TST: migrate from nosetest to pytest

.circleci/config.yml

@@ -7,20 +7,17 @@ commands:
       - run:
           name:  "Set environment variables."
           command: |
-            echo 'export GOLD_STANDARD=HEAD' >> $BASH_ENV
             echo 'export ROCKSTAR_DIR=$HOME/rockstar-galaxies' >> $BASH_ENV
             echo 'export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$ROCKSTAR_DIR' >> $BASH_ENV
             echo 'export YT_DATA=$HOME/yt_test' >> $BASH_ENV
-            echo 'export TEST_DIR=$HOME/test_results' >> $BASH_ENV
-            echo 'export TEST_NAME=astro_analysis' >> $BASH_ENV
-            echo 'export TEST_FLAGS="--nologcapture -v --with-answer-testing --local --local-dir $TEST_DIR --answer-name=$TEST_NAME --answer-big-data"' >> $BASH_ENV
 
   install-with-yt-dev:
     description: "Install dependencies with yt from source."
     steps:
       - run:
           name: "Install dependencies with yt from source."
           command: |
+            set -x
             source $BASH_ENV
             sudo apt update
             sudo apt upgrade
@@ -75,30 +72,7 @@ commands:
                 girder-cli --api-url https://girder.hub.yt/api/v1 download 577c09480d7c6b0001ad5be2 $YT_DATA/enzo_tiny_cosmology
             fi
 
-  build-and-test-nose:
-    description: "Build yt_astro_analysis and run tests (nose)."
-    steps:
-      - run:
-          name: "Build yt_astro_analysis and run tests."
-          command: |
-            # tag the tip so we can get back there
-            git tag tip
-            source $BASH_ENV
-            source $HOME/venv/bin/activate
-            # generate answers if not cached
-            if [ ! -f ${TEST_DIR}/${TEST_NAME}/${TEST_NAME} ]; then
-              git checkout $GOLD_STANDARD
-              python -m pip install -e .
-              nosetests $TEST_FLAGS --answer-store
-            fi
-            # return to tip and run comparison tests
-            git checkout tip
-            python -m pip install -e .
-            coverage run `which nosetests` $TEST_FLAGS
-            # code coverage report
-            codecov
-
-  build-and-test-pytest:
+  build-and-test:
     description: "Build yt_astro_analysis and run tests (pytest)."
     steps:
       - run:
@@ -107,7 +81,7 @@ commands:
             source $BASH_ENV
             source $HOME/venv/bin/activate
             python -m pip install -e .
-            pytest
+            pytest --color=yes -ra -s
 
   build-docs:
     description: "Test the docs build."
@@ -142,62 +116,6 @@ jobs:
 
     working_directory: ~/yt_astro_analysis
 
-    steps:
-      - checkout
-      - set-env
-
-      - restore_cache:
-          name: "Restore dependencies cache."
-          key: python-<< parameters.tag >>-dependencies-bonxie
-
-      - install-with-yt-dev
-
-      - save_cache:
-          name: "Save dependencies cache"
-          key: python-<< parameters.tag >>-dependencies-bonxie
-          paths:
-            - ~/.cache/pip
-            - ~/venv
-            - ~/yt-git
-            - ~/rockstar-galaxies
-
-      - restore_cache:
-          name: "Restore test data cache."
-          key: test-data-bonxie
-
-      - download-test-data
-
-      - save_cache:
-          name: "Save test data cache."
-          key: test-data-bonxie
-          paths:
-            - ~/yt_test
-
-      - restore_cache:
-          name: "Restore test answers."
-          key: python-<< parameters.tag >>-test-answers-bonxie
-
-      - build-and-test-nose
-
-      - save_cache:
-          name: "Save test answers cache."
-          key: python-<< parameters.tag >>-test-answers-bonxie
-          paths:
-            - ~/test_results
-
-  run-tests-pytest:
-    # Run a subset of the test suite (yield-based tests are not supported by pytest)
-    # this is necessary to test in Python 3.10+ because it's not compatible with nose
-    parameters:
-      tag:
-        type: string
-        default: latest
-    executor:
-      name: python
-      tag: << parameters.tag >>
-
-    working_directory: ~/yt_astro_analysis
-
     steps:
       - checkout
       - set-env
@@ -233,7 +151,7 @@ jobs:
           name: "Restore test answers."
           key: python-<< parameters.tag >>-test-answers-bonxie-pytest
 
-      - build-and-test-pytest
+      - build-and-test
 
       - save_cache:
           name: "Save test answers cache."
@@ -282,14 +200,10 @@ workflows:
            name: "Python 3.9 tests"
            tag: "3.9"
 
-       - run-tests-pytest:
+       - run-tests:
            name: "Python 3.10 tests"
            tag: "3.10"
 
-       - run-tests-pytest:
-           name: "Python 3.11 tests"
-           tag: "3.11"
-
        - docs-test:
            name: "Test docs build"
            tag: "3.9"
@@ -307,9 +221,9 @@ workflows:
            name: "Python 3.9 tests"
            tag: "3.9"
 
-       - run-tests-pytest:
-           name: "Python 3.11 tests"
-           tag: "3.11"
+       - run-tests:
+           name: "Python 3.10 tests"
+           tag: "3.10"
 
        - docs-test:
            name: "Test docs build"

pyproject.toml

@@ -97,7 +97,6 @@ select = [
 combine-as-imports = true
 known-third-party = [
   "IPython",
-  "nose",
   "numpy",
   "sympy",
   "matplotlib",

requirements/tests.txt

@@ -3,8 +3,5 @@ astropy
 scipy
 
 # test dependencies
-nose
-nose-timer
 pytest
 girder-client
-codecov

yt_astro_analysis/cosmological_observation/light_cone/tests/test_light_cone.py

@@ -14,96 +14,79 @@
 # -----------------------------------------------------------------------------
 
 import os
-import shutil
-import tempfile
 
+import h5py
 import numpy as np
+import numpy.testing as npt
+import pytest
+import unyt as un
 
-from yt.testing import assert_equal
-from yt.units.yt_array import YTQuantity
-from yt.utilities.answer_testing.framework import AnswerTestingTest
-from yt.utilities.on_demand_imports import _h5py as h5py
+import yt  # noqa
+from yt.testing import requires_file
 from yt_astro_analysis.cosmological_observation.api import LightCone
-from yt_astro_analysis.utilities.testing import requires_sim
 
 ETC = "enzo_tiny_cosmology/32Mpc_32.enzo"
 _funits = {
-    "density": YTQuantity(1, "g/cm**3"),
-    "temperature": YTQuantity(1, "K"),
-    "length": YTQuantity(1, "cm"),
+    "density": un.unyt_quantity(1, "g/cm**3"),
+    "temperature": un.unyt_quantity(1, "K"),
+    "length": un.unyt_quantity(1, "cm"),
 }
 
 
-class LightConeProjectionTest(AnswerTestingTest):
-    _type_name = "LightConeProjection"
-    _attrs = ()
-
-    def __init__(self, parameter_file, simulation_type, field, weight_field=None):
-        self.parameter_file = parameter_file
-        self.simulation_type = simulation_type
-        self.ds = os.path.basename(self.parameter_file)
-        self.field = field
-        self.weight_field = weight_field
-
-    @property
-    def storage_name(self):
-        return "_".join(
-            (os.path.basename(self.parameter_file), self.field, str(self.weight_field))
-        )
-
-    def run(self):
-        # Set up in a temp dir
-        tmpdir = tempfile.mkdtemp()
-        curdir = os.getcwd()
-        os.chdir(tmpdir)
-
-        lc = LightCone(
-            self.parameter_file,
-            self.simulation_type,
-            0.0,
-            0.1,
-            observer_redshift=0.0,
-            time_data=False,
-        )
-        lc.calculate_light_cone_solution(seed=123456789, filename="LC/solution.txt")
-        lc.project_light_cone(
-            (600.0, "arcmin"),
-            (60.0, "arcsec"),
-            self.field,
-            weight_field=self.weight_field,
-            save_stack=True,
-        )
-
-        dname = f"{self.field}_{self.weight_field}"
-        fh = h5py.File("LC/LightCone.h5", mode="r")
+@requires_file(ETC)
+@pytest.mark.parametrize(
+    "field, weight_field, expected",
+    [
+        (
+            "density",
+            None,
+            [6.0000463633868075e-05, 1.1336502301470154e-05, 0.08970763360935877],
+        ),
+        (
+            "temperature",
+            "density",
+            [37.79481498628398, 0.018410545597485613, 543702.4613479003],
+        ),
+    ],
+)
+def test_light_cone_projection(tmp_path, field, weight_field, expected):
+    parameter_file = ETC
+    simulation_type = "Enzo"
+    field = field
+    weight_field = weight_field
+
+    os.chdir(tmp_path)
+    lc = LightCone(
+        parameter_file,
+        simulation_type,
+        near_redshift=0.0,
+        far_redshift=0.1,
+        observer_redshift=0.0,
+        time_data=False,
+    )
+    lc.calculate_light_cone_solution(seed=123456789, filename="LC/solution.txt")
+    lc.project_light_cone(
+        (600.0, "arcmin"),
+        (60.0, "arcsec"),
+        field,
+        weight_field=weight_field,
+        save_stack=True,
+    )
+
+    dname = f"{field}_{weight_field}"
+    with h5py.File("LC/LightCone.h5", mode="r") as fh:
         data = fh[dname][()]
         units = fh[dname].attrs["units"]
-        if self.weight_field is None:
-            punits = _funits[self.field] * _funits["length"]
+        if weight_field is None:
+            punits = _funits[field] * _funits["length"]
         else:
-            punits = (
-                _funits[self.field] * _funits[self.weight_field] * _funits["length"]
-            )
-            wunits = fh["weight_field_%s" % self.weight_field].attrs["units"]
-            pwunits = _funits[self.weight_field] * _funits["length"]
+            punits = _funits[field] * _funits[weight_field] * _funits["length"]
+            wunits = fh[f"weight_field_{weight_field}"].attrs["units"]
+            pwunits = _funits[weight_field] * _funits["length"]
             assert wunits == str(pwunits.units)
-        assert units == str(punits.units)
-        fh.close()
-
-        # clean up
-        os.chdir(curdir)
-        shutil.rmtree(tmpdir)
-
-        mean = data.mean()
-        mi = data[data.nonzero()].min()
-        ma = data.max()
-        return np.array([mean, mi, ma])
-
-    def compare(self, new_result, old_result):
-        assert_equal(new_result, old_result, verbose=True)
-
+    assert units == str(punits.units)
 
-@requires_sim(ETC, "Enzo")
-def test_light_cone_projection():
-    yield LightConeProjectionTest(ETC, "Enzo", "density")
-    yield LightConeProjectionTest(ETC, "Enzo", "temperature", weight_field="density")
+    mean = np.nanmean(data)
+    mi = np.nanmin(data[data.nonzero()])
+    ma = np.nanmax(data)
+    npt.assert_equal([mean, mi, ma], expected, verbose=True)

yt_astro_analysis/halo_analysis/halo_catalog/analysis_operators.py

@@ -63,6 +63,12 @@ def add_quantity(name, function):
     quantity_registry[name] = AnalysisQuantity(function)
 
 
+def _remove_quantity(name):
+    # this is useful to avoid test pollution when using add_quantity in tests
+    # but it's not meant as public API
+    quantity_registry.pop(name)
+
+
 class AnalysisQuantity(AnalysisCallback):
     r"""
     An AnalysisQuantity is a function that takes minimally a target object,