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GonghuaLi / FastMM

FastMM: an ultra-efficient toolbox for constraint-based metabolic modeling
GNU General Public License v3.0
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COBRA Toolbox submodule #1

Open rmtfleming opened 3 years ago

rmtfleming commented 3 years ago

Hi, it would be preferable if this: https://github.com/GonghuaLi/FastMM/tree/d32df20ccfcd462e7e92edb7d6bb02b82b4cc2ee/bin/extern/cobratoolbox-3.0.4_base were a submodule of the cobra toolbox. Thanks. Regards, Ronan

GonghuaLi commented 3 years ago

Hi, it would be preferable if this: https://github.com/GonghuaLi/FastMM/tree/d32df20ccfcd462e7e92edb7d6bb02b82b4cc2ee/bin/extern/cobratoolbox-3.0.4_base were a submodule of the cobra toolbox. Thanks. Regards, Ronan

Hi Ronan, Thanks very much for your suggestion. I will edit this part and use a submodule of cobra toolbox. Best, Gonghua

GonghuaLi commented 3 years ago

Thanks again for this good suggestion.

Now we released FastMM version v1.2 : smallar but more independent.

---1. removed most of cobra functions and just remained miminal functions for FastMM in ./bin/extern/cobra3_submodule.

---2. removed lung_TCGA.txt which is previously for demo.

---3. edited README.md

Best, Gonghua

rmtfleming commented 3 years ago

Hi Gonghua, the idea of a submodule is that it can automatically pull in updates to the cobra toolbox and it maintains a single working copy of the functions. The way you have implemented it achieves neither of those goals. It actually makes the problem of code maintenance worse, because there are now duplicate copies in your repo. Regards, Ronan

On Mon, 8 Feb 2021 at 08:32, Gonghua Li notifications@github.com wrote:

Thanks again for this good suggestion.

Now we released FastMM version v1.2 : smallar but more independent.

---1. removed most of cobra functions and just remained miminal functions for FastMM in ./bin/extern/cobra3_submodule.

---2. removed lung_TCGA.txt which is previously for demo.

---3. edited README.md

Best, Gonghua

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Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.

Assistant Professor, Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University. https://www.universiteitleiden.nl/en/staffmembers/ronan-fleming & H2020 Project Coordinator, Systems Medicine of Mitochondrial Parkinson’s Disease, http://sysmedpd.eu & Senior Lecturer, School of Medicine, National University of Ireland, Galway.

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