@rhydb/rhydb-wasm 0.14.1 → 0.14.2

package/README.md

@@ -1,16 +1,16 @@
-# SILO WASM
+# RhyDB WASM
 
-This directory builds a browser-usable version of SILO using WebAssembly (WASM). It uses Emscripten to compile the C++ sources to a `.wasm` binary and generates a small JavaScript loader that lets browser code call selected C++ functions.
+This directory builds a browser-usable version of RhyDB using WebAssembly (WASM). It uses Emscripten to compile the C++ sources to a `.wasm` binary and generates a small JavaScript loader that lets browser code call selected C++ functions.
 
-`CMakeLists.txt` collects SILO core sources, excludes the CLI, HTTP API, tests, and benchmark code, and links the dependencies needed for preprocessing and SaneQL query execution. `src/rhydb_wasm.cpp` is the boundary between JavaScript and C++.
+`CMakeLists.txt` collects RhyDB core sources, excludes the CLI, HTTP API, tests, and benchmark code, and links the dependencies needed for preprocessing and SaneQL query execution. `src/rhydb_wasm.cpp` is the boundary between JavaScript and C++.
 
 ## What It Exposes
 
 The generated JavaScript module exports these embind functions:
 
-- `preprocess(preprocessingConfigPath)`: reads a SILO preprocessing config from Emscripten's virtual filesystem and returns a database handle.
-- `save(handle, outputDirectory)`: writes the in-memory database as SILO's normal processed-state files into the virtual filesystem.
-- `load(stateDirectory)`: loads a saved SILO processed state from the virtual filesystem and returns a database handle.
+- `preprocess(preprocessingConfigPath)`: reads a RhyDB preprocessing config from Emscripten's virtual filesystem and returns a database handle.
+- `save(handle, outputDirectory)`: writes the in-memory database as RhyDB's normal processed-state files into the virtual filesystem.
+- `load(stateDirectory)`: loads a saved RhyDB processed state from the virtual filesystem and returns a database handle.
 - `query(handle, saneqlQuery)`: runs SaneQL and returns the result as NDJSON.
 - `info(handle)`: returns database information as JSON.
 - `dispose(handle)`: releases a database handle.
@@ -19,15 +19,15 @@ The module also exposes Emscripten's `FS` runtime API. Browser code uses `FS` to
 
 The WASM build supports raw and `.zst` preprocessing inputs. The native `.xz` input path is not included in the WASM target.
 
-Browser queries use a smaller materialization cutoff than native SILO to keep intermediate batches within browser memory limits, especially when projecting full nucleotide sequences.
+Browser queries use a smaller materialization cutoff than native RhyDB to keep intermediate batches within browser memory limits, especially when projecting full nucleotide sequences.
 
 ## Artifacts
 
-Building the WASM target creates these files relative to the SILO repository root:
+Building the WASM target creates these files relative to the RhyDB repository root:
 
 - `wasm/dist/rhydb_wasm.js`: ES module loader generated by Emscripten. Import this from browser code.
 - `wasm/dist/rhydb_wasm.d.ts`: Autogenerated type declarations.
-- `wasm/dist/rhydb_wasm.wasm`: compiled SILO C++ code and linked dependencies.
+- `wasm/dist/rhydb_wasm.wasm`: compiled RhyDB C++ code and linked dependencies.
 
 All files must be served by the web app. The JavaScript loader fetches the `.wasm` file at runtime.
 
@@ -42,21 +42,21 @@ npm install @rhydb/rhydb-wasm
 The package is an ES module. Import the loader as a default import:
 
 ```js
-import createRhyDbModule from "@rhydb/rhydb-wasm";
+import createRhydbModule from "@rhydb/rhydb-wasm";
 
-const silo = await createRhyDbModule();
+const rhydb = await createRhydbModule();
 ```
 
-The `.wasm` file ships alongside `rhydb_wasm.js` and must be resolvable by your bundler so the loader can fetch it at runtime. The package version matches the SILO release version.
+The `.wasm` file ships alongside `rhydb_wasm.js` and must be resolvable by your bundler so the loader can fetch it at runtime. The package version matches the RhyDB release version.
 
-The current build uses pthreads, so the page serving the module must be cross-origin isolated. Pthreads are the POSIX thread API that Emscripten maps to Web Workers, and SILO uses them because its dependencies and query execution are built around threaded native code. Serve it over HTTP with these headers:
+The current build uses pthreads, so the page serving the module must be cross-origin isolated. Pthreads are the POSIX thread API that Emscripten maps to Web Workers, and RhyDB uses them because its dependencies and query execution are built around threaded native code. Serve it over HTTP with these headers:
 
 ```text
 Cross-Origin-Opener-Policy: same-origin
 Cross-Origin-Embedder-Policy: require-corp
 ```
 
-For a local example server, run this from the SILO repository root:
+For a local example server, run this from the RhyDB repository root:
 
 ```sh
 python3 - <<'PY'
@@ -89,7 +89,7 @@ Prerequisites:
 - uv
 - a native C++ compiler for Conan build tools
 
-From the SILO repository root, build the WASM artifacts:
+From the RhyDB repository root, build the WASM artifacts:
 
 ```sh
 make wasm
@@ -120,7 +120,7 @@ Import and initialize the module:
 ```js
 import createRhydbModule from "./rhydb_wasm.js";
 
-const silo = await createRhydbModule();
+const rhydb = await createRhydbModule();
 ```
 
 This assumes `rhydb_wasm.js` and `rhydb_wasm.wasm` are served from the same URL directory. If a web app serves them from different locations, pass Emscripten's `locateFile` option to tell the loader where to fetch `rhydb_wasm.wasm`.
@@ -132,26 +132,26 @@ function mkdirp(path) {
   let current = "";
   for (const part of path.split("/").filter(Boolean)) {
     current += `/${part}`;
-    if (!silo.FS.analyzePath(current).exists) {
-      silo.FS.mkdir(current);
+    if (!rhydb.FS.analyzePath(current).exists) {
+      rhydb.FS.mkdir(current);
     }
   }
 }
 
 mkdirp("/input");
-silo.FS.writeFile("/input/preprocessing_config.yaml", preprocessingConfigBytes);
-silo.FS.writeFile("/input/database_config.yaml", databaseConfigBytes);
-silo.FS.writeFile("/input/reference_genomes.json", referenceGenomeBytes);
-silo.FS.writeFile("/input/sequences.ndjson.zst", ndjsonBytes);
+rhydb.FS.writeFile("/input/preprocessing_config.yaml", preprocessingConfigBytes);
+rhydb.FS.writeFile("/input/database_config.yaml", databaseConfigBytes);
+rhydb.FS.writeFile("/input/reference_genomes.json", referenceGenomeBytes);
+rhydb.FS.writeFile("/input/sequences.ndjson.zst", ndjsonBytes);
 
-silo.FS.chdir("/input");
-const handle = silo.preprocess("preprocessing_config.yaml");
+rhydb.FS.chdir("/input");
+const handle = rhydb.preprocess("preprocessing_config.yaml");
 ```
 
 Query an in-memory database:
 
 ```js
-const ndjson = silo.query(handle, "default.groupBy({count:=count()})");
+const ndjson = rhydb.query(handle, "default.groupBy({count:=count()})");
 console.log(ndjson);
 ```
 
@@ -159,9 +159,9 @@ Save a processed state and read the files back:
 
 ```js
 mkdirp("/state");
-silo.save(handle, "/state");
+rhydb.save(handle, "/state");
 
-for (const entry of silo.FS.readdir("/state")) {
+for (const entry of rhydb.FS.readdir("/state")) {
   if (entry !== "." && entry !== "..") {
     console.log(entry);
   }
@@ -172,16 +172,16 @@ Load an existing processed state:
 
 ```js
 mkdirp("/loaded-state");
-// Write the saved SILO state files under /loaded-state first.
-const loadedHandle = silo.load("/loaded-state");
-console.log(silo.info(loadedHandle));
+// Write the saved RhyDB state files under /loaded-state first.
+const loadedHandle = rhydb.load("/loaded-state");
+console.log(rhydb.info(loadedHandle));
 ```
 
 Release memory when a database is no longer needed:
 
 ```js
-silo.dispose(handle);
-silo.dispose(loadedHandle);
+rhydb.dispose(handle);
+rhydb.dispose(loadedHandle);
 ```
 
 For a complete browser example that uploads input files, downloads a saved state, uploads that state again, and runs a query, see `example/`.