Merge pull request #15 from moshi4/develop

Bump to v0.5.0
moshi4 · Sep 14, 2024 · 50e287a · 50e287a
2 parents b540ae7 + 25f2aff
commit 50e287a
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -14,29 +14,26 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
-      - name: Setup Python ${{ matrix.python-version}}
-        uses: actions/setup-python@v4
-        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" >> $GITHUB_PATH
-
-      - name: Install Dependencies
-        run: poetry install -n
+          curl -sSf https://rye.astral.sh/get | RYE_INSTALL_OPTION="--yes" bash
+          echo "$HOME/.rye/shims" >> $GITHUB_PATH
 
-      - name: Run black format check
-        run: poetry run black src tests --check --diff --verbose
+      - 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 .
+        run: rye run ruff check --diff
+
+      - name: Run ruff format check
+        run: rye run ruff format --check --diff
 
       - name: Run pytest
-        run: poetry run pytest tests --tb=line --cov=src --cov-report=xml --cov-report=term
+        run: rye run pytest
diff --git a/.github/workflows/publish_mkdocs.yml b/.github/workflows/publish_mkdocs.yml
@@ -10,17 +10,15 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
-      - name: Setup Python 3.9
-        uses: actions/setup-python@v4
-        with:
-          python-version: 3.9
-
-      - name: Install MkDocs & Plugins
+      - name: Install Rye
         run: |
-          pip install .
-          pip install mkdocs mkdocs-material mkdocs-jupyter mkdocstrings[python] black
+          curl -sSf https://rye.astral.sh/get | RYE_INSTALL_OPTION="--yes" bash
+          echo "$HOME/.rye/shims" >> $GITHUB_PATH
+
+      - name: Install Python & MkDocs & Plugins
+        run: rye sync
 
       - name: Publish document
-        run: mkdocs gh-deploy --force
+        run: rye run mkdocs gh-deploy --force
diff --git a/.github/workflows/publish_to_pypi.yml b/.github/workflows/publish_to_pypi.yml
@@ -13,20 +13,15 @@ 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
-        with:
-          python-version: 3.9
-
-      - 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
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,11 @@
+# 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: v0.6.4
+    hooks:
+      - id: ruff
+        name: ruff lint check
+        args: [--fix]
+      - id: ruff-format
+        name: ruff format check
diff --git a/README.md b/README.md
@@ -30,7 +30,7 @@ More detailed documentation is available [here](https://moshi4.github.io/pyMSAvi
 
 ## Installation
 
-`Python 3.8 or later` is required for installation.
+`Python 3.9 or later` is required for installation.
 
 **Install PyPI package:**
 
@@ -110,28 +110,33 @@ pyMSAviz provides simple MSA visualization CLI.
 
 ### Options
 
-    -i I, --infile I    Input MSA file
-    -o O, --outfile O   Output MSA visualization file (*.png|*.jpg|*.svg|*.pdf)
-    --format            MSA file format (Default: 'fasta')
-    --color_scheme      Color scheme (Default: 'Zappo')
-    --start             Start position of MSA visualization (Default: 1)
-    --end               End position of MSA visualization (Default: 'MSA Length')
-    --wrap_length       Wrap length (Default: None)
-    --wrap_space_size   Space size between wrap MSA plot area (Default: 3.0)
-    --label_type        Label type ('id'[default]|'description')
-    --show_grid         Show grid (Default: OFF)
-    --show_count        Show seq char count without gap on right side (Default: OFF)
-    --show_consensus    Show consensus sequence (Default: OFF)
-    --consensus_color   Consensus identity bar color (Default: '#1f77b4')
-    --consensus_size    Consensus identity bar height size (Default: 2.0)
-    --sort              Sort MSA order by NJ tree constructed from MSA distance matrix (Default: OFF)
-    --dpi               Figure DPI (Default: 300)
-    -v, --version       Print version information
-    -h, --help          Show this help message and exit
+    $ pymsaviz --help
+    usage: pymsaviz [options] -i msa.fa -o msa_viz.png
+
+    MSA(Multiple Sequence Alignment) visualization CLI tool
+
+    optional arguments:
+      -i I, --infile I    Input MSA file
+      -o O, --outfile O   Output MSA visualization file (*.png|*.jpg|*.svg|*.pdf)
+      --format            MSA file format (Default: 'fasta')
+      --color_scheme      Color scheme (Default: 'Zappo')
+      --start             Start position of MSA visualization (Default: 1)
+      --end               End position of MSA visualization (Default: 'MSA Length')
+      --wrap_length       Wrap length (Default: None)
+      --wrap_space_size   Space size between wrap MSA plot area (Default: 3.0)
+      --label_type        Label type ('id'[default]|'description')
+      --show_grid         Show grid (Default: OFF)
+      --show_count        Show seq char count without gap on right side (Default: OFF)
+      --show_consensus    Show consensus sequence (Default: OFF)
+      --consensus_color   Consensus identity bar color (Default: '#1f77b4')
+      --consensus_size    Consensus identity bar height size (Default: 2.0)
+      --sort              Sort MSA order by NJ tree constructed from MSA distance matrix (Default: OFF)
+      --dpi               Figure DPI (Default: 300)
+      -v, --version       Print version information
+      -h, --help          Show this help message and exit
 
     Available Color Schemes:
-    ['Clustal', 'Zappo', 'Taylor', 'Flower', 'Blossom', 'Sunset', 'Ocean', 'Hydrophobicity', 'HelixPropensity', 
-     'StrandPropensity', 'TurnPropensity', 'BuriedIndex', 'Nucleotide', 'Purine/Pyrimidine', 'Identity', 'None']
+    ['Clustal', 'Zappo', 'Taylor', 'Flower', 'Blossom', 'Sunset', 'Ocean', 'Hydrophobicity', 'HelixPropensity', 'StrandPropensity', 'TurnPropensity', 'BuriedIndex', 'Nucleotide', 'Purine/Pyrimidine', 'Identity', 'None']
 
 ### CLI Example
 

diff --git a/docs/cli-docs/pymsaviz.md b/docs/cli-docs/pymsaviz.md
@@ -8,28 +8,33 @@
 
 ### Options
 
-    -i I, --infile I    Input MSA file
-    -o O, --outfile O   Output MSA visualization file (*.png|*.jpg|*.svg|*.pdf)
-    --format            MSA file format (Default: 'fasta')
-    --color_scheme      Color scheme (Default: 'Zappo')
-    --start             Start position of MSA visualization (Default: 1)
-    --end               End position of MSA visualization (Default: 'MSA Length')
-    --wrap_length       Wrap length (Default: None)
-    --wrap_space_size   Space size between wrap MSA plot area (Default: 3.0)
-    --label_type        Label type ('id'[default]|'description')
-    --show_grid         Show grid (Default: OFF)
-    --show_count        Show seq char count without gap on right side (Default: OFF)
-    --show_consensus    Show consensus sequence (Default: OFF)
-    --consensus_color   Consensus identity bar color (Default: '#1f77b4')
-    --consensus_size    Consensus identity bar height size (Default: 2.0)
-    --sort              Sort MSA order by NJ tree constructed from MSA distance matrix (Default: OFF)
-    --dpi               Figure DPI (Default: 300)
-    -v, --version       Print version information
-    -h, --help          Show this help message and exit
+    $ pymsaviz --help
+    usage: pymsaviz [options] -i msa.fa -o msa_viz.png
+
+    MSA(Multiple Sequence Alignment) visualization CLI tool
+
+    optional arguments:
+      -i I, --infile I    Input MSA file
+      -o O, --outfile O   Output MSA visualization file (*.png|*.jpg|*.svg|*.pdf)
+      --format            MSA file format (Default: 'fasta')
+      --color_scheme      Color scheme (Default: 'Zappo')
+      --start             Start position of MSA visualization (Default: 1)
+      --end               End position of MSA visualization (Default: 'MSA Length')
+      --wrap_length       Wrap length (Default: None)
+      --wrap_space_size   Space size between wrap MSA plot area (Default: 3.0)
+      --label_type        Label type ('id'[default]|'description')
+      --show_grid         Show grid (Default: OFF)
+      --show_count        Show seq char count without gap on right side (Default: OFF)
+      --show_consensus    Show consensus sequence (Default: OFF)
+      --consensus_color   Consensus identity bar color (Default: '#1f77b4')
+      --consensus_size    Consensus identity bar height size (Default: 2.0)
+      --sort              Sort MSA order by NJ tree constructed from MSA distance matrix (Default: OFF)
+      --dpi               Figure DPI (Default: 300)
+      -v, --version       Print version information
+      -h, --help          Show this help message and exit
 
     Available Color Schemes:
-    ['Clustal', 'Zappo', 'Taylor', 'Flower', 'Blossom', 'Sunset', 'Ocean', 'Hydrophobicity', 'HelixPropensity', 
-     'StrandPropensity', 'TurnPropensity', 'BuriedIndex', 'Nucleotide', 'Purine/Pyrimidine', 'Identity', 'None']
+    ['Clustal', 'Zappo', 'Taylor', 'Flower', 'Blossom', 'Sunset', 'Ocean', 'Hydrophobicity', 'HelixPropensity', 'StrandPropensity', 'TurnPropensity', 'BuriedIndex', 'Nucleotide', 'Purine/Pyrimidine', 'Identity', 'None']
 
 ### Example Command
 

diff --git a/docs/index.md b/docs/index.md
@@ -25,7 +25,7 @@ pyMSAviz was developed inspired by [Jalview](https://www.jalview.org/) and [ggms
 
 ## Installation
 
-`Python 3.8 or later` is required for installation.
+`Python 3.9 or later` is required for installation.
 
 **Install PyPI package:**