Merge pull request #35 from COMBINE-lab/main

merge main back into dev

.github/workflows/release.yml

@@ -1,10 +1,12 @@
+# This file was autogenerated by dist: https://opensource.axo.dev/cargo-dist/
+#
 # Copyright 2022-2024, axodotdev
 # SPDX-License-Identifier: MIT or Apache-2.0
 #
 # CI that:
 #
 # * checks for a Git Tag that looks like a release
-# * builds artifacts with cargo-dist (archives, installers, hashes)
+# * builds artifacts with dist (archives, installers, hashes)
 # * uploads those artifacts to temporary workflow zip
 # * on success, uploads the artifacts to a GitHub Release
 #
@@ -22,10 +24,10 @@ permissions:
 # must be a Cargo-style SemVer Version (must have at least major.minor.patch).
 #
 # If PACKAGE_NAME is specified, then the announcement will be for that
-# package (erroring out if it doesn't have the given version or isn't cargo-dist-able).
+# package (erroring out if it doesn't have the given version or isn't dist-able).
 #
 # If PACKAGE_NAME isn't specified, then the announcement will be for all
-# (cargo-dist-able) packages in the workspace with that version (this mode is
+# (dist-able) packages in the workspace with that version (this mode is
 # intended for workspaces with only one dist-able package, or with all dist-able
 # packages versioned/released in lockstep).
 #
@@ -43,7 +45,7 @@ on:
       - '**[0-9]+.[0-9]+.[0-9]+*'
 
 jobs:
-  # Run 'cargo dist plan' (or host) to determine what tasks we need to do
+  # Run 'dist plan' (or host) to determine what tasks we need to do
   plan:
     runs-on: "ubuntu-20.04"
     outputs:
@@ -57,25 +59,25 @@ jobs:
       - uses: actions/checkout@v4
         with:
           submodules: recursive
-      - name: Install cargo-dist
+      - name: Install dist
         # we specify bash to get pipefail; it guards against the `curl` command
         # failing. otherwise `sh` won't catch that `curl` returned non-0
         shell: bash
-        run: "curl --proto '=https' --tlsv1.2 -LsSf https://github.com/axodotdev/cargo-dist/releases/download/v0.18.0/cargo-dist-installer.sh | sh"
-      - name: Cache cargo-dist
+        run: "curl --proto '=https' --tlsv1.2 -LsSf https://github.com/axodotdev/cargo-dist/releases/download/v0.24.1/cargo-dist-installer.sh | sh"
+      - name: Cache dist
         uses: actions/upload-artifact@v4
         with:
           name: cargo-dist-cache
-          path: ~/.cargo/bin/cargo-dist
+          path: ~/.cargo/bin/dist
       # sure would be cool if github gave us proper conditionals...
       # so here's a doubly-nested ternary-via-truthiness to try to provide the best possible
       # functionality based on whether this is a pull_request, and whether it's from a fork.
       # (PRs run on the *source* but secrets are usually on the *target* -- that's *good*
       # but also really annoying to build CI around when it needs secrets to work right.)
       - id: plan
         run: |
-          cargo dist ${{ (!github.event.pull_request && format('host --steps=create --tag={0}', github.ref_name)) || 'plan' }} --output-format=json > plan-dist-manifest.json
-          echo "cargo dist ran successfully"
+          dist ${{ (!github.event.pull_request && format('host --steps=create --tag={0}', github.ref_name)) || 'plan' }} --output-format=json > plan-dist-manifest.json
+          echo "dist ran successfully"
           cat plan-dist-manifest.json
           echo "manifest=$(jq -c "." plan-dist-manifest.json)" >> "$GITHUB_OUTPUT"
       - name: "Upload dist-manifest.json"
@@ -93,12 +95,12 @@ jobs:
     if: ${{ fromJson(needs.plan.outputs.val).ci.github.artifacts_matrix.include != null && (needs.plan.outputs.publishing == 'true' || fromJson(needs.plan.outputs.val).ci.github.pr_run_mode == 'upload') }}
     strategy:
       fail-fast: false
-      # Target platforms/runners are computed by cargo-dist in create-release.
+      # Target platforms/runners are computed by dist in create-release.
       # Each member of the matrix has the following arguments:
       #
       # - runner: the github runner
-      # - dist-args: cli flags to pass to cargo dist
-      # - install-dist: expression to run to install cargo-dist on the runner
+      # - dist-args: cli flags to pass to dist
+      # - install-dist: expression to run to install dist on the runner
       #
       # Typically there will be:
       # - 1 "global" task that builds universal installers
@@ -115,7 +117,7 @@ jobs:
       - uses: actions/checkout@v4
         with:
           submodules: recursive
-      - name: Install cargo-dist
+      - name: Install dist
         run: ${{ matrix.install_dist }}
       # Get the dist-manifest
       - name: Fetch local artifacts
@@ -130,8 +132,8 @@ jobs:
       - name: Build artifacts
         run: |
           # Actually do builds and make zips and whatnot
-          cargo dist build ${{ needs.plan.outputs.tag-flag }} --print=linkage --output-format=json ${{ matrix.dist_args }} > dist-manifest.json
-          echo "cargo dist ran successfully"
+          dist build ${{ needs.plan.outputs.tag-flag }} --print=linkage --output-format=json ${{ matrix.dist_args }} > dist-manifest.json
+          echo "dist ran successfully"
       - id: cargo-dist
         name: Post-build
         # We force bash here just because github makes it really hard to get values up
@@ -166,12 +168,12 @@ jobs:
       - uses: actions/checkout@v4
         with:
           submodules: recursive
-      - name: Install cached cargo-dist
+      - name: Install cached dist
         uses: actions/download-artifact@v4
         with:
           name: cargo-dist-cache
           path: ~/.cargo/bin/
-      - run: chmod +x ~/.cargo/bin/cargo-dist
+      - run: chmod +x ~/.cargo/bin/dist
       # Get all the local artifacts for the global tasks to use (for e.g. checksums)
       - name: Fetch local artifacts
         uses: actions/download-artifact@v4
@@ -182,8 +184,8 @@ jobs:
       - id: cargo-dist
         shell: bash
         run: |
-          cargo dist build ${{ needs.plan.outputs.tag-flag }} --output-format=json "--artifacts=global" > dist-manifest.json
-          echo "cargo dist ran successfully"
+          dist build ${{ needs.plan.outputs.tag-flag }} --output-format=json "--artifacts=global" > dist-manifest.json
+          echo "dist ran successfully"
 
           # Parse out what we just built and upload it to scratch storage
           echo "paths<<EOF" >> "$GITHUB_OUTPUT"
@@ -215,12 +217,12 @@ jobs:
       - uses: actions/checkout@v4
         with:
           submodules: recursive
-      - name: Install cached cargo-dist
+      - name: Install cached dist
         uses: actions/download-artifact@v4
         with:
           name: cargo-dist-cache
           path: ~/.cargo/bin/
-      - run: chmod +x ~/.cargo/bin/cargo-dist
+      - run: chmod +x ~/.cargo/bin/dist
       # Fetch artifacts from scratch-storage
       - name: Fetch artifacts
         uses: actions/download-artifact@v4
@@ -231,7 +233,7 @@ jobs:
       - id: host
         shell: bash
         run: |
-          cargo dist host ${{ needs.plan.outputs.tag-flag }} --steps=upload --steps=release --output-format=json > dist-manifest.json
+          dist host ${{ needs.plan.outputs.tag-flag }} --steps=upload --steps=release --output-format=json > dist-manifest.json
           echo "artifacts uploaded and released successfully"
           cat dist-manifest.json
           echo "manifest=$(jq -c "." dist-manifest.json)" >> "$GITHUB_OUTPUT"

Cargo.toml

@@ -33,28 +33,26 @@ opt-level = 3
 [profile.dist]
 inherits = "release"
 
-# Config for 'cargo dist'
+# Config for 'dist'
 [workspace.metadata.dist]
-# The preferred cargo-dist version to use in CI (Cargo.toml SemVer syntax)
-cargo-dist-version = "0.18.0"
+# The preferred dist version to use in CI (Cargo.toml SemVer syntax)
+cargo-dist-version = "0.24.1"
 # The installers to generate for each app
 installers = ["shell"]
 # Target platforms to build apps for (Rust target-triple syntax)
-targets = [
-  "aarch64-apple-darwin",
-  "x86_64-apple-darwin",
-  "x86_64-unknown-linux-gnu",
-]
+targets = ["aarch64-apple-darwin", "x86_64-apple-darwin", "x86_64-unknown-linux-gnu"]
 # The archive format to use for non-windows builds (defaults .tar.xz)
 unix-archive = ".tar.gz"
 # CI backends to support
 ci = "github"
-# Publish jobs to run in CI
+# Which actions to run on pull requests
 pr-run-mode = "plan"
 # Whether to install an updater program
 install-updater = true
 # Generate and dist a source tarball
 source-tarball = false
+# Path that installers should place binaries in
+install-path = "CARGO_HOME"
 ## since this is cross-language and 
 ## we are not including C++ debug 
 ## symbols, this currently doesn't work 

README.md

@@ -17,6 +17,7 @@ $ ulimit -n 2048
 
 before running `piscem`.
 
+- **The pre-compiled executables (including those installed via bioconda)** require that the underlying processor support [the BMI2 instruction set](https://en.wikipedia.org/wiki/X86_Bit_manipulation_instruction_set). If you are running on a CPU from ~2012 or earlier, these instructions may not be available and the pre-compiled executable may not work. In that case, you should compile from source using the `NO_BMI2` environement variable (i.e. `NO_BMI2=TRUE cargo build --release`).
 
 Building
 ========

build.rs

@@ -87,11 +87,36 @@ fn main() {
         dst_piscem_cpp.join("lib64").display()
     );
 
+    let profile = std::env::var("PROFILE").unwrap();
+    match profile.as_str() {
+        "debug" => {
+            println!(
+                "cargo:rustc-link-search=native={}",
+                dst_piscem_cpp.join("Debug").join("lib64").display()
+            );
+            println!(
+                "cargo:rustc-link-search=native={}",
+                dst_piscem_cpp.join("Debug").join("lib").display()
+            );
+        }
+        "release" => {
+            println!(
+                "cargo:rustc-link-search=native={}",
+                dst_piscem_cpp.join("Release").join("lib64").display()
+            );
+            println!(
+                "cargo:rustc-link-search=native={}",
+                dst_piscem_cpp.join("Release").join("lib").display()
+            );
+        }
+        _ => (),
+    }
+
     println!("cargo:rustc-link-lib=static=kmc_core");
     //println!("cargo:rustc-link-lib=static=pesc_static");
     //println!("cargo:rustc-link-lib=static=build_static");
     println!("cargo:rustc-link-lib=static=sshash_static");
-    println!("cargo:rustc-link-lib=static=z");
+    println!("cargo:rustc-link-lib=static=zcf");
     println!("cargo:rustc-link-lib=static=bz2");
 
     #[cfg(target_os = "linux")]