Implement GitHub action that automatically builds sa binaries

.devcontainer/devcontainer.json

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+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/anaconda
+{
+  "name": "Unipept Index",
+  "image": "mcr.microsoft.com/devcontainers/base:ubuntu",
+
+  // Features to add to the dev container. More info: https://containers.dev/features.
+  "features": {
+    "ghcr.io/devcontainers/features/rust:1": {}
+  },
+
+  // Use 'forwardPorts' to make a list of ports inside the container available locally.
+  // "forwardPorts": [],
+
+  // Use 'postCreateCommand' to run commands after the container is created.
+  // "postCreateCommand": "",
+
+  // Configure tool-specific properties.
+  // "customizations": {},
+
+  // Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+  // "remoteUser": "root"
+}

.github/workflows/build_index.yml

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+name: Build index binaries
+
+on:
+  schedule:
+    # Run on the first day of every month at midnight UTC
+    - cron: '0 0 1 * *'
+  push:
+    branches:
+      - feature/build_index_action
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      # Check out the most recent version of the repository with submodules
+      - name: Check out repository
+        uses: actions/checkout@v3
+        with:
+          submodules: recursive
+
+      # Set up Rust toolchain
+      - name: Set up Rust
+        uses: dtolnay/rust-toolchain@stable
+
+      # Compile Rust code
+      - name: Compile Rust code
+        run: cargo build --release
+
+      # Create a directory "build"
+      - name: Create build directory
+        run: mkdir -p build/input
+
+      # Download the file "suffix-array.zip" from the most recent release of "unipept-database"
+      - name: Download suffix-array.zip
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          latest_release_url=$(curl -s https://api.github.com/repos/unipept/unipept-database/releases/latest | grep "browser_download_url.*suffix-array.zip" | cut -d '"' -f 4)
+          release_date=$(curl -s https://api.github.com/repos/unipept/unipept-database/releases/latest | grep '"published_at":' | cut -d '"' -f 4 | cut -d'T' -f1)
+          release_date_formatted=$(date -d $release_date "+%Y-%m-%d")
+          SP_VERSION="SP_$release_date_formatted"
+          echo "SP_VERSION=$SP_VERSION" >> $GITHUB_ENV
+          curl -L -o build/suffix-array.zip $latest_release_url
+
+      # Extract the contents of this zip into a folder "build/input"
+      - name: Extract zip contents
+        run: unzip build/suffix-array.zip -d build/input
+
+      # Make a directory with the SP_VERSION and process files
+      - name: Process files
+        run: |
+          mkdir -p build/$SP_VERSION
+          lz4 -d build/input/uniprot_entries.tsv.lz4 | cut -f2,4,7,8 > build/$SP_VERSION/proteins.tsv
+          lz4 -d build/input/taxons.tsv.lz4 > build/$SP_VERSION/taxons.tsv
+
+      # Step 8: Run the sa-builder command
+      - name: Run sa-builder
+        run: |
+          prefix="build/$SP_VERSION"
+          ./target/release/sa-builder -d "$prefix/proteins.tsv" -t "$prefix/taxons.tsv" -o "$prefix/sa_sparse3_compressed.bin" -s 3 -a lib-div-suf-sort -c
+          
+      # Zip the contents of the build/$SP_VERSION directory
+      - name: Zip build contents
+        run: |
+          prefix="build/$SP_VERSION"
+          zip -r "build/$SP_VERSION.zip" "$prefix"
+
+      # Create a GitHub release and upload the zip file
+      - name: Upload or Update Release
+        id: upload_or_update_release
+        uses: softprops/action-gh-release@v1
+        with:
+          files: build/$SP_VERSION.zip
+          tag_name: index-${{ env.SP_VERSION }}
+          name: Index ${{ env.SP_VERSION }}
+          commitish: ${{ github.sha }}
+          draft: false
+          prerelease: false
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

unipept-index.iml

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+<?xml version="1.0" encoding="UTF-8"?>
+<module type="WEB_MODULE" version="4">
+  <component name="NewModuleRootManager" inherit-compiler-output="true">
+    <exclude-output />
+    <content url="file://$MODULE_DIR$" />
+    <orderEntry type="inheritedJdk" />
+    <orderEntry type="sourceFolder" forTests="false" />
+  </component>
+</module>