Re: Bug: Duplicate logbook entry for repeated tasks [9.4.6 (9.4.6-gab9f2a @ /home/gustavo/.emacs.d/elpa/org-9.4.6/)]
I can confirm the same is happening here for me with Org mode version 9.4.6 (9.4.6-4-g093c94-elpa @ /home/jeff/.emacs.d/elpa/org-20210607/) on GNU Emacs 28.0.50 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.20, cairo version 1.16.0) of 2021-06-16 The duplicate LOGBOOK entries also seem to be messing up the graphical display of habit records in the agenda. Deleting the duplicates returns the habit display to expected output. I'd be happy to share details of that symptom, but the root cause seems to clearly be the duplicates in the LOGBOOK Jeff Kowalski
[PATCH] ob-core: tangle check library of babel after current buffer
Hi,
This is a patch that fixes tangling behavior when a block has been
ingested into the library of babel and then modified. Best!
Tom
From 22d0689257f977d09b013a143e899f788b45a039 Mon Sep 17 00:00:00 2001
From: Tom Gillespie
Date: Mon, 14 Jun 2021 19:18:28 -0700
Subject: [PATCH] ob-core: tangle check library of babel after current buffer
* lisp/ob-core.el (org-babel-expand-noweb-references): Fix order when
searching for named babel blocks so that blocks in the current buffer
are always found first. This fixes a bug where stale versions of
blocks that have been ingested into the library of babel were being
preferentially tangled instead of newly modified versions from the
current buffer.
---
lisp/ob-core.el | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/lisp/ob-core.el b/lisp/ob-core.el
index 857e03e55..384c06c9a 100644
--- a/lisp/ob-core.el
+++ b/lisp/ob-core.el
@@ -2828,8 +2828,6 @@ block but are passed literally to the \"example-block\"."
(setq cache nil)
(let ((raw (org-babel-ref-resolve id)))
(if (stringp raw) raw (format "%S" raw
- ;; Retrieve from the Library of Babel.
- ((nth 2 (assoc-string id org-babel-library-of-babel)))
;; Return the contents of headlines literally.
((org-babel-ref-goto-headline-id id)
(org-babel-ref-headline-body))
@@ -2842,6 +2840,8 @@ block but are passed literally to the \"example-block\"."
(not (org-in-commented-heading-p))
(funcall expand-body
(org-babel-get-src-block-info t))
+ ;; Retrieve from the Library of Babel.
+ ((nth 2 (assoc-string id org-babel-library-of-babel)))
;; All Noweb references were cached in a previous
;; run. Extract the information from the cache.
((hash-table-p cache)
--
2.31.1
Re: some progress matlab-kernel, a python path problem?
>>> "JK" == John Kitchin writes: > I would see if you can open a jupyter notebook and start a notebook with > the mat lab kernel. If not, it either isn’t installed, or maybe is > installed in a different jupyter. > If you get errors here, the issue is outside of org mode. For example, the > hylang kernel quit working for me a while ago. > See > https://github.com/Calysto/matlab_kernel#kernel-times-out-while-starting > for some troubleshooting tips. > On Wed, Jun 16, 2021 at 11:48 AM Uwe Brauer wrote: Thanks that looks very interesting. smime.p7s Description: S/MIME cryptographic signature
Re: some progress matlab-kernel, a python path problem?
I would see if you can open a jupyter notebook and start a notebook with the mat lab kernel. If not, it either isn’t installed, or maybe is installed in a different jupyter. If you get errors here, the issue is outside of org mode. For example, the hylang kernel quit working for me a while ago. See https://github.com/Calysto/matlab_kernel#kernel-times-out-while-starting for some troubleshooting tips. On Wed, Jun 16, 2021 at 11:48 AM Uwe Brauer wrote: > > > Hi > > So I switched from finks python 3.7 to MacOS 3.8 > I think I set all paths (mac does not locate them in > HOME/.local but in > HOME/Library > > However when I fire up the org-babel command the iphthon console reads > as > > , > | Traceback (most recent call last): > | File "/Users/oub/Library/Python/3.8/bin/jupyter-console", line 10, in > > | sys.exit(main()) > | File > "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_core/application.py", > line 254, in launch_instance > | return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs) > | File > "/Users/oub/Library/Python/3.8/lib/python/site-packages/traitlets/config/application.py", > line 844, in launch_instance > | app.initialize(argv) > | File > "/Users/oub/Library/Python/3.8/lib/python/site-packages/traitlets/config/application.py", > line 87, in inner > | return method(app, *args, **kwargs) > | File > "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_console/app.py", > line 136, in initialize > | self.init_shell() > | File > "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_console/app.py", > line 103, in init_shell > | JupyterConsoleApp.initialize(self) > | File > "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_client/consoleapp.py", > line 343, in initialize > | self.init_kernel_manager() > | File > "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_client/consoleapp.py", > line 295, in init_kernel_manager > | self.kernel_manager.start_kernel(**kwargs) > | File > "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_client/manager.py", > line 337, in start_kernel > | kernel_cmd, kw = self.pre_start_kernel(**kw) > | File > "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_client/manager.py", > line 292, in pre_start_kernel > | kernel_cmd = self.format_kernel_cmd(extra_arguments=extra_arguments) > | File > "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_client/manager.py", > line 210, in format_kernel_cmd > | cmd = self.kernel_spec.argv + extra_arguments > | File > "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_client/manager.py", > line 114, in kernel_spec > | self._kernel_spec = > self.kernel_spec_manager.get_kernel_spec(self.kernel_name) > | File > "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_client/kernelspec.py", > line 230, in get_kernel_spec > | raise NoSuchKernel(kernel_name) > | jupyter_client.kernelspec.NoSuchKernel: No such kernel named matlab > | > | Process kernel-matlab exited abnormally with code 1 > ` > > But the matlab_kernel is installed > > I am puzzled, any python guru could enlighten me please? > > Regards > > Uwe Brauer > > > -- John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803 @johnkitchin http://kitchingroup.cheme.cmu.edu
some progress matlab-kernel, a python path problem?
Hi So I switched from finks python 3.7 to MacOS 3.8 I think I set all paths (mac does not locate them in HOME/.local but in HOME/Library However when I fire up the org-babel command the iphthon console reads as , | Traceback (most recent call last): | File "/Users/oub/Library/Python/3.8/bin/jupyter-console", line 10, in | sys.exit(main()) | File "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_core/application.py", line 254, in launch_instance | return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs) | File "/Users/oub/Library/Python/3.8/lib/python/site-packages/traitlets/config/application.py", line 844, in launch_instance | app.initialize(argv) | File "/Users/oub/Library/Python/3.8/lib/python/site-packages/traitlets/config/application.py", line 87, in inner | return method(app, *args, **kwargs) | File "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_console/app.py", line 136, in initialize | self.init_shell() | File "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_console/app.py", line 103, in init_shell | JupyterConsoleApp.initialize(self) | File "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_client/consoleapp.py", line 343, in initialize | self.init_kernel_manager() | File "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_client/consoleapp.py", line 295, in init_kernel_manager | self.kernel_manager.start_kernel(**kwargs) | File "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_client/manager.py", line 337, in start_kernel | kernel_cmd, kw = self.pre_start_kernel(**kw) | File "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_client/manager.py", line 292, in pre_start_kernel | kernel_cmd = self.format_kernel_cmd(extra_arguments=extra_arguments) | File "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_client/manager.py", line 210, in format_kernel_cmd | cmd = self.kernel_spec.argv + extra_arguments | File "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_client/manager.py", line 114, in kernel_spec | self._kernel_spec = self.kernel_spec_manager.get_kernel_spec(self.kernel_name) | File "/Users/oub/Library/Python/3.8/lib/python/site-packages/jupyter_client/kernelspec.py", line 230, in get_kernel_spec | raise NoSuchKernel(kernel_name) | jupyter_client.kernelspec.NoSuchKernel: No such kernel named matlab | | Process kernel-matlab exited abnormally with code 1 ` But the matlab_kernel is installed I am puzzled, any python guru could enlighten me please? Regards Uwe Brauer
Re: URL woes that never end
Hello, Rudolf Adamkovič writes: > I lamented a while ago about URL handling in Org. To provide > a concrete example, below is a shell script that Org does not export > correctly to HTML. More specifically, Org considers the script to be > a URL. Further, and amazingly, even if I change “see .” to “see > to learn more”, Org *still* does not parse the URL correctly, > even with a valid URL per RFC *and* surrounding angle brackets (<>) > *and* spaces on both sides. This seems to be an issue in htmlize package, not Org. Org does not parse anything in a source block. Regards, -- Nicolas Goaziou
Re: no inline images anymore after reinstall
Hi Johanna,
I don't have much knowledge of Python, but I have done this, in case it
helps you locate the problem:
- I have tried to evaluate your block (previously I have installed in my
Arch system python-matplotlib). Output:
#+RESULTS: fig-zeitverlaufspgendrehstrom
[[file:]]
but
- I have noticed that if you comment on these two lines:
# plt.rcParams.update({'font.size':fontsize})
# rcParams.update({'figure.autolayout': True})
output:
#+RESULTS: fig-zeitverlaufspgendrehstrom
[[file:/tmp/babel-yXFqLG/figurepLRhLV.png]]
(Python console was returning these two errors before commenting
the lines:
NameError: name 'fontsize' is not defined
NameError: name 'rcParams' is not defined)
Best regards,
Juan Manuel
Prof. Dr. Johanna May writes:
> Hi guys,
>
> I've been trying on the web and in "known as good" config files to solve
> this but cannot seem to find the solution:
>
> After reinstalling linux (openSuse leap 15.3) and finding out that
> unfortunately the distro is too new, so 27.1 does not yet get offered
> and switching back to 25.3 most of the stuff that I need works again.
>
> Except for including python output diagrams in org-babel. I put the
> diagram code at the very bottom since it takes up some space. At the very end
> you also see the output: it is not a file, it is just a link called
> [[file:]]. That cannot be right and then, of course, there are no inline
> images displayed and not exported either. It is remarkable though, that
> latex gets the link to the file, but just does not seem to show it
> right. This might point to a latex problem, but the inline images aren't
> shown in org-babel. Therefore I'm trying to find a solution here.
>
> In my dotemacs I included what I thought relevant to get it working, but
> it doesn't (below).
>
> I would be very glad about a hint where to look for a solution. Maybe
> some package-install (but which). Or some other configuration ... Or
> maybe I'm still lacking an important distro package that just does not
> get output on any error buffer?
>
> Thank you very much, any help is appreciated
>
> Johanna May
>
> --- some of my dotemacs lines ---
> ;; === org-babel - Code einbinden ===
> ;; ### Darstellung ###
> (setq org-startup-with-inline-images t)
> (setq org-confirm-babel-evaluate nil)
> (setq org-src-fontify-natively t)
> (setq org-src-tab-acts-natively t)
> (setq org-hide-emphasis-markers t)
>
> ;; ### Statistik mit R ESS ###
> (require 'ess-site)
>
> ;; ### org-babel Sprachen ###
> (require 'ob-python)
> (setq org-babel-python-command "python3")
> ;;(setq python-shell-interpreter "python3")
> (org-babel-do-load-languages
> 'org-babel-load-languages
> '((emacs-lisp . t)
>(python . t)
>(ipython . t)
>(shell . t)
>(js . t)
>(latex . t)
>(org . t)
>(octave . t)
>(R . t)
>(plantuml . t)
>(dot . t)
>(gnuplot . t)
>(ruby . t)
>(screen . nil)
>(ledger . t)
>(C . t)
>(sql . t)
>(ditaa . t)))
>
> ;; ### Einrückungen beachten (z. B. python) ###
> (setq org-edit-src-content-indentation 0)
> (setq org-src-tab-acts-natively t)
> (setq org-src-preserve-indentation t)
>
> ;; ### python-Coding ###
> (require 'epc)
> (require 'company)
> (add-hook 'after-init-hook 'global-company-mode)
> (global-font-lock-mode t)
> (setq font-lock-maximum-decoration t)
> (setq-default indent-tabs-mode nil) ;; nicht Tabs sondern 4 Leerzeichen
> (setq default-tab-width 4)
> (add-hook 'python-mode-hook 'anaconda-mode)
> (add-hook 'python-mode-hook 'eldoc-mode)
> (eval-after-load "company"
> '(progn
> (add-to-list 'company-backends 'company-anaconda)))
> (add-hook 'python-mode-hook 'anaconda-mode)
>
> ;; ### Bilder aus python inline anzeigen ###
> (add-hook 'org-babel-after-execute-hook 'org-display-inline-images 'append)
> (add-hook 'org-mode-hook 'org-display-inline-images)
> --- snip ---
>
>
> ---diagram code in org---
>
> #+name: fig-zeitverlaufspgendrehstrom
> #+begin_src python :results file :session :var
> matplot_lib_filename=(org-babel-temp-file "figure" ".png"),fontsize=fs
> :exports results
>
> import matplotlib.pyplot as plt
> plt.style.use('classic')
> import numpy as np
> from matplotlib.ticker import FuncFormatter, MultipleLocator
> plt.style.use('classic')
>
> plt.rcParams.update({'font.size':fontsize})
> rcParams.update({'figure.autolayout': True})
>
> fig=plt.figure(figsize=(6,3))
>
> x=np.linspace(0,5*np.pi,1000)
> udach=230*np.sqrt(2)
> phi1=0
> phi2=-np.pi*2/3
> phi3=-np.pi*4/3
> u1=udach*np.cos(x+phi1)
> u2=udach*np.cos(x+phi2)
> u3=udach*np.cos(x+phi3)
>
> plt.plot(x,u1,label='$u_1(t)$')
> plt.plot(x,u2,label='$u_2(t)$')
> plt.plot(x,u3,label='$u_3(t)$')
> plt.xlabel('$t$')
> plt.ylabel('$u$')
> plt.xticks([])
> plt.yticks([])
> plt.legend(fontsize='small',bbox_to_anchor=(0,1.02,1.02,0),loc=3,ncol=3,mode="expand",borderaxespad=0.)
> plt.grid(True)
> plt.axhline(0,color='black',lw=1)
>
> #plt.tight_layout()
> plt.savefig(matplot_lib_filename,bbox_inches='tight')
> matplot
insert @6=vsum(@I..@II) interactively HOWTO?
>>> "UB" == Uwe Brauer writes: >>> "UB" == Uwe Brauer writes: >> Hi > | result1 | result2 | result3 | > |-+-+-| > | 14 | 5 | 1 | > | 3 | 5 | 3 | > | 4 | 19 | 4 | > | 6 | 3 | 8 | > |-+-+-| > | 27 | 32 | 16 | > #+TBLFM: @6=vsum(@I..@II) Why can't I insert this interactively? smime.p7s Description: S/MIME cryptographic signature
Re: when importing xlsx via ssconvert (gnumeric) unwanted digits appear
>>> "UB" == Uwe Brauer writes: > Hi > I import xls(x) files, via ssconvert (-->csv) and then into org. > However sometimes I obtain digits like this > 0.5925925925925927 > But I prefer just one digit. > The culprit seems to be ssconvert, but I am curious to hear how people > might treat similar situations and avoid unnecessary digits. It seems that xlsx2csv does a more «common sense» conversion in that particular case. smime.p7s Description: S/MIME cryptographic signature
when importing xlsx via ssconvert (gnumeric) unwanted digits appear
Hi I import xls(x) files, via ssconvert (-->csv) and then into org. However sometimes I obtain digits like this 0.5925925925925927 But I prefer just one digit. The culprit seems to be ssconvert, but I am curious to hear how people might treat similar situations and avoid unnecessary digits. Regards Uwe Brauer
no inline images anymore after reinstall
Hi guys,
I've been trying on the web and in "known as good" config files to solve
this but cannot seem to find the solution:
After reinstalling linux (openSuse leap 15.3) and finding out that
unfortunately the distro is too new, so 27.1 does not yet get offered
and switching back to 25.3 most of the stuff that I need works again.
Except for including python output diagrams in org-babel. I put the
diagram code at the very bottom since it takes up some space. At the very end
you also see the output: it is not a file, it is just a link called
[[file:]]. That cannot be right and then, of course, there are no inline
images displayed and not exported either. It is remarkable though, that
latex gets the link to the file, but just does not seem to show it
right. This might point to a latex problem, but the inline images aren't
shown in org-babel. Therefore I'm trying to find a solution here.
In my dotemacs I included what I thought relevant to get it working, but
it doesn't (below).
I would be very glad about a hint where to look for a solution. Maybe
some package-install (but which). Or some other configuration ... Or
maybe I'm still lacking an important distro package that just does not
get output on any error buffer?
Thank you very much, any help is appreciated
Johanna May
--- some of my dotemacs lines ---
;; === org-babel - Code einbinden ===
;; ### Darstellung ###
(setq org-startup-with-inline-images t)
(setq org-confirm-babel-evaluate nil)
(setq org-src-fontify-natively t)
(setq org-src-tab-acts-natively t)
(setq org-hide-emphasis-markers t)
;; ### Statistik mit R ESS ###
(require 'ess-site)
;; ### org-babel Sprachen ###
(require 'ob-python)
(setq org-babel-python-command "python3")
;;(setq python-shell-interpreter "python3")
(org-babel-do-load-languages
'org-babel-load-languages
'((emacs-lisp . t)
(python . t)
(ipython . t)
(shell . t)
(js . t)
(latex . t)
(org . t)
(octave . t)
(R . t)
(plantuml . t)
(dot . t)
(gnuplot . t)
(ruby . t)
(screen . nil)
(ledger . t)
(C . t)
(sql . t)
(ditaa . t)))
;; ### Einrückungen beachten (z. B. python) ###
(setq org-edit-src-content-indentation 0)
(setq org-src-tab-acts-natively t)
(setq org-src-preserve-indentation t)
;; ### python-Coding ###
(require 'epc)
(require 'company)
(add-hook 'after-init-hook 'global-company-mode)
(global-font-lock-mode t)
(setq font-lock-maximum-decoration t)
(setq-default indent-tabs-mode nil) ;; nicht Tabs sondern 4 Leerzeichen
(setq default-tab-width 4)
(add-hook 'python-mode-hook 'anaconda-mode)
(add-hook 'python-mode-hook 'eldoc-mode)
(eval-after-load "company"
'(progn
(add-to-list 'company-backends 'company-anaconda)))
(add-hook 'python-mode-hook 'anaconda-mode)
;; ### Bilder aus python inline anzeigen ###
(add-hook 'org-babel-after-execute-hook 'org-display-inline-images 'append)
(add-hook 'org-mode-hook 'org-display-inline-images)
--- snip ---
---diagram code in org---
#+name: fig-zeitverlaufspgendrehstrom
#+begin_src python :results file :session :var
matplot_lib_filename=(org-babel-temp-file "figure" ".png"),fontsize=fs :exports
results
import matplotlib.pyplot as plt
plt.style.use('classic')
import numpy as np
from matplotlib.ticker import FuncFormatter, MultipleLocator
plt.style.use('classic')
plt.rcParams.update({'font.size':fontsize})
rcParams.update({'figure.autolayout': True})
fig=plt.figure(figsize=(6,3))
x=np.linspace(0,5*np.pi,1000)
udach=230*np.sqrt(2)
phi1=0
phi2=-np.pi*2/3
phi3=-np.pi*4/3
u1=udach*np.cos(x+phi1)
u2=udach*np.cos(x+phi2)
u3=udach*np.cos(x+phi3)
plt.plot(x,u1,label='$u_1(t)$')
plt.plot(x,u2,label='$u_2(t)$')
plt.plot(x,u3,label='$u_3(t)$')
plt.xlabel('$t$')
plt.ylabel('$u$')
plt.xticks([])
plt.yticks([])
plt.legend(fontsize='small',bbox_to_anchor=(0,1.02,1.02,0),loc=3,ncol=3,mode="expand",borderaxespad=0.)
plt.grid(True)
plt.axhline(0,color='black',lw=1)
#plt.tight_layout()
plt.savefig(matplot_lib_filename,bbox_inches='tight')
matplot_lib_filename
#+end_src
#+CAPTION: Zeitverlauf symmetrischer Spannungen
#+LABEL: fig-zeitverlaufspgendrehstrom
#+ATTR_LATEX: :width \textwidth :height \textheight :options
angle=0,keepaspectratio :float nil
#+RESULTS: fig-zeitverlaufspgendrehstrom
[[file:]]
---snip ---
[SOLVED] (was: org-table-eval-formula for rows?)
>>> "UB" == Uwe Brauer writes: > Hi > I know it is perfectly possible to have org-table-eval-formula for > columns, however sometimes I have tables with very many columns that are > difficult to read and even org-table-toggle-column-width does not help. > That is why I would like to transpose the table but then there seems no > equivalent of org-table-eval-formula for rows? > I can only perform such operation of a cell as in the following example > | result1 | result2 | > |-+-| > | 14 | 5 | > | 3 | 5 | > | 4 | 19 | > | 6 | 3 | > |-+-| > | 27 | | > #+TBLFM: @6$1=vsum(@I$1..@II$1) I did not think when I wrote this | result1 | result2 | result3 | |-+-+-| | 14 | 5 | 1 | | 3 | 5 | 3 | | 4 | 19 | 4 | | 6 | 3 | 8 | |-+-+-| | 27 | 32 | 16 | #+TBLFM: @6=vsum(@I..@II) Is the solution, of course smime.p7s Description: S/MIME cryptographic signature
org-table-eval-formula for rows?
Hi I know it is perfectly possible to have org-table-eval-formula for columns, however sometimes I have tables with very many columns that are difficult to read and even org-table-toggle-column-width does not help. That is why I would like to transpose the table but then there seems no equivalent of org-table-eval-formula for rows? I can only perform such operation of a cell as in the following example | result1 | result2 | |-+-| | 14 | 5 | | 3 | 5 | | 4 | 19 | | 6 | 3 | |-+-| | 27 | | #+TBLFM: @6$1=vsum(@I$1..@II$1) But I would like to get the elements of the second column *automatically* summed up as in the case of columns. Any idea how to achieve that? Thanks and regards Uwe Brauer
Re: [BUG] org babel fails with matlab+python kernel on MacOS-10.15 [9.4.6 (release_9.4.6-541-g52b097 @ /Users/oub/emacs/site-lisp/packages/org/)]
>>> "ND" == Nick Dokos writes:
> Uwe Brauer writes:
>>
>>> | ob-ipython--dump-error("Traceback (most recent call last):\n File
>>> \"/Users/...")
>>
>>
>>
>>> This line seems to be the critical one in the error output. If you can
>>> expand out the full error message, it may elucidate what the problem is.
>>
>> This message drives my crazy since the most important information is
>> just not shown.
>>
> IIUC, clicking on the three dots should expand the message to its full
> glory. You'll probably need to cut-n-past it to another buffer and
> replace "\n" with "real" newlines to make it readable.
Thanks, I will try that out.
smime.p7s
Description: S/MIME cryptographic signature
