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r-darwish / topgrade

Upgrade everything
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git repositories not being pulled with new topgrade.toml syntax #425

Closed comatosejones closed 4 years ago

comatosejones commented 4 years ago

What did you expect to happen? ... that git repositories would be pulled

What actually happened? ... they weren't pulled -- if I manually pull them, changes are downloaded

Additional details:

―― 07:44:50 - System update ――――――――――――――――――――――――――――――――――――――――――――――――――――
Dry running: /usr/bin/sudo /usr/bin/apt update
Dry running: /usr/bin/sudo /usr/bin/apt dist-upgrade

―― 07:44:50 - Flatpak User Packages ――――――――――――――――――――――――――――――――――――――――――――
Dry running: /usr/bin/flatpak update --user -y
Dry running: /usr/bin/flatpak update --system -y

―― 07:44:50 - Firmware upgrades ――――――――――――――――――――――――――――――――――――――――――――――――
Dry running: /usr/bin/fwupdmgr refresh
Dry running: /usr/bin/fwupdmgr get-updates

―― 07:44:50 - Summary ――――――――――――――――――――――――――――――――――――――――――――――――――――――――――
System update: OK
Flatpak: OK
Firmware upgrades: OK
r-darwish commented 4 years ago

Can you please also post the content of topgrade.toml?

comatosejones commented 4 years ago

Thanks for your response; pls see below. Also, pls not that, if iI revert to the old syntax, changes are pulled. This is important to me in that I administrate Linux bioinformatics with many cloned git repositories...had worked like a charm until this change.

cat .config/topgrade.toml

# Disable specific steps - same options as the command line flag
#disable = ["system", "emacs"]

# Run specific steps - same options as the command line flag
#only = ["system", "emacs"]

# Do not ask to retry failed steps (default: false)
#no_retry = true

# Run inside tmux
#run_in_tmux = true

# List of remote machines with Topgrade installed on them
#remote_topgrades = ["toothless", "pi", "parnas"]

# Arguments to pass SSH when upgrading remote systems
#ssh_arguments = "-o ConnectTimeout=2"

# Arguments to pass tmux when pulling Repositories
#tmux_arguments = "-S /var/tmux.sock"

# Do not set the terminal title
#set_title = false

# Cleanup temporary or old files
#cleanup = true

[git]
max_concurrency = 5
# Additional git repositories to pull
repos = [
#    "~/src/*/",
    "~/.zsh/zsh-autosuggestions"
]

# Don't pull the predefined git repos
# predefined_repos = false

# Arguments to pass Git when pulling Repositories
#arguments = "--rebase --autostash"

#[composer]
#self_update = true

# Commands to run before anything
#[pre_commands]
#"Emacs Snapshot" = "rm -rf ~/.emacs.d/elpa.bak && cp -rl ~/.emacs.d/elpa ~/.emacs.d/elpa.bak"

# Custom commands
#[commands]
#"Python Environment" = "~/dev/.env/bin/pip install -i https://pypi.python.org/simple -U --upgrade-strategy eager jupyter"

#[brew]
#greedy_cask = true

#[linux]
# Arguments to pass yay when updating packages
#yay_arguments = "--nodevel"
#trizen_arguments = "--devel"
#enable_tlmgr = true

#[windows]
# Manually select Windows updates
# accept_all_updates = false
comatosejones commented 4 years ago

working on it...

comatosejones commented 4 years ago

same result

comatosejones commented 4 years ago

topgrade -v 2020-06-10T15:46:24.366Z DEBUG topgrade::config > Configuration at /home/marler/.config/topgrade.toml 2020-06-10T15:46:24.366Z DEBUG topgrade::config > Loaded configuration: ConfigFile { pre_commands: None, commands: None, git_repos: None, predefined_git_repos: None, disable: None, remote_topgrades: None, ssh_arguments: None, git_arguments: None, tmux_arguments: None, set_title: None, assume_yes: None, yay_arguments: None, no_retry: None, run_in_tmux: None, cleanup: None, notify_each_step: None, accept_all_windows_updates: None, only: None, composer: None, brew: None, linux: None, git: Some(Git { max_concurrency: None, arguments: None, repos: Some(["~/topgrade/"]), pull_predefined: None }), windows: None } 2020-06-10T15:46:24.366Z DEBUG topgrade::utils > Detected "/usr/bin/notify-send" as "notify-send" 2020-06-10T15:46:24.366Z DEBUG topgrade > Version: 4.6.0 2020-06-10T15:46:24.366Z DEBUG topgrade > OS: x86_64-unknown-linux-gnu 2020-06-10T15:46:24.366Z DEBUG topgrade > Args { inner: ["topgrade", "-v"] } 2020-06-10T15:46:24.366Z DEBUG topgrade > Binary path: Ok("/home/marler/.local/bin/topgrade") 2020-06-10T15:46:24.366Z DEBUG topgrade > Self Update: true 2020-06-10T15:46:24.366Z DEBUG topgrade::utils > Detected "/usr/bin/git" as "git" 2020-06-10T15:46:24.366Z DEBUG topgrade::utils > Detected "/usr/bin/sudo" as "sudo"

―― 11:46:24 - Self update ―――――――――――――――――――――――――――――――――――――――――――――――――――――― Topgrade is up-to-date 2020-06-10T15:46:24.641Z DEBUG topgrade::utils > Cannot find "pwsh" 2020-06-10T15:46:24.641Z DEBUG topgrade::utils > Cannot find "powershell" 2020-06-10T15:46:24.641Z DEBUG topgrade::runner > Step "System update"

―― 11:46:24 - System update ―――――――――――――――――――――――――――――――――――――――――――――――――――― 2020-06-10T15:46:24.641Z DEBUG topgrade::utils > Cannot find "apt-fast" 2020-06-10T15:46:24.641Z DEBUG topgrade::executor > Running "/usr/bin/sudo" "/usr/bin/apt" "update" Hit:1 http://us.archive.ubuntu.com/ubuntu focal InRelease Hit:2 https://brave-browser-apt-release.s3.brave.com stable InRelease

Hit:3 http://us.archive.ubuntu.com/ubuntu focal-updates InRelease

Hit:4 http://security.ubuntu.com/ubuntu focal-security InRelease Hit:5 http://us.archive.ubuntu.com/ubuntu focal-backports InRelease Reading package lists... Done Building dependency tree Reading state information... Done All packages are up to date. 2020-06-10T15:46:26.228Z DEBUG topgrade::executor > Running "/usr/bin/sudo" "/usr/bin/apt" "dist-upgrade" Reading package lists... Done Building dependency tree Reading state information... Done Calculating upgrade... Done 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 2020-06-10T15:46:26.733Z DEBUG topgrade::runner > Step "etc-update" 2020-06-10T15:46:26.733Z DEBUG topgrade::utils > Cannot find "etc-update" 2020-06-10T15:46:26.733Z DEBUG topgrade::runner > Step "brew" 2020-06-10T15:46:26.733Z DEBUG topgrade::utils > Cannot find "brew" 2020-06-10T15:46:26.733Z DEBUG topgrade::runner > Step "nix" 2020-06-10T15:46:26.733Z DEBUG topgrade::utils > Cannot find "nix" 2020-06-10T15:46:26.733Z DEBUG topgrade::runner > Step "home-manager" 2020-06-10T15:46:26.733Z DEBUG topgrade::utils > Cannot find "home-manager" 2020-06-10T15:46:26.733Z DEBUG topgrade::runner > Step "asdf" 2020-06-10T15:46:26.733Z DEBUG topgrade::utils > Cannot find "asdf" 2020-06-10T15:46:26.733Z DEBUG topgrade::steps::git > /home/marler/.doom.d does not exists 2020-06-10T15:46:26.733Z DEBUG topgrade::steps::git > Checking if /home/marler/.vim is a git repository 2020-06-10T15:46:26.735Z TRACE topgrade::executor > Output of "/usr/bin/git" "rev-parse" "--show-toplevel": Output { status: ExitStatus(ExitStatus(32768)), stdout: "", stderr: "fatal: not a git repository (or any of the parent directories): .git\n" } 2020-06-10T15:46:26.735Z DEBUG topgrade::steps::git > /home/marler/.config/nvim does not exists 2020-06-10T15:46:26.735Z DEBUG topgrade::steps::git > /home/marler/.zshrc is a file. Checking /home/marler 2020-06-10T15:46:26.735Z DEBUG topgrade::steps::git > Checking if /home/marler is a git repository 2020-06-10T15:46:26.736Z TRACE topgrade::executor > Output of "/usr/bin/git" "rev-parse" "--show-toplevel": Output { status: ExitStatus(ExitStatus(32768)), stdout: "", stderr: "fatal: not a git repository (or any of the parent directories): .git\n" } 2020-06-10T15:46:26.736Z DEBUG topgrade::steps::git > /home/marler/.tmux does not exists 2020-06-10T15:46:26.736Z DEBUG topgrade::steps::git > /home/marler/.config/fish does not exists 2020-06-10T15:46:26.736Z DEBUG topgrade::steps::git > /home/marler/.config/openbox does not exists 2020-06-10T15:46:26.736Z DEBUG topgrade::steps::git > /home/marler/.config/bspwm does not exists 2020-06-10T15:46:26.736Z DEBUG topgrade::steps::git > /home/marler/.config/i3 does not exists 2020-06-10T15:46:26.736Z DEBUG topgrade::steps::git > /home/marler/.config/sway does not exists 2020-06-10T15:46:26.736Z DEBUG topgrade::runner > Step "Git repositories" 2020-06-10T15:46:26.736Z DEBUG topgrade::runner > Step "zr" 2020-06-10T15:46:26.736Z DEBUG topgrade::utils > Detected "/usr/bin/zsh" as "zsh" 2020-06-10T15:46:26.736Z DEBUG topgrade::utils > Path "/home/marler/.zr" doesn't exist 2020-06-10T15:46:26.736Z DEBUG topgrade::runner > Step "antibody" 2020-06-10T15:46:26.736Z DEBUG topgrade::utils > Detected "/usr/bin/zsh" as "zsh" 2020-06-10T15:46:26.736Z DEBUG topgrade::utils > Cannot find "antibody" 2020-06-10T15:46:26.736Z DEBUG topgrade::runner > Step "antigen" 2020-06-10T15:46:26.736Z DEBUG topgrade::utils > Detected "/usr/bin/zsh" as "zsh" 2020-06-10T15:46:26.736Z DEBUG topgrade::utils > Path "/home/marler/.zshrc" exists 2020-06-10T15:46:26.736Z DEBUG topgrade::utils > Path "/home/marler/antigen.zsh" doesn't exist 2020-06-10T15:46:26.736Z DEBUG topgrade::runner > Step "zplug" 2020-06-10T15:46:26.736Z DEBUG topgrade::utils > Detected "/usr/bin/zsh" as "zsh" 2020-06-10T15:46:26.736Z DEBUG topgrade::utils > Path "/home/marler/.zshrc" exists 2020-06-10T15:46:26.736Z DEBUG topgrade::utils > Path "/home/marler/zplug" doesn't exist 2020-06-10T15:46:26.736Z DEBUG topgrade::runner > Step "zinit" 2020-06-10T15:46:26.736Z DEBUG topgrade::utils > Detected "/usr/bin/zsh" as "zsh" 2020-06-10T15:46:26.736Z DEBUG topgrade::utils > Path "/home/marler/.zshrc" exists 2020-06-10T15:46:26.736Z DEBUG topgrade::utils > Path "/home/marler/.zinit" doesn't exist 2020-06-10T15:46:26.736Z DEBUG topgrade::runner > Step "oh-my-zsh" 2020-06-10T15:46:26.736Z DEBUG topgrade::utils > Detected "/usr/bin/zsh" as "zsh" 2020-06-10T15:46:26.736Z DEBUG topgrade::utils > Path "/home/marler/.oh-my-zsh" doesn't exist 2020-06-10T15:46:26.736Z DEBUG topgrade::runner > Step "fisher" 2020-06-10T15:46:26.736Z DEBUG topgrade::utils > Cannot find "fish" 2020-06-10T15:46:26.736Z DEBUG topgrade::runner > Step "tmux" 2020-06-10T15:46:26.736Z DEBUG topgrade::utils > Path "/home/marler/.tmux/plugins/tpm/bin/update_plugins" doesn't exist 2020-06-10T15:46:26.736Z DEBUG topgrade::runner > Step "TLDR" 2020-06-10T15:46:26.736Z DEBUG topgrade::utils > Cannot find "tldr" 2020-06-10T15:46:26.736Z DEBUG topgrade::runner > Step "rustup" 2020-06-10T15:46:26.736Z DEBUG topgrade::utils > Cannot find "rustup" 2020-06-10T15:46:26.736Z DEBUG topgrade::runner > Step "cargo" 2020-06-10T15:46:26.736Z DEBUG topgrade::utils > Cannot find "cargo-install-update" 2020-06-10T15:46:26.736Z DEBUG topgrade::runner > Step "Flutter" 2020-06-10T15:46:26.736Z DEBUG topgrade::utils > Cannot find "flutter" 2020-06-10T15:46:26.736Z DEBUG topgrade::runner > Step "Go" 2020-06-10T15:46:26.736Z DEBUG topgrade::utils > Cannot find "go" 2020-06-10T15:46:26.736Z DEBUG topgrade::runner > Step "Emacs" 2020-06-10T15:46:26.736Z DEBUG topgrade::utils > Cannot find "emacs" 2020-06-10T15:46:26.736Z DEBUG topgrade::runner > Step "opam" 2020-06-10T15:46:26.736Z DEBUG topgrade::utils > Cannot find "opam" 2020-06-10T15:46:26.736Z DEBUG topgrade::runner > Step "vcpkg" 2020-06-10T15:46:26.736Z DEBUG topgrade::utils > Cannot find "vcpkg" 2020-06-10T15:46:26.736Z DEBUG topgrade::runner > Step "pipx" 2020-06-10T15:46:26.736Z DEBUG topgrade::utils > Cannot find "pipx" 2020-06-10T15:46:26.736Z DEBUG topgrade::runner > Step "stack" 2020-06-10T15:46:26.736Z DEBUG topgrade::utils > Cannot find "stack" 2020-06-10T15:46:26.736Z DEBUG topgrade::runner > Step "tlmgr" 2020-06-10T15:46:26.736Z DEBUG topgrade::runner > Step "myrepos" 2020-06-10T15:46:26.736Z DEBUG topgrade::utils > Cannot find "mr" 2020-06-10T15:46:26.736Z DEBUG topgrade::runner > Step "pearl" 2020-06-10T15:46:26.736Z DEBUG topgrade::utils > Cannot find "pearl" 2020-06-10T15:46:26.736Z DEBUG topgrade::runner > Step "jetpak" 2020-06-10T15:46:26.736Z DEBUG topgrade::utils > Cannot find "jetpack" 2020-06-10T15:46:26.736Z DEBUG topgrade::runner > Step "vim" 2020-06-10T15:46:26.736Z DEBUG topgrade::utils > Detected "/usr/bin/vim" as "vim" 2020-06-10T15:46:26.739Z TRACE topgrade::executor > Output of "/usr/bin/vim" "--version": Output { status: ExitStatus(ExitStatus(0)), stdout: "VIM - Vi IMproved 8.1 (2018 May 18, compiled Apr 15 2020 06:40:31)\nIncluded patches: 1-2269\nModified by team+vim@tracker.debian.org\nCompiled by team+vim@tracker.debian.org\nHuge version without GUI. Features included (+) or not (-):\n+acl -farsi -mouse_sysmouse -tag_any_white\n+arabic +file_in_path +mouse_urxvt -tcl\n+autocmd +find_in_path +mouse_xterm +termguicolors\n+autochdir +float +multi_byte +terminal\n-autoservername +folding +multi_lang +terminfo\n-balloon_eval -footer -mzscheme +termresponse\n+balloon_eval_term +fork() +netbeans_intg +textobjects\n-browse +gettext +num64 +textprop\n++builtin_terms -hangul_input +packages +timers\n+byte_offset +iconv +path_extra +title\n+channel +insert_expand -perl -toolbar\n+cindent +job +persistent_undo +user_commands\n-clientserver +jumplist +postscript +vartabs\n-clipboard +keymap +printer +vertsplit\n+cmdline_compl +lambda +profile +virtualedit\n+cmdline_hist +langmap -python +visual\n+cmdline_info +libcall +python3 +visualextra\n+comments +linebreak +quickfix +viminfo\n+conceal +lispindent +reltime +vreplace\n+cryptv +listcmds +rightleft +wildignore\n+cscope +localmap -ruby +wildmenu\n+cursorbind -lua +scrollbind +windows\n+cursorshape +menu +signs +writebackup\n+dialog_con +mksession +smartindent -X11\n+diff +modify_fname +sound -xfontset\n+digraphs +mouse +spell -xim\n-dnd -mouseshape +startuptime -xpm\n-ebcdic +mouse_dec +statusline -xsmp\n+emacs_tags +mouse_gpm -sun_workshop -xterm_clipboard\n+eval -mouse_jsbterm +syntax -xterm_save\n+ex_extra +mouse_netterm +tag_binary \n+extra_search +mouse_sgr -tag_old_static \n system vimrc file: \"$VIM/vimrc\"\n user vimrc file: \"$HOME/.vimrc\"\n 2nd user vimrc file: \"~/.vim/vimrc\"\n user exrc file: \"$HOME/.exrc\"\n defaults file: \"$VIMRUNTIME/defaults.vim\"\n fall-back for $VIM: \"/usr/share/vim\"\nCompilation: gcc -c -I. -Iproto -DHAVE_CONFIG_H -Wdate-time -g -O2 -fdebug-prefix-map=/build/vim-iU6mZD/vim-8.1.2269=. -fstack-protector-strong -Wformat -Werror=format-security -D_REENTRANT -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 \nLinking: gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o vim -lm -ltinfo -lnsl -lselinux -lcanberra -lacl -lattr -lgpm -ldl -L/usr/lib/python3.8/config-3.8-x86_64-linux-gnu -lpython3.8 -lcrypt -lpthread -ldl -lutil -lm -lm \n", stderr: "" } 2020-06-10T15:46:26.740Z DEBUG topgrade::runner > Step "Neovim" 2020-06-10T15:46:26.741Z DEBUG topgrade::utils > Cannot find "nvim" 2020-06-10T15:46:26.741Z DEBUG topgrade::runner > Step "voom" 2020-06-10T15:46:26.741Z DEBUG topgrade::utils > Cannot find "voom" 2020-06-10T15:46:26.741Z DEBUG topgrade::runner > Step "NPM" 2020-06-10T15:46:26.741Z DEBUG topgrade::utils > Cannot find "npm" 2020-06-10T15:46:26.741Z DEBUG topgrade::runner > Step "yarn" 2020-06-10T15:46:26.741Z DEBUG topgrade::utils > Cannot find "yarn" 2020-06-10T15:46:26.741Z DEBUG topgrade::runner > Step "composer" 2020-06-10T15:46:26.741Z DEBUG topgrade::utils > Cannot find "composer" 2020-06-10T15:46:26.741Z DEBUG topgrade::runner > Step "apm" 2020-06-10T15:46:26.741Z DEBUG topgrade::utils > Cannot find "apm" 2020-06-10T15:46:26.741Z DEBUG topgrade::runner > Step "gem" 2020-06-10T15:46:26.741Z DEBUG topgrade::utils > Cannot find "gem" 2020-06-10T15:46:26.741Z DEBUG topgrade::runner > Step "Flatpak" 2020-06-10T15:46:26.741Z DEBUG topgrade::utils > Cannot find "flatpak" 2020-06-10T15:46:26.741Z DEBUG topgrade::runner > Step "snap" 2020-06-10T15:46:26.741Z DEBUG topgrade::utils > Detected "/usr/bin/snap" as "snap"

―― 11:46:26 - snap ――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― 2020-06-10T15:46:26.742Z DEBUG topgrade::executor > Running "/usr/bin/sudo" "/usr/bin/snap" "refresh" All snaps up to date. 2020-06-10T15:46:28.040Z DEBUG topgrade::runner > Step "pihole" 2020-06-10T15:46:28.040Z DEBUG topgrade::utils > Cannot find "pihole" 2020-06-10T15:46:28.040Z DEBUG topgrade::runner > Step "Firmware upgrades" 2020-06-10T15:46:28.040Z DEBUG topgrade::utils > Detected "/usr/bin/fwupdmgr" as "fwupdmgr"

―― 11:46:28 - Firmware upgrades ―――――――――――――――――――――――――――――――――――――――――――――――― 2020-06-10T15:46:28.040Z DEBUG topgrade::executor > Running "/usr/bin/fwupdmgr" "refresh" Firmware metadata last refresh: 4 hours ago. Use --force to refresh again. 2020-06-10T15:46:28.064Z DEBUG topgrade::executor > Running "/usr/bin/fwupdmgr" "get-updates" No updatable devices 2020-06-10T15:46:28.088Z DEBUG topgrade::runner > Step "Restarts" 2020-06-10T15:46:28.088Z DEBUG topgrade::utils > Cannot find "needrestart" 2020-06-10T15:46:28.088Z DEBUG topgrade::runner > Step "SDKMAN!" 2020-06-10T15:46:28.088Z DEBUG topgrade::utils > Detected "/usr/bin/bash" as "bash" 2020-06-10T15:46:28.088Z DEBUG topgrade::utils > Path "/home/marler/.sdkman/bin/sdkman-init.sh" doesn't exist

On Wed, Jun 10, 2020 at 10:33 AM Roey Darwish Dror notifications@github.com wrote:

Looks okay. Can you show me the output of topgrade -v?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/r-darwish/topgrade/issues/425#issuecomment-642049475, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC3J5PWIDSGG7IV6VPOSQRDRV6KRVANCNFSM4N2JVHDQ .

-- Barry Marler Systems Manager Plant Genome Mapping Laboratory University of Georgia Athens, GA USA

r-darwish commented 4 years ago

Does it work when you write a the full path of the repository without ~?

comatosejones commented 4 years ago

Yes!

r-darwish commented 4 years ago

Weird. That's actually the bug that I tried to fix. I'll try to push more debug logs.

comatosejones commented 4 years ago

Thanks for your time.

r-darwish commented 4 years ago

Can you please pull the git-fix branch and run topgrade with -v again?

comatosejones commented 4 years ago

URL? I don't see it.

r-darwish commented 4 years ago

I pushed this branch to this repository

comatosejones commented 4 years ago

Same as before, out put is identical.

r-darwish commented 4 years ago

Are you sure you're running the latest git-fix branch? You should see logs saying: "Path {} expanded to {}"

comatosejones commented 4 years ago

on the road now, will check later today

comatosejones commented 4 years ago

Later today, I will try from scratch on a VM...please send me the exact steps you want me to try, being as detailed as possible.

On Thu, Jun 11, 2020 at 7:17 AM Roey Darwish Dror notifications@github.com wrote:

Are you sure you're running the latest git-fix branch? You should see logs saying: "Path {} expanded to {}"

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/r-darwish/topgrade/issues/425#issuecomment-642578174, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC3J5PT24O7RXYSHLHHMYVDRWC4MDANCNFSM4N2JVHDQ .

-- Barry Marler Systems Manager Plant Genome Mapping Laboratory University of Georgia Athens, GA USA

r-darwish commented 4 years ago

I'm pretty convinced that I managed to fix this bug so I merged this pull request. Please reopen this if it still happens once the next version of Topgrade is released.

comatosejones commented 4 years ago

Yes, working here when run from source. TY!