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dagou committed Sep 9, 2024
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233 changes: 96 additions & 137 deletions .github/workflows/release.yaml
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Original file line number Diff line number Diff line change
@@ -1,18 +1,13 @@
name: Release
on:
# schedule:
# - cron: '0 0 * * *' # midnight UTC

push:
tags:
- 'v[0-9]+.[0-9]+.[0-9]+'
## - release

env:
# BIN_NAME: clade
PROJECT_NAME: clade
REPO_NAME: eric9n/clade
# BREW_TAP: eric9n/homebrew-tap
REPO_NAME: ${{ github.repository }}
BREW_TAP: eric9n/homebrew-tap

jobs:
dist:
Expand All @@ -21,43 +16,26 @@ jobs:
name: Dist
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false # don't fail other jobs if one fails
fail-fast: false
matrix:
build: [x86_64-linux, x86_64-macos, x86_64-windows, aarch64-macos] # Added platforms
build: [x86_64-linux, x86_64-macos, x86_64-windows, aarch64-macos]
include:
- build: x86_64-linux
os: ubuntu-latest
rust: stable
target: x86_64-unknown-linux-gnu
cross: false
# - build: aarch64-linux
# os: ubuntu-latest
# rust: stable
# target: aarch64-unknown-linux-gnu
# cross: false
- build: x86_64-macos
os: macos-latest
rust: stable
target: x86_64-apple-darwin
cross: false
- build: x86_64-windows
os: windows-latest
rust: stable
target: x86_64-pc-windows-msvc
cross: false
- build: aarch64-macos
os: macos-latest
rust: stable
target: aarch64-apple-darwin
cross: false
# - build: x86_64-win-gnu
# os: windows-2019
# rust: stable-x86_64-gnu
# target: x86_64-pc-windows-gnu
# - build: win32-msvc
# os: windows-2019
# rust: stable
# target: i686-pc-windows-msvc

steps:
- name: Checkout sources
Expand Down Expand Up @@ -92,9 +70,9 @@ jobs:
run: |
mkdir dist
if [ "${{ matrix.os }}" = "windows-latest" ]; then
cp "target/${{ matrix.target }}/release/${{ matrix.target }}.exe" "dist/"
cp "target/${{ matrix.target }}/release/${{ env.PROJECT_NAME }}.exe" "dist/${{ env.PROJECT_NAME }}-${{ github.ref_name }}-${{ matrix.target }}.exe"
else
cp "target/${{ matrix.target }}/release/${{ matrix.target }}" "dist/"
cp "target/${{ matrix.target }}/release/${{ env.PROJECT_NAME }}" "dist/${{ env.PROJECT_NAME }}-${{ github.ref_name }}-${{ matrix.target }}"
fi
# Set up the GitHub CLI
Expand All @@ -119,118 +97,99 @@ jobs:

- name: Upload Release Asset
run: |
if [ "${{ matrix.os }}" = "windows-latest" ]; then
ASSET_NAME="${{ env.PROJECT_NAME }}-${{ github.ref_name }}-${{ matrix.target }}.exe"
else
ASSET_NAME="${{ env.PROJECT_NAME }}-${{ github.ref_name }}-${{ matrix.target }}"
fi
gh release upload ${{ github.ref_name }} \
"./dist/${{ matrix.target }}" \
"./dist/$ASSET_NAME" \
--clobber
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
shell: bash

# - uses: actions/[email protected]
# with:
# # name: bins-${{ matrix.build }}
# path: dist

# publish:
# name: Publish
# needs: [dist]
# runs-on: ubuntu-latest
# steps:
# - name: Checkout sources
# uses: actions/checkout@v2
# with:
# submodules: false

# - uses: actions/download-artifact@v4

# - name: Calculate tag name
# run: |
# name=dev
# if [[ $GITHUB_REF == refs/tags/v* ]]; then
# name=${GITHUB_REF:10}
# fi
# echo "val=$name" >> $GITHUB_OUTPUT
# echo "TAG=$name" >> $GITHUB_ENV
# id: tagname

# - name: Build archive
# shell: bash
# run: |
# set -ex

# rm -rf tmp
# mkdir tmp
# mkdir dist

# for dir in bins-* ; do
# platform=${dir#"bins-"}
# unset exe
# if [[ $platform =~ "windows" ]]; then
# exe=".exe"
# fi
# pkgname=$PROJECT_NAME-$TAG-$platform
# mkdir tmp/$pkgname
# # cp LICENSE README.md tmp/$pkgname
# mv bins-$platform/$BIN_NAME$exe tmp/$pkgname
# chmod +x tmp/$pkgname/$BIN_NAME$exe

# if [ "$exe" = "" ]; then
# tar cJf dist/$pkgname.tar.xz -C tmp $pkgname
# else
# (cd tmp && 7z a -r ../dist/$pkgname.zip $pkgname)
# fi
# done

# - name: Upload binaries to release
# uses: svenstaro/upload-release-action@v2
# with:
# repo_token: ${{ secrets.GITHUB_TOKEN }}
# file: dist/*
# file_glob: true
# tag: ${{ steps.tagname.outputs.val }}
# overwrite: true

# - name: Extract version
# id: extract-version
# run: |
# echo "tag-name=${GITHUB_REF#refs/tags/}" >> $GITHUB_OUTPUT

# # - uses: mislav/bump-homebrew-formula-action@v1
# # with:
# # formula-path: ${{env.PROJECT_NAME}}.rb
# # homebrew-tap: ${{ env.BREW_TAP }}
# # download-url: "https://github.com/${{ env.REPO_NAME }}/releases/download/${{ steps.extract-version.outputs.tag-name }}/${{env.PROJECT_NAME}}-${{ steps.extract-version.outputs.tag-name }}-x86_64-macos.tar.xz"
# # commit-message: updating formula for ${{ env.PROJECT_NAME }}
# # env:
# # COMMITTER_TOKEN: ${{ secrets.COMMITTER_TOKEN }}
# #
# # you can use this initial file in your homebrew-tap if you don't have an initial formula:
# # <projectname>.rb
# #
# # class <Projectname capitalized> < Formula
# # desc "A test formula"
# # homepage "http://www.example.com"
# # url "-----"
# # version "-----"
# # sha256 "-----"

# # def install
# # bin.install "<bin-name>"
# # end
# # end


# # Uncomment this section if you want to release your package to crates.io
# # Before publishing, make sure you have filled out the following fields:
# # license or license-file, description, homepage, documentation, repository, readme.
# # Read more: https://doc.rust-lang.org/cargo/reference/publishing.html

# # - name: Install ${{ matrix.rust }} toolchain
# # uses: actions-rs/toolchain@v1
# # with:
# # profile: minimal
# # toolchain: ${{ matrix.rust }}
# # target: ${{ matrix.target }}
# # - run: cargo publish --token ${CRATES_TOKEN}
# # env:
# # CRATES_TOKEN: ${{ secrets.CRATES_TOKEN }}
- name: Set macOS artifact name
if: matrix.os == 'macos-latest' && matrix.target == 'x86_64-apple-darwin'
run: echo "macos_artifact=${{ env.PROJECT_NAME }}-${{ github.ref_name }}-${{ matrix.target }}" >> $GITHUB_OUTPUT
id: artifact_name

update-formula:
needs: dist
runs-on: ubuntu-latest
steps:
- name: Checkout code
uses: actions/checkout@v2

- name: Extract version
id: extract-version
run: echo "tag-name=${GITHUB_REF#refs/tags/}" >> $GITHUB_OUTPUT

- name: Set environment variables
run: |
echo "PROJECT_NAME=${{ env.PROJECT_NAME }}" >> $GITHUB_ENV
echo "REPO_NAME=${{ env.REPO_NAME }}" >> $GITHUB_ENV
- name: Verify release assets
run: |
VERSION=${{ steps.extract-version.outputs.tag-name }}
REPO=${{ env.REPO_NAME }}
PROJECT=${{ env.PROJECT_NAME }}
X86_64_URL="https://github.com/${REPO}/releases/download/${VERSION}/${PROJECT}-${VERSION}-x86_64-apple-darwin"
AARCH64_URL="https://github.com/${REPO}/releases/download/${VERSION}/${PROJECT}-${VERSION}-aarch64-apple-darwin"
if curl --output /dev/null --silent --head --fail "$X86_64_URL"; then
echo "x86_64 binary exists"
else
echo "x86_64 binary does not exist"
exit 1
fi
if curl --output /dev/null --silent --head --fail "$AARCH64_URL"; then
echo "aarch64 binary exists"
else
echo "aarch64 binary does not exist"
exit 1
fi
- name: Update Homebrew formula
env:
COMMITTER_TOKEN: ${{ secrets.COMMITTER_TOKEN }}
run: |
VERSION=${{ steps.extract-version.outputs.tag-name }}
REPO=${{ env.REPO_NAME }}
PROJECT=${{ env.PROJECT_NAME }}
X86_64_URL="https://github.com/${REPO}/releases/download/${VERSION}/${PROJECT}-${VERSION}-x86_64-apple-darwin"
AARCH64_URL="https://github.com/${REPO}/releases/download/${VERSION}/${PROJECT}-${VERSION}-aarch64-apple-darwin"
# 下载并更新formula
git clone https://github.com/${{ env.BREW_TAP }}.git homebrew-tap
cd homebrew-tap
cat > Formula/${PROJECT}.rb <<EOL
class $(echo $PROJECT | perl -pe 's/(^|-)(\w)/\U$2/g') < Formula
desc "A tool for phylogenetic tree construction and pruning based on NCBI taxonomy data and GTDB (Genome Taxonomy Database) data."
homepage "https://github.com/${REPO}"
version "${VERSION}"
on_macos do
if Hardware::CPU.intel?
url "${X86_64_URL}"
sha256 "$(curl -sL ${X86_64_URL} | shasum -a 256 | cut -d ' ' -f 1)"
else
url "${AARCH64_URL}"
sha256 "$(curl -sL ${AARCH64_URL} | shasum -a 256 | cut -d ' ' -f 1)"
end
end
def install
bin.install "${PROJECT}"
end
end
EOL
git config user.name github-actions
git config user.email [email protected]
git add Formula/${PROJECT}.rb
git commit -m "Updating formula for ${PROJECT} to ${VERSION}"
git push https://${{ secrets.COMMITTER_TOKEN }}@github.com/${{ env.BREW_TAP }}.git main
70 changes: 47 additions & 23 deletions README.md
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@@ -1,14 +1,57 @@
# Clade

A tool for phylogenetic tree construction and pruning based on NCBI taxonomy data and GTDB data.
A tool for phylogenetic tree construction and pruning based on NCBI taxonomy data and GTDB (Genome Taxonomy Database) data.

## Features

1. Fetch and process NCBI taxonomy data
2. Fetch and process GTDB (Genome Taxonomy Database) data
2. Fetch and process GTDB data
3. Parse taxonomy data into efficient vector structures
4. Prune phylogenetic trees based on user input
5. Generate Newick format output from pruned trees
6. Support for both NCBI and GTDB data sources


## Usage

The Clade tool supports the following commands:

1. `update`: Update NCBI taxdump files
2. `gtdb`: GTDB related operations
- `list`: List all GTDB release versions
- `sync`: Download GTDB data files and parse metadata
- `download`: Download GTDB data files
- `parse`: Parse GTDB metadata and create database
- `newick`: Generate Newick format from GTDB database
3. `generate`: Generate and print taxonomy summary from taxdump files
4. `prune`: Prune the taxonomy tree and generate Newick format

### Examples

1. Update NCBI taxdump files:
```
clade -t /path/to/taxo update
```

2. List GTDB release versions:
```
clade -t /path/to/taxo gtdb list
```

3. Download and parse GTDB data:
```
clade -t /path/to/taxo gtdb sync --version 220.0
```

4. Generate Newick format from GTDB database:
```
clade -t /path/to/taxo gtdb newick --version 220.0 --domain bacteria --input-file input.txt --output output.newick
```

5. Prune taxonomy tree:
```
clade -t /path/to/taxo prune --taxids 9606,9605 --output pruned.newick
```

## Workflow

Expand All @@ -17,27 +60,8 @@ A tool for phylogenetic tree construction and pruning based on NCBI taxonomy dat
- Fetch the latest tree and taxonomy data from GTDB
2. **Data Processing**:
- Decompress the downloaded data
- Parse the taxonomy information into five synchronized vectors:
- taxid vector
- parentid vector
- name vector
- rank vector
- parent_distances vector
- Each vector has the same length, and their indices correspond to each other
- Parse the taxonomy information into efficient vector structures
3. **Tree Pruning and Newick Generation**:
- Accept user input in the form of:
- A list of taxids, or
- A list of taxonomic names
- Accept user input in the form of taxids or taxonomic names
- Prune the phylogenetic tree to include only the branches related to the input
- Generate a Newick format file representing the pruned phylogenetic tree

## Usage

The Clade tool supports the following commands:

1. `update`: Update taxdump files from NCBI
2. `generate`: Generate and print taxonomy summary from taxdump files
3. `prune`: Prune the taxonomy tree based on given taxids or names and generate a Newick format file
4. `gtdb`: Download and process GTDB data

Example usage:

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