Python: fatal: not a git repository Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set)

Question

When I run

proc = subprocess.Popen(['git', 'add', '-A'], stdout=subprocess.PIPE)

I get this error

fatal: not a git repository (or any parent up to mount point /media)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).

But running

os.system('git add -A')

Does the job perfectly.

If you think the folder does not have a .git file,

proc = subprocess.Popen(['ls', '-a'], stdout=subprocess.PIPE)

shows that it is already in the cwd.

Why Popen cannot stage the files, nor can it do the commit while os.system does both?

---

Update:

Here is my failed MWE

import subprocess
import os

cwd = os.getcwd()
proj_path = os.path.join(cwd, 'newproj')
os.makedirs(proj_path)
os.chdir(proj_path)
proc = subprocess.Popen(['git', 'init'], stdout=subprocess.PIPE)
proc = subprocess.Popen(['ls', '-a'], stdout=subprocess.PIPE)
print(proc.stdout.read().decode('ascii'))
proc = subprocess.Popen(['git', 'add', '-A'], stdout=subprocess.PIPE)
out, err = proc.communicate()
if err:
    print('Error:\n', err.decode())
print(out.decode('ascii'))

output

.
..
.git

fatal: not a git repository (or any parent up to mount point /media)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).

Answer 1

My Python version is a little behind yours, but I was able to reproduce the problem, which is actually pretty simple:

proc = subprocess.Popen(['git', 'init'], stdout=subprocess.PIPE)
proc = subprocess.Popen(['ls', '-a'], stdout=subprocess.PIPE)
print(proc.stdout.read().decode('ascii'))
proc = subprocess.Popen(['git', 'add', '-A'], stdout=subprocess.PIPE)

Note the lack of any calls to proc.wait() or similar. This means we spin off a git init and do not wait for it.

Next, we run ls -a. Here we do wait a little bit—long enough to read its output to EOF, which is actually relatively long as EOF only occurs because ls -a finishes—and meanwhile the git init is still running. Depending on how fast git init is doing its work, we may or may not find the .git directory here. If this takes long enough, the git init may also finish. Fortunately the git init on my system is sufficiently slower than the ls -a that I see the same effect as you. (Well, I found that the .git directory sometimes doesn't exist yet.)

Last, we run git add -A. The git init may or may not still be running. As it turns out, it is still running, and has not yet gotten far enough to establish the .git directory as a Git repository. So git add -A complains, with the error you observed.

If we add proc.wait() right after the git init—ideally, we should check the return code, or simply use subprocess.check_call or subprocess.run here—the problem goes away.