Newmana/stlearn 1.3.0#343

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Merged
newmana merged 8 commits into from
Feb 24, 2026
Merged

Newmana/stlearn 1.3.0 #343

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d93fcff
* Fix zip id.
newmana Feb 23, 2026
41fc0f7
Try fix legend layout.
newmana Feb 23, 2026
828be72
Merge branch 'master' into newmana/stlearn-1.3.0
newmana Feb 24, 2026
929fbeb
Revert tensorflow and keras version.
newmana Feb 24, 2026
fb486d0
Update release notes.
newmana Feb 24, 2026
03989d5
Reformat.
newmana Feb 24, 2026
d9f1313
Update instructions.
newmana Feb 24, 2026
10f81ea
Fix URL.
newmana Feb 24, 2026
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11 changes: 3 additions & 8 deletions CONTRIBUTING.rst
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Original file line numberDiff line numberDiff line change
Expand Up@@ -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:

Expand DownExpand Up@@ -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::

Expand DownExpand Up@@ -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
----
Expand Down
10 changes: 10 additions & 0 deletions HISTORY.rst
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -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.
Expand Down
26 changes: 13 additions & 13 deletions docs/api.rst
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -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`
Expand DownExpand Up@@ -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`
-------------------
Expand All@@ -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
Expand All@@ -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
Expand DownExpand Up@@ -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`
---------------------------
Expand Down
2 changes: 2 additions & 0 deletions docs/index.rst
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -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
Expand Down
16 changes: 0 additions & 16 deletions docs/interactive.rst
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10 changes: 10 additions & 0 deletions docs/release_notes/1.3.0.rst
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Original file line numberDiff line numberDiff line change
@@ -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.


2 changes: 2 additions & 0 deletions docs/release_notes/index.rst
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Open in desktop
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,8 @@
Release Notes
===================================================

.. include:: 1.3.0.rst

.. include:: 1.2.2.rst

.. include:: 1.1.5.rst
Expand Down
56 changes: 35 additions & 21 deletions pyproject.toml
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Original file line numberDiff line numberDiff line change
Expand Up@@ -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",
Expand All@@ -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",
]

Expand All@@ -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]
Expand Down
15 changes: 0 additions & 15 deletions requirements.txt
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This file was deleted.

24 changes: 12 additions & 12 deletions stlearn/__init__.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -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
Expand All@@ -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",
Expand Down
12 changes: 4 additions & 8 deletions stlearn/adds/add_image.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -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
Loading
Loading
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
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})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

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Newmana/stlearn 1.3.0#343

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Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

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to your account

 Merged

newmana
merged 8 commits into

from

Feb 24, 2026
 Merged


Newmana/stlearn 1.3.0
#343
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d93fcff

* Fix zip id.


newmana Feb 23, 2026
41fc0f7

Try fix legend layout.


newmana Feb 23, 2026
828be72

Merge branch 'master' into newmana/stlearn-1.3.0


newmana Feb 24, 2026
929fbeb

Revert tensorflow and keras version.


newmana Feb 24, 2026
fb486d0

Update release notes.


newmana Feb 24, 2026
03989d5

Reformat.


newmana Feb 24, 2026
d9f1313

Update instructions.


newmana Feb 24, 2026
10f81ea

Fix URL.


newmana Feb 24, 2026

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11 changes: 3 additions & 8 deletions
CONTRIBUTING.rst

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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:

Expand DownExpand Up@@ -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::

Expand DownExpand Up@@ -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
----
Expand Down

10 changes: 10 additions & 0 deletions
HISTORY.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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.
Expand Down

26 changes: 13 additions & 13 deletions
docs/api.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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`
Expand DownExpand Up@@ -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`
-------------------
Expand All@@ -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
Expand All@@ -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
Expand DownExpand Up@@ -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`
---------------------------
Expand Down

2 changes: 2 additions & 0 deletions
docs/index.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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
Expand Down

16 changes: 0 additions & 16 deletions
docs/interactive.rst

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10 changes: 10 additions & 0 deletions
docs/release_notes/1.3.0.rst

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Open in desktop

Original file line numberDiff line numberDiff line change
@@ -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.



2 changes: 2 additions & 0 deletions
docs/release_notes/index.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,6 +1,8 @@
Release Notes
===================================================

.. include:: 1.3.0.rst

.. include:: 1.2.2.rst

.. include:: 1.1.5.rst
Expand Down

56 changes: 35 additions & 21 deletions
pyproject.toml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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",
Expand All@@ -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",
]

Expand All@@ -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]
Expand Down

15 changes: 0 additions & 15 deletions
requirements.txt

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This file was deleted.


24 changes: 12 additions & 12 deletions
stlearn/__init__.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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
Expand All@@ -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",
Expand Down

12 changes: 4 additions & 8 deletions
stlearn/adds/add_image.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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
Loading
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
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newmana
merged 8 commits into

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Feb 24, 2026
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Newmana/stlearn 1.3.0
#343
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d93fcff

* Fix zip id.


newmana Feb 23, 2026
41fc0f7

Try fix legend layout.


newmana Feb 23, 2026
828be72

Merge branch 'master' into newmana/stlearn-1.3.0


newmana Feb 24, 2026
929fbeb

Revert tensorflow and keras version.


newmana Feb 24, 2026
fb486d0

Update release notes.


newmana Feb 24, 2026
03989d5

Reformat.


newmana Feb 24, 2026
d9f1313

Update instructions.


newmana Feb 24, 2026
10f81ea

Fix URL.


newmana Feb 24, 2026

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11 changes: 3 additions & 8 deletions
CONTRIBUTING.rst

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Original file line numberDiff line numberDiff line change
Expand Up@@ -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:

Expand DownExpand Up@@ -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::

Expand DownExpand Up@@ -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
----
Expand Down

10 changes: 10 additions & 0 deletions
HISTORY.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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.
Expand Down

26 changes: 13 additions & 13 deletions
docs/api.rst

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Original file line numberDiff line numberDiff line change
Expand Up@@ -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`
Expand DownExpand Up@@ -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`
-------------------
Expand All@@ -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
Expand All@@ -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
Expand DownExpand Up@@ -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`
---------------------------
Expand Down

2 changes: 2 additions & 0 deletions
docs/index.rst

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Original file line numberDiff line numberDiff line change
Expand Up@@ -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
Expand Down

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docs/interactive.rst

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docs/release_notes/1.3.0.rst

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Original file line numberDiff line numberDiff line change
@@ -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.



2 changes: 2 additions & 0 deletions
docs/release_notes/index.rst

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Original file line numberDiff line numberDiff line change
@@ -1,6 +1,8 @@
Release Notes
===================================================

.. include:: 1.3.0.rst

.. include:: 1.2.2.rst

.. include:: 1.1.5.rst
Expand Down

56 changes: 35 additions & 21 deletions
pyproject.toml

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Expand Up@@ -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",
Expand All@@ -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",
]

Expand All@@ -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]
Expand Down

15 changes: 0 additions & 15 deletions
requirements.txt

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24 changes: 12 additions & 12 deletions
stlearn/__init__.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -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
Expand All@@ -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",
Expand Down

12 changes: 4 additions & 8 deletions
stlearn/adds/add_image.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -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
Loading
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
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try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Newmana/stlearn 1.3.0#343

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 Merged

newmana
merged 8 commits into

from

Feb 24, 2026
 Merged


Newmana/stlearn 1.3.0
#343
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d93fcff

* Fix zip id.


newmana Feb 23, 2026
41fc0f7

Try fix legend layout.


newmana Feb 23, 2026
828be72

Merge branch 'master' into newmana/stlearn-1.3.0


newmana Feb 24, 2026
929fbeb

Revert tensorflow and keras version.


newmana Feb 24, 2026
fb486d0

Update release notes.


newmana Feb 24, 2026
03989d5

Reformat.


newmana Feb 24, 2026
d9f1313

Update instructions.


newmana Feb 24, 2026
10f81ea

Fix URL.


newmana Feb 24, 2026

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11 changes: 3 additions & 8 deletions
CONTRIBUTING.rst

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Original file line numberDiff line numberDiff line change
Expand Up@@ -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:

Expand DownExpand Up@@ -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::

Expand DownExpand Up@@ -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
----
Expand Down

10 changes: 10 additions & 0 deletions
HISTORY.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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.
Expand Down

26 changes: 13 additions & 13 deletions
docs/api.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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`
Expand DownExpand Up@@ -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`
-------------------
Expand All@@ -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
Expand All@@ -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
Expand DownExpand Up@@ -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`
---------------------------
Expand Down

2 changes: 2 additions & 0 deletions
docs/index.rst

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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
Expand Down

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docs/interactive.rst

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docs/release_notes/1.3.0.rst

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Original file line numberDiff line numberDiff line change
@@ -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.



2 changes: 2 additions & 0 deletions
docs/release_notes/index.rst

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Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,6 +1,8 @@
Release Notes
===================================================

.. include:: 1.3.0.rst

.. include:: 1.2.2.rst

.. include:: 1.1.5.rst
Expand Down

56 changes: 35 additions & 21 deletions
pyproject.toml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -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",
Expand All@@ -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",
]

Expand All@@ -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]
Expand Down

15 changes: 0 additions & 15 deletions
requirements.txt

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24 changes: 12 additions & 12 deletions
stlearn/__init__.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -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
Expand All@@ -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",
Expand Down

12 changes: 4 additions & 8 deletions
stlearn/adds/add_image.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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
Loading
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

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 Merged

newmana
merged 8 commits into

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Feb 24, 2026
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Newmana/stlearn 1.3.0
#343
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d93fcff

* Fix zip id.


newmana Feb 23, 2026
41fc0f7

Try fix legend layout.


newmana Feb 23, 2026
828be72

Merge branch 'master' into newmana/stlearn-1.3.0


newmana Feb 24, 2026
929fbeb

Revert tensorflow and keras version.


newmana Feb 24, 2026
fb486d0

Update release notes.


newmana Feb 24, 2026
03989d5

Reformat.


newmana Feb 24, 2026
d9f1313

Update instructions.


newmana Feb 24, 2026
10f81ea

Fix URL.


newmana Feb 24, 2026

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11 changes: 3 additions & 8 deletions
CONTRIBUTING.rst

View file


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Original file line numberDiff line numberDiff line change
Expand Up@@ -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:

Expand DownExpand Up@@ -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::

Expand DownExpand Up@@ -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
----
Expand Down

10 changes: 10 additions & 0 deletions
HISTORY.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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.
Expand Down

26 changes: 13 additions & 13 deletions
docs/api.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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`
Expand DownExpand Up@@ -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`
-------------------
Expand All@@ -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
Expand All@@ -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
Expand DownExpand Up@@ -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`
---------------------------
Expand Down

2 changes: 2 additions & 0 deletions
docs/index.rst

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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
Expand Down

16 changes: 0 additions & 16 deletions
docs/interactive.rst

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10 changes: 10 additions & 0 deletions
docs/release_notes/1.3.0.rst

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Original file line numberDiff line numberDiff line change
@@ -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.



2 changes: 2 additions & 0 deletions
docs/release_notes/index.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,6 +1,8 @@
Release Notes
===================================================

.. include:: 1.3.0.rst

.. include:: 1.2.2.rst

.. include:: 1.1.5.rst
Expand Down

56 changes: 35 additions & 21 deletions
pyproject.toml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -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",
Expand All@@ -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",
]

Expand All@@ -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]
Expand Down

15 changes: 0 additions & 15 deletions
requirements.txt

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This file was deleted.


24 changes: 12 additions & 12 deletions
stlearn/__init__.py

View file


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Original file line numberDiff line numberDiff line change
Expand Up@@ -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
Expand All@@ -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",
Expand Down

12 changes: 4 additions & 8 deletions
stlearn/adds/add_image.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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
Loading
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Newmana/stlearn 1.3.0#343

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

 Sign up for GitHub

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privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Merged

newmana
merged 8 commits into

from

Feb 24, 2026
 Merged


Newmana/stlearn 1.3.0
#343
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d93fcff

* Fix zip id.


newmana Feb 23, 2026
41fc0f7

Try fix legend layout.


newmana Feb 23, 2026
828be72

Merge branch 'master' into newmana/stlearn-1.3.0


newmana Feb 24, 2026
929fbeb

Revert tensorflow and keras version.


newmana Feb 24, 2026
fb486d0

Update release notes.


newmana Feb 24, 2026
03989d5

Reformat.


newmana Feb 24, 2026
d9f1313

Update instructions.


newmana Feb 24, 2026
10f81ea

Fix URL.


newmana Feb 24, 2026

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11 changes: 3 additions & 8 deletions
CONTRIBUTING.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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:

Expand DownExpand Up@@ -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::

Expand DownExpand Up@@ -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
----
Expand Down

10 changes: 10 additions & 0 deletions
HISTORY.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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.
Expand Down

26 changes: 13 additions & 13 deletions
docs/api.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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`
Expand DownExpand Up@@ -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`
-------------------
Expand All@@ -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
Expand All@@ -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
Expand DownExpand Up@@ -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`
---------------------------
Expand Down

2 changes: 2 additions & 0 deletions
docs/index.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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
Expand Down

16 changes: 0 additions & 16 deletions
docs/interactive.rst

View file


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This file was deleted.


10 changes: 10 additions & 0 deletions
docs/release_notes/1.3.0.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -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.



2 changes: 2 additions & 0 deletions
docs/release_notes/index.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,6 +1,8 @@
Release Notes
===================================================

.. include:: 1.3.0.rst

.. include:: 1.2.2.rst

.. include:: 1.1.5.rst
Expand Down

56 changes: 35 additions & 21 deletions
pyproject.toml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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",
Expand All@@ -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",
]

Expand All@@ -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]
Expand Down

15 changes: 0 additions & 15 deletions
requirements.txt

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This file was deleted.


24 changes: 12 additions & 12 deletions
stlearn/__init__.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -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
Expand All@@ -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",
Expand Down

12 changes: 4 additions & 8 deletions
stlearn/adds/add_image.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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
Loading
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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Newmana/stlearn 1.3.0#343

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 Merged

newmana
merged 8 commits into

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Feb 24, 2026
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Newmana/stlearn 1.3.0
#343
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d93fcff

* Fix zip id.


newmana Feb 23, 2026
41fc0f7

Try fix legend layout.


newmana Feb 23, 2026
828be72

Merge branch 'master' into newmana/stlearn-1.3.0


newmana Feb 24, 2026
929fbeb

Revert tensorflow and keras version.


newmana Feb 24, 2026
fb486d0

Update release notes.


newmana Feb 24, 2026
03989d5

Reformat.


newmana Feb 24, 2026
d9f1313

Update instructions.


newmana Feb 24, 2026
10f81ea

Fix URL.


newmana Feb 24, 2026

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11 changes: 3 additions & 8 deletions
CONTRIBUTING.rst

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Original file line numberDiff line numberDiff line change
Expand Up@@ -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:

Expand DownExpand Up@@ -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::

Expand DownExpand Up@@ -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
----
Expand Down

10 changes: 10 additions & 0 deletions
HISTORY.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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.
Expand Down

26 changes: 13 additions & 13 deletions
docs/api.rst

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Original file line numberDiff line numberDiff line change
Expand Up@@ -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`
Expand DownExpand Up@@ -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`
-------------------
Expand All@@ -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
Expand All@@ -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
Expand DownExpand Up@@ -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`
---------------------------
Expand Down

2 changes: 2 additions & 0 deletions
docs/index.rst

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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
Expand Down

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docs/interactive.rst

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10 changes: 10 additions & 0 deletions
docs/release_notes/1.3.0.rst

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Original file line numberDiff line numberDiff line change
@@ -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.



2 changes: 2 additions & 0 deletions
docs/release_notes/index.rst

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Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,6 +1,8 @@
Release Notes
===================================================

.. include:: 1.3.0.rst

.. include:: 1.2.2.rst

.. include:: 1.1.5.rst
Expand Down

56 changes: 35 additions & 21 deletions
pyproject.toml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -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",
Expand All@@ -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",
]

Expand All@@ -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]
Expand Down

15 changes: 0 additions & 15 deletions
requirements.txt

View file


Open in desktop


This file was deleted.


24 changes: 12 additions & 12 deletions
stlearn/__init__.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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
Expand All@@ -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",
Expand Down

12 changes: 4 additions & 8 deletions
stlearn/adds/add_image.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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
Loading
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

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Newmana/stlearn 1.3.0#343

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Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

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 Merged

newmana
merged 8 commits into

from

Feb 24, 2026
 Merged


Newmana/stlearn 1.3.0
#343
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d93fcff

* Fix zip id.


newmana Feb 23, 2026
41fc0f7

Try fix legend layout.


newmana Feb 23, 2026
828be72

Merge branch 'master' into newmana/stlearn-1.3.0


newmana Feb 24, 2026
929fbeb

Revert tensorflow and keras version.


newmana Feb 24, 2026
fb486d0

Update release notes.


newmana Feb 24, 2026
03989d5

Reformat.


newmana Feb 24, 2026
d9f1313

Update instructions.


newmana Feb 24, 2026
10f81ea

Fix URL.


newmana Feb 24, 2026

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11 changes: 3 additions & 8 deletions
CONTRIBUTING.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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:

Expand DownExpand Up@@ -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::

Expand DownExpand Up@@ -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
----
Expand Down

10 changes: 10 additions & 0 deletions
HISTORY.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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.
Expand Down

26 changes: 13 additions & 13 deletions
docs/api.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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`
Expand DownExpand Up@@ -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`
-------------------
Expand All@@ -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
Expand All@@ -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
Expand DownExpand Up@@ -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`
---------------------------
Expand Down

2 changes: 2 additions & 0 deletions
docs/index.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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
Expand Down

16 changes: 0 additions & 16 deletions
docs/interactive.rst

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10 changes: 10 additions & 0 deletions
docs/release_notes/1.3.0.rst

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Original file line numberDiff line numberDiff line change
@@ -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.



2 changes: 2 additions & 0 deletions
docs/release_notes/index.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,6 +1,8 @@
Release Notes
===================================================

.. include:: 1.3.0.rst

.. include:: 1.2.2.rst

.. include:: 1.1.5.rst
Expand Down

56 changes: 35 additions & 21 deletions
pyproject.toml

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -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",
Expand All@@ -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",
]

Expand All@@ -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]
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15 changes: 0 additions & 15 deletions
requirements.txt

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24 changes: 12 additions & 12 deletions
stlearn/__init__.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -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
Expand All@@ -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",
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12 changes: 4 additions & 8 deletions
stlearn/adds/add_image.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -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
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