Refresh test infrastructure

.github/workflows/python-package.yml

@@ -17,14 +17,14 @@ jobs:
             fail-fast: true
             matrix:
                 os: [ubuntu-latest]
-                python-version: [3.8]  # fitsio does not like Python < 3.7, astropy does not like Python < 3.8, might be too soon for 3.9.
-                astropy-version: ['==4.0.1.post1', '==5.0']  # everest & fuji versions
-                fitsio-version: ['==1.1.2', '==1.1.6']  # everest & fuji versions
+                python-version: [3.9]
+                astropy-version: ['==5.0', '<6']  # fuji version
+                fitsio-version: ['==1.1.6']  # fuji version
                 numpy-version: ['<1.23']  # to keep asscalar, used by astropy
 
         env:
-            DESIUTIL_VERSION: 3.2.3
-            DESIMODEL_DATA: branches/test-0.12
+            DESIUTIL_VERSION: 3.2.5
+            DESIMODEL_DATA: branches/test-0.17
 
         steps:
             - name: Checkout code
@@ -56,12 +56,12 @@ jobs:
             fail-fast: true
             matrix:
                 os: [ubuntu-latest]
-                python-version: [3.8]
-                fitsio-version: ['==1.1.2']  # everest version
+                python-version: [3.9]
+                fitsio-version: ['==1.1.6']  # fuji version
                 numpy-version: ['<1.23']  # to keep asscalar, used by astropy
         env:
-            DESIUTIL_VERSION: 3.2.3
-            DESIMODEL_DATA: branches/test-0.12
+            DESIUTIL_VERSION: 3.2.5
+            DESIMODEL_DATA: branches/test-0.17
 
         steps:
             - name: Checkout code
@@ -75,7 +75,7 @@ jobs:
             - name: Install Python dependencies
               run: |
                 python -m pip install --upgrade pip wheel
-                python -m pip install pytest pytest-cov coveralls
+                python -m pip install pytest\<7 pytest-cov\<4 coveralls
                 python -m pip install git+https://github.com/desihub/desiutil.git@${DESIUTIL_VERSION}#egg=desiutil
                 python -m pip install -r requirements.txt
                 python -m pip install -U 'numpy${{ matrix.numpy-version }}'
@@ -97,7 +97,7 @@ jobs:
             fail-fast: false
             matrix:
                 os: [ubuntu-latest]
-                python-version: [3.8]
+                python-version: [3.9]
 
         steps:
             - name: Checkout code
@@ -120,7 +120,7 @@ jobs:
             fail-fast: false
             matrix:
                 os: [ubuntu-latest]
-                python-version: [3.8]
+                python-version: [3.9]
 
         steps:
             - name: Checkout code

.gitignore

@@ -1,7 +1,7 @@
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
-.ipynb_checkpoints                                                                                            
+.ipynb_checkpoints
 # C extensions
 *.so
 
@@ -36,7 +36,7 @@ pip-delete-this-directory.txt
 # Unit test / coverage reports
 htmlcov/
 .tox/
-.coverage
+.coverage*
 .cache
 nosetests.xml
 coverage.xml
@@ -60,3 +60,7 @@ target/
 # VIM stuff
 *.swo
 *.swp
+
+# VS Code stuff
+.vscode
+.env

doc/Makefile

@@ -2,7 +2,7 @@
 #
 
 # You can set these variables from the command line.
-SPHINXOPTS    =
+SPHINXOPTS    = -W --keep-going
 SPHINXBUILD   = sphinx-build
 PAPER         =
 BUILDDIR      = _build

doc/changes.rst

@@ -5,11 +5,13 @@ desitarget Change Log
 2.5.1 (unreleased)
 ------------------
 
-* Address deprecated np.int and np.float dependencies [`PR #797`_]
-* Functionality to download and reformat files for Gaia DR3 [`PR #796`_]
+* Address deprecated np.int and np.float dependencies [`PR #797`_].
+* Functionality to download and reformat files for Gaia DR3 [`PR #796`_].
+* Restore coverage for svX code [`PR #799`_].
 
 .. _`PR #796`: https://github.com/desihub/desitarget/pull/796
 .. _`PR #797`: https://github.com/desihub/desitarget/pull/797
+.. _`PR #799`: https://github.com/desihub/desitarget/pull/799
 
 2.5.0 (2022-04-22)
 ------------------

py/desitarget/cuts.py

@@ -2890,8 +2890,11 @@ def apply_cuts(objects, qso_selection='randomforest',
     # code or an iteration of SV.
     if survey == 'main':
         import desitarget.cuts as targcuts
+        assert targcuts.__name__ == 'desitarget.cuts'
     elif survey[:2] == 'sv':
-        targcuts = import_module("desitarget.{}.{}_cuts".format(survey, survey))
+        sv_module = "desitarget.{}.{}_cuts".format(survey, survey)
+        targcuts = import_module(sv_module)
+        assert targcuts.__name__ == sv_module
     else:
         msg = "survey must be either 'main'or 'svX', not {}!!!".format(survey)
         log.critical(msg)

py/desitarget/test/test_brightmask.py

@@ -5,6 +5,7 @@
 import unittest
 from pkg_resources import resource_filename
 import os
+import sys
 import fitsio
 import numpy as np
 import numpy.lib.recfunctions as rfn
@@ -18,6 +19,8 @@
 
 from desiutil import brick
 
+_macos = sys.platform == 'darwin'
+
 
 class TestBRIGHTMASK(unittest.TestCase):
 
@@ -106,6 +109,7 @@ def test_make_bright_star_mask(self):
         self.assertTrue(len(set(mx["REF_ID"]) - set(self.allmx["REF_ID"])) == 0)
         self.assertTrue(len(set(self.allmx["REF_ID"]) - set(mx["REF_ID"])) > 0)
 
+    @unittest.skipIf(_macos, "Skipping parallel test that fails on macOS.")
     def test_make_bright_star_mask_parallel(self):
         """Check running the mask-making code in parallel.
         """

py/desitarget/test/test_cmx.py

@@ -3,6 +3,7 @@
 """Test desitarget.cmx.
 """
 import unittest
+import sys
 from pkg_resources import resource_filename
 import os.path
 from uuid import uuid4
@@ -18,6 +19,8 @@
 from desitarget import io
 from desitarget.cmx import cmx_cuts as cuts
 
+_macos = sys.platform == 'darwin'
+
 
 class TestCMX(unittest.TestCase):
 
@@ -140,6 +143,7 @@ def test_missing_files(self):
         with self.assertRaises(ValueError):
             targets = cuts.select_targets(['blat.foo1234', ], numproc=1)
 
+    @unittest.skipIf(_macos, "Skipping parallel test that fails on macOS.")
     def test_parallel_select(self):
         """Test multiprocessing parallelization works
         """

py/desitarget/test/test_cuts.py

@@ -3,6 +3,7 @@
 """Test desitarget.cuts.
 """
 import unittest
+import sys
 from pkg_resources import resource_filename
 import os.path
 from uuid import uuid4
@@ -19,6 +20,8 @@
 from desitarget.targetmask import desi_mask
 from desitarget.geomask import hp_in_box, pixarea2nside, box_area
 
+_macos = sys.platform == 'darwin'
+
 
 class TestCuts(unittest.TestCase):
 
@@ -298,6 +301,7 @@ def test_select_targets(self):
 
                 self.assertTrue(np.all(t1[col][notNaN] == t2[col][notNaN]))
 
+    @unittest.skipIf(_macos, "Skipping parallel test that fails on macOS.")
     def test_qso_selection_options(self):
         """Test the QSO selection options are passed correctly
         """
@@ -329,6 +333,7 @@ def test_missing_files(self):
         with self.assertRaises(ValueError):
             targets = cuts.select_targets(['blat.foo1234', ], numproc=1)
 
+    @unittest.skipIf(_macos, "Skipping parallel test that fails on macOS.")
     def test_parallel_select(self):
         """Test multiprocessing parallelization works
         """

py/desitarget/test/test_qa.py

@@ -4,6 +4,7 @@
 """
 import unittest
 import os
+import sys
 import shutil
 import tempfile
 import warnings
@@ -16,6 +17,8 @@
 from desiutil.log import get_logger
 log = get_logger()
 
+_macos = sys.platform == 'darwin'
+
 
 class TestQA(unittest.TestCase):
 
@@ -56,6 +59,7 @@ def tearDown(self):
                 if os.path.exists(filename):
                     os.remove(filename)
 
+    @unittest.skipIf(_macos, "Skipping parallel test that fails on macOS.")
     def test_qa_main(self):
         """Test plots/pages made for some main survey target types.
         """
@@ -80,6 +84,7 @@ def test_qa_main(self):
         # ADM there are only .html, .dat and .png files.
         self.assertEqual(pngs+htmls+dats, alls)
 
+    @unittest.skipIf(_macos, "Skipping parallel test that fails on macOS.")
     def test_qa_cmx(self):
         """Test plots/pages are made for some commissioning targets.
         """

py/desitarget/test/test_secondary.py

@@ -30,6 +30,7 @@ def test_flavors(self):
         """Test that secondary masks only have the allowed flavors.
         """
         # ADM for each mask...
+        self.assertEqual(len(self.Mxs), 4)
         for Mx in self.Mxs:
             # ADM ...if we've already defined the flavor property...
             if "flavor" in dir(Mx[Mx[0]]):

py/desitarget/test/test_sv.py

@@ -3,6 +3,7 @@
 """Test desitarget.sv.
 """
 import unittest
+import sys
 import fitsio
 import os
 import numpy as np
@@ -13,6 +14,8 @@
 from desitarget import io, cuts
 from desitarget.targetmask import desi_mask
 
+_macos = sys.platform == 'darwin'
+
 
 class TestSV(unittest.TestCase):
 
@@ -42,16 +45,19 @@ def tearDownClass(cls):
         if cls.gaiadir_orig is not None:
             os.environ["GAIA_DIR"] = cls.gaiadir_orig
 
+    @unittest.skipIf(_macos, "Skipping parallel test that fails on macOS.")
     def test_sv_cuts(self):
         """Test SV cuts work.
         """
         # ADM find all svX sub-directories in the desitarget directory.
         fns = sorted(glob(resource_filename('desitarget', 'sv*')))
         svlist = [os.path.basename(fn) for fn in fns if os.path.isdir(fn)]
+        self.assertEqual(len(svlist), 3)
 
         for survey in svlist:
             desicol, bgscol, mwscol = ["{}_{}_TARGET".format(survey.upper(), tc)
                                        for tc in ["DESI", "BGS", "MWS"]]
+            number_of_calls = 0
             for filelist in [self.tractorfiles, self.sweepfiles]:
                 # ADM set backup to False as the Gaia unit test
                 # ADM files only cover a limited pixel range.
@@ -66,8 +72,12 @@ def test_sv_cuts(self):
                 bgs1 = (targets[desicol] & desi_mask.BGS_ANY) != 0
                 bgs2 = targets[bgscol] != 0
                 self.assertTrue(np.all(bgs1 == bgs2))
+                number_of_calls += 1
+
+            self.assertEqual(number_of_calls, 2)
 
             # ADM backup targets can only be run on sweep files.
+            number_of_calls = 0
             for filelist in self.sweepfiles:
                 # ADM also test the backup targets in the pixels covered
                 # ADM by the Gaia unit test files.
@@ -76,6 +86,9 @@ def test_sv_cuts(self):
                 for col in desicol, bgscol, mwscol:
                     self.assertTrue(col in targets.dtype.names)
                 self.assertEqual(len(targets), np.count_nonzero(targets[desicol]))
+                number_of_calls += 1
+
+            self.assertEqual(number_of_calls, 3)
 
 
 if __name__ == '__main__':

requirements.txt

@@ -1,7 +1,7 @@
-# Based on desimodules/20.8.
+# Based on desimodules/22.5.
 pytz
 requests
-astropy==4.0.1.post1
+astropy==5.0
 numba
 healpy
 speclite
@@ -10,8 +10,9 @@ fitsio
 photutils
 # Install desiutil separately since it is needed for the other installs.
 # git+https://github.com/desihub/desiutil.git@3.1.0#egg=desiutil
-git+https://github.com/desihub/specter.git@0.9.4#egg=specter
-git+https://github.com/desihub/desimodel.git@0.13.0#egg=desimodel
+git+https://github.com/desihub/specter.git@0.10.0#egg=specter
+git+https://github.com/desihub/desimodel.git@0.17.0#egg=desimodel
 # Don't forget to install desimodel test data.
-git+https://github.com/desihub/desispec.git@0.36.1#egg=desispec
-git+https://github.com/desihub/desisim.git@main#egg=desisim
+git+https://github.com/desihub/desispec.git@0.53.1#egg=desispec
+git+https://github.com/desihub/desisim.git@0.36.0#egg=desisim
+git+https://github.com/desihub/redrock.git@0.15.4#egg=redrock