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 ---
Re: Overleaf equivalent for org-babel users?
Dear Ken, thank you very much. I'm looking into cocalc now. I already got it to compile some test.org file as pdf. I also set up a test file there in order to start finding out how to do this. Next step, I guess, would be to see, if org-babel works. Unfortunately, it looks like a bit more work since for collaboration I need to find out about versioning and testing the stuff and also about how to get some very simple interface working there, maybe for small edits github is nicer. But I have to admit, my experience on tramp (what is that?) and git is very limited, so I don't yet have an idea of how to set that up in a good way. Jupyter Notebooks are not what I feel is right for lecture notes in that subject since they cannot display circuitikz and latex export is not the way it should be. It's not a programming class I'm teaching and many students do prefer the pdf they can either print out or annotate in some software on their tablets or just display on their smartphone. The exam is in writing and on paper. I do also provide some jupyter notebooks, but only for the interested part of the class and they surely can manage without that. As always, such options are rather taken up by the more skilled, and not so much by the weaker students, unfortunately. Cheers, have a good weekend! J Am Samstag, 18. April 2020 um 15:59 schrieb Ken Mankoff ... > Hi Dr. May, > > Unfortunately I have not found Emacs + Org to be the right tools when > collaborating. What we need is a way for Org wrap/interface/edit Jupyter > Notebooks, since that seems to be becoming the standard. Unfortunately. > > I have had some luck with a hybrid approach using the Sage Notebook server. > That project is no longer active (perhaps due to the success of Jupyter > Notebooks?), but I think you can do something similar with either Google > Colab https://colab.research.google.com or more likely CoCalc > https://cocalc.com/ > > Google Collab is just an interface to Jupyter Notebooks. > > CoCalc can also just run Jupyter Notebooks, but also lets you have a full > Linux environment, bash shell, ssh, git, etc. I think you may need to pay for > this level of service, but you could then run emacs remotely via ssh, or > locally and use tramp. If the backend is git you may be able to work locally > and sync with the webserver interface to the tools that your colleagues would > see. > > I still don't think your colleagues would be directly editing your Org source > though, but you may be able to get close to what you're looking for on those > sites. Good luck, and please do post back here if you come up with a good > solution. > > -k. > > On 2020-04-16 at 10:22 -07, Prof. Dr. Johanna May > wrote... >> Hey there, >> >> I've been preparing lecture notes with org-mode and lualatex export >> that include python diagrams and so on for about more than a year. Now >> my colleagues and team start to get interested in tweaking the >> results. Therefore, we would need some kind of online collaboration >> solution similar to overleaf that can compile the latex including the >> python (org-babel) inserts. And, obviously, versioning would also come >> in handy, so that would rather be github / gitlab functionality. >> >> Does anyone know of a solution like overleaf that can be used for >> that? Could you point me at your description of any setup needed? Or, >> alternatively, do you have some good description of how to set up a >> server / virtual machine that can do that? (at best including a >> virtual emacs interface, so not all users have to do all the >> installations locally)? If so, that description would also interest >> me. >> >> I would like to either use some online platform like overleaf or >> explain to my university colleagues who already have servers running >> what they could do for me. >> >> The problem is, that the collaboration colleagues are not good friends >> with coding (they prefer word to latex, excel to python ... until now, >> at least), so I'm not very inclined to suggest them to start using >> emacs. I would very much prefer some web-based solution to get them >> started. Also, such a solution might provide ways of having students >> contribute smaller bits and pieces without having to go thru the whole >> learning curve of learning the use of emacs, installing all the tools, >> etc.pp. Any ideas? >> >> Thank you very much! >> >> Cheers, >> >> J. May -- Prof. Dr. Johanna May Stellvertretende Institutsleiterin CIRE Fakultät für Informations-, Medien- und Elektrotechnik (F07) Institut für Elektrische Energietechnik (IET) Cologne Institute for Renewable Energy (CIRE) Lehrgebiete: Energieeffizienz und Grundlagen Elektrotechnik T: +49 221-8275-2697 M: +49 174 891 9002 E: johanna@th-koeln.de Technische Hochschule Köln Campus Deutz Betzdorfer Str. 2 50679 Köln Raum: HW2-40 www.th-koeln.de
Overleaf equivalent for org-babel users?
Hey there, I've been preparing lecture notes with org-mode and lualatex export that include python diagrams and so on for about more than a year. Now my colleagues and team start to get interested in tweaking the results. Therefore, we would need some kind of online collaboration solution similar to overleaf that can compile the latex including the python (org-babel) inserts. And, obviously, versioning would also come in handy, so that would rather be github / gitlab functionality. Does anyone know of a solution like overleaf that can be used for that? Could you point me at your description of any setup needed? Or, alternatively, do you have some good description of how to set up a server / virtual machine that can do that? (at best including a virtual emacs interface, so not all users have to do all the installations locally)? If so, that description would also interest me. I would like to either use some online platform like overleaf or explain to my university colleagues who already have servers running what they could do for me. The problem is, that the collaboration colleagues are not good friends with coding (they prefer word to latex, excel to python ... until now, at least), so I'm not very inclined to suggest them to start using emacs. I would very much prefer some web-based solution to get them started. Also, such a solution might provide ways of having students contribute smaller bits and pieces without having to go thru the whole learning curve of learning the use of emacs, installing all the tools, etc.pp. Any ideas? Thank you very much! Cheers, J. May
solved partly: exporting ics files with broken link
Hey there, in the end I did find that link in my file. Probably I was using the wrong search function (C-s) which did not show text inside links whereas console grep did the job in the end. And then exporting via C-c c f exported one file for me. Cheers, J Prof. Dr. Johanna May writes: > Hey there, > > using https://orgmode.org/manual/iCalendar-export.html I wanted to > export my agenda files. I tried exporting just one file, or combining > the agenda files. But I always get an error message about an unresolved > link to "selfhosted.libhunt.com". - This link is not in any of my agenda > files or .org files. So it must be sitting somewhere else but I cannot > find out where. Any hints on how to repair that? Any hints in which file > that strange link may sit? And: how can I make sure my files stay > exportable? > > Thanks, > > Cheers, > > J -- Prof. Dr. Johanna May Stellvertretende Institutsleiterin CIRE Fakultät für Informations-, Medien- und Elektrotechnik (F07) Institut für Elektrische Energietechnik (IET) Cologne Institute for Renewable Energy (CIRE) Lehrgebiete: Energieeffizienz und Grundlagen Elektrotechnik T: +49 221-8275-2697 M: +49 174 891 9002 E: johanna@th-koeln.de Technische Hochschule Köln Campus Deutz Betzdorfer Str. 2 50679 Köln Raum: HW2-40 www.th-koeln.de
exporting ics files with broken link
Hey there, using https://orgmode.org/manual/iCalendar-export.html I wanted to export my agenda files. I tried exporting just one file, or combining the agenda files. But I always get an error message about an unresolved link to "selfhosted.libhunt.com". - This link is not in any of my agenda files or .org files. So it must be sitting somewhere else but I cannot find out where. Any hints on how to repair that? Any hints in which file that strange link may sit? And: how can I make sure my files stay exportable? Thanks, Cheers, J
[O] ipython integration fails
Hi everybody,
I am creating lecture notes including some python snippets. Now, in
order to teach jupyter notebook use I would like to include just the
same code as in a python snippet in an ipython snippet.
However ipython blocks don't work in my set up and I could not figure
out which dependency or config line I might need to add in order to do
this properly (and scimax also creates errors, but since I have my own
config running I thought ipython might already do the job).
The ipython snippet I used is:
#+BEGIN_SRC ipython :session :results raw drawer
%matplotlib inline
import matplotlib.pyplot as plt
import numpy as np
#+END_SRC
The error message is:
Traceback (most recent call last):
File "/home/username/.emacs.d/elpa/ob-ipython-20180224.953/client.py", line
60, in
c = create_client(args.conn_file)
File "/home/username/.emacs.d/elpa/ob-ipython-20180224.953/client.py", line
43, in create_client
cf = find_connection_file('emacs-' + name)
File "/usr/lib/python3.6/site-packages/jupyter_client/connect.py", line 218,
in find_connection_file
raise IOError("Could not find %r in %r" % (filename, path))
OSError: Could not find 'emacs-default' in ['.', '/run/user/1000/jupyter']
Maybe I do not need ipython anyway. What works are python code snippets
like the following one. Minted exports both, code and results and they
are both displayed in the pdf slides/manuscript (using lualatex,
beamerarticle etc.)
#+begin_src python :results output :session :exports both
import time
time.sleep(3)
#+end_src
However, then, what does not work properly is several code blocks in one
session, e.g.
(1)
#+begin_src python :results output :session :exports both
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import datetime as dt
import seaborn as sns
sns.set(style="darkgrid")
#+end_src
(2)
#+begin_src python :results output :session :exports both
df = pd.read_csv('./household_data_1min_singleindex.csv')
#+end_src
(3)
#+begin_src python :results output :session :exports both
zeit=df.utc_timestamp.apply(lambda x: dt.datetime.strptime(x,
"%Y-%m-%dT%H:%M:%SZ"))
#+end_src
(4)
#+begin_src python :results file :session :var
matplot_lib_filename=(org-babel-temp-file "figu" ".png"),fontsize=fs :exports
both
plt.rcParams.update({'font.size':fontsize})
rcParams.update({'figure.autolayout': True})
plt.plot(zeit,df.DE_KN_residential2_washing_machine)
plt.savefig(matplot_lib_filename)
matplot_lib_filename
#+end_src
I do not like the fact that plt.rcParams.update and other lines that
jupyter does not need get exported - is there a simple way to exclude
certain lines from export?
And I do get in serious trouble when I add a second data set (another csv) and
do
further analysis steps - all graphics then look the same and bad and do
not represent the actual result of the code block. It seems that all get
the same wrong name and then at each graphics location this same png
gets displayed.
So, maybe there is a good tutorial on using sessions in ob-python or
some other hint that I could use?
Is there a way to restart the (python) kernel with some header message
in the src block?
Thank you very much,
Cheers,
J. May
Re: [O] change font-size in python plots depending on context
Hi there, thanks to Thomas and Eric. I actually found a rather stupid mistake: I was already using a var (for the png filename generation) and the header did not read the next :var. So I added ,fs=fontsize to the first :var and now it works. I will have a look Eric's function of how to get the value of e.g. fontsize and so on (btw, I also need textwidth and textheight from somewhere). I also found a python pgf package but I couldn't figure out fast how to implement that (it sounds as if instead of png a pgf is generated and then everything has the right latex layout, so pretty cool, but it seemed not so easy to implement). So long, cheers! J Thomas S. Dye writes: > Aloha Johanna May, > > This works: > > #+name: fs > #+BEGIN_SRC emacs-lisp > 10 > #+END_SRC > > #+RESULTS: fs > : 10 > > #+header: :var fontsize=fs() :results output > #+begin_src python > print(fontsize) > #+end_src > > #+RESULTS: > : 10 > > Note "fs()" instead of "fs". > > All the best, > Tom -- Prof. Dr. Johanna May Stellvertretende Institutsleiterin CIRE Fakultät für Informations-, Medien- und Elektrotechnik (F07) Institut für Elektrische Energietechnik (IET) Cologne Institute for Renewable Energy (CIRE) Lehrgebiete: Energieeffizienz und Grundlagen Elektrotechnik T: +49 221-8275-2697 M: +49 174 891 9002 E: johanna@th-koeln.de Technische Hochschule Köln Campus Deutz Betzdorfer Str. 2 50679 Köln Raum: HW2-40 www.th-koeln.de
[O] change font-size in python plots depending on context
Dear org-mode fans, I have various files that go together in one document, either chapterwise or the whole book. And just as with tikz (latex) I want the font size of python plots to change automatically when the context changes. So I tried to define a variable in one of the header files like this: #+name: fs #+BEGIN_SRC emacs-lisp 10 #+END_SRC I also tried to define it like this #+name: fs #+begin_src python :results output :session :exports none fontsize=10 return fontsize #+end_src And then, in another file (that is being included by the header file) I added :var fontsize=fs to the header and replaced the number by this variable. I understand it complained that fs could not be found if I used C-c C-c directly to test, since apparently the variable fs only belongs to the other buffer (This is the first problem). However, it doesn't work either when I compile everything (the second problem). Probably it is also possible to solve this with some function in elisp. But, I have to admit, that I haven't started learning elisp yet. Does anyone have a solution to this problem? Any hints to helpful blogs or stackexchange pages would be appreciated. I did a search but probably not using the right keywords. Thanks! J
Re: [O] Show weekday in daily agenda view
Hey there, thank you very much, that is now perfect: I use (setq org-agenda-format-date ;; (1) "%Y-%m-%d %A ") ;; (1) (the (1) in brackets gives me an indication of where I got the initial code from) and it gives me 2019-05-15 Mittwoch all I want :) Cheers and have a good week J Richard Lawrence writes: > Hi Johanna, > > "Prof. Dr. Johanna May" writes: > >> thanks for pointing me at the variable org-agenda-format-date. There >> was a line in my dotemacs that included a formatting without the >> weekday (something like %y-%w-%d). > > Ah, ok, great! > >> I could not figure out how the name-of-the-weekday format would be >> called. But for now I'm fine with returning to the default which gives >> me an English date including the weekday. > > You probably want "%a" or "%A" somewhere in there, if you want a > locale-specific name of the weekday. See the docstring for the > format-time-string function.
Re: [O] Show weekday in daily agenda view
Hi Richard, thanks for pointing me at the variable org-agenda-format-date. There was a line in my dotemacs that included a formatting without the weekday (something like %y-%w-%d). I could not figure out how the name-of-the-weekday format would be called. But for now I'm fine with returning to the default which gives me an English date including the weekday. Cheers, J Richard Lawrence writes: > Hi Johanna, > > johanna@th-koeln.de writes: > >> maybe I did not search the right way in google alias startpage. But I >> could not figure out how to write next to the date e.g. 2000-04-01 the >> weekday, i.e. the specific day of the week. It would come very handy to >> have the date displayed as 2019-05-14 Tu and 2019-05-15 We and so on. Or >> even have it spelled out as 2019-05-14 Tuesday. >> >> Probably there is a way of setting this. How does it work? > > Hmm. My daily agenda (the default one) starts like this: > > Day-agenda (W20): > Tuesday14 May 2019 > > and tasks, etc. are listed below that. I don't think I've ever > customized this. Are you seeing something different? Or maybe you mean > something else by "agenda"? > > If you're talking about Org's built-in agenda, you might want to take a > look at the `org-agenda-format-date' variable. Mine is set to the > org-agenda-format-date-aligned function, which I assume is what outputs > the example above. > > If you're just talking about timestamps in Org files, you might want to > look at the `org-time-stamp-custom-formats' and > `org-display-custom-times' variables. > > Hope that helps!
[O] Show weekday in daily agenda view
Hi org-mode community, maybe I did not search the right way in google alias startpage. But I could not figure out how to write next to the date e.g. 2000-04-01 the weekday, i.e. the specific day of the week. It would come very handy to have the date displayed as 2019-05-14 Tu and 2019-05-15 We and so on. Or even have it spelled out as 2019-05-14 Tuesday. Probably there is a way of setting this. How does it work? Thanks and cheers, J
[O] Dual document export slides and lecture notes title slide issue
Dear org-mode community, I'm a noob, started using org-mode about probably only 9 months ago. However, I'd say my latex knowledge is intermediate, so that helps. I followed some of the instruction in https://orgmode.org/worg/exporters/beamer/beamer-dual-format.html in order to get dual beamer and scrrprt document export. In this link the author mentions the following: "In my environment, I used a hack that assumes Beamer has been added to |org-latex-classes| under the exact string "beamer." This is not ideal, because a user might have added a custom class under a different name. Nicolas Goaziou proposed an alternate approach using regular expressions, but I didn't implement it in my environment." Since in my set-up (probably newer than this 2014 instruction) I cannot find ox-beamer.el as a separate file - and this hack seems fishy to me - I tried to find Nicolas Goaziou's regexp instructions of how to include the titlepage in the beamer presentation in spite of the ignorenonframetext option. However, I could not find anything that was related by him in my searches. So, my question is: Could I add this titlepage by making some sort of copy of the beamer class (something like mybeamer, similar to myscrartcl in https://www.suenkler.info/notes/emacs-config/) in my dotemacs, just adding a few lines there? And what would I add there? Or the other option would be to switch on the ignorenonframetext option later in the document, i.e. after the title slide - how could I get that done? Something like :beamer_opt: ignorenonframetext in every section's property drawer? I don't really care about elegance, I'm interested in stable function. It would be great if you could just point me at well documented examples of other people who are making dual documents for both teaching (slides) and for students to recap with notes (lecture notes) based on the same diagrams. I also am considering using html instead of pdf for the slides, but I haven't so far because I haven't come across any tablet annotating possibility for browser pages: In some slides I want to leave blank spaces in order to demonstrate the calculations live. So, thank you very much for your ideas in advance. I subscribed to the digest, not the single emails, so I probably won't read your answers before this evening (and also not reply to questions about clarification of my issue). I have to say, that I really like what org-mode, and org-babel can do. And I want to thank all of you who are contributing on this. At some point of time I also want to start a blog and share my working examples so that others can profit. But I first need to re-make my lecture notes in a more sustainable and reproducible way. Cheers, J. M.
