Developer and curator setup guide

Windows

• Package manager
  

  For managing a windows development/curation environment I highly recommend using the chocolatey package manager. Install chocolatey.

  choco install `
  autohotkey `
  clisp `
  emacs `
  firefox `
  GoogleChrome `
  nodejs `
  poshgit `
  procexp `
  python `
  racket `
  rsync `
  vim `
  wsl2 `
  wsl-ubuntu-2004 `
  vcxsrv `
  docker-desktop `
  docker
  
  

  Update system Path to include packages that don't add themselves. This needs to be run as administrator.

  $path = [Environment]::GetEnvironmentVariable("Path", [EnvironmentVariableTarget]::Machine)
  $prefix_path = "C:\Program Files\Racket;C:\Program Files\Git\cmd;C:\Program Files\Git\bin;"
  [Environment]::SetEnvironmentVariable("Path",
                                        $prefix_path + $path,
                                        [EnvironmentVariableTarget]::Machine)
  

  If you are logged in remotely restarting sshd is the easiest way to refresh the environment so commands are in PATH. This is because new shells inherit the environment of sshd at the time that it was started.

  Restart-Service sshd
  

  You will need to reconnect to a new ssh session in order to have access to git and other newly installed commands.

• Config
  
  • Environment variables
    

    In order for Emacs to work in a way that is similar to other operating systems the HOME environment variable needs to be set. You can run these commands as a regular user.

    setx HOME %USERPROFILE%
    setx PATH "C:\Program Files\Git\bin;%PATH%"
    

  • Group policy for file system issues
    
    • Long Paths
      

      Datasets in SPARC often have long names. Windows 10 default settings break long paths in Python. To fix this enable win32 long paths.

      Microsoft Documentation

      You can use gpedit.msc to grant these permissions by navigating the menu tree below and adding the user. You can run gpedit.msc directly with Win-r or often Win gpedit enter.

      Computer configuration
      └── Administrative Templates
          Enable Win32 long paths
      

      Set-ItemProperty -Path HKLM:\SYSTEM\CurrentControlSet\Policies  -Name LongPathsEnabled -Value 1
      

      Double click to open the setting dialogue, select the enable radio button on the left and then click the ok button.

      Any program that is run after this is enabled will work as expected if it supports long paths. No restart or logout is required.

    • Symlinks
      

      augpathlib makes extensive use of symlinks to store metadata for remote files that have not been downloaded. By default normal users cannot create symlinks on windows. The best way to fix this is by granting the user that will run sparcur permission to create symlinks (do NOT run the process as Administrator).

      Three relevant links: stackoverflow superuser powershell script source.

      You will need to log out and log back in for the setting to take effect.

      You can use gpedit.msc to grant these permissions by adding the user by navigating the menu tree below. You can run gpedit.msc directly with Win-r or often Win gpedit enter.

      Computer configuration
      └── Windows Settings
          └── Security Settings
              └── Local Policies
                  └── User Rights Assignment
                      Create symbolic links
      

      Once symlinks are working it is safe to continue on to user setup.

      Alternately you can define and run the function below as Administrator. Run it as addSymLinkPermissions("user-to-add").

      function addSymLinkPermissions($accountToAdd){
          Write-Host "Checking SymLink permissions.."
          $sidstr = $null
          try {
              $ntprincipal = new-object System.Security.Principal.NTAccount "$accountToAdd"
              $sid = $ntprincipal.Translate([System.Security.Principal.SecurityIdentifier])
              $sidstr = $sid.Value.ToString()
          } catch {
              $sidstr = $null
          }
          Write-Host "Account: $($accountToAdd)" -ForegroundColor DarkCyan
          if( [string]::IsNullOrEmpty($sidstr) ) {
              Write-Host "Account not found!" -ForegroundColor Red
              exit -1
          }
          Write-Host "Account SID: $($sidstr)" -ForegroundColor DarkCyan
          $tmp = [System.IO.Path]::GetTempFileName()
          Write-Host "Export current Local Security Policy" -ForegroundColor DarkCyan
          secedit.exe /export /cfg "$($tmp)" 
          $c = Get-Content -Path $tmp 
          $currentSetting = ""
          foreach($s in $c) {
              if( $s -like "SECreateSymbolicLinkPrivilege*") {
                  $x = $s.split("=",[System.StringSplitOptions]::RemoveEmptyEntries)
                  $currentSetting = $x[1].Trim()
              }
          }
          if( $currentSetting -notlike "*$($sidstr)*" ) {
              Write-Host "Need to add permissions to SymLink" -ForegroundColor Yellow
      
              Write-Host "Modify Setting ""Create SymLink""" -ForegroundColor DarkCyan
      
              if( [string]::IsNullOrEmpty($currentSetting) ) {
                  $currentSetting = "*$($sidstr)"
              } else {
                  $currentSetting = "*$($sidstr),$($currentSetting)"
              }
              Write-Host "$currentSetting"
          $outfile = @"
      [Unicode]
      Unicode=yes
      [Version]
      signature="`$CHICAGO`$"
      Revision=1
      [Privilege Rights]
      SECreateSymbolicLinkPrivilege = $($currentSetting)
      "@
          $tmp2 = [System.IO.Path]::GetTempFileName()
              Write-Host "Import new settings to Local Security Policy" -ForegroundColor DarkCyan
              $outfile | Set-Content -Path $tmp2 -Encoding Unicode -Force
              Push-Location (Split-Path $tmp2)
              try {
                  secedit.exe /configure /db "secedit.sdb" /cfg "$($tmp2)" /areas USER_RIGHTS 
              } finally { 
                  Pop-Location
              }
          } else {
              Write-Host "NO ACTIONS REQUIRED! Account already in ""Create SymLink""" -ForegroundColor DarkCyan
              Write-Host "Account $accountToAdd already has permissions to SymLink" -ForegroundColor Green
              return $true;
          }
      }
      

• Manual install
  
  • texlive
    

    https://www.tug.org/texlive/windows.html https://www.tug.org/texlive/acquire-netinstall.html http://mirror.ctan.org/systems/texlive/tlnet/install-tl-windows.exe This takes quite a while, about 50 mins on a good connection with a fast computer.

  • protege
    

    https://github.com/protegeproject/protege-distribution/releases/latest

  • redland
    

    rdf tools http://librdf.org/raptor/INSTALL.html https://github.com/dajobe/raptor Unfortunately to get the latest version of these it seems you have to build them yourself.

• ssh   optional
  

  You can skip this if you will only be using the windows computer locally. In a local administrator powershell install OpenSSH. The rest can then be done remotely.

  Get-WindowsCapability -Online | ? Name -like 'OpenSSH*'
  Add-WindowsCapability -Online -Name OpenSSH.Client~~~~0.0.1.0
  Add-WindowsCapability -Online -Name OpenSSH.Server~~~~0.0.1.0
  Set-Service sshd -StartupType Automatic
  Start-Service sshd
  # add your ssh key to %programdata%\ssh\administrators_authorized_keys
  # disable password login in %programdata%\ssh\sshd_config
  Restart-Service sshd
  

  Set default login shell.

  New-ItemProperty -Path "HKLM:\SOFTWARE\OpenSSH" -Name DefaultShell -Value "C:\Windows\System32\WindowsPowerShell\v1.0\powershell.exe" -PropertyType String -Force
  

macOS

• Package manager
  

  Install homebrew.

  set -e  # this will exit your shell if you run at the top level and something fails
  
  curl -fsSL https://raw.githubusercontent.com/Homebrew/install/fcfea5bbf7130d754360d3056601bad131b09762/install.sh -o brew-install.sh
  test $(shasum -a 256 brew-install.sh | awk '{print $1}') = bcdaa4ade908e3766c74883f829c3dbb553a9808899bf58702651bd229d0c463 || { echo FAIL; rm brew-install.sh }
  
  /bin/bash brew-install.sh
  rm brew-install.sh
  
  brew install --cask \
  docker \
  emacs \
  firefox \
  gimp \
  google-chrome \
  inkscape \
  krita \
  mactex \
  macvim \
  protege \
  racket
  
  brew install \
  coreutils \
  curl \
  git \
  htop \
  hunspell \
  libmagic \
  pandoc \
  postgres \
  pyenv \
  python \
  python3 \
  redland \
  rxvt-unicode \
  sbcl \
  sqlite \
  tree \
  virtualbox \
  xquartz \
  imagemagick@6 \
  poppler \
  cmake \
  ninja \
  berkeley-db
  
  

  Add the following to your ~/.bash_profile

  # This file is sourced by bash for login shells.  The following line
  # runs your .bashrc and is recommended by the bash info pages.
  [[ -f ~/.bashrc ]] && . ~/.bashrc
  

  Add the following to your ~/.bashrc

  export PATH=${HOME}/bin:${HOME}/Library/Python/3.10/bin:${PATH}
  

  Run the following to symlink python3 to python. Note that python3 is now legacy as of 2022-12-21, this is retained for the record.

  mkdir ~/bin
  ln -s /usr/local/bin/python3 ~/bin/python
  ln -s /usr/local/bin/pip3 ~/bin/pip
  

  At this point it is safe to continue on to user setup.

• ssh   optional
  

  You can skip this if you will only be using the osx computer locally.

  sudo systemsetup -setremotelogin on
  # scp your key over to ~/.ssh/authorized_keys
  # set PasswordAuthentication no in /etc/ssh/sshd_config
  # set ChallengeResponseAuthentication no in /etc/ssh/sshd_config
  sudo launchctl unload  /System/Library/LaunchDaemons/ssh.plist
  sudo launchctl load -w /System/Library/LaunchDaemons/ssh.plist
  

Ubuntu

apt install openssh-server net-tools

wget -q -O - https://dl-ssl.google.com/linux/linux_signing_key.pub | apt-key add -
echo 'deb [arch=amd64] http://dl.google.com/linux/chrome/deb/ stable main' \
>> /etc/apt/sources.list.d/google-chrome.list
add-apt-repository ppa:plt/racket
add-apt-repository ppa:kelleyk/emacs
add-apt-repository ppa:pypy/ppa
apt update
apt install build-essential lib64readline-dev rxvt-unicode htop attr tree sqlite curl git
apt install emacs26 vim-gtk3 texlive-full pandoc hunspell
apt install librdf0-dev python3-dev python3-pip pypy3 jupyter racket sbcl r-base r-base-dev maven
apt install inkscape gimp krita graphviz firefox google-chrome-stable xfce4
apt install nginx
update-alternatives --install /usr/bin/python python /usr/bin/python3 10
update-alternatives --install /usr/bin/pip pip /usr/bin/pip3 10

{ cat <<EOL
# set PATH so it includes user's private bin if it exists
if [ -d "$HOME/bin" ] ; then
    PATH="$HOME/bin:$PATH"
fi

# set PATH so it includes user's private bin if it exists
if [ -d "$HOME/.local/bin" ] ; then
    PATH="$HOME/.local/bin:$PATH"
fi
EOL
} > /etc/profile.d/user-home-paths.sh

Gentoo

app-editors/emacs
app-editors/gvim
app-text/texlive
dev-vcs/git
dev-scheme/racket
dev-lisp/sbcl
www-client/google-chrome-stable

Docker

Git name and email

git config --global user.name "FIRST_NAME LAST_NAME"
git config --global user.email "MY_NAME@example.com"

Bootstrapping this setup.org file

mkdir -p ~/.local/bin
mkdir ~/bin
mkdir ~/opt
mkdir ~/git
mkdir ~/files
source .profile

pushd ~/git
git clone https://github.com/SciCrunch/sparc-curation.git
git clone https://github.com/tgbugs/orgstrap.git
popd

emacs -q --eval '(setq init-simple-testing t)' -l ~/git/orgstrap/init-simple.el --eval '(progn (with-current-buffer (find-file (pop argv)) (goto-char (org-find-exact-headline-in-buffer (pop argv))) (recenter-top-bottom 0)))' ~/git/sparc-curation/docs/setup.org "Per user setup"

Per user setup

Configuration files

scig t brain

scimax --find-file ~/git/sparc-curation/docs/setup.org --eval "(add-hook 'window-setup-hook (lambda () (org-goto-section *section-accounts-and-api-access*)))"

Accounts and API access

key1:
  key2:
    key3: fake-value

• Pennsieve
  

  Once you have a Pennsieve account on the sparc org go to your profile and create an API key. Put they key in (-> blackfynn sparc key) and the secret in (-> blackfynn sparc secret). While you are there you should also connect your ORCiD (button at the bottom of the page).

• Google API
  

  Enable the google sheets API from the google api dashboard. If you need other APIs you can enable them via the library page.

  If you do not do this then at the end of the client flow you will receive a invalid_clientUnauthorized error.

  The instructions below are probably incomplete/missing steps.
  

  Useful docs for (-> google api creds-file)
  https://developers.google.com/identity/protocols/OAuth2
  https://developers.google.com/api-client-library/python/guide/aaa_oauth
  

  You will need to get API access for an OAuth client.

  1. https://console.developers.google.com/apis/credentials
  2. create credentials -> OAuth client ID
  3. Fill in the consent screen, you only need the Application name field.
  4. Download JSON
  5. Add the name of the downloaded JSON file to (-> google api creds-file).
  6. Run the following
     googapis auth drive sheets --drive-scopes metadata.readonly and
     googapis auth drive sheets --readonly --drive-scopes metadata.readonly.

  Those commands will run the auth workflow and create the file specified at (-> google api store-file) for you. During the process you will be taken to (or need to paste a link to) a google login page to confirm that you want to give the google API project you created access to your account.

• Google sheets
  

  Get the document ids for the following.

  • (-> google sheets sparc-master)
  • (-> google sheets sparc-consistency)
  • (-> google sheets sparc-affiliations)
  • (-> google sheets sparc-field-alignment)

  Document id matches this pattern https://docs.google.com/spreadsheets/d/{document_id}/edit.

• protocols.io
  

  To get protocols.io API keys create an account, login, and go to your developer page.

  You will need to set the redirect uri on that page to match the redirect uri in the json below.

  Use the information from that page to fill in a json file with the structure below. Add the full path to that json file to (-> protocols-io api creds-file) in secrets.yaml like you did for the google json file.

  {
      "installed": {
          "client_id": "pr_live_id_fake-client-id<<<",
          "client_secret": "pr_live_sc_fake-client-secret<<<",
          "auth_uri": "https://www.protocols.io/api/v3/oauth/authorize",
          "token_uri": "https://www.protocols.io/api/v3/oauth/token",
          "redirect_uris": [
              "https://sparc.olympiangods.org/curation/"
          ]
      }
  }
  

  You will be prompted for your protocols.io email and password the first time you run.

  • Refresh
    

    If you hit a refresh error because something expired, run the following block

    _file_name=$(python3 -c "from idlib.config import auth;print(auth.get_path('protocols-io-api-store-file').as_posix())")
    echo "${_file_name}"
    mv "${_file_name}" "${_file_name}.$(date -I)"
    pushd ~/git/idlib
    # you will be promted for email and password for protocols.io after running this
    python3 -m pytest -k TestPio -s
    

    and you should be prompted to renew the token you will have to install and manually fix robobrowser at the moment and you may need to install pytest

• Hypothes.is
  

  As your user Install the hypothesis client in chrome.

  google-chrome-stable https://chrome.google.com/webstore/detail/hypothesis-web-pdf-annota/bjfhmglciegochdpefhhlphglcehbmek
  

  To get Hypothes.is API keys create an account, login, and go to your developer page.

  Add your the API key to (-> hypothesis api user-default-hypothesis)

• SciGraph
  

  For some use cases you will need access to the SciCrunch production SciGraph endpoint. Register for an account and get an api key. Edit ${HOME}/.config/pyontutils/config.yaml and update the scigraph-api-key: path: entry to point to scicrunch api name-of-user-or-name-for-the-key. Edit ${HOME}/.config/orthauth/secrets.yaml and add the api key to (-> scicrunch api name-of-user-or-name-for-the-key).

Python debugger settings

• POSIX
  

  If you can use python3.7 (>=ubuntu-19.04) you can set the embedded debugger as follows.

  pip install --user pudb
  

  Add the following to ~/.bashrc.

  export PYTHONBREAKPOINT=pudb.set_trace
  

• Windows
  

  Sadly pudb doesn't support windows so we have to use ipdb instead.

  pip install --user ipdb
  

  Add the following to your powershell $profile.

  $Env:PYTHONBREAKPOINT = "ipdb.set_trace"
  

Prevent vim from removing xattrs

augroup HasXattrs
 autocmd BufRead,BufNewFile * let x=system('getfattr ' . bufname('%')) | if len(x) | call HasXattrs() | endif
augroup END

function HasXattrs()
 " don't create new inodes
 setlocal backupcopy=yes
endfunction

Config Templates

mkdir /tmp/fakehome
HOME=/tmp/fakehome python -m sparcur.cli
less /tmp/fakehome/.config/*/*.yaml

auth-stores:
  secrets:
    path: '{:user-config-path}/orthauth/secrets.yaml'
auth-variables:
  cache-path:
  log-path:
  protocols-io-api-creds-file: protocols-io api creds-file
  protocols-io-api-store-file: protocols-io api store-file

auth-stores:
  secrets:
    path: '{:user-config-path}/orthauth/secrets.yaml'
auth-variables:
  curies:
  git-local-base: ~/git
  git-remote-base:
  google-api-creds-file:
    path: google api creds-file
  google-api-store-file:
    path: google api store-file
  google-api-store-file-readonly:
    path: google api store-file-readonly
  nifstd-checkout-ok:
  ontology-local-repo:
  ontology-org:
  ontology-repo:
  patch-config:
  resources:
  scigraph-api: https://scigraph.olympiangods.org/scigraph
  scigraph-api-key:
  scigraph-graphload:
  scigraph-services:
  zip-location:

auth-stores:
  secrets:
    path: '{:user-config-path}/orthauth/secrets.yaml'
auth-variables:
  cache-path:
  datasets-no:
  datasets-noexport:
  datasets-sparse:
  datasets-test:
  export-path:
  google-api-service-account-file-readonly: google api saro
  google-api-service-account-file-rw:
  hypothesis-api-key: hypothesis api default-user
  hypothesis-group: hypothesis group sparc-curation
  hypothesis-user:
  log-path:
  never-update:
  preview:
  remote-backoff-factor:
  remote-cli-path:
  remote-organization: N:organization:618e8dd9-f8d2-4dc4-9abb-c6aaab2e78a0
  resources:
  sparse-limit:

pennsieve:
  N:organization:618e8dd9-f8d2-4dc4-9abb-c6aaab2e78a0:
    key: *replace-me-with:your-pennsieve-api-key*
    secret: *replace-me-with:your-pennsieve-api-secret*
google:
  api:
    creds-file: *replace-me-with:/path/to/creds-file.json*
    store-file: google-api-token-rw.pickle
    store-file-readonly: google-api-token.pickle
  sheets:
    sparc-consistency: *replace-me-with:document-hash-id*
    sparc-master: *replace-me-with:document-hash-id*
    sparc-affiliations: *replace-me-with:document-hash-id*
    sparc-field-alignment: *replace-me-with:document-hash-id*
    spc-reports: *replace-me-with:document-hash-id*
    spc-reports-preview: *replace-me-with:document-hash-id*
    anno-tags: *replace-me-with:document-hash-id*
hypothesis:
  api:
    user-default-hypothesis: *replace-me-with:your-hypothesis-api-key*
  group:
    sparc-curation: *replace-me-with:sparc-curation-group-id*
protocols-io:
  api:
    creds-file: *replace-me-with:/path/to/creds-file.json*
    store-file: protocols-io-api-token-rw.pickle

pennsieve:
  N:organization:618e8dd9-f8d2-4dc4-9abb-c6aaab2e78a0:
    key: *replace-me-with:your-pennsieve-api-key*
    secret: *replace-me-with:your-pennsieve-api-secret*
google:
  api:
    saro: *replace-me-with:path-to-service-account.json*
  sheets:
    sparc-field-alignment: *replace-me-with:document-hash-id*
    sparc-affiliations: *replace-me-with:document-hash-id*
    anno-tags: *replace-me-with:document-hash-id*
protocols-io:
  # FIXME robobrowser not a dependency in some setup.py
  # FIXME robobrowser has a broken werkzeug import that has to be fixed manually
  api:
    creds-file: client_secret_protocols.io.json
    store-file: protocols-io-api-token-rw.pickle

pennsieve:
  N:organization:618e8dd9-f8d2-4dc4-9abb-c6aaab2e78a0:
    key: *replace-me-with:your-pennsieve-api-key*
    secret: *replace-me-with:your-pennsieve-api-secret*

Bootstrap code

• user.el
  

  Tangle the following blocks with C-c C-v C-t in vanilla emacs or paste it into scimax's

  ;; silence ob-ipython complaining about missing command
  ;; THIS CAN CAUSE RUNTIME ERRORS
  (setq ob-ipython-html-to-image-program "/dev/null")
  

  (defun config-paths (&optional os)
    (cl-case (or os system-type)
      ;; ucp udp uchp ulp
      (gnu/linux '("~/.config"
                   "~/.local/share"
                   "~/.cache"
                   "~/.cache/log"))
      (darwin '("~/Library/Application Support"
                "~/Library/Application Support"
                "~/Library/Caches"
                "~/Library/Logs"))
      (windows-nt (let ((ucp "~/AppData/Local"))
                    (list ucp ucp ucp (concat ucp "/Logs"))))
      (otherwise (error (format "Unknown OS %s" (or os system-type))))))
  
  (eval-when-compile (defvar *config-paths* (config-paths)))
  
  (defun fcp (position &optional suffix)
    (let ((base-path (funcall position *config-paths*)))
      (if suffix
          (format "%s/%s" base-path suffix)
        base-path)))
  
  (defun user-config-path (&optional suffix) (fcp #'cl-first  suffix))
  (defun user-data-path   (&optional suffix) (fcp #'cl-second suffix))
  (defun user-cache-path  (&optional suffix) (fcp #'cl-third  suffix))
  (defun user-log-path    (&optional suffix) (fcp #'cl-fourth suffix))
  

  ;; org goto heading
  (defun org-goto-section (heading)
    "\`heading' should be a string matching the desired heading"
    (goto-char (org-find-exact-headline-in-buffer heading)))
  
  ;; workaround for powershell cmd windows braindead handling of strings
  (defvar *section-per-user-setup* "Per user setup")
  (defvar *section-accounts-and-api-access* "Accounts and API access")
  
  ;; recenter a line set using --eval to be at the top of the buffer
  (add-hook 'emacs-startup-hook (lambda () (recenter-top-bottom 0)))
  
  ;; line numbers so it is harder to get lost in a big file
  (when (>= emacs-major-version 26)
    (setq display-line-numbers-grow-only 1)
    (global-display-line-numbers-mode 1))
  
  ;; open setup.org symlink without prompt
  (setq vc-follow-symlinks 1)
  
  ;; sane python indenting
  (setq-default indent-tabs-mode nil)
  (setq tab-width 4)
  (setq org-src-preserve-indentation nil)
  (setq org-src-tab-acts-natively nil)
  
  ;; don't hang on tlmgr since it is broken on ubuntu
  (setq scimax-installed-latex-packages t)
  
  ;; save command history
  (setq history-length t)
  (savehist-mode 1)
  (setq savehist-additional-variables '(kill-ring search-ring regexp-search-ring))
  
  ;; racket
  (when (fboundp 'use-package)
    (use-package racket-mode
      :mode "\\.ptc\\'" "\\.rkt\\'" "\\.sxml\\'"
      :bind (:map racket-mode-map
                  ("<f5>" . recompile-quietly))
      :init
      (defun my/buffer-local-tab-complete ()
        "Make \`tab-always-indent' a buffer-local variable and set it to 'complete."
        (make-local-variable 'tab-always-indent)
        (setq tab-always-indent 'complete))
      (defun rcc ()
        (set (make-local-variable 'compile-command)
             (format "raco make %s" (file-name-nondirectory buffer-file-name))))
      (add-hook 'racket-mode-hook 'rcc)
      (add-hook 'racket-mode-hook 'hs-minor-mode)
      (add-hook 'racket-mode-hook 'goto-address-mode)
      (add-hook 'racket-mode-hook 'my/buffer-local-tab-complete)
      (add-hook 'racket-repl-mode-hook 'my/buffer-local-tab-complete)))
  
  ;; config paths
  
  (defun config-paths (&optional os)
    (cl-case (or os system-type)
      ;; ucp udp uchp ulp
      (gnu/linux '("~/.config"
                   "~/.local/share"
                   "~/.cache"
                   "~/.cache/log"))
      (darwin '("~/Library/Application Support"
                "~/Library/Application Support"
                "~/Library/Caches"
                "~/Library/Logs"))
      (windows-nt (let ((ucp "~/AppData/Local"))
                    (list ucp ucp ucp (concat ucp "/Logs"))))
      (otherwise (error (format "Unknown OS %s" (or os system-type))))))
  
  (eval-when-compile (defvar *config-paths* (config-paths)))
  
  (defun fcp (position &optional suffix)
    (let ((base-path (funcall position *config-paths*)))
      (if suffix
          (format "%s/%s" base-path suffix)
        base-path)))
  
  (defun user-config-path (&optional suffix) (fcp #'cl-first  suffix))
  (defun user-data-path   (&optional suffix) (fcp #'cl-second suffix))
  (defun user-cache-path  (&optional suffix) (fcp #'cl-third  suffix))
  (defun user-log-path    (&optional suffix) (fcp #'cl-fourth suffix))
  
  ;; vim bindings if you need them
  ;; if undo-tree fails to install for strange reasons M-x list-packages C-s undo-tree
  ;; to manually install, mega gnu elpa weirdness
  (setq evil-want-keybinding nil)
  (when (fboundp 'use-package)
    (require 'scimax-evil))
  

• scimax launch scripts
  

  emacs -q -l ~/opt/scimax/init.el $args
  

  emacs -q -l ~/opt/scimax/init.el $@
  

Developer setup code

# implicit check for bash by being able to run this block at all

# git check on the off chance that we made it here without cloning this repo
git --version || { echo git is missing; exit 1; }

# python version check
python -c "print('python ok') if __import__('sys').version_info.major >= 3 else __import__('sys').exit(1)" || { echo bad python version; exit 2; }
pip --version || { echo pip is missing; exit 3; }

# git email check
[[ -n "$(git config --list | grep user.email)" ]] || { echo git user.email has not been configured; exit 4; }

pushd ~/git
for repo_url in ${REPOS}; do git clone ${repo_url}.git 2>&1; done
popd

[ -z $VIRTUAL_ENV ] || pip install --user wheel  # if in a venv wheel will be missing
pushd ~/git
for repo in ${PYROOTS}; do pushd ${repo}; python3 -m pip install --user --editable .[dev,test] 2>&1 || break; popd; done
popd

ln -s ~/git/rkdf/bin/ttl-to-rkt ~/bin/ttl-to-rkt
ln -s ~/git/rkdf/bin/rkdf-convert-all ~/bin/rkdf-convert-all
pushd ~/git/NIF-Ontology
git checkout dev
rkdf-convert-all
git checkout master
popd

pushd ~/git
# XXX note the special cases
raco pkg install --name breadcrumb racket-breadcrumb/
raco pkg install --name json-view racket-json-view/
raco pkg install --skip-installed --auto --batch ${RKTROOTS} 2>&1
popd

Remote exports

export REPOS='
https://github.com/tgbugs/sxpyr
https://github.com/tgbugs/augpathlib
https://github.com/tgbugs/idlib
https://github.com/tgbugs/hyputils
https://github.com/tgbugs/orthauth
https://github.com/tgbugs/ontquery
https://github.com/tgbugs/parsercomb
https://github.com/tgbugs/pyontutils
https://github.com/tgbugs/protc
https://github.com/tgbugs/rrid-metadata
https://github.com/tgbugs/rkdf
https://github.com/tgbugs/orgstrap
https://github.com/tgbugs/racket-breadcrumb
https://github.com/tgbugs/racket-json-view
https://github.com/SciCrunch/NIF-Ontology
https://github.com/SciCrunch/scibot
https://github.com/SciCrunch/sparc-curation
https://github.com/Ophirr33/pda
https://github.com/zussitarze/qrcode
'
export PYROOTS='
sxpyr
augpathlib
idlib
pyontutils/htmlfn
pyontutils/ttlser
hyputils
orthauth
ontquery
parsercomb
pyontutils
pyontutils/nifstd
pyontutils/neurondm
protc/protcur
sparc-curation
scibot
'
export RKTROOTS='
qrcode/
pda/
protc/protc-lib
protc/protc-tools-lib
protc/protc
protc/protc-tools
rkdf/rkdf-lib
rkdf/rkdf
rrid-metadata/rrid
sparc-curation/sparcur_internal/sparcur
NIF-Ontology/
'