Merge branch 'master' into pep621

spacetelescope · Aug 21, 2023 · ce9248c · ce9248c
2 parents 1e1155e + d6a9b6f
commit ce9248c
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diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -0,0 +1,26 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  builder: html
+  configuration: docs/conf.py
+  fail_on_warning: true
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: 3.7
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats:
+  - htmlzip
+  - pdf
diff --git a/CHANGES.rst b/CHANGES.rst
@@ -1,4 +1,3 @@
-Changes included in this version
---------------------------------
-
-Edit this template to detail updates to the codebase
+v0.19.1
+-------
+- Patch for new numpy version release (1.25.0). This version deprecated np.int and np.float. This release removes mention of these old methods.
diff --git a/README.md b/README.md
@@ -59,37 +59,37 @@ Plotting (only a small subset of options is illustrated):
 </p>
 
 ````
-    import matplotlib.pyplot as pl
+    import matplotlib.pyplot as plt
 
-    pl.figure(figsize=(4, 4), facecolor='w', edgecolor='k'); pl.clf()
+    plt.figure(figsize=(4, 4), facecolor='w', edgecolor='k'); plt.clf()
 
     # plot single aperture
     nis_cen.plot()
 
     # plot all apertures in SIAF
     for aperture_name, aperture in siaf.apertures.items():
         aperture.plot()
-    pl.show()
+    plt.show()
 ````
 ````
     # plot 'master' apertures
     from pysiaf.siaf import plot_master_apertures
-    pl.figure(figsize=(8, 8), facecolor='w', edgecolor='k'); pl.clf()
+    plt.figure(figsize=(8, 8), facecolor='w', edgecolor='k'); plt.clf()
     plot_master_apertures(mark_ref=True)
-    pl.show()
+    plt.show()
 ````
 ````
     # plot HST apertures
     siaf = pysiaf.Siaf('HST')
     aperture_names = ['FGS1', 'FGS2', 'FGS3', 'IUVIS1FIX', 'IUVIS2FIX', 'JWFC1FIX', 'JWFC2FIX']
 
-    pl.figure(figsize=(4, 4), facecolor='w', edgecolor='k')
+    plt.figure(figsize=(4, 4), facecolor='w', edgecolor='k')
     for aperture_name in aperture_names:
         siaf[aperture_name].plot(color='r', fill_color='darksalmon', mark_ref=True)
-    ax = pl.gca()
+    ax = plt.gca()
     ax.set_aspect('equal')
     ax.invert_yaxis()
-    pl.show()
+    plt.show()
 
 ````
 
@@ -133,7 +133,7 @@ The following describes the typical work flow for contributing to the pysiaf pro
 11. Delete your local copy of your branch.
 
 ### Installation  
-This package is supported in python 3.7, 3.8 and 3.9
+This package is supported in python 3.8 and 3.9
 
 `pip install pysiaf`
 

diff --git a/docs/conf.py b/docs/conf.py
@@ -430,3 +430,6 @@ def check_sphinx_version(expected_version):
 
 # If false, no index is generated.
 # epub_use_index = True
+
+# Enable nitpicky mode - which ensures that all references in the docs resolve.
+nitpicky = True
diff --git a/generate/generate_fgs.py b/generate/generate_fgs.py
@@ -129,7 +129,7 @@
         polynomial_coefficients = iando.read.read_siaf_distortion_coefficients(instrument, AperName)
 
         number_of_coefficients = len(polynomial_coefficients)
-        polynomial_degree = np.int((np.sqrt(8 * number_of_coefficients + 1) - 3) / 2)
+        polynomial_degree = int((np.sqrt(8 * number_of_coefficients + 1) - 3) / 2)
 
         # set polynomial coefficients
         siaf_indices = ['{:02d}'.format(d) for d in polynomial_coefficients['siaf_index'].tolist()]

diff --git a/generate/generate_nircam.py b/generate/generate_nircam.py
@@ -108,7 +108,7 @@
         polynomial_coefficients = iando.read.read_siaf_distortion_coefficients(instrument, AperName)
 
         number_of_coefficients = len(polynomial_coefficients)
-        polynomial_degree = np.int((np.sqrt(8 * number_of_coefficients + 1) - 3) / 2)
+        polynomial_degree = int((np.sqrt(8 * number_of_coefficients + 1) - 3) / 2)
         aperture.Sci2IdlDeg = polynomial_degree
 
         # set polynomial coefficients
@@ -163,8 +163,8 @@
                 if (sca_name == 'NRCA5') and (('MASK335R' in aperture.AperName) or ('MASK430R' in aperture.AperName)):
                     # see https://jira.stsci.edu/browse/JWSTSIAF-77
                     sca_name += '335R430R'
-                v2_offset = np.float(wedge_offsets['v2_offset'][wedge_offsets['name'] == sca_name])
-                v3_offset = np.float(wedge_offsets['v3_offset'][wedge_offsets['name'] == sca_name])
+                v2_offset = float(wedge_offsets['v2_offset'][wedge_offsets['name'] == sca_name])
+                v3_offset = float(wedge_offsets['v3_offset'][wedge_offsets['name'] == sca_name])
                 aperture.V2Ref += v2_offset
                 aperture.V3Ref += v3_offset
             elif dependency_type == 'dhspil_wedge':
@@ -388,21 +388,31 @@
 
         create_jira_plots = True
         if create_jira_plots:
-            # # make figures for JWSTSIAF-245 Jira ticket
-            selected_aperture_names = [['NRCA1_FULL_WEDGE_RND','NRCA2_FULL_WEDGE_RND','NRCA3_FULL_WEDGE_RND','NRCA4_FULL_WEDGE_RND','NRCA2_MASK210R'],
-                                       ['NRCA1_FULL_WEDGE_BAR','NRCA2_FULL_WEDGE_BAR','NRCA3_FULL_WEDGE_BAR','NRCA4_FULL_WEDGE_BAR','NRCA4_MASKSWB'],
-                                       ['NRCA5_FULL_WEDGE_RND','NRCA5_MASK335R','NRCA5_MASK430R'],
-                                       ['NRCA5_FULL_WEDGE_BAR','NRCA5_MASKLWB'],
-                                       ['NRCA2_MASK210R','NRCA2_TAMASK210R','NRCA2_FSTAMASK210R'],
-                                       ['NRCA4_MASKSWB','NRCA4_MASKSWB_F182M','NRCA4_MASKSWB_F187N','NRCA4_MASKSWB_F210M','NRCA4_MASKSWB_F212N','NRCA4_MASKSWB_F200W','NRCA4_MASKSWB_NARROW',
-                                        'NRCA4_TAMASKSWB','NRCA4_TAMASKSWBS','NRCA4_FSTAMASKSWB'  ],
-                                       ['NRCA5_MASK335R','NRCA5_TAMASK335R','NRCA5_FSTAMASK335R'],
-                                       ['NRCA5_MASK430R','NRCA5_TAMASK430R','NRCA5_FSTAMASK430R'],
-                                       ['NRCA5_MASKLWB','NRCA5_MASKLWB_F250M','NRCA5_MASKLWB_F300M','NRCA5_MASKLWB_F277W','NRCA5_MASKLWB_F335M','NRCA5_MASKLWB_F360M','NRCA5_MASKLWB_F356W',
-                                        'NRCA5_MASKLWB_F410M','NRCA5_MASKLWB_F430M','NRCA5_MASKLWB_F460M','NRCA5_MASKLWB_F480M','NRCA5_MASKLWB_F444W','NRCA5_MASKLWB_NARROW',
-                                        'NRCA5_TAMASKLWB','NRCA5_TAMASKLWBL','NRCA5_FSTAMASKLWB']
-                                        ]
-
+            # # make figures for JWSTSIAF-189 Jira ticket
+            selected_aperture_names = [['NRCA2_MASK210R', 'NRCA5_MASK210R','NRCA2_FULL_MASK210R', 'NRCA5_FULL_MASK210R'],
+                                       ['NRCA5_MASK335R', 'NRCA2_MASK335R','NRCA5_FULL_MASK335R', 'NRCA2_FULL_MASK335R','NRCA5_MASK430R', 'NRCA2_MASK430R',
+                                        'NRCA5_FULL_MASK430R', 'NRCA2_FULL_MASK430R'],
+                                       ['NRCA4_MASKSWB', 'NRCA5_MASKSWB','NRCA4_MASKSWB_F182M', 'NRCA5_MASKSWB_F182M','NRCA4_MASKSWB_F187N', 
+                                        'NRCA5_MASKSWB_F187N','NRCA4_MASKSWB_F210M', 'NRCA5_MASKSWB_F210M','NRCA4_MASKSWB_F212N',
+                                        'NRCA5_MASKSWB_F212N','NRCA4_MASKSWB_F200W', 'NRCA5_MASKSWB_F200W','NRCA4_MASKSWB_NARROW', 'NRCA5_MASKSWB_NARROW'],
+                                       ['NRCA4_FULL_MASKSWB', 'NRCA5_FULL_MASKSWB','NRCA4_FULL_MASKSWB_F182M', 'NRCA5_FULL_MASKSWB_F182M','NRCA4_FULL_MASKSWB_F187N',
+                                        'NRCA5_FULL_MASKSWB_F187N','NRCA4_FULL_MASKSWB_F210M', 'NRCA5_FULL_MASKSWB_F210M','NRCA4_FULL_MASKSWB_F212N', 'NRCA5_FULL_MASKSWB_F212N',
+                                        'NRCA4_FULL_MASKSWB_F200W', 'NRCA5_FULL_MASKSWB_F200W','NRCA4_FULL_MASKSWB_NARROW', 'NRCA5_FULL_MASKSWB_NARROW'],
+                                       ['NRCA5_400X256_MASKLWB', 'NRCA4_400X256_MASKLWB','NRCA5_400X256_MASKLWB_F250M', 'NRCA4_400X256_MASKLWB_F250M',
+                                        'NRCA5_400X256_MASKLWB_F300M', 'NRCA4_400X256_MASKLWB_F300M','NRCA5_400X256_MASKLWB_F277W', 'NRCA4_400X256_MASKLWB_F277W',
+                                        'NRCA5_400X256_MASKLWB_F335M', 'NRCA4_400X256_MASKLWB_F335M','NRCA5_400X256_MASKLWB_F360M', 'NRCA4_400X256_MASKLWB_F360M',
+                                        'NRCA5_400X256_MASKLWB_F356W', 'NRCA4_400X256_MASKLWB_F356W','NRCA5_400X256_MASKLWB_F410M', 'NRCA4_400X256_MASKLWB_F410M',
+                                        'NRCA5_400X256_MASKLWB_F430M', 'NRCA4_400X256_MASKLWB_F430M','NRCA5_400X256_MASKLWB_F460M', 'NRCA4_400X256_MASKLWB_F460M',
+                                        'NRCA5_400X256_MASKLWB_F480M', 'NRCA4_400X256_MASKLWB_F480M','NRCA5_400X256_MASKLWB_F444W', 'NRCA4_400X256_MASKLWB_F444W',
+                                        'NRCA5_400X256_MASKLWB_NARROW', 'NRCA4_400X256_MASKLWB_NARROW'],
+                                        ['NRCA5_FULL_MASKLWB', 'NRCA4_FULL_MASKLWB','NRCA5_FULL_MASKLWB_F250M', 'NRCA4_FULL_MASKLWB_F250M',
+                                        'NRCA5_FULL_MASKLWB_F300M', 'NRCA4_FULL_MASKLWB_F300M','NRCA5_FULL_MASKLWB_F277W', 'NRCA4_FULL_MASKLWB_F277W',
+                                        'NRCA5_FULL_MASKLWB_F335M', 'NRCA4_FULL_MASKLWB_F335M','NRCA5_FULL_MASKLWB_F360M', 'NRCA4_FULL_MASKLWB_F360M',
+                                        'NRCA5_FULL_MASKLWB_F356W', 'NRCA4_FULL_MASKLWB_F356W','NRCA5_FULL_MASKLWB_F410M', 'NRCA4_FULL_MASKLWB_F410M',
+                                        'NRCA5_FULL_MASKLWB_F430M', 'NRCA4_FULL_MASKLWB_F430M','NRCA5_FULL_MASKLWB_F460M', 'NRCA4_FULL_MASKLWB_F460M',
+                                        'NRCA5_FULL_MASKLWB_F480M', 'NRCA4_FULL_MASKLWB_F480M','NRCA5_FULL_MASKLWB_F444W', 'NRCA4_FULL_MASKLWB_F444W',
+                                        'NRCA5_FULL_MASKLWB_NARROW', 'NRCA4_FULL_MASKLWB_NARROW']
+                                       ]
 
             for selected_aperture_name in selected_aperture_names:
                 compare.compare_inspection_figures(pre_delivery_siaf, reference_siaf_input=ref_siaf,

diff --git a/generate/generate_niriss.py b/generate/generate_niriss.py
@@ -101,7 +101,7 @@
         polynomial_coefficients = iando.read.read_siaf_distortion_coefficients(instrument, AperName)
 
         number_of_coefficients = len(polynomial_coefficients)
-        polynomial_degree = np.int((np.sqrt(8 * number_of_coefficients + 1) - 3) / 2)
+        polynomial_degree = int((np.sqrt(8 * number_of_coefficients + 1) - 3) / 2)
 
         # set polynomial coefficients
         siaf_indices = ['{:02d}'.format(d) for d in polynomial_coefficients['siaf_index'].tolist()]

diff --git a/generate/generate_nirspec.py b/generate/generate_nirspec.py
@@ -297,7 +297,7 @@ def read_pcf_gtp(file_name):
     # transform to numpy array when possible
     for key in data.keys():
         try:
-            data[key] = np.array(data[key][0].split()).astype(np.float)
+            data[key] = np.array(data[key][0].split()).astype(float)
         except:
             pass
 
@@ -802,7 +802,7 @@ def rows(pcfName, new_pcf_format=False):
     # 'F140X_GWA_OTE', 'F110W_GWA_OTE', 'CLEAR_GWA_OTE']
     elif AperName in pcf_file_mapping.keys():
         number_of_coefficients = len(pcf_data[AperName]['A'])
-        polynomial_degree = np.int((np.sqrt(8 * number_of_coefficients + 1) - 3) / 2)
+        polynomial_degree = int((np.sqrt(8 * number_of_coefficients + 1) - 3) / 2)
         aperture.Sci2IdlDeg = polynomial_degree
         k = 0
         # polynomial coefficients for transformation that goes directly from the GWA pupil plane to the sky
@@ -816,10 +816,10 @@ def rows(pcfName, new_pcf_format=False):
 
         # coefficients to apply the reflection in the MIRROR taking into account the correction
         # to the GWA position as derived from the sensor readings and their calibration relation
-        aperture.XSciScale = np.float(disperser_mirror_tiltx['CoeffsTemperature00'][0])
-        aperture.YSciScale = np.float(disperser_mirror_tilty['CoeffsTemperature00'][0])
-        aperture.XSciRef = np.float(disperser_mirror_tiltx['Zeroreadings'][0])
-        aperture.YSciRef = np.float(disperser_mirror_tilty['Zeroreadings'][0])
+        aperture.XSciScale = float(disperser_mirror_tiltx['CoeffsTemperature00'][0])
+        aperture.YSciScale = float(disperser_mirror_tilty['CoeffsTemperature00'][0])
+        aperture.XSciRef = float(disperser_mirror_tiltx['Zeroreadings'][0])
+        aperture.YSciRef = float(disperser_mirror_tilty['Zeroreadings'][0])
         aperture.DDCName = 'None'
 
     # TRANSFORM apertures for the conversion between the OTE image plane and the MSA plane
@@ -838,7 +838,7 @@ def rows(pcfName, new_pcf_format=False):
         fore_pcf_data = read_pcf_gtp(fore_pcf)
 
         # deal with different formats of the .pcf files
-        fore_year = np.int(fore_pcf_data['DATE'][0][0:4])
+        fore_year = int(fore_pcf_data['DATE'][0][0:4])
         if fore_year > 2016:
             new_pcf_format = True
         else:

diff --git a/generate/generate_reference_files.py b/generate/generate_reference_files.py
@@ -669,7 +669,7 @@ def generate_siaf_pre_flight_reference_files_nircam():
 
             #generate distortion reference file
             number_of_coefficients = len(A)
-            polynomial_degree = np.int((np.sqrt(8 * number_of_coefficients + 1) - 3) / 2)
+            polynomial_degree = int((np.sqrt(8 * number_of_coefficients + 1) - 3) / 2)
             siaf_index = []
             exponent_x = []
             exponent_y = []
@@ -1143,7 +1143,7 @@ def generate_siaf_pre_flight_reference_files_niriss(distortion_file_name, verbos
 
 
         number_of_coefficients = len(AR)
-        polynomial_degree = np.int((np.sqrt(8 * number_of_coefficients + 1) - 3) / 2)
+        polynomial_degree = int((np.sqrt(8 * number_of_coefficients + 1) - 3) / 2)
 
         # if oss is False:
         if 1:
@@ -1294,7 +1294,7 @@ def generate_siaf_pre_flight_reference_files_fgs(verbose=False, mode='siaf'):
                  -2.81501600E-15, -1.73025000E-15, 2.57732600E-15, 1.75268080E-15, 2.95238320E-15])
 
         number_of_coefficients = len(A)
-        polynomial_degree = np.int((np.sqrt(8 * number_of_coefficients + 1) - 3) / 2)
+        polynomial_degree = int((np.sqrt(8 * number_of_coefficients + 1) - 3) / 2)
 
         # generate distortion coefficient files
         siaf_index = []

diff --git a/pysiaf/__init__.py b/pysiaf/__init__.py
@@ -30,7 +30,7 @@
 # Check PRD version is up to date
 try:
     req = requests.get('https://github.com/spacetelescope/pysiaf/tree/master/pysiaf/prd_data/JWST').text
-    p = re.compile("/spacetelescope/pysiaf/tree/master/pysiaf/prd_data/JWST/(.*?)/SIAFXML")
+    p = re.compile("pysiaf/prd_data/JWST/(.*?)/SIAFXML")
     prd_list = p.findall(req)
     prd_list.sort()
     newest_prd = [prd for i, prd in enumerate(prd_list) if

diff --git a/pysiaf/aperture.py b/pysiaf/aperture.py
@@ -288,7 +288,7 @@ def set_distortion_coefficients_from_file(self, file_name):
         polynomial_coefficients = read.read_siaf_distortion_coefficients(file_name=file_name)
 
         number_of_coefficients = len(polynomial_coefficients)
-        polynomial_degree = np.int((np.sqrt(8 * number_of_coefficients + 1) - 3) / 2)
+        polynomial_degree = int((np.sqrt(8 * number_of_coefficients + 1) - 3) / 2)
         self.Sci2IdlDeg = polynomial_degree
 
         # set polynomial coefficients
@@ -910,7 +910,7 @@ def distortion_transform(self, from_system, to_system, include_offset=True):
         # Get the coefficients for "science" to "ideal" transformation (and back)
 
         # degree of distortion polynomial
-        degree = np.int(getattr(self, 'Sci2IdlDeg'))
+        degree = int(getattr(self, 'Sci2IdlDeg'))
 
         number_of_coefficients = polynomial.number_of_coefficients(degree)
         all_keys = self.__dict__.keys()
@@ -1513,8 +1513,8 @@ def dms_corner(self):
         This corresponds to the OSS corner position (x: ColCorner, y: RowCorner).
         The notation for OSS is 1-based, i.e. the lower left corner of a FULL subarray is (1,1)
         """
-        col_corner = np.ceil(np.min(self.corners('det')[0])).astype(np.int_)
-        row_corner = np.ceil(np.min(self.corners('det')[1])).astype(np.int_)
+        col_corner = np.ceil(np.min(self.corners('det')[0])).astype(int)
+        row_corner = np.ceil(np.min(self.corners('det')[1])).astype(int)
 
         return col_corner, row_corner