RFC: refactor benchmarks setups and customize pytest's discovery rule…

… to enable running benchmarks through pytest

benchmarks/coordinates.py

@@ -51,6 +51,9 @@ def setup(self):
         self.array_rep = CartesianRepresentation(np.ones((3, 1000)) * u.kpc)
         self.array_dif = CartesianDifferential(np.ones((3, 1000)) * u.km / u.s)
 
+    # pytest compat
+    setup_method = setup
+
     def time_with_differentials_scalar(self):
         self.scalar_rep.with_differentials(self.scalar_dif)
 
@@ -129,6 +132,9 @@ def setup(self):
             xyz_clustered2, representation_type=CartesianRepresentation
         )
 
+    # pytest compat
+    setup_method = setup
+
     def time_init_nodata(self):
         FK5()
 
@@ -188,6 +194,9 @@ def setup(self):
             lat=self.array_q_dec, lon=self.array_q_ra
         )
 
+    # pytest compat
+    setup_method = setup
+
     def time_init_scalar(self):
         SkyCoord(1, 2, unit="deg", frame="icrs")
 

benchmarks/io_ascii/core.py

@@ -41,6 +41,9 @@ def setup(self):
         for col, x in izip(self.cols, lst):
             col.str_vals = [str(s) for s in x]
 
+    # pytest compat
+    setup_method = setup
+
     def time_continuation_inputter(self):
         core.ContinuationLinesInputter().process_lines(self.lines)
 

benchmarks/io_ascii/fixedwidth.py

@@ -18,6 +18,9 @@ def setup(self):
         self.splitter.cols = self.header.cols
         self.data = ascii.FixedWidthData()
 
+    # pytest compat
+    setup_method = setup
+
     def time_splitter(self):
         self.splitter(self.lines[1:])
 

benchmarks/io_ascii/ipac.py

@@ -26,6 +26,9 @@ def setup(self):
         self.data.cols = list(self.table.columns.values())
         self.data._set_fill_values(self.data.cols)
 
+    # pytest compat
+    setup_method = setup
+
     def time_splitter(self):
         self.splitter.join(self.vals, self.widths)
 

benchmarks/io_ascii/main.py

@@ -43,6 +43,9 @@ def setup(self):
         if self.file_format != "sextractor":
             self.table = self.read()
 
+    # pytest compat
+    setup_method = setup
+
     def read(self):
         return ascii.read(BytesIO(self.data), format=self.file_format, guess=False)
 

benchmarks/io_ascii/rdb.py

@@ -13,5 +13,8 @@ def setup(self):
         self.lines = f.read().split("\n")
         f.close()
 
+    # pytest compat
+    setup_method = setup
+
     def time_get_cols(self):
         self.header.get_cols(self.lines)

benchmarks/io_ascii/sextractor.py

@@ -23,5 +23,8 @@ def setup(self):
             self.lines.append("# {} {} Description [pixel**2]".format(i, randword()))
         self.lines.append("Non-header line")
 
+    # pytest compat
+    setup_method = setup
+
     def time_header(self):
         self.header.get_cols(self.lines)

benchmarks/io_ascii/table.py

@@ -28,6 +28,9 @@ def setup(self):
         self.outputter = core.TableOutputter()
         self.table = table.Table()
 
+    # pytest compat
+    setup_method = setup
+
     def time_table_outputter(self):
         self.outputter(self.cols, {"table": {}})
 

benchmarks/io_fits.py

@@ -25,6 +25,9 @@ def setup(self):
             t["booleans"] = t["floats"] > 0.5
             t.write(temp, format="fits")
 
+    # pytest compat
+    setup_method = setup
+
     def time_read_nommap(self):
         try:
             Table.read(self.table_file, format="fits", memmap=False)
@@ -42,7 +45,7 @@ def time_write(self):
         t.write(table_bytes, format="fits")
 
 
-class FITSBinTableHDU:
+class FITSBinTableHDUBenchmarks:
     def time_from_columns_bytes(self):
         x = np.repeat(b"a", 2_000_000)
         array = np.array(x, dtype=[("col", "S1")])
@@ -57,7 +60,7 @@ def make_header(ncards=1000):
     return fits.Header(cards)
 
 
-class FITSHeader:
+class FITSHeaderBenchmarks:
     """
     Tests of the Header interface
     """
@@ -66,6 +69,9 @@ def setup(self):
         self.hdr = make_header()
         self.hdr_string = self.hdr.tostring()
 
+    # pytest compat
+    setup_method = setup
+
     def time_get_int(self):
         self.hdr.get("INT999")
 
@@ -85,21 +91,23 @@ def time_fromstring(self):
         fits.Header.fromstring(self.hdr_string)
 
 
-class FITSHDUList:
+class FITSHDUListBenchmarks:
     """
     Tests of the HDUList interface
     """
 
-    filename = "many_hdu.fits"
-
     def setup_cache(self):
+        self.filename = NamedTemporaryFile(delete=False).name
         hdr = make_header()
         hdul = fits.HDUList(
             [fits.PrimaryHDU(header=hdr)]
             + [fits.ImageHDU(header=hdr) for _ in range(30)]
         )
         hdul.writeto(self.filename)
 
+    # pytest compat
+    setup_method = setup_cache
+
     def time_getheader(self):
         fits.getheader(self.filename)
 

benchmarks/modeling/compound.py

@@ -47,6 +47,9 @@ def setup(self):
             | models.RotateNative2Celestial(5.6, -72.05, 180)
         )
 
+    # pytest compat
+    setup_method = setup
+
     def time_scalar(self):
         r, d = self.model(x_no_units_scalar, x_no_units_scalar)
 
@@ -77,6 +80,9 @@ def setup(self):
             | models.RotateNative2Celestial(5.6 * u.deg, -72.05 * u.deg, 180 * u.deg)
         )
 
+    # pytest compat
+    setup_method = setup
+
     def time_scalar(self):
         r, d = self.model(x_no_units_scalar * u.pix, x_no_units_scalar * u.pix)
 

benchmarks/stats/sigma_clipping.py

@@ -26,6 +26,9 @@ def setup(self):
             # deviation as the stdfunc.  The default iters is 5.
             self.sigclip = SigmaClip(sigma=3)
 
+    # pytest compat
+    setup_method = setup
+
     def time_3d_array(self):
         self.sigclip(self.data[:, :1024, :1024])
 

benchmarks/table.py

@@ -42,6 +42,9 @@ def setup(self):
 
         self.bool_mask = self.table["a"] > 0.6
 
+    # pytest compat
+    setup_method = setup
+
     def time_table_slice_bool(self):
         self.table[self.bool_mask]
 
@@ -148,6 +151,9 @@ class TimeMaskedColumn:
     def setup(self):
         self.dat = np.arange(1e7)
 
+    # pytest compat
+    setup_method = setup
+
     def time_masked_column_init(self):
         MaskedColumn(self.dat)
 
@@ -156,6 +162,9 @@ class TimeTableInitWithLists:
     def setup(self):
         self.dat = list(range(100_000))
 
+    # pytest compat
+    setup_method = setup
+
     def time_init_lists(self):
         Table([self.dat, self.dat, self.dat], names=["time", "rate", "error"])
 
@@ -183,6 +192,9 @@ def setup(self):
         self.data_str_masked_1d = self.data_str_1d.copy()
         self.data_str_masked_1d[-1] = np.ma.masked
 
+    # pytest compat
+    setup_method = setup
+
     def time_init_int_1d(self):
         Table([self.data_int_1d])
 

benchmarks/units.py

@@ -119,6 +119,9 @@ def setup(self):
         self.out_sq = data * u.g**2
         self.out_sqrt = data * u.g**0.5
 
+    # pytest compat
+    setup_method = setup
+
     def time_quantity_square(self):
         self.data**2
 
@@ -149,6 +152,8 @@ def setup(self):
         self.out_sq = data * u.g**2
         self.out_sqrt = data * u.g**0.5
 
+    # pytest compat
+    setup_method = setup
 
 class TimeQuantityOpSmallArrayDiffUnit:
     """
@@ -163,6 +168,9 @@ def setup(self):
         # A different but dimensionally compatible unit
         self.data2 = 0.001 * data * u.kg
 
+    # pytest compat
+    setup_method = setup
+
     def time_quantity_equal(self):
         # Same as operator.eq
         self.data == self.data2
@@ -211,6 +219,8 @@ def setup(self):
         self.data = data * u.g
         self.data2 = self.data.copy()
 
+    # pytest compat
+    setup_method = setup
 
 class TimeQuantityOpLargeArrayDiffUnit(TimeQuantityOpSmallArrayDiffUnit):
     """
@@ -224,6 +234,8 @@ def setup(self):
         # A different but dimensionally compatible unit
         self.data2 = 0.001 * data * u.kg
 
+    # pytest compat
+    setup_method = setup
 
 class TimeQuantityOpLargeArraySameUnit(TimeQuantityOpSmallArrayDiffUnit):
     """
@@ -234,3 +246,6 @@ def setup(self):
         data = np.arange(1e6) + 1
         self.data = data * u.g
         self.data2 = self.data.copy()
+
+    # pytest compat
+    setup_method = setup

pytest.ini

@@ -0,0 +1,9 @@
+[pytest]
+# customize test discovery to treat benchmarks as tests
+python_files = *.py
+python_classes = Time *Benchmarks
+python_functions = time_*, timeraw_*, mem_*, peakmem_*, and track_*
+addopts =
+  # ignored because pytest interprets some method arguments as missing fixtures
+  --ignore=benchmarks/cosmology.py
+  --ignore=benchmarks/convolve.py