Prepare for stable 2.0 release

CHANGELOG.md

@@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [2.0.0] - 2026-07-13
+
 ### Added
 - New `core` module with `predict` and `predict_and_calibrate` as main public API
 - New `calibration` module replacing `calibrate`, with `Calibration` and `LinearCCSCalibration` classes
@@ -28,15 +30,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - **Breaking:** Minimum Python version raised from 3.10 to 3.11
 - **Breaking:** Switched from Keras/TensorFlow models to PyTorch Lightning models (`.ckpt`)
 - Switched build system from setuptools to uv
-- Replaced `deeplc<4` dependency with `deeplc>=4.0.0a1`
-- Removed pinned `numpy==1.26.0` dependency
-- Removed `im2deeptrainer` optional dependency
 - CLI restructured as click command group with `predict` as default command
 - Renamed reference data files for clarity
 - Linting moved from black/isort to ruff
+- Upgrade `deeplc` dependency to `deeplc>=4.0.0b1,<5`
+- Added explicit lower/upper version bounds to all core dependencies.
 
 ### Removed
 - `im2deep.py` module (replaced by `core.py`)
 - `calibrate.py` module (replaced by `calibration.py`)
 - `predict_multi.py` module (functionality merged into architecture subpackage)
 - Keras model files
+- Removed pinned `numpy==1.26.0` dependency
+- Removed `im2deeptrainer` optional dependency

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "im2deep"
-version = "2.0.0-alpha.3"
+version = "2.0.0"
 description = "Framework for prediction of collisional cross-section of peptides."
 readme = "README.md"
 license = { file = "LICENSE" }
@@ -19,14 +19,14 @@ classifiers = [
 ]
 requires-python = ">=3.11"
 dependencies = [
-    "click",
-    "deeplc>=4.0.0a1",
-    "psm_utils",
-    "pandas",
-    "numpy",
-    "rich",
-    "torch",
-    "lightning",
+    "click>=8,<9",
+    "deeplc>=4.0.0b1,<5",
+    "psm_utils>=1.5.1,<2",
+    "pandas>=1.5,<3",
+    "numpy>=1.25,<3",
+    "rich>=13,<15",
+    "torch>=2.6.0,<3",
+    "lightning>=2.1,<3",
 ]
 
 [dependency-groups]