Thanks Geoff,
Absolutely right. and wonderful to know.
I've not been doing much chemistry recently so am out of touch
with cclib, etc. I think Python was less advanced 10 years ago when I wrote
JumboConverters. I would love to do chemistry but haven't found many people
who want to extract
> I write them as a nested lookahead parser, relying on end-of-sections. I
> would now rewrite in Python + a parser like ANTLR which Lezan and I used for
> NLP of phrases in ChemicalTagger. We probably need to have more heuristics
> for blocks of numbers and relate them to presumed atom
On Fri, Jun 25, 2021 at 8:00 PM Oliver Stueker
wrote:
>
> And Peter:
> A big thumbs up for Python. It would really be great to port the
> CML-validator and later even the JUMBO-converters to Python. It was a wise
> decision to encode the "rules" in XML so they can be re-used when
>
On Fri, Jun 25, 2021 at 4:23 PM Egon Willighagen
wrote:
> But if you need CMLXOM or other parts to be published in Maven Central,
>> I'd say go ahead.
>>
>
> Okay, going ahead and will use org.blueoblelisk as Maven groupId
>
GroupId requested: https://issues.sonatype.org/browse/OSSRH-70540
Thanks Noel,
Yes, I used GitHub's import function when I imported the Mercurial repos
from BitBucket. That worked quite well.
Indeed Jekyll is not necessarily needed. However the xml-cml.org pages (as
they exist right now) rely on some server-side-includes to paste common
elements (like headers,
Just to note that importing from Bitbucket is handled by GitHub. Also that
GitHub pages can serve HTML by turning off Jekyll (a process which I'd
recommend).
- Noel
On Fri, 25 Jun 2021, 16:19 Peter Murray-Rust, wrote:
> Oliver and colleagues did a really great job in porting CML code.
>
> It
Oliver and colleagues did a really great job in porting CML code.
It is valuable and will continue to be. Wikidata+CML adds a lot of
potential to semantic chemistry.
We are still continuing to work on (a) plant science and (b) battery
materials , both of which will need a semantic framework.
I
On Fri, Jun 25, 2021 at 3:25 PM Oliver Stueker
wrote:
> Back between Christmas 2019 and the early days of 2020, Mark and I made
> good progress in enabling CI (Travis) on many of the projects.
> At some point I had to stop because I needed to get access to publish
> modules on Maven Central,
Hi Egon and all,
Back between Christmas 2019 and the early days of 2020, Mark and I made
good progress in enabling CI (Travis) on many of the projects.
At some point I had to stop because I needed to get access to publish
modules on Maven Central, which took a few days.
Then 2020 happened.
At
Hi Oliver, Mark, all
On Fri, Dec 13, 2019 at 9:01 PM Oliver Stueker
wrote:
> 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
>
Thanks that's really valuable in stabilising the framework
On Tue, 31 Dec 2019, 14:07 Egon Willighagen,
wrote:
>
> In related news... XOMCML is now distributed as part of Debian
> GNU/Linux!!! https://packages.debian.org/sid/libcmlxom-java
>
> It was a dependency for CDK 2.3, that's why.
>
>
In related news... XOMCML is now distributed as part of Debian GNU/Linux!!!
https://packages.debian.org/sid/libcmlxom-java
It was a dependency for CDK 2.3, that's why.
Egon
On Mon, Dec 30, 2019 at 12:04 PM Peter Murray-Rust wrote:
>
>
> On Sun, Dec 29, 2019 at 10:00 AM Egon Willighagen <
>
On Sun, Dec 29, 2019 at 10:00 AM Egon Willighagen <
egon.willigha...@gmail.com> wrote:
>
> Dear Oliver,
>
>
> BTW2, do we have a critical mass of potential mentor and project ideas to
> propose the Blue Obelisk as mentoring organization?
>
It's a really good idea to have projects that drive the
On Sat, Dec 28, 2019 at 11:38 PM Peter Murray-Rust wrote:
> Many thanks indeed!
> I'll try to scan the import for any gross errors.
>
> Thanks again,
I have summarised the role of almost all repos and they were all useful at
some stage. Some are now obsolete.
I suggest we have a github tool
Thanks everyone,
Yes, maintaining history was always my plan. I have already (locally)
cloned all hg-repositories in question using git-remote-hg (
https://github.com/felipec/git-remote-hg) and have them as git repositories
that contain the whole history.
I've been using git-remote-hg for quite
On Sat, Dec 28, 2019 at 11:38 PM Peter Murray-Rust wrote:
> Many thanks indeed!
> I'll try to scan the import for any gross errors.
>
>
> ** we should discuss this *on the site*, not email. We need a discussion
forum - Github supports blogs. Do we need a general repo to discuss issues?
Until
I made a few small edits :)
Egon
On Sun, Dec 29, 2019 at 4:12 PM Mark Williamson wrote:
>
>
> On 29/12/2019 09:59, Egon Willighagen wrote:
>
> > Within the BlueObelisk-org, I've also created the teams CML and WWMM
> > and assigned the repos to those teams based on their location on
> >
On 29/12/2019 09:59, Egon Willighagen wrote:
Within the BlueObelisk-org, I've also created the teams CML and WWMM
and assigned the repos to those teams based on their location on
Bitbucket.
Could someone with higher privileges than myself within the
BlueObelisk GH-org add
Dear Oliver,
On Sat, Dec 28, 2019 at 11:24 PM Oliver Stueker
wrote:
> Happy Holidays everyone,
>
Same here.
As discussed a couple of weeks ago, I have today imported the 50
> repositories from the WWMM and CML users/teams on Bitbucket into the Blue
> Obelisk GitHub-org
Many thanks indeed!
I'll try to scan the import for any gross errors.
On Sat, Dec 28, 2019 at 10:24 PM Oliver Stueker
wrote:
> Happy Holidays everyone,
>
> As discussed a couple of weeks ago, I have today imported the 50
> repositories from the WWMM and CML users/teams on Bitbucket into the
Happy Holidays everyone,
As discussed a couple of weeks ago, I have today imported the 50
repositories from the WWMM and CML users/teams on Bitbucket into the Blue
Obelisk GitHub-org (https://github.com/BlueObelisk; I apologize for the
flood of emails that I have probably triggered by that).
Many Many thanks Oliver,
If/when we start using the Github repo, suggest we copy any key mails OR
links to to the blue-obelisk discuss list.
It might make sense to see if we could shift blue-obelisk to NumFocus. This
is a non-profit fiscal sponsor who can apply for funding . I have had
dealing
GitHub has an import button that will import directly from a mercurial
repository on BitBucket. I've already done this for some of my projects. It
maintains history.
- Noel
On Tue, 17 Dec 2019 at 08:05, Mark Williamson wrote:
>
>
> On 17/12/2019 02:06, Oliver Stueker wrote:
> > Dear All
On 17/12/2019 02:06, Oliver Stueker wrote:
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.
Hello Oliver,
Sounds fine to me; just make sure that it is
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 wrote:
> Sounds good to me. I'll add your account when
Sounds good to me. I'll add your account when at my computer.
On Tue, 17 Dec 2019, 06:48 Rzepa, Henry S, wrote:
> I am happy for you to go ahead!
>
> Thanks.
>
> Henry Rzepa
>
> On 17 Dec 2019, at 02:04, Oliver Stueker wrote:
>
>
>
> This email from oliver.stue...@mun.ca originates from
I am happy for you to go ahead!
Thanks.
Henry Rzepa
On 17 Dec 2019, at 02:04, Oliver Stueker 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
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
Many thanks Oliver,
Copying Mark Williamson
On Fri, Dec 13, 2019 at 8:01 PM Oliver Stueker
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
I have been on the mailing list for a long time but only have a minor interest,
plus the fact that at 80 I am now slowing down considerably. I think your
suggestion is a good one.
Regards, Brian Duke.
On Fri, Dec 13, 2019 at 04:31:18PM -0330, Oliver Stueker wrote:
> Dear Henry, Egon and Blue
Dear Henry, Egon and Blue Obelisk team,
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. The
repositories in https://bitbucket.org/cml and https://bitbucket.org/wwmm are
all using Mercurial (hg) and as
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