[BUG FIX] DONE Python session evaluation bug
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Eric Schulte
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367072d11b
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@ -153,14 +153,15 @@ last statement in BODY, as elisp."
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(with-temp-buffer (insert-file-contents tmp-file) (buffer-string)))))))
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;; comint session evaluation
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(org-babel-comint-in-buffer buffer
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(let* ((full-body
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(mapconcat
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#'org-babel-trim
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(list body org-babel-python-last-value-eval org-babel-python-eoe-indicator) "\n"))
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(raw (org-babel-comint-with-output buffer org-babel-python-eoe-indicator t
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(let* ((raw (org-babel-comint-with-output buffer org-babel-python-eoe-indicator t
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;; for some reason python is fussy, and likes enters after every input
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(mapc (lambda (statement) (insert statement) (comint-send-input nil t))
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(split-string full-body "[\r\n]+"))))
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(split-string (org-babel-trim full-body) "[\r\n]+"))
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(comint-send-input nil t) (comint-send-input nil t)
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(insert org-babel-python-last-value-eval)
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(comint-send-input nil t)
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(insert org-babel-python-eoe-indicator)
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(comint-send-input nil t)))
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(results (delete org-babel-python-eoe-indicator
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(cdr (member org-babel-python-eoe-indicator
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(reverse (mapcar #'org-babel-trim raw)))))))
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@ -2819,8 +2819,8 @@ dot("$(2a,0)$",(2,0),N+E);
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*** DONE sh
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* Bugs [35/41]
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** TODO Python session evaluation bug
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* Bugs [36/41]
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** DONE Python session evaluation bug
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The following block evaluates correctly with :session none
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(set :results to output), but fails with session-based evaluation
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(with :results value, as below, you see the error message)
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@ -2844,6 +2844,7 @@ dot("$(2a,0)$",(2,0),N+E);
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outfile = os.path.join(outdir, '%s-vs-%s-direct' % (case, control))
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cmd = 'snptest %s -frequentist 1 -hwe ' % ('-gen_gz' if format == '.gen.gz' else '')
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cmd += '-cases %s %s ' % (case + format, case + '.sample')
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cmd += '-controls %s %s ' % (control + format, control + '.sample')
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cmd += '-exclude_samples %s ' % os.path.join(outdir, 'exclusions')
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cmd += '-o %s ' % outfile
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@ -2854,10 +2855,20 @@ dot("$(2a,0)$",(2,0),N+E);
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#+end_src
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#+resname:
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: File "<stdin>", line 14
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: _
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: ^
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: SyntaxError: invalid syntax
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#+begin_example
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snptest -gen_gz -frequentist 1 -hwe -cases 58C.gen.gz 58C.sample -controls NBS.gen.gz NBS.sample -exclude_samples exclusion-study/none/exclusions -o exclusion-study/none/58C-vs-NBS-direct -chunk 10000 > exclusion-study/none/58C-vs-NBS-direct.log
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snptest -gen_gz -frequentist 1 -hwe -cases 58C.gen.gz 58C.sample -controls POBI.gen.gz POBI.sample -exclude_samples exclusion-study/none/exclusions -o exclusion-study/none/58C-vs-POBI-direct -chunk 10000 > exclusion-study/none/58C-vs-POBI-direct.log
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snptest -gen_gz -frequentist 1 -hwe -cases NBS.gen.gz NBS.sample -controls POBI.gen.gz POBI.sample -exclude_samples exclusion-study/none/exclusions -o exclusion-study/none/NBS-vs-POBI-direct -chunk 10000 > exclusion-study/none/NBS-vs-POBI-direct.log
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snptest -gen_gz -frequentist 1 -hwe -cases 58C.gen.gz 58C.sample -controls NBS.gen.gz NBS.sample -exclude_samples exclusion-study/noscots/exclusions -o exclusion-study/noscots/58C-vs-NBS-direct -chunk 10000 > exclusion-study/noscots/58C-vs-NBS-direct.log
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snptest -gen_gz -frequentist 1 -hwe -cases 58C.gen.gz 58C.sample -controls POBI.gen.gz POBI.sample -exclude_samples exclusion-study/noscots/exclusions -o exclusion-study/noscots/58C-vs-POBI-direct -chunk 10000 > exclusion-study/noscots/58C-vs-POBI-direct.log
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snptest -gen_gz -frequentist 1 -hwe -cases NBS.gen.gz NBS.sample -controls POBI.gen.gz POBI.sample -exclude_samples exclusion-study/noscots/exclusions -o exclusion-study/noscots/NBS-vs-POBI-direct -chunk 10000 > exclusion-study/noscots/NBS-vs-POBI-direct.log
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snptest -gen_gz -frequentist 1 -hwe -cases 58C.gen.gz 58C.sample -controls NBS.gen.gz NBS.sample -exclude_samples exclusion-study/lax/exclusions -o exclusion-study/lax/58C-vs-NBS-direct -chunk 10000 > exclusion-study/lax/58C-vs-NBS-direct.log
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snptest -gen_gz -frequentist 1 -hwe -cases 58C.gen.gz 58C.sample -controls POBI.gen.gz POBI.sample -exclude_samples exclusion-study/lax/exclusions -o exclusion-study/lax/58C-vs-POBI-direct -chunk 10000 > exclusion-study/lax/58C-vs-POBI-direct.log
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snptest -gen_gz -frequentist 1 -hwe -cases NBS.gen.gz NBS.sample -controls POBI.gen.gz POBI.sample -exclude_samples exclusion-study/lax/exclusions -o exclusion-study/lax/NBS-vs-POBI-direct -chunk 10000 > exclusion-study/lax/NBS-vs-POBI-direct.log
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snptest -gen_gz -frequentist 1 -hwe -cases 58C.gen.gz 58C.sample -controls NBS.gen.gz NBS.sample -exclude_samples exclusion-study/strict/exclusions -o exclusion-study/strict/58C-vs-NBS-direct -chunk 10000 > exclusion-study/strict/58C-vs-NBS-direct.log
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snptest -gen_gz -frequentist 1 -hwe -cases 58C.gen.gz 58C.sample -controls POBI.gen.gz POBI.sample -exclude_samples exclusion-study/strict/exclusions -o exclusion-study/strict/58C-vs-POBI-direct -chunk 10000 > exclusion-study/strict/58C-vs-POBI-direct.log
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snptest -gen_gz -frequentist 1 -hwe -cases NBS.gen.gz NBS.sample -controls POBI.gen.gz POBI.sample -exclude_samples exclusion-study/strict/exclusions -o exclusion-study/strict/NBS-vs-POBI-direct -chunk 10000 > exclusion-study/strict/NBS-vs-POBI-direct.log
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#+end_example
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** PROPOSED require users to explicitly turn on each language
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As we continue to add more languages to org-babel, many of which will
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@ -3102,8 +3113,6 @@ the same for the other languages. [Dan]
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find . \( -path \*/SCCS -o -path \*/RCS -o -path \*/CVS -o -path \*/MCVS -o -path \*/.svn -o -path \*/.git -o -path \*/.hg -o -path \*/.bzr -o -path \*/_MTN -o -path \*/_darcs -o -path \*/\{arch\} \) -prune -o -type f \( -iname \*.el \) -exec grep -i -nH -e org-babel-trim {} \;
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#+end_src
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#+resname:
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** DONE Allow source blocks to be recognised when #+ are not first characters on the line
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I think Carsten has recently altered the core so that #+ can have
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preceding whitespace, at least for literal/code examples. org-babel
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