Macau-LYXia
commented
10 months ago The latest document about Code has been put in Zenodo( https://zenodo.org/record/8285174). Thanks a lot!
Charles Tapley Hoyt @.***> 于2023年8月28日周一 04:57写道：
Below, I apply the seven point reproducibility review prescribed by Improving reproducibility and reusability in the Journal of Cheminformatics https://doi.org/10.1186/s13321-023-00730-y based on the state of the repository in c0858c8 https://github.com/Macau-LYXia/MVAE-DFDTnet/commit/c0858c8cdf61d62f945fbd74d0d60f2531394287 (accessed on August 27th, 2023).
1.
Does the repository contain a LICENSE file in its root?
No. The GitHub license picker can be used to facilitate adding one by following this link: https://github.com/Macau-LYXia/MVAE-DFDTnet/community/license/new?branch=main. Ideal software licenses for open source software include the MIT License, BSD family of licenses, and other licenses approved by the Open Source Initiative https://opensource.org/licenses. A simple, informative guide for picking a license can be found at https://choosealicense.com. 2.
Does the repository contain a README file in its root?
No. A minimal viable README file contains:
A short, one line description of the project
- Information on how to download, install, and run the code locally
- Brief documentation describing the single most important use case for the repository. For scientific code, this is ideally a one-liner in Python code, a shell script, or a command line interface (CLI) that can be used to reproduce the results of the analysis presented in a corresponding manuscript, use the tool presented in the manuscript, etc.
- Link to an archive on an external system like Zenodo, FigShare, or an equivalent.
- Citation information, e.g., for a pre-print then later for a peer reviewed manuscript
GitHub can be used to create a README file with https://github.com/Macau-LYXia/MVAE-DFDTnet/new/main?filename=README.md. Repositories typically use the Markdown format, which is explained here https://docs.github.com/en/get-started/writing-on-github/getting-started-with-writing-and-formatting-on-github/basic-writing-and-formatting-syntax . 3.
Does the repository contain an associated public issue tracker?
Yes. It is available at https://github.com/Macau-LYXia/MVAE-DFDTnet/issues. 4.
Has the repository been externally archived on Zenodo, FigShare, or an equivalent that is referenced in the README?
No, there is no README. This is also not mentioned in the manuscript. See https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content for a tutorial on how to do this. 5.
Does the README contain installation documentation?
No, there is no README. This is also not mentioned in the manuscript. 6.
Is the code in the repository installable in a straight-forward manner?
No, the code is not laid out in a typical structure, e.g., as described in https://blog.ionelmc.ro/2014/05/25/python-packaging. Further, there is no setup configuration that encodes the dependencies or facilitates reuse of the code. 7.
Does the code in the repository conform to an external linter (e.g., black for Python)?
No. The Python code has not been linted, e.g., using black https://github.com/psf/black. Similarly, the Matlab code has not been linted, e.g. using checkcode https://de.mathworks.com/help/matlab/ref/checkcode.html.
Scientific integrity depends on enabling others to understand the methodology (written as computer code) and reproduce the results generated from it. This reproducibility review reflects steps towards this goal that may be new for some researchers, but will ultimately raise standards across our community and lead to better science.
— Reply to this email directly, view it on GitHub https://github.com/Macau-LYXia/MVAE-DFDTnet/issues/1, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKPICPGME2VQOURJ2UHPIHDXXOYD3ANCNFSM6AAAAAA4ARPVGM . You are receiving this because you are subscribed to this thread.Message ID: @.***>
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夏良永 / Liangyong Xia
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生物医学工程学院 / School of Biomedical Engineering
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cthoyt
Below, I apply the seven point reproducibility review prescribed by Improving reproducibility and reusability in the Journal of Cheminformatics based on the state of the repository in https://github.com/Macau-LYXia/MVAE-DFDTnet/commit/c0858c8cdf61d62f945fbd74d0d60f2531394287 (accessed on August 27th, 2023).
No. The GitHub license picker can be used to facilitate adding one by following this link: https://github.com/Macau-LYXia/MVAE-DFDTnet/community/license/new?branch=main. Ideal software licenses for open source software include the MIT License, BSD family of licenses, and other licenses approved by the Open Source Initiative. A simple, informative guide for picking a license can be found at https://choosealicense.com.
Does the repository contain a README file in its root?
No. A minimal viable README file contains:
GitHub can be used to create a README file with https://github.com/Macau-LYXia/MVAE-DFDTnet/new/main?filename=README.md. Repositories typically use the Markdown format, which is explained here.
Yes. It is available at https://github.com/Macau-LYXia/MVAE-DFDTnet/issues.
No, there is no README. This is also not mentioned in the manuscript. See https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content for a tutorial on how to do this.
No, there is no README. This is also not mentioned in the manuscript.
No, the code is not laid out in a typical structure, e.g., as described in https://blog.ionelmc.ro/2014/05/25/python-packaging. Further, there is no setup configuration that encodes the dependencies or facilitates reuse of the code.
blackfor Python)?No. The Python code has not been linted, e.g., using
black. Similarly, the Matlab code has not been linted, e.g. usingcheckcode.Scientific integrity depends on enabling others to understand the methodology (written as computer code) and reproduce the results generated from it. This reproducibility review reflects steps towards this goal that may be new for some researchers, but will ultimately raise standards across our community and lead to better science.