refactor!: rename c4gh-experimental to experimental

mmalenic · mmalenic · commit d60770bfdb87 · 2024-09-19T14:43:14.000+10:00
diff --git a/htsget-actix/Cargo.toml b/htsget-actix/Cargo.toml
@@ -13,12 +13,12 @@ repository = "https://github.com/umccr/htsget-rs"
 [features]
 s3-storage = ["htsget-config/s3-storage", "htsget-search/s3-storage", "htsget-http/s3-storage", "htsget-axum/s3-storage", "htsget-test/s3-storage"]
 url-storage = ["htsget-config/url-storage", "htsget-search/url-storage", "htsget-http/url-storage", "htsget-axum/url-storage", "htsget-test/url-storage"]
-c4gh-experimental = [
-    "htsget-config/c4gh-experimental",
-    "htsget-search/c4gh-experimental",
-    "htsget-http/c4gh-experimental",
-    "htsget-axum/c4gh-experimental",
-    "htsget-test/c4gh-experimental"
+experimental = [
+    "htsget-config/experimental",
+    "htsget-search/experimental",
+    "htsget-http/experimental",
+    "htsget-axum/experimental",
+    "htsget-test/experimental"
 ]
 default = []
 
diff --git a/htsget-actix/README.md b/htsget-actix/README.md
@@ -31,7 +31,7 @@ This crate is used for running a local instance of htsget-rs. It is based on:
 
 ## Usage
 
-This application has the same functionality as [htsget-axum]. To use it, following the [htsget-axum][htsget-axum-usage] instructions, and
+This application has the same functionality as [htsget-axum]. To use it, following the [htsget-axum][htsget-axum] instructions, and
 replace any calls to `htsget-axum` with `htsget-actix`.
 
 It is recommended to use [htsget-axum] because it better fits with the rest of [htsget-rs]. For example [htsget-actix]
@@ -50,7 +50,7 @@ are exposed in the public API.
 This crate has the following features:
 * `s3-storage`: used to enable `S3Storage` functionality.
 * `url-storage`: used to enable `UrlStorage` functionality.
-* `c4gh-experimental`: used to enable `C4GHStorage` functionality.
+* `experimental`: used to enable `C4GHStorage` functionality.
 
 ## Benchmarks
 Benchmarks for this crate written using [Criterion.rs][criterion-rs], and aim to compare the performance of this crate with the
@@ -76,6 +76,7 @@ cargo bench -p htsget-axum -- HEAVY
 [criterion-rs]: https://github.com/bheisler/criterion.rs
 [htsget-refserver]: https://github.com/ga4gh/htsget-refserver
 [data-vcf]: ../data/vcf
+[htsget-axum]: ../htsget-axum/README.md#usage
 
 ## License
 
diff --git a/htsget-axum/Cargo.toml b/htsget-axum/Cargo.toml
@@ -24,11 +24,11 @@ url-storage = [
     "htsget-test/url-storage",
     "htsget-http/url-storage"
 ]
-c4gh-experimental = [
-    "htsget-config/c4gh-experimental",
-    "htsget-search/c4gh-experimental",
-    "htsget-test/c4gh-experimental",
-    "htsget-http/c4gh-experimental"
+experimental = [
+    "htsget-config/experimental",
+    "htsget-search/experimental",
+    "htsget-test/experimental",
+    "htsget-http/experimental"
 ]
 default = []
 
diff --git a/htsget-axum/README.md b/htsget-axum/README.md
@@ -108,7 +108,7 @@ for more details on how to configure this.
 Run the server with the following to enable Crypt4GH support using the [example config][example-config]:
 
 ```sh
-cargo run -p htsget-axum --features c4gh-experimental -- --config htsget-config/examples/config-files/c4gh.toml
+cargo run -p htsget-axum --features experimental -- --config htsget-config/examples/config-files/c4gh.toml
 ```
 
 Crypt4GH encrypted byte ranges can be queried:
@@ -171,7 +171,7 @@ htsget-rs. It also contains the data block server which fetches data from a `Loc
 This crate has the following features:
 * `s3-storage`: used to enable `S3Storage` functionality.
 * `url-storage`: used to enable `UrlStorage` functionality.
-* `c4gh-experimental`: used to enable `C4GHStorage` functionality.
+* `experimental`: used to enable `C4GHStorage` functionality.
 
 ## License
 
diff --git a/htsget-config/Cargo.toml b/htsget-config/Cargo.toml
@@ -13,7 +13,7 @@ repository = "https://github.com/umccr/htsget-rs"
 [features]
 s3-storage = []
 url-storage = ["dep:reqwest"]
-c4gh-experimental = ["dep:crypt4gh"]
+experimental = ["dep:crypt4gh"]
 default = []
 
 [dependencies]
diff --git a/htsget-config/README.md b/htsget-config/README.md
@@ -491,7 +491,7 @@ See the MinIO deployment [example][minio-deployment] for more information on how
 ### Crypt4GH
 
 There is experimental support for serving [Crypt4GH][c4gh] encrypted files. This can be enabled by compiling with the 
-`c4gh-experimental` feature flag.
+`experimental` feature flag.
 
 This allows htsget-rs to read Crypt4GH files and serve them encrypted, directly to the client. In the process of
 serving the data, htsget-rs will decrypt the headers of the Crypt4GH files and reencrypt them so that the client can read
@@ -535,7 +535,7 @@ regex, and changing it by using a substitution string.
 This crate has the following features:
 * `s3-storage`: used to enable `S3Storage` functionality.
 * `url-storage`: used to enable `UrlStorage` functionality.
-* `c4gh-experimental`: used to enable `C4GHStorage` functionality.
+* `experimental`: used to enable `C4GHStorage` functionality.
 
 ## License
 
diff --git a/htsget-config/examples/config-files/c4gh.toml b/htsget-config/examples/config-files/c4gh.toml
@@ -1,5 +1,5 @@
 # An example of running htsget-rs with Crypt4GH enabled.
-# Run with `cargo run -p htsget-axum --features c4gh-experimental -- --config htsget-config/examples/config-files/c4gh.toml`
+# Run with `cargo run -p htsget-axum --features experimental -- --config htsget-config/examples/config-files/c4gh.toml`
 
 ticket_server_addr = "127.0.0.1:8080"
 data_server_addr = "127.0.0.1:8081"
diff --git a/htsget-config/src/storage/object/mod.rs b/htsget-config/src/storage/object/mod.rs
@@ -1,10 +1,10 @@
 //! Defines the type of object used by storage.
 //!
 
-#[cfg(feature = "c4gh-experimental")]
+#[cfg(feature = "experimental")]
 pub mod c4gh;
 
-#[cfg(feature = "c4gh-experimental")]
+#[cfg(feature = "experimental")]
 use crate::storage::object::c4gh::C4GHKeys;
 use serde::{Deserialize, Serialize};
 
@@ -15,7 +15,7 @@ use serde::{Deserialize, Serialize};
 pub enum ObjectType {
   #[default]
   Regular,
-  #[cfg(feature = "c4gh-experimental")]
+  #[cfg(feature = "experimental")]
   C4GH {
     #[serde(flatten, skip_serializing)]
     keys: C4GHKeys,
diff --git a/htsget-http/Cargo.toml b/htsget-http/Cargo.toml
@@ -13,7 +13,7 @@ repository = "https://github.com/umccr/htsget-rs"
 [features]
 s3-storage = ["htsget-config/s3-storage", "htsget-search/s3-storage", "htsget-test/s3-storage"]
 url-storage = ["htsget-config/url-storage", "htsget-search/url-storage", "htsget-test/url-storage"]
-c4gh-experimental = ["htsget-config/c4gh-experimental", "htsget-search/c4gh-experimental", "htsget-test/c4gh-experimental"]
+experimental = ["htsget-config/experimental", "htsget-search/experimental", "htsget-test/experimental"]
 default = []
 
 [dependencies]
diff --git a/htsget-http/README.md b/htsget-http/README.md
@@ -38,7 +38,7 @@ These functions take query and endpoint information, and process it using [htsge
 This crate has the following features:
 * `s3-storage`: used to enable `S3Storage` functionality.
 * `url-storage`: used to enable `UrlStorage` functionality.
-* `c4gh-experimental`: used to enable `C4GHStorage` functionality.
+* `experimental`: used to enable `C4GHStorage` functionality.
 
 [warp]: https://github.com/seanmonstar/warp
 [htsget-search]: ../htsget-search
diff --git a/htsget-lambda/Cargo.toml b/htsget-lambda/Cargo.toml
@@ -13,12 +13,12 @@ repository = "https://github.com/umccr/htsget-rs"
 [features]
 s3-storage = ["htsget-axum/s3-storage", "htsget-config/s3-storage", "htsget-search/s3-storage", "htsget-http/s3-storage", "htsget-test/s3-storage"]
 url-storage = ["htsget-axum/url-storage", "htsget-config/url-storage", "htsget-search/url-storage", "htsget-http/url-storage", "htsget-test/url-storage"]
-c4gh-experimental = [
-    "htsget-axum/c4gh-experimental",
-    "htsget-config/c4gh-experimental",
-    "htsget-search/c4gh-experimental",
-    "htsget-http/c4gh-experimental",
-    "htsget-test/c4gh-experimental"
+experimental = [
+    "htsget-axum/experimental",
+    "htsget-config/experimental",
+    "htsget-search/experimental",
+    "htsget-http/experimental",
+    "htsget-test/experimental"
 ]
 default = []
 
diff --git a/htsget-lambda/README.md b/htsget-lambda/README.md
@@ -46,7 +46,7 @@ library code, and it instead uses `htsget-axum`. Please use that crate for funct
 This crate has the following features:
 * `s3-storage`: used to enable `S3Storage` functionality.
 * `url-storage`: used to enable `UrlStorage` functionality.
-* `c4gh-experimental`: used to enable `C4GHStorage` functionality.
+* `experimental`: used to enable `C4GHStorage` functionality.
 
 ## License
 
diff --git a/htsget-search/Cargo.toml b/htsget-search/Cargo.toml
@@ -22,10 +22,10 @@ url-storage = [
     "htsget-config/url-storage",
     "htsget-test/url-storage"
 ]
-c4gh-experimental = [
-    "htsget-storage/c4gh-experimental",
-    "htsget-config/c4gh-experimental",
-    "htsget-test/c4gh-experimental"
+experimental = [
+    "htsget-storage/experimental",
+    "htsget-config/experimental",
+    "htsget-test/experimental"
 ]
 default = []
 
diff --git a/htsget-search/README.md b/htsget-search/README.md
@@ -59,7 +59,7 @@ used to process requests.
 This crate has the following features:
 * `s3-storage`: used to enable `S3Storage` functionality.
 * `url-storage`: used to enable `UrlStorage` functionality.
-* `c4gh-experimental`: used to enable `C4GHStorage` functionality.
+* `experimental`: used to enable `C4GHStorage` functionality.
 
 ## Minimising Byte Ranges
 
diff --git a/htsget-search/src/bam_search.rs b/htsget-search/src/bam_search.rs
@@ -156,7 +156,7 @@ pub(crate) mod tests {
   use htsget_test::http::concat::ConcatResponse;
   use std::future::Future;
   use std::sync::Arc;
-  #[cfg(feature = "c4gh-experimental")]
+  #[cfg(feature = "experimental")]
   use {
     crate::from_storage::tests::with_local_storage_c4gh,
     htsget_storage::c4gh::storage::C4GHStorage, htsget_test::c4gh::get_decryption_keys,
@@ -594,7 +594,7 @@ pub(crate) mod tests {
     .await
   }
 
-  #[cfg(feature = "c4gh-experimental")]
+  #[cfg(feature = "experimental")]
   #[tokio::test]
   async fn search_all_c4gh() {
     with_local_storage_c4gh(|storage| async move {
@@ -613,7 +613,7 @@ pub(crate) mod tests {
     .await;
   }
 
-  #[cfg(feature = "c4gh-experimental")]
+  #[cfg(feature = "experimental")]
   #[tokio::test]
   async fn search_all_range_c4gh() {
     with_local_storage_c4gh(|storage| async move {
diff --git a/htsget-search/src/bcf_search.rs b/htsget-search/src/bcf_search.rs
@@ -121,7 +121,7 @@ mod tests {
   use crate::search::SearchAll;
   use crate::{Class::Header, Headers, HtsGetError::NotFound, Response, Url};
   use htsget_storage::local::LocalStorage;
-  #[cfg(feature = "c4gh-experimental")]
+  #[cfg(feature = "experimental")]
   use {
     crate::from_storage::tests::with_local_storage_c4gh,
     htsget_storage::c4gh::storage::C4GHStorage, htsget_test::c4gh::get_decryption_keys,
@@ -387,7 +387,7 @@ mod tests {
     .await
   }
 
-  #[cfg(feature = "c4gh-experimental")]
+  #[cfg(feature = "experimental")]
   #[tokio::test]
   async fn search_all_c4gh() {
     with_local_storage_c4gh(|storage| async move {
@@ -406,7 +406,7 @@ mod tests {
     .await;
   }
 
-  #[cfg(feature = "c4gh-experimental")]
+  #[cfg(feature = "experimental")]
   #[tokio::test]
   async fn search_range_c4gh() {
     with_local_storage_c4gh(|storage| async move {
diff --git a/htsget-search/src/cram_search.rs b/htsget-search/src/cram_search.rs
@@ -283,7 +283,7 @@ mod tests {
   use crate::from_storage::tests::with_local_storage_fn;
   use crate::{Class::Header, Headers, HtsGetError::NotFound, Response, Url};
   use htsget_storage::local::LocalStorage;
-  #[cfg(feature = "c4gh-experimental")]
+  #[cfg(feature = "experimental")]
   use {
     crate::from_storage::tests::with_local_storage_c4gh,
     htsget_storage::c4gh::storage::C4GHStorage, htsget_test::c4gh::get_decryption_keys,
@@ -600,7 +600,7 @@ mod tests {
     .await
   }
 
-  #[cfg(feature = "c4gh-experimental")]
+  #[cfg(feature = "experimental")]
   #[tokio::test]
   async fn search_all_c4gh() {
     with_local_storage_c4gh(|storage| async move {
@@ -619,7 +619,7 @@ mod tests {
     .await;
   }
 
-  #[cfg(feature = "c4gh-experimental")]
+  #[cfg(feature = "experimental")]
   #[tokio::test]
   async fn search_range_c4gh() {
     with_local_storage_c4gh(|storage| async move {
diff --git a/htsget-search/src/from_storage.rs b/htsget-search/src/from_storage.rs
@@ -119,7 +119,7 @@ pub(crate) mod tests {
   use htsget_config::types::Class::Body;
   use htsget_config::types::Scheme::Http;
   use htsget_storage::local::LocalStorage;
-  #[cfg(feature = "c4gh-experimental")]
+  #[cfg(feature = "experimental")]
   use htsget_test::c4gh::decrypt_data;
   use htsget_test::http::concat::ConcatResponse;
 
@@ -321,7 +321,7 @@ pub(crate) mod tests {
     .await;
   }
 
-  #[cfg(feature = "c4gh-experimental")]
+  #[cfg(feature = "experimental")]
   pub(crate) async fn with_local_storage_c4gh<F, Fut>(test: F)
   where
     F: FnOnce(Arc<LocalStorage<LocalStorageConfig>>) -> Fut,
diff --git a/htsget-search/src/vcf_search.rs b/htsget-search/src/vcf_search.rs
@@ -132,7 +132,7 @@ pub(crate) mod tests {
   use crate::search::SearchAll;
   use crate::{Class::Header, Headers, HtsGetError::NotFound, Response, Url};
   use htsget_storage::local::LocalStorage;
-  #[cfg(feature = "c4gh-experimental")]
+  #[cfg(feature = "experimental")]
   use {
     crate::from_storage::tests::with_local_storage_c4gh,
     htsget_storage::c4gh::storage::C4GHStorage, htsget_test::c4gh::get_decryption_keys,
@@ -397,7 +397,7 @@ pub(crate) mod tests {
     .await
   }
 
-  #[cfg(feature = "c4gh-experimental")]
+  #[cfg(feature = "experimental")]
   #[tokio::test]
   async fn search_all_c4gh() {
     with_local_storage_c4gh(|storage| async move {
@@ -413,7 +413,7 @@ pub(crate) mod tests {
     .await;
   }
 
-  #[cfg(feature = "c4gh-experimental")]
+  #[cfg(feature = "experimental")]
   #[tokio::test]
   async fn search_all_range_c4gh() {
     with_local_storage_c4gh(|storage| async move {
diff --git a/htsget-storage/Cargo.toml b/htsget-storage/Cargo.toml
@@ -25,7 +25,7 @@ url-storage = [
     "htsget-config/url-storage",
     "htsget-test/url-storage"
 ]
-c4gh-experimental = ["dep:crypt4gh", "dep:bincode", "htsget-config/c4gh-experimental", "htsget-test/c4gh-experimental"]
+experimental = ["dep:crypt4gh", "dep:bincode", "htsget-config/experimental", "htsget-test/experimental"]
 default = []
 
 [dependencies]
diff --git a/htsget-storage/README.md b/htsget-storage/README.md
@@ -49,7 +49,7 @@ and [url] modules implement the `Storage` functionality.
 This crate has the following features:
 * `s3-storage`: used to enable `S3Storage` functionality.
 * `url-storage`: used to enable `UrlStorage` functionality.
-* `c4gh-experimental`: used to enable `C4GHStorage` functionality.
+* `experimental`: used to enable `C4GHStorage` functionality.
 
 [local]: src/local.rs
 [s3]: src/s3.rs
diff --git a/htsget-storage/src/lib.rs b/htsget-storage/src/lib.rs
@@ -25,7 +25,7 @@ use std::pin::Pin;
 use std::task::{Context, Poll};
 use tokio::io::{AsyncRead, ReadBuf};
 
-#[cfg(feature = "c4gh-experimental")]
+#[cfg(feature = "experimental")]
 use crate::c4gh::storage::C4GHStorage;
 use crate::error::Result;
 use crate::error::StorageError;
@@ -38,7 +38,7 @@ use crate::url::UrlStorage;
 use htsget_config::storage::object::ObjectType;
 use htsget_config::types::Scheme;
 
-#[cfg(feature = "c4gh-experimental")]
+#[cfg(feature = "experimental")]
 pub mod c4gh;
 pub mod error;
 pub mod local;
@@ -134,7 +134,7 @@ impl Storage {
     let storage = LocalStorage::new(config.local_path(), config.clone())?;
     match config.object_type() {
       ObjectType::Regular => Ok(Storage::new(storage)),
-      #[cfg(feature = "c4gh-experimental")]
+      #[cfg(feature = "experimental")]
       ObjectType::C4GH { keys } => Ok(Storage::new(C4GHStorage::new(
         keys.clone().into_inner(),
         storage,
diff --git a/htsget-test/Cargo.toml b/htsget-test/Cargo.toml
@@ -36,7 +36,7 @@ aws-mocks = [
 ]
 s3-storage = ["htsget-config?/s3-storage"]
 url-storage = ["htsget-config?/url-storage"]
-c4gh-experimental = ["dep:crypt4gh", "dep:htsget-config", "htsget-config/c4gh-experimental"]
+experimental = ["dep:crypt4gh", "dep:htsget-config", "htsget-config/experimental"]
 default = []
 
 [dependencies]
diff --git a/htsget-test/README.md b/htsget-test/README.md
@@ -40,7 +40,7 @@ This crate has the following features:
 * `aws-mocks`: used to enable AWS mocking for tests.
 * `s3-storage`: used to enable `S3Storage` functionality.
 * `url-storage`: used to enable `UrlStorage` functionality.
-* `c4gh-experimental`: used to enable `C4GHStorage` functionality.
+* `experimental`: used to enable `C4GHStorage` functionality.
 
 [dev-dependencies]: https://doc.rust-lang.org/cargo/reference/specifying-dependencies.html#development-dependencies
 
diff --git a/htsget-test/src/lib.rs b/htsget-test/src/lib.rs
