Re: [GRASS-user] Trying to use GRASS with Jupyter note books in Windows
On Thu, 28 Sept 2023 at 16:09, Vishal Mehta wrote: > > Also, can I use bash within the jupyter notebook? I'm not familiar with > the gs.script syntax; I'm very comfortable with the old bash ways.. > so any day I would rather > glist rast than > gs.list_grouped(type=['raster']) > That's really your choice as a user of Jupyter, GRASS GIS just provides the Python API in addition to the command line interface. The command line interface is there and you can use it from Bash or whatever else. > What i'm hoping for is a way to mix and match within a single workflow, > taking advantage of things like the interactive map via python > what-have-you's, but sticking to the bash commands for pretty much > everything else. > Use the exclamation mark lines in Jupyter (with IPython kernel). That passes the line to your operating system. If you simply want general command line syntax, that's the way to go on any platform. With that, you can mix and match easily and that's relatively common thing to do. I'm doing it a lot when experimenting, but for sharing I usually go with one syntax which then needs to be Python. > I saw some notebooks with something like > %%bash > > > but that didn't work for me.. > I would have to check, but the I would guess that your Windows does not have Bash on path? This %%bash creates quite nice experience on Linux (locally, cloud, etc.), but I don't know if it is the right choice on Windows, but that's up to you to decide. ___ grass-user mailing list grass-user@lists.osgeo.org https://lists.osgeo.org/mailman/listinfo/grass-user
Re: [GRASS-user] Trying to use GRASS with Jupyter note books in Windows
On Sat, Sep 30, 2023 at 12:36 AM Vishal Mehta wrote: > > Thanks Markus, > I installed bash kernel; and it seems that it is there (#lsmagic lists bash > as one of the cell magics) > > but I get the error below: > > ##bash > g.list type=rast [...] Probably worth a bug report in GitHub. > Also I am unable to install extensions r.stream.distance: > > !g.extension r.stream.distance > > as well as through the GUI > > > both give me a "cannot find executable git" error This has been this bug: https://github.com/OSGeo/grass/issues/3077 which was fixed last week: https://github.com/OSGeo/grass/pull/3166 It will be fixed in GRASS GIS 8.3.1 - release in preparation. Best, Markus ___ grass-user mailing list grass-user@lists.osgeo.org https://lists.osgeo.org/mailman/listinfo/grass-user
Re: [GRASS-user] Trying to use GRASS with Jupyter note books in Windows
Thanks Markus,
I installed bash kernel; and it seems that it is there (#lsmagic lists bash
as one of the cell magics)
but I get the error below:
##bash
g.list type=rast
---CalledProcessError
Traceback (most recent call last)
Cell In[20], line 1> 1 get_ipython().run_cell_magic('bash', '',
'g.list rast\n')
File C:\GRASS GIS
8.3\Python39\lib\site-packages\IPython\core\interactiveshell.py:2493,
in InteractiveShell.run_cell_magic(self, magic_name, line, cell)
2491 with self.builtin_trap: 2492 args = (magic_arg_s, cell)->
2493 result = fn(*args, **kwargs) 2495 # The code below prevents
the output from being displayed 2496 # when using magics with
decorator @output_can_be_silenced 2497 # when the last Python token
in the expression is a ';'. 2498 if getattr(fn,
magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False):
File C:\GRASS GIS
8.3\Python39\lib\site-packages\IPython\core\magics\script.py:154, in
ScriptMagics._make_script_magic..named_script_magic(line,
cell)152 else:153 line = script--> 154 return
self.shebang(line, cell)
File C:\GRASS GIS
8.3\Python39\lib\site-packages\IPython\core\magics\script.py:314, in
ScriptMagics.shebang(self, line, cell)309 if args.raise_error and
p.returncode != 0:310 # If we get here and p.returncode is
still None, we must have311 # killed it but not yet seen its
return code. We don't wait for it,312 # in case it's stuck in
uninterruptible sleep. -9 = SIGKILL313 rc = p.returncode or
-9--> 314 raise CalledProcessError(rc, cell)
CalledProcessError: Command 'b'g.list rast\n'' returned non-zero exit
status 127.
--
Also I am unable to install extensions r.stream.distance:
!g.extension r.stream.distance
as well as through the GUI
both give me a "cannot find executable git" error
Best,
Vishal
On Fri, Sep 29, 2023 at 11:53 AM Markus Neteler wrote:
> On Thu, Sep 28, 2023 at 10:09 PM Vishal Mehta
> wrote:
> >
> > Thanks Markus and Vaclav,
> >
> > This is what worked for me on Windows:
> > # Ask GRASS GIS where its Python packages are.
> > sys.path.append(
> > subprocess.check_output(["C:\GRASS GIS 8.3/grass83.bat", "--config",
> "python_path"], text=True).strip()
> > )
>
> Perfect, added to the Wiki page, too.
>
> > Also, can I use bash within the jupyter notebook?
>
> Seems yes, after:
>
> pip install bash_kernel
>
> Markus
>
--
Vishal K. Mehta, PhD
Sr. Scientist
Stockholm Environment Institute - US
501 D St
Davis CA 95616
https://www.sei.org/people/vishal-mehta/
___
grass-user mailing list
grass-user@lists.osgeo.org
https://lists.osgeo.org/mailman/listinfo/grass-user
Re: [GRASS-user] Trying to use GRASS with Jupyter note books in Windows
On Thu, Sep 28, 2023 at 10:09 PM Vishal Mehta wrote: > > Thanks Markus and Vaclav, > > This is what worked for me on Windows: > # Ask GRASS GIS where its Python packages are. > sys.path.append( > subprocess.check_output(["C:\GRASS GIS 8.3/grass83.bat", "--config", > "python_path"], text=True).strip() > ) Perfect, added to the Wiki page, too. > Also, can I use bash within the jupyter notebook? Seems yes, after: pip install bash_kernel Markus ___ grass-user mailing list grass-user@lists.osgeo.org https://lists.osgeo.org/mailman/listinfo/grass-user
Re: [GRASS-user] Trying to use GRASS with Jupyter note books in Windows
Thanks Markus and Vaclav, This is what worked for me on Windows: # Ask GRASS GIS where its Python packages are. sys.path.append( subprocess.check_output(["C:\GRASS GIS 8.3/grass83.bat", "--config", "python_path"], text=True).strip() ) Also, can I use bash within the jupyter notebook? I'm not familiar with the gs.script syntax; I'm very comfortable with the old bash ways.. so any day I would rather glist rast than gs.list_grouped(type=['raster']) What i'm hoping for is a way to mix and match within a single workflow, taking advantage of things like the interactive map via python what-have-you's, but sticking to the bash commands for pretty much everything else. I saw some notebooks with something like %%bash but that didn't work for me.. Thanks, Vishal On Thu, Sep 28, 2023 at 12:46 AM Markus Neteler wrote: > On Thu, Sep 28, 2023 at 5:22 AM Vaclav Petras via grass-user > wrote: > > > > Hi Vishal, > > > > The executable on Windows is not called "grass" like on Linux but > "grass8" or "grass83" (to avoid a strange Python > > import error). That should do the trick. If not, try simply providing a > full path yourself including the extension (C:\...\...bat). > > I have taken liberty to cite this note here: > > https://grasswiki.osgeo.org/wiki/GRASS_GIS_Jupyter_notebooks#Windows_tricks > > Best, > Markus > ___ grass-user mailing list grass-user@lists.osgeo.org https://lists.osgeo.org/mailman/listinfo/grass-user
Re: [GRASS-user] Trying to use GRASS with Jupyter note books in Windows
On Thu, Sep 28, 2023 at 5:22 AM Vaclav Petras via grass-user wrote: > > Hi Vishal, > > The executable on Windows is not called "grass" like on Linux but "grass8" or > "grass83" (to avoid a strange Python > import error). That should do the trick. If not, try simply providing a full > path yourself including the extension (C:\...\...bat). I have taken liberty to cite this note here: https://grasswiki.osgeo.org/wiki/GRASS_GIS_Jupyter_notebooks#Windows_tricks Best, Markus ___ grass-user mailing list grass-user@lists.osgeo.org https://lists.osgeo.org/mailman/listinfo/grass-user
Re: [GRASS-user] Trying to use GRASS with Jupyter note books in Windows
Hi Vishal, The executable on Windows is not called "grass" like on Linux but "grass8" or "grass83" (to avoid a strange Python import error). That should do the trick. If not, try simply providing a full path yourself including the extension (C:\...\...bat). Best, Vaclav On Wed, 27 Sept 2023 at 21:20, Vishal Mehta via grass-user < grass-user@lists.osgeo.org> wrote: > I'm trying to follow this setup: > > https://github.com/ncsu-geoforall-lab/GIS714-assignments/blob/main/GRASS_GIS_Foundations/JupyterOnWindows_Tutorial.ipynb > > I have stand-alone GRASS GIS 8.3 installed in Windows in C:\GRASS GIS 8.3 > > I followed the 7 setup steps (changing set path to reflect that its > installed in C:\GRASS GIS 8.3 > Then when i run this first part: > > import os > import subprocess > import sys > > # Ask GRASS GIS where its Python packages are. > sys.path.append( > subprocess.check_output(["grass", "--config", "python_path"], > text=True).strip() > ) > > # Import GRASS packages > import grass.script as gs > import grass.jupyter as gj > -- > I get the following error: > > ---FileNotFoundError > Traceback (most recent call last) > Cell In[1], line 7 3 import sys 5 # Ask GRASS GIS where its Python > packages are. 6 sys.path.append(> 7 > subprocess.check_output(["grass", "--config", "python_path"], > text=True).strip() 8 ) 10 # Import GRASS packages 11 import > grass.script as gs > > File C:\GRASS GIS 8.3\Python39\lib\subprocess.py:424, in > check_output(timeout, *popenargs, **kwargs)421 empty = b''422 > kwargs['input'] = empty--> 424 return run(*popenargs, stdout=PIPE, > timeout=timeout, check=True,425**kwargs).stdout > > File C:\GRASS GIS 8.3\Python39\lib\subprocess.py:505, in run(input, > capture_output, timeout, check, *popenargs, **kwargs)502 > kwargs['stdout'] = PIPE503 kwargs['stderr'] = PIPE--> 505 with > Popen(*popenargs, **kwargs) as process:506 try:507 > stdout, stderr = process.communicate(input, timeout=timeout) > > File C:\GRASS GIS 8.3\Python39\lib\subprocess.py:951, in Popen.__init__(self, > args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, > shell, cwd, env, universal_newlines, startupinfo, creationflags, > restore_signals, start_new_session, pass_fds, user, group, extra_groups, > encoding, errors, text, umask)947 if self.text_mode:948 > self.stderr = io.TextIOWrapper(self.stderr,949 > encoding=encoding, errors=errors)--> 951 self._execute_child(args, > executable, preexec_fn, close_fds,952 pass_fds, > cwd, env,953 startupinfo, creationflags, shell, > 954 p2cread, p2cwrite,955 > c2pread, c2pwrite,956 errread, errwrite,957 >restore_signals,958 gid, > gids, uid, umask,959 start_new_session)960 > except:961 # Cleanup if the child failed starting.962 for f > in filter(None, (self.stdin, self.stdout, self.stderr)): > > File C:\GRASS GIS 8.3\Python39\lib\subprocess.py:1420, in > Popen._execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, > cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, > c2pwrite, errread, errwrite, unused_restore_signals, unused_gid, unused_gids, > unused_uid, unused_umask, unused_start_new_session) 1418 # Start the > process 1419 try:-> 1420 hp, ht, pid, tid = > _winapi.CreateProcess(executable, args, 1421 # > no special security 1422 None, None, 1423 > int(not close_fds), 1424 > creationflags, 1425 env, 1426 > cwd, 1427 startupinfo) > 1428 finally: 1429 # Child is launched. Close the parent's copy of > those pipe 1430 # handles that only the child should have open. You > need (...) 1433 # pipe will not close when the child process exits > and the 1434 # ReadFile will hang. 1435 > self._close_pipe_fds(p2cread, p2cwrite, 1436 > c2pread, c2pwrite, 1437 errread, errwrite) > FileNotFoundError: [WinError 2] The system cannot find the file specified > > > Can someone help figure out what the issue is? > Thanks, > Vishal > ___ > grass-user mailing list > grass-user@lists.osgeo.org > https://lists.osgeo.org/mailman/listinfo/grass-user > ___ grass-user mailing list grass-user@lists.osgeo.org https://
