Merge pull request #326 from BiomedicalMachineLearning/newmana/upgrade

Upgrade to Python 3.10

Author: newmana

.github/workflows/python-package.yml

@@ -26,8 +26,14 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install pytest
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        pip install -e .[dev,test]
+    - name: Check style
+      run: |
+        black stlearn tests
+        ruff check stlearn tests
+    - name: Check types
+      run: |
+        mypy stlearn tests
     - name: Test with pytest
       run: |
-        pytest
+        pytest

.gitignore

@@ -1,21 +1,71 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
 *.pyc
-.ipynb_checkpoints
-*/.ipynb_checkpoints/*
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
 build/
+docs/api/
+docs/_build/
+docs/generated/
+data/samples
+develop-eggs/
 dist/
-*.egg-info
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# Unit tests / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+*/.ipynb_checkpoints/*
 /*.ipynb
+
+# Data files
 /*.csv
-output/
+
+# MacOS caching
 .DS_Store
 */.DS_Store
+
+# PyCharm etc
 .idea/
-docs/_build
+
+# Sphinx documentation
+docs.bk/_build
+
+# Distribution/package/temporary files
 data/
 tiling/
-.pytest_cache
 figures/
 *.h5ad
-inferCNV/
-stlearn/tools/microenv/cci/junk_code.py
-stlearn/tools/microenv/cci/.Rhistory

.readthedocs.yml

@@ -1,4 +1,25 @@
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version, and other tools you might need
 build:
-  image: latest
+  os: ubuntu-24.04
+  tools:
+    python: "3.10"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Optionally, but recommended,
+# declare the Python requirements required to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
 python:
-  version: 3.8
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - dev

AUTHORS.rst

@@ -5,9 +5,12 @@ Credits
 Development Lead
 ----------------
 
-* Genomics and Machine Learning lab
+* Genomics and Machine Learning Lab
 
 Contributors
 ------------
 
-None yet. Why not be the first?
+* Brad Balderson
+* Andrew Newman
+* Duy Pham
+* Xiao Tan

CONTRIBUTING.rst

@@ -64,26 +64,36 @@ Ready to contribute? Here's how to set up `stlearn` for local development.
 
     $ git clone git@github.com:your_name_here/stlearn.git
 
-3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
+3. Install your local copy into a virtualenv. This is how you set up your fork for local development::
 
-    $ mkvirtualenv stlearn
+    $ conda create -n stlearn-dev python=3.10 --y
+    $ conda activate stlearn-dev
     $ cd stlearn/
-    $ python setup.py develop
+    $ pip install -e .[dev,test]
+
+   Or if you prefer pip/virtualenv::
+
+    $ python -m venv stlearn-env
+    $ source stlearn-env/bin/activate  # On Windows: stlearn-env\Scripts\activate
+    $ cd stlearn/
+    $ pip install -e .[dev,test]
 
 4. Create a branch for local development::
 
     $ git checkout -b name-of-your-bugfix-or-feature
 
    Now you can make your changes locally.
 
-5. When you're done making changes, check that your changes pass flake8 and the
-   tests, including testing other Python versions with tox::
+5. When you're done making changes, check that your changes pass linters and tests::
 
-    $ flake8 stlearn tests
-    $ python setup.py test or pytest
-    $ tox
+    $ black stlearn tests
+    $ ruff check stlearn tests
+    $ mypy stlearn tests
+    $ pytest
+
+Or run everything with tox::
 
-   To get flake8 and tox, just pip install them into your virtualenv.
+    $ tox
 
 6. Commit your changes and push your branch to GitHub::
 

HISTORY.rst

@@ -2,24 +2,51 @@
 History
 =======
 
+1.1.0 (2025-07-02)
+------------------
+* Support Python 3.10.x
+* Added quality checks black, ruff and mypy and fixed appropriate source code.
+* Copy parameters now work with the same semantics as scanpy.
+* Library upgrades for leidenalg, louvain, numba, numpy, scanpy, and tensorflow.
+* datasets.xenium_sge - loads Xenium data (and caches it) similar to scanpy.visium_sge.
+
+API and Bug Fixes:
+* Xenium TIFF and cell positions are now aligned.
+* Consistent with type annotations - mainly missing None annotations.
+* pl.cluster_plot - Does not keep colours from previous runs when clustering.
+* pl.trajectory.pseudotime_plot - Fix typing of cluster values in .uns["split_node"].
+* Removed datasets.example_bcba - Replaced with wrapper for scanpy.visium_sge.
+* Moved spatials directory to spatial, cleaned up pl and tl packages.
+
 0.4.11 (2022-11-25)
 ------------------
+
 0.4.10 (2022-11-22)
 ------------------
+
 0.4.8 (2022-06-15)
 ------------------
+
 0.4.7 (2022-03-28)
 ------------------
+
 0.4.6 (2022-03-09)
 ------------------
+
 0.4.5 (2022-03-02)
 ------------------
+
 0.4.0 (2022-02-03)
 ------------------
+
 0.3.2 (2021-03-29)
 ------------------
+
 0.3.1 (2020-12-24)
 ------------------
+
 0.2.7 (2020-09-12)
 ------------------
+
 0.2.6 (2020-08-04)
+------------------

LICENSE

@@ -1,8 +1,6 @@
-
-
 BSD License
 
-Copyright (c) 2020, Genomics and Machine Learning lab
+Copyright (c) 2020-2025, Genomics and Machine Learning lab
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without modification,

docs/Makefile

@@ -1,10 +1,10 @@
 # Minimal makefile for Sphinx documentation
 #
 
-# You can set these variables from the command line.
-SPHINXOPTS    =
-SPHINXBUILD   = python -msphinx
-SPHINXPROJ    = stlearn
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
 SOURCEDIR     = .
 BUILDDIR      = _build
 

docs/_static/css/custom.css

@@ -0,0 +1,5 @@
+/* Custom styling for stLearn documentation */
+
+p img {
+    vertical-align: bottom
+}