diff --git a/Cargo.toml b/Cargo.toml
index 8ab386045e0f8e12380479442f2efdf72fcb87cb..c256cf0d2ab12a3f8ba40447dc76bfc08edbcc65 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -10,7 +10,6 @@ edition = "2021"
[dependencies]
arrayvec = { version = "0.7.4", features = ["serde"] }
clap = { version = "4.5.0", features = ["derive"] }
-colored = "2.1.0"
itertools = "0.12.1"
lexical-sort = "0.3.1"
num-traits = "0.2.18"
@@ -28,6 +27,8 @@ unicode-width = "0.1.11"
float_eq = { version = "1.0.1", features = ["derive"] }
snafu = "0.8.2"
serde_json = { version = "1.0.127", features = ["preserve_order"] }
+color-print = { git = "https://gitlab.com/iago-lito/color-print", branch = "dev", version = "0.3.6" }
+color-print-proc-macro = { git = "https://gitlab.com/iago-lito/color-print", branch = "dev", version = "0.3.6" }
[dev-dependencies]
rand = "0.8.5"
diff --git a/src/bin/aphid/main.rs b/src/bin/aphid/main.rs
index 415a42f1a9d4fe8ef4fa379d715b9fe47cc2b06c..bbeb0821e05049b81015f65a4ec4c7cb940c486f 100644
--- a/src/bin/aphid/main.rs
+++ b/src/bin/aphid/main.rs
@@ -15,7 +15,7 @@ use aphid::{
Config, GeneTree, GeneTriplet, GenesForest, LocalGeneTriplet, VERSION,
};
use clap::Parser;
-use colored::Colorize;
+use color_print::{ceprintln, cformat, cprintln};
use float_eq::float_eq;
use serde_json::json;
use snafu::{ensure, Snafu};
@@ -33,10 +33,10 @@ fn main() {
println!("Running Aphid v{VERSION}.");
match run() {
Ok(()) => {
- println!("Success. {}", "✓".bold().green());
+ cprintln!("Success. <bold,green>✓</>");
}
Err(e) => {
- eprintln!("{} {e}", "🗙 Error:".bold().red());
+ ceprintln!("<bold,red>🗙 Error:</> {e}");
process::exit(1);
}
}
@@ -100,13 +100,13 @@ fn run() -> Result<(), Error> {
fn read_inputs(args: &args::Args, interner: &mut Interner) -> Result<(Config, GenesForest), Error> {
let path = &args.config;
- println!("Read config from {}.", format!("{path:?}").blue());
+ cprintln!("Read config from <b>{}</>.", path.display());
let config = Config::from_file(path, interner)?;
let path = &config.trees;
- println!("Read gene trees from {}:", format!("{path:?}").blue());
+ cprintln!("Read gene trees from <b>{}</>:", path.display());
let forest = GenesForest::from_file(path, interner)?;
- println!(" Found {} gene trees.", forest.len());
+ cprintln!(" Found <g>{}</> gene trees.", forest.len());
Ok((config, forest))
}
@@ -151,19 +151,15 @@ fn prepare_output(args: &args::Args) -> Result<PathBuf, Error> {
let output = path::absolute(&args.output)?;
match (output.exists(), args.force) {
(true, true) => {
- println!(
- " {} existing folder: {}.",
- "Removing".yellow(),
- format!("{}", output.display()).blue()
+ cprintln!(
+ " <y>Removing</> existing folder: <b>{}</>.",
+ output.display()
);
fs::remove_dir_all(&output)?;
}
(true, false) => OutputExistsErr { path: &output }.fail()?,
(false, _) => {
- println!(
- " Creating empty folder: {}.",
- format!("{}", output.display()).blue()
- );
+ cprintln!(" Creating empty folder: <b>{}</>.", output.display());
}
};
fs::create_dir_all(&output)?;
@@ -173,10 +169,7 @@ fn prepare_output(args: &args::Args) -> Result<PathBuf, Error> {
fn write_config(output: &Path, config: &Config, interner: &Interner) -> Result<(), Error> {
let path = output.join(out::CONFIG);
- println!(
- " Write full configuration to {}.",
- format!("{}", path.display()).blue()
- );
+ cprintln!(" Write full configuration to <b>{}</>.", path.display());
let mut file = File::create(path)?;
writeln!(file, "{:#}", config.resolve(interner).json())?;
Ok(())
@@ -272,13 +265,13 @@ fn topology_filter<'i>(
}
// Report.
- println!(
- " {n_excluded} tree{s_were} excluded from analysis based on their topology.",
+ cprintln!(
+ " <g>{n_excluded}</> tree{s_were} excluded from analysis based on their topology.",
s_were = if n_excluded > 1 { "s were" } else { " was" },
);
if let Some(min) = unrl {
- println!(
- " {n_unresolved} included triplet{s_were} unresolved (internal length <= {min}).",
+ cprintln!(
+ " <g>{n_unresolved}</> included triplet{s_were} unresolved (internal length ⩽ {min}).",
s_were = if n_unresolved > 1 { "s were" } else { " was" },
);
}
@@ -307,12 +300,12 @@ fn geometry_filter(
let (triplet_longer, imbalance) = imbalance(triplet_means_sum, rest_means_sum);
let (t, r) = ("'triplet' section", "'outgroup' and 'other' section");
let (small, large) = if triplet_longer { (t, r) } else { (r, t) };
- println!(
- " Branch lengths in {large} are on average {imbalance} times longer \
+ cprintln!(
+ " Branch lengths in {large} are on average <g>{imbalance}</> times longer \
than in {small}."
);
let global_shape = triplet_means_sum / rest_means_sum;
- println!(" Mean tree shape: {global_shape}");
+ cprintln!(" Mean tree shape: <g>{global_shape}</>");
for i in topology_included {
let tree = &pruned[i];
@@ -344,8 +337,8 @@ fn geometry_filter(
// Report.
if n_excluded > 0 {
- println!(
- " --> {n_excluded} tree{s_were} excluded from analysis based on their geometry.",
+ cprintln!(
+ " --> <g>{n_excluded}</> tree{s_were} excluded from analysis based on their geometry.",
s_were = if n_excluded > 1 { "s were" } else { " was" },
);
} else {
@@ -366,7 +359,7 @@ fn final_tree_selection(
.map(|&i| details[i].mean_lengths.total.unwrap())
.summed_mean::<usize>();
- println!(" mean branch length accross trees: l = {global_mean}");
+ cprintln!(" mean branch length accross trees: l = <g>{global_mean}</>");
let mut triplets = Vec::new();
for i in included {
let local = local_triplets[i].take().unwrap(); // Exists since included.
@@ -382,9 +375,9 @@ fn final_tree_selection(
fn write_detail(output: &Path, details: &[detail::Tree]) -> Result<(), Error> {
let path = output.join(out::DETAIL);
- println!(
- "Write full trees analysis/filtering detail to {}.",
- format!("{}", path.display()).blue()
+ cprintln!(
+ "Write full trees analysis/filtering detail to <b>{}</>.",
+ path.display()
);
let mut file = File::create(path)?;
writeln!(file, "{:#}", json!(details))?;
@@ -396,8 +389,8 @@ fn display_summary(included: &[usize], details: &[detail::Tree], config: &Config
let s = |n| if n > 1 { "s" } else { "" };
let n = details.iter().map(|d| u64::from(!d.triplet.included)).sum();
- println!(
- " - {n} triplet{} rejected (incomplete or non-monophyletic).",
+ cprintln!(
+ " - <g>{n}</> triplet{} rejected (incomplete or non-monophyletic).",
s(n),
);
@@ -406,8 +399,8 @@ fn display_summary(included: &[usize], details: &[detail::Tree], config: &Config
.iter()
.filter_map(|d| d.triplet.analysis.as_ref().map(|a| u64::from(!a.resolved)))
.sum();
- println!(
- " - {n} triplet{} considered unresolved (internal branch length ⩽ {min}).",
+ cprintln!(
+ " - <g>{n}</> triplet{} considered unresolved (internal branch length ⩽ {min}).",
s(n),
);
}
@@ -416,8 +409,8 @@ fn display_summary(included: &[usize], details: &[detail::Tree], config: &Config
.iter()
.map(|d| u64::from(!d.outgroup.included))
.sum();
- println!(
- " - {n} outgroup{} rejected (empty or non-monophyletic).",
+ cprintln!(
+ " - <g>{n}</> outgroup{} rejected (empty or non-monophyletic).",
s(n)
);
@@ -425,8 +418,8 @@ fn display_summary(included: &[usize], details: &[detail::Tree], config: &Config
.iter()
.map(|d| d.top.as_ref().map_or(1, |top| (!top.included).into()))
.sum::<u64>();
- println!(
- " - {n} tree top{} rejected (non-root LCA(triplet, outgroup){}).",
+ cprintln!(
+ " - <g>{n}</> tree top{} rejected (non-root LCA(triplet, outgroup){}).",
s(n),
if config.filters.triplet_other_monophyly {
" or non-monophyletic (triplet, other)"
@@ -440,15 +433,15 @@ fn display_summary(included: &[usize], details: &[detail::Tree], config: &Config
.iter()
.map(|d| u64::from(!d.included_geometry))
.sum();
- println!(
- " - {n} tree shape{} rejected \
+ cprintln!(
+ " - <g>{n}</> tree shape{} rejected \
(triplet/outgroup imbalance larger than {max} times the average).",
s(n)
);
}
let n = included.len() as u64;
- println!(" => {n} tree{} kept for analysis.", s(n));
+ cprintln!(" ==> <s,g>{n}</> tree{} kept for analysis.", s(n));
}
fn learn(triplets: &[GeneTriplet], config: &Config) -> Result<(), Error> {
@@ -456,8 +449,8 @@ fn learn(triplets: &[GeneTriplet], config: &Config) -> Result<(), Error> {
let parms = &config.search.init_parms;
let (opt, opt_lnl) = optimize_likelihood(triplets, parms, &config.search)?;
- println!("Optimized ln-likelihood: {opt_lnl}");
- println!("Optimized parameters: {opt:#?}\n");
+ cprintln!("Optimized ln-likelihood: <g>{opt_lnl}</>");
+ println!("Optimized parameters: {}\n", opt.colored());
// Smoke test:
// TODO: turn into actual testing by including 'official' example data.
@@ -479,7 +472,8 @@ enum Error {
Io { source: std::io::Error },
#[snafu(transparent)]
Check { source: aphid::config::check::Error },
- #[snafu(display("Output folder already exists: {}.", format!("{}", path.display()).blue()))]
+ // TODO: have color_print feature this without the need to allocate an intermediate string?
+ #[snafu(display("Output folder already exists: {}.", cformat!("<b>{}</>", path.display())))]
OutputExists { path: PathBuf },
#[snafu(transparent)]
ForestParse {
diff --git a/src/config/check.rs b/src/config/check.rs
index 16bb02207142c12663d24c3a2cb6e522306ae931..0d855f6f97695975435d715fd50a5ecd2137e474 100644
--- a/src/config/check.rs
+++ b/src/config/check.rs
@@ -8,7 +8,6 @@ use std::{
};
use arrayvec::ArrayVec;
-use colored::Colorize;
use regex::Regex;
use snafu::{ensure, Snafu};
@@ -212,14 +211,12 @@ impl BfgsConfig {
let linsearch_trace_path = check_path(linsearch_trace)?;
if let (None, Some(path)) = (&main_trace_path, &linsearch_trace) {
return err!((
- "A path is specified with {linopt} \
+ "A path is specified with <b>`search.bfgs.linsearch_trace`</> \
to log the detailed trace of BFGS linear search during each step, \
but none is specified to log the global trace of each step. \
- Consider setting {mainopt} option.\n\
- The path given was: {path}",
- linopt = "`search.bfgs.linsearch_trace`".blue(),
- mainopt = "`search.bfgs.main_trace`".blue(),
- path = format!("{:?}", path.to_string_lossy()).black(),
+ Consider setting <b>`search.bfgs.main_trace`</> option.\n\
+ The path given was: <k>{}</>",
+ path.display(),
))
.fail();
}
diff --git a/src/model/parameters.rs b/src/model/parameters.rs
index bc59a80716189e603c0a68824a1eb564c98c03f3..b570a860c337e227886df3a96c6c65760e52212b 100644
--- a/src/model/parameters.rs
+++ b/src/model/parameters.rs
@@ -4,6 +4,7 @@
use std::fmt::{self, Display};
use arrayvec::ArrayVec;
+use color_print::cwriteln;
use serde::Serialize;
use tch::Tensor;
@@ -102,3 +103,41 @@ impl fmt::Debug for ValGrad {
write!(f, "{self}")
}
}
+
+// Colored parameters for stdout.
+pub struct Colored<'p, F: Num + Display + Sized>(&'p Parameters<F>);
+
+impl<F: Num + Display + Sized + fmt::Debug> Display for Colored<'_, F> {
+ fn fmt(&self, f: &mut fmt::Formatter) -> fmt::Result {
+ writeln!(f, "Parameters {{")?;
+ let Parameters {
+ theta,
+ tau_1,
+ tau_2,
+ p_ab,
+ p_ac,
+ p_bc,
+ p_ancient,
+ gf_times,
+ } = &self.0;
+ cwriteln!(f, " theta: <b>{theta:?}</>,")?;
+ cwriteln!(f, " tau_1: <b>{tau_1:?}</>,")?;
+ cwriteln!(f, " tau_2: <b>{tau_2:?}</>,")?;
+ cwriteln!(f, " p_ab: <b>{p_ab:?}</>,")?;
+ cwriteln!(f, " p_ac: <b>{p_ac:?}</>,")?;
+ cwriteln!(f, " p_bc: <b>{p_bc:?}</>,")?;
+ cwriteln!(f, " p_ancient: <b>{p_ancient:?}</>,")?;
+ writeln!(f, " gf_times: [")?;
+ for t in &gf_times.0 {
+ cwriteln!(f, " <b>{t}</>,")?;
+ }
+ writeln!(f, " ]")?;
+ writeln!(f, "}}")
+ }
+}
+
+impl<F: Num + Display + Sized> Parameters<F> {
+ pub fn colored(&self) -> Colored<F> {
+ Colored(self)
+ }
+}