Merge pull request #464 from desihub/remove-desi-test

Remove DesiTest and update to work with pytest
desihub · Jan 29, 2025 · 4127563 · 4127563
2 parents 3b6a44b + 37fd43f
commit 4127563
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Showing 14 changed files with 133 additions and 167 deletions.
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -15,37 +15,38 @@ jobs:
         strategy:
             fail-fast: true
             matrix:
-                os: [ubuntu-latest]
-                python-version: ['3.8', '3.9', '3.10']
-                numpy-version: ['<1.22', '<1.23']
-                astropy-version: ['<5.1']
+                os: [ubuntu-22.04]  # , ubuntu-24.04]
+                python-version: ['3.10']  # '3.11', '3.12']
+                numpy-version: ['<1.23']
+                astropy-version: ['<6.1', '<7']
 
         env:
-            DESIUTIL_VERSION: 3.2.1
-            DESIMODEL_VERSION: main
-            DESIMETER_VERSION: 0.6.5
-            DESIMODEL_DATA: branches/test-0.17
+            DESIUTIL_VERSION: 3.4.3
+            DESIMODEL_VERSION: 0.19.2
+            DESIMETER_VERSION: 0.7.1
+            DESIMODEL_DATA: branches/test-0.19
             DESIMODEL: ${{ github.workspace }}/desimodel
-            DESITARGET_VERSION: 2.2.1
+            DESITARGET_VERSION: 2.5.0
 
         steps:
             - name: Cancel Previous Runs
-              uses: styfle/cancel-workflow-action@0.8.0
+              uses: styfle/cancel-workflow-action@0.12.1
               with:
                   access_token: ${{ github.token }}
-            - name: Checkout
-              uses: actions/checkout@v2
+            - name: Install System Packages
+              run: sudo apt install libbz2-dev subversion
+            - name: Checkout Package
+              uses: actions/checkout@v4
               with:
                   fetch-depth: 0
             - name: Set up Python ${{ matrix.python-version }}
-              uses: actions/setup-python@v2
+              uses: actions/setup-python@v5
               with:
                   python-version: ${{ matrix.python-version }}
             - name: Install Python dependencies
               run: |
-                python -m pip install --no-cache-dir --upgrade pip wheel
-                python -m pip install --no-cache-dir pyyaml requests
-                python -m pip install --no-cache-dir scipy matplotlib healpy
+                python -m pip install --no-cache-dir --upgrade pip setuptools wheel pytest
+                python -m pip install --no-cache-dir pyyaml requests scipy matplotlib healpy
                 python -m pip install --no-cache-dir --upgrade "numpy${{ matrix.numpy-version }}"
                 python -m pip install --no-cache-dir --upgrade "astropy${{ matrix.astropy-version }}"
                 python -m pip install --no-cache-dir fitsio
@@ -55,38 +56,42 @@ jobs:
                 python -m pip install --no-cache-dir git+https://github.com/desihub/desimeter.git@${{ env.DESIMETER_VERSION }}#egg=desimeter
                 mkdir -p ${{ env.DESIMODEL }}
                 svn export https://desi.lbl.gov/svn/code/desimodel/${{ env.DESIMODEL_DATA }}/data ${{ env.DESIMODEL }}/data
-            - name: Install Fiberassign
-              run: CC=g++ CXX=g++ CFLAGS="-fPIC" LDSHARED="g++ -shared" python -m pip install -vvv .
+            # - name: Install Fiberassign
+            #   run: CC=g++ CXX=g++ CFLAGS="-fPIC" LDSHARED="g++ -shared" python -m pip install -vvv .
+            # - name: Run Tests
+            #   run: python -c 'import fiberassign.test; fiberassign.test.runtests()'
+            - name: Compile the package
+              run: CC=g++ CXX=g++ CFLAGS="-fPIC" LDSHARED="g++ -shared" python setup.py build_ext --inplace
             - name: Run Tests
-              run: python -c 'import fiberassign.test; fiberassign.test.runtests()'
+              run: pytest
 
     docs:
         name: Doc test
         runs-on: ${{ matrix.os }}
         strategy:
             fail-fast: false
             matrix:
-                os: [ubuntu-latest]
-                python-version: ['3.9']
+                os: [ubuntu-22.04]
+                python-version: ['3.10']
 
         env:
-            DESIUTIL_VERSION: 3.2.1
+            DESIUTIL_VERSION: 3.5.0
 
         steps:
             - name: Checkout code
-              uses: actions/checkout@v2
+              uses: actions/checkout@v4
               with:
                   fetch-depth: 0
             - name: Set up Python ${{ matrix.python-version }}
-              uses: actions/setup-python@v2
+              uses: actions/setup-python@v5
               with:
                   python-version: ${{ matrix.python-version }}
             - name: Install Python dependencies
               run: |
-                python -m pip install --upgrade pip wheel
+                python -m pip install --upgrade pip setuptools wheel
                 python -m pip install -r doc/rtd_requirements.txt
-            - name: Install desiutil
-              run: python -m pip install --no-cache-dir git+https://github.com/desihub/desiutil.git@${{ env.DESIUTIL_VERSION }}#egg=desiutil
+            # - name: Install desiutil
+            #   run: python -m pip install --no-cache-dir git+https://github.com/desihub/desiutil.git@${{ env.DESIUTIL_VERSION }}#egg=desiutil
             - name: Compile the package
               run: CC=g++ CXX=g++ CFLAGS="-fPIC" LDSHARED="g++ -shared" python setup.py build_ext --inplace
             - name: Test the documentation

diff --git a/doc/Makefile b/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

diff --git a/doc/changes.rst b/doc/changes.rst
@@ -6,7 +6,9 @@ fiberassign change log
 5.7.3 (unreleased)
 ------------------
 
-* No changes yet.
+* Remove ``DesiTest`` from setup.py and warn about other deprecated features (PR `#464`_).
+
+.. _`#464`: https://github.com/desihub/fiberassign/pull/464
 
 5.7.2 (2023-10-04)
 ------------------

diff --git a/doc/conf.py b/doc/conf.py
@@ -46,17 +46,18 @@
     'sphinx.ext.todo',
     'sphinx.ext.mathjax',
     'sphinx.ext.viewcode',
-    'sphinx.ext.napoleon'
+    'sphinx.ext.napoleon',
+    'sphinx_rtd_theme'
 ]
 
 # Configuration for intersphinx, copied from astropy.
 intersphinx_mapping = {
     'python': ('https://docs.python.org/3/', None),
     'numpy': ('https://numpy.org/doc/stable/', None),
     'scipy': ('https://docs.scipy.org/doc/scipy/reference/', None),
-    'matplotlib': ('https://matplotlib.org/', None),
+    'matplotlib': ('https://matplotlib.org/stable/', None),
     'astropy': ('https://docs.astropy.org/en/stable/', None),
-    'h5py': ('https://docs.h5py.org/en/latest/', None)
+    'h5py': ('https://docs.scipy.org/doc/scipy/', None)
     }
 
 # Add any paths that contain templates here, relative to this directory.
@@ -73,7 +74,7 @@
 
 # General information about the project.
 project = 'fiberassign'
-copyright = '2014-2022, DESI Collaboration'
+copyright = '2014-2025, DESI Collaboration'
 author = 'Robert Cahn, Jaime E. Forero-Romero, Ted Kisner'
 
 # The version info for the project you're documenting, acts as replacement for
@@ -150,12 +151,7 @@
 # a list of builtin themes.
 #html_theme = 'default'
 #html_theme = 'haiku'
-try:
-    import sphinx_rtd_theme
-    html_theme = 'sphinx_rtd_theme'
-    html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
-except ImportError:
-    pass
+html_theme = 'sphinx_rtd_theme'
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
@@ -234,82 +230,3 @@
 
 # Output file base name for HTML help builder.
 htmlhelp_basename = 'fiberassigndoc'
-
-
-# -- Options for LaTeX output ---------------------------------------------
-
-latex_elements = {
-# The paper size ('letterpaper' or 'a4paper').
-#'papersize': 'letterpaper',
-
-# The font size ('10pt', '11pt' or '12pt').
-#'pointsize': '10pt',
-
-# Additional stuff for the LaTeX preamble.
-#'preamble': '',
-}
-
-# Grouping the document tree into LaTeX files. List of tuples
-# (source start file, target name, title,
-#  author, documentclass [howto, manual, or own class]).
-latex_documents = [
-  ('index', 'fiberassign.tex', 'fiberassign Documentation',
-   'DESI Collaboration', 'manual'),
-]
-
-# The name of an image file (relative to this directory) to place at the top of
-# the title page.
-#latex_logo = None
-
-# For "manual" documents, if this is true, then toplevel headings are parts,
-# not chapters.
-#latex_use_parts = False
-
-# If true, show page references after internal links.
-#latex_show_pagerefs = False
-
-# If true, show URL addresses after external links.
-#latex_show_urls = False
-
-# Documents to append as an appendix to all manuals.
-#latex_appendices = []
-
-# If false, no module index is generated.
-#latex_domain_indices = True
-
-
-# -- Options for manual page output ---------------------------------------
-
-# One entry per manual page. List of tuples
-# (source start file, name, description, authors, manual section).
-man_pages = [
-    ('index', 'fiberassign', 'fiberassign Documentation',
-     ['DESI Collaboration'], 1)
-]
-
-# If true, show URL addresses after external links.
-#man_show_urls = False
-
-
-# -- Options for Texinfo output -------------------------------------------
-
-# Grouping the document tree into Texinfo files. List of tuples
-# (source start file, target name, title, author,
-#  dir menu entry, description, category)
-texinfo_documents = [
-  ('index', 'fiberassign', 'fiberassign Documentation',
-   'DESI Collaboration', 'fiberassign', 'One line description of project.',
-   'Miscellaneous'),
-]
-
-# Documents to append as an appendix to all manuals.
-#texinfo_appendices = []
-
-# If false, no module index is generated.
-#texinfo_domain_indices = True
-
-# How to display URL addresses: 'footnote', 'no', or 'inline'.
-#texinfo_show_urls = 'footnote'
-
-# If true, do not generate a @detailmenu in the "Top" node's menu.
-#texinfo_no_detailmenu = False
diff --git a/doc/rtd_requirements.txt b/doc/rtd_requirements.txt
@@ -1,3 +1,3 @@
-Sphinx>6,<7
-sphinx-rtd-theme>1
-git+https://github.com/desihub/desiutil.git@main#egg=desiutil
+Sphinx
+sphinx-rtd-theme
+git+https://github.com/desihub/desiutil.git@3.5.0#egg=desiutil
diff --git a/py/fiberassign/test/simulate.py b/py/fiberassign/test/simulate.py
@@ -24,7 +24,7 @@
                                  TARGET_TYPE_SUPPSKY,
                                  TARGET_TYPE_SUPPSKY, TARGET_TYPE_STANDARD)
 
-test_assign_date = "2020-01-01T00:00:00+00:00"
+sim_assign_date = "2020-01-01T00:00:00+00:00"
 
 def sim_data_dir():
     dir = "test_fiberassign_output"
@@ -33,7 +33,7 @@ def sim_data_dir():
     return dir
 
 
-def test_subdir_create(name):
+def sim_data_subdir_create(name):
     test_dir = os.path.join(sim_data_dir(), name)
     if os.path.isdir(test_dir):
         shutil.rmtree(test_dir)

diff --git a/py/fiberassign/test/test_assign.py b/py/fiberassign/test/test_assign.py
@@ -50,8 +50,8 @@
 from fiberassign.scripts.qa_plot import parse_plot_qa, run_plot_qa
 
 
-from .simulate import (test_subdir_create, sim_tiles, sim_targets,
-                       sim_focalplane, petal_rotation, test_assign_date,
+from .simulate import (sim_data_subdir_create, sim_tiles, sim_targets,
+                       sim_focalplane, petal_rotation, sim_assign_date,
                        sim_stuck_sky)
 
 
@@ -73,7 +73,7 @@ def tearDown(self):
 
     def test_io(self):
         np.random.seed(123456789)
-        test_dir = test_subdir_create("assign_test_io")
+        test_dir = sim_data_subdir_create("assign_test_io")
         input_mtl = os.path.join(test_dir, "mtl.fits")
         input_std = os.path.join(test_dir, "standards.fits")
         input_sky = os.path.join(test_dir, "sky.fits")
@@ -115,10 +115,10 @@ def test_io(self):
         load_target_file(tgs, tagalong, input_suppsky)
 
         # Compute the targets available to each fiber for each tile.
-        fp, exclude, state = sim_focalplane(rundate=test_assign_date)
+        fp, exclude, state = sim_focalplane(rundate=sim_assign_date)
         hw = load_hardware(
             focalplane=(fp, exclude, state),
-            rundate=test_assign_date
+            rundate=sim_assign_date
         )
         tfile = os.path.join(test_dir, "footprint.fits")
         sim_tiles(tfile)
@@ -285,7 +285,7 @@ def test_stucksky(self):
         return self.test_full(do_stucksky=True)
 
     def test_full(self, do_stucksky=False):
-        test_dir = test_subdir_create("assign_test_full")
+        test_dir = sim_data_subdir_create("assign_test_full")
         np.random.seed(123456789)
         input_mtl = os.path.join(test_dir, "mtl.fits")
         input_std = os.path.join(test_dir, "standards.fits")
@@ -328,8 +328,8 @@ def test_full(self, do_stucksky=False):
         load_target_file(tgs, tagalong, input_suppsky)
 
         # Read hardware properties
-        fp, exclude, state = sim_focalplane(rundate=test_assign_date)
-        hw = load_hardware(focalplane=(fp, exclude, state), rundate=test_assign_date)
+        fp, exclude, state = sim_focalplane(rundate=sim_assign_date)
+        hw = load_hardware(focalplane=(fp, exclude, state), rundate=sim_assign_date)
         tfile = os.path.join(test_dir, "footprint.fits")
         sim_tiles(tfile)
         tiles = load_tiles(tiles_file=tfile)
@@ -394,7 +394,7 @@ def test_full(self, do_stucksky=False):
         return
 
     def test_cli(self):
-        test_dir = test_subdir_create("assign_test_cli")
+        test_dir = sim_data_subdir_create("assign_test_cli")
         np.random.seed(123456789)
         input_mtl = os.path.join(test_dir, "mtl.fits")
         input_std = os.path.join(test_dir, "standards.fits")
@@ -439,7 +439,7 @@ def test_cli(self):
             "standards_per_petal": 10,
             "sky_per_petal": 40,
             "overwrite": True,
-            "rundate": test_assign_date
+            "rundate": sim_assign_date
         }
         optlist = option_list(opts)
         args = parse_assign(optlist)
@@ -482,7 +482,7 @@ def test_cli(self):
         return
 
     def test_fieldrot(self):
-        test_dir = test_subdir_create("assign_test_fieldrot")
+        test_dir = sim_data_subdir_create("assign_test_fieldrot")
         np.random.seed(123456789)
         input_mtl = os.path.join(test_dir, "mtl.fits")
         input_std = os.path.join(test_dir, "standards.fits")
@@ -544,12 +544,12 @@ def test_fieldrot(self):
                 tile_ids = list(tiles.id)
 
             # Simulate a fake focalplane
-            fp, exclude, state = sim_focalplane(rundate=test_assign_date, fakepos=True)
+            fp, exclude, state = sim_focalplane(rundate=sim_assign_date, fakepos=True)
 
             # Load the focalplane
             hw = load_hardware(
                 focalplane=(fp, exclude, state),
-                rundate=test_assign_date
+                rundate=sim_assign_date
             )
 
             # Precompute target positions