updating workflow action versions, adding latest python version to ac…

…tions, adding repo link to readme, adding error handling test functions to pytest, adding latest python version to pytest

.github/workflows/build.yaml

@@ -14,9 +14,9 @@ jobs:
   package:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python 3.10
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.10"
           cache: "pip"

.github/workflows/release.yaml

@@ -14,7 +14,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
           python-version: "3.11"
       - name: Install dependencies

.github/workflows/test.yaml

@@ -26,9 +26,15 @@ jobs:
           - os: ubuntu-latest
             python: "3.9"
           - os: ubuntu-latest
-            python: "3.12"
+            python: "3.10"
+          - os: ubuntu-latest
+            python: "3.11"
           - os: ubuntu-latest
             python: "3.12"
+          - os: ubuntu-latest
+            python: "3.13"
+          - os: ubuntu-latest
+            python: "3.13"
             pip-flags: "--pre"
             name: PRE-RELEASE DEPENDENCIES
 
@@ -39,9 +45,9 @@ jobs:
       PYTHON: ${{ matrix.python }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python }}
           cache: "pip"

.python-version

@@ -1 +1 @@
-3.9
+3.10

CITATION.cff

@@ -1,12 +1,12 @@
 cff-version: 1.2.0
 message: "If you use pyclustree, please cite it as below. Please also cite the original clustree package."
 authors:
-  - family-names: "Kuehl"
-    given-names: "Malte"
-  - family-names: "Hellmig"
-    given-names: "Malte"
-  - family-names: "Puelles"
-    given-names: "Victor G."
+    - family-names: "Kuehl"
+      given-names: "Malte"
+    - family-names: "Hellmig"
+      given-names: "Malte"
+    - family-names: "Puelles"
+      given-names: "Victor G."
 title: "pyclustree: Visualizing cluster resolution optimization for biomedical data"
 version: 0.3.1
 date-released: 2024-10-24

Makefile

@@ -1,39 +1,60 @@
-.DEFAULT_GOAL := test
+
+
+.DEFAULT_GOAL := help
+
+
+.PHONY : help
+help:
+	@awk 'BEGIN {FS = ":.*?## "} /^[a-zA-Z_-]+:.*?## / {printf "\033[36m%-30s\033[0m %s\n", $$1, $$2}' $(MAKEFILE_LIST)
+
 
 #
 # Virtual environment setup
 # You may want to replace python3 with the path to your python3 executable,
 # e.g. the output of `pyenv which python3`when using pyenv
 #
-create-venv:
-	python3 -m venv '.venv'
+.PHONY : create-venv
+create-venv: ## Create virtualenv
+	python3 -m virtualenv '.venv'
 	echo "Don't forget to activate with 'source .venv/bin/activate'"
 
 #
 # Install requirements
 #
-install:
-	python3 -m pip install --upgrade pip
-	python3 -m pip install flit poetry
+.PHONY : install
+install: ## Install dependencies for production
+	python3 -m pip --require-virtualenv install --upgrade pip
+	python3 -m pip --require-virtualenv install flit poetry
 	python3 -m flit install --deps production
 
-install-dev: install
-	python3 -m pip install '.[dev]'
+.PHONY : install-dev
+install-dev: install ## Install dependencies for development and production
+	python3 -m pip --require-virtualenv install '.[dev]'
 	python3 -m certifi
 	pre-commit install --hook-type pre-commit --hook-type pre-push
 	echo "Please also install pandoc to create the documentation."
 
-upload: check
-	flit publish
 
 #
-# Testing
+# Build and upload package
 #
-unittest:
-	coverage run -m pytest --maxfail=10
+.PHONY : build
+build: ## Build python package
+	python3 -m build
+	python3 -m twine check --strict dist/*.whl
+
+.PHONY : upload
+upload: ## Publish package with flit
+	python3 -m flit publish
 
-coverage-report: unittest
-	coverage report
-	coverage html
+#
+# Testing
+#
+.PHONY : pytest
+pytest: ## Run pytest with coverage
+	python3 -m coverage run -m pytest --maxfail=10
 
-test: check unittest
+.PHONY : coverage-report
+coverage-report: pytest ## Generate coverage report
+	python3 -m coverage report -m
+	python3 -m coverage html

README.md

@@ -11,7 +11,7 @@
 Visualize cluster assignments at different resolutions. Possbile applications include finding the optimal resolution for
 single-cell RNA-sequencing clusterings.
 
-`pyclustree` is inspired by the R package `clustree`, however, while we aim to provide the same functionality, the API
+`pyclustree` is inspired by the R package `clustree` ([Github repository](https://github.com/lazappi/clustree)), however, while we aim to provide the same functionality, the API
 will differ between the implementations.
 
 ## Getting started

pyclustree/__init__.py

@@ -2,8 +2,6 @@
 
 from ._clustree import clustree
 
-pyclustree = clustree
-
-__all__ = ["clustree", "pyclustree"]
+__all__ = ["clustree"]
 
 __version__ = version("pyclustree")

pyproject.toml

@@ -10,7 +10,7 @@ description = "Visualize cluster assignments at different resolutions"
 readme = "README.md"
 license = { file = "LICENSE" }
 maintainers = [
-  { name = "Malte Hellmig", email = "[email protected]" },
+  { name = "Malte Hellmig", email = "[email protected]" },
   { name = "Malte Kuehl", email = "[email protected]" },
 ]
 authors = [ { name = "Malte Hellmig" }, { name = "Malte Kuehl" } ]
@@ -47,6 +47,7 @@ optional-dependencies.dev = [
   "furo",
   "ipykernel",
   "ipython",
+  "ipywidgets",
   "myst-parser",
   "nbsphinx",
   "pandas",

tests/test_pyclustree.py

@@ -1,4 +1,5 @@
 import matplotlib.pyplot as plt
+import pytest
 import scanpy as sc
 
 import pyclustree
@@ -61,3 +62,31 @@ def test_scatter_reference():
     )
 
     assert isinstance(fig, plt.Figure), "pyclustree should return a matplotlib Figure object."
+
+    # Testing errorhandling
+
+    # Testing none existing gene fo node color
+    with pytest.raises(AssertionError):
+        clustree(
+            adata,
+            [f"leiden_{str(resolution).replace('.', '_')}" for resolution in [0.2, 1.0]],
+            node_color_gene="Non-existing gene",
+        )
+
+    with pytest.raises(AssertionError):
+        clustree(
+            adata,
+            [f"leiden_{str(resolution).replace('.', '_')}" for resolution in [0.2, 1.0]],
+            node_color_gene="Non-existing gene",
+            node_color_gene_use_raw=False,
+        )
+
+    # Testing node colormap argument
+    with pytest.raises(AssertionError):
+        cluster_keys = [f"leiden_{str(resolution).replace('.', '_')}" for resolution in [0.2, 1.0]]
+        clustree(adata, cluster_keys, node_colormap=["#FF0000"] * (len(cluster_keys) + 1))
+
+    # Testing node_color_gene when node colormap argument is provided
+    with pytest.raises(AssertionError):
+        cluster_keys = [f"leiden_{str(resolution).replace('.', '_')}" for resolution in [0.2, 1.0]]
+        clustree(adata, cluster_keys, node_colormap=["#FF0000"] * len(cluster_keys), node_color_gene="CD8A")