release: 0.3.0

CHANGELOG.md

@@ -7,6 +7,10 @@ All notable changes to MuMDIA are recorded here. The format follows
 `0.1.0` is the first tagged release of the Rust engine. The superseded
 Python implementation remains available at the tag `legacy-python-v1`.
 
+`0.3.0` raises the DeepLC floor to 4.4.0, so every environment must be rebuilt
+before upgrading. It also adds multi-head retention-time calibration, off by
+default.
+
 `0.2.0` is a minor rather than a patch release: it changes behaviour a user can
 see. The default MS2PIP model is `HCDch2`, configurations with out-of-range
 numeric values are refused at load instead of running, both TSV reports gain two
@@ -23,6 +27,20 @@ than a number. Both are recorded in every run's `manifest.json`.
 
 ## [Unreleased]
 
+### Fixed
+
+- Nine desktop test fixtures used a fixed temporary directory and deleted it on entry, so
+  two `cargo test` runs on one machine raced and one lost its files mid-test. They are
+  unique per process, like every other temporary fixture in the workspace (`docs/14`). Hit
+  twice while preparing releases; two concurrent runs now both pass.
+
+## [0.3.0] - 2026-09-09
+
+Multi-head retention-time calibration and the DeepLC 4.4.0 floor it needs, plus
+the sha2 0.11 bump. `rt_im_train.multihead_calibration` is off by default;
+turning it on measured +4.8% stripped peptides on the HYE AIF benchmark and
++14.3% on HYE Astral, at an unchanged empirical decoy fraction.
+
 ### Added
 
 - `rt_im_train.multihead_calibration` (default 0, off): calibrate the DeepLC base model

bench/pb_eval.py

@@ -41,7 +41,7 @@ def main() -> int:
     a = ap.parse_args()
 
     user_input = {
-        "software_version": "0.2.0", "search_engine": "MuMDIA", "search_engine_version": "0.2.0",
+        "software_version": "0.3.0", "search_engine": "MuMDIA", "search_engine_version": "0.3.0",
         "ident_fdr_psm": 0.01, "ident_fdr_peptide": 0.01, "ident_fdr_protein": 0.01,
         "enable_match_between_runs": True, "precursor_mass_tolerance": "20 ppm",
         "fragment_mass_tolerance": "20 ppm", "enzyme": "Trypsin", "allowed_miscleavages": 1,

desktop/src-tauri/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "mumdia-console"
-version = "0.2.0"
+version = "0.3.0"
 edition = "2021"
 description = "Desktop interface for the MuMDIA DIA search engine"
 license = "Apache-2.0"

desktop/src-tauri/src/diann.rs

@@ -1607,7 +1607,11 @@ mod tests {
 
     #[test]
     fn the_predicted_parquet_is_found_by_name_or_by_search() {
-        let dir = std::env::temp_dir().join("mumdia-diann-test-lib");
+        // Unique per process, like every other temp fixture in the workspace: a fixed name
+        // plus the delete-on-entry below races a second `cargo test` on one machine
+        // (docs/14). Hit twice during the 0.2.0 and 0.3.0 releases.
+        let dir =
+            std::env::temp_dir().join(format!("mumdia-diann-test-lib-{}", std::process::id()));
         let _ = std::fs::remove_dir_all(&dir);
         std::fs::create_dir_all(&dir).unwrap();
 
@@ -1900,7 +1904,7 @@ mod tests {
         // `.speclib`; only an empirical one is Parquet. Without recognising the
         // `.speclib`, a successful prediction was reported as "DIA-NN finished but
         // wrote no Parquet library" and the user was left with a file nothing reads.
-        let dir = std::env::temp_dir().join("mumdia-diann-speclib");
+        let dir = std::env::temp_dir().join(format!("mumdia-diann-speclib-{}", std::process::id()));
         let _ = std::fs::remove_dir_all(&dir);
         std::fs::create_dir_all(&dir).unwrap();
 
@@ -2011,7 +2015,8 @@ mod tests {
         // search, and the engine then either rejected the library or accepted a
         // partial decoy population -- with no eviction and no way to force a rebuild.
         // The marker is written last, after both tables are complete.
-        let dir = std::env::temp_dir().join("mumdia-diann-halfcache");
+        let dir =
+            std::env::temp_dir().join(format!("mumdia-diann-halfcache-{}", std::process::id()));
         let _ = std::fs::remove_dir_all(&dir);
         std::fs::create_dir_all(&dir).unwrap();
 
@@ -2104,7 +2109,7 @@ mod tests {
         // `pop()` returned `lib_precursors_targets.parquet` and MuMDIA's own schema
         // table was imported as the DIA-NN library, reporting success on a library
         // that did not match the FASTA.
-        let dir = std::env::temp_dir().join("mumdia-diann-anchor");
+        let dir = std::env::temp_dir().join(format!("mumdia-diann-anchor-{}", std::process::id()));
         let _ = std::fs::remove_dir_all(&dir);
         std::fs::create_dir_all(&dir).unwrap();
 

desktop/src-tauri/src/run.rs

@@ -1530,7 +1530,11 @@ mod multifile_tests {
         // the results screen blank after every experiment. And the counts it does
         // yield are experiment-wide: the grouped q columns are grouped across the whole
         // experiment, so a per-file reading of them is diluted by ~1/n_runs.
-        let dir = std::env::temp_dir().join("mumdia-results-experiment");
+        // Unique per process, like every other temp fixture in the workspace: a fixed name
+        // plus the delete-on-entry below races a second `cargo test` on one machine
+        // (docs/14). Hit twice during the 0.2.0 and 0.3.0 releases.
+        let dir =
+            std::env::temp_dir().join(format!("mumdia-results-experiment-{}", std::process::id()));
         let _ = std::fs::remove_dir_all(&dir);
         std::fs::create_dir_all(&dir).unwrap();
 

desktop/src-tauri/src/thermo.rs

@@ -789,7 +789,10 @@ mod tests {
         // The collision. A Waters `.raw` directory sent to ThermoRawFileParser fails
         // with something unhelpful, and the interface would have offered the wrong
         // Install button.
-        let d = std::env::temp_dir().join("mumdia-thermo-waters");
+        // Unique per process, like every other temp fixture in the workspace: a fixed name
+        // plus the delete-on-entry below races a second `cargo test` on one machine
+        // (docs/14). Hit twice during the 0.2.0 and 0.3.0 releases.
+        let d = std::env::temp_dir().join(format!("mumdia-thermo-waters-{}", std::process::id()));
         let _ = std::fs::remove_dir_all(&d);
         std::fs::create_dir_all(d.join("waters.raw")).unwrap();
         let p = d.join("waters.raw");
@@ -802,7 +805,7 @@ mod tests {
 
     #[test]
     fn a_d_directory_is_labelled_by_its_contents() {
-        let d = std::env::temp_dir().join("mumdia-thermo-dlabel");
+        let d = std::env::temp_dir().join(format!("mumdia-thermo-dlabel-{}", std::process::id()));
         let _ = std::fs::remove_dir_all(&d);
         let tims = d.join("tims.d");
         std::fs::create_dir_all(&tims).unwrap();
@@ -825,7 +828,8 @@ mod tests {
     fn a_zip_entry_that_escapes_the_target_is_refused() {
         // A zip is untrusted input even from a trusted publisher. Without the
         // `enclosed_name` check this entry would be written outside the target.
-        let dir = std::env::temp_dir().join("mumdia-thermo-traversal");
+        let dir =
+            std::env::temp_dir().join(format!("mumdia-thermo-traversal-{}", std::process::id()));
         let _ = std::fs::remove_dir_all(&dir);
         std::fs::create_dir_all(&dir).unwrap();
         let archive = dir.join("evil.zip");
@@ -858,7 +862,7 @@ mod tests {
 
     #[test]
     fn a_normal_zip_round_trips_with_its_directory_structure() {
-        let dir = std::env::temp_dir().join("mumdia-thermo-unzip");
+        let dir = std::env::temp_dir().join(format!("mumdia-thermo-unzip-{}", std::process::id()));
         let _ = std::fs::remove_dir_all(&dir);
         std::fs::create_dir_all(&dir).unwrap();
         let archive = dir.join("ok.zip");

desktop/src-tauri/tauri.conf.json

@@ -1,7 +1,7 @@
 {
   "$schema": "https://schema.tauri.app/config/2",
   "productName": "MuMDIA",
-  "version": "0.2.0",
+  "version": "0.3.0",
   "identifier": "be.ugent.compomics.mumdia.console",
   "build": {
     "frontendDist": "../ui"

docs/14_build_test_deploy_gotchas.md

@@ -106,7 +106,7 @@ mzML, FASTA, and library Parquets remain user data and must be mounted.
 
 **Build configuration.** The workspace declares three members
 (`Cargo.toml:3`) sharing one `[workspace.package]` (`Cargo.toml:5-23`): version
-`0.2.0`, `edition = "2021"`, `rust-version = "1.96"`, license `Apache-2.0`, plus
+`0.3.0`, `edition = "2021"`, `rust-version = "1.96"`, license `Apache-2.0`, plus
 the crates.io metadata (description, repository, homepage, keywords, categories)
 and `publish = false`. The declared MSRV deliberately tracks
 `rust-toolchain.toml` (channel `1.96.1`), which is the only Rust version CI

rust/mumdia/Cargo.toml

@@ -3,7 +3,7 @@ resolver = "2"
 members = ["crates/mumdia-core", "crates/mumdia-io", "crates/mumdia"]
 
 [workspace.package]
-version = "0.2.0"
+version = "0.3.0"
 edition = "2021"
 # Tracks rust-toolchain.toml, which is the only Rust version CI builds and tests.
 # A lower floor may well work, but claiming one we do not verify is a guess; lower

sbom.cdx.json

@@ -5,16 +5,16 @@
   "metadata": {
     "component": {
       "type": "application",
-      "bom-ref": "pkg:cargo/mumdia@0.2.0",
+      "bom-ref": "pkg:cargo/mumdia@0.3.0",
       "name": "mumdia",
-      "version": "0.2.0",
+      "version": "0.3.0",
       "description": "Clean-room Rust DIA proteomics search engine",
       "licenses": [
         {
           "expression": "Apache-2.0"
         }
       ],
-      "purl": "pkg:cargo/mumdia@0.2.0"
+      "purl": "pkg:cargo/mumdia@0.3.0"
     },
     "tools": [
       {
@@ -1905,10 +1905,10 @@
     },
     {
       "type": "library",
-      "bom-ref": "pkg:cargo/mumdia-core@0.2.0",
+      "bom-ref": "pkg:cargo/mumdia-core@0.3.0",
       "name": "mumdia-core",
-      "version": "0.2.0",
-      "purl": "pkg:cargo/mumdia-core@0.2.0",
+      "version": "0.3.0",
+      "purl": "pkg:cargo/mumdia-core@0.3.0",
       "description": "Typed configuration, mass model, artifact schemas, and run manifest for MuMDIA",
       "licenses": [
         {
@@ -1924,10 +1924,10 @@
     },
     {
       "type": "library",
-      "bom-ref": "pkg:cargo/mumdia-io@0.2.0",
+      "bom-ref": "pkg:cargo/mumdia-io@0.3.0",
       "name": "mumdia-io",
-      "version": "0.2.0",
-      "purl": "pkg:cargo/mumdia-io@0.2.0",
+      "version": "0.3.0",
+      "purl": "pkg:cargo/mumdia-io@0.3.0",
       "description": "Parquet/JSON artifact layer, content hashing, and logging for MuMDIA",
       "licenses": [
         {
@@ -4126,7 +4126,7 @@
       ]
     },
     {
-      "ref": "pkg:cargo/mumdia-core@0.2.0",
+      "ref": "pkg:cargo/mumdia-core@0.3.0",
       "dependsOn": [
         "pkg:cargo/serde@1.0.228",
         "pkg:cargo/serde_json@1.0.150",
@@ -4135,12 +4135,12 @@
       ]
     },
     {
-      "ref": "pkg:cargo/mumdia-io@0.2.0",
+      "ref": "pkg:cargo/mumdia-io@0.3.0",
       "dependsOn": [
         "pkg:cargo/anyhow@1.0.103",
         "pkg:cargo/arrow@59.0.0",
         "pkg:cargo/blake3@1.8.5",
-        "pkg:cargo/mumdia-core@0.2.0",
+        "pkg:cargo/mumdia-core@0.3.0",
         "pkg:cargo/parquet@59.0.0",
         "pkg:cargo/serde@1.0.228",
         "pkg:cargo/serde_json@1.0.150",
@@ -4150,15 +4150,15 @@
       ]
     },
     {
-      "ref": "pkg:cargo/mumdia@0.2.0",
+      "ref": "pkg:cargo/mumdia@0.3.0",
       "dependsOn": [
         "pkg:cargo/anyhow@1.0.103",
         "pkg:cargo/arrow@59.0.0",
         "pkg:cargo/blake3@1.8.5",
         "pkg:cargo/clap@4.6.1",
         "pkg:cargo/mimalloc@0.1.52",
-        "pkg:cargo/mumdia-core@0.2.0",
-        "pkg:cargo/mumdia-io@0.2.0",
+        "pkg:cargo/mumdia-core@0.3.0",
+        "pkg:cargo/mumdia-io@0.3.0",
         "pkg:cargo/mzdata@0.65.5",
         "pkg:cargo/parquet@59.0.0",
         "pkg:cargo/rayon@1.12.0",