Make the sourmash crate library-only (#812)

* fix test data paths
* split draff and smrs out of sourmash
* depend only on primal_check
* move sourmash crate into src/core
* add README for rust crate
* update main README

.github/workflows/rust.yml

@@ -180,7 +180,7 @@ jobs:
           args: -- -D warnings
 
   wasm-pack:
-    name: Check if wasm-pack builds a valid package
+    name: Check if wasm-pack builds a valid package for the sourmash crate
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@master
@@ -193,7 +193,7 @@ jobs:
           command: install
           args: --force wasm-pack
       - name: run wasm-pack
-        run: wasm-pack build
+        run: wasm-pack build src/core -d ../../pkg
 
   wasm32-wasi:
     name: Run tests under wasm32-wasi
@@ -240,11 +240,11 @@ jobs:
           toolchain: stable
           override: true
 
-      - name: Make sure we can publish the crate
+      - name: Make sure we can publish the sourmash crate
         uses: actions-rs/cargo@v1
         with:
           command: publish
-          args: --dry-run
+          args: --dry-run --manifest-path src/core/Cargo.toml
 
   minimum_rust_version:
     runs-on: ubuntu-latest

Cargo.toml

@@ -1,86 +1,5 @@
-[package]
-name = "sourmash"
-version = "0.3.0"
-authors = ["Luiz Irber <luiz.irber@gmail.com>"]
-description = "MinHash sketches for genomic data"
-repository = "https://github.com/luizirber/sourmash-rust"
-keywords = ["minhash", "bioinformatics"]
-categories = ["science", "algorithms", "data-structures"]
-license = "BSD-3-Clause"
-edition = "2018"
-autoexamples = false
-autobins = false
-
-[lib]
-name = "sourmash"
-crate-type = ["cdylib", "rlib"]
-bench = false
-
-[profile.release]
-lto=true
-
-[features]
-from-finch = ["finch"]
-
 [workspace]
-
-#[build-dependencies]
-#cbindgen = "~0.6.7"
-
-[dependencies]
-byteorder = "1.3.2"
-cfg-if = "0.1.10"
-clap = { version = "2.33.0", features = ["yaml"] }
-env_logger = "0.7.1"
-exitfailure = "0.5.1"
-failure = "0.1.6"
-failure_derive = "0.1.6"
-finch = { version = "0.3.0", optional = true }
-fixedbitset = "0.2.0"
-log = "0.4.8"
-md5 = "0.7.0"
-murmurhash3 = "0.0.5"
-once_cell = "1.2.0"
-serde = "1.0.103"
-serde_derive = "1.0.103"
-serde_json = "1.0.44"
-#ukhs = { git = "https://github.com/luizirber/ukhs", branch = "feature/alternative_backends", features = ["boomphf_mphf"], default-features = false}
-primal = "0.2.3"
-#pdatastructs = { git = "https://github.com/luizirber/pdatastructs.rs", branch = "succinct_wasm" }
-itertools = "0.8.2"
-typed-builder = "0.4.0"
-csv = "1.1.1"
-tempfile = "3.1.0"
-
-[dependencies.needletail]
-version = "0.3.2"
-default-features = false
-#features = ["compression"]
-
-[target.'cfg(all(target_arch = "wasm32", target_vendor="unknown"))'.dependencies.wasm-bindgen]
-version = "0.2.55"
-features = ["serde-serialize"]
-
-[target.'cfg(not(all(target_arch = "wasm32", target_vendor="unknown")))'.dependencies.niffler]
-version = "1.0"
-default-features = false
-
-[target.'cfg(not(target_arch = "wasm32"))'.dev-dependencies]
-proptest = "0.9.4"
-
-[dev-dependencies]
-criterion = "0.3.0"
-rand = "0.7.2"
-tempfile = "3.1.0"
-assert_matches = "1.3.0"
-assert_cmd = "0.12.0"
-predicates = "1.0.2"
-
-[[bench]]
-name = "index"
-harness = false
-
-[[bin]]
-name = "smrs"
-path = "src/bin/smrs.rs"
-bench = false
+members = [
+  "src/core",
+]
+default-members = ["src/core"]

Makefile

@@ -27,9 +27,14 @@ test: all
 doc: .PHONY
 	cd doc && make html
 
-include/sourmash.h: src/lib.rs src/ffi/minhash.rs src/ffi/signature.rs src/ffi/nodegraph.rs src/errors.rs
+include/sourmash.h: src/core/src/lib.rs \
+                    src/core/src/ffi/minhash.rs \
+                    src/core/src/ffi/signature.rs \
+                    src/core/src/ffi/nodegraph.rs \
+                    src/core/src/errors.rs
 	rustup override set nightly
-	RUST_BACKTRACE=1 cbindgen --clean -c cbindgen.toml -o $@
+	cd src/core && \
+	RUST_BACKTRACE=1 cbindgen -c cbindgen.toml -o ../../$@
 	rustup override set stable
 
 coverage: all
@@ -49,7 +54,7 @@ last-tag:
 	git fetch -p -q; git tag -l | sort -V | tail -1
 
 wasm:
-	wasm-pack build
+	wasm-pack build src/core -d ../../pkg
 
 wasi:
 	cargo wasi build

README.md

@@ -9,10 +9,6 @@
 [![DOI](http://joss.theoj.org/papers/10.21105/joss.00027/status.svg)](http://joss.theoj.org/papers/10.21105/joss.00027)
 <a href="https://github.com/dib-lab/sourmash/blob/master/LICENSE"><img alt="License: 3-Clause BSD" src="https://img.shields.io/badge/License-BSD%203--Clause-blue.svg"></a>
 
-🦀
-[![](http://meritbadge.herokuapp.com/sourmash)](https://crates.io/crates/sourmash)
-[![Rust API Documentation on docs.rs](https://docs.rs/sourmash/badge.svg)](https://docs.rs/sourmash)
-
 ---
 
 Compute MinHash signatures for nucleotide (DNA/RNA) and protein sequences.
@@ -45,7 +41,7 @@ We recommend using bioconda to install sourmash:
 ```
 conda install -c conda-forge -c bioconda sourmash
 ```
-This will install the latest stable version of sourmash 2.
+This will install the latest stable version of sourmash 3.
 
 You can also use pip to install sourmash:
 
@@ -95,7 +91,10 @@ After installation, `sourmash` is the main command-line entry point;
 run it with `python -m sourmash`, or do `pip install -e /path/to/repo` to
 do a developer install in a virtual environment.
 
-The `sourmash/` directory contains the library code.
+The `sourmash/` directory contains the Python library and command-line interface code.
+
+The `src/core/` directory contains the Rust library implementing core
+functionality.
 
 Tests require py.test and can be run with `make test`.
 
@@ -104,4 +103,4 @@ Please see [the developer notes](doc/developer.md) for more information.
 ----
 
 CTB
-Dec 2018
+Jan 2020