From ee8c814af195544792ac96a3f8c06508444f02e2 Mon Sep 17 00:00:00 2001
From: ChrisGadek1 <krzysztof.gadek15@gmail.com>
Date: Thu, 26 Mar 2026 22:50:37 +0100
Subject: [PATCH] Add packaging configuration and update .gitignore for build
 artifacts

---
 .gitignore     |  5 ++++-
 MANIFEST.in    |  9 +++++++++
 README.md      | 22 ++++++++++++++++++++++
 pyproject.toml | 48 ++++++++++++++++++++++++++++++++++++++++++++++++
 4 files changed, 83 insertions(+), 1 deletion(-)
 create mode 100644 MANIFEST.in
 create mode 100644 pyproject.toml

diff --git a/.gitignore b/.gitignore
index 9beeac1..31833e9 100644
--- a/.gitignore
+++ b/.gitignore
@@ -24,4 +24,7 @@ dask-scratch-space
 
 *.h5
 !tests/data/distograms_pdbs/pdbs.h5
-!tests/data/dataset_expected/structures/*/*/*/*/*.h5
\ No newline at end of file
+!tests/data/dataset_expected/structures/*/*/*/*/*.h5
+
+*.egg-info
+build
diff --git a/MANIFEST.in b/MANIFEST.in
new file mode 100644
index 0000000..9311c11
--- /dev/null
+++ b/MANIFEST.in
@@ -0,0 +1,9 @@
+# include everything in the sdist (be careful — this will bundle all files)
+global-include *
+
+recursive-exclude tests *
+recursive-exclude .github *
+recursive-exclude .pytest_cache *
+recursive-exclude build *
+recursive-exclude *.egg-info *
+recursive-exclude dist *
\ No newline at end of file
diff --git a/README.md b/README.md
index 644c481..be2e84b 100644
--- a/README.md
+++ b/README.md
@@ -86,6 +86,28 @@ PYTHONPATH='.' python3 -u ${FRIDATA_PATH}/fridata.py \
  -e ${EMBEDDER_TYPE}
 ```
 
+## Running as a CLI tool
+
+Assuming all `Instalation and activation` steps succeeded.
+
+0. Go into `FRIdata` directory
+
+```
+cd <path into FRIdata>
+```
+
+1. Install as a CLI tool
+
+```
+python3 -m pip install -e .
+```
+
+2. Now FRIdata can be run as a CLI tool
+
+```
+$ fridata <...>
+```
+
 ## Running on HPC
 
 Running FRIdata on HPC differs on CPU and GPU nodes. This instruction set is valid for HPC hosted in PLGrid infrastructure. Running on other infrastructures may require additional adjustments.
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..80b81eb
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,48 @@
+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "FRIdata"
+version = "0.1.0"
+readme = "README.md"
+requires-python = ">=3.10"
+dependencies = [
+    "foldcomp",
+    "pydantic>=2.8.2",
+    "scipy>=1.14.0",
+    "h5py",
+    "matplotlib",
+    "biotite>=0.41.2",
+    "numpy>=1.26.4,<1.27.0",
+    "genson",
+    "bs4",
+    "bio~=1.7.0",
+    "pytest",
+    "pytest-order",
+    "dask>=2024.4.2,<2025.0.0",
+    "dask[dataframe]",
+    "distributed>=2024.4.2,<2025.0.0",
+    "python-dotenv",
+    "tables",
+    "biopython",
+    "bokeh>=2.4.2,<3.0.0",
+    "pdbfixer",
+    "mamba",
+    "transformers",
+    "tqdm",
+    "pytorch-gpu",
+    "esm"
+]
+
+[project.scripts]
+fridata = "fridata:main"
+
+[tool.setuptools]
+# fridata.py is a single-module at project root; install as py-module
+py-modules = ["fridata"]
+include-package-data = true
+
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["toolbox*"]
\ No newline at end of file