fix: run pixplot on more recent M1 mac

.gitignore

@@ -5,6 +5,7 @@
 *.ipynb
 *.egg-info
 *.ruby-version
+.idea
 manifest.txt
 missing-metadata.txt
 dist

README.md

@@ -10,11 +10,11 @@ See the [change log](https://github.com/YaleDHLab/pix-plot/wiki/Change-Log) for
 
 We maintain several platform-specific [installation cookbooks](https://github.com/YaleDHLab/pix-plot/wiki) online.
 
-Broadly speaking, to install the Python dependencies, we recommend you [install Anaconda](https://www.anaconda.com/products/individual#Downloads) and then create a conda environment with a Python 3.7 runtime:
+Broadly speaking, to install the Python dependencies, we recommend you [install Anaconda](https://www.anaconda.com/products/individual#Downloads) and then create a conda environment with a Python 3.x runtime:
 
 ```bash
-conda create --name=3.7 python=3.7
-source activate 3.7
+conda create --name=3.10 python=3.10
+source activate 3.10
 ```
 
 Then you can install the dependencies by running:
@@ -64,7 +64,7 @@ image_datasets.oslomini.download()
 The `.download()` command will make a directory named `datasets` in your current working directory. That `datasets` directory will contain a subdirectory named 'oslomini', which contains a directory of images and another directory with a CSV file of image metadata. Using that data, we can next build a plot:
 
 ```bash
-pixplot --images "datasets/oslomini/images/*" --metadata "datasets/oslomini/metadata/metadata.csv"
+pixplot --images "datasets/oslomini/images/**" --metadata "datasets/oslomini/metadata/metadata.csv"
 ```
 
 ## Creating Massive Plots

pixplot/pixplot.py

@@ -7,6 +7,7 @@
 
 from os.path import basename, join, exists, dirname, realpath
 from distutils.dir_util import copy_tree
+import numpy as np
 import pkg_resources
 import datetime
 import argparse
@@ -16,6 +17,9 @@
 import sys
 import os
 
+if not hasattr(np, 'float'):
+  np.float = float
+
 def timestamp():
   '''Return a string for printing the current time'''
   return str(datetime.datetime.now()) + ':'
@@ -606,7 +610,7 @@ def process_single_layout_umap(v, **kwargs):
   if cuml_ready:
     z = model.fit(v).embedding_
   else:
-    if os.path.exists(out_path) and kwargs['use_cache']: 
+    if os.path.exists(out_path) and kwargs['use_cache']:
       return {
         'variants': [
           {

setup.py

@@ -39,17 +39,17 @@
     'cmake>=3.15.3',
     'Cython>=0.29.21',
     'glob2>=0.6',
-    'h5py~=3.1.0',
+    'h5py==3.15.1',
     'iiif-downloader>=0.0.6',
-    'numba==0.53',
-    'numpy==1.19.5',
+    'numba==0.57.1',
+    'numpy==1.24',
     'Pillow>=6.1.0',
     'pointgrid>=0.0.2',
     'python-dateutil>=2.8.0',
-    'scikit-learn==0.24.2',
-    'scipy==1.4.0',
+    'scikit-learn==1.2.2',
+    'scipy==1.15.3',
     'six==1.15.0',
-    'tensorflow==2.5.0',
+    'tensorflow==2.13.0',
     'tqdm==4.61.1',
     'umap-learn==0.5.1',
     'yale-dhlab-rasterfairy>=1.0.3',