Merge pull request #852 from bhilbert4/modernize-packaging

Modernize packaging

Author: bhilbert4

.github/workflows/ci.yml

@@ -2,9 +2,9 @@ name: Python Package CI
 
 on:
   push:
-    branches: [ "master" ]
+    branches: [ "main" ]
   pull_request:
-    branches: [ "master" ]
+    branches: [ "main" ]
 
 jobs:
   build:

.gitignore

@@ -7,6 +7,7 @@
 
 # Package Stuff #
 #################
+build/
 build/*
 dist/*
 mirages.egg-info/*

MANIFEST.in

@@ -1,18 +1,5 @@
-include mirage/config/NIRCam_subarray_definitions.list
-include mirage/config/NIRCam_zeropoints.list
-include mirage/config/__init__.py
-include mirage/config/dq_init.cfg
-include mirage/config/linearity.cfg
-include mirage/config/nircam_filter_pupil_pairings.list
-include mirage/config/nircam_read_pattern_definitions.list
-include mirage/config/refpix.cfg
-include mirage/config/saturation.cfg
-include mirage/config/superbias.cfg
-include mirage/config/xtalk20150303g0.errorcut.txt
+recursive-include mirage/config *
 include tests/test_data/NIRISS/niriss_soss_substrip256_clear.yaml
 include mirage/reference_files/jband_transmission.dat
 include mirage/reference_files/alpha_lyr_stis_009.fits
 include examples/niriss_soss_example_data/*
-exclude mirage/reference_files/stellarmodels/atlas/*
-exclude mirage/reference_files/stellarmodels/phoenix/*
-exclude mirage/version.py

environment_python_3.11.yml

@@ -8,29 +8,27 @@ dependencies:
 - pip
 - python==3.11.13
 - pip:
-    - asdf==4.5.0
-    - astropy==7.1.0
+    - asdf==5.3.0
+    - astropy==7.2.0
     - astroquery==0.4.11
     - batman-package>=2.5.2
-    - bokeh==3.8.0
-    - crds==13.0.6
-    - grismconf==1.51
-    - h5py==3.14.0
+    - bokeh==3.9.0
+    - crds==13.1.6
+    - grismconf>=1.60
+    - h5py==3.16.0
     - hotsoss==0.1.10
-    - ipython==9.6.0
-    - jupyter==1.1.1
-    - jwst==1.19.2
+    - jwst==2.0.0
     - jwst-backgrounds==1.3.0
     - jwst_gtvt==1.1.1
-    - lxml==6.0.2
-    - matplotlib==3.10.7
+    - lxml==6.1.0
+    - matplotlib==3.10.9
     - nircam_gsim>=1.71
-    - numpy==2.2.6
+    - numpy==2.3.5
     - photutils==2.3.0
-    - pysiaf==0.24.1
-    - pytest==8.4.2
+    - pysiaf>=0.25.0
+    - pytest==9.0.3
     - pyyaml==6.0.3
-    - scipy==1.16.2
-    - sphinx==8.2.3
-    - synphot==1.6.0
-    - webbpsf==2.0.0
+    - scipy==1.17.1
+    - setuptools==81.0.0
+    - stpsf==2.2.0
+    - synphot==1.7.0

environment_python_3.12.yml

@@ -8,28 +8,27 @@ dependencies:
 - pip
 - python==3.12.11
 - pip:
-    - asdf==4.5.0
-    - astropy==7.1.0
+    - asdf==5.3.0
+    - astropy==7.2.0
     - astroquery==0.4.11
-    - bokeh==3.8.0
-    - crds==13.0.6
-    - grismconf==1.51
-    - h5py==3.14.0
+    - batman-package>=2.5.2
+    - bokeh==3.9.0
+    - crds==13.1.6
+    - grismconf>=1.60
+    - h5py==3.16.0
     - hotsoss==0.1.10
-    - ipython==9.6.0
-    - jupyter==1.1.1
-    - jwst==1.19.2
+    - jwst==2.0.0
     - jwst-backgrounds==1.3.0
     - jwst_gtvt==1.1.1
-    - lxml==6.0.2
-    - matplotlib==3.10.7
+    - lxml==6.1.0
+    - matplotlib==3.10.9
     - nircam_gsim>=1.71
-    - numpy==2.2.6
+    - numpy==2.3.5
     - photutils==2.3.0
-    - pysiaf==0.24.1
-    - pytest==8.4.2
+    - pysiaf>=0.25.0
+    - pytest==9.0.3
     - pyyaml==6.0.3
-    - scipy==1.16.2
-    - sphinx==8.2.3
-    - synphot==1.6.0
-    - webbpsf==2.0.0
+    - scipy==1.17.1
+    - setuptools==81.0.0
+    - stpsf==2.2.0
+    - synphot==1.7.0

mirage/psf/deployments.py

@@ -20,7 +20,7 @@
 
 from astropy.io import fits
 import numpy as np
-import webbpsf
+import stpsf as webbpsf
 
 from mirage.logging import logging_functions
 from mirage.utils.constants import LOG_CONFIG_FILENAME, STANDARD_LOGFILE_NAME

mirage/psf/psf_selection.py

@@ -37,7 +37,7 @@
 
 from astropy.io import fits
 import numpy as np
-from webbpsf.utils import to_griddedpsfmodel
+from stpsf.utils import to_griddedpsfmodel
 
 from mirage.logging import logging_functions
 from mirage.utils.constants import NIRISS_PUPIL_WHEEL_FILTERS, NIRCAM_PUPIL_WHEEL_FILTERS, \

mirage/psf/segment_psfs.py

@@ -26,9 +26,9 @@
 from astropy.io import fits
 import numpy as np
 import pysiaf
-import webbpsf
-from webbpsf.gridded_library import CreatePSFLibrary
-from webbpsf.utils import to_griddedpsfmodel
+import stpsf
+from stpsf.gridded_library import CreatePSFLibrary
+from stpsf.utils import to_griddedpsfmodel
 
 import multiprocessing
 import functools
@@ -56,7 +56,7 @@ def _generate_psfs_for_one_segment(inst, ote, segment_tilts, out_dir, boresight,
 
     i_segment = i + 1
 
-    segname = webbpsf.webbpsf_core.segname(i_segment)
+    segname = stpsf.stpsf_core.segname(i_segment)
     logger.info('GENERATING SEGMENT {} DATA'.format(segname))
 
     det_filt_match = False
@@ -76,12 +76,12 @@ def _generate_psfs_for_one_segment(inst, ote, segment_tilts, out_dir, boresight,
             inst.detector = det
 
             # Restrict the pupil to the current segment
-            pupil = webbpsf.webbpsf_core.one_segment_pupil(i_segment)
+            pupil = stpsf.stpsf_core.one_segment_pupil(i_segment)
             ote.amplitude = pupil[0].data
             inst.pupil = ote
 
             # Determine normalization factor - what fraction of total pupil is in this one segment?
-            full_pupil = fits.getdata(os.path.join(webbpsf.utils.get_webbpsf_data_path(), 'jwst_pupil_RevW_npix1024.fits.gz'))
+            full_pupil = fits.getdata(os.path.join(stpsf.utils.get_stpsf_data_path(), 'jwst_pupil_RevW_npix1024.fits.gz'))
             pupil_fraction_for_this_segment = pupil[0].data.sum() / full_pupil.sum()
 
             # Generate the PSF grid
@@ -191,7 +191,12 @@ def generate_segment_psfs(ote, segment_tilts, out_dir, filters=['F212N', 'F480M'
     logger = logging.getLogger('mirage.psf.segment_psfs.generate_segment_psfs')
 
     # Create webbpsf NIRCam instance
-    inst = webbpsf.Instrument(instrument)
+    if instrument.lower() == 'nircam':
+        inst = stpsf.NIRCam()
+    elif instrument.lower() == 'fgs':
+        inst = stpsf.FGS()
+    else:
+        raise ValueError(f'Unsupported instrument: {instrument}')
 
     # Create dummy CreatePSFLibrary instance to get lists of filter and detectors
     lib = CreatePSFLibrary
@@ -415,14 +420,14 @@ def get_segment_offset(segment_number, detector, library_list):
     }
 
     x_rot = control_xaxis_rotations[segment]  # degrees
-    x_rot_rad = x_rot * np.pi / 180  # radians
+    x_rot_rad = np.float64(x_rot * np.pi / 180)  # radians
 
     # Note that y is defined as the x component and x is defined as the y component.
     # This is because "xtilt" moves the PSF in the y direction, and vice versa.
-    tilt_onto_y = (xtilt * np.cos(x_rot_rad)) - (ytilt * np.sin(x_rot_rad))
-    tilt_onto_x = (xtilt * np.sin(x_rot_rad)) + (ytilt * np.cos(x_rot_rad))
+    tilt_onto_y = np.float64((xtilt * np.cos(x_rot_rad)) - (ytilt * np.sin(x_rot_rad)))
+    tilt_onto_x = np.float64((xtilt * np.sin(x_rot_rad)) + (ytilt * np.cos(x_rot_rad)))
 
-    umrad_to_arcsec = 1e-6 * (180./np.pi) * 3600
+    umrad_to_arcsec = np.float64(1e-6 * (180./np.pi) * 3600)
     x_arcsec = 2 * umrad_to_arcsec * tilt_onto_x
     y_arcsec = 2 * umrad_to_arcsec * tilt_onto_y
 
@@ -450,11 +455,11 @@ def get_segment_offset(segment_number, detector, library_list):
     # between different OTE pose terms into optical tip and tilt. In particular, this is needed for
     # accurate modeling of radial translation corrections when using incoherent PSF calculations.
     if f'S{segment_number:02d}XTILT' in header:
-        hexike_to_arcsec = 206265/webbpsf.constants.JWST_SEGMENT_RADIUS
+        hexike_to_arcsec = 206265/stpsf.constants.JWST_SEGMENT_RADIUS
         # recall that Hexike tilt _around the X axis_ produces an offset _into Y_, and vice versa.
-        x_arcsec =  header[f'S{segment_number:02d}YTILT'] * hexike_to_arcsec
+        x_arcsec =  np.float64(header[f'S{segment_number:02d}YTILT'] * hexike_to_arcsec)
         # also recall coord flip of Y axis from OTE L.O.M in entrance pupil to exit pupil
-        y_arcsec = -header[f'S{segment_number:02d}XTILT'] * hexike_to_arcsec
+        y_arcsec = np.float64(-header[f'S{segment_number:02d}XTILT'] * hexike_to_arcsec)
 
     # Optionally, arbitrary boresight offset may also be present in the FITS header metadata.
     # If so, include that in the PSF too. Be careful about coordinate sign for the V2 axis!

mirage/psf/soss_trace.py

@@ -194,7 +194,7 @@ def generate_SOSS_psfs(filt):
         The filter to use, ['CLEAR', 'F277W']
     """
     try:
-        import webbpsf
+        import stpsf as webbpsf
 
     except ImportError:
         raise ("Could not import `webbpsf` package. Functionality limited. Generating dummy file.")

mirage/psf/tools.py

@@ -10,7 +10,7 @@
 from astropy.modeling.models import Gaussian2D
 import numpy as np
 from photutils.datasets import load_irac_psf
-import webbpsf
+import stpsf as webbpsf
 
 from mirage.psf.psf_selection import get_psf_wings
 from mirage.utils.siaf_interface import get_instance