Newmana/stlearn 1.3.0

CONTRIBUTING.rst

@@ -15,7 +15,7 @@ Types of Contributions
 Report Bugs
 ~~~~~~~~~~~
 
-Report bugs at https://github.com/duypham2108/stlearn/issues.
+Report bugs at https://github.com/BiomedicalMachineLearning/stLearn/issues
 
 If you are reporting a bug, please include:
 
@@ -72,11 +72,8 @@ Ready to contribute? Here's how to set up `stlearn` for local development.
     $ cd stlearn/
     $ pip install -e .[dev,test]
 
-    If you get an error for louvain package on MacOS, make sure you have cmake installed first (if you have brew):
-    $ brew install cmake
-
     You can also use conda to install these dependencies (after creating the environment):
-    $ conda install -c conda-forge louvain leidenalg python-igraph
+    $ conda install -c conda-forge leidenalg python-igraph
 
    Or if you prefer pip/virtualenv::
 
@@ -119,9 +116,7 @@ Before you submit a pull request, check that it meets these guidelines:
 2. If the pull request adds functionality, the docs should be updated. Put
    your new functionality into a function with a docstring, and add the
    feature to the list in README.rst.
-3. The pull request should work for Python 3.5, 3.6, 3.7 and 3.8, and for PyPy. Check
-   https://travis-ci.org/duypham2108/stlearn/pull_requests
-   and make sure that the tests pass for all supported Python versions.
+3. The pull request should work for Python 3.12 and above.
 
 Tips
 ----

HISTORY.rst

@@ -2,6 +2,16 @@
 History
 =======
 
+1.3.0 (2026-02-24)
+------------------
+* Removed interactive stLearn/embedded web application.
+* Removed louvain clustering - replaced with leiden.
+
+API and Bug Fixes:
+* Fix import on MutableVertexPartition to use leidenalg.VertexPartition.
+* Switch default flavour in leiden to use igraph (and its required parameters).
+* Renamed methods and classes to follow lowercase standard.
+
 1.2.2 (2025-10-20)
 ------------------
 * Added support for Python 3.11 and 3.12.

docs/api.rst

@@ -18,13 +18,14 @@ Wrapper functions: `wrapper`
 .. autosummary::
    :toctree: api/
 
-   Read10X
-   ReadOldST
-   ReadSlideSeq
-   ReadMERFISH
-   ReadSeqFish
-   convert_scanpy
+   read_10x
+   read_old_st
+   read_slide_seq
+   read_merfish
+   read_seq_fish
+   read_xenium
    create_stlearn
+   convert_scanpy
 
 
 Add: `add`
@@ -115,15 +116,15 @@ Spatial: `spatial`
 
    spatial.morphology.adjust
 
-.. module:: stlearn.spatial.SME
+.. module:: stlearn.spatial.sme
 .. currentmodule:: stlearn
 
 .. autosummary::
    :toctree: api/
 
-   spatial.SME.SME_impute0
-   spatial.SME.pseudo_spot
-   spatial.SME.SME_normalize
+   spatial.sme.sme_impute0
+   spatial.sme.pseudo_spot
+   spatial.sme.sme_normalize
 
 Tools: `tl`
 -------------------
@@ -135,7 +136,6 @@ Tools: `tl`
 
    tl.clustering.kmeans
    tl.clustering.leiden
-   tl.clustering.louvain
    tl.cci.load_lrs
    tl.cci.grid
    tl.cci.run
@@ -151,7 +151,7 @@ Plot: `pl`
 .. autosummary::
    :toctree: api/
 
-   pl.QC_plot
+   pl.qc_plot
    pl.gene_plot
    pl.gene_plot_interactive
    pl.cluster_plot
@@ -183,7 +183,7 @@ Plot: `pl`
    pl.trajectory.local_plot
    pl.trajectory.tree_plot
    pl.trajectory.transition_markers_plot
-   pl.trajectory.DE_transition_plot
+   pl.trajectory.de_transition_plot
 
 Datasets: `datasets`
 ---------------------------

docs/index.rst

@@ -38,6 +38,8 @@ undissociated tissue sample.
 Latest Additions
 ----------------
 
+.. include:: release_notes/1.3.0.rst
+
 .. include:: release_notes/1.2.2.rst
 
 .. include:: release_notes/1.1.5.rst

docs/release_notes/1.3.0.rst

@@ -0,0 +1,10 @@
+1.3.0 `2026-02-24`
+~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. rubric:: Features
+
+* Removed interactive stLearn/embedded web application.
+* Removed louvain clustering.
+* Renamed methods and classes to follow lowercase standard.
+
+

docs/release_notes/index.rst

@@ -1,6 +1,8 @@
 Release Notes
 ===================================================
 
+.. include:: 1.3.0.rst
+
 .. include:: 1.2.2.rst
 
 .. include:: 1.1.5.rst

pyproject.toml

@@ -4,26 +4,46 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "stlearn"
-version = "1.2.2"
+version = "1.3.0"
 authors = [
-    {name = "Genomics and Machine Learning lab", email = "andrew.newman@uq.edu.au"},
+    { name = "Genomics and Machine Learning Lab", email = "andrew.newman@uq.edu.au" },
 ]
 description = "A downstream analysis toolkit for Spatial Transcriptomic data"
-readme = {file = "README.md", content-type = "text/markdown"}
-license = {text = "BSD license"}
-requires-python = ">=3.10,<3.13"
+readme = { file = "README.md", content-type = "text/markdown" }
+license = { text = "BSD license" }
+requires-python = ">=3.12"
+dependencies = [
+    "bokeh>=3.7.0,<4.0",
+    "click>=8.2.0,<9.0",
+    "igraph>=1.0.0",
+    "leidenalg>=0.11.0",
+    "numba>=0.58.1",
+    "numpy>=1.26.0,<2.0",
+    "pillow>=11.0.0,<12.0",
+    "scanpy>=1.11.0,<2.0",
+    "scikit-image>=0.22.0",
+    "tensorflow>=2.14.1",
+    "keras>=2.14.0",
+    "pandas>=2.3.0",
+    "imageio>=2.37.0,<3.0",
+    "scipy>=1.11.0,<2.0",
+    "scikit-learn>=1.7.0,<2.0",
+]
 keywords = ["stlearn"]
 classifiers = [
     "Development Status :: 5 - Production/Stable",
+    "Environment :: Console",
+    "Framework :: Jupyter",
     "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
     "License :: OSI Approved :: BSD License",
     "Natural Language :: English",
-    "Programming Language :: Python :: 3.10",
-    "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Scientific/Engineering :: Visualization",
 ]
-dynamic = ["dependencies"]
-
 [project.optional-dependencies]
 dev = [
     "black>=23.0",
@@ -44,18 +64,12 @@ test = [
     "pytest",
     "pytest-cov",
 ]
-webapp = [
-    "flask>=2.0.0",
-    "flask-wtf>=1.0.0",
-    "wtforms>=3.0.0",
-    "markupsafe>2.1.0",
-]
 jupyter = [
     "jupyter>=1.0.0",
     "jupyterlab>=3.0.0",
-    "ipywidgets>=7.6.0",
+    "ipywidgets>=8.0.0",
     "plotly>=5.0.0",
-    "bokeh>=2.4.0",
+    "bokeh>=3.7.0,<4.0",
     "rpy2>=3.4.0",
 ]
 
@@ -73,15 +87,15 @@ include = ["stlearn", "stlearn.*"]
 "*" = ["*"]
 
 [tool.setuptools.dynamic]
-dependencies = {file = ["requirements.txt"]}
+dependencies = { file = ["requirements.txt"] }
 
 [tool.ruff]
-line-length=88
-target-version = "py310"
+target-version = "py311"
+line-length = 88
 
 [tool.ruff.lint]
 select = ["E", "F", "W", "I", "N", "UP"]
-ignore = ["E722", "F811", "N802", "N803", "N806", "N818", "N999", "UP031"]
+ignore = ["E722", "F811", "N803", "N806", "N818"]
 exclude = [".git", "__pycache__", "build", "dist"]
 
 [tool.ruff.format]

stlearn/__init__.py

@@ -11,13 +11,13 @@
 
 # Wrapper
 from .wrapper.read import (
-    Read10X,
-    ReadMERFISH,
-    ReadOldST,
-    ReadSeqFish,
-    ReadSlideSeq,
-    ReadXenium,
     create_stlearn,
+    read_10x,
+    read_merfish,
+    read_old_st,
+    read_seq_fish,
+    read_slide_seq,
+    read_xenium,
 )
 
 # from . import cli
@@ -29,12 +29,12 @@
     "pl",
     "spatial",
     "datasets",
-    "ReadSlideSeq",
-    "Read10X",
-    "ReadOldST",
-    "ReadMERFISH",
-    "ReadSeqFish",
-    "ReadXenium",
+    "read_slide_seq",
+    "read_10x",
+    "read_old_st",
+    "read_merfish",
+    "read_seq_fish",
+    "read_xenium",
     "create_stlearn",
     "settings",
     "types",

stlearn/adds/add_image.py

@@ -71,15 +71,11 @@ def image(
 
             print("Added tissue image to the object!")
         except:
-            raise ValueError(
-                f"""\
+            raise ValueError(f"""\
             {imgpath!r} does not end on a valid extension.
-            """
-            )
+            """)
     else:
-        raise ValueError(
-            f"""\
+        raise ValueError(f"""\
         {imgpath!r} does not end on a valid extension.
-        """
-        )
+        """)
     return adata if copy else None