From ff0f0e2799295ad2559c9d3782c57778dc2e7c24 Mon Sep 17 00:00:00 2001
From: jasonfan1997 <fkt8356@gmail.com>
Date: Fri, 18 Oct 2024 11:17:36 -0400
Subject: [PATCH] update README and add requirements.txt

---
 GUI_cal_metrics.py |  3 ---
 README.md          | 21 ++++++++++++++++++---
 cal_metrics.py     |  2 ++
 citation.cff       | 11 +++++++++++
 requirements.txt   |  4 ++++
 5 files changed, 35 insertions(+), 6 deletions(-)
 create mode 100644 citation.cff
 create mode 100644 requirements.txt

diff --git a/GUI_cal_metrics.py b/GUI_cal_metrics.py
index 28cf70a..f6dd1c2 100644
--- a/GUI_cal_metrics.py
+++ b/GUI_cal_metrics.py
@@ -1,8 +1,5 @@
 import argparse
-import numpy as np
 import subprocess
-import time
-import matplotlib.pyplot as plt
 from nicegui import ui, app
 
 
diff --git a/README.md b/README.md
index d5ea8f2..2030979 100644
--- a/README.md
+++ b/README.md
@@ -14,13 +14,28 @@ calzone is a comprehensive Python package for calculating and visualizing variou
 
 ## Installation
 
-You can install calzone using pip:
-pip install -e "git+https://github.com/DIDSR/calzone.git"
+`calzone` package require installation of `numpy`, `scipy`, `matplotlib` and `statsmodels`. If you need to run GUI, `nicegui` is also required.
 
+You can install calzone using pip:
+```
+pip install -e "git+https://github.com/DIDSR/calzone.git"#egg=calzone`
+```
+
+Alternatively, you can clone the repository and install it locally:
+```
+git clone https://github.com/DIDSR/calzone.git
+cd calzone
+pip install .
+```
 ## Usage
 
-run `python cal_metrics.py -h` to see the help information and usage. To use the package in your Python code, please refer to the examples in the documentation pages.
+run `python cal_metrics.py -h` to see the help information and usage. To use the package in your Python code, please refer to the examples in the documentation pages. 
+
+To use GUI, run `python GUI_cal_metrics.py` (GUI is under development, use with caution.)
 
 ## Documentation
 
 For detailed documentation and API reference, please visit our [documentation pdf](https://github.com/DIDSR/calzone/blob/main/docs/build/latex/calzone.pdf).
+
+
+## Disclaimer 
diff --git a/cal_metrics.py b/cal_metrics.py
index ad6ce33..39995a4 100755
--- a/cal_metrics.py
+++ b/cal_metrics.py
@@ -55,10 +55,12 @@ def perform_calculation(probs, labels, args, suffix=""):
 
     # Save metrics to CSV
     if args.save_metrics:
+        print("Saving result to", args.save_metrics)
         save_metrics_to_csv(result, keys, args.save_metrics, suffix)
 
     # Plot reliability diagram
     if args.plot:
+        print("Saving plot to", args.save_plot)
         plot_reliability(labels, probs, args, suffix)
 
     return result
diff --git a/citation.cff b/citation.cff
new file mode 100644
index 0000000..8ec7c5d
--- /dev/null
+++ b/citation.cff
@@ -0,0 +1,11 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+- family-names: "Fan"
+  given-names: "Kwok Lung"
+  orcid: "https://orcid.org/0000-0002-2180-9082"
+- family-names: "Cao"
+  given-names: "Qian"
+title: "calzone: A Python package for measring calibration of probablistic models for classification"
+date-released: 2024-10-18
+url: "https://github.com/DIDSR/calzone"
\ No newline at end of file
diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 0000000..a15297a
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,4 @@
+numpy == 1.26.4
+scipy == 1.14.1
+matplotlib == 3.8.0
+statsmodels == 0.14.2
\ No newline at end of file