emacs-orgmode@gnu.org archives
 help / color / mirror / code / Atom feed
From: "Adolfo De Unanue" <adolfo+org@unanue.mx>
To: emacs-orgmode@gnu.org
Subject: org-babel not finding executables when using direnv [Was: Re: ob-sql is not finding psql when using direnv+guix]
Date: Thu, 13 May 2021 12:12:03 -0500	[thread overview]
Message-ID: <99230428-5576-4f08-8312-935967822eb8@www.fastmail.com> (raw)
In-Reply-To: <DM6PR20MB34105EF06BDAEDA0E679F83BBE529@DM6PR20MB3410.namprd20.prod.outlook.com>



On Wed, May 12, 2021, at 08:49, Cook, Malcolm wrote:
> > > >I am using Guix with direnv.
> > > 
> > > What is your shell?
> > > 
> > 
> > My shell is bash, originally I was using zsh and I thought that was the problem, so I switched to bash and still not working.
> > 
> > > How/When do you "hook direnv into your shell" (https://direnv.net/)?
> > > 
> > 
> > In the .profile file, at login.
> > 
> > > > In an specific folder I am installing and using psql and postgresql using direnv+guix as follows:
> > > >use guix --manifest=cdpp-manifest.scm
> > > >
> > > >export PGUSER=food_user
> > > >export PGPASSWORD=some_password
> > > >export PGDATABASE=food
> > > >
> > > >layout postgres
> > > 
> > > When are you doing this?
> > > 
> > > a) in the "specific folder"'s .envrc file?
> > > b) in an org-mode shell block that you execute prior to the sql block?
> > > c) ??
> > 
> > Option (a)
> > 
> > 
> > > You seem to be following [Per\-project 
> > > Postgres](https://jamey.thesharps.us/2019/05/29/per-project-postgres/) 
> > > but with guix instead of nix. Nice.
> > > 
> > 
> > Yep, great post. direnv + guix change the way I develop software, do data science and write lectures and papers.
> > 
> > > If you enter the directory and then call emacs, earthing should just 
> > > work, no changes neede.
> > > 
> > 
> > It works for almost everything (sql-buffers, python buffers, etc), except for org-babel sql blocks.
> > 
> > I am using EXWM, so emacs is always on.
> > 
> > 
> > > If you want to tell emacs to adopt the environment established by a 
> > > .direnv, you probably want [direnv integration for 
> > > emacs\.](https://github.com/wbolster/emacs-direnv)
> > > 
> > 
> > emacs-direnv was my first choice, but then I changed to envrc (https://github.com/purcell/envrc) . In both I got the error.
> > 
> 
> I see.  Envrc looks superior.  Good to know.
> 
> You've covered all my bases.  Shooting in the dark,  I would 
> confirm/check the following:
> 

I have news:

It fails for python too. Using the same files as before and this block:

#+begin_src python 
import pandas as pd
import matplotlib.pyplot as plt
#+end_src

It finds matplotlib, but fails to find pandas. I tried the same trick as before (but with the python executable, no psql), added the line

    (org-babel-python-command . ".direnv/.guix-profile/bin/python3")

but is not working. 

But if I am in shell, or in a python buffer or in a inferior-python process Emacs is finding all the libraries and executables.

So, I am assumming that the problem lies in how org-babel searchs the path ...

Answers to your questions below:


> How do you know that envrc is working otherwise?
> 
> When you switch to a direnv controlled buffer do you get any 
> informative diagnostics in *Messages*?
> 

Yes

> Do you get any more if you first `(setq envrc-debug t)`?
> 
Didn't try, Will do later

> Is this buffer in the same directory as the .direnvrc file?
> 

Yes

> Presumably TRAMP is not in the mix in any way.
>

No
 
> Variable sql-postgres-program is unchanged from default value of psql
> 
> What is result of
> 
> 	m-x shell-command
> 	which psql
> 

Is empty when I am not in a direnv controlled directory, the correct path when I enter to those directories.

> and does it change as expected/required depending on the current active 
> .direnvrc?
> 
> What happens if you eval (getenv 'psql) while in buffer governed by 
> direnv, or alternatively
> 
> 	m-x getenv
> 	psql
> 
> If you `m-x shell`, does normal direnv work as expected in the created shell?
> 

Yes, also works in vterm

> > > I've got to try this!
> > > 
> > > Cheers
> > > 
> > 
> > Please tell me how that works for you
> 
> Gotta get guix rolling again.  Hope to do this RSN.
> 
> Cheers,
> 
> ~Malcolm
> 
> > 
> > Thanks
> > 
> > - A
> > 
> > 
> > > >
> > > >
> > > >Where cdpp-manifest.scm contains the following:
> > > >
> > > >(specifications->manifest
> > > >'("python"
> > > >   "python-pandas"
> > > >   "python-numpy"
> > > >   "python-flask"
> > > >   "python-graphene"
> > > >   "postgresql"
> > > >   "jupyter"))
> > > >
> > > >I am able to use sql-mode and run queries against the database, in order to achieve that I am using the following .dir-locals.el
> > > >
> > > >;;; Directory Local Variables
> > > >;;; For more information see (info "(emacs) Directory Variables")
> > > >
> > > >
> > > >((nil .
> > > >      ((projectile-project-test-cmd . "pytest --color=no --failed-first --maxfail=5")))
> > > >(python-mode .
> > > >              ((python-shell-buffer-name . "Python [CDPP-Inspecciones]")))
> > > >
> > > >(org-mode . (
> > > >              (indent-tabs-mode . nil)
> > > >              (org-src-preserve-indentation . t)
> > > >              (org-footnote-auto-adjust . t)
> > > >              (org-footnote-auto-label . t)
> > > >              (ispell-local-dictionary . "spanish")
> > > >              (org-export-allow-bind-keywords . t)
> > > >              (org-footnote-define-inline . nil)
> > > >              (org-footnote-section . "Footnotes")))
> > > >
> > > >(sql-mode . ((sql-connection-alist . ((mydb
> > > >                                        (sql-product 'postgres)
> > > >                                        (sql-database "mydb")
> > > >                                        (sql-user "db_user")
> > > >                                        (sql-server (expand-file-name ".direnv/postgres"))
> > > >                                        (sql-port 5432)
> > > >                                        )
> > > >                                      )))))
> > > >
> > > >But If I try to use an sql org-babel block
> > > >
> > > >#+begin_src sql
> > > >select 1;
> > > >#+end_src
> > > >
> > > >(I am setting the connection variables in a PROPERTY)
> > > >
> > > >I get the error: `psql is not found`
> > > >
> > > >
> > > >I was reading about the variable sql-postgres-program, so if I set the following in dir-locals.el
> > > >
> > > >(sql-postgres-program . "/gnu/store/f2v92bkx2vfzmkl14qxj3hlmby4dy9x0-profile/bin/psql")
> > > >
> > > >It works (note that psql ONLY lives inside the profile defined by direnv+guix), but I don't like the idea of hardcode the path.
> > > >
> > > >Is there a better way?
> > > >
> > > >Ideally I will expect that the org block will read it from the environment, but is not working. 
> > > >
> > > >Thanks in advance
> > > >
> > > 
> > 
> 


  reply	other threads:[~2021-05-13 17:16 UTC|newest]

Thread overview: 7+ messages / expand[flat|nested]  mbox.gz  Atom feed  top
2021-05-09  8:07 ob-sql is not finding psql when using direnv+guix Adolfo De Unanue
2021-05-10 18:14 ` Cook, Malcolm
2021-05-11 20:54   ` Adolfo De Unanue
2021-05-12 13:49     ` Cook, Malcolm
2021-05-13 17:12       ` Adolfo De Unanue [this message]
2021-05-13 18:23         ` org-babel not finding executables when using direnv [Was: Re: ob-sql is not finding psql when using direnv+guix] Cook, Malcolm
2021-05-13 22:54         ` Tim Cross

Reply instructions:

You may reply publicly to this message via plain-text email
using any one of the following methods:

* Save the following mbox file, import it into your mail client,
  and reply-to-all from there: mbox

  Avoid top-posting and favor interleaved quoting:
  https://en.wikipedia.org/wiki/Posting_style#Interleaved_style

  List information: https://www.orgmode.org/

* Reply using the --to, --cc, and --in-reply-to
  switches of git-send-email(1):

  git send-email \
    --in-reply-to=99230428-5576-4f08-8312-935967822eb8@www.fastmail.com \
    --to=adolfo+org@unanue.mx \
    --cc=emacs-orgmode@gnu.org \
    --subject='org-babel not finding executables when using direnv [Was: Re: ob-sql is not finding psql when using direnv+guix]' \
    /path/to/YOUR_REPLY

  https://kernel.org/pub/software/scm/git/docs/git-send-email.html

* If your mail client supports setting the In-Reply-To header
  via mailto: links, try the mailto: link

Code repositories for project(s) associated with this inbox:

	https://git.savannah.gnu.org/cgit/emacs/org-mode.git

This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox;
as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).