Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add Devcontainer and GitHub Action #28

Merged
merged 14 commits into from
Sep 19, 2024
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension


Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
23 changes: 23 additions & 0 deletions .devcontainer/devcontainer.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,23 @@
// 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"
}
82 changes: 82 additions & 0 deletions .github/workflows/build_index.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,82 @@
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 the output folder from the 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" -o "$prefix/sa_sparse3_compressed.bin" -s 3 -a lib-div-suf-sort -c

# Zip the contents of the build/$SP_VERSION directory
- name: Zip build contents
run: |
cd "build/$SP_VERSION" && zip "index_$SP_VERSION.zip" "proteins.tsv" "taxons.tsv" "sa_sparse3_compressed.bin"

# 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/${{ env.SP_VERSION }}/index_${{ env.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 }}
8 changes: 8 additions & 0 deletions .idea/.gitignore

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

6 changes: 6 additions & 0 deletions .idea/misc.xml

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

8 changes: 8 additions & 0 deletions .idea/modules.xml

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

6 changes: 6 additions & 0 deletions .idea/vcs.xml

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

9 changes: 9 additions & 0 deletions unipept-index.iml
Original file line number Diff line number Diff line change
@@ -0,0 +1,9 @@
<?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>
Loading