[PRE REVIEW]: OPTIMUS: a multidimensional global optimization package #7352

editorialbot · 2024-10-14T20:55:24Z

Submitting author: @itsoulos (Ioannis Tsoulos)
Repository: https://github.com/itsoulos/GlobalOptimus/
Branch with paper.md (empty if default branch):
Version: 1.0
Editor: @diehlpk
Reviewers: Pending
Managing EiC: Daniel S. Katz

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/d956fb8adc59fca0b422a43fef85dbf3"><img src="https://joss.theoj.org/papers/d956fb8adc59fca0b422a43fef85dbf3/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/d956fb8adc59fca0b422a43fef85dbf3/status.svg)](https://joss.theoj.org/papers/d956fb8adc59fca0b422a43fef85dbf3)

Author instructions

Thanks for submitting your paper to JOSS @itsoulos. Currently, there isn't a JOSS editor assigned to your paper.

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The text was updated successfully, but these errors were encountered:

editorialbot · 2024-10-14T20:55:26Z

Hello human, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

editorialbot · 2024-10-14T20:55:58Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.39 s (886.4 files/s, 233170.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TeX                             47           4418           2227          40411
C++                            140           3886           3700          24409
C/C++ Header                   134            537           1184           3524
make                             1            183             14           2590
ProGuard                         3             24             13            800
XML                              3              0              3            703
Markdown                         2            142              0            443
Bourne Shell                     4             92            254            236
R                                7             78              0            115
DOS Batch                        1             12             63             46
MATLAB                           1              5            110              2
-------------------------------------------------------------------------------
SUM:                           343           9377           7568          73279
-------------------------------------------------------------------------------

Commit count by author:

   347	Ioannis G. Tsoulos

editorialbot · 2024-10-14T20:56:00Z

⚠️ An error happened when generating the pdf.

editorialbot · 2024-10-14T20:56:02Z

Paper file info:

📄 Wordcount for paper.md is 5353

🔴 Failed to discover a Statement of need section in paper

editorialbot · 2024-10-14T20:56:06Z

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

danielskatz · 2024-10-14T20:57:34Z

👋 @itsoulos - note that your paper does not compile. Please follow the example paper and note that you can click on the error above to find out more about it. Please feel free to make changes to your .md file, then use the command @editorialbot generate pdf to make a new PDF. editorialbot commands need to be the first entry in a new comment.

danielskatz · 2024-10-14T21:00:15Z

👋 @itsoulos - Also, I notice your paper is about 5x as long as a JOSS paper should be. Please see the example paper for this as well, and reduce your paper to be more like the 250-1000 words that JOSS expects. You can possible put a lot of text elsewhere in the repo or docs, and then point to it there. Alternatively, it could be that JOSS is not the right venue for your publication, which would be ok, too, but if so, please tell me so I can mark this submission as withdrawn. You can use the command @editorialbot check repository to check a few things, including the length of the paper

itsoulos · 2024-10-16T03:55:03Z

Dear editor,
We have again upload the paper in the relevant github repository and we have reduced the size to the required one.
Also, in order to compile the GlobalOptimus the used should follow the instructions provided in the README.md
In most unix systems the user should invoke the following commands:

qmake GlobalOptimus.pro
make
Also, we have included msi files for Windows users, where no compilation is required

Best regards,
Ioannis G. Tsoulos
Professor

danielskatz · 2024-10-16T13:31:32Z

@editorialbot generate pdf

@itsoulos - as mentioned above, the next step is to check that the paper compiles, which I am doing, but I asked you to do... I will also do the other step I asked you to do next

danielskatz · 2024-10-16T13:31:39Z

@editorialbot check repository

editorialbot · 2024-10-16T13:32:13Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.39 s (889.9 files/s, 233138.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TeX                             47           4418           2227          40411
C++                            140           3888           3700          24409
C/C++ Header                   134            537           1184           3524
make                             1            183             14           2590
ProGuard                         3             24             13            800
XML                              3              0              3            703
Bourne Shell                     4             92            254            236
Markdown                         2             62              0            155
R                                7             78              0            115
DOS Batch                        1             12             63             46
MATLAB                           1              5            110              2
-------------------------------------------------------------------------------
SUM:                           343           9299           7568          72991
-------------------------------------------------------------------------------

Commit count by author:

   349	Ioannis G. Tsoulos

editorialbot · 2024-10-16T13:32:19Z

Paper file info:

📄 Wordcount for paper.md is 1031

🔴 Failed to discover a Statement of need section in paper

editorialbot · 2024-10-16T13:32:20Z

⚠️ An error happened when generating the pdf.

editorialbot · 2024-10-16T13:32:22Z

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

danielskatz · 2024-10-16T13:33:06Z

👋 @itsoulos - you now need to keep working on the paper until it compiles. The word count is good, however.

itsoulos · 2024-10-16T13:34:46Z

Dear editor,
in order to compile the package you need the QT library as we mention in the git repository. After that, the user should invoke two commands

qmake GlobalOptimus.pro
make

itsoulos · 2024-10-16T13:35:36Z

Sorry, my mistake you mean that the md file can not be compiled?

itsoulos · 2024-10-16T13:41:26Z

We will add a "statement of need" later today.
Best regards

danielskatz · 2024-10-16T14:10:22Z

Sorry, my mistake you mean that the md file can not be compiled?

correct. see the thread above

editorialbot · 2024-10-16T18:17:35Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.38 s (891.5 files/s, 233914.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TeX                             47           4440           2227          40516
C++                            140           3888           3700          24409
C/C++ Header                   134            537           1184           3524
make                             1            183             14           2590
ProGuard                         3             24             13            800
XML                              3              0              3            703
Bourne Shell                     4             92            254            236
Markdown                         2             49              0            180
R                                7             78              0            115
DOS Batch                        1             12             63             46
MATLAB                           1              5            110              2
-------------------------------------------------------------------------------
SUM:                           343           9308           7568          73121
-------------------------------------------------------------------------------

Commit count by author:

   363	Ioannis G. Tsoulos

editorialbot · 2024-10-16T18:17:44Z

Paper file info:

📄 Wordcount for paper.md is 971

✅ The paper includes a Statement of need section

editorialbot · 2024-10-16T18:17:47Z

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

itsoulos · 2024-10-16T18:18:50Z

@editorialbot check repository

editorialbot · 2024-10-16T18:19:25Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.38 s (894.5 files/s, 234702.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TeX                             47           4440           2227          40516
C++                            140           3888           3700          24409
C/C++ Header                   134            537           1184           3524
make                             1            183             14           2590
ProGuard                         3             24             13            800
XML                              3              0              3            703
Bourne Shell                     4             92            254            236
Markdown                         2             49              0            180
R                                7             78              0            115
DOS Batch                        1             12             63             46
MATLAB                           1              5            110              2
-------------------------------------------------------------------------------
SUM:                           343           9308           7568          73121
-------------------------------------------------------------------------------

Commit count by author:

   363	Ioannis G. Tsoulos

editorialbot · 2024-10-16T18:19:30Z

Paper file info:

📄 Wordcount for paper.md is 971

✅ The paper includes a Statement of need section

itsoulos · 2024-10-16T18:23:22Z

@editorialbot check repository

editorialbot · 2024-10-16T18:23:57Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.39 s (882.8 files/s, 231636.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TeX                             47           4440           2227          40516
C++                            140           3888           3700          24409
C/C++ Header                   134            537           1184           3524
make                             1            183             14           2590
ProGuard                         3             24             13            800
XML                              3              0              3            703
Bourne Shell                     4             92            254            236
Markdown                         2             49              0            180
R                                7             78              0            115
DOS Batch                        1             12             63             46
MATLAB                           1              5            110              2
-------------------------------------------------------------------------------
SUM:                           343           9308           7568          73121
-------------------------------------------------------------------------------

Commit count by author:

   364	Ioannis G. Tsoulos

editorialbot · 2024-10-16T18:24:09Z

Paper file info:

📄 Wordcount for paper.md is 971

✅ The paper includes a Statement of need section

editorialbot · 2024-10-16T18:24:12Z

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

itsoulos · 2024-10-16T18:27:13Z

@editorialbot generate pdf

editorialbot · 2024-10-16T18:28:03Z

⚠️ An error happened when generating the pdf.

itsoulos · 2024-10-16T18:31:01Z

@editorialbot check repository

editorialbot · 2024-10-16T18:31:29Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.39 s (881.4 files/s, 231263.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TeX                             47           4440           2227          40516
C++                            140           3888           3700          24409
C/C++ Header                   134            537           1184           3524
make                             1            183             14           2590
ProGuard                         3             24             13            800
XML                              3              0              3            703
Bourne Shell                     4             92            254            236
Markdown                         2             49              0            179
R                                7             78              0            115
DOS Batch                        1             12             63             46
MATLAB                           1              5            110              2
-------------------------------------------------------------------------------
SUM:                           343           9308           7568          73120
-------------------------------------------------------------------------------

Commit count by author:

   365	Ioannis G. Tsoulos

editorialbot · 2024-10-16T18:31:34Z

Paper file info:

📄 Wordcount for paper.md is 967

✅ The paper includes a Statement of need section

editorialbot · 2024-10-16T18:31:37Z

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

itsoulos · 2024-10-16T18:31:46Z

@editorialbot generate pdf

editorialbot · 2024-10-16T18:33:15Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

editorialbot · 2024-10-16T18:33:57Z

Five most similar historical JOSS papers:

Metaheuristics: A Julia Package for Single- and Multi-Objective Optimization
Submitting author: @jmejia8
Handling editor: @vissarion (Active)
Reviewers: @idoby, @PaulDebus
Similarity score: 0.7396

Limbo: A Flexible High-performance Library for Gaussian Processes modeling and Data-Efficient Optimization
Submitting author: @aneoshun
Handling editor: @arfon (Active)
Reviewers: @dfm
Similarity score: 0.7314

pyGOURGS - global optimization of n-ary tree representable problems using uniform random global search
Submitting author: @pySRURGS
Handling editor: @arokem (Retired)
Reviewers: @iljah, @nicoguaro
Similarity score: 0.7269

Optim: A mathematical optimization package for Julia
Submitting author: @anriseth
Handling editor: @labarba (Retired)
Reviewers: @ahwillia
Similarity score: 0.7253

A parallel global multiobjective framework for optimization: pagmo
Submitting author: @bluescarni
Handling editor: @eloisabentivegna (Retired)
Reviewers: @dgoldri25, @jangmys
Similarity score: 0.7223

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

itsoulos · 2024-10-16T18:35:12Z

Dear editor,
I have managed to create the proof!
Is this ok now?

danielskatz · 2024-10-16T19:16:27Z

@itsoulos - yes, though I will also check the references now to make sure those with DOIs do have the DOIs listed

danielskatz · 2024-10-16T19:16:33Z

@editorialbot check references

editorialbot · 2024-10-16T19:17:23Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- None

🟡 SKIP DOIs

- No DOI given, and none found for title: An improved parallel particle swarm optimization
- No DOI given, and none found for title: Optimization by simulated annealing
- No DOI given, and none found for title: Adam: A method for stochastic optimization
- No DOI given, and none found for title: Protein structure prediction by global optimizatio...

❌ MISSING DOIs

- 10.1016/j.cpc.2016.09.006 may be a valid DOI for title: PDoublePop: An implementation of parallel genetic ...
- 10.1016/j.engappai.2020.103479 may be a valid DOI for title: Differential Evolution: A review of more than two ...
- 10.3390/analytics2010002 may be a valid DOI for title: A parallel implementation of the differential evol...
- 10.1016/j.amc.2008.05.005 may be a valid DOI for title: Modifications of real code genetic algorithm for g...
- 10.3390/info13050217 may be a valid DOI for title: Toward an ideal particle swarm optimizer for multi...
- 10.3390/info14020066 may be a valid DOI for title: NeuralMinimizer: A Novel Method for Global Optimiz...
- 10.3390/computation12080158 may be a valid DOI for title: EOFA: An Extended Version of the Optimal Foraging ...
- 10.1007/bf01589118 may be a valid DOI for title: A tolerant algorithm for linearly constrained opti...
- 10.1016/0925-2312(93)90006-o may be a valid DOI for title: Backpropagation and stochastic gradient descent me...
- 10.2307/1267998 may be a valid DOI for title: The Nelder-Mead simplex procedure for function min...
- 10.1007/bf01589116 may be a valid DOI for title: On the limited memory BFGS method for large scale ...
- 10.1007/s10439-007-9317-7 may be a valid DOI for title: Large-scale optimization-based classification mode...
- 10.18576/amis/110602 may be a valid DOI for title: Neural networks optimization through genetic algor...
- 10.1029/91wr02985 may be a valid DOI for title: Effective and efficient global optimization for co...
- 10.3390/su13063208 may be a valid DOI for title: An improved gray wolf optimization algorithm to so...
- 10.1007/978-1-4419-1665-5_9 may be a valid DOI for title: Advanced multi-start methods
- 10.20944/preprints202404.1784.v1 may be a valid DOI for title: Improving the Giant-Armadillo Optimization Method
- 10.1038/s41598-017-18940-4 may be a valid DOI for title: On the efficiency of nature-inspired metaheuristic...
- 10.1016/j.cpc.2008.01.040 may be a valid DOI for title: GenMin: An enhanced genetic algorithm for global o...

❌ INVALID DOIs

- None

danielskatz · 2024-10-16T19:19:35Z

@itsoulos - it looks like a lot of your references might need DOIs. Please add them to the .bib file, e.g. doi={10.1016/j.cpc.2016.09.006}, and then re-run the check references command

itsoulos · 2024-10-16T19:31:16Z

@editorialbot check references

editorialbot · 2024-10-16T19:31:40Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.1016/j.engappai.2020.103479 is OK
- 10.3390/analytics2010002 is OK
- 10.1016/j.amc.2008.05.005 is OK
- 10.3390/info13050217 is OK
- 10.3390/info14020066 is OK
- 10.1007/s42979-023-02227-9 is OK
- 10.1126/science.220.4598.671 is OK
- 10.3390/computation12080158 is OK
- 10.1007/bf01589118 is OK
- 10.1016/0925-2312(93)90006-o is OK
- 10.48550/arXiv.1412.6980 is OK
- 10.2307/1267998 is OK
- 10.1007/bf01589116 is OK
- 10.1007/s10439-007-9317-7 is OK
- 10.18576/amis/110602 is OK
- 10.1073/pnas.96.10.5482 is OK
- 10.1029/91wr02985 is OK
- 10.3390/su13063208 is OK
- 10.1007/978-1-4419-1665-5_9 is OK
- 10.20944/preprints202404.1784.v1 is OK
- 10.1038/s41598-017-18940-4 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

itsoulos · 2024-10-16T19:32:06Z

Dear editor,
I think that they are ok now

Giannis

itsoulos · 2024-10-16T19:38:03Z

@editorialbot generate pdf

editorialbot · 2024-10-16T19:39:40Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

editorialbot · 2024-10-16T19:40:28Z

Five most similar historical JOSS papers:

Metaheuristics: A Julia Package for Single- and Multi-Objective Optimization
Submitting author: @jmejia8
Handling editor: @vissarion (Active)
Reviewers: @idoby, @PaulDebus
Similarity score: 0.7267

pyGOURGS - global optimization of n-ary tree representable problems using uniform random global search
Submitting author: @pySRURGS
Handling editor: @arokem (Retired)
Reviewers: @iljah, @nicoguaro
Similarity score: 0.7158

A parallel global multiobjective framework for optimization: pagmo
Submitting author: @bluescarni
Handling editor: @eloisabentivegna (Retired)
Reviewers: @dgoldri25, @jangmys
Similarity score: 0.7127

Limbo: A Flexible High-performance Library for Gaussian Processes modeling and Data-Efficient Optimization
Submitting author: @aneoshun
Handling editor: @arfon (Active)
Reviewers: @dfm
Similarity score: 0.6994

Optim: A mathematical optimization package for Julia
Submitting author: @anriseth
Handling editor: @labarba (Retired)
Reviewers: @ahwillia
Similarity score: 0.6969

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

danielskatz · 2024-10-16T19:40:35Z

👋 @diehlpk - Would you be able to edit this submission?

danielskatz · 2024-10-16T19:40:45Z

@editorialbot invite @diehlpk as editor

editorialbot · 2024-10-16T19:40:48Z

Invitation to edit this submission sent!

diehlpk · 2024-10-16T20:24:04Z

@editorialbot add @diehlpk as editor

editorialbot · 2024-10-16T20:24:07Z

Assigned! @diehlpk is now the editor

editorialbot added pre-review Track: 7 (CSISM) Computer science, Information Science, and Mathematics labels Oct 14, 2024

editorialbot added C++ Makefile Shell labels Oct 14, 2024

editorialbot assigned diehlpk Oct 16, 2024

[PRE REVIEW]: OPTIMUS: a multidimensional global optimization package #7352

[PRE REVIEW]: OPTIMUS: a multidimensional global optimization package #7352

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