ghuls
commented
6 months ago Github might temporarily be unavailable during the download.
Closed hshcao closed 6 months ago
ghuls
commented
6 months ago Github might temporarily be unavailable during the download.
Describe the bug in the downloading process, the git close using https url did not work, but the ssh git worked (see extra note at bottom) in the installation process, the https url needs to be replaced. in which file do I change that? i.e., which installation file is called by 'pip install .' I just need to change the following line in the installation file: git clone --filter=blob:none --quiet https://github.com/aertslab/pycisTopic to git clone --filter=blob:none --quiet git@github.com:aertslab/pycisTopic.git
To Reproduce (scenicplus) test@master:~$ git clone git@github.com:aertslab/scenicplus.git Cloning into 'scenicplus'... remote: Enumerating objects: 3513, done. remote: Counting objects: 100% (823/823), done. remote: Compressing objects: 100% (314/314), done. remote: Total 3513 (delta 458), reused 733 (delta 398), pack-reused 2690 Receiving objects: 100% (3513/3513), 44.54 MiB | 37.00 KiB/s, done. Resolving deltas: 100% (1959/1959), done.
(scenicplus) test@master:~$ cd scenicplus/
(scenicplus) test@master:~/scenicplus$ pip install . Processing /home/test/scenicplus Installing build dependencies ... done Getting requirements to build wheel ... done Installing backend dependencies ... done Preparing metadata (pyproject.toml) ... done
Error output Processing /home/test/scenicplus Installing build dependencies ... done Getting requirements to build wheel ... done Installing backend dependencies ... done Preparing metadata (pyproject.toml) ... done Collecting loomxpy@ git+https://github.com/aertslab/LoomXpy@main (from scenicplus==1.0a1) Cloning https://github.com/aertslab/LoomXpy (to revision main) to /tmp/pip-install-vpx3jhvt/loomxpy_610499f5ef5449f58836ab45717056d2 Running command git clone --filter=blob:none --quiet https://github.com/aertslab/LoomXpy /tmp/pip-install-vpx3jhvt/loomxpy_610499f5ef5449f58836ab45717056d2 Resolved https://github.com/aertslab/LoomXpy to commit 61995ff10940968eac2cee8fe48300ab477a15d0 Installing build dependencies ... done Getting requirements to build wheel ... done Preparing metadata (pyproject.toml) ... done Collecting pycistarget@ git+https://github.com/aertslab/pycistarget (from scenicplus==1.0a1) Cloning https://github.com/aertslab/pycistarget to /tmp/pip-install-vpx3jhvt/pycistarget_af4fb4b1cd484b65975527308e2c309d Running command git clone --filter=blob:none --quiet https://github.com/aertslab/pycistarget /tmp/pip-install-vpx3jhvt/pycistarget_af4fb4b1cd484b65975527308e2c309d Resolved https://github.com/aertslab/pycistarget to commit 8cd78f110f4eeeb38d8f7006a1100a13d636d984 Installing build dependencies ... done Getting requirements to build wheel ... done Preparing metadata (pyproject.toml) ... done Collecting pycistopic@ git+https://github.com/aertslab/pycisTopic (from scenicplus==1.0a1) Cloning https://github.com/aertslab/pycisTopic to /tmp/pip-install-vpx3jhvt/pycistopic_caad988ea2164e85a363175e1f402b49 Running command git clone --filter=blob:none --quiet https://github.com/aertslab/pycisTopic /tmp/pip-install-vpx3jhvt/pycistopic_caad988ea2164e85a363175e1f402b49 error: RPC failed; curl 92 HTTP/2 stream 0 was not closed cleanly: CANCEL (err 8) fatal: the remote end hung up unexpectedly fatal: early EOF fatal: index-pack failed warning: Clone succeeded, but checkout failed. You can inspect what was checked out with 'git status' and retry with 'git restore --source=HEAD :/'
error: subprocess-exited-with-error
× git clone --filter=blob:none --quiet https://github.com/aertslab/pycisTopic /tmp/pip-install-vpx3jhvt/pycistopic_caad988ea2164e85a363175e1f402b49 did not run successfully. │ exit code: 128 ╰─> See above for output.
note: This error originates from a subprocess, and is likely not a problem with pip. error: subprocess-exited-with-error
× git clone --filter=blob:none --quiet https://github.com/aertslab/pycisTopic /tmp/pip-install-vpx3jhvt/pycistopic_caad988ea2164e85a363175e1f402b49 did not run successfully. │ exit code: 128 ╰─> See above for output.
note: This error originates from a subprocess, and is likely not a problem with pip. (scenicplus) test@master:~/scenicplus$ git status On branch main Your branch is up to date with 'origin/main'.
Untracked files: (use "git add..." to include in what will be committed)
src/scenicplus.egg-info/
nothing added to commit but untracked files present (use "git add" to track)
Expected behavior Collecting pycistopic@ git+https://github.com/aertslab/pycisTopic (from scenicplus==1.0a1) Cloning https://github.com/aertslab/pycisTopic to /tmp/pip-install-vpx3jhvt/pycistopic_caad988ea2164e85a363175e1f402b49 Running command git clone --filter=blob:none --quiet https://github.com/aertslab/pycisTopic /tmp/pip-install-vpx3jhvt/pycistopic_caad988ea2164e85a363175e1f402b49
Screenshots
Version (please complete the following information):
Additional context it seems to the url is the problem: the http url does not work but ssh url does. e.g., http did not work (scenicplus) test@master:~$ git clone https://github.com/aertslab/scenicplus Cloning into 'scenicplus'... remote: Enumerating objects: 3513, done. remote: Counting objects: 100% (823/823), done. remote: Compressing objects: 100% (314/314), done. fatal: the remote end hung up unexpectedlyMiB | 23.00 KiB/s fatal: early EOF fatal: index-pack failed
ssh url work:
(scenicplus) test@master:~$ git clone git@github.com:aertslab/scenicplus.git Cloning into 'scenicplus'... remote: Enumerating objects: 3513, done. remote: Counting objects: 100% (823/823), done. remote: Compressing objects: 100% (314/314), done. remote: Total 3513 (delta 458), reused 733 (delta 398), pack-reused 2690 Receiving objects: 100% (3513/3513), 44.54 MiB | 37.00 KiB/s, done. Resolving deltas: 100% (1959/1959), done.