update packages and fix CI (#518)

* sep_pjw

* update precommit

* gitignore

* update various packages

* run poetry update

* ruff notebooks

* add 3.12 to test

.github/workflows/pytest.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
       - name: Checkout github repo

.gitignore

@@ -9,3 +9,5 @@
 /dist/
 /docs/build
 /data/cache
+Dockerfile
+.devcontainer

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 ---
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: trailing-whitespace
         exclude: ^.*fits
@@ -15,7 +15,7 @@ repos:
         exclude: ^.*fits
 
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.7.1
+    rev: 0.8.1
     hooks:
       - id: nbstripout
         args:

btk/deblend.py

@@ -6,7 +6,7 @@
 from typing import Dict, List, Optional, Tuple, Union
 
 import numpy as np
-import sep
+import sep_pjw as sep
 from astropy import units
 from astropy.coordinates import SkyCoord
 from astropy.table import Table

btk/measure.py

@@ -4,7 +4,7 @@
 
 import galsim
 import numpy as np
-import sep
+import sep_pjw as sep
 from galsim import GSObject
 
 

notebooks/01-advanced-deblending.ipynb

@@ -316,7 +316,7 @@
     "plt.imshow(blend_batch.blend_images[3, 2, :, :], cmap=\"gray\")\n",
     "\n",
     "# plot centers of truth\n",
-    "plt.scatter(blend_batch.catalog_list[3][\"x_peak\"], blend_batch.catalog_list[3][\"y_peak\"], \n",
+    "plt.scatter(blend_batch.catalog_list[3][\"x_peak\"], blend_batch.catalog_list[3][\"y_peak\"],\n",
     "            c=\"r\", marker=\"x\", label=\"targets\")\n",
     "\n",
     "# plot centers of prediction\n",

notebooks/01-advanced-generation.ipynb

@@ -449,7 +449,7 @@
     "from btk.catalog import CosmosCatalog\n",
     "\n",
     "cosmos_files = [\n",
-    "\"../data/cosmos/real_galaxy_catalog_23.5_example.fits\", \n",
+    "\"../data/cosmos/real_galaxy_catalog_23.5_example.fits\",\n",
     "\"../data/cosmos/real_galaxy_catalog_23.5_example_fits.fits\"\n",
     "]\n",
     "\n",

notebooks/02-advanced-plots.ipynb

@@ -204,7 +204,7 @@
     "plt.imshow(blend_batch.blend_images[ii, 2, :, :], cmap=\"gray\")\n",
     "\n",
     "# plot centers\n",
-    "plt.scatter(blend_batch.catalog_list[ii][\"x_peak\"], \n",
+    "plt.scatter(blend_batch.catalog_list[ii][\"x_peak\"],\n",
     "            blend_batch.catalog_list[ii][\"y_peak\"], c=\"r\", marker=\"x\")"
    ]
   },
@@ -423,7 +423,7 @@
     "r, c  = mat1.shape\n",
     "_mat1[:r, :c] = mat1[:, :]\n",
     "\n",
-    "# plot \n",
+    "# plot\n",
     "im1 = ax1.imshow(_mat1, vmin=0, vmax=1, cmap='binary')\n",
     "im2 = ax2.imshow(_mat2, vmin=0, vmax=1, cmap='binary')\n",
     "\n",
@@ -435,7 +435,7 @@
     "\n",
     "ax1.set_yticks([0, 1, 2, 3, 4, 5, 6])\n",
     "ax2.set_yticks([0, 1, 2, 3, 4, 5, 6])\n",
-    "ax2.set_xticks([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10]); "
+    "ax2.set_xticks([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10]);"
    ]
   },
   {
@@ -574,7 +574,7 @@
     "# join data from all batches into single array\n",
     "\n",
     "# sep\n",
-    "all_sep = {'mse': np.array([]), 'psnr': np.array([]), 'ssim': np.array([])} \n",
+    "all_sep = {'mse': np.array([]), 'psnr': np.array([]), 'ssim': np.array([])}\n",
     "for metric_name, metric in metrics_sep.items():\n",
     "    for mvalues in metric.all_data:\n",
     "        all_sep[metric_name] = np.concatenate([all_sep[metric_name], mvalues[metric_name]])\n",
@@ -610,15 +610,15 @@
     }
    ],
    "source": [
-    "# plot histograms of each metric for both deblenders \n",
+    "# plot histograms of each metric for both deblenders\n",
     "fig, axes = plt.subplots(1, 3, figsize=(15, 5))\n",
     "ranges = [(0, 200), (20, 70), (0.9, 1.0)]\n",
     "latex_metric_names = [r'\\rm MSE', r'\\rm PSNR', r'\\rm SSIM']\n",
     "for ii, metric_name in enumerate(['mse', 'psnr', 'ssim']):\n",
     "    ax = axes[ii]\n",
     "    _, bins, _ = ax.hist(all_sep[metric_name], bins=25, alpha=0.5, label=r'\\rm SEP',\n",
     "                         color='C0', histtype='stepfilled',  range=ranges[ii])\n",
-    "    ax.hist(all_scarlet[metric_name], bins=bins, alpha=0.5, label=r'\\rm Scarlet', \n",
+    "    ax.hist(all_scarlet[metric_name], bins=bins, alpha=0.5, label=r'\\rm Scarlet',\n",
     "            color='C1', histtype='stepfilled',  range=ranges[ii])\n",
     "    ax.set_xlabel(latex_metric_names[ii], fontsize=20)\n",
     "    if ii == 0:\n",
@@ -670,10 +670,10 @@
     "min_distance = int(get_psf_size(survey)) # needs to be an integer\n",
     "\n",
     "# setup both deblenders\n",
-    "peak_finder = PeakLocalMax(max_n_sources=max_n_sources+10, \n",
+    "peak_finder = PeakLocalMax(max_n_sources=max_n_sources+10,\n",
     "                           sky_level=sky_level,\n",
-    "                           threshold_scale=5, \n",
-    "                           min_distance=min_distance*2, \n",
+    "                           threshold_scale=5,\n",
+    "                           min_distance=min_distance*2,\n",
     "                           use_band=2 # r-band\n",
     "                           )\n",
     "\n",