Merge pull request #96 from COMBINE-lab/clap_v4

Clap v4

Cargo.toml

@@ -67,7 +67,7 @@ csv = "1.1.6"
 mimalloc = { version = "0.1.34", default-features = false }
 num-format = "0.4.4"
 num_cpus = "1.15.0"
-bio-types = "0.13.0"
+bio-types = { version = "0.13.0", default-features = true, features = ["serde"] }
 itertools = "0.10.5"
 thiserror = "1.0.38"
 statrs = "0.16.0"
@@ -79,7 +79,7 @@ sce = { git = "https://github.com/parazodiac/SingleCellExperiment", version = "0
 
 # no shenanigans; clap makes breaking "fixes" too often to allow variability
 # in the version different from what we tested with
-clap = { version = "=3.2.23", features = ["derive", "wrap_help", "cargo"] }
+clap = { version = "=4.0.32", features = ["derive", "wrap_help", "cargo", "help", "usage", "string", "error-context"] }
 
 [profile.release]
 #debug = true

src/cellfilter.rs

@@ -23,6 +23,7 @@ use libradicl::rad_types;
 use libradicl::BarcodeLookupMap;
 use needletail::bitkmer::*;
 use num_format::{Locale, ToFormattedString};
+use serde::Serialize;
 use serde_json::json;
 use std::cmp;
 use std::collections::HashMap;
@@ -32,7 +33,7 @@ use std::io::{BufWriter, Write};
 use std::path::{Path, PathBuf};
 use std::time::Instant;
 
-#[derive(Debug)]
+#[derive(Clone, Debug, Serialize)]
 pub enum CellFilterMethod {
     // cut off at this cell in
     // the frequency sorted list
@@ -230,6 +231,7 @@ fn process_unfiltered(
     velo_mode: bool,
     cmdline: &str,
     log: &slog::Logger,
+    gpl_opts: &GenPermitListOpts,
 ) -> anyhow::Result<u64> {
     let parent = std::path::Path::new(output_dir);
     std::fs::create_dir_all(&parent)
@@ -418,7 +420,8 @@ fn process_unfiltered(
     "version_str" : version,
     "max-ambig-record" : max_ambiguity_read,
     "cmd" : cmdline,
-    "permit-list-type" : "unfiltered"
+    "permit-list-type" : "unfiltered",
+    "gpl_options" : &gpl_opts
     });
 
     let m_path = parent.join("generate_permit_list.json");
@@ -451,6 +454,7 @@ fn process_filtered(
     velo_mode: bool,
     cmdline: &str,
     log: &slog::Logger,
+    gpl_opts: &GenPermitListOpts,
 ) -> anyhow::Result<u64> {
     let valid_bc: Vec<u64>;
     let mut freq: Vec<u64> = hm.values().cloned().collect();
@@ -557,7 +561,8 @@ fn process_filtered(
     "version_str" : version,
     "max-ambig-record" : max_ambiguity_read,
     "cmd" : cmdline,
-    "permit-list-type" : "filtered"
+    "permit-list-type" : "filtered",
+    "gpl_options" : &gpl_opts
     });
 
     let m_path = parent.join("generate_permit_list.json");
@@ -586,7 +591,7 @@ fn process_filtered(
 pub fn generate_permit_list(gpl_opts: GenPermitListOpts) -> anyhow::Result<u64> {
     let rad_dir = gpl_opts.input_dir;
     let output_dir = gpl_opts.output_dir;
-    let filter_meth = gpl_opts.fmeth;
+    let filter_meth = gpl_opts.fmeth.clone();
     let expected_ori = gpl_opts.expected_ori;
     let version = gpl_opts.version;
     let velo_mode = gpl_opts.velo_mode;
@@ -728,6 +733,7 @@ pub fn generate_permit_list(gpl_opts: GenPermitListOpts) -> anyhow::Result<u64>
                     velo_mode,
                     cmdline,
                     log,
+                    &gpl_opts,
                 )
             } else {
                 Ok(0)
@@ -757,6 +763,7 @@ pub fn generate_permit_list(gpl_opts: GenPermitListOpts) -> anyhow::Result<u64>
                 velo_mode,
                 cmdline,
                 log,
+                &gpl_opts,
             )
         }
     }

src/cmd_parse_utils.rs

@@ -15,15 +15,15 @@ impl clap::ValueEnum for ResolutionStrategy {
         ]
     }
 
-    fn to_possible_value<'a>(&self) -> Option<clap::PossibleValue<'a>> {
+    fn to_possible_value(&self) -> Option<clap::builder::PossibleValue> {
         match self {
-            Self::Trivial => Some(clap::PossibleValue::new("trivial")),
-            Self::CellRangerLike => Some(clap::PossibleValue::new("cr-like")),
-            Self::CellRangerLikeEm => Some(clap::PossibleValue::new("cr-like-em")),
-            Self::ParsimonyEm => Some(clap::PossibleValue::new("parsimony-em")),
-            Self::Parsimony => Some(clap::PossibleValue::new("parsimony")),
-            Self::ParsimonyGeneEm => Some(clap::PossibleValue::new("parsimony-gene-em")),
-            Self::ParsimonyGene => Some(clap::PossibleValue::new("parsimony-gene")),
+            Self::Trivial => Some(clap::builder::PossibleValue::new("trivial")),
+            Self::CellRangerLike => Some(clap::builder::PossibleValue::new("cr-like")),
+            Self::CellRangerLikeEm => Some(clap::builder::PossibleValue::new("cr-like-em")),
+            Self::ParsimonyEm => Some(clap::builder::PossibleValue::new("parsimony-em")),
+            Self::Parsimony => Some(clap::builder::PossibleValue::new("parsimony")),
+            Self::ParsimonyGeneEm => Some(clap::builder::PossibleValue::new("parsimony-gene-em")),
+            Self::ParsimonyGene => Some(clap::builder::PossibleValue::new("parsimony-gene")),
         }
     }
 }
@@ -33,10 +33,10 @@ impl clap::ValueEnum for SplicedAmbiguityModel {
         &[Self::PreferAmbiguity, Self::WinnerTakeAll]
     }
 
-    fn to_possible_value<'a>(&self) -> Option<clap::PossibleValue<'a>> {
+    fn to_possible_value(&self) -> Option<clap::builder::PossibleValue> {
         match self {
-            Self::PreferAmbiguity => Some(clap::PossibleValue::new("prefer-ambig")),
-            Self::WinnerTakeAll => Some(clap::PossibleValue::new("winner-take-all")),
+            Self::PreferAmbiguity => Some(clap::builder::PossibleValue::new("prefer-ambig")),
+            Self::WinnerTakeAll => Some(clap::builder::PossibleValue::new("winner-take-all")),
         }
     }
 }