From a653781dd5fb70d52760df508ddd137af182803d Mon Sep 17 00:00:00 2001
From: Cunliang Geng <c.geng@esciencecenter.nl>
Date: Mon, 25 Mar 2024 17:11:08 +0100
Subject: [PATCH] move dependencies to pyproject.toml file

Major changes
- move dependencies to pyproject.toml file
- remove files `requirements.txt` and `requirements.dev.txt`
---
 pyproject.toml       | 74 ++++++++++++++++++++++++++++++++------------
 requirements.dev.txt | 23 --------------
 requirements.txt     | 12 -------
 setup.py             |  1 -
 4 files changed, 55 insertions(+), 55 deletions(-)
 delete mode 100644 requirements.dev.txt
 delete mode 100644 requirements.txt

diff --git a/pyproject.toml b/pyproject.toml
index acf50b91..a4ff4d48 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,9 +1,7 @@
-# We use setup.cfg to set project metadata and setuptools configs.
-# All the other configs (e.g. pytest, coverage) are set in this file.
 # see https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html
 
 [build-system]
-requires      = ["setuptools", "wheel"]
+requires = ["setuptools"]
 build-backend = "setuptools.build_meta"
 
 [project]
@@ -26,42 +24,80 @@ classifiers = [
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+]
+dependencies = [
+    "beautifulsoup4",
+    "biopython",
+    "deprecated",
+    "dynaconf",
+    "httpx",
+    "jsonschema",
+    "numpy",
+    "pandas",
+    "pyteomics",
+    "scipy",
+    "sortedcontainers",
+    "tqdm",
 ]
-dynamic = ["dependencies", "optional-dependencies"]
 
-[tool.setuptools.dynamic]
-dependencies              = { file = ["requirements.txt"] }
-optional-dependencies.dev = { file = ["requirements.dev.txt"] }
+[project.optional-dependencies]
+dev = [
+    # packaging
+    "build",
+    "bump2version",
+    "wheel",
+    # formatting and linting
+    "ruff",
+    # testing
+    "pytest",
+    "pytest-cov",
+    "pytest-xdist",
+    "coverage[toml]",
+    # static typing
+    "mypy",
+    "types-toml",
+    "types-Deprecated",
+    "typing_extensions",
+    # docs
+    "mkdocs",
+    "mkdocs-material",
+    "mkdocs-exclude",
+    "mkdocs-redirects",
+    "mkdocstrings-python",
+    "mike",
+]
 
 [project.urls]
-"Homepage"    = "https://github.com/NPLinker/nplinker"
-"Bug Tracker" = "https://github.com/NPLinker/nplinker/issues"
+"Documentation" = "https://nplinker.github.io/nplinker"
+"Repository" = "https://github.com/NPLinker/nplinker"
+"Issues" = "https://github.com/NPLinker/nplinker/issues"
 
 [tool.setuptools.packages.find]
-where      = ["src"]
-namespaces = true    # enable data directory to be identified
+where = ["src"]
+namespaces = true # enable data directory to be identified
 
 [tool.setuptools.package-data]
-"nplinker.data"    = ["*"]
+"nplinker.data" = ["*"]
 "nplinker.schemas" = ["*"]
 "nplinker" = ["nplinker_default.toml"]
 
 [tool.pytest.ini_options]
 minversion = "6.0"
-addopts    = "-ra -n auto"   # -ra: show summary info for all test outcomes; -n auto: run tests in parallel
-testpaths  = ["tests/unit"]
+addopts = "-ra -n auto"    # -ra: show summary info for all test outcomes; -n auto: run tests in parallel
+testpaths = ["tests/unit"]
 
 [tool.coverage.run]
-branch       = true
-source       = ["src"]
+branch = true
+source = ["src"]
 command_line = "-m pytest"
 
 # Mypy: to check static type
 # see https://mypy.readthedocs.io/en/stable/config_file.html#example-pyproject-toml
 [tool.mypy]
-python_version         = "3.10"
-warn_return_any        = true
-warn_unused_configs    = true
+python_version = "3.10"
+warn_return_any = true
+warn_unused_configs = true
 ignore_missing_imports = true
 
 [tool.ruff]
diff --git a/requirements.dev.txt b/requirements.dev.txt
deleted file mode 100644
index 68b381fd..00000000
--- a/requirements.dev.txt
+++ /dev/null
@@ -1,23 +0,0 @@
-# packaging
-build
-bump2version
-wheel
-# formatting and linting
-ruff
-# testing
-pytest
-pytest-cov
-pytest-xdist
-coverage[toml]
-# static typing
-mypy
-types-toml
-types-Deprecated
-typing_extensions
-# docs
-mkdocs
-mkdocs-material
-mkdocs-exclude
-mkdocs-redirects
-mkdocstrings-python
-mike
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index 1d4e512f..00000000
--- a/requirements.txt
+++ /dev/null
@@ -1,12 +0,0 @@
-beautifulsoup4
-biopython
-deprecated
-dynaconf
-httpx
-jsonschema
-numpy
-pandas
-pyteomics
-scipy
-sortedcontainers
-tqdm
diff --git a/setup.py b/setup.py
index 81a328bd..d00a42cc 100644
--- a/setup.py
+++ b/setup.py
@@ -6,5 +6,4 @@
 if sys.version_info[:2] < (3, 9):
     raise RuntimeError("Python version >= 3.9 required.")
 
-# see setup.cfg
 setup(scripts=["bin/install-nplinker-deps"])