Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

cc: refactor DeepPot to support multiple backends #3142

Merged
merged 5 commits into from
Jan 15, 2024

Conversation

njzjz
Copy link
Member

@njzjz njzjz commented Jan 13, 2024

See #3119.
At this time, only TF is supported in such the multiple-backend framework.

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Copy link

codecov bot commented Jan 13, 2024

Codecov Report

Attention: 87 lines in your changes are missing coverage. Please review.

Comparison is base (ae90498) 76.18% compared to head (0a52f7f) 76.24%.
Report is 1 commits behind head on devel.

Files Patch % Lines
source/api_cc/src/DeepPotTF.cc 78.62% 56 Missing and 25 partials ⚠️
source/api_cc/src/DeepPot.cc 76.00% 5 Missing and 1 partial ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##            devel    #3142      +/-   ##
==========================================
+ Coverage   76.18%   76.24%   +0.05%     
==========================================
  Files         252      269      +17     
  Lines       25374    25516     +142     
  Branches     1579     1583       +4     
==========================================
+ Hits        19332    19455     +123     
- Misses       5117     5134      +17     
- Partials      925      927       +2     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

Copy link

@github-advanced-security github-advanced-security bot left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

CodeQL found more than 20 potential problems in the proposed changes. Check the Files changed tab for more details.

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
See https://stackoverflow.com/a/13444839/9567349

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
source/api_cc/include/DeepPotTF.h Fixed Show fixed Hide fixed
nlist_data.make_inlist(nlist);
}
if (dtype == tensorflow::DT_DOUBLE) {
int ret = session_input_tensors<double>(

Check notice

Code scanning / CodeQL

Unused local variable

Variable ret is not used.
run_model<double>(dener, dforce_, dvirial, session, input_tensors, atommap,
nframes, nghost);
} else {
int ret = session_input_tensors<float>(

Check notice

Code scanning / CodeQL

Unused local variable

Variable ret is not used.
std::vector<std::pair<std::string, Tensor>> input_tensors;

if (dtype == tensorflow::DT_DOUBLE) {
int nloc = session_input_tensors_mixed_type<double>(

Check notice

Code scanning / CodeQL

Unused local variable

Variable nloc is not used.
run_model<double>(dener, dforce_, dvirial, datom_energy_, datom_virial_,
session, input_tensors, atommap, nframes);
} else {
int nloc = session_input_tensors_mixed_type<float>(

Check notice

Code scanning / CodeQL

Unused local variable

Variable nloc is not used.
run_model<double>(dener, dforce_, dvirial, datom_energy_, datom_virial_,
session, input_tensors, atommap, nframes);
} else {
int nloc = session_input_tensors_mixed_type<float>(

Check notice

Code scanning / CodeQL

Declaration hides variable

Variable nloc hides another variable of the same name (on [line 1153](1)).
source/api_cc/src/DeepPotTF.cc Fixed Show fixed Hide fixed
source/api_cc/src/DeepPotTF.cc Fixed Show fixed Hide fixed
std::vector<std::pair<std::string, Tensor>> input_tensors;

if (dtype == tensorflow::DT_DOUBLE) {
int ret = session_input_tensors<double>(input_tensors, dcoord_, ntypes,

Check notice

Code scanning / CodeQL

Unused local variable

Variable ret is not used.
run_model<double>(dener, dforce_, dvirial, datom_energy_, datom_virial_,
session, input_tensors, atommap, nframes);
} else {
int ret = session_input_tensors<float>(input_tensors, dcoord_, ntypes,

Check notice

Code scanning / CodeQL

Unused local variable

Variable ret is not used.
@njzjz
Copy link
Member Author

njzjz commented Jan 13, 2024

@CodiumAI-Agent /review --pr_reviewer.inline_code_comments=true

@CodiumAI-Agent
Copy link
Contributor

CodiumAI-Agent commented Jan 13, 2024

PR Analysis

(review updated until commit 5903415)

  • 🎯 Main theme: Refactoring the DeepPot module to support multiple backends
  • 📝 PR summary: This PR is a refactoring effort to allow the DeepPot module to support multiple backends. At the moment, only TensorFlow is supported, but the changes lay the groundwork for adding support for other backends like PyTorch and Paddle in the future.
  • 📌 Type of PR: Enhancement
  • 🧪 Relevant tests added: No
  • ⏱️ Estimated effort to review [1-5]: 4, because the PR involves refactoring of a core module and addition of new files. It requires a deep understanding of the existing codebase and the changes made.
  • 🔒 Security concerns: No security concerns found

PR Feedback

💡 General suggestions: The PR seems to be a significant refactoring effort. It would be beneficial to include more detailed comments explaining the changes and their implications. Also, it would be helpful to add tests to ensure that the refactoring does not break existing functionality.


✨ Usage guide:

Overview:
The review tool scans the PR code changes, and generates a PR review. The tool can be triggered automatically every time a new PR is opened, or can be invoked manually by commenting on any PR.
When commenting, to edit configurations related to the review tool (pr_reviewer section), use the following template:

/review --pr_reviewer.some_config1=... --pr_reviewer.some_config2=...

With a configuration file, use the following template:

[pr_reviewer]
some_config1=...
some_config2=...
Utilizing extra instructions

The review tool can be configured with extra instructions, which can be used to guide the model to a feedback tailored to the needs of your project.

Be specific, clear, and concise in the instructions. With extra instructions, you are the prompter. Specify the relevant sub-tool, and the relevant aspects of the PR that you want to emphasize.

Examples for extra instructions:

[pr_reviewer] # /review #
extra_instructions="""
In the code feedback section, emphasize the following:
- Does the code logic cover relevant edge cases?
- Is the code logic clear and easy to understand?
- Is the code logic efficient?
...
"""

Use triple quotes to write multi-line instructions. Use bullet points to make the instructions more readable.

How to enable\disable automation
  • When you first install PR-Agent app, the default mode for the review tool is:
pr_commands = ["/review", ...]

meaning the review tool will run automatically on every PR, with the default configuration.
Edit this field to enable/disable the tool, or to change the used configurations

About the 'Code feedback' section

The review tool provides several type of feedbacks, one of them is code suggestions.
If you are interested only in the code suggestions, it is recommended to use the improve feature instead, since it dedicated only to code suggestions, and usually gives better results.
Use the review tool if you want to get a more comprehensive feedback, which includes code suggestions as well.

Auto-labels

The review tool can auto-generate two specific types of labels for a PR:

  • a possible security issue label, that detects possible security issues (enable_review_labels_security flag)
  • a Review effort [1-5]: x label, where x is the estimated effort to review the PR (enable_review_labels_effort flag)
Extra sub-tools

The review tool provides a collection of possible feedbacks about a PR.
It is recommended to review the possible options, and choose the ones relevant for your use case.
Some of the feature that are disabled by default are quite useful, and should be considered for enabling. For example:
require_score_review, require_soc2_review, enable_review_labels_effort, and more.

More PR-Agent commands

To invoke the PR-Agent, add a comment using one of the following commands:

  • /review: Request a review of your Pull Request.
  • /describe: Update the PR title and description based on the contents of the PR.
  • /improve [--extended]: Suggest code improvements. Extended mode provides a higher quality feedback.
  • /ask <QUESTION>: Ask a question about the PR.
  • /update_changelog: Update the changelog based on the PR's contents.
  • /add_docs 💎: Generate docstring for new components introduced in the PR.
  • /generate_labels 💎: Generate labels for the PR based on the PR's contents.
  • /analyze 💎: Automatically analyzes the PR, and presents changes walkthrough for each component.

See the tools guide for more details.
To list the possible configuration parameters, add a /config comment.

See the review usage page for a comprehensive guide on using this tool.

@CodiumAI-Agent
Copy link
Contributor

Persistent review updated to latest commit 5903415

@wanghan-iapcm wanghan-iapcm merged commit e218f9c into deepmodeling:devel Jan 15, 2024
46 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
Projects
None yet
Development

Successfully merging this pull request may close these issues.

3 participants