Added autoformatting and updated README

.flake8

@@ -0,0 +1,3 @@
+[flake8]
+extend-ignore = E203
+max-line-length = 100

.github/workflows/black.yml

@@ -0,0 +1,12 @@
+name: Lint
+
+on: [push, pull_request]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: psf/black@stable
+        with:
+          src: "./src"

.gitignore

@@ -0,0 +1,164 @@
+### Python template
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be foud at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# User-specific stuff
+*.whl

.pre-commit-config.yaml

@@ -0,0 +1,15 @@
+repos:
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 23.7.0
+    hooks:
+      - id: black
+        language_version: python3.9
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-executables-have-shebangs
+      - id: check-shebang-scripts-are-executable
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace

README.md

@@ -1,5 +1,4 @@
-hyakvnc
-=======
+# hyakvnc
 
 Create and manage VNC Slurm jobs on UW HYAK Klone cluster.
 
@@ -15,94 +14,115 @@ time.
 ### Prerequisites
 
 Before running `hyakvnc`, you'll need the following:
+
 - SSH client
 - VNC client/viewer
-    - TigerVNC viewer is recommended for all platforms
+  - TigerVNC viewer is recommended for all platforms
 - HYAK Klone access with compute resources
 - VNC Apptainer with TigerVNC server and a desktop environment
-    - Install additional tools and libraries to the container as required by
-      programs running within the VNC session.
-- xstartup script used to launch a desktop environment
+  - Install additional tools and libraries to the container as required by programs running within the VNC session.
+- `xstartup` script used to launch a desktop environment
+- A Python interpreter (version **3.9** or higher)
 
 ### Building
 
-Update pip:
+`hyakvnc` is a Python package that can be installed with `pip`. The minimum Python version required is **3.9**. You can check the version of the default Python 3 interpreter with:
+
 ```bash
-python3 -m pip install --upgrade --user pip
+python3 -V
+```
+
+As of 2021-09-30, the default Python 3 interpreter on Klone is version 3.6.8. Because `hyakvnc` requires version 3.9 or higher, it is necessary to specify the path to a Python 3.9 or newer interpreter when installing `hyakvnc`. You can list the Python 3 interpreters you have available with:
+
+```bash
+compgen -c | grep '^python3\.[[:digit:]]$'
+```
+
+At this time, Klone supports Python 3.9, which can be run with the command `python3.9`. The following instructions are written with `python3.9` in mind. If you use another version, such as `python3.11`, you will need to substitute `python3.9` with, e.g., `python3.11` in the instructions.
+
+```bash
+python3.9 -m pip install --upgrade --user pip
 ```
 
 Build and install the package:
 
 ```bash
-python3 -m pip install --user git+https://github.com/uw-psych/hyakvnc
+python3.9 -m pip install --user git+https://github.com/uw-psych/hyakvnc
 ```
 
 Or, clone the repo and install the package locally:
 
 ```bash
 git clone https://github.com/uw-psych/hyakvnc
-python3 -m pip install --user .
+python3.9 -m pip install --user .
 ```
 
 If successful, then `hyakvnc` should be installed to `~/.local/bin/`.
 
+#### Optional dependencies for development
+
+The optional dependency group `[dev]` in `pyroject.toml` includes dependencies useful for development, including [pre-commit](https://pre-commit.com/) hooks that run in order to commit to the `git` repository.
+These apply various checks, including running the `black` code formatter before the commit takes place.
+
+To ensure `pre-commit` and other development packages are installed, run:
+
+```bash
+python3.9 -m pip install --user '.[dev]'
+```
+
 ### General usage
 
 `hyakvnc` is command-line tool that only works while on the login node.
 
 ### Creating a VNC session
 
-1. Start a VNC session with the `hyakvnc create` command followed by arguments
-   to specify the Slurm account and partition, compute resource needs,
-   reservation time, and paths to a VNC apptainer and xstartup script.
+1. Start a VNC session with the `hyakvnc create` command followed by arguments to specify the Slurm account and partition, compute resource needs, reservation time, and paths to a VNC apptainer and xstartup script.
 
-```bash
-# example: Starting VNC session on `ece` compute resources for 5 hours on a
-# node with 16 cores and 32GB of memory
-hyakvnc create -A ece -p compute-hugemem \
-    -t 5 -c 16 --mem 32G \
-    --container /path/to/container.sif \
-    --xstartup /path/to/xstartup
-```
+   ```bash
+   # example: Starting VNC session on `ece` compute resources for 5 hours on a
+   # node with 16 cores and 32GB of memory
+   hyakvnc create -A ece -p compute-hugemem \
+     -t 5 -c 16 --mem 32G \
+     --container /path/to/container.sif \
+     --xstartup /path/to/xstartup
+    ```
 
 2. If successful, `hyakvnc` should print a unique port forward command:
 
-```
-...
-=====================
-Run the following in a new terminal window:
-        ssh -N -f -L AAAA:127.0.0.1:BBBB [email protected]
-then connect to VNC session at localhost:AAAA
-=====================
-```
+   ```text
+   ...
+   =====================
+   Run the following in a new terminal window:
+       ssh -N -f -L AAAA:127.0.0.1:BBBB [email protected]
+   then connect to VNC session at localhost:AAAA
+   =====================
+   ```
 
-Copy this port forward command for the following step.
+   Copy this port forward command for the following step.
 
-3. Set up port forward between your computer and HYAK login node. On your
-   machine, in a new terminal window, run the the copied command.
+3. Set up port forward between your computer and HYAK login node. On your machine, in a new terminal window, run the the copied command.
 
-Following the example, run:
+    Following the example, run:
 
-```bash
-ssh -N -f -L AAAA:127.0.0.1:BBBB [email protected]
-```
+   ```bash
+   ssh -N -f -L AAAA:127.0.0.1:BBBB [email protected]
+   ```
 
-Alternatively, for PuTTY users, navigate to
-PuTTY Configuration->Connection->SSH->Tunnels, then set:
-  - source port to `AAAA`
-  - destination to `127.0.0.1:BBBB`
+   Alternatively, for PuTTY users, navigate to `PuTTY Configuration->Connection->SSH->Tunnels`, then set:
+   - source port to `AAAA`
+   - destination to `127.0.0.1:BBBB`
 
-Press `Add`, then connect to Klone as normal. Keep this window open as it
-maintains a connection to the VNC session running on Klone.
+   Press `Add`, then connect to Klone as normal. Keep this window open as it
+   maintains a connection to the VNC session running on Klone.
 
 4. Connect to the VNC session at instructed address (in this example:
    `localhost:AAAA`)
 
 5. To close the VNC session, run the following
 
-```bash
-hyakvnc kill-all
-```
+   ```bash
+   hyakvnc kill-all
+   ```
 
 ### Checking active VNC sessions
 
@@ -135,7 +155,7 @@ re-established with new port mappings via the `hyakvnc repair` command.
 
 Before repairing:
 
-```
+```text
 Active hyakvnc jobs:
         Job ID: NNNNNNNN
                 SubNode: n3050
@@ -145,7 +165,7 @@ Active hyakvnc jobs:
 
 After repairing port forwarding:
 
-```
+```text
 Active hyakvnc jobs:
         Job ID: NNNNNNNN
                 SubNode: n3050
@@ -162,7 +182,7 @@ which may require the user to set up new port forward(s).
 
 ### Override Apptainer bind paths
 
-If present, `hyakvnc` will use `APPTAINER_BINDPATH` or `SINGULARITY_BINDPATH` to
+If present, `hyakvnc` will use the [environment variables](https://tldp.org/LDP/Bash-Beginners-Guide/html/sect_03_02.html)  `APPTAINER_BINDPATH` or `SINGULARITY_BINDPATH` to
 determine how paths are mounted in the VNC container environment. If neither is
 defined, `hyakvnc` will use its default bindpath.