RAVEN

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fix: disable adding prefix 'M_' and 'R_' in exportModel function

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### Main improvements in this PR: Duplicate of #356, reverting the revert by #359 :) (see explanation there). The changes made in PR are based on the discussion and consensus...

edkerk

help: randomSampling with human-GEM

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Hello everyone! I tried to perform random sampling on a model generated by tINIT from the human1 model but the program appears to be hung. I set the show Progress...

manas-kohli

feat: importYaml and exportYaml functions

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### Description of the issue: Adapt https://github.com/SysBioChalmers/Human-GEM/pull/392 for native support in RAVEN. #### System information * Please report: 1. RAVEN version (stabile [release](https://github.com/SysBioChalmers/RAVEN/releases), `devel` branch?) 2. Operating system (Windows/Mac/Linux; include...

edkerk

refactor: remove prefix 'M_' and 'R_' in exprotModel/importModel functions

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### Description of the issue: * Prefixes `M_` and `R_` are added by `exprotModel` function while exporting, and removed by `importModel` while importing. This was initially designed to [follow](https://github.com/SysBioChalmers/RAVEN/blob/17df2147f604951705bdb2fbfcf12dac913a491e/io/importModel.m#L71) the...

haowang-bioinfo

The `testing/unit_tests` folder now already includes tests for many functions (as of 5a65fe0455ac41e6cab4826981cf268a4127f057). Ideally this should cover all functions (`*.m` files, except from those in the `legacy` and `software` folders)....

edkerk

Excel I/O problems using MATLAB 2017b and later

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**Edit: a workaround for this problem is provided, see: https://github.com/SysBioChalmers/RAVEN/issues/55#issuecomment-478980100** Attempting to import an Excel model (.xlsx) using the command "importExcelModel" results in the following error: Error using importExcelModel (line...

danieljcook

support for export to cobrapy-compatible yaml format

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RAVEN should support writing a [cobrapy](http://cobrapy.readthedocs.io/en/latest/_autogen/cobra.io.yaml.html)-compatible yaml format, as this format is very concise. - [x] make `writeYaml` function that writes a text file, and parses through the model structure....

edkerk

bug: predictLocalization error when using DeepLoc results

10

### Description of the issue: Hello, I am trying to incorporate location for my reactions. But I getting following error: Please find attached location file with my model. [predict_location_juv.txt](https://github.com/SysBioChalmers/RAVEN/files/4977738/predict_location_juv.txt) [juvenile_model_ori_gpr.xlsx](https://github.com/SysBioChalmers/RAVEN/files/4977749/juvenile_model_ori_gpr.xlsx)...

SPD20

feat: add a delta G field for reactions/metabolites

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### Description of the issue: * It would be great if delta G field can be added for each reaction/metabolite * Metacyc offers this information at pH 7.3 and ionic...

feiranl

doc: update contribution guidelines

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### Description of the issue: Leveraging on the work done for [`yeast-GEM`](https://github.com/SysBioChalmers/yeast-GEM/pull/175), the contribution guidelines should be updated, to clarify the following: - [ ] when major, minor and patch...

edkerk