From 6e76adcac3c2d695e94c73b37e6071fa0f88ca00 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Anton=C3=ADn=20Dufka?= <xdufka1@fi.muni.cz>
Date: Tue, 1 Aug 2023 17:01:29 +0200
Subject: [PATCH] Update package specification

---
 .dockerignore    |  2 ++
 .gitignore       |  3 ++-
 Dockerfile       |  5 ++---
 pyproject.toml   | 35 +++++++++++++++++++++++++++++++++++
 requirements.txt |  5 -----
 setup.py         | 32 --------------------------------
 6 files changed, 41 insertions(+), 41 deletions(-)
 create mode 100644 .dockerignore
 create mode 100644 pyproject.toml
 delete mode 100644 requirements.txt
 delete mode 100644 setup.py

diff --git a/.dockerignore b/.dockerignore
new file mode 100644
index 0000000..8a8d38c
--- /dev/null
+++ b/.dockerignore
@@ -0,0 +1,2 @@
+*venv/
+build/
diff --git a/.gitignore b/.gitignore
index a22771e..f24c9dc 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,5 +1,6 @@
 data/
 local/
+build/
 *venv/
 .idea/
 *.log
@@ -13,5 +14,5 @@ dissect/traits/sample_curves.py
 dissect/traits/**/*.json
 !dissect/traits/**/*_structure.json
 dissect/traits/**/*.txt
-DiSSECT.egg-info
+*.egg-info
 /dissect/results/
diff --git a/Dockerfile b/Dockerfile
index 514d246..db15d6c 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM sagemath/sagemath:9.4
+FROM sagemath/sagemath:9.8
 
 # Setup sage and jupyter
 RUN sage --pip3 install --no-cache-dir notebook
@@ -9,12 +9,11 @@ ARG NB_UID=1000
 ENV USER ${NB_USER}
 ENV HOME /home/sage
 ENV TARGET "${HOME}/dissect"
-COPY . ${TARGET}
 
 USER root
-RUN sed -i -re 's/([a-z]{2}.)?archive.ubuntu.com|security.ubuntu.com/old-releases.ubuntu.com/g' /etc/apt/sources.list
 RUN apt-get update && apt-get install ca-certificates
 RUN usermod -l ${NB_USER} sage
+COPY . ${TARGET}
 RUN chown -R ${NB_UID} ${TARGET}
 
 # Install DiSSECT
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..3255e08
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,35 @@
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "dissect"
+version = "0.3.0"
+description = "Distinguisher of Standard & Simulated Elliptic Curves through Traits."
+authors = [
+    {name = "Vladimír Sedláček", email = "vlada.sedlacek@mail.muni.cz"},
+    {name = "Vojtěch Suchánek"},
+    {name = "Antonín Dufka"},
+]
+readme = "README.md"
+license = {text = "MIT License"}
+requires-python = ">=3.8"
+dependencies = [
+    "pathlib==1.0.1",
+    "pymongo==4.4.1",
+    "pandas==2.0.3",
+    "scikit-learn==1.3.0",
+    "plotly==5.15.0",
+]
+
+[project.urls]
+Homepage = "https://dissect.crocs.fi.muni.cz/"
+Repository = "https://github.com/crocs-muni/DiSSECT.git"
+
+[project.scripts]
+dissect-database = "dissect.utils.database_handler:main"
+dissect-compute-database = "dissect.traits.run:main"
+dissect-compute-file = "dissect.traits.compute:main"
+dissect-feature_builder = "dissect.analysis.feature_builder:main"
+dissect-find_outliers = "dissect.analysis.find_outliers:main"
+dissect-detail = "dissect.analysis.detail:main"
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index dedebb0..0000000
--- a/requirements.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-pathlib==1.0.1
-pymongo==4.4.1
-pandas==2.0.3
-scikit-learn==1.3.0
-plotly==5.15.0
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 8340581..0000000
--- a/setup.py
+++ /dev/null
@@ -1,32 +0,0 @@
-#!/usr/bin/env sage
-
-import importlib.util
-from pathlib import Path
-
-from setuptools import setup, find_packages
-
-from dissect.definitions import TRAIT_PATH
-
-with open('requirements.txt') as f:
-    install_requires = f.read().splitlines()
-
-setup(name='DiSSECT',
-      version='0.3',
-      description='Distinguisher of Standard & Simulated Elliptic Curves through Traits.',
-      url='https://github.com/crocs-muni/DiSSECT',
-      author='Vladimír Sedláček, Vojtěch Suchánek and Antonín Dufka',
-      author_email='vlada.sedlacek@mail.muni.cz',
-      license='MIT',
-      packages=find_packages(),
-      install_requires=install_requires,
-      entry_points={
-          'console_scripts': [
-              'dissect-database=dissect.utils.database_handler:main',
-              'dissect-compute-database=dissect.traits.run:main',
-              'dissect-compute-file=dissect.traits.compute:main',
-              'dissect-feature_builder=dissect.analysis.feature_builder:main',
-              'dissect-find_outliers=dissect.analysis.find_outliers:main',
-              'dissect-detail=dissect.analysis.detail:main'
-          ]
-      }
-)