sync torsion tree update from nashtools #43
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
caic99
approved these changes
Sep 26, 2023
zhengh96
pushed a commit
that referenced
this pull request
Feb 29, 2024
* get template parameter * add small size template mode * add small config template * success run template docking * add large medium extra_large template * fix missing template parameter * fix template parameter error * adjust ExtraLarge template parameter * update Version number to 1.1.0 * success run template mode docking * Add GPU model support policy * feat: remove template code * create issue templates (#18) * create issue templates * Create CONTRIBUTING.md * refactor of unidock_tools (#19) * unidock tools 2 * unidock and mcdock runner * fix unidock pipeline runner * fix mcdock * main entry * fix savedir name * feat:pdb2pdbqt and ligprep module * build:use toml * fix toml * fix: package data * fix: toml package data * (feat):Update time measurement in vina.h * refactor unidock tools cicd workflow (#25) * refactor:ut by module * rm old ut * refactor:use pytest syntex for ut * fix:ut * fix static type * fix static type 2 * fix static type 3 * build:base env dockerfile * feat:add application e2e tests * fix:e2e tests * fix:app test read score * fix:app test * build:update unidocktools ci * test:update tools ci trigger condition * build:fix tool yaml * build:fix ci yaml variable * build:fix build ninja dep * build:fix ninja dep * test: ut unidock input change to 1iep * test: skip ad4 test * build:change push image condition * feat(unidock):add energy_range arg * build:downgrade docker login action * build:reupdate docker login action * build:dockerhub token * build:add checkout * build:change docker login action version * build:change docker login action version 2 * build:docker login action 3 * build:docker build job * build image workflow trigger after push * style:pyright check * build:fix toml pyright setting --------- Co-authored-by: Yuan Yannan <[email protected]> * rename dockerfile name * Update unidock/CMakeLists.txt * Feature:Refactor docking process and remove unnecessary code * Found a situation where the program hang without printf * Create dependabot.yml * Add instructions to build a docker image for unidock * format cdpkit dockerfile * use CDPKit from release * set default cuda version * Bump actions/setup-python from 3 to 5 Bumps [actions/setup-python](https://github.com/actions/setup-python) from 3 to 5. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v3...v5) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> * Bump docker/build-push-action from 2 to 5 Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 2 to 5. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](docker/build-push-action@v2...v5) --- updated-dependencies: - dependency-name: docker/build-push-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> * Bump docker/login-action from 1 to 3 Bumps [docker/login-action](https://github.com/docker/login-action) from 1 to 3. - [Release notes](https://github.com/docker/login-action/releases) - [Commits](docker/login-action@v1...v3) --- updated-dependencies: - dependency-name: docker/login-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> * Bump actions/checkout from 2 to 4 Bumps [actions/checkout](https://github.com/actions/checkout) from 2 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v2...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> * build:unidock_tools image base on unidock image * flatten folder structure * Update CUDA device synchronization and CUDA architectures * Remove cudaMalloc output * Delete test data files * Update MAX_NUM_OF_RIGID and MAX_NUM_OF_ATOMS constants * Update MAX_NUM_OF_ATOMS_ constant values * Update CI workflows and add benchmark (#32) * Refactor Docker image building workflow * remove outdated actions * add benchmark workflow * download test dataset * fix requirements * upload test result in benchmark * build:fix bm test vs result * fix missing path for python scripts --------- Co-authored-by: Yuan Yannan <[email protected]> * update issue template for bug report (#34) * fix:tool dockerfile * Set `wget --quiet` in Dockerfile * Update MAX_NUM_OF_LIG_TORSION and MAX_NUM_OF_ATOMS constants * Update MAX_NUM_OF_ATOMS_ constant values * Update kernel.h * doc: update unidock_tools README (#42) * doc:tool readme 1 * update unidocktools readme * update readme --------- Co-authored-by: Yuan Yannan <[email protected]> * Update Readme Files (#41) * Update readme files * Update README.md * Unify the spelling * Prompt source code access * Update deepmodeling badge * re-organize paragraphs * Remove unidock-tools subtitles --------- Co-authored-by: Yuan Yannan <[email protected]> * doc:update unidock new bm test result images (#43) * Add unit test case (#40) * Add Catch2 unit test * Fix unit test * Add git support in Dockerfile * Add git in CI basic packages * Fix file path in parse_pdqt_test.cpp * Update CMakeLists.txt to link unit_tests with lib and cuda --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: ysy <[email protected]> Co-authored-by: dp-yuanyn <[email protected]> Co-authored-by: Yuan Yannan <[email protected]> Co-authored-by: YANG SHAOYI <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.