GitHub integration error

[navidcy]

I did

git clone layer2_tau1e-1_manyshortridges layer2_tau6e-1_manyshortridges
cd newfolder

various changes

git commit -am"new setup"
payu ghsetup
git push

and I get this:

[nc3020@raijin2 layer2_tau6e-1_manyshortridges]$ git commit la2* -am"run for 30 years"; git push;
fatal: Paths with -a does not make sense.
Counting objects: 7, done.
Delta compression using up to 32 threads.
Compressing objects: 100% (7/7), done.
Writing objects: 100% (7/7), 701 bytes | 0 bytes/s, done.
Total 7 (delta 5), reused 0 (delta 0)
remote: error: refusing to update checked out branch: refs/heads/master
remote: error: By default, updating the current branch in a non-bare repository
remote: error: is denied, because it will make the index and work tree inconsistent
remote: error: with what you pushed, and will require 'git reset --hard' to match
remote: error: the work tree to HEAD.
remote: error:
remote: error: You can set 'receive.denyCurrentBranch' configuration variable to
remote: error: 'ignore' or 'warn' in the remote repository to allow pushing into
remote: error: its current branch; however, this is not recommended unless you
remote: error: arranged to update its work tree to match what you pushed in some
remote: error: other way.
remote: error:
remote: error: To squelch this message and still keep the default behaviour, set
remote: error: 'receive.denyCurrentBranch' configuration variable to 'refuse'.
To /home/552/nc3020/SOchanBcBtEddySat/layer2/layer2_tau1e-1_manyshortridges
 ! [remote rejected] master -> master (branch is currently checked out)
error: failed to push some refs to '/home/552/nc3020/SOchanBcBtEddySat/layer2/layer2_tau1e-1_manyshortridges'
[nc3020@raijin2 layer2_tau6e-1_manyshortridges]$ git push
Counting objects: 7, done.
Delta compression using up to 32 threads.
Compressing objects: 100% (7/7), done.
Writing objects: 100% (7/7), 701 bytes | 0 bytes/s, done.
Total 7 (delta 5), reused 0 (delta 0)
remote: error: refusing to update checked out branch: refs/heads/master
remote: error: By default, updating the current branch in a non-bare repository
remote: error: is denied, because it will make the index and work tree inconsistent
remote: error: with what you pushed, and will require 'git reset --hard' to match
remote: error: the work tree to HEAD.
remote: error:
remote: error: You can set 'receive.denyCurrentBranch' configuration variable to
remote: error: 'ignore' or 'warn' in the remote repository to allow pushing into
remote: error: its current branch; however, this is not recommended unless you
remote: error: arranged to update its work tree to match what you pushed in some
remote: error: other way.
remote: error:
remote: error: To squelch this message and still keep the default behaviour, set
remote: error: 'receive.denyCurrentBranch' configuration variable to 'refuse'.
To /home/552/nc3020/SOchanBcBtEddySat/layer2/layer2_tau1e-1_manyshortridges
 ! [remote rejected] master -> master (branch is currently checked out)
error: failed to push some refs to '/home/552/nc3020/SOchanBcBtEddySat/layer2/layer2_tau1e-1_manyshortridges'
[nc3020@raijin2 layer2_tau6e-1_manyshortridges]$ git commit la2* -m"run for 30 years"; git push;
[master 608a040] run for 30 years
 2 files changed, 1098 insertions(+)
 create mode 100644 la2_t6e-1ms.e1500038
 create mode 100644 la2_t6e-1ms.o1500038
Counting objects: 11, done.
Delta compression using up to 32 threads.
Compressing objects: 100% (11/11), done.
Writing objects: 100% (11/11), 4.95 KiB | 0 bytes/s, done.
Total 11 (delta 6), reused 0 (delta 0)
remote: error: refusing to update checked out branch: refs/heads/master
remote: error: By default, updating the current branch in a non-bare repository
remote: error: is denied, because it will make the index and work tree inconsistent
remote: error: with what you pushed, and will require 'git reset --hard' to match
remote: error: the work tree to HEAD.
remote: error:
remote: error: You can set 'receive.denyCurrentBranch' configuration variable to
remote: error: 'ignore' or 'warn' in the remote repository to allow pushing into
remote: error: its current branch; however, this is not recommended unless you
remote: error: arranged to update its work tree to match what you pushed in some
remote: error: other way.
remote: error:
remote: error: To squelch this message and still keep the default behaviour, set
remote: error: 'receive.denyCurrentBranch' configuration variable to 'refuse'.
To /home/552/nc3020/SOchanBcBtEddySat/layer2/layer2_tau1e-1_manyshortridges
 ! [remote rejected] master -> master (branch is currently checked out)
error: failed to push some refs to '/home/552/nc3020/SOchanBcBtEddySat/layer2/layer2_tau1e-1_manyshortridges'

Any ideas?

And now I can't even commit to GitHub the "usual" way? Or can I?

[marshallward]

Best guess is that the glob in `git commit la2 -am"..."picked up something unexpected here. (Actually, I'm not even sure that's a validgit commit`).

This error also does not bode well

fatal: Paths with -a does not make sense.

Is this just a bad commit throwing git into a spiral?

Maybe re-try as separate steps rather than one line.

[navidcy]

I did that previously and got the same error.

On Oct 24, 2018, at 11:05, Marshall Ward notifications@github.com wrote:

Best guess is that the glob in git commit la2 -am"..." picked up something unexpected here. (Actually, I'm not even sure that's a valid git commit).

This error also does not bode well

fatal: Paths with -a does not make sense. Is this just a bad commit throwing git into a spiral?

Maybe re-try as separate steps rather than one line.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

[marshallward]

I think there might be some role of payu here, but I think the underlying problem is that git commit la2* -am"..." is not a valid git command. If I do git help commit then I can see no use case where something like la2* is supposed to precede a flag. Are you sure this is what you mean to do here?

If you want to just try git commit -am"some msg" without the glob and see what happens?

Even if this does explain the problem, there might be room for payu to be more resilient to this problem.

[navidcy]

my bad: I actually did git commit la2* -m"run for 30 years"; git push; N

On Oct 24, 2018, at 2:01 PM, Marshall Ward notifications@github.com wrote:

I think there might be some role of payu here, but I think the underlying problem is that git commit la2 -am"..." is not a valid git command. If I do git help commit then I can see no use case where something like la2 is supposed to precede a flag. Are you sure this is what you mean to do here?

If you want to just try git commit -am"some msg" without the glob and see what happens?

Even if this does explain the problem, there might be room for payu to be more resilient to this problem.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/marshallward/payu/issues/133#issuecomment-432495185, or mute the thread https://github.com/notifications/unsubscribe-auth/AGyIQKlGab82dLaX03MNwz0rA3UNKCBIks5un9fvgaJpZM4X1OKW.

[AndyHoggANU]

Hi @marshallward -- I'm also having a but of trouble with this aspect of payu. I can commit OK, but I get this error:

amh157@raijin3:025deg_jra55_iaf_pipes %% payu ghsetup
Traceback (most recent call last):
 File "/apps/payu/0.10/bin/payu", line 8, in <module>
   cli.parse()
 File "/apps/payu/0.10/lib/payu/cli.py", line 61, in parse
   run_cmd(**args)
 File "/apps/payu/0.10/lib/payu/subcommands/ghsetup_cmd.py", line 24, in runcmd
   runlog.github_setup()
 File "/apps/payu/0.10/lib/payu/runlog.py", line 118, in github_setup
   github_auth = self.authenticate()
 File "/apps/payu/0.10/lib/payu/runlog.py", line 247, in authenticate
   github_username = runlog_config.get('username')
AttributeError: 'list' object has no attribute 'get'
amh157@raijin3:025deg_jra55_iaf_pipes %%```

[marshallward]

I think that's a bug that Paul found. It's been fixed in master but not 0.10.

If you delete the runlog: True entry then it should be ok.

[navidcy]

1) what/where is the runlog: True entry? 2) why don't you release a 0.10.1 then with the bug fixed?

[marshallward]

1. runlog: True would be in config.yaml
2. Because this particular problem is avoidable, and I'm in the middle of a much more delicate update, and would rather focus on that than on minor updates.

If you want to use the latest version, you can try to do a python setup.py install --user, although that is what I am currently testing.

[marshallward]

I think this was resolved as "git command broke the runlog". With a special guest issue from Andy that will be fixed in the next release.

There's a broader discussion of how to handle stray git commands, but those are being discussed in #135.