Refactor to tidy, remove duplication, and increase usability

.gitignore

@@ -1,5 +1,4 @@
-python_runs/__pycache__
-python_runs/IOR_config
+__pycache__
 examples/test_files
 logs
 tmp

LICENSE

@@ -0,0 +1,7 @@
+Copyright (c) 2025 Shaker Krit, Flatiron Institute
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

README.md

@@ -1,14 +1,26 @@
 # PyBenchFramework
-#throw this change out
-This application is being used with slurm but it can run on its own.
-
-User must set the environment variable "PyBench_root_dir" to run run.py. Try to use mdtest_env to start the environment for MDTEST or env_start for FIO. Don't use both at the same time.
-
-The app needs a root directory to read templates and store intermediate config files as well as log files and the like.
-
-Options can be included as arguments to 'run.py' or as fields in a YAML config file. The config file for an FIO job looks like so:
-
-<pre>
+This application is designed to be used with `slurm` but it can run on its own.
+
+## Installation (development)
+```sh
+python3 -m venv /path/to/venv
+source /path/to/venv/bin/activate
+git clone https://github.com/flatironinstitute/PyBenchFramework --branch cleanup
+cd PyBenchFramework
+pip install -e .
+rehash # might not be necessary, depending on shell
+```
+
+## Running
+```sh
+source /path/to/venv/bin/activate
+mpirun -n 2 pybench-run --benchmark "fio-independent-ranks" --slurm-job-number 0 --io-type "read" --config examples/YAML_templates/FIO_templates/test_kernel_rep3_ssd.yml --block-size 4M --first-node $(hostname -s) --total-node-count 1
+```
+Options can be included as arguments to 'run.py' or as fields in a YAML config file. The config
+file for an FIO job looks like so:
+
+### Configuration
+```yaml
 slurm_job_number: 
 block_size: "4M,64K,4K"
 directory: /mnt/cephtest-fi5k/test-rep3-ssd/skrit/fio
@@ -22,11 +34,11 @@ hosts_file:
 no_scrub: 0
 unit_restart: 1
 template_path: /mnt/home/skrit/Documents/testing_clones/clone1/PyBenchFramework/examples/template/template.fio
-</pre>
+```
 
 The config file for an mdtest job looks like so:
 
-<pre>
+```yaml
 mpi_ranks: 40,30,20,10,5 
 directory: /mnt/cephtestk/test-ec63/skrit/mdtest
 files_per_rank: 20,10,5
@@ -38,10 +50,7 @@ offset: 1
 write_data: '3901'
 read_data: '3901'
 node_count: 10,5,1
-</pre>
-
-One thing to note is that the main loop takes mpi ranks and multiplies it to the node count. For example, when mpi_ranks is 5 and node_count is 1, mpirun is given '-n 5' for a total of 5 mpi ranks. When mpi_ranks is 5 and node_count is 10, mpirun is given '-n 50' (5 * 10) which is distributed across 10 nodes (--map-by node -N 10).
-
-'slurm_job_number' should, at least for now, be an inline argument. Keep in mind inline arguments are likely separated by - rather than _ --help should show all arguments as they should be inline.
+```
 
-Under the 'submit_scripts' folder, you'll see several slurm scripts. 'mdtest.sh' is a good template for submitting mdtest jobs and the scripts starting with 'ssd...' or 'hdd...' are good templates for FIO jobs.
+## Slurm submission
+All `submit_scripts` are currently broken.

pyproject.toml

@@ -0,0 +1,39 @@
+[build-system]
+requires = ["hatchling >= 1.26"]
+build-backend = "hatchling.build"
+
+[project]
+name = "BenchmarkToolkit"
+version = "0.0.1"
+authors = [
+  { name="Shaker Krit", email="skrit@flatironinstitute.org" },
+]
+description = "BenchmarkToolkit is a Python library designed to simplify and streamline benchmarking tasks. This library provides a high-level abstraction over various benchmarking functions, allowing developers to easily perform performance testing and analysis with minimal setup."
+readme = "README.md"
+requires-python = ">=3.9"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Operating System :: OS Independent",
+]
+license = "MIT"
+license-files = ["LICENSE"]
+dependencies = [
+    "cryptography", # FIXME was: 42.0.8
+    "matplotlib",   # FIXME was: 3.9.2
+    "pandas",       # FIXME was: 2.2.2
+    "paramiko",     # FIXME was: 3.4.0
+    "psutil",       # FIXME was: 6.0.0
+    "PyYAML",
+    "mpi4py",
+]
+
+[tool.hatch.build.targets.wheel]
+packages = [
+    "src/BenchmarkToolkit",
+]
+
+[project.urls]
+Repository = "https://github.com/flatironinstitute/PyBenchFramework"
+
+[project.scripts]
+pybench-run = "BenchmarkToolkit.run:main"