Merge pull request #1685 from pypeit/pkgrsrc

Tests pass
```
Test Summary
--------------------------------------------------------
--- PYTEST PYPEIT UNIT TESTS PASSED  239 passed, 70 warnings in 549.16s (0:09:09) ---
--- PYTEST UNIT TESTS PASSED  133 passed, 171 warnings in 1006.59s (0:16:46) ---
--- PYTEST VET TESTS PASSED  58 passed, 68 warnings in 1070.66s (0:17:50) ---
--- PYPEIT DEVELOPMENT SUITE PASSED 231/231 TESTS  ---
Testing Started at 2023-10-02T21:32:49.404150
Testing Completed at 2023-10-03T14:51:06.930614
Total Time: 17:18:17.526464
```

CHANGES.rst

@@ -1,8 +1,8 @@
 
-1.14.1dev
----------
-
-PLEASE ADD TO doc/releases/1.14.1dev.rst!
+****************************************************************************
+USE OF THIS FILE IS NOW DEPRECATED.  CHANGES SHOULD BE ADDED TO THE RELEVANT
+RELEASE FILE IN doc/releases
+****************************************************************************
 
 
 1.14.0 (18 Sep 2023)

doc/conf.py

@@ -12,21 +12,20 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import os
-import sys
-from pkg_resources import get_distribution
+from configparser import ConfigParser
+from importlib import metadata
+import pathlib
 
 # Get configuration information from setup.cfg
-from configparser import ConfigParser
 conf = ConfigParser()
-
-conf.read([os.path.join(os.path.dirname(__file__), '..', 'setup.cfg')])
+conf.read([pathlib.Path(__file__).resolve().parents[1] / 'setup.cfg'])
 setup_cfg = dict(conf.items('metadata'))
 
 #
 ## If extensions (or modules to document with autodoc) are in another directory,
 ## add these directories to sys.path here. If the directory is relative to the
 ## documentation root, use os.path.abspath to make it absolute, like shown here.
+#import sys
 #sys.path.insert(0, os.path.abspath('../pypeit'))
 
 # -- General configuration ------------------------------------------------
@@ -99,7 +98,9 @@
 # built documents.
 
 # The full version, including alpha/beta/rc tags.
-version = get_distribution(setup_cfg['name']).version
+#from pkg_resources import get_distribution
+#version = get_distribution(setup_cfg['name']).version
+version = metadata.version(setup_cfg['name'])
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/installing.rst

@@ -563,7 +563,7 @@ same in bash) that will locate a test spec1D file and attempt to use
 
 .. code-block:: console
 
-    python -c "from pkg_resources import resource_filename; print(resource_filename('pypeit', 'tests/files/spec1d_r153-J0025-0312_KASTr_20150123T025323.850.fits'))" | xargs -I {} pypeit_show_1dspec {}
+    python -c "from importlib import resources; print(resources.files('pypeit') / 'tests/files/spec1d_r153-J0025-0312_KASTr_20150123T025323.850.fits')" | xargs -I {} pypeit_show_1dspec {}
 
 If ``pyqt6`` or another Qt backend is correctly installed, this should show a test
 spectrum from the Shane/KAST spectrograph.

doc/releases/1.14.1dev.rst

@@ -5,6 +5,8 @@ Version 1.14.1dev
 Dependency Changes
 ------------------
 
+- Removes use of deprecated ``pkg_resources``.
+
 Functionality/Performance Improvements and Additions
 ----------------------------------------------------
 

doc/scripts/build_afterburn_datamodels_rst.py

@@ -2,8 +2,7 @@
 Dynamically build the rst documentation for the Calibration Images
 """
 
-from pathlib import Path
-from pkg_resources import resource_filename
+from importlib import resources
 
 import numpy
 
@@ -142,7 +141,7 @@ def telluric_datamodel(output_root):
 
 if __name__ == '__main__':
     # Set the output directory
-    output_root = Path(resource_filename('pypeit', '')).resolve().parent / 'doc' / 'include'
+    output_root = resources.files('pypeit').parent / 'doc' / 'include'
 
     # Sensitivity file
     sens_datamodel(output_root)

doc/scripts/build_bitmask_rst.py

@@ -2,11 +2,11 @@
 Dynamically build tables for the bitmasks.
 """
 
-import os
+from importlib import resources
 import time
+
 import numpy
 
-from pkg_resources import resource_filename
 from pypeit.utils import to_string, string_table
 
 from IPython import embed
@@ -15,7 +15,7 @@
 
 def write_bitmask_table(obj, path):
     bm = obj()
-    ofile = os.path.join(path, '{0}_table.rst'.format(obj.__name__.lower()))
+    ofile = path / f'{obj.__name__.lower()}_table.rst'
 
     data_table = numpy.empty((bm.nbits+1, 4), dtype=object)
     data_table[0,:] = ['Bit Name', 'Bit Number', 'Decimal Value', 'Description']
@@ -34,10 +34,9 @@ def write_bitmask_table(obj, path):
 if __name__ == '__main__':
     t = time.perf_counter()
 
-    pypeit_root = os.path.dirname(resource_filename('pypeit', ''))
-    path = os.path.join(pypeit_root, 'doc', 'include')
-    if not os.path.isdir(path):
-        os.makedirs(path)
+    path = resources.files('pypeit').parent / 'doc' / 'include'
+    if not path.is_dir():
+        path.mkdir(parents=True)
 
     from pypeit.images.imagebitmask import ImageBitMask
     write_bitmask_table(ImageBitMask, path)

doc/scripts/build_calib_images_rst.py

@@ -2,8 +2,7 @@
 Dynamically build the rst documentation for the Calibration Images
 """
 
-from pathlib import Path
-from pkg_resources import resource_filename
+from importlib import resources
 
 import numpy
 
@@ -287,7 +286,7 @@ def flatfield_datamodel(output_root):
 
 if __name__ == '__main__':
     # Set the output directory
-    output_root = Path(resource_filename('pypeit', '')).resolve().parent / 'doc' / 'include'
+    output_root = resources.files('pypeit').parent / 'doc' / 'include'
 
     # Simple datamodels for Arc, Bias, Dark, Tiltimg
     for obj in [buildimage.ArcImage, buildimage.BiasImage, buildimage.DarkImage,

doc/scripts/build_datacontainer_datamodels.py

@@ -2,8 +2,7 @@
 Dynamically build the rst documentation for the Calibration Images
 """
 
-from pathlib import Path
-from pkg_resources import resource_filename
+from importlib import resources
 
 from IPython import embed
 
@@ -59,7 +58,7 @@ def build_datamodel_tbl(obj):
 if __name__ == '__main__':
 
     # Set the output directory
-    output_root = Path(resource_filename('pypeit', '')).resolve().parent / 'doc' / 'include'
+    output_root = resources.files('pypeit').parent / 'doc' / 'include'
 
     # All DataContainer objects
     # TODO: automate this?

doc/scripts/build_dependency_rst.py

@@ -2,18 +2,18 @@
 Construct an rst table with the dependencies
 """
 
-from IPython import embed
-import os
 import configparser
-from pkg_resources import resource_filename
+from importlib import resources
 
 import numpy
 
 from pypeit.utils import string_table
 
+from IPython import embed
+
 
 def write_dependency_table(setup_file, path):
-    ofile = os.path.join(path, 'dependencies_table.rst')
+    ofile = path / 'dependencies_table.rst'
 
     setup = configparser.ConfigParser()
     setup.read(setup_file)
@@ -34,14 +34,13 @@ def write_dependency_table(setup_file, path):
 
 
 def main():
-    output_root = os.path.join(os.path.split(os.path.abspath(resource_filename('pypeit', '')))[0],
-                               'doc', 'include')
-    if not os.path.isdir(output_root):
+    pypeit_root = resources.files('pypeit').parent
+    output_root = pypeit_root / 'doc' / 'include'
+    if not output_root.is_dir():
         raise NotADirectoryError(f'{output_root} does not exist!')
 
-    setup_file = os.path.join(os.path.split(os.path.abspath(resource_filename('pypeit', '')))[0],
-                               'setup.cfg')
-    if not os.path.isfile(setup_file):
+    setup_file = pypeit_root / 'setup.cfg'
+    if not setup_file.is_file():
         raise FileNotFoundError(f'{setup_file} does not exist!')
     write_dependency_table(setup_file, output_root)
 

doc/scripts/build_detector_table.py

@@ -2,17 +2,17 @@
 Construct an rst table with the detector properties
 """
 
-from IPython import embed
-import os
-from pkg_resources import resource_filename
+from importlib import resources
 
 import numpy
 
 from pypeit.utils import string_table
 from pypeit.spectrographs import spectrograph_classes
-from pypeit.images.detector_container import DetectorContainer
+
+from IPython import embed
 
 #def write_detector_datamodel(ofile):
+#    from pypeit.images.detector_container import DetectorContainer
 #    det_dm = DetectorContainer.datamodel
 #    keys = numpy.sort(list(det_dm.keys()))
 #    nkeys = len(keys)
@@ -72,15 +72,14 @@ def write_detector_table(ofile):
 
 
 def main():
-    output_root = os.path.join(os.path.split(os.path.abspath(resource_filename('pypeit', '')))[0],
-                               'doc', 'include')
-    if not os.path.isdir(output_root):
+    output_root = resources.files('pypeit').parent / 'doc' / 'include'
+    if not output_root.is_dir():
         raise NotADirectoryError(f'{output_root} does not exist!')
 
-#    ofile = os.path.join(output_root, 'datamodel_detector.rst')
+#    ofile = output_root / 'datamodel_detector.rst'
 #    write_detector_datamodel(ofile)
 
-    ofile = os.path.join(output_root, 'inst_detector_table.rst')
+    ofile = output_root / 'inst_detector_table.rst'
     write_detector_table(ofile)
 
 

doc/scripts/build_imgproc_defaults.py

@@ -2,15 +2,14 @@
 Construct an rst table with the dependencies
 """
 
-from IPython import embed
-import os
-from pkg_resources import resource_filename
+from importlib import resources
 
 import numpy
 
 from pypeit.utils import string_table
 from pypeit.par.pypeitpar import ProcessImagesPar, PypeItPar
-from pypeit.spectrographs import spectrograph_classes
+
+from IPython import embed
 
 
 def write_imgproc_def_table(ofile, spec=None):
@@ -73,17 +72,16 @@ def write_imgproc_def_table(ofile, spec=None):
 
 
 def main():
-    output_root = os.path.join(os.path.split(os.path.abspath(resource_filename('pypeit', '')))[0],
-                               'doc', 'include')
-    if not os.path.isdir(output_root):
+    output_root = resources.files('pypeit').parent / 'doc' / 'include'
+    if not output_root.is_dir():
         raise NotADirectoryError(f'{output_root} does not exist!')
 
-    ofile = os.path.join(output_root, 'imgproc_defaults_table.rst')
+    ofile = output_root / 'imgproc_defaults_table.rst'
     write_imgproc_def_table(ofile)
 
 #    allspec = spectrograph_classes()
 #    for key, spec_c in allspec.items():
-#        ofile = os.path.join(output_root, f'imgproc_{key}_table.rst')
+#        ofile = output_root / f'imgproc_{key}_table.rst'
 #        write_imgproc_def_table(ofile, spec=spec_c())
 
 if __name__ == '__main__':

doc/scripts/build_par_rst.py

@@ -2,20 +2,17 @@
 Dynamically build the rst documentation of the pypeit parameters.
 """
 
-import os
+from importlib import resources
 import time
 import textwrap
 
-from IPython import embed
-
-import numpy
-
-from pkg_resources import resource_filename
 from pypeit.par import pypeitpar
 from pypeit.par.parset import ParSet
 from pypeit.spectrographs.util import load_spectrograph
 from pypeit.spectrographs import available_spectrographs
 
+from IPython import embed
+
 #-----------------------------------------------------------------------------
 #def class_name(p):
 #    return '.'.join([type(p).__module__, type(p).__name__])
@@ -48,8 +45,8 @@ def par_hierarchy(p, indent_level=0, key=''):
 
     # Read the baseline file that is not changed and must be edited by
     # the person building the documentation as necessary.
-    pypeit_root = os.path.dirname(resource_filename('pypeit', ''))
-    input_base = os.path.join(pypeit_root, 'doc', 'scripts', 'base_par.rst')
+    pypeit_root = resources.files('pypeit').parent 
+    input_base = pypeit_root / 'doc' / 'scripts' / 'base_par.rst'
     with open(input_base, 'r') as f:
         lines = [ l.replace('\n','') for l in f.readlines() ]
     lines += ['']
@@ -99,7 +96,7 @@ def par_hierarchy(p, indent_level=0, key=''):
         lines += ['']
     lines += ['']
 
-    output_rst = os.path.join(pypeit_root, 'doc', 'pypeit_par.rst')
+    output_rst = pypeit_root / 'doc' / 'pypeit_par.rst'
     with open(output_rst, 'w') as f:
         f.write('\n'.join(lines))
 

doc/scripts/build_specobj_rst.py

@@ -2,11 +2,11 @@
 Dynamically build the rst documentation for the specobj and spec2dobj objects
 """
 
-import os
+from importlib import resources
 import time
+
 import numpy
 
-from pkg_resources import resource_filename
 from pypeit.utils import to_string, string_table
 from pypeit import specobj
 from pypeit import spec2dobj
@@ -20,13 +20,12 @@
     t = time.perf_counter()
 
     # Set the output directory
-    output_root = os.path.join(os.path.split(os.path.abspath(resource_filename('pypeit', '')))[0],
-                               'doc', 'include')
+    output_root = resources.files('pypeit').parent / 'doc' / 'include'
 
     # Iterate through all the specobj classes
     for obj in [specobj.SpecObj, spec2dobj.Spec2DObj, coadd1d.OneSpec]:
 
-        ofile = os.path.join(output_root, 'datamodel_{0}.rst'.format(obj.__name__.lower()))
+        ofile = output_root / f'datamodel_{obj.__name__.lower()}.rst'
 
         lines = []
         lines += ['']