Merge pull request #15 from moshi4/develop

Bump to v1.4.0
moshi4 · Jul 13, 2024 · 538e7da · 538e7da
2 parents e67d670 + 7792820
commit 538e7da
Show file tree

Hide file tree

Showing 7 changed files with 515 additions and 525 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -1,10 +1,10 @@
 name: CI
 on:
   push:
-    branches: [main]
+    branches: [main, develop]
     paths: ["src/**", "tests/**", ".github/workflows/ci.yml"]
   pull_request:
-    branches: [main]
+    branches: [main, develop]
     paths: ["src/**", "tests/**", ".github/workflows/ci.yml"]
   workflow_dispatch:
 
@@ -17,10 +17,10 @@ jobs:
         python-version: ["3.8", "3.9", "3.10", "3.11"]
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup Python ${{ matrix.python-version}}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -32,11 +32,11 @@ jobs:
       - name: Install Dependencies
         run: poetry install -n
 
-      - name: Run black format check
-        run: poetry run black src tests --check --diff --verbose
-
       - name: Run ruff lint check
-        run: poetry run ruff .
+        run: poetry run ruff check --diff
+
+      - name: Run ruff format check
+        run: poetry run ruff format --check --diff
 
       - name: Run pytest
-        run: poetry run pytest tests --tb=line --cov=src --cov-report=xml --cov-report=term
+        run: poetry run pytest
diff --git a/.github/workflows/publish_to_pypi.yml b/.github/workflows/publish_to_pypi.yml
@@ -12,12 +12,12 @@ jobs:
       PYPI_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
-      - name: Setup Python 3.9
-        uses: actions/setup-python@v4
+      - name: Setup Python 3.12
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: 3.12
 
       - name: Install Poetry
         run: |

diff --git a/README.md b/README.md
@@ -49,21 +49,28 @@ Description of ANIclustermap's automated workflow.
 
 ### Options
 
-    -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)
-    -v, --version        Print version information
-    -h, --help           Show this help message and exit
+    $ 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
 
 ### Example Command