diff --git a/Cargo.toml b/Cargo.toml
index 692d90069e4aed5316eb66edc68cf731ae8b846f..78ba00ceae0c53cd137229f65ab659808c2791d9 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -30,6 +30,7 @@ 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" }
csv = "1.3.0"
+pathdiff = "0.2.1"
[dev-dependencies]
rand = "0.8.5"
diff --git a/src/bin/aphid/main.rs b/src/bin/aphid/main.rs
index 3ad4f38d32170c1d9910968c443c238772b8a595..d03727778af5d2a8e2eb118fb6c792a8643fc4ad 100644
--- a/src/bin/aphid/main.rs
+++ b/src/bin/aphid/main.rs
@@ -3,12 +3,14 @@ use std::{
fs::{self, File},
io::Write as IoWrite,
path::{self, Path, PathBuf},
- process, time::Instant,
+ process,
+ time::Instant,
};
use aphid::{
extract_local_triplet, imbalance,
interner::{Interner, ResolvedSymbol, SpeciesSymbol},
+ io::ToRelative,
it_mean::SummedMean,
ln_likelihood, optimize_likelihood,
output::{self, detail, file},
@@ -98,8 +100,12 @@ fn run() -> Result<(), Error> {
Ok(())
}
-fn read_inputs(args: &args::Args, output_folder: &Path, interner: &mut Interner) -> Result<(Config, GenesForest), Error> {
- let path = &args.config;
+fn read_inputs(
+ args: &args::Args,
+ output_folder: &Path,
+ interner: &mut Interner,
+) -> Result<(Config, GenesForest), Error> {
+ let path = &args.config.canonicalize()?;
cprintln!("Read config from <b>{}</>.", path.display());
let config = Config::from_file(path, output_folder, interner)?;
@@ -151,23 +157,26 @@ fn prepare_output(output: &Path, args: &args::Args) -> Result<(), Error> {
match (output.exists(), args.force) {
(true, true) => {
cprintln!(
- " <y>Removing</> existing folder: <b>{}</>.",
+ " <y>Replacing</> existing folder: <b>{}</>.",
output.display()
);
- fs::remove_dir_all(&output)?;
+ fs::remove_dir_all(output)?;
}
(true, false) => OutputExistsErr { path: &output }.fail()?,
(false, _) => {
cprintln!(" Creating empty folder: <b>{}</>.", output.display());
}
};
- fs::create_dir_all(&output)?;
+ fs::create_dir_all(output)?;
Ok(())
}
fn write_config(output: &Path, config: &Config, interner: &Interner) -> Result<(), Error> {
let path = output.join(file::CONFIG);
- cprintln!(" Write full configuration to <b>{}</>.", path.display());
+ cprintln!(
+ " Write full configuration to <b>{}</>.",
+ path.to_relative()?.display()
+ );
let mut file = File::create(path)?;
writeln!(file, "{:#}", config.resolve(interner).json())?;
Ok(())
@@ -375,7 +384,7 @@ fn write_detail(output: &Path, details: &[detail::Tree]) -> Result<(), Error> {
let path = output.join(file::DETAIL);
cprintln!(
"Write full trees analysis/filtering detail to <b>{}</>.",
- path.display()
+ path.to_relative()?.display()
);
let mut file = File::create(path)?;
writeln!(file, "{:#}", json!(details))?;
@@ -384,7 +393,10 @@ fn write_detail(output: &Path, details: &[detail::Tree]) -> Result<(), Error> {
fn write_csv(output: &Path, details: &[detail::Tree]) -> Result<(), Error> {
let path = output.join(file::CSV);
- cprintln!("Summarize scalar values to <b>{}</>.", path.display());
+ cprintln!(
+ "Summarize scalar values to <b>{}</>.",
+ path.to_relative()?.display()
+ );
let file = File::create(path)?;
let mut wtr = csv::Writer::from_writer(file);
for detail in details {
@@ -496,4 +508,6 @@ enum Error {
Learn { source: aphid::learn::Error },
#[snafu(display("Could not serialize record to CSV:\n{source}"))]
Csv { source: csv::Error },
+ #[snafu(transparent)]
+ AphidIo { source: aphid::io::Error },
}
diff --git a/src/config/deserialize.rs b/src/config/deserialize.rs
index 18b2700f71a6091971ce81051a3698c54fd2042d..f44fd121916e085d03f79d4e1786db975eaf8891 100644
--- a/src/config/deserialize.rs
+++ b/src/config/deserialize.rs
@@ -144,7 +144,7 @@ pub(crate) struct BfgsConfig {
}
#[derive(Deserialize)]
-#[serde(rename_all="snake_case")]
+#[serde(rename_all = "snake_case")]
pub(crate) enum RecordTrace {
No,
Global,
diff --git a/src/io.rs b/src/io.rs
index bebe8cede22218993c7e5c62fb38088f49a795b9..ecb6b4b5dbb5e0db2bf4ba8bd99b1be84014f4fa 100644
--- a/src/io.rs
+++ b/src/io.rs
@@ -1,6 +1,8 @@
// Reading from / writing to files on disk.
use std::{
+ borrow::Cow,
+ env,
fs::File,
io::{self, Read},
path::{Path, PathBuf},
@@ -25,6 +27,21 @@ pub fn canonicalize(path: &Path) -> Result<PathBuf, Error> {
.with_context(|_| CanonicalizeErr { path })
}
+// Display canonicalized paths relatively to current directory.
+pub trait ToRelative {
+ fn to_relative(&self) -> Result<Cow<Path>, Error>;
+}
+impl ToRelative for Path {
+ fn to_relative(&self) -> Result<Cow<Path>, Error> {
+ let cwd = env::current_dir().with_context(|_| CurDirErr)?;
+ Ok(if let Some(diff) = pathdiff::diff_paths(self, cwd) {
+ Cow::Owned(diff)
+ } else {
+ Cow::Borrowed(self)
+ })
+ }
+}
+
#[derive(Debug, Snafu)]
#[snafu(context(suffix(Err)))]
pub enum Error {
@@ -40,4 +57,6 @@ pub enum Error {
source: std::io::Error,
path: PathBuf,
},
+ #[snafu(display("Could not locate current directory: {source:?}"))]
+ CurDir { source: std::io::Error },
}
diff --git a/src/learn.rs b/src/learn.rs
index 217db857e43e408309996c7708f880f06e84ef18..02ec07a9e58a3f2c7c638ed181e0d93c0b9705a1 100644
--- a/src/learn.rs
+++ b/src/learn.rs
@@ -11,6 +11,7 @@ use tch::{Device, Tensor};
use crate::{
config::Search,
+ io::{self, ToRelative},
model::{
likelihood::{data_tensors, ln_likelihood_tensors},
parameters::GeneFlowTimes,
@@ -151,13 +152,13 @@ pub fn optimize_likelihood(
if let Some(main) = &search.bfgs.main_trace_path {
cprintln!(
" Recording main BFGS search trace at <b>{}</>.",
- main.display()
+ main.to_relative()?.display()
);
}
if let Some(lins) = &search.bfgs.linsearch_trace_path {
cprintln!(
" Recording detailed Wolfe linear search traces at <b>{}</>.",
- lins.display()
+ lins.to_relative()?.display()
);
}
// Log every step if a file was provided.
@@ -177,7 +178,11 @@ pub fn optimize_likelihood(
<g>{n_eval}</> evaluations and \
<g>{n_diff}</> differentiations."
);
- cprintln!("<s>--</> Final location: <k,i>{}value 'gradient{}</>:\n{grad:#}", '<', '>');
+ cprintln!(
+ "<s>--</> Final location: <k,i>{}value 'gradient{}</>:\n{grad:#}",
+ '<',
+ '>'
+ );
let parms: Parameters<f64> = (&scores).into();
let opt_lnl = -opt.best_loss();
@@ -255,4 +260,6 @@ pub enum Error {
NonFiniteLikelihood { lnl: f64, parms: Parameters<f64> },
#[snafu(transparent)]
Optim { source: OptimError },
+ #[snafu(transparent)]
+ IO { source: io::Error },
}
diff --git a/src/lib.rs b/src/lib.rs
index ced4954e68919311934d4eda0e9efdf989bca24c..e07a4111bdd36d96c1ddda0ebc9129a2db59a7c4 100644
--- a/src/lib.rs
+++ b/src/lib.rs
@@ -2,7 +2,7 @@ pub mod config;
mod gene_tree;
pub mod genes_forest;
pub mod interner;
-mod io;
+pub mod io;
pub mod it_mean;
pub mod learn;
mod lexer;
diff --git a/src/model/parameters.rs b/src/model/parameters.rs
index 3bc67951797084790d89b9190f070eecd725e456..ae55e8f59c477120dd1183f456dd22f360d0fb50 100644
--- a/src/model/parameters.rs
+++ b/src/model/parameters.rs
@@ -120,16 +120,16 @@ impl<F: Num + Display + Sized + fmt::Debug> Display for Colored<'_, F> {
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:?}</>,")?;
+ cwriteln!(f, " theta: <c>{theta:?}</>,")?;
+ cwriteln!(f, " tau_1: <c>{tau_1:?}</>,")?;
+ cwriteln!(f, " tau_2: <c>{tau_2:?}</>,")?;
+ cwriteln!(f, " p_ab: <c>{p_ab:?}</>,")?;
+ cwriteln!(f, " p_ac: <c>{p_ac:?}</>,")?;
+ cwriteln!(f, " p_bc: <c>{p_bc:?}</>,")?;
+ cwriteln!(f, " p_ancient: <c>{p_ancient:?}</>,")?;
writeln!(f, " gf_times: [")?;
for t in &gf_times.0 {
- cwriteln!(f, " <b>{t}</>,")?;
+ cwriteln!(f, " <c>{t}</>,")?;
}
writeln!(f, " ]")?;
writeln!(f, "}}")
diff --git a/src/output.rs b/src/output.rs
index 9bebdcd15b652c6a5cdb200392c198990e138e57..42391064f1d4bded5470c8a102bfb91a18268cf6 100644
--- a/src/output.rs
+++ b/src/output.rs
@@ -1,8 +1,8 @@
// Use this module to specify the possible output(s) of aphid.
mod config;
-pub mod detail;
pub mod csv;
+pub mod detail;
// Standard output filenames.
pub mod file {
@@ -12,4 +12,3 @@ pub mod file {
pub const MAIN_TRACE: &str = "search_global.csv";
pub const LINSEARCH_TRACE: &str = "search_detail.csv";
}
-