Merge pull request #1206 from wright-group/faster-pytest

faster pytest

Author: rpm4

.readthedocs.yml

@@ -3,7 +3,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.9"
+    python: "3.11"
 
 python:
   install:

CHANGELOG.md

@@ -18,6 +18,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/).
 - `data.from_LabRAM`:  small tweaks to deal with newly emerged test failure in python 3.11 tests
 
 ### Changed
+- various unit tests were altered to speed up CI
 - default colorbar is sampled at 4096 points (was 256)
 - packaging now done through pyproject.toml
 

WrightTools/data/_data.py

@@ -790,6 +790,8 @@ def norm_for_each(
         norm_vals = np.expand_dims(np.nanmax(channel[:], axis=trivial), trivial)
         new = (channel[:] - channel.null) / (norm_vals - channel.null)
         if new_channel:
+            if not isinstance(new_channel, dict):
+                new_channel = {}
             self.create_channel(
                 new_channel.pop("name", f"{channel.natural_name}_{variable.natural_name}_norm"),
                 values=new,

tests/artists/test_interact2D.py

@@ -1,5 +1,6 @@
 #! /usr/bin/env python3
 
+import pytest
 import numpy as np
 import WrightTools as wt
 from WrightTools import datasets
@@ -49,6 +50,7 @@ def test_skewed():
     return wt.artists.interact2D(data, xaxis=0, yaxis=1)
 
 
+@pytest.mark.xfail(reason="sometimes fails for artificial reasons")
 def test_4D():
     w1 = np.linspace(-5, 5, 31)
     w2 = w1[::2].copy()

tests/collection/from_directory.py

@@ -1,25 +1,23 @@
 #! /usr/bin/env python3
 
-import os
+import pathlib
 import WrightTools as wt
 from WrightTools import datasets
 
 
 def test_from_directory():
     from_dict = {
-        "*.data": wt.data.from_PyCMDS,
         "*.csv": wt.collection.from_Cary,
+        "*.txt": wt.data.from_JASCO,
         "KENT": None,
-        "COLORS": None,
+        "Shimadzu": None,
     }
     p = datasets.PyCMDS.w1_000
-    p = os.path.dirname(p)
-    p = os.path.dirname(p)
-    col = wt.collection.from_directory(p, from_dict)
+    col = wt.collection.from_directory(pathlib.Path(*p.parts[:-2]), from_dict)
     # Print the tree in case tests fail, also will catch errors in printing
     col.print_tree()
     assert col.natural_name == "datasets"
-    assert col.PyCMDS["w1 000"]
+    assert col.JASCO["PbSe batch 1"]
     assert col.Cary["CuPCtS_H2O_vis"]
     assert "KENT" not in col.item_names
     col.close()

tests/data/axis/convert_axis.py

@@ -50,24 +50,24 @@ def test_exception():
     data.close()
 
 
-def test_w1_wa():
-    p = datasets.PyCMDS.w1_wa_000
-    data = wt.data.from_PyCMDS(p)
-    assert data.wa.units == "wn"
-    data.wa.convert("eV")
-    assert data.wa.units == "eV"
-    assert np.isclose(data.wa.max(), 1.5800551001941774)
-    assert np.isclose(data.wa.min(), 0.6725528801867734)
-    assert data["wa"].units == "nm"
+def test_w1_wm():
+    p = datasets.wt5.v1p0p1_MoS2_TrEE_movie
+    data = wt.open(p).at(d2=[0, "fs"])
+    assert data.w2.units == "nm"
+    data.w2.convert("eV")
+    assert data.w2.units == "eV"
+    assert np.isclose(data.w2.max(), 2.120129779494837)
+    assert np.isclose(data.w2.min(), 1.6241930110774845)
+    assert data["w2"].units == "nm"
     data.close()
 
 
 def test_wigner():
-    p = datasets.COLORS.v2p2_WL_wigner
-    data = wt.data.from_COLORS(p)
-    data.d1.convert("ns")
-    assert data.d1.units == "ns"
-    assert data["d1"].units == "fs"
+    p = datasets.wt5.v1p0p1_MoS2_TrEE_movie
+    data = wt.open(p).at(w2=[680, "nm"])
+    data.d2.convert("ns")
+    assert data.d2.units == "ns"
+    assert data["d2"].units == "fs"
     data.close()
 
 
@@ -78,5 +78,5 @@ def test_wigner():
     test_convert_variables()
     test_units_preserved_on_copy()
     test_exception()
-    test_w1_wa()
+    test_w1_wm()
     test_wigner()

tests/data/channel/normalize.py

@@ -33,17 +33,17 @@ def test_LDS821_mag_0p5():
 
 
 def test_wigner():
-    p = datasets.COLORS.v2p2_WL_wigner
-    data = wt.data.from_COLORS(p)
+    p = datasets.wt5.v1p0p1_MoS2_TrEE_movie
+    data = wt.open(p).at(w2=[680, "nm"])
     data.ai0.normalize()
     assert np.isclose(data.ai0.null, 0.0)
     assert np.isclose(data.ai0.max(), 1.0)
     data.close()
 
 
 def test_negative_wigner():
-    p = datasets.COLORS.v2p2_WL_wigner
-    data = wt.data.from_COLORS(p)
+    p = datasets.wt5.v1p0p1_MoS2_TrEE_movie
+    data = wt.open(p).at(w2=[680, "nm"])
     data.ai0 *= -1
     data.ai0.signed = True
     data.ai0.normalize()
@@ -54,8 +54,8 @@ def test_negative_wigner():
 
 
 def test_negative_wigner_mag_1p1():
-    p = datasets.COLORS.v2p2_WL_wigner
-    data = wt.data.from_COLORS(p)
+    p = datasets.wt5.v1p0p1_MoS2_TrEE_movie
+    data = wt.open(p).at(w2=[680, "nm"])
     data.ai0 *= -1
     data.ai0.signed = True
     data.ai0.normalize(1.1)

tests/data/chop.py

@@ -15,11 +15,11 @@
 
 def test_2D_to_1D():
     p = datasets.PyCMDS.w2_w1_000
-    data = wt.data.from_PyCMDS(p)
+    data = wt.data.from_PyCMDS(p)[:, ::10]
     chop = data.chop("w2")
-    assert len(chop) == 81
+    assert len(chop) == data.w1.size
     for d in chop.values():
-        assert d.w2.size == 81
+        assert d.w2.size == data.w2.size
         assert d.axis_expressions == ("w2",)
         for k in data.variable_names:
             assert d[k].label == data[k].label
@@ -29,11 +29,11 @@ def test_2D_to_1D():
 
 def test_3D_to_1D():
     p = datasets.PyCMDS.wm_w2_w1_000
-    data = wt.data.from_PyCMDS(p)
+    data = wt.data.from_PyCMDS(p)[::10, :, ::3]
     chop = data.chop("w2")
-    assert len(chop) == 385
+    assert len(chop) == data.wm.size * data.w1.size
     for d in chop.values():
-        assert d.w2.size == 11
+        assert d.w2.size == data.w2.size
         assert d.axis_expressions == ("w2",)
     data.close()
     chop.close()

tests/data/convert_data.py

@@ -44,8 +44,10 @@ def test_w1_wa():
 
 
 def test_wigner():
-    p = datasets.COLORS.v2p2_WL_wigner
-    data = wt.data.from_COLORS(p)
+    data = wt.Data()
+    data.create_variable("wm", values=np.linspace(100, 300)[:, None], units="nm")
+    data.create_variable("d1", values=np.linspace(-100, 100)[None, :], units="fs")
+    data.transform("d1", "wm")
     data.convert("ns")
     assert data.d1.units == "ns"
     assert data["d1"].units == "fs"

tests/data/from_COLORS.py

@@ -4,7 +4,7 @@
 
 # --- import --------------------------------------------------------------------------------------
 
-
+import pytest
 import numpy as np
 import glob
 import os
@@ -47,6 +47,7 @@ def test_v0p2_d1_d2_diagonal():
     data.close()
 
 
+@pytest.mark.skip(reason="This test takes a long time and examines rarely used code.")
 def test_v2p1_MoS2_TrEE_movie():
     ps = sorted(
         glob.glob(
@@ -61,6 +62,7 @@ def test_v2p1_MoS2_TrEE_movie():
     data.close()
 
 
+@pytest.mark.skip(reason="This test takes a long time and examines rarely used code.")
 def test_v2p2_WL_wigner():
     p = datasets.COLORS.v2p2_WL_wigner
     data = wt.data.from_COLORS(p)