Dear All (especially Egon and Henry), I'd really like to hear your opinion (in favor or against) adding these WWMM and CML source-code repositories to https://github.com/BlueObelisk.
If you agree that BlueObelisk is a suitable destination, someone (Egon?) would need to add my GitHub account (ostueker) to that GH-organization, so that I can create the repos. If you have concerns about adding this to BlueObelisk, please let me know and I'll simply create a new GH-organization (how about WWMolecularMatrix or ChemicalMarkupLanguage ?). Cheers, Oliver On Sat, Dec 14, 2019 at 2:40 AM Peter Murray-Rust <pm...@cam.ac.uk> wrote: > Many thanks Oliver, > Copying Mark Williamson > > > On Fri, Dec 13, 2019 at 8:01 PM Oliver Stueker <oliver.stue...@mun.ca> > wrote: > >> Dear Henry, Egon and Blue Obelisk team, >> >> > I'd first like to thank Oliver for the several years that he has forked > and maintained JUMBO-converters software in the context of > https://retrievium.com/ . Oliver was on this project which develops > computational chemistry tools and has a CML component. I has used > JUMBO-converters in the past and may do again. > > Oliver is now in Newfoundland, Canada and no longer in chemistry but has > generously offered to help this migration. He knows more about the details > of this than I. > > His JUMBO fork has taken place since my last commits (which will have > been about 2013 - with minor additional features in 2017 (Scala). > > >> Today Peter (Murray-Rust) and I had a conversation about the future of >> the source-code repositories of the WWMM and CML (XML-CML.org) projects. >> > ... > > Makes complete sense. I use only Github at present. > >> >> Peter and I have agreed that we want to transfer all of the repositories >> (which include projects like oscar4, JUMBO, the JUMBO-converters, the CML >> schema and dictionaries) over into a new "Organization" on GitHub which >> would then allow to grant merge privileges or even transfer ownership in >> case a new "Doctor Who" wants to take on development. >> > > Absolutely. I am very happy to hand over to a new Doctor Who - including > Oliver if he wishes - and also to take his current forks if there are no > other developments in the last few years that conflict with Oliver's fork. > >> >> Peter suggested that the "Blue Obelisk" might be a good place for the >> repositories and I see that https://github.com/BlueObelisk already >> exists and contain the code for the Blue Obelisk website and Blue Obelisk >> Data Repository. >> >> > Makes sense - we have suffered from having to migrate at verious times and > keep services running and Github looks like a one-stop shop. > > We would like to get your feedback on a number of points: >> >> - Do you also think that https://github.com/BlueObelisk would be a >> good home for the WWMM and CML repositories? The names wwmm and cml are >> already taken on GitHub.com. >> >> >> I think the names may belong to me and I may have forgotten passwords . > >> >> - >> - With https://github.com/BlueObelisk already containing data, should >> we create "Teams" within the "BlueObelisk-org" to keep things tidy and >> manage access? >> >> I don't think I ised teamns on BB. What is the virtue if the numbers are > small? > >> >> - >> - Should we at some point migrate the xml-cml.org website to be >> hosted directly out of the Git-repository? >> This would allow publishing updates simply by merging Pull Requests. >> Who runs the current website (and manages the xml-cml.org domain)? >> Henry? >> >> I'd be happy to work on migrating the repositories from Bitbucket (hg) to >> GitHub (git) over the holidays and even try using GitHub Actions or >> Travis-CI for building for some select repositories. >> >> What are your thoughts? >> >> Cheers, >> Peter and Oliver >> >> <https://bitbucket.org/blog/sunsetting-mercurial-support-in-bitbucket> >>> >> > >> >>> >>> From 2014 to 2016, our team at Memorial University has expanded the >>> JUMBO-converters as well as a few CML-CompChem dictionaries, however so far >>> we fell short at contributing our changes back to the original projects. >>> >> > Ideally dictionaries shiudl be centrally maintained but I suspect this has > been patchy. > >> >>> Now with the risk of all the work being lost when Bitbucket pulls the >>> plug on Mercurial, it's time to take action. >>> >>> The first course of action from my side will be to create Pull-Requests >>> containing our work done in the JUMBO-converters and xml-cml.org >>> repositories, because it will be much harder to merge them after the >>> Mercurial-repositories have been moved elsewhere or converted to Git. >>> >> > Agreed > >> >>> Next is the question of what will happen to all the Mercurial >>> repositories at https://bitbucket.org/wwmm/ and >>> https://bitbucket.org/cml/ ? >>> >>> - Do all repositories need to be migrated? >>> I think I've counted 50 repositories but I have no idea how many of >>> them contain data that has later-on been combined into other >>> repositories. >>> >>> It depends on the effort. it may be harder to work out what to migrate > than actually to migrate it. But I can try to annotate. > >> >>> - Should they be converted to Git and re-uploaded to BitBucket? >>> As I understand, data about issues and pull-requests will likely get >>> lost during the process. >>> >>> I don't think this matters from my side. I don't think we have many > issues that are active? > >> >>> - Wikis are repositories as well and can/need to be converted from >>> Mercurial to Git as well. >>> It might be possible to export and re-import the issues though. >>> - Maybe move to another hosting site? GitHub? GitLab? >>> Unfortunately https://github.com/wwmm and https://github.com/cml are >>> already taken. >>> >>> >>> I don't have absolute objections to Github (I know some people do) > > >> I'm happy to pitch in and work on migrating *some* of the repositories. >>> >>> As I had been working with Git quite a lot before my work on >>> JUMBO-converters, I have been using the git-remote-gh plugin >>> <https://github.com/felipec/git-remote-hg> the whole time. This allows >>> you to use the Git command line tools to work on hg repositories >>> transparently. >>> >>> > Thank you. > P. > > >> >>> >>> > > -- > "I always retain copyright in my papers, and nothing in any contract I > sign with any publisher will override that fact. You should do the same". > > Peter Murray-Rust > Reader Emeritus in Molecular Informatics > Unilever Centre, Dept. Of Chemistry > University of Cambridge > CB2 1EW, UK > +44-1223-763069 > _______________________________________________ > Blueobelisk-discuss mailing list > Blueobelisk-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss > -- Oliver Stueker, Dr.rer.nat. - Computational Research Consultant Memorial University of Newfoundland - ACENET - Compute Canada Email: supp...@ace-net.ca Web: http://www.ace-net.ca Phone: +1 (709) 864-3021 Office: HH2033
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