Merge pull request #79 from desihub/update-api

Update api.rst

.github/workflows/python-package.yml

@@ -17,7 +17,7 @@ jobs:
             fail-fast: true
             matrix:
                 os: [ubuntu-latest]
-                python-version: [3.6, 3.7, 3.8]
+                python-version: ['3.8', '3.9']
 
         steps:
             - name: Checkout code
@@ -30,9 +30,9 @@ jobs:
                 python-version: ${{ matrix.python-version }}
             - name: Install Python dependencies
               run: |
-                python -m pip install --upgrade pip wheel
+                python -m pip install --upgrade pip setuptools wheel
                 python -m pip install pytest
-                if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+                if [ -f requirements.txt ]; then python -m pip install -r requirements.txt; fi
             - name: Run the test
               run: pytest
 
@@ -43,7 +43,7 @@ jobs:
             fail-fast: true
             matrix:
                 os: [ubuntu-latest]
-                python-version: [3.8]
+                python-version: ['3.9']
 
         steps:
             - name: Checkout code
@@ -56,9 +56,9 @@ jobs:
                 python-version: ${{ matrix.python-version }}
             - name: Install Python dependencies
               run: |
-                python -m pip install --upgrade pip wheel
+                python -m pip install --upgrade pip setuptools wheel
                 python -m pip install pytest pytest-cov coveralls
-                if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+                if [ -f requirements.txt ]; then python -m pip install -r requirements.txt; fi
             - name: Run the test with coverage
               run: pytest --cov
             - name: Coveralls
@@ -74,7 +74,7 @@ jobs:
             fail-fast: false
             matrix:
                 os: [ubuntu-latest]
-                python-version: [3.8]
+                python-version: ['3.9']
 
         steps:
             - name: Checkout code
@@ -86,7 +86,7 @@ jobs:
               with:
                 python-version: ${{ matrix.python-version }}
             - name: Install Python dependencies
-              run: python -m pip install --upgrade pip wheel Sphinx
+              run: python -m pip install --upgrade pip setuptools wheel Sphinx
             - name: Test the documentation
               run: sphinx-build -W --keep-going -b html doc doc/_build/html
 
@@ -97,7 +97,7 @@ jobs:
             fail-fast: false
             matrix:
                 os: [ubuntu-latest]
-                python-version: [3.8]
+                python-version: ['3.9']
 
         steps:
             - name: Checkout code
@@ -109,7 +109,7 @@ jobs:
               with:
                 python-version: ${{ matrix.python-version }}
             - name: Install Python dependencies
-              run: python -m pip install --upgrade pip wheel pycodestyle
+              run: python -m pip install --upgrade pip setuptools wheel pycodestyle
             - name: Test the style; failures are allowed
               # This is equivalent to an allowed falure.
               continue-on-error: true

doc/Makefile

@@ -2,7 +2,7 @@
 #
 
 # You can set these variables from the command line.
-SPHINXOPTS    =
+SPHINXOPTS    = -W --keep-going
 # For macports, use the second line...
 SPHINXBUILD   = sphinx-build
 # SPHINXBUILD   = sphinx-build-2.7

doc/api.rst

@@ -5,10 +5,10 @@ prospect API
 .. automodule:: prospect
     :members:
 
-.. automodule:: prospect.grid_thumbs
+.. automodule:: prospect.coaddcam
     :members:
 
-.. automodule:: prospect.coaddcam
+.. automodule:: prospect.grid_thumbs
     :members:
 
 .. automodule:: prospect.scripts
@@ -17,6 +17,9 @@ prospect API
 .. automodule:: prospect.scripts.prospect_pages
     :members:
 
+.. automodule:: prospect.scripts.prospect_std_templates
+    :members:
+
 .. automodule:: prospect.specutils
     :members:
 
@@ -35,8 +38,8 @@ prospect API
 .. automodule:: prospect.viewer.plots
     :members:
 
-.. automodule:: prospect.viewer.widgets
+.. automodule:: prospect.viewer.vi_widgets
     :members:
 
-.. automodule:: prospect.viewer.vi_widgets
+.. automodule:: prospect.viewer.widgets
     :members:

doc/changes.rst

@@ -5,7 +5,9 @@ prospect's Change Log
 1.2.4 (unreleased)
 ------------------
 
-* No changes yet.
+* Update API documentation and test infrastructure (PR `#79`_).
+
+.. _`#79`: https://github.com/desihub/prospect/pull/79
 
 1.2.3 (2022-09-15)
 ------------------

py/prospect/scripts/prospect_std_templates.py

@@ -10,6 +10,7 @@
 """
 
 import os
+import sys
 import numpy as np
 from astropy.table import Table
 from astropy.io import fits
@@ -20,31 +21,43 @@
 # Log of previous versions:
 #  std_templates_v0.fits : old Redrock templates only
 
-std_template_file = os.path.join(os.environ['HOME'], 'prospect/py/prospect/data/std_templates.fits')
-if os.path.isfile(std_template_file):
-    print('Error std template file already exists')
-
-#- Templates produced from 1st component of old (pre-Aug 2022) Redrock templates:
-template_dir = os.path.join(os.environ['DESICONDA'], '../code/redrock-templates/0.7.2')
-#std_templates = {'QSO': ('QSO',''), 'GALAXY': ('GALAXY',''), 'STAR': ('STAR','F') }
-std_templates = {'GALAXY': ('GALAXY',''), 'STAR': ('STAR','F') }
-delta_lambd_templates = 3
-
-rr_templts = load_redrock_templates(template_dir=template_dir)
-for key,rr_key in std_templates.items() :
-    wave_array = np.arange(rr_templts[rr_key].wave[0], rr_templts[rr_key].wave[-1], delta_lambd_templates)
-    flux_array = resample_flux(wave_array, rr_templts[rr_key].wave, rr_templts[rr_key].flux[0,:])
-    table_templates = Table(data=[wave_array, flux_array], names=['wave_'+key, 'flux_'+key], meta={'name':key})
+def main():
+    """Entry-point for command-line scripts.
+
+    Returns
+    -------
+    :class:`int`
+        An integer suitable for passing to :func:`sys.exit`.
+    """
+    std_template_file = os.path.join(os.environ['HOME'], 'prospect/py/prospect/data/std_templates.fits')
+    if os.path.isfile(std_template_file):
+        print('Error std template file already exists')
+
+    #- Templates produced from 1st component of old (pre-Aug 2022) Redrock templates:
+    template_dir = os.path.join(os.environ['DESICONDA'], '../code/redrock-templates/0.7.2')
+    #std_templates = {'QSO': ('QSO',''), 'GALAXY': ('GALAXY',''), 'STAR': ('STAR','F') }
+    std_templates = {'GALAXY': ('GALAXY',''), 'STAR': ('STAR','F') }
+    delta_lambd_templates = 3
+
+    rr_templts = load_redrock_templates(template_dir=template_dir)
+    for key,rr_key in std_templates.items() :
+        wave_array = np.arange(rr_templts[rr_key].wave[0], rr_templts[rr_key].wave[-1], delta_lambd_templates)
+        flux_array = resample_flux(wave_array, rr_templts[rr_key].wave, rr_templts[rr_key].flux[0,:])
+        table_templates = Table(data=[wave_array, flux_array], names=['wave_'+key, 'flux_'+key], meta={'name':key})
+        table_templates.write(std_template_file, append=True)
+
+    #- Case of QSO (Summer 2022): use new template provided by A. Brodzeller
+    qsotemplate_file = os.environ['HOME'] + '/stdtemplate-qso.fits'
+    hdul = fits.open(qsotemplate_file)
+    qsowave = 10**(hdul[0].header['CRVAL1']+np.arange(hdul[0].header['NAXIS1'])*hdul[0].header['CDELT1'])
+    qsoflux = hdul[0].data
+    # Resample as previously:
+    wave_array = np.arange(qsowave[0], qsowave[-1], delta_lambd_templates)
+    flux_array = resample_flux(wave_array, qsowave, qsoflux)
+    table_templates = Table(data=[wave_array, flux_array], names=['wave_QSO', 'flux_QSO'], meta={'name':'QSO'})
     table_templates.write(std_template_file, append=True)
+    return 0
 
-#- Case of QSO (Summer 2022): use new template provided by A. Brodzeller
-qsotemplate_file = os.environ['HOME'] + '/stdtemplate-qso.fits'
-hdul = fits.open(qsotemplate_file)
-qsowave = 10**(hdul[0].header['CRVAL1']+np.arange(hdul[0].header['NAXIS1'])*hdul[0].header['CDELT1'])
-qsoflux = hdul[0].data
-# Resample as previously:
-wave_array = np.arange(qsowave[0], qsowave[-1], delta_lambd_templates)
-flux_array = resample_flux(wave_array, qsowave, qsoflux)
-table_templates = Table(data=[wave_array, flux_array], names=['wave_QSO', 'flux_QSO'], meta={'name':'QSO'})
-table_templates.write(std_template_file, append=True)
 
+if __name__ == '__main__':
+    sys.exit(main())

requirements.txt

@@ -1,4 +1,4 @@
 specutils
 bokeh
 jinja2
-git+https://github.com/desihub/desiutil.git@3.0.3#egg=desiutil
+git+https://github.com/desihub/desiutil.git@3.2.5#egg=desiutil