Slipmap

.github/workflows/python-publish.yml

@@ -11,23 +11,19 @@ on:
 jobs:
   deploy:
     runs-on: ubuntu-latest
+    permissions:
+      id-token: write
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
           python-version: "3.x"
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          python -m pip install build
+          python -m pip install --upgrade pip build
       - name: Build package
-        run: |
-          python -m build
-          python -c "import os, glob; assert os.path.getsize(sorted(glob.glob('dist/*-*.whl'))[-1]) > 10_000"
-      - name: Publish package
-        uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
-        with:
-          user: __token__
-          password: ${{ secrets.PYPI_API_TOKEN }}
+        run: python -m build
+      - name: Publish package to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/python-pytest.yml

@@ -4,35 +4,57 @@
 name: tests
 
 on:
-  workflow_dispatch:
   push:
     branches: [master, main]
     paths: ["**.py"]
   pull_request:
     paths: ["**.py"]
 
 jobs:
-  build:
+  test:
     runs-on: ubuntu-latest
     strategy:
       matrix:
         python-version: ["3.8", "3.9", "3.10", "3.11"]
-
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+          cache: "pip"
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install pytest build
-          python -m pip install --editable .
+          python -m pip install xiplot pytest pytest-cov
+          python -m pip install -e .
+      - name: Test with pytest
+        run: |
+          pytest --cov-report term --cov=slisemap_interactive --cov-fail-under=70
+
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+      - run: python -m pip install --upgrade pip build
       - name: Build package
         run: |
+          rm -f dist/*.whl
           python -m build
-          python -c "import os, glob; assert os.path.getsize(sorted(glob.glob('dist/*-*.whl'))[-1]) > 10_000"
-      - name: Test with pytest
+          python -c "import os, glob; assert os.path.getsize(glob.glob('dist/*.whl')[-1]) > 10_000"
+
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+      - run: python -m pip install --upgrade pip ruff
+      - name: Lint with Ruff
         run: |
-          pytest
+          ruff check --output-format=github
+          ruff format --check

.gitignore

@@ -169,4 +169,4 @@ poetry.toml
 *.sm
 *.tmp
 *.txt
-!*requitements*.txt
+*.sp

README.md

@@ -23,9 +23,11 @@ To use the plugin, just install the package in the same Python environment as [
 
 ## Installation
 
-To install __slisemap_interactive__ without manually downloading the repository run:
+To install __slisemap_interactive__ run one of the following commands:
 
 ```bash
+pip install slisemap_interactive
+pip install slisemap_interactive[xiplot]
 pip install git+https://github.com/edahelsinki/slisemap_interactive
 ```
 

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "slisemap_interactive"
-version = "0.5.0"
+version = "0.6.0"
 description = "Interactive plots for Slisemap using Dash"
 readme = "README.md"
 license = { text = "MIT" }
@@ -29,13 +29,14 @@ dependencies = [
 
 [project.optional-dependencies]
 xiplot = ["xiplot"]
-dev = ["pytest", "black[jupyter]", "pylint", "jupyter", "IPython"]
+dev = ["pytest", "pytest-cov", "black[jupyter]", "ruff", "jupyter", "IPython"]
 
 [project.urls]
 github = "https://github.com/edahelsinki/slisemap_interactive"
 
 [project.entry-points."xiplot.plugin.read"]
-xiplot_plugin_load = "slisemap_interactive.xiplot:plugin_load"
+xiplot_plugin_load_slisemap = "slisemap_interactive.xiplot:load_slisemap"
+xiplot_plugin_load_slipmap = "slisemap_interactive.xiplot:load_slipmap"
 
 [project.entry-points."xiplot.plugin.plot"]
 xiplot_plugin_embeddingplot = "slisemap_interactive.xiplot:SlisemapEmbeddingPlot"
@@ -50,3 +51,47 @@ slisemap_interactive = "slisemap_interactive.app:cli"
 
 [tool.setuptools]
 packages = ["slisemap_interactive"]
+
+[tool.coverage.run]
+branch = true
+
+[tool.coverage.report]
+exclude_also = ["print", "ImportError"]
+
+[tool.ruff.lint]
+select = [
+    "I",
+    "E",
+    "F",
+    "B",
+    "C4",
+    "W",
+    "D",
+    "UP",
+    "ANN",
+    "SIM",
+    "RUF",
+    "S",
+    "N",
+]
+ignore = [
+    "E501",
+    "B006",
+    "D105",
+    "D203",
+    "D204",
+    "D406",
+    "D213",
+    "D407",
+    "D413",
+    "ANN101",
+    "ANN102",
+    "ANN401",
+    "S101",
+    "N802",
+    "N803",
+    "N806",
+]
+
+[tool.ruff.lint.per-file-ignores]
+"tests/**" = ["D", "ANN"]

slisemap_interactive/__init__.py

@@ -1,25 +1,27 @@
-"""
-    Slisemap - Interactive: A Dash app for interactively visualising Slisemap objects
-    =================================================================================
+"""Slisemap - Interactive: A Dash app for interactively visualising Slisemap objects.
+=================================================================================
 
-    Use the `plot` function for non-blocking interactive plots in notebooks and interactive interpreters.
-    In (non-Python) terminals you can call `slisemap_interactive` to start a standalone application.
-    Finally, this package also integrates into χiplot as a plugin.
+Use the `plot` function for non-blocking interactive plots in notebooks and interactive interpreters.
+In (non-Python) terminals you can call `slisemap_interactive` to start a standalone application.
+Finally, this package also integrates into χiplot as a plugin.
 
-    Relevant links:
-    ---------------
+Relevant links:
+---------------
 
-    - [GitHub repository](https://github.com/edahelsinki/slisemap_interactive)
-    - [Slisemap](https://github.com/edahelsinki/slisemap)
-    - [χiplot](https://github.com/edahelsinki/xiplot)
-    - [Dash](https://dash.plotly.com/)
-"""
+- [GitHub repository](https://github.com/edahelsinki/slisemap_interactive)
+- [Slisemap](https://github.com/edahelsinki/slisemap)
+- [χiplot](https://github.com/edahelsinki/xiplot)
+- [Dash](https://dash.plotly.com/)
+"""  # noqa: D205
 
-from slisemap_interactive.app import plot, shutdown, BackgroundApp, ForegroundApp
-from slisemap_interactive.load import load, slisemap_to_dataframe
-
-
-def __version__():
-    from importlib.metadata import version
-
-    return version("slisemap_interactive")
+from slisemap_interactive.app import (  # noqa: F401
+    BackgroundApp,
+    ForegroundApp,
+    plot,
+    shutdown,
+)
+from slisemap_interactive.load import (  # noqa: F401
+    load,
+    slipmap_to_dataframe,
+    slisemap_to_dataframe,
+)

slisemap_interactive/__main__.py

@@ -1,4 +1,7 @@
+"""Run the slisemap_interactive app."""
+
 import sys
+
 from slisemap_interactive.app import cli
 
 # This script is only called when there is a local copy of the repository,