release: v0.4.2 — republish the stack to close the PyPI version skew

CLAUDE.md

@@ -63,7 +63,7 @@ Additional MS utilities:
 - `algorithm/` - Isotope and peptide algorithms
 - `ms/` - Spectrum utilities
 
-### imspy_connector (Rust/PyO3) — v0.4.1
+### imspy_connector (Rust/PyO3) — v0.4.2
 Python bindings organized as 21 submodules:
 - `py_mz_spectrum`, `py_peptide`, `py_tims_frame`, `py_tims_slice`, `py_dataset`
 - `py_dda`, `py_dia`, `py_quadrupole`, `py_feature`, `py_pseudo`
@@ -76,12 +76,12 @@ Python bindings organized as 21 submodules:
 
 | Package | Version | Module | Description |
 |---------|---------|--------|-------------|
-| **imspy-core** | 0.4.1 | `imspy_core` | Base data structures, timsTOF dataset access |
-| **imspy-predictors** | 0.5.1 | `imspy_predictors` | PyTorch models for CCS, RT, fragment intensities |
+| **imspy-core** | 0.4.2 | `imspy_core` | Base data structures, timsTOF dataset access |
+| **imspy-predictors** | 0.5.2 | `imspy_predictors` | PyTorch models for CCS, RT, fragment intensities |
 | **imspy-dia** | 0.4.0 | `imspy_dia` | DIA-PASEF clustering and feature extraction |
-| **imspy-search** | 0.4.0 | `imspy_search` | Database search integration (sagepy, mokapot) |
+| **imspy-search** | 0.4.1 | `imspy_search` | Database search integration (sagepy, mokapot) |
 | **imspy-simulation** | 0.4.2 | `imspy_simulation` | TimSim synthetic data generation & EVAL pipeline |
-| **imspy-vis** | 0.4.0 | `imspy_vis` | Visualization and plotting tools |
+| **imspy-vis** | 0.4.1 | `imspy_vis` | Visualization and plotting tools |
 
 #### imspy-core
 - `core/` - RustWrapperObject base class
@@ -306,13 +306,13 @@ Versions are maintained in:
 - `mscore/Cargo.toml` (0.4.1)
 - `rustdf/Cargo.toml` (0.4.1)
 - `rustms/Cargo.toml` (0.1.0)
-- `imspy_connector/Cargo.toml` (0.4.1)
-- `packages/imspy-core/pyproject.toml` (0.4.1)
-- `packages/imspy-predictors/pyproject.toml` (0.5.1)
+- `imspy_connector/Cargo.toml` (0.4.2)
+- `packages/imspy-core/pyproject.toml` (0.4.2)
+- `packages/imspy-predictors/pyproject.toml` (0.5.2)
 - `packages/imspy-dia/pyproject.toml` (0.4.0)
-- `packages/imspy-search/pyproject.toml` (0.4.0)
+- `packages/imspy-search/pyproject.toml` (0.4.1)
 - `packages/imspy-simulation/pyproject.toml` (0.4.2)
-- `packages/imspy-vis/pyproject.toml` (0.4.0)
+- `packages/imspy-vis/pyproject.toml` (0.4.1)
 
 Dependencies between Rust crates reference specific versions (e.g., `mscore = { version = "0.4.1" }`).
 

imspy_connector/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "imspy-connector"
-version = "0.4.1"
+version = "0.4.2"
 edition = "2021"
 
 [lib]

imspy_connector/pyproject.toml

@@ -7,7 +7,7 @@ name = "imspy_connector"
 dependencies = [
     "opentims-bruker-bridge>=1.1.0",
 ]
-version = "0.4.1"
+version = "0.4.2"
 requires-python = ">=3.11"
 classifiers = [
     "Programming Language :: Rust",

packages/imspy-core/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "imspy-core"
-version = "0.4.1"
+version = "0.4.2"
 description = "Core data structures and utilities for processing timsTOF ion mobility spectrometry data."
 authors = [
     { name = "theGreatHerrLebert", email = "davidteschner@googlemail.com" }
@@ -20,7 +20,7 @@ dependencies = [
     "pyarrow>=13.0",
     "mendeleev>=0.7.0",
     "toml>=0.10.2",
-    "imspy-connector>=0.3.0",
+    "imspy-connector>=0.4.2",
     "opentims-bruker-bridge>=1.1.0",
 ]
 

packages/imspy-dia/pyproject.toml

@@ -24,8 +24,8 @@ classifiers = [
 
 [tool.poetry.dependencies]
 python = "^3.11"
-imspy-core = ">=0.4.0"
-imspy-connector = ">=0.4.0"
+imspy-core = ">=0.4.2"
+imspy-connector = ">=0.4.2"
 pandas = ">=2.0.0"
 numpy = ">=1.24.0"
 torch = ">=2.0.0"

packages/imspy-predictors/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "imspy-predictors"
-version = "0.5.1"
+version = "0.5.2"
 description = "ML-based predictors for CCS, retention time, and fragment intensity in mass spectrometry."
 authors = [
     { name = "theGreatHerrLebert", email = "davidteschner@googlemail.com" }
@@ -10,7 +10,7 @@ license = "MIT"
 requires-python = ">=3.11,<3.14"
 
 dependencies = [
-    "imspy-core>=0.4.0",
+    "imspy-core>=0.4.2",
     # PyTorch - deep learning framework
     "torch>=2.0.0",
     # Scientific computing

packages/imspy-search/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "imspy-search"
-version = "0.4.0"
+version = "0.4.1"
 description = "Database search functionality for timsTOF proteomics data using sagepy."
 authors = [
     { name = "theGreatHerrLebert", email = "davidteschner@googlemail.com" }
@@ -10,8 +10,8 @@ license = "MIT"
 requires-python = ">=3.11,<3.14"
 
 dependencies = [
-    "imspy-core>=0.4.0",
-    "imspy-predictors>=0.4.0",
+    "imspy-core>=0.4.2",
+    "imspy-predictors>=0.5.2",
     "sagepy>=0.4.0",
     "mokapot>=0.9.0",
     "scikit-learn>=1.0",

packages/imspy-simulation/pyproject.toml

@@ -10,8 +10,9 @@ license = "MIT"
 requires-python = ">=3.11,<3.14"
 
 dependencies = [
-    "imspy-core>=0.4.0",
-    "imspy-predictors[koina]>=0.4.0",  # Include Koina support for intensity prediction
+    "imspy-connector>=0.4.2",
+    "imspy-core>=0.4.2",
+    "imspy-predictors[koina]>=0.5.2",  # Include Koina support for intensity prediction
     "pandas>=2.0",
     "numpy>=1.24",
     "numba>=0.53",
@@ -20,7 +21,7 @@ dependencies = [
     "tqdm>=4.66",
     "zstd>=1.5",
     "matplotlib>=3.5",
-    "imspy-search>=0.4.0",
+    "imspy-search>=0.4.1",
 ]
 
 [project.optional-dependencies]

packages/imspy-vis/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "imspy-vis"
-version = "0.4.0"
+version = "0.4.1"
 description = "Lightweight visualization tools for timsTOF proteomics data."
 authors = [
     { name = "theGreatHerrLebert", email = "davidteschner@googlemail.com" }
@@ -10,7 +10,7 @@ license = "MIT"
 requires-python = ">=3.11,<3.14"
 
 dependencies = [
-    "imspy-core>=0.4.0",
+    "imspy-core>=0.4.2",
     "plotly>=5.0",
     "ipywidgets>=8.0",
     "matplotlib>=3.5",