- Improve text file parsing by @robomics in https://github.com/paulsengroup/modle/pull/107
- Add modle_tools annotate-barriers by @robomics in https://github.com/paulsengroup/modle/pull/109
- Bump deps by @robomics in https://github.com/paulsengroup/modle/pull/113 https://github.com/paulsengroup/modle/pull/114
Bugfix
- Bugfix by @robomics in https://github.com/paulsengroup/modle/pull/115
- Fix logic used to generate MoDLE version string from git metadata by @robomics in https://github.com/paulsengroup/modle/pull/111
Full Changelog: https://github.com/paulsengroup/modle/compare/v1.0.1...v1.1.0
Docker images
- GHCR: ghcr.io/paulsengroup/modle:1.1.0
- DockerHub: paulsengroup/modle:1.1.0
Checksums (SHA256)
sha256
52da81d4365ef7889945f863743c177b8d2f41c3dcbfcd8f1f4c19a9cbccf52a modle-1.1.0-x86_64-linux.tar.xz
fc96ec3f6c494b0de2bd6936d61ee87a364e3932fe2476cd94739ebb4c4f4567 modle-1.1.0.zip
f1bfd2c98ff131d555bc1504fab5c86f35521e51da87d5f66435c145e11a26e3 modle-1.1.0.tar.gz
- C++
Published by robomics over 2 years ago
modle - 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-positionis now true by default
What's Changed
- Bump deps by @robomics in https://github.com/paulsengroup/modle/pull/88 https://github.com/paulsengroup/modle/pull/92 https://github.com/paulsengroup/modle/pull/96 https://github.com/paulsengroup/modle/pull/98
- Migrate to Conan v2 by @robomics in https://github.com/paulsengroup/modle/pull/90
- Build Docker images for
platform=linux/arm64by @robomics in https://github.com/paulsengroup/modle/pull/89 https://github.com/paulsengroup/modle/pull/97 - Add CI for macos-13 by @robomics in https://github.com/paulsengroup/modle/pull/99
- Improvements to simulation scheduling by @robomics in https://github.com/paulsengroup/modle/pull/95
- Make formatting of log/error messages more consistent by @robomics in https://github.com/paulsengroup/modle/pull/101
- Update CLI by @robomics in https://github.com/paulsengroup/modle/pull/100
- Update parser for BED and .chrom.sizes files to support files enclosing strings using quotes by @robomics in https://github.com/paulsengroup/modle/pull/106
Bugfix
- Fix incorrect handling of
--target-number-of-epochsby @robomics in https://github.com/paulsengroup/modle/pull/91
Full Changelog: https://github.com/paulsengroup/modle/compare/v1.0.0...v1.0.1
Docker images
- GHCR: ghcr.io/paulsengroup/modle:1.0.1
- DockerHub: paulsengroup/modle:1.0.1
Checksums (SHA256)
sha256
ca752f97ebf184701cf683dbd148988ad33815303e9ea4c36fb281e4aba4a592 modle-1.0.1-x86_64-linux.tar.xz
ec665ad19576c045fff445aa8cfac2a2bd4a6b7f2f022c0d617231d6dad09388 modle-1.0.1.zip
66135d77127abac89fae1309346decd179a96ba512ded58dbdc3a8c802ca87f7 modle-1.0.1.tar.gz
- C++
Published by robomics almost 3 years ago
modle - v1.0.0 - First stable release!
First stable release! :partyingface: :partyingface:
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 perturbateandmodle replay
What's Changed
- Bump dependencies by @robomics in https://github.com/paulsengroup/modle/pull/50 https://github.com/paulsengroup/modle/pull/61 https://github.com/paulsengroup/modle/pull/62 https://github.com/paulsengroup/modle/pull/67
- Update Dockerfile by @robomics in https://github.com/paulsengroup/modle/pull/51
- Update CI by @robomics in https://github.com/paulsengroup/modle/pull/53 https://github.com/paulsengroup/modle/pull/54 https://github.com/paulsengroup/modle/pull/59 https://github.com/paulsengroup/modle/pull/60 https://github.com/paulsengroup/modle/pull/68 https://github.com/paulsengroup/modle/pull/69
- Add GHA workflow to build portable Linux binaries by @robomics in https://github.com/paulsengroup/modle/pull/55
- Fix bugs in modle_tools (#46, #47) by @robomics in https://github.com/paulsengroup/modle/pull/56
- Remove unused subcommands by @robomics in https://github.com/paulsengroup/modle/pull/57
- Use coolerpp for Cooler IO by @robomics in https://github.com/paulsengroup/modle/pull/58
- Update test suites by @robomics in https://github.com/paulsengroup/modle/pull/64
- Enable LTO by default by @robomics in https://github.com/paulsengroup/modle/pull/65
- Remove support for
-DBUILD_SHARED_LIBS=ONby @robomics in https://github.com/paulsengroup/modle/pull/66 - Update test dataset by @robomics in https://github.com/paulsengroup/modle/pull/71
- Update integration test scripts by @robomics in https://github.com/paulsengroup/modle/pull/74
- Fix
generated-byattr by @robomics in https://github.com/paulsengroup/modle/pull/79 - Fix broken error message by @robomics in https://github.com/paulsengroup/modle/pull/80
- Add
--assembly-nameCLI option to modle by @robomics in https://github.com/paulsengroup/modle/pull/81 - Add missing SPDX headers [no ci] by @robomics in https://github.com/paulsengroup/modle/pull/84
- Update README by @robomics in https://github.com/paulsengroup/modle/pull/85
Full Changelog: https://github.com/paulsengroup/modle/compare/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)
sha256
df4a73d60a8b8518a6189cc164103cea139c4f6c828f7f1393acc6ff06836b3f modle-1.0.0-x86_64-linux.tar.xz
5ac837be47c28c027a5a5c05ab7b365ae86c9080ca562ac910aabaab0d08ec0a modle-1.0.0.zip
dd9ea8c08f3c5c7acc00996b8dde96bd321805f8a3f070f9a22f5be9d7240e5b modle-1.0.0.tar.gz
- C++
Published by robomics about 3 years ago
modle - 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 https://github.com/paulsengroup/modle/pull/31
- Bump dependencies. Let Conan manage thread-pool and xoshiro by @robomics in https://github.com/paulsengroup/modle/pull/34
- Various small bugfixes by @robomics in https://github.com/paulsengroup/modle/pull/35
- Extend contact matrix class by @robomics in https://github.com/paulsengroup/modle/pull/33
- Update README by @robomics in https://github.com/paulsengroup/modle/pull/39
- Update integration test by @robomics in https://github.com/paulsengroup/modle/pull/38
- Bugfix for modle_tools by @robomics in https://github.com/paulsengroup/modle/pull/41
- Bump dependencies by @robomics in https://github.com/paulsengroup/modle/pull/42
- Update bigwig-related code by @robomics in https://github.com/paulsengroup/modle/pull/43
- Make puu tunable for each individual barrier by @robomics in https://github.com/paulsengroup/modle/pull/45
- Track LEF positions in 1D space by @robomics in https://github.com/paulsengroup/modle/pull/44
Full Changelog: https://github.com/paulsengroup/modle/compare/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
- C++
Published by robomics over 3 years ago
modle - 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: https://github.com/paulsengroup/modle/compare/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
- C++
Published by robomics over 3 years ago
modle - 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-sizehas been replaced by--resolution--num-loop-contacts-per-sampling-eventand--num-tad-ontacts-per-sampling-eventhave been replaced by--tad-to-loop-contact-ratio--ctcf-occupied-probability-of-transition-to-selfhas been replaced with--extrusion-barrier-bound-stp-
--ctcf-not-occupied-probability-of-transition-to-selfhas been replaced with--extrusion-barrier-not-bound-stp --lef-fraction-for-contact-samplinghas been removed. Use--contact-sampling-intervalto 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 https://github.com/paulsengroup/modle/pull/12
- Bump dependencies by @robomics in https://github.com/paulsengroup/modle/pull/13
- Bugfix in CLI validation by @robomics in https://github.com/paulsengroup/modle/pull/14
- Various small bugfix and improvements by @robomics in https://github.com/paulsengroup/modle/pull/15
- Make Lef and ExtrusionBarrier (mostly) constexpr by @robomics in https://github.com/paulsengroup/modle/pull/16
- Rework contact sampling by @robomics in https://github.com/paulsengroup/modle/pull/17
- Remove support for using Mersenne Twister as PRNG by @robomics in https://github.com/paulsengroup/modle/pull/19
- Update datasets for unit and integration test by @robomics in https://github.com/paulsengroup/modle/pull/20
- Rework extrusion barriers by @robomics in https://github.com/paulsengroup/modle/pull/18
- Various small bugfixes by @robomics in https://github.com/paulsengroup/modle/pull/27
- Add CI for macOS by @robomics in https://github.com/paulsengroup/modle/pull/28
Full Changelog: https://github.com/paulsengroup/modle/compare/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
- C++
Published by robomics over 3 years ago
modle - v1.0.0-rc.4
What's Changed
- Hide experimental subcommands by @robomics
- Update Ubuntu CI by @robomics in https://github.com/paulsengroup/modle/pull/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: https://github.com/paulsengroup/modle/compare/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
- C++
Published by robomics almost 4 years ago
modle - v1.0.0-rc.3
What's Changed
- Fix build on AppleClang 12 and update README by @robomics in https://github.com/paulsengroup/modle/pull/6
- Bugfix contact registration by @robomics in https://github.com/paulsengroup/modle/pull/7
- Bump dependencies by @robomics in https://github.com/paulsengroup/modle/pull/8
- Add CITATION.cff by @robomics in https://github.com/paulsengroup/modle/pull/9
- Update CI pipeline by @robomics in https://github.com/paulsengroup/modle/pull/10
Full Changelog: https://github.com/paulsengroup/modle/compare/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
- C++
Published by robomics almost 4 years ago
modle - v1.0.0-rc.2
What's Changed
- Fix segfault introduced by 3425928
Full Changelog: https://github.com/paulsengroup/modle/compare/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
- C++
Published by robomics almost 4 years ago
modle - 1.0.0-rc.1
First release candidate! :tada:
Docker images
- GHCR: ghcr.io/paulsengroup/modle:1.0.0-rc.1
- DockerHub: paulsengroup/modle:1.0.0-rc.1
- C++
Published by robomics almost 4 years ago