Bump to v2.0.0

.github/workflows/ci.yml

@@ -11,32 +11,39 @@ on:
 jobs:
   CI:
     runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
     steps:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Setup Python ${{ matrix.python-version}}
-        uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
-
-      - name: Install Poetry
+      - name: Install Rye
         run: |
-          curl -sSL https://install.python-poetry.org | python3 -
-          echo "$HOME/.local/bin" >> $GITHUB_PATH
+          curl -sSf https://rye.astral.sh/get | RYE_INSTALL_OPTION="--yes" bash
+          echo "$HOME/.rye/shims" >> $GITHUB_PATH
 
-      - name: Install Dependencies
-        run: poetry install -n
+      - name: Setup Python ${{matrix.python-version}} & Dependencies
+        run: |
+          rye pin ${{ matrix.python-version }}
+          rye sync --update-all --all-features
 
       - name: Run ruff lint check
-        run: poetry run ruff check --diff
+        run: rye run ruff check --diff
 
       - name: Run ruff format check
-        run: poetry run ruff format --check --diff
+        run: rye run ruff format --check --diff
 
       - name: Run pytest
-        run: poetry run pytest
+        run: rye run pytest --junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=src | tee pytest-coverage.txt
+
+      - name: Pytest Coverage Comment
+        uses: MishaKav/pytest-coverage-comment@main
+        with:
+          pytest-coverage-path: pytest-coverage.txt
+          junitxml-path: pytest.xml
+        if: ${{ matrix.os=='ubuntu-latest' && matrix.python-version=='3.12' }}

.github/workflows/publish_to_pypi.yml

@@ -2,6 +2,7 @@ name: Publish to PyPI
 on:
   release:
     types: [released]
+  workflow_dispatch:
 
 jobs:
   publish_to_pypi:
@@ -14,18 +15,13 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Setup Python 3.12
-        uses: actions/setup-python@v5
-        with:
-          python-version: 3.12
-
-      - name: Install Poetry
+      - name: Install Rye
         run: |
-          curl -sSL https://install.python-poetry.org | python3 -
-          echo "$HOME/.local/bin" >> $GITHUB_PATH
+          curl -sSf https://rye.astral.sh/get | RYE_INSTALL_OPTION="--yes" bash
+          echo "$HOME/.rye/shims" >> $GITHUB_PATH
 
       - name: Build
-        run: poetry build
+        run: rye build
 
       - name: Publish
-        run: poetry publish -u $PYPI_USERNAME -p $PYPI_PASSWORD
+        run: rye publish -u $PYPI_USERNAME --token $PYPI_PASSWORD -y

.gitignore

@@ -1,6 +1,8 @@
 output/
 example/
 .vscode/
+notebooks/
+**.fna.gz
 
 # Byte-compiled / optimized / DLL files
 __pycache__/
@@ -60,7 +62,7 @@ coverage.xml
 *.pot
 
 # Django stuff:
-*.log
+# *.log
 local_settings.py
 db.sqlite3
 db.sqlite3-journal

.pre-commit-config.yaml

@@ -0,0 +1,13 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.11.6
+    hooks:
+      - id: ruff
+        name: ruff lint check
+        types_or: [python, pyi]
+        args: [--fix]
+      - id: ruff-format
+        name: ruff format check
+        types_or: [python, pyi]

README.md

@@ -20,7 +20,7 @@ Fig2. ANI clustermap between all-vs-all 18 genomes. If no similarity detected by
 
 ## Installation
 
-`Python 3.8 or later` is required for installation.
+`Python 3.9 or later` is required for installation.
 [fastANI](https://github.com/ParBLiSS/FastANI) or [skani](https://github.com/bluenote-1577/skani) is required to calculate ANI.  
 
 **Install bioconda package:**
@@ -38,7 +38,7 @@ Description of ANIclustermap's automated workflow.
 1. Calculate ANI between all-vs-all microbial genomes by fastANI (or skani).  
    If no similarity detected by fastANI, NA is output. In that case, NA is replaced by 0.0.  
    If previous result available at the time of re-run, reuse previous result.
-2. Clustering ANI matrix by scipy's UPGMA method.  
+2. Clustering ANI matrix by scipy UPGMA method.  
 3. Using clustered matrix, draw ANI clustermap by seaborn.  
 
 ## Usage
@@ -50,37 +50,40 @@ Description of ANIclustermap's automated workflow.
 ### Options
 
     $ ANIclustermap --help
-    usage: ANIclustermap -i [Genome fasta directory] -o [output directory]
-
-    Draw ANI(Average Nucleotide Identity) clustermap
-
-    optional arguments:
-      -i I, --indir I      Input genome fasta directory (*.fa|*.fna[.gz]|*.fasta)
-      -o O, --outdir O     Output directory
-      -m , --mode          ANI calculation mode ('fastani'[default]|'skani')
-      -t , --thread_num    Thread number parameter (Default: MaxThread - 1)
-      --overwrite          Overwrite previous ANI calculation result (Default: OFF)
-      --fig_width          Figure width (Default: 10)
-      --fig_height         Figure height (Default: 10)
-      --dendrogram_ratio   Dendrogram ratio to figsize (Default: 0.15)
-      --cmap_colors        cmap interpolation colors parameter (Default: 'lime,yellow,red')
-      --cmap_gamma         cmap gamma parameter (Default: 1.0)
-      --cmap_ranges        Range values (e.g. 80,90,95,100) for discrete cmap (Default: None)
-      --cbar_pos           Colorbar position (Default: (0.02, 0.8, 0.05, 0.18))
-      --annotation         Show ANI value annotation (Default: OFF)
-      --annotation_fmt     Annotation value format (Default: '.3g')
-      -v, --version        Print version information
-      -h, --help           Show this help message and exit
+
+    Usage: ANIclustermap [OPTIONS]                                                                                       
+
+    Draw ANI(Average Nucleotide Identity) clustermap                                                                     
+
+    ╭─ Options ────────────────────────────────────────────────────────────────────────────────────────────╮
+    │ *  --indir             -i        Input genome fasta directory (*.fa|*.fna[.gz]|*.fasta) [required]   │
+    │ *  --outdir            -o        Output directory [required]                                         │
+    │    --mode                        ANI calculation tool (fastani|skani) [default: fastani]             │
+    │    --thread_num        -t        Thread number parameter [default: MaxThread - 1]                    │
+    │    --overwrite                   Overwrite previous ANI calculation result                           │
+    │    --fig_width                   Figure width [default: 10]                                          │
+    │    --fig_height                  Figure height [default: 10]                                         │
+    │    --dendrogram_ratio            Dendrogram ratio to figsize [default: 0.15]                         │
+    │    --cmap_colors                 cmap interpolation colors parameter [default: lime,yellow,red]      │
+    │    --cmap_gamma                  cmap gamma parameter [default: 1.0]                                 │
+    │    --cmap_ranges                 Range values (e.g. 80,90,95,100) for discrete cmap                  │
+    │    --cbar_pos                    Colorbar position [default: 0.02, 0.85, 0.04, 0.15]                 │
+    │    --annotation                  Show ANI value annotation                                           │
+    │    --annotation_fmt              Annotation value format [default: .3g]                              │
+    │    --quiet                       No print log on screen                                              │
+    │    --version           -v        Print version information                                           │
+    │    --help              -h        Show this message and exit.                                         │
+    ╰──────────────────────────────────────────────────────────────────────────────────────────────────────╯
 
 ### Example Command
 
-7 genomes minimal dataset. Click [here](https://github.com/moshi4/ANIclustermap/wiki/dataset/minimal_dataset.zip) to download dataset (Size=3.6MB).
+7 genomes minimal dataset. Click [here](https://github.com/moshi4/ANIclustermap/raw/main/example/input/minimal_dataset.zip) to download dataset.
 
     ANIclustermap -i ./minimal_dataset/ -o ./ANIclustermap_result
 
 ## Output Contents
 
-ANIclustermap outputs 3 types of files.
+ANIclustermap outputs 3 types of result files.
 
 - **`ANIclustermap.[png|svg]`**  ([example1](https://github.com/moshi4/ANIclustermap/blob/main/example/output/05_normal_dataset/ANIclustermap.png), [example2](https://github.com/moshi4/ANIclustermap/blob/main/example/output/06_normal_dataset_annotation/ANIclustermap.png))  
   ANI clustermap result figure.
@@ -94,32 +97,32 @@ ANIclustermap outputs 3 types of files.
 ## Gallery
 
 Example gallery of 33 genomes normal dataset.  
-If you want to try it for yourself, click [here](https://github.com/moshi4/ANIclustermap/wiki/dataset/normal_dataset.zip) to donwload dataset (Size=63.5MB).
+If you want to try it for yourself, click [here](https://github.com/moshi4/ANIclustermap/raw/main/example/input/normal_dataset.zip) to donwload dataset.
 
 **Normal parameter:**
 
-    ANIclustermap -i ./normal_dataset -o ./ANIclustermap_result \
+    ANIclustermap -i ./normal_dataset -o ./ANIclustermap_result01 \
                   --fig_width 15
 
 ![ANIclustermap.png](https://raw.githubusercontent.com/moshi4/ANIclustermap/main/images/gallery/01_ANIclustermap.png)  
 
 **Change cmap_gamma parameter:**
 
-    ANIclustermap -i ./normal_dataset -o ./ANIclustermap_result \ 
+    ANIclustermap -i ./normal_dataset -o ./ANIclustermap_result02 \
                   --fig_width 15 --cmap_gamma 0.5
 
 ![ANIclustermap.png](https://raw.githubusercontent.com/moshi4/ANIclustermap/main/images/gallery/02_ANIclustermap.png)  
 
 **Change cmap_colors(=white,orange,red) paramter:**
 
-    ANIclustermap -i ./normal_dataset -o ./ANIclustermap_result \ 
+    ANIclustermap -i ./normal_dataset -o ./ANIclustermap_result03 \
                   --fig_width 15 --cmap_colors white,orange,red
 
 ![ANIclustermap.png](https://raw.githubusercontent.com/moshi4/ANIclustermap/main/images/gallery/03_ANIclustermap.png)  
 
 **Change cmap_ranges paramter:**
 
-    ANIclustermap -i ./normal_dataset -o ./ANIclustermap_result \ 
+    ANIclustermap -i ./normal_dataset -o ./ANIclustermap_result04 \
                   --fig_width 15 --cmap_ranges 80,85,90,92.5,95,97.5,100
 
 > See [this issue](https://github.com/moshi4/ANIclustermap/issues/1) for more details.
@@ -128,7 +131,7 @@ If you want to try it for yourself, click [here](https://github.com/moshi4/ANIcl
 
 **Add ANI value annotation parameter:**
 
-    ANIclustermap -i ./normal_dataset -o ./ANIclustermap_result \ 
+    ANIclustermap -i ./normal_dataset -o ./ANIclustermap_result05 \
                   --fig_width 20 --fig_height 15 --annotation
 
 ![ANIclustermap.png](https://raw.githubusercontent.com/moshi4/ANIclustermap/main/images/gallery/05_ANIclustermap.png)  

example/example_run.sh

@@ -3,19 +3,39 @@ OUTDIR=output
 mkdir -p $OUTDIR
 
 ANIclustermap -i ./input/minimal_dataset -o ${OUTDIR}/01_minimal_dataset \
-              --fig_width 8 --fig_height 5
+    --fig_width 8 --fig_height 5
 
 ANIclustermap -i ./input/minimal_dataset -o ${OUTDIR}/02_minimal_dataset_annotation \
-              --fig_width 8 --fig_height 5 --annotation
+    --fig_width 8 --fig_height 5 --annotation
 
 ANIclustermap -i ./input/small_dataset -o ${OUTDIR}/03_small_dataset \
-              --fig_width 15
+    --fig_width 15
 
 ANIclustermap -i ./input/small_dataset -o ${OUTDIR}/04_small_dataset_annotation \
-              --fig_width 15 --annotation
+    --fig_width 15 --annotation
 
 ANIclustermap -i ./input/normal_dataset -o ${OUTDIR}/05_normal_dataset \
-              --fig_width 15
+    --fig_width 15
 
 ANIclustermap -i ./input/normal_dataset -o ${OUTDIR}/06_normal_dataset_annotation \
-              --fig_width 20 --annotation
+    --fig_width 20 --annotation
+
+# Normal parameter
+ANIclustermap -i ./input/normal_dataset -o ${OUTDIR}/ANIclustermap_result01 \
+    --fig_width 15
+
+# Change cmap_gamma parameter
+ANIclustermap -i ./input/normal_dataset -o ${OUTDIR}/ANIclustermap_result02 \
+    --fig_width 15 --cmap_gamma 0.5
+
+# Change cmap_colors parameter
+ANIclustermap -i ./input/normal_dataset -o ${OUTDIR}/ANIclustermap_result03 \
+    --fig_width 15 --cmap_colors white,orange,red
+
+# Change cmap_ranges parameter
+ANIclustermap -i ./input/normal_dataset -o ${OUTDIR}/ANIclustermap_result04 \
+    --fig_width 15 --cmap_ranges 80,85,90,92.5,95,97.5,100
+
+# Add ANI value annotation parameter
+ANIclustermap -i ./input/normal_dataset -o ${OUTDIR}/ANIclustermap_result05 \
+    --fig_width 20 --fig_height 15 --annotation