Auto publish feature and fix repository links

.github/workflows/release.yml

@@ -54,7 +54,16 @@ jobs:
       - name: Verify the workspace builds before releasing
         run: cargo build --release --workspace --all-targets --exclude timsrust-sdk
 
-      - name: Bump shared version, commit, tag and push
+      - name: Bump shared version, publish to crates.io, commit, tag and push
+        env:
+          # Token used by `cargo publish`; create it on crates.io and store it as
+          # a repository Actions secret (Settings > Secrets and variables > Actions).
+          CARGO_REGISTRY_TOKEN: ${{ secrets.CARGO_REGISTRY_TOKEN }}
         run: |
-          cargo release patch --workspace --no-publish --no-confirm
-          cargo release patch --workspace --no-publish --no-confirm --execute
+          if [ -z "${CARGO_REGISTRY_TOKEN}" ]; then
+            echo "Missing CARGO_REGISTRY_TOKEN secret; required to publish to crates.io." >&2
+            exit 1
+          fi
+          # Dry-run first to surface problems before anything is published or pushed.
+          cargo release patch --workspace --no-confirm
+          cargo release patch --workspace --no-confirm --execute

Cargo.toml

@@ -9,6 +9,8 @@ resolver = "3"
 [workspace.package]
 version = "0.6.1"
 edition = "2024"
+repository = "https://github.com/MannLabs/timsrust"
+
 [workspace.metadata.release]
 # Bump every crate together to one shared version and emit a single tag.
 shared-version = true

clis/timsrust-centroid-cli/Cargo.toml

@@ -2,6 +2,7 @@
 name = "timsrust-centroid-cli"
 version.workspace = true
 edition.workspace = true
+repository.workspace = true
 publish = false
 
 [dependencies]

clis/timsrust-cli-core/Cargo.toml

@@ -2,6 +2,7 @@
 name = "timsrust-cli-core"
 version.workspace = true
 edition.workspace = true
+repository.workspace = true
 publish = false
 
 [dependencies]

clis/timsrust-mgf-cli/Cargo.toml

@@ -2,6 +2,7 @@
 name = "timsrust-mgf-cli"
 version.workspace = true
 edition.workspace = true
+repository.workspace = true
 publish = false
 
 [dependencies]

clis/timsrust-parquet-spectra-cli/Cargo.toml

@@ -2,6 +2,7 @@
 name = "timsrust-parquet-spectra-cli"
 version.workspace = true
 edition.workspace = true
+repository.workspace = true
 publish = false
 
 [dependencies]

crates/filemanager/Cargo.toml

@@ -2,6 +2,7 @@
 name = "filemanager"
 version.workspace = true
 edition.workspace = true
+repository.workspace = true
 description = "Unified file abstraction for local and cloud files with caching options and support for multiple formats."
 license = "Apache-2.0"
 

crates/timsrust-centroid/Cargo.toml

@@ -2,6 +2,7 @@
 name = "timsrust-centroid"
 version.workspace = true
 edition.workspace = true
+repository.workspace = true
 description = "Centroiding algorithms for timsTOF ion mobility spectra"
 license = "Apache-2.0"
 

crates/timsrust-core/Cargo.toml

@@ -2,6 +2,7 @@
 name = "timsrust-core"
 version.workspace = true
 edition.workspace = true
+repository.workspace = true
 description = "Core data types and abstractions for timsTOF data"
 license = "Apache-2.0"
 

crates/timsrust-mgf/Cargo.toml

@@ -2,6 +2,7 @@
 name = "timsrust-mgf"
 version.workspace = true
 edition.workspace = true
+repository.workspace = true
 description = "MGF (Mascot Generic Format) writer for timsTOF spectra"
 license = "Apache-2.0"
 

crates/timsrust-minitdf/Cargo.toml

@@ -2,6 +2,7 @@
 name = "timsrust-minitdf"
 version.workspace = true
 edition.workspace = true
+repository.workspace = true
 description = "Reader for the ProteoScape miniTDF timsTOF file format"
 license = "Apache-2.0"
 

crates/timsrust-parquet-spectra/Cargo.toml

@@ -2,6 +2,7 @@
 name = "timsrust-parquet-spectra"
 version.workspace = true
 edition.workspace = true
+repository.workspace = true
 description = "Parquet-backed spectrum and precursor reader for timsTOF data"
 license = "Apache-2.0"
 

crates/timsrust-sdk/Cargo.toml

@@ -2,10 +2,19 @@
 name = "timsrust-sdk"
 version.workspace = true
 edition.workspace = true
+repository.workspace = true
 build = "build.rs"
 description = "Bruker TimsData SDK bindings for native timsTOF data access"
 license = "Apache-2.0"
 
+[package.metadata.release]
+# The proprietary Bruker native SDK is not available on the CI runners, so this
+# crate cannot be built there. Publish the source without a verification build
+# (`cargo publish --no-verify`). Consumers link the real library themselves via
+# the crate's `lib/` directory or the TIMSDATA_LIB_DIR env var; build.rs
+# tolerates a missing library so docs.rs and plain `cargo build` still succeed.
+verify = false
+
 [dependencies]
 timsrust-core = { workspace = true, features = ["io"] }
 serde = { workspace = true, features = ["derive"] }

crates/timsrust-sdk/build.rs

@@ -53,18 +53,34 @@ fn main() {
 
     // Source file you want to copy
     let source = lib_path.join(&runtime_lib_name);
-    // Destination in the target folder
-    let destination = target_dir.join(&runtime_lib_name);
-    // Create directory if missing
-    fs::create_dir_all(&target_dir).unwrap();
-    // Copy the file
-    fs::copy(&source, &destination).unwrap_or_else(|e| {
-        panic!("Failed to copy {:?} to {:?}: {}", source, destination, e)
-    });
 
-    // Logging
-    println!("cargo:warning=Target dir: {}", target_dir.display());
-    println!("cargo:warning=Source dir: {}", source.display());
+    // The runtime library is gitignored and absent when the crate is built
+    // without the proprietary Bruker SDK (e.g. `cargo publish --no-verify`,
+    // docs.rs, or a plain `cargo build` by a downstream user). Skip the copy
+    // instead of failing; real usage requires the library to be present in
+    // `lib/` or pointed at by TIMSDATA_LIB_DIR.
+    if source.exists() {
+        // Destination in the target folder
+        let destination = target_dir.join(&runtime_lib_name);
+        // Create directory if missing
+        fs::create_dir_all(&target_dir).unwrap();
+        // Copy the file
+        fs::copy(&source, &destination).unwrap_or_else(|e| {
+            panic!("Failed to copy {:?} to {:?}: {}", source, destination, e)
+        });
+
+        // Logging
+        println!("cargo:warning=Target dir: {}", target_dir.display());
+        println!("cargo:warning=Source dir: {}", source.display());
+    } else {
+        println!(
+            "cargo:warning=timsrust-sdk: {} not found in {}; skipping runtime library copy. \
+             Set TIMSDATA_LIB_DIR to the directory containing the Bruker timsdata library to link against it.",
+            runtime_lib_name,
+            lib_path.display()
+        );
+    }
+
     // Re-run this script if the file changes
     println!("cargo:rerun-if-changed={}", source.display());
     println!("cargo:rerun-if-env-changed=TIMSDATA_LIB_DIR");

crates/timsrust-tdf/Cargo.toml

@@ -2,6 +2,7 @@
 name = "timsrust-tdf"
 version.workspace = true
 edition.workspace = true
+repository.workspace = true
 description = "Reader for the Bruker TDF timsTOF file format (.d folders)"
 license = "Apache-2.0"
 

crates/timsrust-tsf/Cargo.toml

@@ -2,6 +2,7 @@
 name = "timsrust-tsf"
 version.workspace = true
 edition.workspace = true
+repository.workspace = true
 description = "Reader for the Bruker TSF timsTOF file format (MALDI/MS imaging)"
 license = "Apache-2.0"
 

crates/timsrust-utils/Cargo.toml

@@ -2,6 +2,7 @@
 name = "timsrust-utils"
 version.workspace = true
 edition.workspace = true
+repository.workspace = true
 description = "Shared utilities for the timsrust crate family (readers, buffers, threading helpers)"
 license = "Apache-2.0"
 

crates/timsrust/Cargo.toml

@@ -2,11 +2,11 @@
 name = "timsrust"
 version.workspace = true
 edition.workspace = true
+repository.workspace = true
 description = "A crate to read Bruker timsTOF data"
 license = "Apache-2.0"
 readme = "README.md"
 documentation = "https://docs.rs/timsrust"
-repository = "https://github.com/mannlabs/timsrust"
 homepage = "https://github.com/mannlabs/timsrust"
 categories = ["accessibility", "data-structures", "parsing", "science"]
 keywords = ["MS", "LC-TIMS-TOF", "PASEF"]

python/timsrust-pyo3/Cargo.toml

@@ -2,6 +2,7 @@
 name = "timsrust-pyo3"
 version.workspace = true
 edition.workspace = true
+repository.workspace = true
 publish = false
 
 [lib]