Merge pull request #146 from XAITK/update-to-v0.8.0

Update to v0.8.0.

.github/workflows/ci-unittests.yml

@@ -82,7 +82,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8","3.9","3.10","3.11"]
+        python-version: ["3.8","3.9","3.10","3.11","3.12"]
         # Extras for included, optional plugin support (space-separated lists)
         opt-extra: [
             "",  # no extras
@@ -128,7 +128,7 @@ jobs:
         run: poetry run pytest
 
       - name: CodeCov report submission
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           fail_ci_if_error: true

.readthedocs.yaml

@@ -1,12 +1,17 @@
 version: 2
 formats:
   - pdf
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.8"
+
 python:
-  version: 3.8
   install:
     - requirements: docs/readthedocs-reqs.txt
     - method: pip
       path: .
+
 sphinx:
   builder: html
   configuration: docs/conf.py

Dockerfile

@@ -1,8 +1,9 @@
 FROM python:3.8 AS xaitk_base
 
 # install poetry and configure to install to pip environment
-RUN pip install poetry \
-&& poetry config virtualenvs.create false
+ENV PATH=/root/.local/bin:${PATH}
+RUN (curl -sSL 'https://install.python-poetry.org' | python3 -) \
+ && poetry config virtualenvs.create false
 
 WORKDIR /xaitk
 
@@ -11,5 +12,9 @@ COPY poetry.lock pyproject.toml /xaitk/
 RUN poetry install --no-root
 
 # install package
-COPY . /xaitk/
+COPY docs /xaitk/docs/
+COPY scripts /xaitk/scripts/
+COPY tests /xaitk/tests/
+COPY xaitk_saliency /xaitk/xaitk_saliency
+COPY .flake8 .mypy.ini CONTRIBUTING.md LICENSE.txt README.md /xaitk/
 RUN poetry install

docs/readthedocs-reqs.txt

@@ -1,2 +1,3 @@
 # Additional requirements for building our documentation in read-the-docs build
-sphinx-prompt
+sphinx-prompt==1.3.0
+sphinx-rtd-theme==1.2.2

docs/release_notes.rst

@@ -12,3 +12,4 @@ Release Notes
    release_notes/v0.6.0
    release_notes/v0.6.1
    release_notes/v0.7.0
+   release_notes/v0.8.0

docs/release_notes/v0.8.0.rst

@@ -0,0 +1,33 @@
+v0.8.0
+======
+
+Updated dependencies to support Python 3.12 along with a few other smaller bug fixes.
+
+Updates / New Features
+----------------------
+
+CI/CD
+
+* Changed CodeCov version from v3 to v4.
+
+* Add python 3.12 to test matrix
+
+Docker
+
+* Update Dockerfile install of poetry, and make separate & specific directory
+  copies.
+
+Utils
+
+* Updated logging format of occlusion masking benchmark utility.
+
+Fixes
+-----
+
+Tests
+
+* Fix various floating point equality comparisons to not use exact match.
+
+* Fix random number usage from numpy to use `np.random.default_rng`.
+
+* Fix error being masked in `test_sal_on_coco_dets`

pyproject.toml

@@ -8,7 +8,7 @@ name = "xaitk_saliency"
 # REMEMBER: `distutils.version.*Version` types can be used to compare versions
 # from strings like this.
 # This package prefers to use the strict numbering standard when possible.
-version = "0.7.0"
+version = "0.8.0"
 description = """\
     Visual saliency map generation interfaces and baseline implementations \
     for explainable AI."""
@@ -29,22 +29,33 @@ classifiers = [
         'Programming Language :: Python :: 3.9',
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
+        'Programming Language :: Python :: 3.12',
 ]
 
 [tool.poetry.dependencies]
 python = "^3.8"
-numpy = ">=1.22"
+numpy = [
+    {version = ">=1.22,<1.26", python = ">=3.8,<3.12"},
+    {version = ">=1.26", python = ">=3.12"}
+]
 scikit-image = [
     # Hinge because minimum support 0.20.0 for py3.11
     { version = ">=0.18.1", python = "<3.11" },
-    { version = ">=0.20.0", python = ">=3.11" }
+    { version = ">=0.20.0", python = ">=3.11, <3.12" },
+    { version = ">=0.22.0", python = ">=3.12" }
+]
+scikit-learn = [
+    {version = ">=1.2, <1.4", python = ">=3.8,<3.12"},
+    {version = ">=1.4", python = ">=3.12"}
 ]
-scikit-learn = ">=1.2"
 smqtk-classifier = ">=0.17.0"
 smqtk-core = ">=0.18.0"
 smqtk-descriptors = ">=0.16.0"
 smqtk-detection = ">=0.19.0"
-scipy = ">=1.8.1"
+scipy = [
+    {version = ">=1.8.1,<1.9", python = ">=3.8,<3.11"},
+    {version = ">=1.9", python = "^3.11"}
+]
 click = ">=8.0.3"
 setuptools = "*"
 # Optionals for "example" extra
@@ -56,10 +67,12 @@ torchvision = {version = ">=0.10.0", optional = true}
 tqdm = { version = ">=4.45.0", optional = true }
 # Optionals for "tools" extra"
 kwcoco = { version = ">=0.2.18", optional = true}
+pyyaml = {version = ">=6.0.1", optional = true, python = ">=3.12"}
+shapely = {version = ">=2.0.2", optional = true, python = ">=3.12"}
 
 [tool.poetry.extras]
 example_deps = [ "jupyter", "matplotlib", "papermill", "torch", "torchvision", "tqdm" ]
-tools = [ "kwcoco", "matplotlib" ]
+tools = [ "kwcoco", "matplotlib", "pyyaml", "shapely" ]
 
 [tool.poetry.dev-dependencies]
 # CI

tests/impls/gen_classifier_conf_sal/test_occlusion_scoring.py

@@ -58,11 +58,11 @@ def test_1class_scores(self) -> None:
         Test basic scoring with a single class for broadcasting sanity check.
         """
         impl = OcclusionScoring()
-        np.random.seed(2)
+        rng = np.random.default_rng(2)
         # Three Perturbation masks of height and width 10px for 1 class
-        image_confs_1_class_ = np.random.rand(1)
-        pertb_confs_1_class_ = np.random.rand(3, 1)
-        mask_confs_1_class_ = np.random.randint(low=0, high=2, size=(3, 10, 10), dtype='int')
+        image_confs_1_class_ = rng.standard_normal((1))
+        pertb_confs_1_class_ = rng.standard_normal((3, 1))
+        mask_confs_1_class_ = rng.integers(low=0, high=2, size=(3, 10, 10), dtype='int')
 
         sal = impl.generate(image_confs_1_class_, pertb_confs_1_class_, mask_confs_1_class_)
         assert sal.shape == (1, 10, 10)
@@ -85,10 +85,10 @@ def test_20class_scores(self) -> None:
         Test scoring for 20 classes.
         """
         impl = OcclusionScoring()
-        np.random.seed(2)
+        rng = np.random.default_rng(2)
         # Three Perturbation masks of height and width 10px for 20 classes
-        image_confs_1_class_ = np.random.rand(20)
-        pertb_confs_1_class_ = np.random.rand(3, 20)
-        mask_confs_1_class_ = np.random.randint(low=0, high=2, size=(3, 10, 10), dtype='int')
+        image_confs_1_class_ = rng.standard_normal((20))
+        pertb_confs_1_class_ = rng.standard_normal((3, 20))
+        mask_confs_1_class_ = rng.integers(low=0, high=2, size=(3, 10, 10), dtype='int')
         sal = impl.generate(image_confs_1_class_, pertb_confs_1_class_, mask_confs_1_class_)
         assert sal.shape == (20, 10, 10)

tests/impls/gen_classifier_conf_sal/test_rise_scoring.py

@@ -31,7 +31,7 @@ def test_configuration(self) -> None:
         """
         inst = RISEScoring(p1=0.747)
         for inst_i in configuration_test_helper(inst):
-            assert inst_i.p1 == 0.747
+            assert np.allclose(inst_i.p1, 0.747)
 
     def test_bad_alignment(self) -> None:
         """

tests/impls/gen_descriptor_sim_sal/test_similarity_scoring.py

@@ -57,11 +57,11 @@ def test_generate_mismatch_ref_descriptors(self) -> None:
         Test that we appropriately error when the input reference descriptors
         are not the same dimensionality.
         """
-        np.random.seed(0)
-        test_ref_descr = np.random.rand(16)
-        test_query_descrs = np.random.rand(5, 15)  # Different than above
-        test_pert_descrs = np.random.rand(32, 16)
-        test_masks = np.random.rand(32, 16, 16)
+        rng = np.random.default_rng(seed=0)
+        test_ref_descr = rng.standard_normal(16)
+        test_query_descrs = rng.standard_normal((5, 15))  # Different than above
+        test_pert_descrs = rng.standard_normal((32, 16))
+        test_masks = rng.standard_normal((32, 16, 16))
 
         impl = SimilarityScoring()
 
@@ -76,11 +76,11 @@ def test_generate_mismatched_perturbed(self) -> None:
         Test that we appropriately error when the input perturbation
         descriptors and mask arrays are not equal in first-dimension length.
         """
-        np.random.seed(0)
-        test_ref_descr = np.random.rand(16)
-        test_query_descrs = np.random.rand(1, 16)
-        test_pert_descrs = np.random.rand(32, 16)
-        test_masks = np.random.rand(30, 16, 16)  # Different than above
+        rng = np.random.default_rng(seed=0)
+        test_ref_descr = rng.standard_normal(16)
+        test_query_descrs = rng.standard_normal((1, 16))
+        test_pert_descrs = rng.standard_normal((32, 16))
+        test_masks = rng.standard_normal((30, 16, 16))  # Different than above
 
         impl = SimilarityScoring()
 
@@ -96,11 +96,11 @@ def test_1_featurevec(self) -> None:
         Test basic scoring with a single feature for broadcasting sanity check.
         """
         impl = SimilarityScoring()
-        np.random.seed(2)
-        ref_feat = np.random.rand(2048)
-        query_feats = np.random.rand(2, 2048)
-        pertb_feats = np.random.rand(3, 2048)
-        pertb_mask = np.random.randint(low=0, high=2, size=(3, 10, 10), dtype='int')
+        rng = np.random.default_rng(2)
+        ref_feat = rng.standard_normal(2048)
+        query_feats = rng.standard_normal((2, 2048))
+        pertb_feats = rng.standard_normal((3, 2048))
+        pertb_mask = rng.integers(low=0, high=2, size=(3, 10, 10), dtype='int')
         sal = impl.generate(ref_feat, query_feats, pertb_feats, pertb_mask)
         assert sal.shape == (2, 10, 10)
 
@@ -123,10 +123,10 @@ def test_512_featdim(self) -> None:
         Test scoring for features of 512 dims.
         """
         impl = SimilarityScoring()
-        np.random.seed(2)
-        ref_feat = np.random.rand(512)
-        query_feats = np.random.rand(1, 512)
-        pertb_feats = np.random.rand(15, 512)
-        pertb_mask = np.random.randint(low=0, high=2, size=(15, 10, 10), dtype='int')
+        rng = np.random.default_rng(2)
+        ref_feat = rng.standard_normal(512)
+        query_feats = rng.standard_normal((1, 512))
+        pertb_feats = rng.standard_normal((15, 512))
+        pertb_mask = rng.integers(low=0, high=2, size=(15, 10, 10), dtype='int')
         sal = impl.generate(ref_feat, query_feats, pertb_feats, pertb_mask)
         assert sal.shape == (1, 10, 10)

tests/impls/gen_detector_prop_sal/test_drise_scoring.py

@@ -23,9 +23,10 @@ def test_shape_sanity(self) -> None:
         Test basic scoring with a single feature for broadcasting sanity check.
         """
         impl = DRISEScoring()
-        ref_dets = np.random.rand(2, 7)
-        pert_dets = np.random.rand(10, 3, 7)
-        pert_mask = np.random.randint(
+        rng = np.random.default_rng(seed=0)
+        ref_dets = rng.standard_normal((2, 7))
+        pert_dets = rng.standard_normal((10, 3, 7))
+        pert_mask = rng.integers(
             low=0, high=2, size=(10, 15, 25), dtype='int')
         sal = impl.generate(ref_dets, pert_dets, pert_mask)
         assert sal.shape == (2, 15, 25)
@@ -52,9 +53,10 @@ def test_mask_detections_size_mismatch(self) -> None:
         Test size mismatch between perturbed detections and masks.
         """
         impl = DRISEScoring()
-        ref_dets = np.random.rand(2, 7)
-        pert_dets = np.random.rand(9, 3, 7)  # ONE LESS than pert mask mat.
-        pert_mask = np.random.randint(
+        rng = np.random.default_rng(seed=0)
+        ref_dets = rng.standard_normal((2, 7))
+        pert_dets = rng.standard_normal((9, 3, 7))  # ONE LESS than pert mask mat.
+        pert_mask = rng.integers(
             low=0, high=2, size=(10, 15, 25), dtype='int')
         with pytest.raises(
             ValueError,
@@ -68,9 +70,10 @@ def test_detections_classes_mismatch(self) -> None:
         Test mismatch in number of classes between perturbed and reference detections.
         """
         impl = DRISEScoring()
-        ref_dets = np.random.rand(2, 8)  # ONE MORE than pert dets mat.
-        pert_dets = np.random.rand(10, 3, 7)
-        pert_mask = np.random.randint(
+        rng = np.random.default_rng(seed=0)
+        ref_dets = rng.standard_normal((2, 8))  # ONE MORE than pert dets mat.
+        pert_dets = rng.standard_normal((10, 3, 7))
+        pert_mask = rng.integers(
             low=0, high=2, size=(10, 15, 25), dtype='int')
         with pytest.raises(
             ValueError,

tests/impls/gen_image_classifier_blackbox_sal/test_rise.py

@@ -35,10 +35,10 @@ def test_configuration(self) -> None:
             assert isinstance(inst_g, RISEScoring)
             assert inst_p.n == 444
             assert inst_p.s == 33
-            assert inst_p.p1 == .22
+            assert np.allclose(inst_p.p1, .22)
             assert inst_p.seed == 42
             assert inst_p.threads == 99
-            assert inst_g.p1 == .22
+            assert np.allclose(inst_g.p1, .22)
             assert inst_i.get_config()['debiased'] is True
 
     def test_configuration_not_debiased(self) -> None:
@@ -58,8 +58,8 @@ def test_configuration_not_debiased(self) -> None:
             inst_g = inst_i._po._generator
             assert isinstance(inst_p, RISEGrid)
             assert isinstance(inst_g, RISEScoring)
-            assert inst_p.p1 == .22
-            assert inst_g.p1 == 0.0
+            assert np.allclose(inst_p.p1, .22)
+            assert np.allclose(inst_g.p1, 0.0)
             assert inst_i.get_config()['debiased'] is False
 
     def test_generation_rgb(self) -> None:

tests/impls/gen_object_detector_blackbox_sal/test_drise.py

@@ -37,7 +37,7 @@ def test_configuration(self) -> None:
             assert isinstance(inst_g, DRISEScoring)
             assert inst_p.n == 123
             assert inst_p.s == 8
-            assert inst_p.p1 == 0.73
+            assert np.allclose(inst_p.p1, .73)
             assert inst_p.seed == 98
             assert inst_p.threads == 5
             assert inst_g.get_config() == {}

tests/impls/gen_object_detector_blackbox_sal/test_random_grid.py

@@ -38,7 +38,7 @@ def test_configuration(self) -> None:
             assert isinstance(inst_g, DRISEScoring)
             assert inst_p.n == 55
             assert inst_p.s == (15, 8)
-            assert inst_p.p1 == 0.34
+            assert np.allclose(inst_p.p1, 0.34)
             assert inst_p.seed == 7
             assert inst_p.threads == 2
             assert inst_g.get_config() == {}