and me, of course. BTW Chan Zuckerberg has a CFP to fund bioscience software and maybe the Blue Obelisk could apply. But someone needs to front it - not me, although I'd be happy to be involved.
On Tue, Dec 17, 2019 at 7:30 AM Noel O'Boyle <baoille...@gmail.com> wrote: > Sounds good to me. I'll add your account when at my computer. > > On Tue, 17 Dec 2019, 06:48 Rzepa, Henry S, <h.rz...@imperial.ac.uk> wrote: > >> I am happy for you to go ahead! >> >> Thanks. >> >> Henry Rzepa >> >> On 17 Dec 2019, at 02:04, Oliver Stueker <oliver.stue...@mun.ca> wrote: >> >> >> >> This email from oliver.stue...@mun.ca originates from outside Imperial. >> Do not click on links and attachments unless you recognise the sender. If >> you trust the sender, add them to your safe senders list >> <https://spam.ic.ac.uk/SpamConsole/Senders.aspx> to disable email >> stamping for this address. >> >> >> 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 >> >> _______________________________________________ >> Blueobelisk-discuss mailing list >> Blueobelisk-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss >> > -- "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
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