Move code

* move all suffix array code from personal repo to unipept repo * ignore untracked files rom submodule * run cargo fmt * filter away empty fa * run cargo fmt * update actions to checkout submodules * add extra tests * format test code * add back SA search tests (#22) * Add SA compression, fix some tests and refactor some code * bitarray compression * add coverage for bitarray and small README * document library * cargo formatting + better panic message in testing * add is_empty method for clippy * cargo formatting * function to compress data without having to store everything in memory * compressed integration + some major refactoring * dynamic resuired bits per value * update tests and documentation * update coverage config * fmt + clippy * format --all * improve testing * formatting * fix bitarray tests * some additional smaller tests * update codecov config * ignore main files when covering code * test failing reader and writer in test module * small cleanup * small cleanup * some debug information * allow preliminary enzyme numbers (x.x.x.nx) * encode functional annotations on load * more debug info + some movement of SA code --------- Co-authored-by: tibvdm <[email protected]> Co-authored-by: Tibo Vande Moortele <[email protected]>
unipept · Jun 7, 2024 · 76dda83 · 76dda83
1 parent ca12b8b
commit 76dda83
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Showing 41 changed files with 5,131 additions and 206 deletions.
diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
@@ -9,6 +9,8 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
+        with:
+          submodules: recursive
 
       - name: Install minimal nightly toolchain
         uses: actions-rs/toolchain@v1
@@ -17,6 +19,33 @@ jobs:
           toolchain: nightly
           override: true
 
+
+
+      - name: Run cargo test (bitarray)
+        uses: actions-rs/cargo@v1
+        with:
+          command: test
+          args: --all-features --no-fail-fast -p bitarray
+        env:
+          CARGO_INCREMENTAL: 0
+          RUSTFLAGS: '-Zprofile -Ccodegen-units=1 -Cinline-threshold=0 -Clink-dead-code -Coverflow-checks=off -Cpanic=abort -Zpanic_abort_tests'
+          RUSTDOCFLAGS: '-Zprofile -Ccodegen-units=1 -Cinline-threshold=0 -Clink-dead-code -Coverflow-checks=off -Cpanic=abort -Zpanic_abort_tests'
+
+      - name: Gather coverage information (bitarray)
+        id: coverage-bitarray
+        uses: actions-rs/[email protected]
+
+      - name: Upload coverage reports to Codecov (bitarray)
+        uses: codecov/[email protected]
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: ${{ steps.coverage-bitarray.outputs.report }}
+          flags: bitarray
+          verbose: true
+          fail_ci_if_error: true
+
+
+
       - name: Run cargo test (fa-compression)
         uses: actions-rs/cargo@v1
         with:
@@ -40,6 +69,82 @@ jobs:
           verbose: true
           fail_ci_if_error: true
 
+
+
+      - name: Run cargo test (sa-builder)
+        uses: actions-rs/cargo@v1
+        with:
+          command: test
+          args: --all-features --no-fail-fast -p sa-builder
+        env:
+          CARGO_INCREMENTAL: 0
+          RUSTFLAGS: '-Zprofile -Ccodegen-units=1 -Cinline-threshold=0 -Clink-dead-code -Coverflow-checks=off -Cpanic=abort -Zpanic_abort_tests'
+          RUSTDOCFLAGS: '-Zprofile -Ccodegen-units=1 -Cinline-threshold=0 -Clink-dead-code -Coverflow-checks=off -Cpanic=abort -Zpanic_abort_tests'
+
+      - name: Gather coverage information (sa-builder)
+        id: coverage-sa-builder
+        uses: actions-rs/[email protected]
+
+      - name: Upload coverage reports to Codecov (sa-builder)
+        uses: codecov/[email protected]
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: ${{ steps.coverage-sa-builder.outputs.report }}
+          flags: sa-builder
+          verbose: true
+          fail_ci_if_error: true
+
+
+
+      - name: Run cargo test (sa-compression)
+        uses: actions-rs/cargo@v1
+        with:
+          command: test
+          args: --all-features --no-fail-fast -p sa-compression
+        env:
+          CARGO_INCREMENTAL: 0
+          RUSTFLAGS: '-Zprofile -Ccodegen-units=1 -Cinline-threshold=0 -Clink-dead-code -Coverflow-checks=off -Cpanic=abort -Zpanic_abort_tests'
+          RUSTDOCFLAGS: '-Zprofile -Ccodegen-units=1 -Cinline-threshold=0 -Clink-dead-code -Coverflow-checks=off -Cpanic=abort -Zpanic_abort_tests'
+
+      - name: Gather coverage information (sa-compression)
+        id: coverage-sa-compression
+        uses: actions-rs/[email protected]
+
+      - name: Upload coverage reports to Codecov (sa-compression)
+        uses: codecov/[email protected]
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: ${{ steps.coverage-sa-compression.outputs.report }}
+          flags: sa-compression
+          verbose: true
+          fail_ci_if_error: true
+
+
+
+      - name: Run cargo test (sa-index)
+        uses: actions-rs/cargo@v1
+        with:
+          command: test
+          args: --all-features --no-fail-fast -p sa-index
+        env:
+          CARGO_INCREMENTAL: 0
+          RUSTFLAGS: '-Zprofile -Ccodegen-units=1 -Cinline-threshold=0 -Clink-dead-code -Coverflow-checks=off -Cpanic=abort -Zpanic_abort_tests'
+          RUSTDOCFLAGS: '-Zprofile -Ccodegen-units=1 -Cinline-threshold=0 -Clink-dead-code -Coverflow-checks=off -Cpanic=abort -Zpanic_abort_tests'
+
+      - name: Gather coverage information (sa-index)
+        id: coverage-sa-index
+        uses: actions-rs/[email protected]
+
+      - name: Upload coverage reports to Codecov (sa-index)
+        uses: codecov/[email protected]
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: ${{ steps.coverage-sa-index.outputs.report }}
+          flags: sa-index
+          verbose: true
+          fail_ci_if_error: true
+
+
       - name: Run cargo test (sa-mappings)
         uses: actions-rs/cargo@v1
         with:
@@ -61,4 +166,4 @@ jobs:
           file: ${{ steps.coverage-sa-mappings.outputs.report }}
           flags: sa-mappings
           verbose: true
-          fail_ci_if_error: true
+          fail_ci_if_error: true
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
@@ -9,6 +9,8 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
+        with:
+          submodules: recursive
 
       - name: Install minimal nightly toolchain
         uses: actions-rs/toolchain@v1

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -9,6 +9,8 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
+        with:
+          submodules: recursive
 
       - name: Install minimal nightly toolchain
         uses: actions-rs/toolchain@v1

diff --git a/.gitignore b/.gitignore
@@ -1 +1,4 @@
 target/
+data/
+
+.DS_Store
diff --git a/.gitmodules b/.gitmodules
@@ -0,0 +1,4 @@
+[submodule "libsais64-rs/libsais"]
+	path = libsais64-rs/libsais
+	url = https://github.com/IlyaGrebnov/libsais.git
+	ignore = untracked