{"action":"created","issue":{"url":"https://api.github.com/repos/opencobra/cobratoolbox/issues/412","repository_url":"https://api.github.com/repos/opencobra/cobratoolbox","labels_url":"https://api.github.com/repos/opencobra/cobratoolbox/issues/412/labels{/name}","comments_url":"https://api.github.com/repos/opencobra/cobratoolbox/issues/412/comments","events_url":"https://api.github.com/repos/opencobra/cobratoolbox/issues/412/events","html_url":"https://github.com/opencobra/cobratoolbox/issues/412","id":226153987,"number":412,"title":"Bug in updateCobraToolbox.m","user":{"login":"acalapez","id":28373467,"avatar_url":"https://avatars2.githubusercontent.com/u/28373467?v=3","gravatar_id":"","url":"https://api.github.com/users/acalapez","html_url":"https://github.com/acalapez","followers_url":"https://api.github.com/users/acalapez/followers","following_url":"https://api.github.com/users/acalapez/following{/other_user}","gists_url":"https://api.github.com/users/acalapez/gists{/gist_id}","starred_url":"https://api.github.com/users/acalapez/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/acalapez/subscriptions","organizations_url":"https://api.github.com/users/acalapez/orgs","repos_url":"https://api.github.com/users/acalapez/repos","events_url":"https://api.github.com/users/acalapez/events{/privacy}","received_events_url":"https://api.github.com/users/acalapez/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":6,"created_at":"2017-05-04T00:57:01Z","updated_at":"2017-05-04T17:53:19Z","closed_at":"2017-05-04T05:42:01Z","body":"In lines 38,39,51,52 of updateCobraToolbox.m should be = instead of ==\r\nThis prevents updating CTB from matlab. Correcting the code makes it work but still can't update because it complains that there are non commit changes.\r\n\r\n**I hereby confirm that I have:**\r\n\r\n- [x] Tried to solve the issue on my own\r\n- [x] Retried to run my code with the latest version of The COBRA Toolbox\r\n- [x] Checked that a similar issue has not already been opened\r\n"},"comment":{"url":"https://api.github.com/repos/opencobra/cobratoolbox/issues/comments/299260899","html_url":"https://github.com/opencobra/cobratoolbox/issues/412#issuecomment-299260899","issue_url":"https://api.github.com/repos/opencobra/cobratoolbox/issues/412","id":299260899,"user":{"login":"rmtfleming","id":2146874,"avatar_url":"https://avatars3.githubusercontent.com/u/2146874?v=3","gravatar_id":"","url":"https://api.github.com/users/rmtfleming","html_url":"https://github.com/rmtfleming","followers_url":"https://api.github.com/users/rmtfleming/followers","following_url":"https://api.github.com/users/rmtfleming/following{/other_user}","gists_url":"https://api.github.com/users/rmtfleming/gists{/gist_id}","starred_url":"https://api.github.com/users/rmtfleming/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rmtfleming/subscriptions","organizations_url":"https://api.github.com/users/rmtfleming/orgs","repos_url":"https://api.github.com/users/rmtfleming/repos","events_url":"https://api.github.com/users/rmtfleming/events{/privacy}","received_events_url":"https://api.github.com/users/rmtfleming/received_events","type":"User","site_admin":false},"created_at":"2017-05-04T17:53:19Z","updated_at":"2017-05-04T17:53:19Z","body":"https://github.com/acalapez is who?\n\nOn 4 May 2017 at 19:49, Ronan M.T. Fleming <ronan.mt.fleming@gmail.com>\nwrote:\n\n> Hi AC,\n>\n> try http://sbml.org/Facilities/Validator/ this with your xml file.\n>\n> Regards,\n>\n> Ronan\n>\n> On 4 May 2017 at 19:01, acalapez <notifications@github.com> wrote:\n>\n>> Hi Ronan\n>>\n>> I'm working primarily with ADMM based optimization. This is a kind of\n>> side-project someone asked me to look into. Still, I'd be happy to get\n>> involved (at least as much as I could fit into my schedule). In the\n>> weekend\n>> I'll take a look at the link you just sent and see how I may contribute.\n>>\n>> Regarding the SMBL issue, I'll try to figure it out. Indeed, I'm\n>> suspecting\n>> some kind of misspecification (or lack of experience with CTB on my\n>> side), and\n>> for this reason I find it premature to post it as an issue. I can still\n>> send the xml and the matlab (2016b) output if you tell me where (or to\n>> whom) to, if I find no way to circumvent the issue.\n>>\n>> I'll keep you posted (or someone else, if you prefer) as to my\n>> availability\n>> to contribute.\n>>\n>> Best regards\n>>\n>> AC\n>>\n>>\n>>\n>>\n>> On Thu, May 4, 2017 at 5:03 PM, Ronan M.T. Fleming <\n>> notifications@github.com\n>> > wrote:\n>>\n>> > Hi AC,\n>> >\n>> > below is a recent request for contributions.\n>> >\n>> > A function very similar to your update cobra toolbox function is also in\n>> > the devel branch at the moment and undergoing testing. We want to make\n>> it\n>> > as easy as possible for people to contribute and get others\n>> contributions.\n>> >\n>> > As for the yeast model io issue, I am not sure. If you are using all of\n>> the\n>> > latest cobra toolbox functions then it could be a bug in our code, or\n>> the\n>> > code for SBML import or it could be due to misspecification of the .xml\n>> > file somehow. We put a lot of effort into updating the io functionality\n>> > with Sarah. If you post here the detailed warnings/errors then we can\n>> look\n>> > at them, but we are not responsible if it is a misspecification of the\n>> .xml\n>> > file.\n>> >\n>> > Regards,\n>> >\n>> > Ronan\n>> >\n>> >\n>> >\n>> > ==================\n>> >\n>> > Dear user and developer of The COBRA Toolbox,\n>> >\n>> > over the last years, the developer community has assembled a\n>> comprehensive\n>> > suite of COBRA methods and algorithms, tutorials, and tests. As the code\n>> > base grew larger in size, the code complexity inevitably increased. In\n>> > order to redress this situation, we launched a significant effort in\n>> > October 2016 to improve the user friendliness and accessibility through\n>> > easy-to-follow tutorials and documentation. We set up a continuous\n>> > integration (CI) server that is testing automatically every change in\n>> the\n>> > code in order to ensure high quality, stable code, and ultimately,\n>> > guarantee reproducibility of results.\n>> >\n>> > The developer community has been very active over the last months.\n>> > Nonetheless, The COBRA Toolbox cannot be turned into a comprehensive\n>> > professional code base for constraint-based reconstruction and analysis\n>> > without the contributions of the community. That is the reason why we\n>> reach\n>> > out to you - help your community grow!\n>> >\n>> > We aim to submit a publication to Nature Protocols by the end of June\n>> 2017\n>> > that will highlight the user friendliness, new features, and improved\n>> > quality of The COBRA Toolbox. In order to overachieve on this goal, we\n>> need\n>> > your support with code contributions, elaborating tutorials, writing\n>> tests\n>> > for existing code, and feedback.\n>> >\n>> > Please note that while MATLAB is used as the main language within The\n>> COBRA\n>> > Toolbox, we already have selectively interfaced to some algorithms in\n>> other\n>> > languages, including perl, python, C, julia and many binaries. We\n>> welcome\n>> > the computational language agnostic, open source development of all\n>> forms\n>> > of COBRA code and welcome support to integrate with complementary tools,\n>> > including within the broader https://opencobra.github.io/community\n>> effort.\n>> >\n>> > You will find instructions on how to contribute on *\n>> > www.github.com/opencobra/\n>> > <http://www.github.com/opencobra/>cobratoolbox*. As The COBRA Toolbox\n>> is\n>> > tracked using the *git* versioning system, you might feel overwhelmed\n>> with\n>> > submitting your contribution as a pull request (PR). The newly released\n>> > *MATLAB.devTools* (*www.github.com/opencobra/\n>> > <http://www.github.com/opencobra/>MATLAB.devTools*) that we developed\n>> > specifically for this project, allows you to easily submit your\n>> > contribution from within MATLAB. We look forward to hearing from you and\n>> > reading your pull request! If you need help, please feel free to post in\n>> > our forum on www.groups.google.com/forum/#!forum/cobra-toolbox\n>> >\n>> > In order to honor your contribution, we will evaluate your\n>> contributions,\n>> > since the publication of the v2 protocol June 2017, based on the\n>> following\n>> > weighted criteria as a guideline:\n>> >\n>> > 25%: Number of contributed tutorials (*.mlx* format) / Total number of\n>> > tutorials\n>> >\n>> > 15%: Number of commits / Total number of commits (square root)\n>> >\n>> > 15%: Number of submitted & merged PRs / Total number of submitted &\n>> merged\n>> > PRs\n>> >\n>> > 15%: Number of support messages on forum & issues / Total number of\n>> support\n>> > messages on forum & issues\n>> >\n>> > 15%: Number of lines added / Total number of lines added\n>> >\n>> > 15%: Number of lines removed / Total number of lines removed\n>> >\n>> > With a significant contribution based on the weighting above, your\n>> > authorship on the publication will be assured. Principal investigators\n>> of\n>> > the most significantly contributing individuals will also be added to\n>> the\n>> > senior authors list, unless they elect otherwise. The order of authors\n>> on\n>> > the publication will be determined based on the contribution guideline.\n>> The\n>> > basis for this decision will be transparently disseminated via\n>> > *www.github.com/opencobra/\n>> > <http://www.github.com/opencobra/>cobratoolbox.* Please note that the\n>> last\n>>\n>> > COBRA Toolbox protocol paper (doi:10.1038/nprot.2011.308) has been\n>> cited in\n>> > excess of 700 times, illustrating the breadth of our community.\n>> >\n>> > Please also note the citation guideline for users of The COBRA Toolbox,\n>> > where we ask people to cite the original paper that first reported a new\n>> > algorithm as well as the appropriate COBRA Toolbox paper, so that we\n>> ensure\n>> > creation and dissemination are both credited.\n>> >\n>> > We are looking forward to your contributions!\n>> >\n>> > Regards,\n>> >\n>> > Dr. Ronan M.T. Fleming,\n>> >\n>> > Lead COBRA Toolbox developer (since December 2015).\n>> >\n>> > ================\n>> >\n>> > On 4 May 2017 at 17:10, acalapez <notifications@github.com> wrote:\n>> >\n>> > > Hi\n>> > >\n>> > > Thank you so much for your reply. I am familiar with git. I have not\n>> made\n>> > > any pull requests because I am not aware of your policies regarding\n>> > > (outside) contributions and didn't want to mess with your work.\n>> > >\n>> > > I did circumvent the issue by writing an \"updateCobraToolboxFix.m\"\n>> > outside\n>> > > the git repository folder (but still on matlab path) and using it to\n>> > > update. There were a few update issues in the development branch but\n>> > since\n>> > > I'm was trying to make a model work with the code in master I didn't\n>> > > recorded them (I can check that during the weekend if you wish).\n>> > >\n>> > > If I may bother you a little more, I am trying to optimize a yeast\n>> > reaction\n>> > > model written in SMBL that was delivered to me \"as is\". I am getting a\n>> > > number of warnings concerning an entry \"sgd\" that supposedly reports\n>> to\n>> > > some data in the EMBL database. I haven't been able to check exactly\n>> what\n>> > > is it but apparently some reactions are left out. I haven't reported\n>> this\n>> > > because I am not sure if it qualifies as a bug. Probably it qualifies\n>> as\n>> > a\n>> > > \"unsupported\" entry. Are you aware of anything like this and if so,\n>> how\n>> > to\n>> > > solve it? (e.g. alternative SMBL readers)\n>> > >\n>> > > Thank you in advance...\n>> > >\n>> > > Looking forward for the new updates\n>> > >\n>> > > AC\n>> > >\n>> > > On Thu, May 4, 2017 at 6:41 AM, Laurent Heirendt <\n>> > notifications@github.com\n>> > > >\n>> > > wrote:\n>> > >\n>> > > > Thanks @acalapez <https://github.com/acalapez> for reporting this.\n>> The\n>> > > > issue with == has already been fixed on the develop branch and will\n>> be\n>> > > > released soon with other fixes.\n>> > > >\n>> > > > The reason the CBT cannot update is because you have made changes -\n>> and\n>> > > > the updateCobraToolbox function does not overwrite these. You can\n>> check\n>> > > > which files have been changed using (from the Terminal):\n>> > > >\n>> > > > $ git status # check the status and lists your files\n>> > > >\n>> > > > and, in more detail:\n>> > > >\n>> > > > $ git status # check the status and lists your files\n>> > > >\n>> > > > If you want to contribute, you need to make changes to your fork and\n>> > > > submit a Pull Request (PR). If you are not too familiar with git,\n>> you\n>> > can\n>> > > > use the MATLAB.devTools <https://github.com/opencobra/\n>> MATLAB.devTools\n>> > >.\n>> > > >\n>> > > > If you however want to update (⚠️ your changes will be lost), you\n>> can\n>> > do\n>> > > > the following from the terminal:\n>> > > >\n>> > > > $ git stash\n>> > > > $ git clean -d -f # changes will be lost!\n>> > > >\n>> > > > I will close the issue now, as the reported bug has already been\n>> fixed.\n>> > > >\n>> > > > —\n>> > > > You are receiving this because you were mentioned.\n>> > > > Reply to this email directly, view it on GitHub\n>> > > > <https://github.com/opencobra/cobratoolbox/issues/412#\n>> > > issuecomment-299100860 <29%2091%2000%20860>>,\n>> > > > or mute the thread\n>> > > > <https://github.com/notifications/unsubscribe-auth/AbDx2-OW84-Vgjd-\n>> > > hZhg67zcBZRK4fLTks5r2WUjgaJpZM4NQH0r>\n>> > > > .\n>> > > >\n>> > >\n>> > > —\n>> > > You are receiving this because you commented.\n>> > > Reply to this email directly, view it on GitHub\n>> > > <https://github.com/opencobra/cobratoolbox/issues/412#\n>> > issuecomment-299214632 <29%2092%2014%20632>>,\n>> > > or mute the thread\n>> > > <https://github.com/notifications/unsubscribe-auth/ACDCOmxnUN1hx-WFI-\n>> > Y7zFa9Ot2mGf0Pks5r2epmgaJpZM4NQH0r>\n>> > > .\n>>\n>> >\n>> > >\n>> >\n>> >\n>> >\n>> > --\n>> > --\n>> > Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.\n>> > ------------------------------------------------------------\n>> > ----------------\n>> > Senior research associate (EN) == Chercheur (FR),\n>> > Principal investigator,\n>> > Systems Biochemistry Group,\n>> > wwwen.uni.lu/lcsb/research/systems_biochemistry\n>> > Luxembourg Centre for Systems Biomedicine,\n>> > University of Luxembourg,\n>> > Campus Belval,\n>> > 6, avenue du Swing,\n>> > L-4367 Belvaux.\n>> > &\n>> > National Centre of Excellence in Research on Parkinson’s disease\n>> > www.parkinson.lu\n>> > &\n>> > Adjunct Assistant Professor,\n>> > Division of Analytical Biosciences,\n>> > Leiden Academic Centre for Drug Research,\n>> > Faculty of Science,\n>> > University of Leiden.\n>> > http://analyticalbiosciences.leidenuniv.nl\n>> > ------------------------------------------------------------\n>> > ----------------\n>> > Mobile: +352 621 175 112 <621%20175%20112> <+352%20621%20175%20112>\n>> > Office: +352 466 644 5528\n>> > Skype: ronan.fleming\n>> > ------------------------------------------------------------\n>> > ----------------\n>> > (This message is confidential and may contain privileged information.\n>> It is\n>> > intended for the named recipient only. If you receive it in error please\n>> > notify me and permanently delete the original message and any copies.)\n>> >\n>> > —\n>> > You are receiving this because you were mentioned.\n>> > Reply to this email directly, view it on GitHub\n>> > <https://github.com/opencobra/cobratoolbox/issues/412#issuec\n>> omment-299231118>,\n>> > or mute the thread\n>> > <https://github.com/notifications/unsubscribe-auth/AbDx2-NYr\n>> kJOnA2YUPjHmSN3k12MIZ4cks5r2fbJgaJpZM4NQH0r>\n>> > .\n>> >\n>>\n>> —\n>> You are receiving this because you commented.\n>> Reply to this email directly, view it on GitHub\n>> <https://github.com/opencobra/cobratoolbox/issues/412#issuecomment-299246938>,\n>> or mute the thread\n>> <https://github.com/notifications/unsubscribe-auth/ACDCOhOKUSqww8rGcR-VRyuVHUmpzClHks5r2gRegaJpZM4NQH0r>\n>> .\n>>\n>\n>\n>\n> --\n> --\n> Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.\n> -----------------------------------------------------------------\n> -----------\n> Senior research associate (EN) == Chercheur (FR),\n> Principal investigator,\n> Systems Biochemistry Group,\n> wwwen.uni.lu/lcsb/research/systems_biochemistry\n> Luxembourg Centre for Systems Biomedicine,\n> University of Luxembourg,\n> Campus Belval,\n> 6, avenue du Swing,\n> L-4367 Belvaux.\n> &\n> National Centre of Excellence in Research on Parkinson’s disease\n> www.parkinson.lu\n> &\n> Adjunct Assistant Professor,\n> Division of Analytical Biosciences,\n> Leiden Academic Centre for Drug Research,\n> Faculty of Science,\n> University of Leiden.\n> http://analyticalbiosciences.leidenuniv.nl\n> -----------------------------------------------------------------\n> -----------\n> Mobile:  +352 621 175 112 <621%20175%20112>\n> Office: +352 466 644 5528\n> Skype: ronan.fleming\n> -----------------------------------------------------------------\n> -----------\n> (This message is confidential and may contain privileged information. It\n> is intended for the named recipient only. If you receive it in error please\n> notify me and permanently delete the original message and any copies.)\n>\n\n\n\n-- \n--\nMr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.\n----------------------------------------------------------------------------\nSenior research associate (EN) == Chercheur (FR),\nPrincipal investigator,\nSystems Biochemistry Group,\nwwwen.uni.lu/lcsb/research/systems_biochemistry\nLuxembourg Centre for Systems Biomedicine,\nUniversity of Luxembourg,\nCampus Belval,\n6, avenue du Swing,\nL-4367 Belvaux.\n&\nNational Centre of Excellence in Research on Parkinson’s disease\nwww.parkinson.lu\n&\nAdjunct Assistant Professor,\nDivision of Analytical Biosciences,\nLeiden Academic Centre for Drug Research,\nFaculty of Science,\nUniversity of Leiden.\nhttp://analyticalbiosciences.leidenuniv.nl\n----------------------------------------------------------------------------\nMobile:  +352 621 175 112\nOffice: +352 466 644 5528\nSkype: ronan.fleming\n----------------------------------------------------------------------------\n(This message is confidential and may contain privileged information. It is\nintended for the named recipient only. If you receive it in error please\nnotify me and permanently delete the original message and any copies.)\n"}}
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