Rust: check in Cargo.toml with a literal version

.github/workflows/build.yml

@@ -32,8 +32,8 @@ jobs:
     - name: rust lint
       run: |
         cd bindings/rust
-        ./cargo check --no-default-features --locked
-        ./cargo fmt -- --check
+        cargo check --no-default-features --locked
+        cargo fmt -- --check
 
   test:
     runs-on: ubuntu-24.04
@@ -109,7 +109,7 @@ jobs:
         mkdir -p bindings/rust/lib/x86_64-linux-gnu
         cp build/libgenomicsqlite.so bindings/rust/lib/x86_64-linux-gnu/
         ln -sf libsqlite3.so.0 build/libsqlite3.so
-        env LD_LIBRARY_PATH="$(pwd)/build" LIBRARY_PATH="$(pwd)/build" SQLITE_WEB_LOG=99 bindings/rust/cargo test --release --locked
+        env LD_LIBRARY_PATH="$(pwd)/build" LIBRARY_PATH="$(pwd)/build" SQLITE_WEB_LOG=99 cargo test --release --locked --manifest-path bindings/rust/Cargo.toml
     - name: test
       run: |
         export PATH="$FLOOR_PATH"
@@ -198,8 +198,12 @@ jobs:
         mkdir -p bindings/rust/lib/${{ matrix.target }}
         cp build/libgenomicsqlite.so bindings/rust/lib/${{ matrix.target }}/
         ln -sf libsqlite3.so.0 build/libsqlite3.so  # linker name, scoped to build/ like the Dockerfile rust stage
-        env LD_LIBRARY_PATH="$(pwd)/build" LIBRARY_PATH="$(pwd)/build" SQLITE_WEB_LOG=99 bindings/rust/cargo test --release --locked
-        bindings/rust/cargo package --list | grep lib/${{ matrix.target }}/libgenomicsqlite.so
+        env LD_LIBRARY_PATH="$(pwd)/build" LIBRARY_PATH="$(pwd)/build" SQLITE_WEB_LOG=99 cargo test --release --locked --manifest-path bindings/rust/Cargo.toml
+        # --allow-dirty: this crate is packaged from deliberately dirty trees — releases
+        # stamp the version in at publish time rather than committing it, and the library
+        # staged above is git-ignored but manifest-included, so cargo's version-control
+        # check would otherwise refuse.
+        cargo package --list --allow-dirty --manifest-path bindings/rust/Cargo.toml | grep lib/${{ matrix.target }}/libgenomicsqlite.so
     - name: test rust crate (rusqlite ceiling)
       if: matrix.target == 'x86_64-linux-gnu'
       run: |
@@ -209,8 +213,8 @@ jobs:
         mkdir build/rust-ceiling
         tar -C bindings/rust --exclude=target -cf - . | tar -C build/rust-ceiling -xf -
         cd build/rust-ceiling
-        env LD_LIBRARY_PATH="$(pwd)/.." LIBRARY_PATH="$(pwd)/.." ./cargo update -p rusqlite
-        env LD_LIBRARY_PATH="$(pwd)/.." LIBRARY_PATH="$(pwd)/.." SQLITE_WEB_LOG=99 ./cargo test --release --locked
+        env LD_LIBRARY_PATH="$(pwd)/.." LIBRARY_PATH="$(pwd)/.." cargo update -p rusqlite
+        env LD_LIBRARY_PATH="$(pwd)/.." LIBRARY_PATH="$(pwd)/.." SQLITE_WEB_LOG=99 cargo test --release --locked
     - name: installed-package smoke test
       run: |
         python3 -m pip install -q setuptools wheel
@@ -296,8 +300,12 @@ jobs:
         set -e
         mkdir -p bindings/rust/lib/aarch64-darwin
         cp build/libgenomicsqlite.dylib bindings/rust/lib/aarch64-darwin/
-        SQLITE_WEB_LOG=99 bindings/rust/cargo test --release --locked
-        bindings/rust/cargo package --list | grep lib/aarch64-darwin/libgenomicsqlite.dylib
+        SQLITE_WEB_LOG=99 cargo test --release --locked --manifest-path bindings/rust/Cargo.toml
+        # --allow-dirty: this crate is packaged from deliberately dirty trees — releases
+        # stamp the version in at publish time rather than committing it, and the library
+        # staged above is git-ignored but manifest-included, so cargo's version-control
+        # check would otherwise refuse.
+        cargo package --list --allow-dirty --manifest-path bindings/rust/Cargo.toml | grep lib/aarch64-darwin/libgenomicsqlite.dylib
     - name: installed-package smoke test
       run: |
         python3 -m pip install -q setuptools wheel

.github/workflows/release-smoke.yml

@@ -122,11 +122,11 @@ jobs:
           brew install sqlite
           echo "SQLITE3_LIB_DIR=$(brew --prefix sqlite)/lib" >> "$GITHUB_ENV"
           echo "SQLITE3_INCLUDE_DIR=$(brew --prefix sqlite)/include" >> "$GITHUB_ENV"
-      - name: Generate the smoke crate manifest for the release version
+      - name: Pin the smoke crate to the release version
         run: |
-          sed 's/{{GENOMICSQLITE_VERSION}}/=${{ steps.v.outputs.semver }}/' \
-            test/cargo_smoke_test/Cargo.toml.in > test/cargo_smoke_test/Cargo.toml
-          grep '^genomicsqlite' test/cargo_smoke_test/Cargo.toml
+          sed -i -E 's/^genomicsqlite = .*/genomicsqlite = "=${{ steps.v.outputs.semver }}"/' \
+            test/cargo_smoke_test/Cargo.toml
+          grep -Fx 'genomicsqlite = "=${{ steps.v.outputs.semver }}"' test/cargo_smoke_test/Cargo.toml
       - name: Build & run the smoke crate against crates.io
         working-directory: test/cargo_smoke_test
         run: |

CMakeLists.txt

@@ -74,6 +74,6 @@ if(CMAKE_PROJECT_NAME STREQUAL PROJECT_NAME)
     add_test(NAME extension_loading COMMAND python3 ${CMAKE_CURRENT_SOURCE_DIR}/test/extension_loading.py $<TARGET_FILE:genomicsqlite>)
     add_test(NAME capi_smoke_test COMMAND ${GENOMICSQLITE_TEST_ENV} ${CMAKE_BINARY_DIR}/test/capi_smoke_test)
     add_test(NAME JdbcTests COMMAND ${GENOMICSQLITE_TEST_ENV} mvn test -B -f ${CMAKE_CURRENT_SOURCE_DIR}/bindings/jdbc/genomicsqlite-jdbc/pom.xml)
-    add_test(NAME cargo_test COMMAND ${GENOMICSQLITE_TEST_ENV} ${CMAKE_CURRENT_SOURCE_DIR}/bindings/rust/cargo test --no-default-features)
+    add_test(NAME cargo_test COMMAND ${GENOMICSQLITE_TEST_ENV} cargo test --no-default-features --manifest-path ${CMAKE_CURRENT_SOURCE_DIR}/bindings/rust/Cargo.toml)
     add_test(NAME pytest COMMAND ${GENOMICSQLITE_TEST_ENV} python3 -m pytest -xv -n 4 --tb=short ${CMAKE_CURRENT_SOURCE_DIR}/test)
 endif()

Dockerfile

@@ -124,15 +124,11 @@ RUN mkdir -p /work/lib
 WORKDIR /work
 COPY --from=builder /usr/local/lib/libsqlite3.so.0 ./lib/
 RUN ln -s libsqlite3.so.0 lib/libsqlite3.so
-ADD ./.git ./.git
 ADD ./bindings/rust ./rust
 COPY --from=builder /work/GenomicSQLite/build/libgenomicsqlite.so ./libgenomicsqlite.so
 # plant the library in the crate's per-target directory for this build's CPU
 RUN mkdir -p ./rust/lib/$(uname -m)-linux-gnu && cp ./libgenomicsqlite.so ./rust/lib/$(uname -m)-linux-gnu/
-# git in the cargo wrapper must accept the context's .git even if the build
-# host checked it out under a different uid than root
-RUN git config --global --add safe.directory /work
-RUN SQLITE_WEB_LOG=99 LD_LIBRARY_PATH=$(pwd)/lib LIBRARY_PATH=$(pwd)/lib rust/cargo test --release
+RUN SQLITE_WEB_LOG=99 LD_LIBRARY_PATH=$(pwd)/lib LIBRARY_PATH=$(pwd)/lib cargo test --release --manifest-path ./rust/Cargo.toml
 
 ###################################################################################################
 # Run-up in ubuntu 20.04 (final stage: the default docker build target, and the

bindings/rust/.gitignore

@@ -3,14 +3,12 @@
 debug/
 target/
 
-# Cargo.lock is committed (2026-10-22): reproducible CI/dev builds for this
-# repo; cargo ignores it downstream. Refresh it as an early release step.
+# Cargo.lock pins dependencies for reproducible CI and development builds.
+# Downstream consumers resolve their own dependencies.
 
 # These are backup files generated by rustfmt
 **/*.rs.bk
 
-# Cargo.toml is generated from Cargo.toml.in by ./cargo
-Cargo.toml
 # planted prebuilt libraries, in per-target directories (release pipeline)
 lib/*/libgenomicsqlite.so
 lib/*/libgenomicsqlite.dylib

bindings/rust/Cargo.toml.in → bindings/rust/Cargo.toml

@@ -1,6 +1,10 @@
 [package]
 name = "genomicsqlite"
-version = "{{GENOMICSQLITE_VERSION}}"
+# Release versioning: the git tag is the version source of truth; this
+# 0.0.0 is a dummy. At publish time the tag's version is stamped into the
+# publish checkout (cargo set-version), never committed. Cargo.lock pins
+# dependency versions; its root entry follows the stamp there only.
+version = "0.0.0"
 description = "Genomics Extension for SQLite"
 authors = ["Mike Lin <dna@mlin.net>"]
 edition = "2018"

test/cargo_smoke_test/.gitignore

@@ -10,6 +10,4 @@ Cargo.lock
 # These are backup files generated by rustfmt
 **/*.rs.bk
 
-# Cargo.toml is generated from Cargo.toml.in by ./cargo
-Cargo.toml
 libgenomicsqlite.*

test/cargo_smoke_test/Cargo.toml.in → test/cargo_smoke_test/Cargo.toml

@@ -5,6 +5,7 @@ authors = ["Mike Lin <dna@mlin.net>"]
 edition = "2018"
 
 [dependencies]
-genomicsqlite = "{{GENOMICSQLITE_VERSION}}"
+# Dummy pin — the release-smoke workflow rewrites it to the version under test.
+genomicsqlite = "=0.0.0"
 rusqlite = "^0.25"
 json = "^0"