Incomplete files in last dist

Author: Mr-Milk

CHANGES.txt

@@ -0,0 +1,9 @@
+0.1.1
+1. Incomplete files in previous distribution
+2. Fix SettingWithCopy warning in plotting.cell_map
+
+0.1.0
+1. The first major release of SpatialTis
+2. Yank the 1.0.0.dev0 version
+3. Neighbor search, neighborhood analysis, spatial enrichment analysis reimplemented in Rust
+4. Allow Ray runs on Windows

MANIFEST.in

@@ -1,3 +1,4 @@
+# Exclude dev files
 prune tests
 prune docs
 prune src
@@ -7,4 +8,8 @@ exclude .isort.cfg
 exclude .pre-commit-config.yaml
 exclude readthedocs.yaml
 exclude mypy.ini
-exclude MANIFEST.in
+
+# Include published needed files
+include LICENSE
+include CHANGES.txt
+recursive-include spatialtis/ *.py

docs/source/index.rst

@@ -15,13 +15,13 @@ SpatialTis is a spatial analysis toolkit for single-cell multiplexed tissue data
 For a quick view of what it's does, check our following examples:
 
 - MIBI breast cancer 180K cells: |MIBI-tutorial|_
-- IMC diabetes 1.7M cells: |IMC-tutorial|
+- IMC diabetes 1.7M cells: |IMC-tutorial|_
 
 .. |MIBI-tutorial| image:: https://badgen.net/badge/view%20on/nbviewer/orange
 .. _MIBI-tutorial: https://nbviewer.jupyter.org/github/Mr-Milk/SpatialTis-Tutorial/blob/master/Tutorial-1%20%28MIBI-dataset%29.ipynb
 
 .. |IMC-tutorial| image:: https://badgen.net/badge/view%20on/nbviewer/orange
-.. _IMC_tutorial: https://nbviewer.jupyter.org/github/Mr-Milk/SpatialTis-Tutorial/blob/master/Tutorial-2%20%28IMC-dataset%29.ipynb
+.. _IMC-tutorial: https://nbviewer.jupyter.org/github/Mr-Milk/SpatialTis-Tutorial/blob/master/Tutorial-2%20%28IMC-dataset%29.ipynb
 
 
 .. toctree::

docs/source/usage/installation.rst

@@ -1,7 +1,7 @@
 Installation
 ============
 
-SpatialTis requires **Python 3.6+**, it's recommended that you start a new environment.
+SpatialTis requires **Python 3.6+**, it's recommended that you install it in a new environment.
 
 PYPI
 ----
@@ -17,7 +17,7 @@ For windows user
 -----------------
 
 You may find installation problem with following dependencies, please refer to their documentation for detail instructions.
-You can try install them via conda channels, or compile it on your machine:
+You can try install them via conda channels, or compile it from source on your machine:
 
 - `python-igraph <https://igraph.org/python/>`_
 - `leidenalg <https://leidenalg.readthedocs.io/en/stable/install.html>`_

setup.py

@@ -1,15 +1,14 @@
 from pathlib import Path
 
-from setuptools import find_packages, setup
+from setuptools import setup
 
 README = Path("README.md").read_text()
 
 setup(name="spatialtis",
-      packages=find_packages(include=["spatialtis"]),
       description="spatial analysis toolkit for single-cell multiplexed tissue data",
       long_description=README,
       long_description_content_type="text/markdown",
-      version="0.1.0",
+      version="0.1.1",
       author="Mr-Milk",
       url="https://github.com/Mr-Milk/SpatialTis",
       author_email="yb97643@um.edu.mo",
@@ -25,5 +24,5 @@
                         'scipy', 'shapely', 'bokeh',
                         'seaborn', 'colour', 'matplotlib', 'tqdm', 'pyecharts', 'ray',
                         'spatialentropy', 'colorama', 'snapshot_phantomjs', 'neighborhood_analysis'],
-      extra_requires={'all': ['scikit-image', 'python-igraph', 'leidenalg', 'alphashape', 'tifffile', ]}
+      extras_require={'all': ['scikit-image', 'python-igraph', 'leidenalg', 'alphashape', 'tifffile', ]}
       )

spatialtis/plotting/_cell_map.py

@@ -66,7 +66,7 @@ def cell_map(
         if centroid_key not in adata.obs.keys():
             raise KeyError("Centroid key not exist")
 
-    df = adata.obs.query("&".join([f"({k}=='{v}')" for k, v in query.items()]))
+    df = adata.obs.query("&".join([f"({k}=='{v}')" for k, v in query.items()])).copy()
 
     if selected_types is not None:
         new_types = []