From ca1a0b3d6b5c4a98627f2779a019b4aa7d0df038 Mon Sep 17 00:00:00 2001
From: Wid-L-Hacker <nilekim@gmail.com>
Date: Fri, 6 Nov 2026 02:54:51 +0000
Subject: [PATCH] Check in the Rust crate manifest with a literal version

The crate's Cargo.toml was generated on every invocation by a
wrapper script that stamped the package version from the nearest
git tag. Check the manifest in directly, with the current release
version (0.10.0) as a literal, and call plain cargo at every call
site: CI, the CTest cargo_test, and the Dockerfile test stage
(which no longer needs the checkout's .git copied in just so the
wrapper could read the tag).

The crates.io smoke-test crate gets the same treatment: its
checked-in manifest pins the current published release exactly,
and the release smoke workflow rewrites that pin to the version
under test.

With the version a literal in the manifest, the committed
Cargo.lock's root entry agrees with it in every checkout, and a
release version bump is a deliberate manifest edit followed by a
lock refresh.
---
 .github/workflows/build.yml                    | 18 +++++++++---------
 .github/workflows/release-smoke.yml            |  6 +++---
 CMakeLists.txt                                 |  2 +-
 Dockerfile                                     |  6 +-----
 bindings/rust/.gitignore                       |  2 --
 bindings/rust/{Cargo.toml.in => Cargo.toml}    |  2 +-
 bindings/rust/cargo                            | 18 ------------------
 test/cargo_smoke_test/.gitignore               |  2 --
 .../{Cargo.toml.in => Cargo.toml}              |  2 +-
 test/cargo_smoke_test/cargo                    | 18 ------------------
 10 files changed, 16 insertions(+), 60 deletions(-)
 rename bindings/rust/{Cargo.toml.in => Cargo.toml} (96%)
 delete mode 100755 bindings/rust/cargo
 rename test/cargo_smoke_test/{Cargo.toml.in => Cargo.toml} (78%)
 delete mode 100755 test/cargo_smoke_test/cargo

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 617607f6..b70442fc 100644
--- a/.github/workflows/build.yml
+++ b/.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="$FLOOR_PATH"
@@ -198,8 +198,8 @@ jobs:
         mkdir -p bindings/rust/lib/${{ 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
+        cargo package --list --manifest-path bindings/rust/Cargo.toml | grep lib/${{ matrix.target }}/libgenomicsqlite.so
     - name: test rust crate (rusqlite ceiling)
       if: matrix.target == 'x86_64-linux-gnu'
       run: |
@@ -209,8 +209,8 @@ jobs:
         mkdir build/rust-ceiling
         tar -C bindings/rust --exclude=target -cf - . | tar -C build/rust-ceiling -xf -
         cd build/rust-ceiling
-        env LD_LIBRARY_PATH="$(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="$(pwd)/.." SQLITE_WEB_LOG=99 cargo test --release --locked
     - name: installed-package smoke test
       run: |
         python3 -m pip install -q setuptools wheel
@@ -296,8 +296,8 @@ jobs:
         set -e
         mkdir -p bindings/rust/lib/aarch64-darwin
         cp build/libgenomicsqlite.dylib bindings/rust/lib/aarch64-darwin/
-        SQLITE_WEB_LOG=99 bindings/rust/cargo test --release --locked
-        bindings/rust/cargo package --list | grep lib/aarch64-darwin/libgenomicsqlite.dylib
+        SQLITE_WEB_LOG=99 cargo test --release --locked --manifest-path bindings/rust/Cargo.toml
+        cargo package --list --manifest-path bindings/rust/Cargo.toml | grep lib/aarch64-darwin/libgenomicsqlite.dylib
     - name: installed-package smoke test
       run: |
         python3 -m pip install -q setuptools wheel
diff --git a/.github/workflows/release-smoke.yml b/.github/workflows/release-smoke.yml
index 37527291..5115b433 100644
--- a/.github/workflows/release-smoke.yml
+++ b/.github/workflows/release-smoke.yml
@@ -122,10 +122,10 @@ jobs:
           brew install sqlite
           echo "SQLITE3_LIB_DIR=$(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
+          sed -i -E 's/^genomicsqlite = .*/genomicsqlite = "=${{ steps.v.outputs.semver }}"/' \
+            test/cargo_smoke_test/Cargo.toml
           grep '^genomicsqlite' test/cargo_smoke_test/Cargo.toml
       - name: Build & run the smoke crate against crates.io
         working-directory: test/cargo_smoke_test
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 4df53c2e..45eb832c 100644
--- a/CMakeLists.txt
+++ b/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 ${CMAKE_CURRENT_SOURCE_DIR}/test)
 endif()
diff --git a/Dockerfile b/Dockerfile
index 853e3463..1f15c5c1 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -124,15 +124,11 @@ RUN mkdir -p /work/lib
 WORKDIR /work
 COPY --from=builder /usr/local/lib/libsqlite3.so.0 ./lib/
 RUN ln -s libsqlite3.so.0 lib/libsqlite3.so
-ADD ./.git ./.git
 ADD ./bindings/rust ./rust
 COPY --from=builder /work/GenomicSQLite/build/libgenomicsqlite.so ./libgenomicsqlite.so
 # plant the library in the crate's per-target directory for this build's CPU
 RUN mkdir -p ./rust/lib/$(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
diff --git a/bindings/rust/.gitignore b/bindings/rust/.gitignore
index 5041fd10..bec38e17 100644
--- a/bindings/rust/.gitignore
+++ b/bindings/rust/.gitignore
@@ -9,8 +9,6 @@ target/
 # 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
diff --git a/bindings/rust/Cargo.toml.in b/bindings/rust/Cargo.toml
similarity index 96%
rename from bindings/rust/Cargo.toml.in
rename to bindings/rust/Cargo.toml
index 15bc1670..d164af39 100644
--- a/bindings/rust/Cargo.toml.in
+++ b/bindings/rust/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "genomicsqlite"
-version = "{{GENOMICSQLITE_VERSION}}"
+version = "0.10.0"
 description = "Genomics Extension for SQLite"
 authors = ["Mike Lin <dna@mlin.net>"]
 edition = "2018"
diff --git a/bindings/rust/cargo b/bindings/rust/cargo
deleted file mode 100755
index e3227b60..00000000
--- a/bindings/rust/cargo
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/bin/bash
-# wrapper for cargo that generates Cargo.toml from Cargo.toml.in, filling in git revision as
-# crate version
-set -e
-cd `dirname $0`
-
-revision="$(git describe --tags --abbrev=0)"
-# -dirty only for changes other than the tracked Cargo.lock: builds rewrite
-# the lock's root-package version entry, and that must not feed back into
-# the version itself (which would rewrite the lock again on the next run).
-if git status --porcelain --untracked-files=no | grep -v 'Cargo.lock' | grep -q .; then
-    revision="${revision}-dirty"
-fi
-revision="${revision#v}"  # strip 'v' prefix
->&2 echo "$revision"
-
-sed "s/{{GENOMICSQLITE_VERSION}}/${revision}/" Cargo.toml.in > Cargo.toml
-cargo "$@"
diff --git a/test/cargo_smoke_test/.gitignore b/test/cargo_smoke_test/.gitignore
index 2d7878f6..4cfaae23 100644
--- a/test/cargo_smoke_test/.gitignore
+++ b/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.*
diff --git a/test/cargo_smoke_test/Cargo.toml.in b/test/cargo_smoke_test/Cargo.toml
similarity index 78%
rename from test/cargo_smoke_test/Cargo.toml.in
rename to test/cargo_smoke_test/Cargo.toml
index 6f36d5b6..885f98e8 100644
--- a/test/cargo_smoke_test/Cargo.toml.in
+++ b/test/cargo_smoke_test/Cargo.toml
@@ -5,6 +5,6 @@ authors = ["Mike Lin <dna@mlin.net>"]
 edition = "2018"
 
 [dependencies]
-genomicsqlite = "{{GENOMICSQLITE_VERSION}}"
+genomicsqlite = "=0.10.0"
 rusqlite = "^0.25"
 json = "^0"
diff --git a/test/cargo_smoke_test/cargo b/test/cargo_smoke_test/cargo
deleted file mode 100755
index e3227b60..00000000
--- a/test/cargo_smoke_test/cargo
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/bin/bash
-# wrapper for cargo that generates Cargo.toml from Cargo.toml.in, filling in git revision as
-# crate version
-set -e
-cd `dirname $0`
-
-revision="$(git describe --tags --abbrev=0)"
-# -dirty only for changes other than the tracked Cargo.lock: builds rewrite
-# the lock's root-package version entry, and that must not feed back into
-# the version itself (which would rewrite the lock again on the next run).
-if git status --porcelain --untracked-files=no | grep -v 'Cargo.lock' | grep -q .; then
-    revision="${revision}-dirty"
-fi
-revision="${revision#v}"  # strip 'v' prefix
->&2 echo "$revision"
-
-sed "s/{{GENOMICSQLITE_VERSION}}/${revision}/" Cargo.toml.in > Cargo.toml
-cargo "$@"