Merge branch 'master' into tangle
This commit is contained in:
Eric Schulte
commit
89f4d92829
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@ -39,14 +39,6 @@
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(require 'org-babel-lob)
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(require 'org-babel-tangle)
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;; language specific files
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(add-to-list 'load-path (expand-file-name "langs" (file-name-directory (or load-file-name buffer-file-name))))
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(require 'org-babel-ruby)
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(require 'org-babel-python)
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(require 'org-babel-sh)
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(require 'org-babel-lisp)
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(require 'org-babel-R)
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;; load utility files
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(let ((util-dir (expand-file-name
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"util"
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@ -58,5 +50,13 @@
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;; the newest version of inf-ruby.el is required by org-babel-ruby.el
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(load (expand-file-name "inf-ruby.el" util-dir)))
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;; language specific files
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(add-to-list 'load-path (expand-file-name "langs" (file-name-directory (or load-file-name buffer-file-name))))
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(require 'org-babel-ruby)
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(require 'org-babel-python)
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(require 'org-babel-sh)
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(require 'org-babel-lisp)
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(require 'org-babel-R)
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(provide 'org-babel-init)
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;;; org-babel-init.el ends here
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194
org-babel.org
194
org-babel.org
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@ -27,6 +27,7 @@ Also see the [[file:library-of-babel.org][Library of Babel]] an extensible colle
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and easily-shortcut-callable source-code blocks for handling common
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tasks.
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* Introduction
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Org-Babel enables *communication* between programming languages and
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@ -178,6 +179,16 @@ collected after evaluation.
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thought of as similar to a "script" style of evaluation.
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* Getting started
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Add the following lines to your .emacs, replacing the path as
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appropriate. A good place to check that things are up and running
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would then be [[#sandbox][the sandbox]].
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#+begin_src emacs-lisp
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(add-to-list 'load-path "/path/to/org-babel/lisp")
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(require 'org-babel-init)
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#+end_src
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* Tasks [27/42]
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** TODO support for working with =*Org Edit Src Example*= buffers [1/4]
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*** TODO set buffer-local-process variables appropriately [DED]
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@ -330,60 +341,6 @@ msg + " y python"
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#+begin_src emacs-lisp :var msg="org-babel speaks"
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(concat msg " elisp")
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#+end_src
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** TODO re-implement helper functions from org-R
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*** Initial statement [Eric]
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Much of the power of org-R seems to be in it's helper functions for
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the quick graphing of tables. Should we try to re-implement these
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functions on top of org-babel?
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I'm thinking this may be useful both to add features to org-babel-R and
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also to potentially suggest extensions of the framework. For example
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one that comes to mind is the ability to treat a source-code block
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like a function which accepts arguments and returns results. Actually
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this can be it's own TODO (see [[* source blocks as functions][source blocks as functions]]).
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*** Objectives [Dan]
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- We want to provide convenient off-the-shelf actions
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(e.g. plotting data) that make use of our new code evaluation
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environment but do not require any actual coding.
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*** Initial Design proposal [Dan]
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- *Input data* will be specified using the same mechanism as :var
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references, thus the input data may come from a table, or
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another source block, and it is initially available as an elisp
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data structure.
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- We introduce a new #+ line, e.g. #+BABELDO. C-c C-c on that
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line will apply an *action* to the referenced data.
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- *Actions correspond to source blocks*: our library of available
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actions will be a library of org-babel source blocks. Thus the
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code for executing an action, and the code for dealing with the
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output of the action will be the same code as for executing
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source blocks in general
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- Optionally, the user can have the relevant source block inserted
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into the org buffer after the (say) #+BABELDO line. This will
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allow the user to fine tune the action by modifying the code
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(especially useful for plots).
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- So maybe a #+BABELDO line will have header args
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- :data (a reference to a table or source code block)
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- :action (or should that be :srcname?) which will be something
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like :action pie-chart, referring to a source block which will
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be executed with the :data referent passed in using a :var arg.
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- :showcode or something controlling whether to show the code
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*** Modification to design
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I'm implementing this, at least initially, as a new interpreter
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named 'babel', which has an empty body. 'babel' blocks take
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a :srcname header arg, and look for the source-code block with
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that name. They then execute the referenced block, after first
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appending their own header args on to the target block's header
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args.
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If the target block is in the library of babel (a.o.t. e.g. the
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current buffer), then the code in the block will refer to the
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input data with a name dictated by convention (e.g. __data__
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(something which is syntactically legal in all languages...). Thus
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the babel block will use a :var __data__ = whatever header arg to
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reference the data to be plotted.
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** TODO share org-babel
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how should we share org-babel?
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@ -554,6 +511,63 @@ tabel
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Another example is in the [[*operations%20in%20on%20tables][grades example]].
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** TODO re-implement helper functions from org-R
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*** Initial statement [Eric]
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Much of the power of org-R seems to be in it's helper functions for
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the quick graphing of tables. Should we try to re-implement these
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functions on top of org-babel?
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I'm thinking this may be useful both to add features to org-babel-R and
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also to potentially suggest extensions of the framework. For example
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one that comes to mind is the ability to treat a source-code block
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like a function which accepts arguments and returns results. Actually
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this can be it's own TODO (see [[* source blocks as functions][source blocks as functions]]).
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*** Objectives [Dan]
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- We want to provide convenient off-the-shelf actions
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(e.g. plotting data) that make use of our new code evaluation
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environment but do not require any actual coding.
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*** Initial Design proposal [Dan]
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- *Input data* will be specified using the same mechanism as :var
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references, thus the input data may come from a table, or
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another source block, and it is initially available as an elisp
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data structure.
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- We introduce a new #+ line, e.g. #+BABELDO. C-c C-c on that
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line will apply an *action* to the referenced data.
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- *Actions correspond to source blocks*: our library of available
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actions will be a library of org-babel source blocks. Thus the
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code for executing an action, and the code for dealing with the
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output of the action will be the same code as for executing
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source blocks in general
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- Optionally, the user can have the relevant source block inserted
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into the org buffer after the (say) #+BABELDO line. This will
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allow the user to fine tune the action by modifying the code
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(especially useful for plots).
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- So maybe a #+BABELDO line will have header args
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- :data (a reference to a table or source code block)
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- :action (or should that be :srcname?) which will be something
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like :action pie-chart, referring to a source block which will
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be executed with the :data referent passed in using a :var arg.
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- :showcode or something controlling whether to show the code
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*** Modification to design
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I'm implementing this, at least initially, as a new interpreter
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named 'babel', which has an empty body. 'babel' blocks take
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a :srcname header arg, and look for the source-code block with
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that name. They then execute the referenced block, after first
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appending their own header args on to the target block's header
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args.
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If the target block is in the library of babel (a.o.t. e.g. the
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current buffer), then the code in the block will refer to the
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input data with a name dictated by convention (e.g. __data__
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(something which is syntactically legal in all languages...). Thus
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the babel block will use a :var __data__ = whatever header arg to
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reference the data to be plotted.
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*** Current design
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This is covered by the [[file:library-of-babel.org][Library of Babel]], which will contain
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ready-made source blocks designed to carry out useful common tasks.
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** PROPOSED Are we happy with current behaviour regarding vector/scalar output?
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This simple example of multilingual chaining produces vector output if
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there are spaces in the message and scalar otherwise.
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@ -2287,50 +2301,50 @@ of these tests may fail.
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#+TBLNAME: org-babel-tests
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| functionality | block | arg | expected | results | pass |
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|-------------------------+----------------------------+-----+-------------+-------------+------|
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| basic evaluation | | | | | pass |
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| basic evaluation | | | | | |
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|-------------------------+----------------------------+-----+-------------+-------------+------|
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| emacs lisp | basic-elisp | | 5 | 5 | pass |
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| shell | basic-shell | | 6 | 6 | pass |
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| ruby | basic-ruby | | org-babel | org-babel | pass |
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| python | basic-python | | hello world | hello world | pass |
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| R | basic-R | | 13 | 13 | pass |
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| emacs lisp | basic-elisp | | 5 | | |
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| shell | basic-shell | | 6 | | |
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| ruby | basic-ruby | | org-babel | | |
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| python | basic-python | | hello world | | |
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| R | basic-R | | 13 | | |
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|-------------------------+----------------------------+-----+-------------+-------------+------|
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| tables | | | | | pass |
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| tables | | | | | |
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|-------------------------+----------------------------+-----+-------------+-------------+------|
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| emacs lisp | table-elisp | | 3 | 3 | pass |
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| ruby | table-ruby | | 1-2-3 | 1-2-3 | pass |
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| python | table-python | | 5 | 5 | pass |
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| R | table-R | | 3.5 | 3.5 | pass |
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| emacs lisp | table-elisp | | 3 | | |
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| ruby | table-ruby | | 1-2-3 | | |
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| python | table-python | | 5 | | |
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| R | table-R | | 3.5 | | |
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|-------------------------+----------------------------+-----+-------------+-------------+------|
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| source block references | | | | | pass |
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| source block references | | | | | |
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|-------------------------+----------------------------+-----+-------------+-------------+------|
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| all languages | chained-ref-last | | Array | Array | pass |
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| all languages | chained-ref-last | | Array | | |
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|-------------------------+----------------------------+-----+-------------+-------------+------|
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| source block functions | | | | | pass |
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| source block functions | | | | | |
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|-------------------------+----------------------------+-----+-------------+-------------+------|
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| emacs lisp | defun-fibb | | fibbd | fibbd | pass |
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| run over | Fibonacci | 0 | 1 | 1 | pass |
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| a | Fibonacci | 1 | 1 | 1 | pass |
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| variety | Fibonacci | 2 | 2 | 2 | pass |
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| of | Fibonacci | 3 | 3 | 3 | pass |
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| different | Fibonacci | 4 | 5 | 5 | pass |
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| arguments | Fibonacci | 5 | 8 | 8 | pass |
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| emacs lisp | defun-fibb | | fibbd | | |
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| run over | Fibonacci | 0 | 1 | | |
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| a | Fibonacci | 1 | 1 | | |
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| variety | Fibonacci | 2 | 2 | | |
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| of | Fibonacci | 3 | 3 | | |
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| different | Fibonacci | 4 | 5 | | |
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| arguments | Fibonacci | 5 | 8 | | |
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|-------------------------+----------------------------+-----+-------------+-------------+------|
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| bugs and tasks | | | | | pass |
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| bugs and tasks | | | | | |
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|-------------------------+----------------------------+-----+-------------+-------------+------|
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| simple ruby arrays | ruby-array-test | | 3 | 3 | pass |
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| R number evaluation | bug-R-number-evaluation | | 2 | 2 | pass |
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| multi-line ruby blocks | multi-line-ruby-test | | 2 | 2 | pass |
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| forcing vector results | test-forced-vector-results | | Array | Array | pass |
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| simple ruby arrays | ruby-array-test | | 3 | | |
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| R number evaluation | bug-R-number-evaluation | | 2 | | |
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| multi-line ruby blocks | multi-line-ruby-test | | 2 | | |
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| forcing vector results | test-forced-vector-results | | Array | | |
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|-------------------------+----------------------------+-----+-------------+-------------+------|
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| sessions | | | | | pass |
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| sessions | | | | | |
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|-------------------------+----------------------------+-----+-------------+-------------+------|
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| set ruby session | set-ruby-session-var | | :set | :set | pass |
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| get from ruby session | get-ruby-session-var | | 3 | 3 | pass |
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| set python session | set-python-session-var | | set | set | pass |
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| get from python session | get-python-session-var | | 4 | 4 | pass |
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| set R session | set-R-session-var | | set | set | pass |
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| get from R session | get-R-session-var | | 5 | 5 | pass |
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| set ruby session | set-ruby-session-var | | :set | | |
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| get from ruby session | get-ruby-session-var | | 3 | | |
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| set python session | set-python-session-var | | set | | |
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| get from python session | get-python-session-var | | 4 | | |
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| set R session | set-R-session-var | | set | | |
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| get from R session | get-R-session-var | | 5 | | |
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#+TBLFM: $5='(if (= (length $3) 1) (progn (message (format "running %S" '(sbe $2 (n $3)))) (sbe $2 (n $3))) (sbe $2))::$6='(if (string= $4 $5) "pass" (format "expected %S but was %S" $4 $5))
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** basic tests
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@ -2554,10 +2568,14 @@ Time.now
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#+begin_src R :results replace
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a <- 9
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b <- 16
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b <- 17
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a + b
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#+end_src
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#+resname:
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: 26
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: 25
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#+begin_src R
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|
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