I have a user case where I need to execute a magic command and pass an argument to it, for example:
%my_magic_command hello
What I wish is for hello to be a value from an environment variable, e.g. assume I have an environment variable MY_VAR=hello, I want to be able to call something like
%my_magic_command $MY_VAR
Is there a way to achieve this in Jupyter?
Related
It looks like my Jupyter notebook picks up everything that I export in my .bash_profile, but nothing that I alias.
I think ! uses bin/sh, so it's understandable that the aliases from the bash profile don't port over, but the %%bash magic also does not pick up the aliases I've written.
Is there a way to make the aliases in my bash profile available through ! (ideally) or, at the least, using %%bash?
This seems to work (python3, modified from a hack I found in a jupyter issue)
import subprocess
lines = subprocess.check_output('source ~/.bash_profile; alias',shell=True).split(b'\n')
manager = get_ipython().alias_manager
for line in lines:
line = line.decode("utf-8")
split_index = line.find('=')
cmd = line[split_index+1:]
alias = line[:split_index]
cmd = cmd[1:-1]
print ("ALIAS:{}\t\tCMD:{}".format(alias,cmd))
manager.soft_define_alias(alias, cmd)
Here's another alternative, which is less a solution than a workaround: you can define aliases locally to the notebook using the %alias magic, and make those aliases available in the future using the %store magic. More alias trickiness here: https://github.com/ipython/ipython/wiki/Cookbook:-Storing-aliases
More on the %store magic here: http://ipython.readthedocs.io/en/stable/config/extensions/storemagic.html
The next step is hacking the %store magic to persist these aliases: https://github.com/ipython/ipython/blob/master/IPython/extensions/storemagic.py
For posterity, here are the results of some experiments I ran before finally finding a solution:
I sourced my .bash_profile in a %%bash cell. From within that cell, I was able to interrogate the values of variables I defined in my .bash_profile, and was able to list aliased commands by invoking alias. However, I was still not able to use aliased commands. Additionally, variables defined in my .bash_profile were only accessible inside the cell with the source call: trying to access them in subsequent %%bash cell didn't work, and the alias command also failed. More interesting still: if I sourced using !, I wasn't able to interrogate variables defined in my bash profile nor list my aliases with ! shell commands in the same cell.
Suffice it say, the %%bash magic is finicky.
I have looked at documentation of GNU Makefile Conditional Statements, but I couldn't find any information on how to build both the target and its dependencies conditionally.
EDIT: When I say conditionally, I mean dependent on values of variable set in command line while calling make. I apologize for not making it clear earlier.
To add to the above edit. If some variables set in the commandline take a particular value, even if the targets and their dependencies need to be updated, I want to refrain from doing this.
GNU Makefile Conditionals
Thanks!
What about something like:
ALL_TARGETS = foo bar
ifndef SOME_VARIABLE
ALL_TARGETS += biz baz
endif
all: $(ALL_TARGETS)
Now if you run make it will build foo, bar, biz, and baz, but if you run make SOME_VARIABLE=true it will only build foo and bar.
With the very generic, specifics-free question that's about all we can suggest.
Typical use of the magic command %run is
%run foo.py
for some script file foo.py.
Is there a way to use this command to run a cell, e.g. In[83], instead of foo.py?
This can be done simply by executing:
exec(In[83])
Santiago, you can do that simply calling your foo.py each time you need. This is the samr that "call a cell" by their "name" (i.e. In[83] or whatever). That are the advantages of scripts.
%load 83 then Enter will be shorter to write than exec(In[83]) and will work all the time (almost same context).
Furthermore, it allows you to modify the cell (which is often useful)
I am trying to run the following command from Julia:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/user/.julia/v0.3/Smile/deps/downloads
When I run it as-is it tries to replace $LD_LIBRARY_PATH with a local variable.
When I escape the $, it puts quotes around the command, which invalidates it.
julia> cmd = `export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/tim/.julia/v0.3/Smile/deps/downloads`
ERROR: LD_LIBRARY_PATH not defined
julia> cmd = `export LD_LIBRARY_PATH=\$LD_LIBRARY_PATH:/home/tim/.julia/v0.3/Smile/deps/downloads`
`export 'LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/tim/.julia/v0.3/Smile/deps/downloads'`
I would like to run the command in a form similar to:
run(`export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$newpath`)
How do I properly handle the dollar sign?
Thank you
*note: pasting the command directly into terminal and running it does work
In Julia, backticks are not completely equivalent to running the corresponding command at the shell. You can't interpolate environmental variables with $ (although $(get(ENV, "varname", "") should match the shell's behavior), and export is a shell built-in, not a command, so I don't think you can run it. Also, even if backticks shelled out, export would only change the environment of the subshell, not the calling process.
You should be able to set LD_LIBRARY_PATH from Julia as:
ENV["LD_LIBRARY_PATH"] = "$(get(ENV, "LD_LIBRARY_PATH", "")):$newpath"
but you should avoid this if possible. If your intent is to ccall a specific library, you can pass the library path directly to ccall, perhaps using find_library as you indicated in a comment if you don't know the full path advance. If you need to set LD_LIBRARY_PATH because the library needs to load other libraries, I'm not sure if there's a better way, but note that LD_LIBRARY_PATH is platform-specific. You might be able to dlopen the dependent libraries first, but I haven't tested that.
I'm new to zsh and am using the ZSH_THEME="jnrowe", which works great for a little while.
It starts out and I get a prompt that looks like this:
Ξ ~ →
but if I run a command like: ssh it becomes:
↑255 ~ →
I suspect something is messing up the character that was creating the triple bar in the first one, but have no clue really as to what's going on. I could just pick a different theme, but I've noticed most of them with a fancy character in the prompt do the same thing.
Is this a special error code or something? Or is something just borking out?
I don't know the prompt theme "jnrowe" (it's not part of the default zsh distribution afaics), but I suspect this prompt includes the error code of the last command in its output.
Try to run "ls" or "true" and the number will disapper. Run "false" and it will be 1, run ssh without arguments and it will be 255. zsh preserves this value until you run the next command, so pressing ENTER many times will not clear it.
(This will be the same value that is stored in the shell variable "$?")