Bump rustix from 0.36.7 to 0.36.17

.cargo/config

@@ -1,2 +1,85 @@
-[alias]
-t = "test --bin traceback1 --test enclone_test -- --nocapture"
+[target.x86_64-unknown-linux-gnu]
+rustflags = [
+  "--codegen=link-args=-Wl,--compress-debug-sections=zlib",
+  "-C", "target-feature=+sse3,+ssse3,+sse4.1,+sse4.2,+popcnt",
+  "-D", "clippy::perf",
+  "-D", "clippy::style",
+  "-D", "clippy::suspicious",
+  "-A", "clippy::comparison_chain",
+  "-W", "future_incompatible",
+  "-W", "nonstandard_style",
+  "-W", "rust_2018_compatibility",
+  "-W", "rust_2021_compatibility",
+  "-W", "unused",
+  "-D", "clippy::enum_glob_use",
+  "-D", "clippy::needless_lifetimes",
+  "-D", "clippy::redundant_closure_for_method_calls",
+  "-D", "clippy::unused_io_amount",
+  "-D", "clippy::wildcard_imports",
+  "-D", "clippy::unnecessary_unwrap",
+  "-D", "clippy::uninlined_format_args",
+  "-W", "clippy::disallowed_names",
+  "-W", "clippy::enum_variant_names",
+  "-W", "clippy::large-enum-variant",
+  "-W", "clippy::missing_safety_doc",
+  "-A", "clippy::type_complexity",
+  "-A", "clippy::too_many_arguments",
+  "-W", "clippy::result_unit_err",
+]
+
+[target.x86_64-pc-windows-gnu]
+linker = "x86_64-w64-mingw32-gcc"
+rustflags = [
+  "-C", "target-feature=+sse3,+ssse3,+sse4.1,+sse4.2,+popcnt",
+  "-D", "clippy::perf",
+  "-D", "clippy::style",
+  "-D", "clippy::suspicious",
+  "-A", "clippy::comparison_chain",
+  "-W", "future_incompatible",
+  "-W", "nonstandard_style",
+  "-W", "rust_2018_compatibility",
+  "-W", "rust_2021_compatibility",
+  "-W", "unused",
+  "-D", "clippy::enum_glob_use",
+  "-D", "clippy::needless_lifetimes",
+  "-D", "clippy::redundant_closure_for_method_calls",
+  "-D", "clippy::unused_io_amount",
+  "-D", "clippy::wildcard_imports",
+  "-D", "clippy::unnecessary_unwrap",
+  "-D", "clippy::uninlined_format_args",
+  "-W", "clippy::disallowed_names",
+  "-W", "clippy::enum_variant_names",
+  "-W", "clippy::large-enum-variant",
+  "-W", "clippy::missing_safety_doc",
+  "-A", "clippy::type_complexity",
+  "-A", "clippy::too_many_arguments",
+  "-W", "clippy::result_unit_err",
+]
+
+[target.'cfg(target_arch = "x86_64")']
+rustflags = [
+  "-C", "target-feature=+sse3,+ssse3,+sse4.1,+sse4.2,+popcnt",
+  "-D", "clippy::perf",
+  "-D", "clippy::style",
+  "-D", "clippy::suspicious",
+  "-A", "clippy::comparison_chain",
+  "-W", "future_incompatible",
+  "-W", "nonstandard_style",
+  "-W", "rust_2018_compatibility",
+  "-W", "rust_2021_compatibility",
+  "-W", "unused",
+  "-D", "clippy::enum_glob_use",
+  "-D", "clippy::needless_lifetimes",
+  "-D", "clippy::redundant_closure_for_method_calls",
+  "-D", "clippy::unused_io_amount",
+  "-D", "clippy::wildcard_imports",
+  "-D", "clippy::unnecessary_unwrap",
+  "-D", "clippy::uninlined_format_args",
+  "-W", "clippy::disallowed_names",
+  "-W", "clippy::enum_variant_names",
+  "-W", "clippy::large-enum-variant",
+  "-W", "clippy::missing_safety_doc",
+  "-A", "clippy::type_complexity",
+  "-A", "clippy::too_many_arguments",
+  "-W", "clippy::result_unit_err",
+]

.github/dependabot.yml

@@ -0,0 +1,41 @@
+version: 2
+
+updates:
+- package-ecosystem: cargo
+  directory: "/"
+  schedule:
+    interval: weekly
+  open-pull-requests-limit: 10
+  reviewers:
+  - sreenathkrishnan
+  ignore:
+    # ignore crates from rust-toolbox repo other than vdj_ann.
+    # They all get updated together anyway.
+    - dependency-name: align_tools
+    - dependency-name: amino
+    - dependency-name: ansi_escape
+    - dependency-name: binary_vec_io
+    - dependency-name: dna
+    - dependency-name: equiv
+    - dependency-name: exons
+    - dependency-name: expr_tools
+    - dependency-name: fasta_tools
+    - dependency-name: graph_simple
+    - dependency-name: hyperbase
+    - dependency-name: io_utils
+    - dependency-name: kmer_lookup
+    - dependency-name: load_feature_bc
+    - dependency-name: mirror_sparse_matrix
+    - dependency-name: perf_stats
+    - dependency-name: pretty_trace
+    - dependency-name: stats_utils
+    - dependency-name: stirling_numbers
+    - dependency-name: string_utils
+    - dependency-name: tables
+    - dependency-name: vdj_ann_ref
+    - dependency-name: vdj_types
+    - dependency-name: vector_utils
+- package-ecosystem: "github-actions"
+  directory: "/"
+  schedule:
+    interval: weekly

.github/workflows/test.yaml

@@ -4,57 +4,137 @@ on:
   pull_request:
   push:
     branches:
-      - master
+      - main
 
 env:
+  DENY_VERSION: "0.13.9"
+  RUST_VERSION: "1.71.0"
   CARGO_INCREMENTAL: 0
 
+permissions:
+  contents: read
+  # Write permissions are required in order to produce annotations.
+  checks: write
+
 jobs:
   test-mac:
     # This job runs on MacOS Catalina
     runs-on: macos-latest
     steps:
-      - name: rust version
-        run: rustup default 1.43.0
-      - name: add rustfmt
-        run: rustup component add rustfmt
-      - name: install cargo-license
-        run: cargo install cargo-license
+
+      - name: Install protoc
+        run: brew install protobuf
+      - name: Install Rust
+        uses: dtolnay/rust-toolchain@master
+        with:
+          toolchain: ${{ env.RUST_VERSION }}
+          components: rustfmt
+
+      # check out master
+
       - name: Checkout enclone master
         uses: actions/checkout@master
-      - name: Check Rust formatting
-        run: cargo fmt -- --check
+
+      - uses: Swatinem/rust-cache@v2
+
+      # start the real work
+
+      - name: Remove the Cargo target directory
+        if: github.ref == 'refs/heads/master'
+        run: cargo clean
       - name: build-enclone
-        run: cargo build --release
-      - name: download test data
-        run: git clone --depth=1 https://github.com/10XGenomics/enclone-data.git
+        run: cargo build
       - name: unit tests
-        run: cd enclone_main; cargo test --release --features basic -- --nocapture
+        run: cargo test -- --nocapture
 
   test-linux:
     # This job runs on Linux
     runs-on: ubuntu-latest
     steps:
-      - name: rust version
-        run: rustup default 1.43.0
-      - name: add rustfmt
-        run: rustup component add rustfmt
-      - name: install cargo-license
-        run: cargo install cargo-license
-      - name: Checkout enclone master
-        uses: actions/checkout@master
+      - name: Install protoc
+        run: sudo apt-get install -y protobuf-compiler
+
+      - name: Install Rust
+        uses: dtolnay/rust-toolchain@master
+        with:
+          toolchain: ${{ env.RUST_VERSION }}
+          components: rustfmt, clippy
+
+      # check out
+
+      - name: Compute required fetch depth
+        id: fetch_depth
+        run: >
+          echo
+          "depth=$(("${{github.event.pull_request.commits}}" + 2))"
+          >> "$GITHUB_OUTPUT"
+      - uses: actions/checkout@v4
         with:
-          fetch-depth: 100
+          fetch-depth: ${{ steps.fetch_depth.outputs.depth }}
+
+      # set up caching
+
+      - uses: Swatinem/rust-cache@v2
+
+      # start the real work
+
       - name: Check for large files
         run: >
           git rev-list --objects ${{github.event.pull_request.base.sha}}..
           | git cat-file --batch-check='%(objectname) %(objecttype) %(objectsize) %(rest)'
-          | awk '$2 == "blob" && $3 >= 1000000 { print substr($1, 1, 7), $3, $4; fail=1 } END { exit fail }'
+          | awk '$2 == "blob" && $3 >= 1600000 { print substr($1, 1, 7), $3, $4; fail=1 } END { exit fail }'
+      - name: Remove the Cargo target directory
+        if: github.ref == 'refs/heads/master'
+        run: cargo clean
+      - name: Install cargo-deny
+        run: |
+          wget https://github.com/EmbarkStudios/cargo-deny/releases/download/${DENY_VERSION}/cargo-deny-${DENY_VERSION}-x86_64-unknown-linux-musl.tar.gz
+          tar -xvf cargo-deny-${DENY_VERSION}-x86_64-unknown-linux-musl.tar.gz
+          mkdir -p ~/bin/
+          cp cargo-deny-${DENY_VERSION}-x86_64-unknown-linux-musl/cargo-deny ~/bin/
+          rm -r cargo-deny-${DENY_VERSION}-x86_64-unknown-linux-musl*
+          echo "$HOME/bin" >> $GITHUB_PATH
       - name: Check Rust formatting
         run: cargo fmt -- --check
+      - name: Deny duplicate dependencies (lib/rust)
+        run: cargo deny --locked check
+      - name: Run clippy
+        uses: 10XGenomics/clippy-check@main
+        with:
+          # Github limits the number of annotations it will display on a PR for
+          # a given action, so we're going to disable (for now!) some of the
+          # noisier lints so that more important ones are more likely to be
+          # visible.
+          # NOTE: keep this list in sync with lib/rust/.cargo/config, or else
+          #       which is ignored when running in this mode but not when
+          #       running locally.
+          # TODO: re-enable the allowed lints at the end of this list.
+          args: |
+            --all-targets --locked --
+            -D clippy::perf
+            -D clippy::style
+            -D clippy::suspicious
+            -A clippy::comparison_chain
+            -W future_incompatible
+            -W nonstandard_style
+            -W rust_2018_compatibility
+            -W rust_2021_compatibility
+            -W unused
+            -D clippy::enum_glob_use
+            -D clippy::needless_lifetimes
+            -D clippy::redundant_closure_for_method_calls
+            -D clippy::unused_io_amount
+            -D clippy::wildcard_imports
+            -D clippy::unnecessary_unwrap
+            -D clippy::uninlined_format_args
+            -W clippy::disallowed_names
+            -W clippy::enum_variant_names
+            -W clippy::large-enum-variant
+            -W clippy::missing_safety_doc
+            -A clippy::type_complexity
+            -A clippy::too_many_arguments
+            -W clippy::result_unit_err
       - name: build-enclone
-        run: cargo build --release
-      - name: download test data
-        run: git clone --depth=1 https://github.com/10XGenomics/enclone-data.git
+        run: cargo build
       - name: unit tests
-        run: cd enclone_main; cargo test --release --features basic -- --nocapture
+        run: cargo test -- --nocapture