Merge devel into master #3165
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Merge devel into master #3165
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`gelu_tf` is equivalent to `gelu`. --------- Signed-off-by: Jinzhe Zeng <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
By default, SpecifierSet doesn't allow prereleases, which is not our expected behavior. Signed-off-by: Jinzhe Zeng <[email protected]>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.1.1 → v0.1.3](astral-sh/ruff-pre-commit@v0.1.1...v0.1.3) - [github.com/psf/black-pre-commit-mirror: 23.10.0 → 23.10.1](psf/black-pre-commit-mirror@23.10.0...23.10.1) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
to be consistent with Pytorch version --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
See https://astral.sh/blog/the-ruff-formatter --------- Signed-off-by: Jinzhe Zeng <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Add theory to documentation. --------- Signed-off-by: Jinzhe Zeng <[email protected]> Signed-off-by: Han Wang <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Han Wang <[email protected]>
…#2975) See https://docs.github.com/en/repositories/releasing-projects-on-github/automatically-generated-release-notes. We shall add proper labels when submitting and merging PRs, so release notes can be more automatic. --------- Signed-off-by: Jinzhe Zeng <[email protected]>
Signed-off-by: Jinzhe Zeng <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.1.3 → v0.1.4](astral-sh/ruff-pre-commit@v0.1.3...v0.1.4) - [github.com/pre-commit/mirrors-clang-format: v17.0.3 → v17.0.4](pre-commit/mirrors-clang-format@v17.0.3...v17.0.4) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Although we set it to `all` by default, one may manually set it via [CMAKE_CUDA_ARCHITECTURES](https://cmake.org/cmake/help/latest/variable/CMAKE_CUDA_ARCHITECTURES.html) or [CUDAARCHS](https://cmake.org/cmake/help/latest/envvar/CUDAARCHS.html#envvar:CUDAARCHS). Signed-off-by: Jinzhe Zeng <[email protected]>
The current implementation used a complex method to ensure `ixnode`
(int) within `[0, nxnodes-1]`, but why not use mod ("%") to get the same
behavior?
---------
Signed-off-by: Jinzhe Zeng <[email protected]>
Bump scikit-build-core from `>=0.5,<0.6` to `>=0.5,<0.7,!=0.6.0`. (by default it will install 0.6.1) Signed-off-by: Jinzhe Zeng <[email protected]>
Preparation for more methods in the `deepmd_utils` package. (`deepmd_cli` is not a good name for this usage) Enable documentation for the `deepmd_utils` package. --------- Signed-off-by: Jinzhe Zeng <[email protected]>
It has been covered by `quick_start.ipynb` or `lammps-command.md`.
TensorFlow 2.15 bumps the CUDA version to 12.2. See tensorflow/tensorflow@3de4416. --------- Signed-off-by: Jinzhe Zeng <[email protected]>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.1.4 → v0.1.5](astral-sh/ruff-pre-commit@v0.1.4...v0.1.5) - [github.com/scop/pre-commit-shfmt: v3.7.0-1 → v3.7.0-2](scop/pre-commit-shfmt@v3.7.0-1...v3.7.0-2) <!--pre-commit.ci end--> --------- Signed-off-by: Jinzhe Zeng <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Jinzhe Zeng <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…ling#2996) Fix deepmodeling#2989. --------- Signed-off-by: Jinzhe Zeng <[email protected]>
Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 5.0.0 to 5.1.0. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/docker/build-push-action/releases">docker/build-push-action's releases</a>.</em></p> <blockquote> <h2>v5.1.0</h2> <ul> <li>Add <code>annotations</code> input by <a href="https://github.com/crazy-max"><code>@crazy-max</code></a> in <a href="https://redirect.github.com/docker/build-push-action/pull/992">docker/build-push-action#992</a></li> <li>Add <code>secret-envs</code> input by <a href="https://github.com/elias-lundgren"><code>@elias-lundgren</code></a> in <a href="https://redirect.github.com/docker/build-push-action/pull/980">docker/build-push-action#980</a></li> <li>Bump <code>@babel/traverse</code> from 7.17.3 to 7.23.2 in <a href="https://redirect.github.com/docker/build-push-action/pull/991">docker/build-push-action#991</a></li> <li>Bump <code>@docker/actions-toolkit</code> from 0.13.0-rc.1 to 0.14.0 in <a href="https://redirect.github.com/docker/build-push-action/pull/990">docker/build-push-action#990</a> <a href="https://redirect.github.com/docker/build-push-action/pull/1006">docker/build-push-action#1006</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/docker/build-push-action/compare/v5.0.0...v5.1.0">https://github.com/docker/build-push-action/compare/v5.0.0...v5.1.0</a></p> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/docker/build-push-action/commit/4a13e500e55cf31b7a5d59a38ab2040ab0f42f56"><code>4a13e50</code></a> Merge pull request <a href="https://redirect.github.com/docker/build-push-action/issues/1006">#1006</a> from docker/dependabot/npm_and_yarn/docker/actions-t...</li> <li><a href="https://github.com/docker/build-push-action/commit/74166686865cdc289a02f214871fb53447b73447"><code>7416668</code></a> chore: update generated content</li> <li><a href="https://github.com/docker/build-push-action/commit/b4f76a5dc6a67282180eddc6d460f23bc97bfcbc"><code>b4f76a5</code></a> chore(deps): Bump <code>@docker/actions-toolkit</code> from 0.13.0 to 0.14.0</li> <li><a href="https://github.com/docker/build-push-action/commit/b7feb766fae338d85274c87a9d0f24c09690dbe2"><code>b7feb76</code></a> Merge pull request <a href="https://redirect.github.com/docker/build-push-action/issues/1005">#1005</a> from crazy-max/ci-inspect</li> <li><a href="https://github.com/docker/build-push-action/commit/fae8018297c67066fff64a6e9c319c86f89b8982"><code>fae8018</code></a> ci: inspect sbom and provenance</li> <li><a href="https://github.com/docker/build-push-action/commit/b625868b13c3feb675cabbf9bfeb52ae94166606"><code>b625868</code></a> Merge pull request <a href="https://redirect.github.com/docker/build-push-action/issues/1004">#1004</a> from crazy-max/ci-update-buildx</li> <li><a href="https://github.com/docker/build-push-action/commit/5193ef1da6ea0d66de97d22817c258b203ade96a"><code>5193ef1</code></a> ci: update buildx to latest</li> <li><a href="https://github.com/docker/build-push-action/commit/d3afd779e409ac26db5374fb27fe4aae9f6adb42"><code>d3afd77</code></a> Merge pull request <a href="https://redirect.github.com/docker/build-push-action/issues/991">#991</a> from docker/dependabot/npm_and_yarn/babel/traverse-7....</li> <li><a href="https://github.com/docker/build-push-action/commit/7a786bb2b9408f7f997564f677248fabd4b886d5"><code>7a786bb</code></a> Merge pull request <a href="https://redirect.github.com/docker/build-push-action/issues/992">#992</a> from crazy-max/annotations</li> <li><a href="https://github.com/docker/build-push-action/commit/c66ae3adcfbf698ecd851c6bb782654a0c6ffcae"><code>c66ae3a</code></a> chore: update generated content</li> <li>Additional commits viewable in <a href="https://github.com/docker/build-push-action/compare/0565240e2d4ab88bba5387d719585280857ece09...4a13e500e55cf31b7a5d59a38ab2040ab0f42f56">compare view</a></li> </ul> </details> <br /> [](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) --- <details> <summary>Dependabot commands and options</summary> <br /> You can trigger Dependabot actions by commenting on this PR: - `@dependabot rebase` will rebase this PR - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it - `@dependabot merge` will merge this PR after your CI passes on it - `@dependabot squash and merge` will squash and merge this PR after your CI passes on it - `@dependabot cancel merge` will cancel a previously requested merge and block automerging - `@dependabot reopen` will reopen this PR if it is closed - `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually - `@dependabot show <dependency name> ignore conditions` will show all of the ignore conditions of the specified dependency - `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself) </details> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Recently I contributed Horovod to conda-forge at conda-forge/staged-recipes#24472. I have tested it with DeePMD-kit. Now the Conda-forge channel has all the features in our deepmodeling channel and even more available platforms. I wonder if we should recommend Conda-forge in favor of our DeepModeling channel and use it for the offline installer. In 2019, Conda-forge lacked support for TensorFlow, so we hosted and built our own channel against the Anaconda channel. But now Conda-forge has become a mature channel and has better support for TensorFlow than the Anaconda channel. Signed-off-by: Jinzhe Zeng <[email protected]>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.1.5 → v0.1.6](astral-sh/ruff-pre-commit@v0.1.5...v0.1.6) - [github.com/pre-commit/mirrors-clang-format: v17.0.4 → v17.0.5](pre-commit/mirrors-clang-format@v17.0.4...v17.0.5) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Signed-off-by: Jinzhe Zeng <[email protected]>
When the probability of a system is smaller than 1e-3, it is shown as `0.000`, which is useless. This commit changes it to the scientific notation, displaying it like `1.547e-06`. --------- Signed-off-by: Jinzhe Zeng <[email protected]> Co-authored-by: Han Wang <[email protected]>
<!--pre-commit.ci start--> updates: - [github.com/scop/pre-commit-shfmt: v3.7.0-3 → v3.7.0-4](scop/pre-commit-shfmt@v3.7.0-3...v3.7.0-4) <!--pre-commit.ci end--> --------- Signed-off-by: Jinzhe Zeng <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Jinzhe Zeng <[email protected]>
Modified the `DPMD_CVT_STR` macro to handle multiple arguments by using `__VA_ARGS__`. This resolves deepmodeling#2952, the error caused by commas in the branch name during compilation. This commit (including the above message) is entirely generated by ChatGPT 3.5. Signed-off-by: Jinzhe Zeng <[email protected]>
<!--pre-commit.ci start--> updates: - [github.com/pre-commit/mirrors-clang-format: v17.0.5 → v17.0.6](pre-commit/mirrors-clang-format@v17.0.5...v17.0.6) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
No breaking changes there Signed-off-by: Jinzhe Zeng <[email protected]>
…ling#3036) Resolves deepmodeling#3027. --------- Signed-off-by: Jinzhe Zeng <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.1.11 → v0.1.13](astral-sh/ruff-pre-commit@v0.1.11...v0.1.13) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…3151) See deepmodeling#3119 --------- Signed-off-by: Jinzhe Zeng <[email protected]>
…g#3148) See deepmodeling#3119 --------- Signed-off-by: Jinzhe Zeng <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
- strict type hint - allow the last dim to be variable (by setting the dim to -1) - remove variable def, which is not very useful. - _derv_c should be defined for each atom --------- Co-authored-by: Han Wang <[email protected]> Co-authored-by: Jinzhe Zeng <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…ng#3145) Remove 18 member functions from `DeepPotBase` and 4 member functions from `DeepTensor`. --------- Signed-off-by: Jinzhe Zeng <[email protected]>
AmberTools24 should be released in April 2024. --------- Signed-off-by: Jinzhe Zeng <[email protected]>
…#3153) To prevent circular import Signed-off-by: Jinzhe Zeng <[email protected]>
Fix deepmodeling#2523 (comment). [`CMAKE_<LANG>_FLAGS`](https://cmake.org/cmake/help/latest/variable/CMAKE_LANG_FLAGS.html#variable:CMAKE_%3CLANG%3E_FLAGS) is a string, so when using `set`, we should use quotes. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Signed-off-by: Jinzhe Zeng <[email protected]>
…g#3159) Follow up deepmodeling#3149. --------- Signed-off-by: Jinzhe Zeng <[email protected]>
This saves the time to load TensorFlow. Signed-off-by: Jinzhe Zeng <[email protected]>
![github-advanced-security[bot]](https://avatars.githubusercontent.com/in/57789?s=60&v=4){kind=small}
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CodeQL found more than 20 potential problems in the proposed changes. Check the Files changed tab for more details.
Codecov ReportAttention:
Additional details and impacted files@@ Coverage Diff @@
## master #3165 +/- ##
==========================================
+ Coverage 75.22% 76.06% +0.84%
==========================================
Files 245 277 +32
Lines 24678 25603 +925
Branches 1599 1591 -8
==========================================
+ Hits 18565 19476 +911
- Misses 5177 5203 +26
+ Partials 936 924 -12 ☔ View full report in Codecov by Sentry. |
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