Merge pull request #53 from moshi4/develop

Bump to v1.2.0

.github/workflows/ci.yml

@@ -19,25 +19,32 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Setup Python ${{ matrix.python-version}}
-        uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
+      # - name: Setup Python ${{ matrix.python-version}}
+      #   uses: actions/setup-python@v5
+      #   with:
+      #     python-version: ${{ matrix.python-version }}
+
+      - name: Install Rye
+        run: |
+          curl -sSf https://rye.astral.sh/get | RYE_INSTALL_OPTION="--yes" bash
+          echo "$HOME/.rye/shims" >> $GITHUB_PATH
 
       - name: Install python dependencies
-        run: pip install -e . pytest pytest-cov ruff streamlit
+        run: |
+          rye pin ${{ matrix.python-version }}
+          rye sync --update-all --all-features
 
-      - name: Install external dependencies
+      - name: Install external tool dependencies
         run: |
           sudo apt update -y
           sudo apt install -y ncbi-blast+ mmseqs2 mummer progressivemauve
         if: ${{ matrix.os=='ubuntu-latest' }}
 
       - name: Run ruff lint check
-        run: ruff check --diff
+        run: rye run ruff check --diff
 
       - name: Run ruff format check
-        run: ruff format --check --diff
+        run: rye run ruff format --check --diff
 
       - name: Run pytest
-        run: pytest
+        run: rye run pytest

.github/workflows/publish_mkdocs.yml

@@ -17,10 +17,13 @@ jobs:
         with:
           python-version: "3.11"
 
-      - 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 MkDocs & Plugins
+        run: rye sync
 
       - name: Publish document
-        run: mkdocs gh-deploy --force
+        run: rye run mkdocs gh-deploy --force

.github/workflows/publish_to_pypi.yml

@@ -20,13 +20,13 @@ jobs:
         with:
           python-version: "3.11"
 
-      - 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

.pre-commit-config.yaml

@@ -2,7 +2,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.3
+    rev: v0.5.1
     hooks:
       - id: ruff
         name: ruff lint check

README.md

@@ -372,10 +372,11 @@ As shown below, pan/zoom, tooltip display, object color change, text change, etc
 
 Following libraries were used to implement HTML viewer.  
 
-- [jQuery](https://github.com/jquery/jquery): HTML document traversal and manipulation  
-- [jQuery UI](https://github.com/jquery/jquery-ui): Tooltip, Dialog  
 - [Spectrum](https://github.com/bgrins/spectrum): Colorpicker  
-- [panzoom](https://github.com/timmywil/panzoom): SVG panning and zooming  
+- [Panzoom](https://github.com/timmywil/panzoom): SVG panning and zooming  
+- [Tabulator](https://github.com/olifolkerd/tabulator): Interactive Table
+- [Micromodal](https://github.com/Ghosh/micromodal): Modal dialog
+- [Tippy.js](https://github.com/atomiks/tippyjs): Tooltip
 
 ## Inspiration