Bump minimum piscem to 0.18.0 and alevin-fry to 0.13.0, fix clippy warnings

Update all internal version checks and test mocks:
- piscem: >=0.18.0 (was >=0.7.0/0.11.0/0.12.2 in various locations)
- alevin-fry: >=0.13.0 (was >=0.11.2) — required for multi-barcode
  collation fix (trait-based grouping key, record-based sample identity)

Fix all clippy warnings:
- &Vec<PathBuf> -> &[PathBuf] in add_fragment_library_to_piscem
- match { Ok => Some, Err => None } -> .ok() in prog_utils
- Unneeded late initialization in indexing.rs

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: rob-p

src/atac/index.rs

@@ -19,7 +19,7 @@ pub(crate) fn piscem_index(af_home_path: &Path, opts: &IndexOpts) -> anyhow::Res
 
     match prog_utils::check_version_constraints(
         "piscem",
-        ">=0.11.0, <1.0.0",
+        ">=0.18.0, <1.0.0",
         &piscem_prog_info.version,
     ) {
         Ok(af_ver) => info!("found piscem version {:#}, proceeding", af_ver),

src/atac/process.rs

@@ -164,7 +164,7 @@ pub(crate) fn check_progs<P: AsRef<Path>>(
 
     match prog_utils::check_version_constraints(
         "alevin-fry",
-        ">=0.11.2, <1.0.0",
+        ">=0.13.0, <1.0.0",
         &af_prog_info.version,
     ) {
         Ok(af_ver) => info!("found alevin-fry version {:#}, proceeding", af_ver),
@@ -178,7 +178,7 @@ pub(crate) fn check_progs<P: AsRef<Path>>(
 
     match prog_utils::check_version_constraints(
         "piscem",
-        ">=0.11.0, <1.0.0",
+        ">=0.18.0, <1.0.0",
         &piscem_prog_info.version,
     ) {
         Ok(piscem_ver) => info!("found piscem version {:#}, proceeding", piscem_ver),
@@ -255,10 +255,10 @@ pub(crate) fn map_reads(af_home_path: &Path, opts: &ProcessOpts) -> anyhow::Resu
     add_read_args(&mut piscem_map_cmd, opts)?;
 
     // if the user is requesting a mapping option that required
-    // piscem version >= 0.7.0, ensure we have that
+    // piscem version >= 0.18.0, ensure we have that
     match prog_utils::check_version_constraints(
         "piscem",
-        ">=0.11.0, <1.0.0",
+        ">=0.18.0, <1.0.0",
         &piscem_prog_info.version,
     ) {
         Ok(_piscem_ver) => {
@@ -267,9 +267,9 @@ pub(crate) fn map_reads(af_home_path: &Path, opts: &ProcessOpts) -> anyhow::Resu
         Err(_) => {
             info!(
                 r#"
-Simpleaf is currently using piscem version {}, but you must be using version >= 0.11.0 in order to use the 
-mapping options specific to this, or later versions. If you wish to use these options, please upgrade your 
-piscem version or, if you believe you have a sufficiently new version installed, update the executable 
+Simpleaf is currently using piscem version {}, but you must be using version >= 0.18.0 in order to use the
+mapping options specific to this, or later versions. If you wish to use these options, please upgrade your
+piscem version or, if you believe you have a sufficiently new version installed, update the executable
 being used by simpleaf"#,
                 &piscem_prog_info.version
             );

src/core/context.rs

@@ -35,8 +35,8 @@ mod tests {
         let td = tempdir().expect("failed to create tempdir");
         let af_info = json!({
             "prog_info": {
-                "piscem": {"exe_path": "/bin/echo", "version": "0.12.2"},
-                "alevin_fry": {"exe_path": "/bin/echo", "version": "0.11.2"},
+                "piscem": {"exe_path": "/bin/echo", "version": "0.18.0"},
+                "alevin_fry": {"exe_path": "/bin/echo", "version": "0.13.0"},
                 "macs": null
             }
         });

src/simpleaf_commands/indexing.rs

@@ -542,9 +542,6 @@ pub fn build_ref_and_index(af_home_path: &Path, opts: IndexOpts) -> anyhow::Resu
     )?;
 
     let output_index_dir = output.join("index");
-    let index_duration;
-    let index_cmd_string: String;
-
     if rp.piscem.is_none() {
         bail!(
             "The construction of a piscem index was requested, but a valid piscem executable was not available. \n\
@@ -599,7 +596,7 @@ pub fn build_ref_and_index(af_home_path: &Path, opts: IndexOpts) -> anyhow::Resu
     if let Some(decoy_paths) = opts.decoy_paths {
         match prog_utils::check_version_constraints(
             "piscem",
-            ">=0.7.0, <1.0.0",
+            ">=0.18.0, <1.0.0",
             &piscem_prog_info.version,
         ) {
             Ok(_piscem_ver) => {
@@ -613,22 +610,22 @@ pub fn build_ref_and_index(af_home_path: &Path, opts: IndexOpts) -> anyhow::Resu
             Err(_) => {
                 warn!(
                     r#"
-You requested to build a poison k-mer table with {:?}, but you must be using piscem version >= 0.7.0 
-to use this feature. Simpleaf is currently using version {}. Please upgrade your piscem version or, 
-if you believe you have a sufficiently new version installed, update the executable being used by 
+You requested to build a poison k-mer table with {:?}, but you must be using piscem version >= 0.18.0
+to use this feature. Simpleaf is currently using version {}. Please upgrade your piscem version or,
+if you believe you have a sufficiently new version installed, update the executable being used by
 simpleaf"#,
                     decoy_paths, &piscem_prog_info.version
                 );
             }
         }
     }
 
-    index_cmd_string = prog_utils::get_cmd_line_string(&piscem_index_cmd);
+    let index_cmd_string = prog_utils::get_cmd_line_string(&piscem_index_cmd);
     info!("piscem build cmd : {}", index_cmd_string);
 
     let index_start = Instant::now();
     let _cres = exec::run_checked(&mut piscem_index_cmd, "piscem index command")?;
-    index_duration = index_start.elapsed();
+    let index_duration = index_start.elapsed();
 
     let mut t2g_out_path: Option<PathBuf> = None;
     if let Some(t2g_file) = reference_stage.t2g.clone() {

src/simpleaf_commands/quant.rs

@@ -434,7 +434,7 @@ fn run_mapping_stage(
 
                 match prog_utils::check_version_constraints(
                     "piscem",
-                    ">=0.7.0, <1.0.0",
+                    ">=0.18.0, <1.0.0",
                     &piscem_prog_info.version,
                 ) {
                     Ok(_piscem_ver) => {
@@ -443,9 +443,9 @@ fn run_mapping_stage(
                     Err(_) => {
                         info!(
                             r#"
-Simpleaf is currently using piscem version {}, but you must be using version >= 0.7.0 in order to use the 
-mapping options specific to this, or later versions. If you wish to use these options, please upgrade your 
-piscem version or, if you believe you have a sufficiently new version installed, update the executable 
+Simpleaf is currently using piscem version {}, but you must be using version >= 0.18.0 in order to use the
+mapping options specific to this, or later versions. If you wish to use these options, please upgrade your
+piscem version or, if you believe you have a sufficiently new version installed, update the executable
 being used by simpleaf"#,
                             &piscem_prog_info.version
                         );

src/utils/af_utils.rs

@@ -535,8 +535,8 @@ Please consider removing and re-adding this chemistry with a valid permit list."
 /// with the piscem mapping command `quant_cmd`.
 pub fn add_fragment_library_to_piscem(
     fragment_geometry_str: &str,
-    reads1: &Vec<PathBuf>,
-    reads2: &Vec<PathBuf>,
+    reads1: &[PathBuf],
+    reads2: &[PathBuf],
     quant_cmd: &mut std::process::Command,
 ) -> Result<()> {
     let reads1_str = reads1

src/utils/prog_utils.rs

@@ -230,9 +230,9 @@ pub struct ReqProgs {
 
 impl ReqProgs {
     pub fn issue_recommended_version_messages(&self) {
-        // Currently (2/08/2025) want to recommend piscem >= 0.12.2
+        // Currently (3/21/2026) want to recommend piscem >= 0.18.0
         if let Some(ref piscem_info) = self.piscem {
-            let desired_ver = VersionReq::parse(">=0.12.2").unwrap();
+            let desired_ver = VersionReq::parse(">=0.18.0").unwrap();
             let current_ver = Version::parse(&piscem_info.version).unwrap();
             if desired_ver.matches(&current_ver) {
                 // nothing to do here
@@ -364,10 +364,7 @@ pub fn get_required_progs_from_paths(
 
     let opt_piscem = match piscem_exe {
         Some(p) => Some(p),
-        None => match get_which_executable("piscem") {
-            Ok(p) => Some(p),
-            Err(_e) => None,
-        },
+        None => get_which_executable("piscem").ok(),
     };
 
     let alevin_fry = match alevin_fry_exe {

tests/phase1_regressions.rs

@@ -16,8 +16,8 @@ fn legacy_salmon_index_metadata_is_rejected_with_migration_error() {
 
     let af_info = json!({
         "prog_info": {
-            "piscem": {"exe_path": "/bin/echo", "version": "0.12.2"},
-            "alevin_fry": {"exe_path": "/bin/echo", "version": "0.11.2"},
+            "piscem": {"exe_path": "/bin/echo", "version": "0.18.0"},
+            "alevin_fry": {"exe_path": "/bin/echo", "version": "0.13.0"},
             "macs": null
         }
     });