chore: cleanup configs, use mold linker on linux

.cargo/config → .cargo/config.toml

@@ -1,3 +1,22 @@
+[future-incompat-report]
+frequency = 'always'
+
+[profile.dev]
+codegen-units = 32
+incremental = true
+lto = "off"
+
+[profile.release]
+codegen-units = 1
+incremental = false
+lto = "fat"
+opt-level = 3
+panic = "abort"
+strip = true
+
+[profile.test]
+debug = true
+
 [target.aarch64-unknown-linux-gnu]
 linker = "aarch64-linux-gnu-ld"
 ar = "aarch64-linux-gnu-ar"

docker-dev

@@ -43,7 +43,6 @@ export MAKES="make --no-print-directory"
 export NICE="nice -14 ionice -c2 -n3"
 export TIME="/usr/bin/time --quiet -f \"Cmd : %C\nTime: %E\nMem : %M KB\n\""
 
-export RUSTFLAGS="-A dead_code -A unused"
 export RUST_BACKTRACE="full"
 export COLORBT_SHOW_HIDDEN="0"
 export RUST_LOG="warn"
@@ -492,7 +491,6 @@ if [ "${RUN}" != "1" ] && [ "${DOCKER_PS_RESULT}" == "${DOCKER_CONTAINER_NAME}"
     --env="USER=${USER}" \
     --env="GROUP=${GROUP}" \
     --env="PS1=\${USER}@\${HOST}" \
-    --env="RUSTFLAGS=${RUSTFLAGS}" \
     --env="RUST_BACKTRACE=${RUST_BACKTRACE}" \
     --env="COLORBT_SHOW_HIDDEN=${COLORBT_SHOW_HIDDEN}" \
     --env="RUST_LOG=${RUST_LOG}" \
@@ -518,7 +516,6 @@ else
     --env="USER=${USER}" \
     --env="GROUP=${GROUP}" \
     --env="PS1=\${USER}@\${HOST}" \
-    --env="RUSTFLAGS=${RUSTFLAGS}" \
     --env="RUST_BACKTRACE=${RUST_BACKTRACE}" \
     --env="COLORBT_SHOW_HIDDEN=${COLORBT_SHOW_HIDDEN}" \
     --env="RUST_LOG=${RUST_LOG}" \

docker-dev.dockerfile

@@ -1,11 +1,12 @@
 # Freeze base image version to
 # ubuntu:20.04 (pushed 2022-03-18T05:48:59.785294Z)
 # https://hub.docker.com/layers/ubuntu/library/ubuntu/20.04/images/sha256-dcc176d1ab45d154b767be03c703a35fe0df16cfb1cc7ea5dd3b6f9af99b6718
-FROM ubuntu@sha256:dcc176d1ab45d154b767be03c703a35fe0df16cfb1cc7ea5dd3b6f9af99b6718 as dev
+FROM ubuntu@sha256:dcc176d1ab45d154b767be03c703a35fe0df16cfb1cc7ea5dd3b6f9af99b6718 as base
 
 SHELL ["bash", "-c"]
 
 ARG CLANG_VERSION="13"
+ARG MOLD_VERSION="1.1.1"
 ARG DASEL_VERSION="1.22.1"
 ARG WATCHEXEC_VERSION="1.17.1"
 ARG NODEMON_VERSION="2.0.15"
@@ -47,11 +48,21 @@ RUN set -euxo pipefail >/dev/null \
   clang-tools-${CLANG_VERSION} \
   lld-${CLANG_VERSION} \
   lldb-${CLANG_VERSION} \
+  llvm-${CLANG_VERSION} \
+  llvm-${CLANG_VERSION}-dev \
+  llvm-${CLANG_VERSION}-linker-tools \
+  llvm-${CLANG_VERSION}-tools \
 >/dev/null \
 && rm -rf /var/lib/apt/lists/* \
 && apt-get clean autoclean >/dev/null \
 && apt-get autoremove --yes >/dev/null
 
+# Install mold linker (https://github.com/rui314/mold)
+RUN set -euxo pipefail >/dev/null \
+&& cd /tmp \
+&& curl -fsSL "https://github.com/rui314/mold/releases/download/v${MOLD_VERSION}/mold-${MOLD_VERSION}-x86_64-linux.tar.gz" | \
+     tar -xz --strip-components=1 -C /usr
+
 
 ARG USER=user
 ARG GROUP=user
@@ -68,20 +79,22 @@ ENV CARGO_HOME="${HOME}/.cargo"
 ENV CARGO_INSTALL_ROOT="${HOME}/.cargo/install"
 ENV RUSTUP_HOME="${HOME}/.rustup"
 ENV NODE_DIR="/opt/node"
-ENV PATH="${NODE_DIR}/bin:${HOME}/.local/bin:${HOME}/.cargo/bin:${HOME}/.cargo/install/bin:${PATH}"
+ENV PATH="/usr/lib/llvm-13/bin:${NODE_DIR}/bin:${HOME}/.local/bin:${HOME}/.cargo/bin:${HOME}/.cargo/install/bin:${PATH}"
 
+# Install dasel, a tool to query TOML files
 RUN set -euxo pipefail >/dev/null \
 && curl -fsSL "https://github.com/TomWright/dasel/releases/download/v${DASEL_VERSION}/dasel_linux_amd64" -o "/usr/bin/dasel" \
 && chmod +x "/usr/bin/dasel" \
 && dasel --version
 
+# Install watchexec - file watcher
 RUN set -euxo pipefail >/dev/null \
 && curl -sSL "https://github.com/watchexec/watchexec/releases/download/cli-v${WATCHEXEC_VERSION}/watchexec-${WATCHEXEC_VERSION}-x86_64-unknown-linux-musl.tar.xz" | tar -C "/usr/bin/" -xJ --strip-components=1 "watchexec-1.17.1-x86_64-unknown-linux-musl/watchexec" \
 && chmod +x "/usr/bin/watchexec" \
 && watchexec --version
 
+# Install Node.js
 COPY .nvmrc /
-
 RUN set -eux >dev/null \
 && mkdir -p "${NODE_DIR}" \
 && cd "${NODE_DIR}" \
@@ -90,9 +103,6 @@ RUN set -eux >dev/null \
 && npm install -g nodemon@${NODEMON_VERSION} yarn@${YARN_VERSION} >/dev/null \
 && npm config set scripts-prepend-node-path auto
 
-
-COPY rust-toolchain.toml "${HOME}/rust-toolchain.toml"
-
 # Make a user and group
 RUN set -euxo pipefail >/dev/null \
 && \
@@ -119,9 +129,11 @@ RUN set -euxo pipefail >/dev/null \
 && touch ${HOME}/.hushlogin \
 && chown -R ${UID}:${GID} "${HOME}"
 
+
 USER ${USER}
 
 # Install rustup and toolchain from rust-toolchain.toml
+COPY rust-toolchain.toml "${HOME}/rust-toolchain.toml"
 RUN set -euxo pipefail >/dev/null \
 && cd "${HOME}" \
 && RUST_TOOLCHAIN=$(dasel select -p toml -s ".toolchain.channel" -f "${HOME}/rust-toolchain.toml") \
@@ -172,15 +184,32 @@ USER ${USER}
 WORKDIR ${HOME}/src
 
 
-# Cross-compilation for Linux x86_64 with gnu-libc
+
+# Native compilation for Linux x86_64 with gnu-libc
+FROM base as dev
+
+ENV CC_x86_64-unknown-linux-gnu=clang
+ENV CXX_x86_64-unknown-linux-gnu=clang++
+ENV RUSTFLAGS="-C linker=clang -C link-arg=-fuse-ld=mold"
+
+# Cross-compilation for Linux x86_64 with gnu-libc.
+# Same as native, but convenient to have for mass cross-compilation.
 FROM dev as cross-x86_64-unknown-linux-gnu
 
+ENV CC_x86_64-unknown-linux-gnu=clang
+ENV CXX_x86_64-unknown-linux-gnu=clang++
+ENV RUSTFLAGS="-C linker=clang -C link-arg=-fuse-ld=mold"
+
+
+
 # Cross-compilation for Linux x86_64 with libmusl
-FROM dev as cross-x86_64-unknown-linux-musl
+FROM base as cross-x86_64-unknown-linux-musl
+
+ENV RUSTFLAGS="-C linker=clang -C link-arg=-fuse-ld=mold"
 
 
 # Cross-compilation for Linux ARM64
-FROM dev as cross-aarch64-unknown-linux-gnu
+FROM base as cross-aarch64-unknown-linux-gnu
 
 USER 0
 SHELL ["bash", "-c"]
@@ -204,8 +233,9 @@ ENV CXX_aarch64_unknown_linux_gnu=aarch64-linux-gnu-g++
 USER ${USER}
 
 
+
 # Cross-compilation for Windows x86_64
-FROM dev as cross-x86_64-pc-windows-gnu
+FROM base as cross-x86_64-pc-windows-gnu
 
 USER 0
 SHELL ["bash", "-c"]
@@ -223,8 +253,9 @@ RUN set -euxo pipefail >/dev/null \
 USER ${USER}
 
 
+
 # Builds osxcross for Mac cross-compiation
-FROM dev as osxcross
+FROM base as osxcross
 
 SHELL ["bash", "-c"]
 
@@ -236,15 +267,12 @@ RUN set -euxo pipefail >/dev/null \
 && apt-get install -qq --no-install-recommends --yes \
   bash \
   bzip2 \
-  clang \
-  clang \
   cmake \
   cpio \
   gzip \
   libbz2-dev \
   libssl-dev \
   libxml2-dev \
-  llvm-dev \
   make \
   patch \
   sed \
@@ -285,6 +313,7 @@ RUN set -euxo pipefail >/dev/null \
 && UNATTENDED=1 TARGET_DIR=${OSXCROSS_INSTALL_DIR} OSX_VERSION_MIN=${OSX_VERSION_MIN} ./build.sh
 
 
+
 # Cross-compilation for macOS x86_64
 FROM osxcross as cross-x86_64-apple-darwin
 
@@ -293,6 +322,7 @@ ENV CC_x86_64-apple-darwin=x86_64-apple-darwin20.2-clang
 ENV CXX_x86_64-apple-darwin=x86_64-apple-darwin20.2-clang++
 
 
+
 # Cross-compilation for macOS ARM64
 FROM osxcross as cross-aarch64-apple-darwin
 

packages_rs/nextclade-web/Cargo.toml

@@ -9,8 +9,6 @@ publish = false
 [lib]
 crate-type = ["cdylib", "rlib"]
 
-[features]
-
 [dependencies]
 console_error_panic_hook = "0.1.7"
 log = "0.4.14"
@@ -23,8 +21,3 @@ wee_alloc = "0.4.5"
 
 [dev-dependencies]
 wasm-bindgen-test = "0.3.29"
-
-[profile.release]
-codegen-units = 1
-lto = "fat"
-opt-level = "s"

packages_rs/nextclade/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "nextclade"
-description = "Alignment, mutation calling, phylogenetic placement, clade assignment and quality control checks for viral genetic sequences. Library."
+description = "Alignment, mutation calling, phylogenetic placement, clade assignment and quality control checks for viral genetic sequences"
 version = "2.0.0"
 documentation = "https://docs.nextstrain.org/projects/nextclade/en/stable/"
 homepage = "https://clades.nextstrain.org/"
@@ -72,12 +72,3 @@ non-wasm = [
   "rstest",
   "rstest_reuse"
 ]
-
-
-[profile.test]
-debug = true
-
-[profile.release]
-codegen-units = 1
-lto = "fat"
-panic = "abort"