org-mode Clojure babel

[Johannes]

Hi,

I am looking for a working environment for using org-mode with Clojure babel. Googleing for the issue I can only find some apparently outdated hints. I am using org-mode version 8.2.10, Clojure 1.6.0, Leiningen 2.5.1, and CIDER 0.10.0.

Any hints, where I can find the right configuration?

Johannes

[Stuart Sierra]

Hi Johannes

I have a working Org babel & Clojure in my Emacs setup. It's idiosyncratic to my preferences, but maybe it will be useful:
github.com/stuartsierra/dotfiles

–S

[Karsten Schmidt]

Hi Johannes, checkout my leiningen template for org-mode projects
here: http://thi.ng/babel and an example project using this template
here: http://thi.ng/fabric

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[Johannes Brauer]

Hi Stuart,

thanks a lot for your help. I’ve included your settings in my Emacs (Aquamacs) setup. After having activated CIDER I tried to compile (C-c C-c) a little code snippet:

#+begin_src clojure  :results silent

   (+ 1 2)

#+end_src

What happens, is:

Evaluate this clojure code block on your system? (y or n) y

executing Clojure code block...

let: Wrong number of arguments: (3 . 4), 1

What I am doing wrongly?

Johannes

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[Johannes Brauer]

Hi Karsten,

thank you for the links to your project. But until now, I haven’t succeeded to setup my Emacs so that I can evaluate Clojure code snippets in an org file.

Johannes

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[Stuart Sierra]

Hi, Johannes,

Sorry, I don't know. That error looks like an incompatibility of Elisp functions from different libraries.

There are just too many different moving pieces here: Emacs, org-mode, CIDER, and nREPL. These projects are not coordinated with regard to version numbers and API incompatibilities.

The code snippet I linked to only works on the specific versions I have: Emacs (GNU 24.5.1), org-mode (commit d3196f0), CIDER (0.9.1), and nREPL (0.9.1).

You will probably have to debug and tweak the Elisp code to work with your local Emacs installation. I don't know of any easier way to get org-babel & Clojure working together.

Good luck,
–S

[Matching Socks]

If you and your Emacs are happy with cider and clojure-mode, then the leap to Org Babel with Clojure should be a short one.

One thing to do is look at your Org mode's ob-clojure.el and figure out whether it mentions cider.  (The older or "stable" versions use only slime or nrepl.)  The Org website is a house of mirrors, but somewhere you should find a tidy tar.gz of a nicely assembled Org whose ob-clojure.el covers cider.

Another thing that might go wrong, is that the cider-capable version of ob-clojure may try to detect whether it should use cider, nrepl, or slime.  Detection might reach an unfortunate conclusion if Emacs had not loaded cider.  Therefore, it might help to open a cider REPL buffer before opening any Org buffers.  (If I recall, Org Babel will need that REPL sooner or later anyway; it does not open its own REPL.)

[Johannes Brauer]

Hi!

Thank you for your hints.

...

One thing to do is look at your Org mode's ob-clojure.el and figure out whether it mentions cider.  (The older or "stable" versions use only slime or nrepl.)  The Org website is a house of mirrors, but somewhere you should find a tidy tar.gz of a nicely assembled Org whose ob-clojure.el covers cider.

indeed, my version of ob-clojure did not mention cider. I’ve one in the house of mirrors (http://orgmode.org/cgit.cgi/org-mode.git/plain/lisp/ob-clojure.el) which does.

But the error message

     executing Clojure code block...

     let: Wrong number of arguments: (3 . 4), 1

remains.

Another thing that might go wrong, is that the cider-capable version of ob-clojure may try to detect whether it should use cider, nrepl, or slime.  Detection might reach an unfortunate conclusion if Emacs had not loaded cider.  Therefore, it might help to open a cider REPL buffer before opening any Org buffers.  (If I recall, Org Babel will need that REPL sooner or later anyway; it does not open its own REPL.)

I tried this too, but without success

Johannes

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[Phillip Lord]

If you are willing to entertain a slightly different interaction model,
you might want to take a look at the lentic package

https://github.com/phillord/lentic

Instead of Clojure snippets which you can pop out and edit, this gives
you two buffers, one entirely valid clojure (which syntax highlights,
you can eval, test and so forth) and one entirely valid org (which you
can publish, show-hide and so forth). You can edit either one (the
Clojure view or the Org-mode view) and changes percolate backward.

This video shows it working with org-mode and Emacs-lisp.

https://vimeo.com/116078853

And this video shows it working with latex and clojure.

https://vimeo.com/116141808

I don't have a video of it working with org and clojure, but it does
work with them. My tawny-owl library is being (slowly) ported to this
form of literate development.

https://github.com/phillord/tawny-owl/blob/master/src/tawny/owl.clj

It also allows integration with asciidoc, and clojure. I wrote these
slides:

http://homepages.cs.ncl.ac.uk/phillip.lord/download/tawny/icbo_2015/2015_lisbon.html

as literate clojure source.

Have fun.

Phil

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[Johannes Brauer]

it sounds exciting, I’ll give it a try.

Johannes

[Johannes]

I am quite impressed about lentic. I think I will use it. Thank you, Phil. 

Nevertheless I am looking for a working configuration for Emacs org-mode with Clojure babel.

Johannes

Am Freitag, 6. November 2015 18:10:58 UTC+1 schrieb Phillip Lord:

If you are willing to entertain a slightly different interaction model,
you might want to take a look at the lentic package

https://github.com/phillord/lentic

 pInstead of Clojure snippets which you can pop out and edit, this gives

[Matching Socks]

The latest stable Org Babel stopped working with the introduction of Cider 0.10.0. 

You can either go back to Cider 0.9.1, or
(1) get Org 8.3.2,
(2) git-clone Org's repo, and
(3) back-port to 8.3.2 the change in ob-clojure.el that accommodates the latest Cider.

The breakage was raised at https://github.com/clojure-emacs/cider/issues/1302 and closed with a comment, "I don't have nor the time nor the energy to sync up with everyone maintaining a 3rd party extension. I just hope they're following the development and will do the necessary changes when needed." 

But three considerations, which are not Cider's fault, argue for a kinder accommodation.  First, Org freezes for bundling into a major Emacs release only a few times a century, and the resulting Emacs release then enjoys wide distribution for many years.  Second, the bundled Org is unusually significant because overriding it with another version is not always fool-proof.  Third, Org with Clojure snippets is dynamite!  Therefore, I hope Org will get advice from Cider about a more durable technique, so the next Emacs+Org release might be useful even on the glacial Emacs time scale.

On Tuesday, November 3, 2015 at 3:25:51 AM UTC-5, Johannes wrote:

[Johannes Brauer]

Thanks, for the explanations. I hope for the best, that there will be an working org-babel version in the future. In the mean time I will continue using lentilc.

Johannes

[martin_clausen]

I found that

Org-mode version 8.3.2 and CIDER 0.11.0 snapshot (package: 20151212.1044)

works great and can be easily be installed from repos.

[Johannes Brauer]

thanks for the hint; indeed it works 

[Stuart Sierra]

I recently adapted my Emacs config to work with Org 8.3.2 and CIDER 0.10.0. Here it is. This is just my personal setup, not something I can support. Posting here in case someone else might find it useful.
–S

[Johannes]

BUT!!!

With cider-nrepl set to 0.10.0 and cider set to 0.11.0-snapshot emacs complains:

WARNING: CIDER requires nREPL 0.2.12 (or newer) to work properly

WARNING: CIDER's version (0.11.0-snapshot) does not match cider-nrepl's version (0.10.1). Things will break!

That's not an org-bable problem, but perhaps there is a tip what to do.

Johannes

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[Martin Clausen]

If you update to cider/cider-nrepl 0.11.0-snapshot in your .lein/profiles.clj that should fix the problem.

[Johannes Brauer]

I tried this before. But with

{:repl {:plugins [[cider/cider-nrepl " 0.11.0-snapshot"]]}}

in my profiles.clj and cider-jack-in I get a Java exception:

Starting nREPL server via lein repl :headless...

error in process sentinel: Could not start nREPL server: java.lang.IllegalArgumentException: Bad artifact coordinates cider:cider-nrepl:jar: 0.11.0-snapshot, expected format is <groupId>:<artifactId>[:<extension>[:<classifier>]]:<version>

 at org.sonatype.aether.util.artifact.DefaultArtifact.<init> (DefaultArtifact.java:73)

    org.sonatype.aether.util.artifact.DefaultArtifact.<init> (DefaultArtifact.java:56)

    cemerick.pomegranate.aether$artifact.invoke (aether.clj:222)

    cemerick.pomegranate.aether$dependency.invoke (aether.clj:230)

    cemerick.pomegranate.aether$resolve_dependencies_STAR_$fn__190.invoke (aether.clj:708)

…

[Reid McKenzie]

"0.11.0-SNAPSHOT". It's case sensitive.

Reid

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[Johannes Brauer]

okay, that I could have figured out myself, sorry. But now I get another exception:

error in process sentinel: Could not start nREPL server: java.lang.IllegalArgumentException: No value supplied for key: .

 at clojure.lang.PersistentHashMap.create (PersistentHashMap.java:77)

    leiningen.core.project$dependency_map.invoke (project.clj:77)

    leiningen.core.project$dep_key.invoke (project.clj:228)

    leiningen.core.project$reduce_dep_step.invoke (project.clj:232)

    clojure.lang.ArrayChunk.reduce (ArrayChunk.java:58)

…

???

Johannes

[Johannes Brauer]

now my profiles.clj looks like

{:repl {:plugins [[cider/cider-nrepl "0.11.0-SNAPSHOT"]

                  [lein-pprint "1.1.2"]]

        :dependencies [[org.clojure/tools.nrepl "0.2.12"]]}}

 But repl complains:

; CIDER 0.11.0snapshot (package: 20160104.1114) (Java 1.8.0_25, Clojure 1.6.0, nREPL 0.2.6)

WARNING: CIDER requires nREPL 0.2.12 (or newer) to work properly

WARNING: The following required nREPL ops are not supported: 

  apropos classpath complete eldoc format-code format-edn info inspect-pop inspect-push inspect-refresh macroexpand ns-list ns-vars ns-path refresh resource stacktrace toggle-trace-var toggle-trace-ns undef

  Please, install (or update) cider-nrepl 0.11.0-SNAPSHOT and restart CIDER

user> 

Is anything wrong with my profiles.clj?

Johannes

[Martin Clausen]

Have you tried updating leiningen?

[Johannes Brauer]

thanks a lot,Martin, upgrading leiningen from 2.5.1 to 2.5.3 solves the problem

Johannes