Re: good practices in science
Hello— Thank you all the useful comments. I believe that these tips can really help me with my further career. Even as this list's purpose is not to ask personal advice, I am happy that I did ask here. Strangly, I could not get this insight by talking about it with collegues, friends and family (I tried). A main message I got here is that even if things look grim (concerning technology), there are good initatives and people that are improving the situation, or at the very least that there are opportunities out there that can make one's personal and career situation better. Best, take care, —Marco
good practices in science
Hi all— Are there any natural scientists here? I'm asking because at least in my field not the right tools are used to do the work; I'd like to exchange ideas on how to approach these issues. I am sending this to this list because Guix is an obvious tool for scientific (and other) computing. None of my collegues anywhere in the world have heard of it and they are not interested when I mention it. (Furthermore, brendyyn on #guix suggested this list.) Invasion of privacy has been growing over the years, and getting a spurt during the COVID-19 pandemic (maybe not unlike 9/11). Examples include that here at the university we are expected to use Zoom and Skype, and this was a good moment to push through Microsoft Teams (as a "good replacement for mail"). These are all tools that are not open spec, free software or federated. Very few of my collegues care, and those that do have the opinion (or understanding) that it is too late to do something about it. At the University of Bergen it is expected that we install and use proprietary software on our home network (e.g. MS Teams, Skype and Zoom – two of these run luckily in Chromium). Except for the integrity of our scientific results, our privacy and general home security is affected. We have to find ways to mitigate the situation (e.g. laptop dedicated to all the crap on a special subnet). But, in my opinion, such mitigations should not even be necessary in the first place. Especially in an environment of learning and research things should be really different. There are related, even worse, issues outside of academia, like the proprietary COVID-19 tracking apps that several countries are building, mostly independently because "we cannot trust another country's app" (which would be moot point if ...). Discussion of these wider issues would warant a forked or separate thread (or perhaps a different mailinglist). I think it's all connected, but now I'd like to focus on free software and science. When I do science (the ordering and creation of concepts, models, hypotheses and theories; through thinking, programming, simulating, evaluating, discussing and writing), I have a way of working that I think is efficient and in line with the scientific method. In my mind, this must mean that one writes plain text everywhere. This is plain/text for e-mail, LaTeX for papers, code is code, Markdown or similar for most other documents. All this is in version control. You can push, share, collaborate quite easily. Anyone is free to make a pretty PDF of it or do whatever else. Because, of course it is all free as in speech. You know all this. But it doesn't work like this. Collegues don't follow this workflow, and they don't care about freedom. They actually think that Track Changes is the same as version control management. I have some work-arounds for the incompatibility between the workflows. For instance, I write most things in Markdown and use pandoc(1) to convert it to PDF and ODT. The collaborators may use any method to comment on my text and then send it back. They never edit the source, they almost invariably send back a (non-strict OOXML) docx with Track Changes or a PDF with text balloons. In academics, there was recently (in Norway just a year ago) a discussion about open access. The discussion showed that it is very difficult for my collegues to only publish open access – they consider it as a serious problem, even though I would not think twice to publish a paper that restricts its readers. For writing papers I tried the proprietary service Overleaf (and similar) or sending the TeX files, but it doesn't work. They won't use it. They even copy text from a PDF into MS Word and send a Track Changed document in a top-posted HTML e-mail back to me. Some of them expect me to do the same thing (or using Google Docs or Sharepoint or so; sometimes logging in is expected as well). For anyone writing a thesis and having these problems right now: don't think they will go away. It does not even matter if you have your own funding. Most of your partners won't care about anyone's freedom, and you still have to find ways to work with their inefficient workflows. Free software helps a lot dealing with this, but these inefficiencies are not necessary. The inefficiencies arise from naivity about free software and technology, or just not caring and/or trying to follow status quo and writing senseless proposals (with inefficient and non-free tools). This is the state for Earth sciences. My work is appreciated in my field, so I might survive in the system (writing proposals and crap), but these unnecessary inefficiencies are *at least* an annoyance, and it does not appear to get any better. I would like to find a community where I can do science in a good way. I want to use free software and would like to collaborate through version control, IRC, Jitsi, well formatted e-mails. Does such a community exist? I am considering going out of
Re: missing dependency for ungoogled-chromium
Je 25 Mar 16:12 skribis Marco: > [...] > Maybe there should be a link to "Application Setup" from the "After > System Installation" section. Not that I read that section, but at > least everyone should've come across "Application Setup", no matter they > installed the tarball or Guix System. No, sorry. Only the "X11 Fonts" and "Locales" subsections are probably relevant for Guix System. I see your point: maybe nothing should be done. —Marco
Re: missing dependency for ungoogled-chromium
Marius—
Je 25 Mar 11:09 skribis Marius:
> Marco van Hulten writes:
>
> > Hello—
> >
> > In a relatively clean profile, Chromium
> > (ungoogled-chromium@80.0.3987.132-0.7e68f18) was crashing. By
> > trial-and-error, I found out that the crash does not occur when
> > font-liberation is installed.
> >
> > Therefore, I propose to add font-liberation as a dependency to
> > ungoogled-chromium.
>
> Chromium needs _a_ font installed, not font-liberation specifically.
>
> Not sure what to do about it. Mention in the description perhaps?
>
> Maybe guix-install.sh could recommend installing a few fonts when it
> finishes, as I guess few people read the manual section about fonts on
> foreign distribution these days? Not very useful on servers though.
That's an option, but not strictly needed, because guix-install.sh
refers to the Guix manual.
It is clearly described in the installation manual ("Application
Setup"). As long as I have not set up at least a dozen of clean user
profiles, I don't know it by heart so I'll try to remember to go
through this section.
Maybe there should be a link to "Application Setup" from the "After
System Installation" section. Not that I read that section, but at
least everyone should've come across "Application Setup", no matter they
installed the tarball or Guix System.
—Marco
missing dependency for ungoogled-chromium
Hello— In a relatively clean profile, Chromium (ungoogled-chromium@80.0.3987.132-0.7e68f18) was crashing. By trial-and-error, I found out that the crash does not occur when font-liberation is installed. Therefore, I propose to add font-liberation as a dependency to ungoogled-chromium. —Marco
--rollback does not always roll back generation
Hello— guix package --rollback usually rolls back from generation N to N-1 (for any integer N > 0), but this didn't happen when I did this (I wanted the last generation not to be overwritten—that part worked): $ guix package --switch-generation=1 switched from generation 2 to 1 $ mv guix-profile-2-link guix-profile-2-link~ $ guix package -i make autoconf automake glibc-utf8-locales glibc-locales $ guix package --rollback switched from generation 2 to 2 $ guix package --rollback switched from generation 2 to 2 This appears a bug to me. guix package --switch-generation=1 worked fine, though. —Marco
Re: TeX Live 2019 wanted
On 17 Jan 09:53 Ricardo Wurmus wrote: > Mikhail Kryshen writes: > > > - font files are missing from texlive-latex-lh (shouldn't it be > > called texlive-lh?). > > Thank you, that’s a good one. Generally, the texlive-latex-* packages > are of the old type that may very well be incomplete. I’ll replace > this one with texlive-lh which will include all the source files as it > should. TeX Live is a full TeX distribution that includes TeX and variants as well as the macro packages LaTeX and ConTeXt. lh is LaTeX-specific, I think. It could be fine if any CTAN package is included in TeX Live as "texlive-PACKAGENAME"; just wondering if this is done consistently and with good reason. —Marco
Re: Claws Mail missing libetpan
Je 2 jan 20:52 skribis Efraim: > On Thu, Jan 02, 2020 at 12:29:47PM -0500, Julien Lepiller wrote: > > Le 2 janvier 2020 12:14:50 GMT-05:00, Marco van Hulten a > > écrit : > > >Hello— > > > > > >I get an error compiling Claws Mail (claws-mail): > > > > > >checking for libetpan-config... no > > >*** Claws Mail requires libetpan 0.57 or newer. See > > >http://www.etpan.org/ > > >[...] > > > > > >First installing libetpan (the Guix package) does not help. > > > > > >—Marco > > > > There's no reason it should help: builds are completely isolated > > from the host environment. There is nothing you can do to influence > > them. But that means builds may be reproducible! > > [...] > > I recently upgraded libetpan from 1.9.3 to 1.9.4, and with it we lost > the libetpan-config binary. There's an open bug¹ with libetpan > upstream to mention the now missing binary. There's also an upstream > patch² but I'm having a hard time getting it to work. On a different Guix (System) system I already had Claws Mail 3.17.4 running. After 'guix pull' it grabbed libetpan-1.9.4 and wanted to compile Claws Mail anew. Indeed, same compilation error. —Marco
Claws Mail missing libetpan
Hello— I get an error compiling Claws Mail (claws-mail): checking for libetpan-config... no *** Claws Mail requires libetpan 0.57 or newer. See http://www.etpan.org/ *** You can use --disable-libetpan if you don't need IMAP4 and/or NNTP support. configure: error: libetpan 0.57 not found command "/gnu/store/29jhbbg1hf557x8j53f9sxd9imlmf02a-bash-minimal-5.0.7/bin/bash" "./configure" "CONFIG_SHELL=/gnu/store/29jhbbg1hf557x8j53f9sxd9imlmf02a-bash-minimal-5.0.7/bin/bash" "SHELL=/gnu/store/29jhbbg1hf557x8j53f9sxd9imlmf02a-bash-minimal-5.0.7/bin/bash" "--prefix=/gnu/store/knhrmn4cjqyxrmbwqm33vwakma8gcpql-claws-mail-3.17.4" "--enable-fast-install" "--build=x86_64-unknown-linux-gnu" "--enable-gnutls" "--enable-pgpmime-plugin" "--enable-enchant" "--enable-ldap" failed with status 1 First installing libetpan (the Guix package) does not help. —Marco
Re: New POWER9 machines for the Guix build farm?
Hello— On 29 Nov 09:25 dftxbs3e wrote: > I'm really happy to hear this! I also do own a POWER9 machine. > > I have a Talos II with 2x 8 SMT4 cores POWER9 DD2.2 CPUs (64 threads), > 64GB of RAM and an AMD WX7100 GPU (amdgpu libre driver). > > I run Fedora on it since more than a year now, it's been my main > workstation without any major issue. It's great to hear of such an experience! I have an amd64 server at home that makes quite a bit of noise and, standing next to the server, an amd64 workstation that makes even more noise, both of which are over 10 years old. I am considering replacing both systems for a single Talos II. According to the mainboard specifications [1], Ethernet is driven by a proprietary chip (Broadcom BCM5719). Is there libre firmware that is shown to work reliably? I guess it should be because it is FSF-certified to Respect Your Freedom, but could someone confirm this specifically for the network interface? [1]: https://wiki.raptorcs.com/wiki/Talos_II > I'm happy to provide assistance, I encourage GNU Guix developers to join > #talos-workstation on Freenode's IRC, we have a friendly active > community that is always happy to help on POWER9 matters. Fantastic to see this work out! The other free modern architecture, RISC-V, is that like a sort of competitor of POWER9? Or is it more like Talos II being the obvious choice for a server (and workstation) because it is available now/more established? —Marco
Re: ldap support for Claws Mail
Hi Ricardo— On 22 Mar 15:05 Ricardo Wurmus wrote: > > Added configure option is enough (works without the openldap package). > > Thanks for the patch! > > I pushed it to the master branch after changing the commit summary and > the formatting. Thanks for this. Sorry for the late response, but could someone check if LDAP is actually enabled in Claws Mail? It doesn't look like it according to 'claws-mail --version-full'. —Marco
Re: GNU Guix 1.0.0 released
On Thu, 02 May 2019 14:12:01 +0200 Ludovic wrote: > We are thrilled to announce the release of GNU Guix 1.0.0! > [...] Fantastic news. Congratulations! Gratulerer. Gratulon! Gefeliciteerd! Félicitations! —Marco
ldap support for Claws Mail
Added configure option is enough (works without the openldap package).
—Marco
>From 404cf25040fdf84e288170d2c7cc10519144cbec Mon Sep 17 00:00:00 2001
From: Marco van Hulten
Date: Fri, 22 Mar 2019 10:58:51 +0100
Subject: [PATCH 26/26] Claws Mail (claws-mail) LDAP support.
---
gnu/packages/mail.scm | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index 278ad1f7e..81c083773 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -1127,7 +1127,7 @@ compresses it.")
("mime-info" ,shared-mime-info)))
(arguments
'(#:configure-flags
-'("--enable-gnutls" "--enable-pgpmime-plugin" "--enable-enchant")
+'("--enable-gnutls" "--enable-pgpmime-plugin" "--enable-enchant" "--enable-ldap")
#:make-flags
;; Disable updating icon cache since it's done by the profile hook.
;; Conflict with other packages in the profile would be inevitable
--
2.17.1
Re: Guix-HPC activity report
Ludovic— On 12 Feb 14:51 Ludovic Courtès wrote: > We have just published an activity report of Guix-HPC for the past 18 > months: > > > https://guix-hpc.bordeaux.inria.fr/blog/2019/02/guix-hpc-activity-report-2018/ > > As you may know, some of us are involved at work with Guix in a > scientific context. Guix-HPC is about bringing reproducible software > deployment to high-performance computing (HPC) and scientific workflows. This is awesome! I read the report with great attention. Some typos (from the pdf I downloaded two days ago): + footnote 8: https://softwareheritage.org → https://www.softwareheritage.org + page 18: becomming → becoming + page 17 (bottom): worflows → workflows. —Marco
Re: FOSDEM 2019: Thank you!
Hi all— This message is a bit belated... but thank you for the good organisation of the Guix days (that I could only participate near the end), as well as the organisation and high-quality talks in the minimalistic languages track! I only met good people. I knew already that they were pleasant as well as knowledgable through the Internet, and now I experienced that this is also true in real life! Best, —Marco
Re: GDM update!
Ludovic et al—
On 10 Feb 23:30 Ludovic Courtès wrote:
> I’m happy to report that GDM basically works, including choosing among X
> session… and it has a neat Guix theme!
> [...]
>
> The one thing I didn’t get to work is ~/.xsession support. Any ideas?
>
> I’d real like to get that fixed and then we can finally replace SLiM
> with GDM as the default.
>
> BTW, at the Guix Days, there were discussions about defaulting to
> LightDM instead of GDM. I forgot to mention then that using LightDM
> wouldn’t solve the GNOME use case; in particular, closing the lid under
> GNOME wouldn’t lock the screen, and clicking the lock button wouldn’t
> have any effect, which is pretty bad.
I have had problems (on different GNU distro's and OpenBSD) with at
least SLiM, GDM and LightDM, ranging from usability ("Do I press Tab or
Enter now?") to forgettability ("I didn't order GNOME!") to not
using .xsession.
Now I tend to use XDM where I can. For me it is always working as
expected in all the above respects.
—Marco
Re: mismatch of source tar ball hash
update— Je 28 okt 12:23 skribis Marco: > Hi— > > When I try to install calcurse, the hash of the downloaded file is > different from the one specified in the package: > [...] I happened to find the same tar ball that I downloaded on 5 April 2018. As this is quite some time ago, my *guess* is that the issue is related to Guix instead of calcurse.org. —Marco
mismatch of source tar ball hash
Hi— When I try to install calcurse, the hash of the downloaded file is different from the one specified in the package: marco@graviton ~$ guix package --fallback -i calcurse The following package will be installed: calcurse 4.3.0 /gnu/store/a77ap0vw0fnsz138paby8w55rlcd58zi-calcurse-4.3.0 The following derivations will be built: /gnu/store/r44sbjgn7gxwl3nxvlnq6946zc05xq0f-profile.drv /gnu/store/xzvmj17kgc5z97czlw5nrz7afb47cjyh-ca-certificate-bundle.drv /gnu/store/wazkm772ssqj81w9npbfi9531s41rh4w-glib-schemas.drv /gnu/store/kwqvdmcpqrqg1q2gk6zc83c50x8w8198-gtk-icon-themes.drv /gnu/store/fad05ars0k7lnis4pys6bc5n2mrwywqj-xdg-mime-database.drv /gnu/store/dkr1dg622dyaphw66zy2lrb925pkfz0y-xdg-desktop-database.drv /gnu/store/9zqzgm8gybh8a8w05g4151k7bk3wkv7x-fonts-dir.drv /gnu/store/4ccc9liswa27f56867fnsg4xl657irpg-info-dir.drv /gnu/store/35zb2h95ssn189i8y43z54b6jqmngwsp-gtk-im-modules.drv /gnu/store/6abn78c8wa5dkks4pnig5i2mijj0f3lf-manual-database.drv 0.3 MB will be downloaded: /gnu/store/a77ap0vw0fnsz138paby8w55rlcd58zi-calcurse-4.3.0 substitution of /gnu/store/a77ap0vw0fnsz138paby8w55rlcd58zi-calcurse-4.3.0 failed building /gnu/store/ya1v2nv0mq8dzkcik64inlyxxk3skz3h-calcurse-4.3.0.tar.gz.drv... downloading from http://calcurse.org/files/calcurse-4.3.0.tar.gz... sha256 hash mismatch for /gnu/store/873m2xbqxndbhcdfrngpsj7cwflm48d0-calcurse-4.3.0.tar.gz: expected hash: 16jzg0nasnxdlz23i121x41pq5kbxmjzk52c5d863rg117fc7v1i actual hash: 11q0r4dbi8vca22x3q1ad07nr1gs4y17cgnplbjzmmz9r9x0h8m2 build of /gnu/store/ya1v2nv0mq8dzkcik64inlyxxk3skz3h-calcurse-4.3.0.tar.gz.drv failed View build log at '/var/log/guix/drvs/ya/1v2nv0mq8dzkcik64inlyxxk3skz3h-calcurse-4.3.0.tar.gz.drv.bz2'. \guix package: error: build failed: build of `/gnu/store/r44sbjgn7gxwl3nxvlnq6946zc05xq0f-profile.drv' failed Should I contact the calcurse people to ask if the file could have been changed? Or is there a better hypothesis explaining this issue? —Marco
Re: Posts in languages other than English on help-guix?
Hei Marius,
Marius Bakke schreef op 3 maart 2018 21:06:27 CET:
> Marco van Hulten <ma...@hulten.org> writes:
>
> > ("nb"
> > "Abonner på diskusjonlisten «Help» for å få hjelp om GuixSD og
> > GNU Guix via e-post. Du kan legge inn meldinger på norsk.")
>
> Takk! I think "diskusjonliste" should be "diskusjonsliste" as
> "diskusjon" is used in a passive infinite form (though good resources
> regarding this online was surprisingly difficult to come by).
>
> "om" is also not the best preposition here, but I wonder if it's
> better
> to avoid "hjelp" altogether:
>
> ("nb"
>"Meld deg på diskusjonslisten «Help» for å få råd og tips fra
> andre GuixSD- og GNU Guix-brukere via e-post. Du kan legge inn
> meldinger på norsk.")
>
> "Råd" here is used as a kind of advice that is "sought for", implying
> support. Tips is..well, general advice. WDYT?
Sounds very good, let's go with your translation!
Marco
Re: Posts in languages other than English on help-guix?
Ludovic—
Je 2 mrt 17:02 skribis Ludovic:
> What about allowing posts on help-guix in one of the languages that
> regular contributors know, in addition to English?
> [...]
I like the idea.
> To experiment with this on help-guix, I propose the patch below for the
> web site. If you’re a committer, please provide a translation for the
> language(s) you know!
("nl"
"Abonneer je op de discussielijst \"Help\" om hulp te vragen
van de GuixSD- en GNU Guix-gemeenschap. Je kunt berichten sturen in
het Nederlands.")
("nb"
"Abonner på diskusjonlisten «Help» for å få hjelp om GuixSD og
GNU Guix via e-post. Du kan legge inn meldinger på norsk.")
—Marco
patch: partition vs filesystem
Patch for documentation attached.
terminology: replaced partition with filesystem where needed
—Marco
diff --git a/doc/guix.texi b/doc/guix.texi
index 098ff5e..d4a2a69 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -8072,7 +8072,7 @@ types.}. For the ESP, if you have one and assuming it is
mkfs.fat -F32 /dev/sda2
@end example
-Preferably, assign partitions a label so that you can easily and
+Preferably, assign file systems a label so that you can easily and
reliably refer to them in @code{file-system} declarations (@pxref{File
Systems}). This is typically done using the @code{-L} option of
@command{mkfs.ext4} and related commands. So, assuming the target root
@@ -8097,9 +8097,9 @@ cryptsetup open --type luks /dev/sda1 my-partition
mkfs.ext4 -L my-root /dev/mapper/my-partition
@end example
-Once that is done, mount the target root partition under @file{/mnt}
+Once that is done, mount the target file system under @file{/mnt}
with a command like (again, assuming @code{my-root} is the label of the
-root partition):
+root file system):
@example
mount LABEL=my-root /mnt
