Merge pull request #373 from 10XGenomics/macklin/merge-rust-toolbox

Merge rust-toolbox into this repo.

.cargo/config

@@ -1,7 +1,5 @@
-[target.x86_64-unknown-linux-gnu]
+[build]
 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",
@@ -24,62 +22,23 @@ rustflags = [
   "-W", "clippy::missing_safety_doc",
   "-A", "clippy::type_complexity",
   "-A", "clippy::too_many_arguments",
+  "-A", "clippy::needless_range_loop",
   "-W", "clippy::result_unit_err",
 ]
 
+[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",
+]
+
 [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

@@ -8,33 +8,6 @@ updates:
   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:

.github/workflows/test.yaml

@@ -94,46 +94,18 @@ jobs:
           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 that rustflags from config are still valid so Clippy runs the right lints
+        run: >
+          [ -z ${RUSTFLAGS+value} ] &&
+          [ -z ${CARGO_ENCODED_RUSTFLAGS+value} ]
       - 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
+          args: --all-targets --locked --
       - name: build-enclone
         run: cargo build
       - name: unit tests