build!: add features for disabling sqlite-based implementation (#74)

Release-As: 0.7.0

Cargo.toml

@@ -12,12 +12,23 @@ readme = "README.md"
 name = "seqrepo"
 path = "src/lib.rs"
 
+[features]
+# By default, we enable the directory-based implementation.
+default = ["impl"]
+# Directory-based implementation of the interface as provided by the Python
+# reference implementation.  This will create a runtime dependency on
+# `libsqlite3`.
+impl = ["dep:chrono", "dep:noodles-bgzf", "dep:noodles-core", "dep:noodles-fasta", "dep:rusqlite"]
+# Optional caching implementation that is useful in testing scenarios where
+# one only wants to provide minimal data, e.g., in continuous integration.
+cached = ["impl"]
+
 [dependencies]
-chrono = "0.4"
-noodles-bgzf = "0.22"
-noodles-core = "0.12"
-noodles-fasta = "0.25"
-rusqlite = "0.29"
+chrono = { version = "0.4", optional = true }
+noodles-bgzf = { version = "0.22", optional = true }
+noodles-core = { version = "0.12", optional = true }
+noodles-fasta = { version = "0.25", optional = true }
+rusqlite = { version = "0.29", optional = true }
 thiserror = "1.0"
 tracing = "0.1"
 

src/cached.rs

@@ -12,8 +12,11 @@ use std::{
     sync::{Arc, Mutex},
 };
 
-use crate::error::Error;
-use crate::repo::{self, AliasOrSeqId, SeqRepo};
+use crate::repo::SeqRepo;
+use crate::{
+    error::Error,
+    interface::{AliasOrSeqId, Interface},
+};
 
 /// Sequence repository reading from actual implementation and writing to a cache.
 pub struct CacheWritingSeqRepo {
@@ -50,7 +53,7 @@ impl CacheWritingSeqRepo {
     }
 }
 
-impl repo::Interface for CacheWritingSeqRepo {
+impl Interface for CacheWritingSeqRepo {
     fn fetch_sequence_part(
         &self,
         alias_or_seq_id: &AliasOrSeqId,
@@ -122,7 +125,7 @@ impl CacheReadingSeqRepo {
     }
 }
 
-impl repo::Interface for CacheReadingSeqRepo {
+impl Interface for CacheReadingSeqRepo {
     fn fetch_sequence_part(
         &self,
         alias_or_seq_id: &AliasOrSeqId,

src/interface.rs

@@ -0,0 +1,27 @@
+//! Implementation of the interface trait.
+
+use crate::error::Error;
+
+/// Trait describing the interface of a sequence repository.
+pub trait Interface {
+    /// Fetch part sequence given an alias.
+    fn fetch_sequence(&self, alias_or_seq_id: &AliasOrSeqId) -> Result<String, Error> {
+        self.fetch_sequence_part(alias_or_seq_id, None, None)
+    }
+
+    /// Fetch part sequence given an alias.
+    fn fetch_sequence_part(
+        &self,
+        alias_or_seq_id: &AliasOrSeqId,
+        begin: Option<usize>,
+        end: Option<usize>,
+    ) -> Result<String, Error>;
+}
+
+pub enum AliasOrSeqId {
+    Alias {
+        value: String,
+        namespace: Option<String>,
+    },
+    SeqId(String),
+}

src/lib.rs

@@ -1,13 +1,24 @@
 //! This is the `seqrepo` library.
 
-mod aliases;
-mod cached;
-mod error;
-mod fasta;
-mod repo;
+#[cfg(feature = "impl")]
+pub(crate) mod aliases;
+#[cfg(feature = "cached")]
+pub(crate) mod cached;
+pub(crate) mod error;
+#[cfg(feature = "impl")]
+pub(crate) mod fasta;
+#[cfg(feature = "impl")]
+pub(crate) mod interface;
+#[cfg(feature = "impl")]
+pub(crate) mod repo;
 
 pub use crate::aliases::*;
+#[cfg(feature = "cached")]
 pub use crate::cached::*;
 pub use crate::error::*;
+#[cfg(feature = "impl")]
 pub use crate::fasta::*;
+#[cfg(feature = "impl")]
+pub use crate::interface::*;
+#[cfg(feature = "impl")]
 pub use crate::repo::*;

src/repo.rs

@@ -1,25 +1,10 @@
-//! Code providing the interface for sequence repositories and the base `SeqRepo` implementation.
+//! Code providing the base `SeqRepo` implementation.
 
 use std::path::{Path, PathBuf};
 
 use crate::error::Error;
-use crate::{AliasDb, FastaDir, Namespace, Query};
-
-/// Trait describing the interface of a sequence repository.
-pub trait Interface {
-    /// Fetch part sequence given an alias.
-    fn fetch_sequence(&self, alias_or_seq_id: &AliasOrSeqId) -> Result<String, Error> {
-        self.fetch_sequence_part(alias_or_seq_id, None, None)
-    }
-
-    /// Fetch part sequence given an alias.
-    fn fetch_sequence_part(
-        &self,
-        alias_or_seq_id: &AliasOrSeqId,
-        begin: Option<usize>,
-        end: Option<usize>,
-    ) -> Result<String, Error>;
-}
+use crate::interface::Interface;
+use crate::{AliasDb, AliasOrSeqId, FastaDir, Namespace, Query};
 
 /// Provide (read-only) access to a `seqrepo` sequence repository.
 #[derive(Debug)]
@@ -34,14 +19,6 @@ pub struct SeqRepo {
     fasta_dir: FastaDir,
 }
 
-pub enum AliasOrSeqId {
-    Alias {
-        value: String,
-        namespace: Option<String>,
-    },
-    SeqId(String),
-}
-
 impl SeqRepo {
     /// Create new `SeqRepo` at the given path.
     pub fn new<P>(path: P, instance: &str) -> Result<Self, Error>
@@ -120,7 +97,7 @@ impl Interface for SeqRepo {
 
 #[cfg(test)]
 mod test {
-    use crate::{repo::Interface, AliasOrSeqId, SeqRepo};
+    use crate::{AliasOrSeqId, Interface, SeqRepo};
     use anyhow::Error;
 
     #[test]