From 4d41e83e9657f6ec7d9741f610fea7a02792b99b Mon Sep 17 00:00:00 2001
From: Altan Orhon <altan@uw.edu>
Date: Tue, 24 Oct 2023 18:23:11 -0700
Subject: [PATCH 01/19] Build installer

---
 .build/install.j2.sh              | 63 +++++++++++++++++++++++++++++++
 .github/workflows/mkinstaller.yml | 35 +++++++++++++++++
 2 files changed, 98 insertions(+)
 create mode 100755 .build/install.j2.sh
 create mode 100644 .github/workflows/mkinstaller.yml

diff --git a/.build/install.j2.sh b/.build/install.j2.sh
new file mode 100755
index 0000000..d5456b3
--- /dev/null
+++ b/.build/install.j2.sh
@@ -0,0 +1,63 @@
+#!/bin/sh
+
+# install.sh is generated from .build/install.j2.sh. Do not edit it directly.
+# This script is intended to be sourced from the current shell.
+# It will clone the hyakvnc repository to ~/.hyakvnc/hyakvnc and create a symlink in it to ~/.local/bin/hyakvnc.
+# These locations can be changed by setting the following environment variables:
+# - HYAKVNC_DIR: Local directory to store application data (default: `$HOME/.hyakvnc`)
+# - HYAKVNC_REPO_DIR: Local directory to store git repository (default: `$HYAKVNC_DIR/hyakvnc`)
+# - HYAKVNC_REPO_URL: URL of the git repository to clone (default: {{j2_hyakvnc_repo_url}})
+# - BIN_INSTALL_DIR: Local directory to store executable (default: `$HOME/.local/bin`)
+
+_add_hyakvnc_to_path() {
+	[ -z "${_UNEXPANDED_BIN_INSTALL_DIR:-}" ] || [ -z "${_BIN_INSTALL_DIR:-}" ] && return 1
+	case "${PATH:-}" in
+	*"${_BIN_INSTALL_DIR}"*) ;;
+	*)
+		if [ -n "${BASH_VERSION:-}" ]; then
+			echo "export PATH=\"${_UNEXPANDED_BIN_INSTALL_DIR}:\$PATH\"" >>"${HOME:-}/.bashrc"
+			echo "Added hyakvnc to PATH in ${HOME:-}/.bashrc" 2>&1
+			export PATH="${_BIN_INSTALL_DIR}:${PATH:-}"
+		elif [ -n "${ZSH_VERSION:-}" ]; then
+			echo "export PATH=\"${_UNEXPANDED_BIN_INSTALL_DIR}:\$PATH\"" >>"${ZDOTDIR:-${HOME:-}}/.zshrc"
+			echo "Added hyakvnc to PATH in ${ZDOTDIR:-${HOME}}/.zshrc" 2>&1
+			export PATH="${_BIN_INSTALL_DIR}:${PATH}"
+			rehash 2>/dev/null || true
+		else
+			echo "Could not add hyakvnc to PATH. Please add ${_BIN_INSTALL_DIR} to your shell PATH manually." 2>&1
+			return 1
+		fi
+		;;
+	esac
+}
+
+_install_hyakvnc() {
+	_HYAKVNC_DIR="${_HYAKVNC_DIR:-${HOME}/.hyakvnc}"                  # %% Local directory to store application data (default: `$HOME/.hyakvnc`)
+	_HYAKVNC_REPO_DIR="${_HYAKVNC_REPO_DIR:-${_HYAKVNC_DIR}/hyakvnc}" # Local directory to store git repository (default: `$HYAKVNC_DIR/hyakvnc`)
+	_HYAKVNC_REPO_URL="${_HYAKVNC_REPO_URL:-"{{j2_hyakvnc_repo_url}}"}"
+
+	# shellcheck disable=SC2016
+	_UNEXPANDED_BIN_INSTALL_DIR='${HOME}/.local/bin'                          # Local directory to store executable (default: `$HOME/.local/bin`)
+	_EXPANDED_BIN_INSTALL_DIR="$(eval echo "${_UNEXPANDED_BIN_INSTALL_DIR}")" # Expand environment variables in path
+	_BIN_INSTALL_DIR="${_BIN_INSTALL_DIR:-${_EXPANDED_BIN_INSTALL_DIR}}"
+
+	mkdir -p "${_BIN_INSTALL_DIR}" &&
+		rm -rf "${_HYAKVNC_DIR}/hyakvnc-tmp" &&
+		echo "Fetching hyakvnc from ${_HYAKVNC_REPO_URL}" 2>&1 &&
+		git clone --depth 1 --single-branch --quiet "${_HYAKVNC_REPO_URL}" ~/.hyakvnc/hyakvnc-tmp &&
+		rm -rf "${_HYAKVNC_REPO_DIR}" &&
+		mv "${_HYAKVNC_DIR}/hyakvnc-tmp" "${_HYAKVNC_REPO_DIR}" &&
+		ln -sf "${_HYAKVNC_REPO_DIR}/hyakvnc" "${_BIN_INSTALL_DIR}/hyakvnc" &&
+		echo "Installed hyakvnc to ${_BIN_INSTALL_DIR}/hyakvnc linking to hyakvnc in ${_HYAKVNC_REPO_DIR}" 2>&1 ||
+		return 1
+}
+
+if _install_hyakvnc && _add_hyakvnc_to_path; then
+	echo "Successfully installed hyakvnc." 2>&1
+else
+	echo "Failed to install hyakvnc." 2>&1
+fi
+
+# Unset all variables and functions defined in this script:
+unset _HYAKVNC_DIR _HYAKVNC_REPO_DIR _HYAKVNC_REPO_URL _UNEXPANDED_BIN_INSTALL_DIR _EXPANDED_BIN_INSTALL_DIR _BIN_INSTALL_DIR
+unset -f _install_hyakvnc _add_hyakvnc_to_path
diff --git a/.github/workflows/mkinstaller.yml b/.github/workflows/mkinstaller.yml
new file mode 100644
index 0000000..30bdd21
--- /dev/null
+++ b/.github/workflows/mkinstaller.yml
@@ -0,0 +1,35 @@
+name: Build installer
+"on":
+  push:
+
+jobs:
+  build-readme:
+    runs-on: ubuntu-latest
+    name: Build install.sh
+    permissions: write-all
+    steps:
+      - name: Install jinja-cli
+        run: |
+          python3 -m pip install jinja-cli
+      - name: Check out code for the container build
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Check if install.j2.sh has changed
+        id: installer-changed
+        run: |
+          if git --no-pager diff --name-only --quiet --diff-filter=AM ${{ github.event.before }} ${{ github.event.after }} -- .build/install.j2.sh .github/workflows/mkinstaller.yml; then
+            gh run cancel ${{ github.run_id }}
+            gh run watch ${{ github.run_id }}
+          fi
+        env:
+            GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - name: Create and push install.sh
+        run: |
+          jinja -D j2_hyakvnc_repo_url 'https://github.com/${{ github.repository }}' -o install.sh .build/install.sh.j2
+          git config --local user.email "${{ github.event.sender.id }}+${{ github.event.sender.login }}@users.noreply.github.com"
+          git config --local user.name ${{ github.event.sender.login }}
+          git add install.sh
+          git commit -am "Update install.sh"
+          git push
+

From d375f737b887d7a6ae9eedd55d552cb9d68e2c1d Mon Sep 17 00:00:00 2001
From: maouw <62307612+maouw@users.noreply.github.com>
Date: Wed, 25 Oct 2023 01:23:32 +0000
Subject: [PATCH 02/19] Update README.md

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index b3f2024..562bff3 100644
--- a/README.md
+++ b/README.md
@@ -78,7 +78,7 @@ ssh your-uw-netid@klone.hyak.uw.edu
 After you've connected to the login node, you can download and install `hyakvnc` by running the following command. Copy and paste it into the terminal window where you are connected to the login node and press enter:
 
 ```bash
-curl -o ~/.local/bin/hyakvnc --create-dirs -fsSL https://raw.githubusercontent.com/maouw/hyakvnc/main/hyakvnc && chmod +x ~/.local/bin/hyakvnc && [[ ":${PATH}:" != *":$HOME/.local/bin:"* ]] && export PATH="$HOME/.local/bin:$PATH" && [-n "${ZSH_VERSION:-}" ] && rehash
+curl -o ~/.local/bin/hyakvnc --create-dirs -fsSL https://raw.githubusercontent.com/maouw/hyakvnc/install-sh/hyakvnc && chmod +x ~/.local/bin/hyakvnc && [[ ":${PATH}:" != *":$HOME/.local/bin:"* ]] && export PATH="$HOME/.local/bin:$PATH" && [-n "${ZSH_VERSION:-}" ] && rehash
 ```
 
 This will download and install `hyakvnc` to your `~/.local/bin` directory and add it to your `$PATH` so you can run it by typing `hyakvnc` into the terminal window.

From 66dc7a0a19b0e1f52faa5acc33d74bf02bb7b05c Mon Sep 17 00:00:00 2001
From: Altan Orhon <altan@uw.edu>
Date: Tue, 24 Oct 2023 18:24:45 -0700
Subject: [PATCH 03/19] Build installer

---
 .github/workflows/mkinstaller.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/mkinstaller.yml b/.github/workflows/mkinstaller.yml
index 30bdd21..de15c06 100644
--- a/.github/workflows/mkinstaller.yml
+++ b/.github/workflows/mkinstaller.yml
@@ -3,7 +3,7 @@ name: Build installer
   push:
 
 jobs:
-  build-readme:
+  build-installer:
     runs-on: ubuntu-latest
     name: Build install.sh
     permissions: write-all

From 0c5de421e6a9d515f9293592dae51484c9ff0b24 Mon Sep 17 00:00:00 2001
From: Altan Orhon <altan@uw.edu>
Date: Tue, 24 Oct 2023 18:27:42 -0700
Subject: [PATCH 04/19] Build installer

---
 .github/workflows/mkinstaller.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/mkinstaller.yml b/.github/workflows/mkinstaller.yml
index de15c06..7435945 100644
--- a/.github/workflows/mkinstaller.yml
+++ b/.github/workflows/mkinstaller.yml
@@ -26,7 +26,9 @@ jobs:
             GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       - name: Create and push install.sh
         run: |
-          jinja -D j2_hyakvnc_repo_url 'https://github.com/${{ github.repository }}' -o install.sh .build/install.sh.j2
+          pushd .build/
+          jinja -D j2_hyakvnc_repo_url 'https://github.com/${{ github.repository }}' install.sh.j2 > ../install.sh
+          popd
           git config --local user.email "${{ github.event.sender.id }}+${{ github.event.sender.login }}@users.noreply.github.com"
           git config --local user.name ${{ github.event.sender.login }}
           git add install.sh

From b5d4d3c624588f50cc830417b4db90764886b43c Mon Sep 17 00:00:00 2001
From: Altan Orhon <altan@uw.edu>
Date: Tue, 24 Oct 2023 18:32:14 -0700
Subject: [PATCH 05/19] Build installer

---
 .github/workflows/mkinstaller.yml | 35 ++++++++++---------------------
 1 file changed, 11 insertions(+), 24 deletions(-)

diff --git a/.github/workflows/mkinstaller.yml b/.github/workflows/mkinstaller.yml
index 7435945..5e880f1 100644
--- a/.github/workflows/mkinstaller.yml
+++ b/.github/workflows/mkinstaller.yml
@@ -8,30 +8,17 @@ jobs:
     name: Build install.sh
     permissions: write-all
     steps:
-      - name: Install jinja-cli
+      - name: Template, create, and push install.sh
         run: |
-          python3 -m pip install jinja-cli
-      - name: Check out code for the container build
-        uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
-      - name: Check if install.j2.sh has changed
-        id: installer-changed
-        run: |
-          if git --no-pager diff --name-only --quiet --diff-filter=AM ${{ github.event.before }} ${{ github.event.after }} -- .build/install.j2.sh .github/workflows/mkinstaller.yml; then
-            gh run cancel ${{ github.run_id }}
-            gh run watch ${{ github.run_id }}
+          if ! git --no-pager diff --name-only --quiet --diff-filter=AM ${{ github.event.before }} ${{ github.event.after }} -- .build/install.j2.sh .github/workflows/mkinstaller.yml; then
+            python3 -m pip install jinja-cli
+            pushd .build/
+            jinja -D j2_hyakvnc_repo_url 'https://github.com/${{ github.repository }}' install.sh.j2 > ../install.sh
+            popd
+            git config --local user.email "${{ github.event.sender.id }}+${{ github.event.sender.login }}@users.noreply.github.com"
+            git config --local user.name ${{ github.event.sender.login }}
+            git add install.sh
+            git commit -am "Update install.sh"
+            git push
           fi
-        env:
-            GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      - name: Create and push install.sh
-        run: |
-          pushd .build/
-          jinja -D j2_hyakvnc_repo_url 'https://github.com/${{ github.repository }}' install.sh.j2 > ../install.sh
-          popd
-          git config --local user.email "${{ github.event.sender.id }}+${{ github.event.sender.login }}@users.noreply.github.com"
-          git config --local user.name ${{ github.event.sender.login }}
-          git add install.sh
-          git commit -am "Update install.sh"
-          git push
 

From ac9b94f42cb4518b495e74dacbaa589d4cceb66e Mon Sep 17 00:00:00 2001
From: Altan Orhon <altan@uw.edu>
Date: Tue, 24 Oct 2023 18:36:03 -0700
Subject: [PATCH 06/19] Simplified workflows

---
 .github/workflows/mkinstaller.yml |  7 +++++-
 .github/workflows/mkreadme.yml    | 42 ++++++++++---------------------
 2 files changed, 19 insertions(+), 30 deletions(-)

diff --git a/.github/workflows/mkinstaller.yml b/.github/workflows/mkinstaller.yml
index 5e880f1..e4e8a3e 100644
--- a/.github/workflows/mkinstaller.yml
+++ b/.github/workflows/mkinstaller.yml
@@ -8,7 +8,12 @@ jobs:
     name: Build install.sh
     permissions: write-all
     steps:
-      - name: Template, create, and push install.sh
+      - name: Check out code for the container build
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Update install.sh if needed
+        id: update-installer
         run: |
           if ! git --no-pager diff --name-only --quiet --diff-filter=AM ${{ github.event.before }} ${{ github.event.after }} -- .build/install.j2.sh .github/workflows/mkinstaller.yml; then
             python3 -m pip install jinja-cli
diff --git a/.github/workflows/mkreadme.yml b/.github/workflows/mkreadme.yml
index 7d98a26..392a89d 100644
--- a/.github/workflows/mkreadme.yml
+++ b/.github/workflows/mkreadme.yml
@@ -8,39 +8,23 @@ jobs:
     name: Build README.md
     permissions: write-all
     steps:
-      - name: Install jinja-cli
-        run: |
-          python3 -m pip install jinja-cli
       - name: Check out code for the container build
         uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - name: Check if README.md has changed
-        id: readme-changed
+      - name: Update README.md if needed
+        id: update-readme
         run: |
           if git --no-pager diff --name-only --quiet --diff-filter=AM ${{ github.event.before }} ${{ github.event.after }} -- hyakvnc .build/README.j2.md .github/workflows/mkreadme.yml; then
-            gh run cancel ${{ github.run_id }}
-            gh run watch ${{ github.run_id }}
+            pushd .build/
+            sed -E '/^HYAKVNC_.*#\s*%%/!d; s/=.*(#\s*%%)/:/g; s/(^.)/- \1/g' ../hyakvnc > config.inc.md
+            for x in create status show stop config install; do ../hyakvnc help "$x" | sed -E '1 s/(.*)/\n### \1\n/; 2 s/^$/```text/' | pr -e4 -t && echo '```'; done > usage.inc.md
+            jinja -D github_repository "${{ github.repository }}" -D github_ref_name "${{ github.ref_name }}" README.j2.md | sed 's/^.*<!-- markdownlint-disable-file -->.*$//g' > ../README.md
+            popd
+            git config --local user.email "${{ github.event.sender.id }}+${{ github.event.sender.login }}@users.noreply.github.com"
+            git config --local user.name ${{ github.event.sender.login }}
+            git add README.md
+            git commit -am "Update README.md"
+            git push
           fi
-        env:
-            GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      - name: Generate configuration descriptions
-        run: |
-          pushd .build/
-          sed -E '/^HYAKVNC_.*#\s*%%/!d; s/=.*(#\s*%%)/:/g; s/(^.)/- \1/g' ../hyakvnc > config.inc.md
-          popd
-      - name: Generate usage descriptions
-        run: |
-          pushd .build/
-          for x in create status show stop config install; do ../hyakvnc help "$x" | sed -E '1 s/(.*)/\n### \1\n/; 2 s/^$/```text/' | pr -e4 -t && echo '```'; done > usage.inc.md
-          popd
-      - name: Create and push README.md
-        run: |
-          pushd .build/
-          jinja -D github_repository "${{ github.repository }}" -D github_ref_name "${{ github.ref_name }}" README.j2.md | sed 's/^.*<!-- markdownlint-disable-file -->.*$//g' > ../README.md
-          popd
-          git config --local user.email "${{ github.event.sender.id }}+${{ github.event.sender.login }}@users.noreply.github.com"
-          git config --local user.name ${{ github.event.sender.login }}
-          git add README.md
-          git commit -am "Update README.md"
-          git push
+

From 3a517e7388698c1fdfab9298aab2e9e2376d9d7e Mon Sep 17 00:00:00 2001
From: Altan Orhon <altan@uw.edu>
Date: Tue, 24 Oct 2023 18:37:37 -0700
Subject: [PATCH 07/19] Simplified workflows

---
 .github/workflows/mkinstaller.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/mkinstaller.yml b/.github/workflows/mkinstaller.yml
index e4e8a3e..0d264d6 100644
--- a/.github/workflows/mkinstaller.yml
+++ b/.github/workflows/mkinstaller.yml
@@ -17,8 +17,7 @@ jobs:
         run: |
           if ! git --no-pager diff --name-only --quiet --diff-filter=AM ${{ github.event.before }} ${{ github.event.after }} -- .build/install.j2.sh .github/workflows/mkinstaller.yml; then
             python3 -m pip install jinja-cli
-            pushd .build/
-            jinja -D j2_hyakvnc_repo_url 'https://github.com/${{ github.repository }}' install.sh.j2 > ../install.sh
+            jinja -D j2_hyakvnc_repo_url 'https://github.com/${{ github.repository }}' .build/install.j2.sh -o install.sh
             popd
             git config --local user.email "${{ github.event.sender.id }}+${{ github.event.sender.login }}@users.noreply.github.com"
             git config --local user.name ${{ github.event.sender.login }}

From 925907902fffa584b5ec07dd05692237186d9979 Mon Sep 17 00:00:00 2001
From: maouw <62307612+maouw@users.noreply.github.com>
Date: Wed, 25 Oct 2023 01:37:52 +0000
Subject: [PATCH 08/19] Update README.md

---
 README.md | 327 ------------------------------------------------------
 1 file changed, 327 deletions(-)

diff --git a/README.md b/README.md
index 562bff3..e69de29 100644
--- a/README.md
+++ b/README.md
@@ -1,327 +0,0 @@
-# hyakvnc
-
-hyakvnc -- A tool for launching VNC sessions on Hyak.
-
-`hyakvnc` is a command-line tool that makes it easy to start a graphical [VNC](https://en.wikipedia.org/wiki/Virtual_Network_Computing) session on the University of Washington [Hyak](https://hyak.uw.edu/) cluster, allowing you to interact with the system in a point-and-click environment, with support for graphical applications such as [Freesurfer](https://surfer.nmr.mgh.harvard.edu/). `hyakvnc` sessions run in [Apptainer](https://apptainer.org) containers, which provide reproducible environments that can run anywhere and be shared with other researchers.
-
-## Prerequisites
-
-Before running `hyakvnc`, you'll need the following:
-
-- A Linux, macOS, or Windows machine
-- The OpenSSH client (usually included with Linux and macOS, and available for Windows via [WSL2](https://learn.microsoft.com/en-us/windows/wsl/install) or [Cygwin](https://www.cs.odu.edu/~zeil/cs252/latest/Public/loggingin/cygwin.mmd.html) [note that the Windows 10+ built-in OpenSSH client will not work])
-- A VNC client/viewer ([TurboVNC viewer](https://www.turbovnc.org) is recommended for all platforms)
-- HYAK Klone access with compute resources
-- A private SSH key on your local machine which has been added to the authorized keys on the login node of the HYAK Klone cluster (see below)
-- A HyakVNC-compatible Apptainer container image in a directory on Hyak (usually with the file extension `.sif`) or the URL to one (e.g,., `oras://ghcr.io/maouw/hyakvnc_apptainer/ubuntu22.04_turbovnc:latest`)
-
-Follow the instructions below to set up your machine correctly:
-
-### Installing OpenSSH and TurboVNC
-
-#### Linux
-
-If you are using Linux, OpenSSH is probably installed already -- if not, you can install it via `apt-get install openssh-client` on Debian/Ubuntu or `yum install openssh-clients` on RHEL/CentOS/Rocky/Fedora. To open a terminal window, search for "Terminal" in your desktop environment's application launcher.
-
-To install TurboVNC, download the latest version from [here](https://sourceforge.net/projects/turbovnc/files). On Debian/Ubuntu, you will need to download the file ending with `arm64.deb`. On RHEL/CentOS/Rocky/Fedora, you will need to download the file ending with `x86_64.rpm`. Then, install it by running `sudo dpkg -i <filename>` on Debian/Ubuntu or `sudo rpm -i <filename>` on RHEL/CentOS/Rocky/Fedora.
-
-#### macOS
-
-If you're on macOS, OpenSSH will already be installed. To open a terminal window, open `/Applications/Utilities/Terminal.app` or search for "Terminal" in Launchpad or Spotlight.
-
-To install TurboVNC, download the latest version from [here](https://sourceforge.net/projects/turbovnc/files). On an M1 Mac (newer), you will need to download the file ending with `arm64.dmg`. On an Intel Mac (older), you will need the file ending with `x86_64.dmg`. Then, open the `.dmg` file and launch the installer inside.
-
-#### Windows
-
-Windows needs a little more setup. You'll need to install a terminal emulator as well as the OpenSSH client. The easiest way to do this is to install [WSL2](https://learn.microsoft.com/en-us/windows/wsl/install) (recommended for Windows versions 10+, comes with the OpenSSH client already installed) or [Cygwin](https://www.cs.odu.edu/~zeil/cs252/latest/Public/loggingin/cygwin.mmd.html) (not recommended, needs additional setup). See the links for instructions on how to install these. You can start a terminal window by searching for "Terminal" in the Start menu.
-
-To install TurboVNC, download the latest version from [here](https://sourceforge.net/projects/turbovnc/files). You will need the file ending with `x64.exe`. Run the program to install TurboVNC.
-
-### Setting up SSH keys to connect to Hyak compute nodes
-
-Before you are allowed to connect to a compute node where your VNC session will be running, you must add your SSH public key to the authorized keys on the login node of the HYAK Klone cluster.
-
-If you don't, you will receive an error like this when you try to connect:
-
-```text
-Permission denied (publickey,gssapi-keyex,gssapi-with-mic)
-```
-
-To set this up quickly on Linux, macOS, or Windows (WSL2/Cygwin), open a new terminal window on your machine and enter the following 2 commands before you try again. Replace `your-uw-netid` with your UW NetID:
-
-```bash
-[ ! -r ~/.ssh/id_rsa ] && ssh-keygen -t rsa -b 4096 -N '' -C "your-uw-netid@uw.edu" -f ~/.ssh/id_rsa
-ssh-copy-id -o StrictHostKeyChecking=no -i ~/.ssh/id_rsa "your-uw-netid"@klone.hyak.uw.edu
-```
-
-See https://hyak.uw.edu/docs/setup/intracluster-keys for more information.
-
-### Finding a HyakVNC-compatible container image
-
-You'll need to find a HyakVNC-compatible container image to run your VNC session in. The following images are provided by us and can be used with `hyakvnc` by copying and pasting the URL into the `hyakvnc create` command:
-
-- `oras://ghcr.io/maouw/hyakvnc_apptainer/ubuntu22.04_turbovnc:latest` -- Ubuntu 22.04 with TurboVNC
-- `oras://ghcr.io/maouw/ubuntu22.04_freesurfer:latest` -- Ubuntu 22.04 with TurboVNC and Freesurfer
-
-## Installing `hyakvnc`
-
-`hyakvnc` should be installed on the login node of the HYAK Klone cluster.
-
-To connect to the login node, you'll need to enter the following command into a terminal window (replacing `your-uw-netid` with your UW NetID) and provide your password when prompted:
-
-```bash
-ssh your-uw-netid@klone.hyak.uw.edu
-```
-
-### Quick install
-
-After you've connected to the login node, you can download and install `hyakvnc` by running the following command. Copy and paste it into the terminal window where you are connected to the login node and press enter:
-
-```bash
-curl -o ~/.local/bin/hyakvnc --create-dirs -fsSL https://raw.githubusercontent.com/maouw/hyakvnc/install-sh/hyakvnc && chmod +x ~/.local/bin/hyakvnc && [[ ":${PATH}:" != *":$HOME/.local/bin:"* ]] && export PATH="$HOME/.local/bin:$PATH" && [-n "${ZSH_VERSION:-}" ] && rehash
-```
-
-This will download and install `hyakvnc` to your `~/.local/bin` directory and add it to your `$PATH` so you can run it by typing `hyakvnc` into the terminal window.
-
-### Installing manually
-
-In a terminal window connected to a login node, enter this command to clone the repository and navigate into the repository directory:
-
-```bash
-git clone https://github.com/maouw/hyakvnc && cd hyakvnc
-```
-
-Then, run the following command to install `hyakvnc`:
-
-```bash
-./hyakvnc install
-```
-
-If you prefer, you may continue to use `hyakvnc` from the directory where you cloned it by running `./hyakvnc` from that directory instead of using the command `hyakvnc`.
-started
-
-## Getting started
-
-### Creating a VNC session
-
-Start a VNC session with the `hyakvnc create` command followed by arguments to specify the container. In this example, we'll use a basic container for a graphical environment from the HyakVNC GitHub Container Registry:
-
-```bash
-hyakvnc create --container oras://maouw/hyakvnc_apptainer/ubuntu22.04_turbovnc:latest
-```
-
-It may take a few minutes to download the container if you're running it the first time. If successful, `hyakvnc` should print commands and instructions to connect:
-
-```text
-==========
-Copy and paste these instructions into a command line terminal on your local machine to connect to the VNC session.
-You may need to install a VNC client if you don't already have one.
-
-NOTE: If you receive an error that looks like "Permission denied (publickey,gssapi-keyex,gssapi-with-mic)", you don't have an SSH key set up.
-See https://hyak.uw.edu/docs/setup/intracluster-keys for more information.
-To set this up quickly on Linux, macOS, or Windows (WSL2/Cygwin), open a new terminal window on your machine and enter the following 2 commands before you try again:
-
-[ ! -r ~/.ssh/id_rsa ] && ssh-keygen -t rsa -b 4096 -N '' -C "your-uw-netid@uw.edu" -f ~/.ssh/id_rsa
-ssh-copy-id -o StrictHostKeyChecking=no your-uw-netid@klone.hyak.uw.edu
----------
-LINUX TERMINAL (bash/zsh):
-ssh -f -o StrictHostKeyChecking=no -L 5901:/mmfs1/home/your-uw-netid/.hyakvnc/jobs/15042104/vnc/socket.uds -J your-uw-netid@klone.hyak.uw.edu your-uw-netid@g3053 sleep 20 && vncviewer localhost:5901 || xdg-open vnc://localhost:5901 || echo 'No VNC viewer found. Please install one or try entering the connection information manually.'
-
-MACOS TERMINAL
-ssh -f -o StrictHostKeyChecking=no -L 5901:/mmfs1/home/your-uw-netid/.hyakvnc/jobs/15042104/vnc/socket.uds -J your-uw-netid@klone.hyak.uw.edu your-uw-netid@g3053 sleep 20 && open -b com.turbovnc.vncviewer.VncViewer --args localhost:5901 2>/dev/null || open -b com.realvnc.vncviewer --args localhost:5901 2>/dev/null || open -b com.tigervnc.vncviewer --args localhost:5901 2>/dev/null || open vnc://localhost:5901 2>/dev/null || echo 'No VNC viewer found. Please install one or try entering the connection information manually.'
-
-WINDOWS
-ssh -f -o StrictHostKeyChecking=no -L 5901:/mmfs1/home/your-uw-netid/.hyakvnc/jobs/15042104/vnc/socket.uds -J your-uw-netid@klone.hyak.uw.edu your-uw-netid@g3053 sleep 20 && cmd.exe /c cmd /c "$(cmd.exe /c where "C:\Program Files\TurboVNC;C:\Program Files(x86)\TurboVNC:vncviewerw.bat")" localhost:5901 || echo 'No VNC viewer found. Please install one or try entering the connection information manually.'
-
-==========
-```
-
-## Usage
-
-`hyakvnc` is command-line tool that only works on the login node of the Hyak cluster.
-
-### Create a VNC session on Hyak
-
-```text
-Usage: hyakvnc create [create options...] -c <container> [extra args to pass to apptainer...]
-
-Description:
-    Create a VNC session on Hyak.
-
-Options:
-    -h, --help  Show this help message and exit
-    -c, --container Path to container image (required)
-    -A, --account   Slurm account to use (default: )
-    -p, --partition Slurm partition to use (default: )
-    -C, --cpus  Number of CPUs to request (default: 4)
-    -m, --mem   Amount of memory to request (default: 4G)
-    -t, --timelimit Slurm timelimit to use (default: 12:00:00)
-    -g, --gpus  Number of GPUs to request (default: )
-
-Extra arguments:
-    Any extra arguments will be passed to apptainer run.
-    See 'apptainer run --help' for more information.
-
-Examples:
-    # Create a VNC session using the container ~/containers/mycontainer.sif
-    hyakvnc create -c ~/containers/mycontainer.sif
-    # Create a VNC session using the URL for a container:
-    hyakvnc create -c oras://ghcr.io/maouw/hyakvnc_apptainer/ubuntu22.04_turbovnc:latest
-    # Use the SLURM account escience, the partition gpu-a40, 4 CPUs, 1GB of memory, 1 GPU, and 1 hour of time:
-    hyakvnc create -c ~/containers/mycontainer.sif -A escience -p gpu-a40 -C 4 -m 1G -t 1:00:00 -g 1
-
-```
-
-### Show the status of running HyakVNC sessions
-
-```text
-Usage: hyakvnc status [status options...]
-
-Description:
-    Check status of VNC session(s) on Hyak.
-
-Options:
-    -h, --help  Show this help message and exit
-    -d, --debug Print debug info
-    -j, --jobid Only check status of provided SLURM job ID (optional)
-
-Examples:
-    # Check the status of job no. 12345:
-    hyakvnc status -j 12345
-    # Check the status of all VNC jobs:
-    hyakvnc status
-```
-
-### Show connection information for a HyakVNC sesssion
-
-```text
-Usage: hyakvnc show <jobid>
-    
-Description:
-    Show connection information for a HyakVNC sesssion. 
-    If no job ID is provided, a menu will be shown to select from running jobs.
-    
-Options:
-    -h, --help  Show this help message and exit
-
-Examples:
-    # Show connection information for session running on job 123456:
-    hyakvnc show 123456
-    # Interactively select a job to show connection information for:
-    hyakvnc show
-
-    # Show connection information for session running on job 123456 for macOS:
-    hyakvnc show -s mac 123456
-```
-
-### Stop a HyakVNC session
-
-```text
-Usage: hyakvnc stop [-a] [<jobids>...]
-    
-Description:
-    Stop a provided HyakVNC sesssion and clean up its job directory.
-    If no job ID is provided, a menu will be shown to select from running jobs.
-
-Options:
-    -h, --help  Show this help message and exit
-    -n, --no-cancel Don't cancel the SLURM job
-    -a, --all   Stop all jobs
-
-Examples:
-    # Stop a VNC session running on job 123456:
-    hyakvnc stop 123456
-    # Stop a VNC session running on job 123456 and do not cancel the job:
-    hyakvnc stop --no-cancel 123456
-    # Stop all VNC sessions:
-    hyakvnc stop -a
-    # Stop all VNC sessions but do not cancel the jobs:
-    hyakvnc stop -a -n
-```
-
-### Show the current configuration for hyakvnc
-
-```text
-Usage: hyakvnc config [config options...]
-    
-Description:
-    Show the current configuration for hyakvnc, as set in the user configuration file at /home/runner/.hyakvnc/hyakvnc-config.env, in the current environment, or the default values set by hyakvnc.
-
-Options:
-    -h, --help      Show this help message and exit
-
-Examples:
-    # Show configuration
-    hyakvnc config
-```
-
-### Install the hyakvnc command
-
-```text
-Usage: hyakvnc install [install options...]
-    
-Description:
-    Install hyakvnc so the "hyakvnc" command can be run from anywhere.
-
-Options:
-    -h, --help          Show this help message and exit
-    -i, --install-dir       Directory to install hyakvnc to (default: ~/.local/bin)
-    -s, --shell [bash|zsh]  Shell to install hyakvnc for (default: $SHELL or bash)
-
-Examples:
-    # Install
-    hyakvnc install
-    # Install to ~/bin:
-    hyakvnc install -i ~/bin
-```
-
-## Configuration
-
-The following [environment variables](https://wiki.archlinux.org/title/environment_variables) can be used to override the default settings. Any arguments passed to `hyakvnc create` will override the environment variables.
-
-You can modify the values of these variables by:
-
-- Setting and exporting them in your shell session, e.g. `export HYAKVNC_SLURM_MEM='8G'` (which will only affect the current shell session)
-- Setting them in your shell's configuration file, e.g. `~/.bashrc` or `~/.zshrc` (which will affect all shell sessions)
-- Setting them by prefixing the `hyakvnc` command with the variable assignment, e.g. `HYAKVNC_SLURM_MEM='8G' hyakvnc create ...` (which will only affect the current command)
-- Setting them in the file `~/.hyakvnc/hyakvnc-config.env` (which will affect all `hyakvnc` commands)
-
-When you set an environment variable, it is advisable to surround the value with single quotes (`'`) to prevent your shell from interpreting special characters. There should be no spaces between the variable name, the equals sign, and the value.
-
-The following variables are available:
-
-- HYAKVNC_DIR: Local directory to store application data (default: `$HOME/.hyakvnc`)
-- HYAKVNC_CHECK_UPDATE_FREQUENCY: How often to check for updates in `[d]`ays or `[m]`inutes (default: `0` for every time. Use `1d` for daily, `10m` for every 10 minutes, etc. `-1` to disable.)
-- HYAKVNC_CONFIG_FILE: Configuration file to use (default: `$HYAKVNC_DIR/hyakvnc-config.env`)
-- HYAKVNC_LOG_FILE: Log file to use (default: `$HYAKVNC_DIR/hyakvnc.log`)
-- HYAKVNC_LOG_LEVEL: Log level to use for interactive output (default: `INFO`)
-- HYAKVNC_LOG_FILE_LEVEL: Log level to use for log file output (default: `DEBUG`)
-- HYAKVNC_SSH_HOST: Default SSH host to use for connection strings (default: `klone.hyak.uw.edu`)
-- HYAKVNC_DEFAULT_TIMEOUT: Seconds to wait for most commands to complete before timing out (default: `30`)
-- HYAKVNC_VNC_PASSWORD: Password to use for new VNC sessions (default: `password`)
-- HYAKVNC_VNC_DISPLAY: VNC display to use (default: `:1`)
-- HYAKVNC_APPTAINER_BIN: Name of apptainer binary (default: `apptainer`)
-- HYAKVNC_APPTAINER_CONTAINER: Path to container image to use (default: (none; set by `--container` option))
-- HYAKVNC_APPTAINER_APP_VNCSERVER: Name of app in the container that starts the VNC session (default: `vncserver`)
-- HYAKVNC_APPTAINER_APP_VNCKILL: Name of app that cleanly stops the VNC session in the container (default: `vnckill`)
-- HYAKVNC_APPTAINER_WRITABLE_TMPFS: Whether to use a writable tmpfs for the container (default: `1`)
-- HYAKVNC_APPTAINER_CLEANENV: Whether to use a clean environment for the container (default: `1`)
-- HYAKVNC_APPTAINER_ADD_BINDPATHS: Bind paths to add to the container (default: (none))
-- HYAKVNC_APPTAINER_ADD_ENVVARS: Environment variables to add to before invoking apptainer (default: (none))
-- HYAKVNC_APPTAINER_ADD_ARGS: Additional arguments to give apptainer (default: (none))
-- HYAKVNC_SLURM_JOB_PREFIX: Prefix to use for hyakvnc SLURM job names (default: `hyakvnc-`)
-- HYAKVNC_SLURM_SUBMIT_TIMEOUT: Seconds after submitting job to wait for the job to start before timing out (default: `120`)
-- HYAKVNC_SLURM_OUTPUT_DIR: Directory to store SLURM output files (default: `$HYAKVNC_DIR/slurm-output`)
-- HYAKVNC_SLURM_OUTPUT: Where to send SLURM job output (default: `$HYAKVNC_SLURM_OUTPUT_DIR/job-%j.out`)
-- HYAKVNC_SLURM_JOB_NAME: What to name the launched SLURM job (default: (set according to container name))
-- HYAKVNC_SLURM_ACCOUNT: Slurm account to use (default: (autodetected))
-- HYAKVNC_SLURM_PARTITION: Slurm partition to use (default: (autodetected))
-- HYAKVNC_SLURM_CLUSTER: Slurm cluster to use (default: (autodetected))
-- HYAKVNC_SLURM_GPUS: Number of GPUs to request (default: (none))
-- HYAKVNC_SLURM_MEM: Amount of memory to request, in [M]egabytes or [G]igabytes (default: `4G`)
-- HYAKVNC_SLURM_CPUS: Number of CPUs to request (default: `4`)
-- HYAKVNC_SLURM_TIMELIMIT: Time limit for SLURM job (default: `12:00:00`)
-
-## License
-
-`hyakvnc` is licensed under [MIT License](LICENSE).

From 9adb73a39fea95c27e3f8683bd53b9f4e0a2f63f Mon Sep 17 00:00:00 2001
From: Altan Orhon <altan@uw.edu>
Date: Tue, 24 Oct 2023 18:38:09 -0700
Subject: [PATCH 09/19] Simplified workflows

---
 .github/workflows/mkinstaller.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/mkinstaller.yml b/.github/workflows/mkinstaller.yml
index 0d264d6..4997b37 100644
--- a/.github/workflows/mkinstaller.yml
+++ b/.github/workflows/mkinstaller.yml
@@ -18,7 +18,6 @@ jobs:
           if ! git --no-pager diff --name-only --quiet --diff-filter=AM ${{ github.event.before }} ${{ github.event.after }} -- .build/install.j2.sh .github/workflows/mkinstaller.yml; then
             python3 -m pip install jinja-cli
             jinja -D j2_hyakvnc_repo_url 'https://github.com/${{ github.repository }}' .build/install.j2.sh -o install.sh
-            popd
             git config --local user.email "${{ github.event.sender.id }}+${{ github.event.sender.login }}@users.noreply.github.com"
             git config --local user.name ${{ github.event.sender.login }}
             git add install.sh

From c385ffed21a50e15ced2be44b37596dd3d59e741 Mon Sep 17 00:00:00 2001
From: maouw <62307612+maouw@users.noreply.github.com>
Date: Wed, 25 Oct 2023 01:38:36 +0000
Subject: [PATCH 10/19] Update install.sh

---
 install.sh | 63 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 63 insertions(+)
 create mode 100644 install.sh

diff --git a/install.sh b/install.sh
new file mode 100644
index 0000000..7184f18
--- /dev/null
+++ b/install.sh
@@ -0,0 +1,63 @@
+#!/bin/sh
+
+# install.sh is generated from .build/install.j2.sh. Do not edit it directly.
+# This script is intended to be sourced from the current shell.
+# It will clone the hyakvnc repository to ~/.hyakvnc/hyakvnc and create a symlink in it to ~/.local/bin/hyakvnc.
+# These locations can be changed by setting the following environment variables:
+# - HYAKVNC_DIR: Local directory to store application data (default: `$HOME/.hyakvnc`)
+# - HYAKVNC_REPO_DIR: Local directory to store git repository (default: `$HYAKVNC_DIR/hyakvnc`)
+# - HYAKVNC_REPO_URL: URL of the git repository to clone (default: https://github.com/maouw/hyakvnc)
+# - BIN_INSTALL_DIR: Local directory to store executable (default: `$HOME/.local/bin`)
+
+_add_hyakvnc_to_path() {
+	[ -z "${_UNEXPANDED_BIN_INSTALL_DIR:-}" ] || [ -z "${_BIN_INSTALL_DIR:-}" ] && return 1
+	case "${PATH:-}" in
+	*"${_BIN_INSTALL_DIR}"*) ;;
+	*)
+		if [ -n "${BASH_VERSION:-}" ]; then
+			echo "export PATH=\"${_UNEXPANDED_BIN_INSTALL_DIR}:\$PATH\"" >>"${HOME:-}/.bashrc"
+			echo "Added hyakvnc to PATH in ${HOME:-}/.bashrc" 2>&1
+			export PATH="${_BIN_INSTALL_DIR}:${PATH:-}"
+		elif [ -n "${ZSH_VERSION:-}" ]; then
+			echo "export PATH=\"${_UNEXPANDED_BIN_INSTALL_DIR}:\$PATH\"" >>"${ZDOTDIR:-${HOME:-}}/.zshrc"
+			echo "Added hyakvnc to PATH in ${ZDOTDIR:-${HOME}}/.zshrc" 2>&1
+			export PATH="${_BIN_INSTALL_DIR}:${PATH}"
+			rehash 2>/dev/null || true
+		else
+			echo "Could not add hyakvnc to PATH. Please add ${_BIN_INSTALL_DIR} to your shell PATH manually." 2>&1
+			return 1
+		fi
+		;;
+	esac
+}
+
+_install_hyakvnc() {
+	_HYAKVNC_DIR="${_HYAKVNC_DIR:-${HOME}/.hyakvnc}"                  # %% Local directory to store application data (default: `$HOME/.hyakvnc`)
+	_HYAKVNC_REPO_DIR="${_HYAKVNC_REPO_DIR:-${_HYAKVNC_DIR}/hyakvnc}" # Local directory to store git repository (default: `$HYAKVNC_DIR/hyakvnc`)
+	_HYAKVNC_REPO_URL="${_HYAKVNC_REPO_URL:-"https://github.com/maouw/hyakvnc"}"
+
+	# shellcheck disable=SC2016
+	_UNEXPANDED_BIN_INSTALL_DIR='${HOME}/.local/bin'                          # Local directory to store executable (default: `$HOME/.local/bin`)
+	_EXPANDED_BIN_INSTALL_DIR="$(eval echo "${_UNEXPANDED_BIN_INSTALL_DIR}")" # Expand environment variables in path
+	_BIN_INSTALL_DIR="${_BIN_INSTALL_DIR:-${_EXPANDED_BIN_INSTALL_DIR}}"
+
+	mkdir -p "${_BIN_INSTALL_DIR}" &&
+		rm -rf "${_HYAKVNC_DIR}/hyakvnc-tmp" &&
+		echo "Fetching hyakvnc from ${_HYAKVNC_REPO_URL}" 2>&1 &&
+		git clone --depth 1 --single-branch --quiet "${_HYAKVNC_REPO_URL}" ~/.hyakvnc/hyakvnc-tmp &&
+		rm -rf "${_HYAKVNC_REPO_DIR}" &&
+		mv "${_HYAKVNC_DIR}/hyakvnc-tmp" "${_HYAKVNC_REPO_DIR}" &&
+		ln -sf "${_HYAKVNC_REPO_DIR}/hyakvnc" "${_BIN_INSTALL_DIR}/hyakvnc" &&
+		echo "Installed hyakvnc to ${_BIN_INSTALL_DIR}/hyakvnc linking to hyakvnc in ${_HYAKVNC_REPO_DIR}" 2>&1 ||
+		return 1
+}
+
+if _install_hyakvnc && _add_hyakvnc_to_path; then
+	echo "Successfully installed hyakvnc." 2>&1
+else
+	echo "Failed to install hyakvnc." 2>&1
+fi
+
+# Unset all variables and functions defined in this script:
+unset _HYAKVNC_DIR _HYAKVNC_REPO_DIR _HYAKVNC_REPO_URL _UNEXPANDED_BIN_INSTALL_DIR _EXPANDED_BIN_INSTALL_DIR _BIN_INSTALL_DIR
+unset -f _install_hyakvnc _add_hyakvnc_to_path

From a64618cb6b26f5310311f314b9733e4550ef9e98 Mon Sep 17 00:00:00 2001
From: Altan Orhon <altan@uw.edu>
Date: Tue, 24 Oct 2023 18:39:08 -0700
Subject: [PATCH 11/19] Simplified workflows

---
 .github/workflows/mkreadme.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/mkreadme.yml b/.github/workflows/mkreadme.yml
index 392a89d..7e93d6d 100644
--- a/.github/workflows/mkreadme.yml
+++ b/.github/workflows/mkreadme.yml
@@ -16,6 +16,7 @@ jobs:
         id: update-readme
         run: |
           if git --no-pager diff --name-only --quiet --diff-filter=AM ${{ github.event.before }} ${{ github.event.after }} -- hyakvnc .build/README.j2.md .github/workflows/mkreadme.yml; then
+            python3 -m pip install jinja-cli
             pushd .build/
             sed -E '/^HYAKVNC_.*#\s*%%/!d; s/=.*(#\s*%%)/:/g; s/(^.)/- \1/g' ../hyakvnc > config.inc.md
             for x in create status show stop config install; do ../hyakvnc help "$x" | sed -E '1 s/(.*)/\n### \1\n/; 2 s/^$/```text/' | pr -e4 -t && echo '```'; done > usage.inc.md

From 54bdf34d568b5538f7303f5c03102b8473142052 Mon Sep 17 00:00:00 2001
From: Altan Orhon <altan@uw.edu>
Date: Tue, 24 Oct 2023 18:49:29 -0700
Subject: [PATCH 12/19] Simplified workflows

---
 .../{mkreadme.yml => build-documentation.yml} | 25 +++++++++++------
 .github/workflows/mkinstaller.yml             | 27 -------------------
 2 files changed, 17 insertions(+), 35 deletions(-)
 rename .github/workflows/{mkreadme.yml => build-documentation.yml} (51%)
 delete mode 100644 .github/workflows/mkinstaller.yml

diff --git a/.github/workflows/mkreadme.yml b/.github/workflows/build-documentation.yml
similarity index 51%
rename from .github/workflows/mkreadme.yml
rename to .github/workflows/build-documentation.yml
index 7e93d6d..b596d47 100644
--- a/.github/workflows/mkreadme.yml
+++ b/.github/workflows/build-documentation.yml
@@ -1,21 +1,22 @@
-name: Build documentation
+name: Build documentation and installer
 "on":
   push:
 
 jobs:
   build-readme:
     runs-on: ubuntu-latest
-    name: Build README.md
+    name: Build documentation and installer
     permissions: write-all
     steps:
       - name: Check out code for the container build
         uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - name: Update README.md if needed
-        id: update-readme
+      - name: Build documentation and installer in one step
+        id: update-docs-and-installer
         run: |
-          if git --no-pager diff --name-only --quiet --diff-filter=AM ${{ github.event.before }} ${{ github.event.after }} -- hyakvnc .build/README.j2.md .github/workflows/mkreadme.yml; then
+          commit_msg=""
+          if git --no-pager diff --name-only --quiet --diff-filter=AM ${{ github.event.before }} ${{ github.event.after }} -- hyakvnc .build/README.j2.md .github/workflows/build-documentation.yml; then
             python3 -m pip install jinja-cli
             pushd .build/
             sed -E '/^HYAKVNC_.*#\s*%%/!d; s/=.*(#\s*%%)/:/g; s/(^.)/- \1/g' ../hyakvnc > config.inc.md
@@ -25,7 +26,15 @@ jobs:
             git config --local user.email "${{ github.event.sender.id }}+${{ github.event.sender.login }}@users.noreply.github.com"
             git config --local user.name ${{ github.event.sender.login }}
             git add README.md
-            git commit -am "Update README.md"
-            git push
+            commit_msg="Rebuilt README.md"
           fi
-
+          if ! git --no-pager diff --name-only --quiet --diff-filter=AM ${{ github.event.before }} ${{ github.event.after }} -- .build/install.j2.sh; then
+            python3 -m pip install jinja-cli
+            jinja -D j2_hyakvnc_repo_url 'https://github.com/${{ github.repository }}' .build/install.j2.sh -o install.sh
+            git config --local user.email "${{ github.event.sender.id }}+${{ github.event.sender.login }}@users.noreply.github.com"
+            git config --local user.name ${{ github.event.sender.login }}
+            git add install.sh
+            [ -n "${commit_msg:-}" ] && commit_msg="${commit_msg} "
+            commit_msg="${commit_msg:-}Rebuilt install.sh"
+          fi
+          [ -n "${commit_msg:-}" ] && git commit -m "${commit_msg}" && git push
diff --git a/.github/workflows/mkinstaller.yml b/.github/workflows/mkinstaller.yml
deleted file mode 100644
index 4997b37..0000000
--- a/.github/workflows/mkinstaller.yml
+++ /dev/null
@@ -1,27 +0,0 @@
-name: Build installer
-"on":
-  push:
-
-jobs:
-  build-installer:
-    runs-on: ubuntu-latest
-    name: Build install.sh
-    permissions: write-all
-    steps:
-      - name: Check out code for the container build
-        uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
-      - name: Update install.sh if needed
-        id: update-installer
-        run: |
-          if ! git --no-pager diff --name-only --quiet --diff-filter=AM ${{ github.event.before }} ${{ github.event.after }} -- .build/install.j2.sh .github/workflows/mkinstaller.yml; then
-            python3 -m pip install jinja-cli
-            jinja -D j2_hyakvnc_repo_url 'https://github.com/${{ github.repository }}' .build/install.j2.sh -o install.sh
-            git config --local user.email "${{ github.event.sender.id }}+${{ github.event.sender.login }}@users.noreply.github.com"
-            git config --local user.name ${{ github.event.sender.login }}
-            git add install.sh
-            git commit -am "Update install.sh"
-            git push
-          fi
-

From 10b3276c422bf1b3e5e7120f6634bb7d530b7360 Mon Sep 17 00:00:00 2001
From: Altan Orhon <altan@uw.edu>
Date: Tue, 24 Oct 2023 19:05:52 -0700
Subject: [PATCH 13/19] Simplified workflows

---
 .github/workflows/build-documentation.yml | 29 +++++++++++++----------
 1 file changed, 16 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/build-documentation.yml b/.github/workflows/build-documentation.yml
index b596d47..1a7f10c 100644
--- a/.github/workflows/build-documentation.yml
+++ b/.github/workflows/build-documentation.yml
@@ -16,25 +16,28 @@ jobs:
         id: update-docs-and-installer
         run: |
           commit_msg=""
-          if git --no-pager diff --name-only --quiet --diff-filter=AM ${{ github.event.before }} ${{ github.event.after }} -- hyakvnc .build/README.j2.md .github/workflows/build-documentation.yml; then
+          echo "Checking for changes in hyakvnc, .build/README.j2.md, and .github/workflows/build-documentation.yml"
+          if ! git --no-pager diff --name-only --quiet --diff-filter=AM ${{ github.event.before }} ${{ github.event.after }} -- hyakvnc .build/README.j2.md .build/install.j2.sh .github/workflows/build-documentation.yml; then
+            echo "Changes detected in hyakvnc, .build/README.j2.md, or .github/workflows/build-documentation.yml"
             python3 -m pip install jinja-cli
             pushd .build/
             sed -E '/^HYAKVNC_.*#\s*%%/!d; s/=.*(#\s*%%)/:/g; s/(^.)/- \1/g' ../hyakvnc > config.inc.md
             for x in create status show stop config install; do ../hyakvnc help "$x" | sed -E '1 s/(.*)/\n### \1\n/; 2 s/^$/```text/' | pr -e4 -t && echo '```'; done > usage.inc.md
             jinja -D github_repository "${{ github.repository }}" -D github_ref_name "${{ github.ref_name }}" README.j2.md | sed 's/^.*<!-- markdownlint-disable-file -->.*$//g' > ../README.md
+            jinja -D j2_hyakvnc_repo_url 'https://github.com/${{ github.repository }}' install.j2.sh -o ../install.sh
             popd
+
             git config --local user.email "${{ github.event.sender.id }}+${{ github.event.sender.login }}@users.noreply.github.com"
             git config --local user.name ${{ github.event.sender.login }}
-            git add README.md
-            commit_msg="Rebuilt README.md"
-          fi
-          if ! git --no-pager diff --name-only --quiet --diff-filter=AM ${{ github.event.before }} ${{ github.event.after }} -- .build/install.j2.sh; then
-            python3 -m pip install jinja-cli
-            jinja -D j2_hyakvnc_repo_url 'https://github.com/${{ github.repository }}' .build/install.j2.sh -o install.sh
-            git config --local user.email "${{ github.event.sender.id }}+${{ github.event.sender.login }}@users.noreply.github.com"
-            git config --local user.name ${{ github.event.sender.login }}
-            git add install.sh
-            [ -n "${commit_msg:-}" ] && commit_msg="${commit_msg} "
-            commit_msg="${commit_msg:-}Rebuilt install.sh"
+
+            if ! git diff --quiet --stat README.md; then
+                git add README.md && commit_msg="Rebuilt README.md"
+            fi
+
+            if ! git diff --quiet --stat install.sh; then
+                new_commit_msg="${commit_msg:-}"
+                [ -n "${new_commit_msg:-}" ] && new_commit_msg="${new_commit_msg} "
+                git add install.sh && new_commit_msg="Rebuilt install.sh" && commit_msg="${new_commit_msg:-}"
+            fi
+            git commit -am "${commit_msg}" && git push
           fi
-          [ -n "${commit_msg:-}" ] && git commit -m "${commit_msg}" && git push

From 17a2fedaf95a9328521dd05e841cd6f8896a00d8 Mon Sep 17 00:00:00 2001
From: maouw <62307612+maouw@users.noreply.github.com>
Date: Wed, 25 Oct 2023 02:06:07 +0000
Subject: [PATCH 14/19] Rebuilt README.md

---
 README.md | 327 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 327 insertions(+)

diff --git a/README.md b/README.md
index e69de29..562bff3 100644
--- a/README.md
+++ b/README.md
@@ -0,0 +1,327 @@
+# hyakvnc
+
+hyakvnc -- A tool for launching VNC sessions on Hyak.
+
+`hyakvnc` is a command-line tool that makes it easy to start a graphical [VNC](https://en.wikipedia.org/wiki/Virtual_Network_Computing) session on the University of Washington [Hyak](https://hyak.uw.edu/) cluster, allowing you to interact with the system in a point-and-click environment, with support for graphical applications such as [Freesurfer](https://surfer.nmr.mgh.harvard.edu/). `hyakvnc` sessions run in [Apptainer](https://apptainer.org) containers, which provide reproducible environments that can run anywhere and be shared with other researchers.
+
+## Prerequisites
+
+Before running `hyakvnc`, you'll need the following:
+
+- A Linux, macOS, or Windows machine
+- The OpenSSH client (usually included with Linux and macOS, and available for Windows via [WSL2](https://learn.microsoft.com/en-us/windows/wsl/install) or [Cygwin](https://www.cs.odu.edu/~zeil/cs252/latest/Public/loggingin/cygwin.mmd.html) [note that the Windows 10+ built-in OpenSSH client will not work])
+- A VNC client/viewer ([TurboVNC viewer](https://www.turbovnc.org) is recommended for all platforms)
+- HYAK Klone access with compute resources
+- A private SSH key on your local machine which has been added to the authorized keys on the login node of the HYAK Klone cluster (see below)
+- A HyakVNC-compatible Apptainer container image in a directory on Hyak (usually with the file extension `.sif`) or the URL to one (e.g,., `oras://ghcr.io/maouw/hyakvnc_apptainer/ubuntu22.04_turbovnc:latest`)
+
+Follow the instructions below to set up your machine correctly:
+
+### Installing OpenSSH and TurboVNC
+
+#### Linux
+
+If you are using Linux, OpenSSH is probably installed already -- if not, you can install it via `apt-get install openssh-client` on Debian/Ubuntu or `yum install openssh-clients` on RHEL/CentOS/Rocky/Fedora. To open a terminal window, search for "Terminal" in your desktop environment's application launcher.
+
+To install TurboVNC, download the latest version from [here](https://sourceforge.net/projects/turbovnc/files). On Debian/Ubuntu, you will need to download the file ending with `arm64.deb`. On RHEL/CentOS/Rocky/Fedora, you will need to download the file ending with `x86_64.rpm`. Then, install it by running `sudo dpkg -i <filename>` on Debian/Ubuntu or `sudo rpm -i <filename>` on RHEL/CentOS/Rocky/Fedora.
+
+#### macOS
+
+If you're on macOS, OpenSSH will already be installed. To open a terminal window, open `/Applications/Utilities/Terminal.app` or search for "Terminal" in Launchpad or Spotlight.
+
+To install TurboVNC, download the latest version from [here](https://sourceforge.net/projects/turbovnc/files). On an M1 Mac (newer), you will need to download the file ending with `arm64.dmg`. On an Intel Mac (older), you will need the file ending with `x86_64.dmg`. Then, open the `.dmg` file and launch the installer inside.
+
+#### Windows
+
+Windows needs a little more setup. You'll need to install a terminal emulator as well as the OpenSSH client. The easiest way to do this is to install [WSL2](https://learn.microsoft.com/en-us/windows/wsl/install) (recommended for Windows versions 10+, comes with the OpenSSH client already installed) or [Cygwin](https://www.cs.odu.edu/~zeil/cs252/latest/Public/loggingin/cygwin.mmd.html) (not recommended, needs additional setup). See the links for instructions on how to install these. You can start a terminal window by searching for "Terminal" in the Start menu.
+
+To install TurboVNC, download the latest version from [here](https://sourceforge.net/projects/turbovnc/files). You will need the file ending with `x64.exe`. Run the program to install TurboVNC.
+
+### Setting up SSH keys to connect to Hyak compute nodes
+
+Before you are allowed to connect to a compute node where your VNC session will be running, you must add your SSH public key to the authorized keys on the login node of the HYAK Klone cluster.
+
+If you don't, you will receive an error like this when you try to connect:
+
+```text
+Permission denied (publickey,gssapi-keyex,gssapi-with-mic)
+```
+
+To set this up quickly on Linux, macOS, or Windows (WSL2/Cygwin), open a new terminal window on your machine and enter the following 2 commands before you try again. Replace `your-uw-netid` with your UW NetID:
+
+```bash
+[ ! -r ~/.ssh/id_rsa ] && ssh-keygen -t rsa -b 4096 -N '' -C "your-uw-netid@uw.edu" -f ~/.ssh/id_rsa
+ssh-copy-id -o StrictHostKeyChecking=no -i ~/.ssh/id_rsa "your-uw-netid"@klone.hyak.uw.edu
+```
+
+See https://hyak.uw.edu/docs/setup/intracluster-keys for more information.
+
+### Finding a HyakVNC-compatible container image
+
+You'll need to find a HyakVNC-compatible container image to run your VNC session in. The following images are provided by us and can be used with `hyakvnc` by copying and pasting the URL into the `hyakvnc create` command:
+
+- `oras://ghcr.io/maouw/hyakvnc_apptainer/ubuntu22.04_turbovnc:latest` -- Ubuntu 22.04 with TurboVNC
+- `oras://ghcr.io/maouw/ubuntu22.04_freesurfer:latest` -- Ubuntu 22.04 with TurboVNC and Freesurfer
+
+## Installing `hyakvnc`
+
+`hyakvnc` should be installed on the login node of the HYAK Klone cluster.
+
+To connect to the login node, you'll need to enter the following command into a terminal window (replacing `your-uw-netid` with your UW NetID) and provide your password when prompted:
+
+```bash
+ssh your-uw-netid@klone.hyak.uw.edu
+```
+
+### Quick install
+
+After you've connected to the login node, you can download and install `hyakvnc` by running the following command. Copy and paste it into the terminal window where you are connected to the login node and press enter:
+
+```bash
+curl -o ~/.local/bin/hyakvnc --create-dirs -fsSL https://raw.githubusercontent.com/maouw/hyakvnc/install-sh/hyakvnc && chmod +x ~/.local/bin/hyakvnc && [[ ":${PATH}:" != *":$HOME/.local/bin:"* ]] && export PATH="$HOME/.local/bin:$PATH" && [-n "${ZSH_VERSION:-}" ] && rehash
+```
+
+This will download and install `hyakvnc` to your `~/.local/bin` directory and add it to your `$PATH` so you can run it by typing `hyakvnc` into the terminal window.
+
+### Installing manually
+
+In a terminal window connected to a login node, enter this command to clone the repository and navigate into the repository directory:
+
+```bash
+git clone https://github.com/maouw/hyakvnc && cd hyakvnc
+```
+
+Then, run the following command to install `hyakvnc`:
+
+```bash
+./hyakvnc install
+```
+
+If you prefer, you may continue to use `hyakvnc` from the directory where you cloned it by running `./hyakvnc` from that directory instead of using the command `hyakvnc`.
+started
+
+## Getting started
+
+### Creating a VNC session
+
+Start a VNC session with the `hyakvnc create` command followed by arguments to specify the container. In this example, we'll use a basic container for a graphical environment from the HyakVNC GitHub Container Registry:
+
+```bash
+hyakvnc create --container oras://maouw/hyakvnc_apptainer/ubuntu22.04_turbovnc:latest
+```
+
+It may take a few minutes to download the container if you're running it the first time. If successful, `hyakvnc` should print commands and instructions to connect:
+
+```text
+==========
+Copy and paste these instructions into a command line terminal on your local machine to connect to the VNC session.
+You may need to install a VNC client if you don't already have one.
+
+NOTE: If you receive an error that looks like "Permission denied (publickey,gssapi-keyex,gssapi-with-mic)", you don't have an SSH key set up.
+See https://hyak.uw.edu/docs/setup/intracluster-keys for more information.
+To set this up quickly on Linux, macOS, or Windows (WSL2/Cygwin), open a new terminal window on your machine and enter the following 2 commands before you try again:
+
+[ ! -r ~/.ssh/id_rsa ] && ssh-keygen -t rsa -b 4096 -N '' -C "your-uw-netid@uw.edu" -f ~/.ssh/id_rsa
+ssh-copy-id -o StrictHostKeyChecking=no your-uw-netid@klone.hyak.uw.edu
+---------
+LINUX TERMINAL (bash/zsh):
+ssh -f -o StrictHostKeyChecking=no -L 5901:/mmfs1/home/your-uw-netid/.hyakvnc/jobs/15042104/vnc/socket.uds -J your-uw-netid@klone.hyak.uw.edu your-uw-netid@g3053 sleep 20 && vncviewer localhost:5901 || xdg-open vnc://localhost:5901 || echo 'No VNC viewer found. Please install one or try entering the connection information manually.'
+
+MACOS TERMINAL
+ssh -f -o StrictHostKeyChecking=no -L 5901:/mmfs1/home/your-uw-netid/.hyakvnc/jobs/15042104/vnc/socket.uds -J your-uw-netid@klone.hyak.uw.edu your-uw-netid@g3053 sleep 20 && open -b com.turbovnc.vncviewer.VncViewer --args localhost:5901 2>/dev/null || open -b com.realvnc.vncviewer --args localhost:5901 2>/dev/null || open -b com.tigervnc.vncviewer --args localhost:5901 2>/dev/null || open vnc://localhost:5901 2>/dev/null || echo 'No VNC viewer found. Please install one or try entering the connection information manually.'
+
+WINDOWS
+ssh -f -o StrictHostKeyChecking=no -L 5901:/mmfs1/home/your-uw-netid/.hyakvnc/jobs/15042104/vnc/socket.uds -J your-uw-netid@klone.hyak.uw.edu your-uw-netid@g3053 sleep 20 && cmd.exe /c cmd /c "$(cmd.exe /c where "C:\Program Files\TurboVNC;C:\Program Files(x86)\TurboVNC:vncviewerw.bat")" localhost:5901 || echo 'No VNC viewer found. Please install one or try entering the connection information manually.'
+
+==========
+```
+
+## Usage
+
+`hyakvnc` is command-line tool that only works on the login node of the Hyak cluster.
+
+### Create a VNC session on Hyak
+
+```text
+Usage: hyakvnc create [create options...] -c <container> [extra args to pass to apptainer...]
+
+Description:
+    Create a VNC session on Hyak.
+
+Options:
+    -h, --help  Show this help message and exit
+    -c, --container Path to container image (required)
+    -A, --account   Slurm account to use (default: )
+    -p, --partition Slurm partition to use (default: )
+    -C, --cpus  Number of CPUs to request (default: 4)
+    -m, --mem   Amount of memory to request (default: 4G)
+    -t, --timelimit Slurm timelimit to use (default: 12:00:00)
+    -g, --gpus  Number of GPUs to request (default: )
+
+Extra arguments:
+    Any extra arguments will be passed to apptainer run.
+    See 'apptainer run --help' for more information.
+
+Examples:
+    # Create a VNC session using the container ~/containers/mycontainer.sif
+    hyakvnc create -c ~/containers/mycontainer.sif
+    # Create a VNC session using the URL for a container:
+    hyakvnc create -c oras://ghcr.io/maouw/hyakvnc_apptainer/ubuntu22.04_turbovnc:latest
+    # Use the SLURM account escience, the partition gpu-a40, 4 CPUs, 1GB of memory, 1 GPU, and 1 hour of time:
+    hyakvnc create -c ~/containers/mycontainer.sif -A escience -p gpu-a40 -C 4 -m 1G -t 1:00:00 -g 1
+
+```
+
+### Show the status of running HyakVNC sessions
+
+```text
+Usage: hyakvnc status [status options...]
+
+Description:
+    Check status of VNC session(s) on Hyak.
+
+Options:
+    -h, --help  Show this help message and exit
+    -d, --debug Print debug info
+    -j, --jobid Only check status of provided SLURM job ID (optional)
+
+Examples:
+    # Check the status of job no. 12345:
+    hyakvnc status -j 12345
+    # Check the status of all VNC jobs:
+    hyakvnc status
+```
+
+### Show connection information for a HyakVNC sesssion
+
+```text
+Usage: hyakvnc show <jobid>
+    
+Description:
+    Show connection information for a HyakVNC sesssion. 
+    If no job ID is provided, a menu will be shown to select from running jobs.
+    
+Options:
+    -h, --help  Show this help message and exit
+
+Examples:
+    # Show connection information for session running on job 123456:
+    hyakvnc show 123456
+    # Interactively select a job to show connection information for:
+    hyakvnc show
+
+    # Show connection information for session running on job 123456 for macOS:
+    hyakvnc show -s mac 123456
+```
+
+### Stop a HyakVNC session
+
+```text
+Usage: hyakvnc stop [-a] [<jobids>...]
+    
+Description:
+    Stop a provided HyakVNC sesssion and clean up its job directory.
+    If no job ID is provided, a menu will be shown to select from running jobs.
+
+Options:
+    -h, --help  Show this help message and exit
+    -n, --no-cancel Don't cancel the SLURM job
+    -a, --all   Stop all jobs
+
+Examples:
+    # Stop a VNC session running on job 123456:
+    hyakvnc stop 123456
+    # Stop a VNC session running on job 123456 and do not cancel the job:
+    hyakvnc stop --no-cancel 123456
+    # Stop all VNC sessions:
+    hyakvnc stop -a
+    # Stop all VNC sessions but do not cancel the jobs:
+    hyakvnc stop -a -n
+```
+
+### Show the current configuration for hyakvnc
+
+```text
+Usage: hyakvnc config [config options...]
+    
+Description:
+    Show the current configuration for hyakvnc, as set in the user configuration file at /home/runner/.hyakvnc/hyakvnc-config.env, in the current environment, or the default values set by hyakvnc.
+
+Options:
+    -h, --help      Show this help message and exit
+
+Examples:
+    # Show configuration
+    hyakvnc config
+```
+
+### Install the hyakvnc command
+
+```text
+Usage: hyakvnc install [install options...]
+    
+Description:
+    Install hyakvnc so the "hyakvnc" command can be run from anywhere.
+
+Options:
+    -h, --help          Show this help message and exit
+    -i, --install-dir       Directory to install hyakvnc to (default: ~/.local/bin)
+    -s, --shell [bash|zsh]  Shell to install hyakvnc for (default: $SHELL or bash)
+
+Examples:
+    # Install
+    hyakvnc install
+    # Install to ~/bin:
+    hyakvnc install -i ~/bin
+```
+
+## Configuration
+
+The following [environment variables](https://wiki.archlinux.org/title/environment_variables) can be used to override the default settings. Any arguments passed to `hyakvnc create` will override the environment variables.
+
+You can modify the values of these variables by:
+
+- Setting and exporting them in your shell session, e.g. `export HYAKVNC_SLURM_MEM='8G'` (which will only affect the current shell session)
+- Setting them in your shell's configuration file, e.g. `~/.bashrc` or `~/.zshrc` (which will affect all shell sessions)
+- Setting them by prefixing the `hyakvnc` command with the variable assignment, e.g. `HYAKVNC_SLURM_MEM='8G' hyakvnc create ...` (which will only affect the current command)
+- Setting them in the file `~/.hyakvnc/hyakvnc-config.env` (which will affect all `hyakvnc` commands)
+
+When you set an environment variable, it is advisable to surround the value with single quotes (`'`) to prevent your shell from interpreting special characters. There should be no spaces between the variable name, the equals sign, and the value.
+
+The following variables are available:
+
+- HYAKVNC_DIR: Local directory to store application data (default: `$HOME/.hyakvnc`)
+- HYAKVNC_CHECK_UPDATE_FREQUENCY: How often to check for updates in `[d]`ays or `[m]`inutes (default: `0` for every time. Use `1d` for daily, `10m` for every 10 minutes, etc. `-1` to disable.)
+- HYAKVNC_CONFIG_FILE: Configuration file to use (default: `$HYAKVNC_DIR/hyakvnc-config.env`)
+- HYAKVNC_LOG_FILE: Log file to use (default: `$HYAKVNC_DIR/hyakvnc.log`)
+- HYAKVNC_LOG_LEVEL: Log level to use for interactive output (default: `INFO`)
+- HYAKVNC_LOG_FILE_LEVEL: Log level to use for log file output (default: `DEBUG`)
+- HYAKVNC_SSH_HOST: Default SSH host to use for connection strings (default: `klone.hyak.uw.edu`)
+- HYAKVNC_DEFAULT_TIMEOUT: Seconds to wait for most commands to complete before timing out (default: `30`)
+- HYAKVNC_VNC_PASSWORD: Password to use for new VNC sessions (default: `password`)
+- HYAKVNC_VNC_DISPLAY: VNC display to use (default: `:1`)
+- HYAKVNC_APPTAINER_BIN: Name of apptainer binary (default: `apptainer`)
+- HYAKVNC_APPTAINER_CONTAINER: Path to container image to use (default: (none; set by `--container` option))
+- HYAKVNC_APPTAINER_APP_VNCSERVER: Name of app in the container that starts the VNC session (default: `vncserver`)
+- HYAKVNC_APPTAINER_APP_VNCKILL: Name of app that cleanly stops the VNC session in the container (default: `vnckill`)
+- HYAKVNC_APPTAINER_WRITABLE_TMPFS: Whether to use a writable tmpfs for the container (default: `1`)
+- HYAKVNC_APPTAINER_CLEANENV: Whether to use a clean environment for the container (default: `1`)
+- HYAKVNC_APPTAINER_ADD_BINDPATHS: Bind paths to add to the container (default: (none))
+- HYAKVNC_APPTAINER_ADD_ENVVARS: Environment variables to add to before invoking apptainer (default: (none))
+- HYAKVNC_APPTAINER_ADD_ARGS: Additional arguments to give apptainer (default: (none))
+- HYAKVNC_SLURM_JOB_PREFIX: Prefix to use for hyakvnc SLURM job names (default: `hyakvnc-`)
+- HYAKVNC_SLURM_SUBMIT_TIMEOUT: Seconds after submitting job to wait for the job to start before timing out (default: `120`)
+- HYAKVNC_SLURM_OUTPUT_DIR: Directory to store SLURM output files (default: `$HYAKVNC_DIR/slurm-output`)
+- HYAKVNC_SLURM_OUTPUT: Where to send SLURM job output (default: `$HYAKVNC_SLURM_OUTPUT_DIR/job-%j.out`)
+- HYAKVNC_SLURM_JOB_NAME: What to name the launched SLURM job (default: (set according to container name))
+- HYAKVNC_SLURM_ACCOUNT: Slurm account to use (default: (autodetected))
+- HYAKVNC_SLURM_PARTITION: Slurm partition to use (default: (autodetected))
+- HYAKVNC_SLURM_CLUSTER: Slurm cluster to use (default: (autodetected))
+- HYAKVNC_SLURM_GPUS: Number of GPUs to request (default: (none))
+- HYAKVNC_SLURM_MEM: Amount of memory to request, in [M]egabytes or [G]igabytes (default: `4G`)
+- HYAKVNC_SLURM_CPUS: Number of CPUs to request (default: `4`)
+- HYAKVNC_SLURM_TIMELIMIT: Time limit for SLURM job (default: `12:00:00`)
+
+## License
+
+`hyakvnc` is licensed under [MIT License](LICENSE).

From 06130146d47b664f96d64bf33118ff6a58c5a285 Mon Sep 17 00:00:00 2001
From: Altan Orhon <altan@uw.edu>
Date: Tue, 24 Oct 2023 19:16:40 -0700
Subject: [PATCH 15/19] Updated installer

---
 .build/install.j2.sh | 17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/.build/install.j2.sh b/.build/install.j2.sh
index d5456b3..09d4a74 100755
--- a/.build/install.j2.sh
+++ b/.build/install.j2.sh
@@ -19,12 +19,14 @@ _add_hyakvnc_to_path() {
 			echo "Added hyakvnc to PATH in ${HOME:-}/.bashrc" 2>&1
 			export PATH="${_BIN_INSTALL_DIR}:${PATH:-}"
 		elif [ -n "${ZSH_VERSION:-}" ]; then
-			echo "export PATH=\"${_UNEXPANDED_BIN_INSTALL_DIR}:\$PATH\"" >>"${ZDOTDIR:-${HOME:-}}/.zshrc"
-			echo "Added hyakvnc to PATH in ${ZDOTDIR:-${HOME}}/.zshrc" 2>&1
-			export PATH="${_BIN_INSTALL_DIR}:${PATH}"
+			echo "export PATH=\"${_UNEXPANDED_BIN_INSTALL_DIR}:\$PATH\"" >>"${ZDOTDIR:-${HOME:-}}/.zshrc" && echo "Added hyakvnc to PATH in ${ZDOTDIR:-${HOME}}/.zshrc" 2>&1
+			export PATH="${_BIN_INSTALL_DIR}:${PATH:-}"
 			rehash 2>/dev/null || true
+		elif [ "${0:-}" = "dash" ] || [ "${0:-}" = "sh" ]; then
+			echo "export PATH=\"${_UNEXPANDED_BIN_INSTALL_DIR}:\$PATH\"" >>"${HOME}/.profile" && echo "Added hyakvnc to PATH in ${HOME}/.profile" 2>&1
+			export PATH="${_BIN_INSTALL_DIR}:${PATH:-}"
 		else
-			echo "Could not add hyakvnc to PATH. Please add ${_BIN_INSTALL_DIR} to your shell PATH manually." 2>&1
+			echo "Could not add hyakvnc to PATH." 2>&1
 			return 1
 		fi
 		;;
@@ -52,8 +54,13 @@ _install_hyakvnc() {
 		return 1
 }
 
-if _install_hyakvnc && _add_hyakvnc_to_path; then
+if _install_hyakvnc; then
 	echo "Successfully installed hyakvnc." 2>&1
+	if _add_hyakvnc_to_path; then
+		echo "Added hyakvnc to PATH." 2>&1
+	else
+		echo "Could not add hyakvnc to PATH." 2>&1
+	fi
 else
 	echo "Failed to install hyakvnc." 2>&1
 fi

From 02476d71ee33f4b6bc2c3d02620b564e6d58aba8 Mon Sep 17 00:00:00 2001
From: maouw <62307612+maouw@users.noreply.github.com>
Date: Wed, 25 Oct 2023 02:17:05 +0000
Subject: [PATCH 16/19] Rebuilt install.sh

---
 install.sh | 17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/install.sh b/install.sh
index 7184f18..9f5d66f 100644
--- a/install.sh
+++ b/install.sh
@@ -19,12 +19,14 @@ _add_hyakvnc_to_path() {
 			echo "Added hyakvnc to PATH in ${HOME:-}/.bashrc" 2>&1
 			export PATH="${_BIN_INSTALL_DIR}:${PATH:-}"
 		elif [ -n "${ZSH_VERSION:-}" ]; then
-			echo "export PATH=\"${_UNEXPANDED_BIN_INSTALL_DIR}:\$PATH\"" >>"${ZDOTDIR:-${HOME:-}}/.zshrc"
-			echo "Added hyakvnc to PATH in ${ZDOTDIR:-${HOME}}/.zshrc" 2>&1
-			export PATH="${_BIN_INSTALL_DIR}:${PATH}"
+			echo "export PATH=\"${_UNEXPANDED_BIN_INSTALL_DIR}:\$PATH\"" >>"${ZDOTDIR:-${HOME:-}}/.zshrc" && echo "Added hyakvnc to PATH in ${ZDOTDIR:-${HOME}}/.zshrc" 2>&1
+			export PATH="${_BIN_INSTALL_DIR}:${PATH:-}"
 			rehash 2>/dev/null || true
+		elif [ "${0:-}" = "dash" ] || [ "${0:-}" = "sh" ]; then
+			echo "export PATH=\"${_UNEXPANDED_BIN_INSTALL_DIR}:\$PATH\"" >>"${HOME}/.profile" && echo "Added hyakvnc to PATH in ${HOME}/.profile" 2>&1
+			export PATH="${_BIN_INSTALL_DIR}:${PATH:-}"
 		else
-			echo "Could not add hyakvnc to PATH. Please add ${_BIN_INSTALL_DIR} to your shell PATH manually." 2>&1
+			echo "Could not add hyakvnc to PATH." 2>&1
 			return 1
 		fi
 		;;
@@ -52,8 +54,13 @@ _install_hyakvnc() {
 		return 1
 }
 
-if _install_hyakvnc && _add_hyakvnc_to_path; then
+if _install_hyakvnc; then
 	echo "Successfully installed hyakvnc." 2>&1
+	if _add_hyakvnc_to_path; then
+		echo "Added hyakvnc to PATH." 2>&1
+	else
+		echo "Could not add hyakvnc to PATH." 2>&1
+	fi
 else
 	echo "Failed to install hyakvnc." 2>&1
 fi

From a116e29235e0d846193f6508c9930791f79bcb1b Mon Sep 17 00:00:00 2001
From: Altan Orhon <altan@uw.edu>
Date: Tue, 24 Oct 2023 19:31:39 -0700
Subject: [PATCH 17/19] Update README.md for new installer

---
 .build/README.j2.md | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.build/README.j2.md b/.build/README.j2.md
index ae43b52..50d2833 100644
--- a/.build/README.j2.md
+++ b/.build/README.j2.md
@@ -4,6 +4,8 @@ hyakvnc -- A tool for launching VNC sessions on Hyak.
 
 `hyakvnc` is a command-line tool that makes it easy to start a graphical [VNC](https://en.wikipedia.org/wiki/Virtual_Network_Computing) session on the University of Washington [Hyak](https://hyak.uw.edu/) cluster, allowing you to interact with the system in a point-and-click environment, with support for graphical applications such as [Freesurfer](https://surfer.nmr.mgh.harvard.edu/). `hyakvnc` sessions run in [Apptainer](https://apptainer.org) containers, which provide reproducible environments that can run anywhere and be shared with other researchers.
 
+*If you're already familiar with Hyak and VNC and you just want to install `hyakvnc` immediately, you can skip to the [quick install](#quick-install) section.*
+
 ## Prerequisites
 
 Before running `hyakvnc`, you'll need the following:
@@ -78,7 +80,7 @@ ssh your-uw-netid@klone.hyak.uw.edu
 After you've connected to the login node, you can download and install `hyakvnc` by running the following command. Copy and paste it into the terminal window where you are connected to the login node and press enter:
 
 ```bash
-curl -o ~/.local/bin/hyakvnc --create-dirs -fsSL https://raw.githubusercontent.com/{{github_repository}}/{{github_ref_name}}/hyakvnc && chmod +x ~/.local/bin/hyakvnc && [[ ":${PATH}:" != *":$HOME/.local/bin:"* ]] && export PATH="$HOME/.local/bin:$PATH" && [-n "${ZSH_VERSION:-}" ] && rehash
+eval "$(curl -fsSL https://raw.githubusercontent.com//{{github_repository}}/{{github_ref_name}}/install.sh)"
 ```
 
 This will download and install `hyakvnc` to your `~/.local/bin` directory and add it to your `$PATH` so you can run it by typing `hyakvnc` into the terminal window.
@@ -88,7 +90,7 @@ This will download and install `hyakvnc` to your `~/.local/bin` directory and ad
 In a terminal window connected to a login node, enter this command to clone the repository and navigate into the repository directory:
 
 ```bash
-git clone https://github.com/{{github_repository}} && cd hyakvnc
+git clone --depth 1 --single-branch https://github.com/{{github_repository}} && cd hyakvnc
 ```
 
 Then, run the following command to install `hyakvnc`:

From df0413f5817d97adc85a98d2a388cd2f370eea92 Mon Sep 17 00:00:00 2001
From: maouw <62307612+maouw@users.noreply.github.com>
Date: Wed, 25 Oct 2023 02:31:56 +0000
Subject: [PATCH 18/19] Rebuilt README.md

---
 README.md | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 562bff3..c3af2e1 100644
--- a/README.md
+++ b/README.md
@@ -4,6 +4,8 @@ hyakvnc -- A tool for launching VNC sessions on Hyak.
 
 `hyakvnc` is a command-line tool that makes it easy to start a graphical [VNC](https://en.wikipedia.org/wiki/Virtual_Network_Computing) session on the University of Washington [Hyak](https://hyak.uw.edu/) cluster, allowing you to interact with the system in a point-and-click environment, with support for graphical applications such as [Freesurfer](https://surfer.nmr.mgh.harvard.edu/). `hyakvnc` sessions run in [Apptainer](https://apptainer.org) containers, which provide reproducible environments that can run anywhere and be shared with other researchers.
 
+*If you're already familiar with Hyak and VNC and you just want to install `hyakvnc` immediately, you can skip to the [quick install](#quick-install) section.*
+
 ## Prerequisites
 
 Before running `hyakvnc`, you'll need the following:
@@ -78,7 +80,7 @@ ssh your-uw-netid@klone.hyak.uw.edu
 After you've connected to the login node, you can download and install `hyakvnc` by running the following command. Copy and paste it into the terminal window where you are connected to the login node and press enter:
 
 ```bash
-curl -o ~/.local/bin/hyakvnc --create-dirs -fsSL https://raw.githubusercontent.com/maouw/hyakvnc/install-sh/hyakvnc && chmod +x ~/.local/bin/hyakvnc && [[ ":${PATH}:" != *":$HOME/.local/bin:"* ]] && export PATH="$HOME/.local/bin:$PATH" && [-n "${ZSH_VERSION:-}" ] && rehash
+eval "$(curl -fsSL https://raw.githubusercontent.com//maouw/hyakvnc/install-sh/install.sh)"
 ```
 
 This will download and install `hyakvnc` to your `~/.local/bin` directory and add it to your `$PATH` so you can run it by typing `hyakvnc` into the terminal window.
@@ -88,7 +90,7 @@ This will download and install `hyakvnc` to your `~/.local/bin` directory and ad
 In a terminal window connected to a login node, enter this command to clone the repository and navigate into the repository directory:
 
 ```bash
-git clone https://github.com/maouw/hyakvnc && cd hyakvnc
+git clone --depth 1 --single-branch https://github.com/maouw/hyakvnc && cd hyakvnc
 ```
 
 Then, run the following command to install `hyakvnc`:

From be85b97bccfb9eb739f8e3bd37e32e720ccbf965 Mon Sep 17 00:00:00 2001
From: Altan Orhon <altan@uw.edu>
Date: Wed, 25 Oct 2023 10:05:30 -0700
Subject: [PATCH 19/19] Clarify install.sh execution in comments

---
 install.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/install.sh b/install.sh
index 9f5d66f..da58716 100644
--- a/install.sh
+++ b/install.sh
@@ -2,7 +2,7 @@
 
 # install.sh is generated from .build/install.j2.sh. Do not edit it directly.
 # This script is intended to be sourced from the current shell.
-# It will clone the hyakvnc repository to ~/.hyakvnc/hyakvnc and create a symlink in it to ~/.local/bin/hyakvnc.
+# It will clone the hyakvnc repository from GitHub to ~/.hyakvnc/hyakvnc and create a symlink in it to ~/.local/bin/hyakvnc.
 # These locations can be changed by setting the following environment variables:
 # - HYAKVNC_DIR: Local directory to store application data (default: `$HOME/.hyakvnc`)
 # - HYAKVNC_REPO_DIR: Local directory to store git repository (default: `$HYAKVNC_DIR/hyakvnc`)