Repository: impactchart/impactchart (language: python)

Issue:
Update to SHAP 0.44.1
We are pinned to 0.41.0, which in turn requires a pin to an older versions of numpy. We did this to support MacOS, but a wheel for 0.44.1 is avaialble now so we should upgrade.


Discussion / hints:

Fix patch:
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index 04dbf5d..f81a1ca 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -18,14 +18,14 @@ jobs:
       #----------------------------------------------
       #       check-out repo and set-up python
       #----------------------------------------------
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: 3.11
       #----------------------------------------------
       #        load pip cache if cache exists
       #----------------------------------------------
-      - uses: actions/cache@v3
+      - uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: ${{ runner.os }}-pip
diff --git a/impactchart/cli/main.py b/impactchart/cli/main.py
index 4c8d3b3..34ac0c5 100644
--- a/impactchart/cli/main.py
+++ b/impactchart/cli/main.py
@@ -148,14 +148,12 @@ def optimize(args):
 def read_and_filter_data(data_path, y_col: str, filters: Iterable[str]):
     """Read and filter the data."""
     filter_names = [f.split("=")[0] for f in filters]
-    
+
     str_col_types = {
         col: str for col in set(["STATE", "COUNTY", "TRACT"] + filter_names)
     }
 
-    df = pd.read_csv(
-        data_path, header=0, dtype=str_col_types
-    )
+    df = pd.read_csv(data_path, header=0, dtype=str_col_types)
 
     logger.info(f"Initial rows: {len(df.index)}")
 
@@ -233,9 +231,7 @@ def plot_impact_charts(
         lambda d, pos: f"\\${d:,.0f}" if d >= 0 else f"(\\${-d:,.0f})"
     )
 
-    comma_formatter = FuncFormatter(
-        lambda d, pos: f"{d:,.0f}"
-    )
+    comma_formatter = FuncFormatter(lambda d, pos: f"{d:,.0f}")
 
     if filename_prefix is None:
         filename_prefix = ""
@@ -333,7 +329,7 @@ def plot(args):
         w = df[args.w_column]
     else:
         w = None
-        
+
     k = args.k
     seed = int(args.seed, 0)
 
@@ -391,12 +387,7 @@ def add_data_arguments(parser) -> None:
         help="Weight column.",
     )
 
-    parser.add_argument(
-        "-f",
-        "--filter",
-        type=str,
-        nargs="*"
-    )
+    parser.add_argument("-f", "--filter", type=str, nargs="*")
 
     parser.add_argument("data", help="Input data file.")
 
@@ -420,7 +411,9 @@ def main():
     optimize_parser.add_argument(
         "--scoring",
         type=str,
-        help="Scoring method to use when optimizing. See https://scikit-learn.org/stable/modules/model_evaluation.html#scoring-parameter")
+        help="Scoring method to use when optimizing."
+        "See https://scikit-learn.org/stable/modules/model_evaluation.html#scoring-parameter",
+    )
     optimize_parser.add_argument("-S", "--seed", type=str, default="17")
 
     plot_parser = subparsers.add_parser("plot", help="Generate an impact chart.")
diff --git a/poetry.lock b/poetry.lock
index 91be376..8a74852 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -238,53 +238,53 @@ pyflakes = ">=3.1.0,<3.2.0"
 
 [[package]]
 name = "fonttools"
-version = "4.47.0"
+version = "4.47.2"
 description = "Tools to manipulate font files"
 optional = false
 python-versions = ">=3.8"
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 ]
 
 [package.dependencies]
@@ -1337,14 +1307,15 @@ pandas = "*"
 scikit-learn = "*"
 scipy = "*"
 slicer = "0.0.7"
-tqdm = ">4.25.0"
+tqdm = ">=4.27.0"
 
 [package.extras]
-all = ["catboost", "ipython", "lightgbm", "lime", "matplotlib", "nbsphinx", "numpydoc", "opencv-python", "pyod", "pyspark", "pytest", "pytest-cov", "pytest-mpl", "sentencepiece", "sphinx", "sphinx-rtd-theme", "torch", "transformers", "xgboost"]
-docs = ["ipython", "matplotlib", "nbsphinx", "numpydoc", "sphinx", "sphinx-rtd-theme"]
+docs = ["ipython", "matplotlib", "myst-parser (==2.0.0)", "nbsphinx (==0.9.3)", "numpydoc", "requests", "sphinx (==7.2.6)", "sphinx-github-changelog (==1.2.1)", "sphinx-rtd-theme (==2.0.0)"]
 others = ["lime"]
 plots = ["ipython", "matplotlib"]
-test = ["catboost", "lightgbm", "opencv-python", "pyod", "pyspark", "pytest", "pytest-cov", "pytest-mpl", "sentencepiece", "torch", "transformers", "xgboost"]
+test = ["catboost", "gpboost", "lightgbm", "ngboost", "opencv-python", "protobuf (==3.20.3)", "pyod", "pyspark", "pytest", "pytest-cov", "pytest-mpl", "sentencepiece", "tensorflow", "torch", "torchvision", "transformers", "xgboost"]
+test-core = ["pytest", "pytest-cov", "pytest-mpl"]
+test-notebooks = ["datasets", "jupyter", "keras", "nbconvert", "nbformat", "nlp", "transformers"]
 
 [[package]]
 name = "six"
@@ -1429,17 +1400,17 @@ files = [
 
 [[package]]
 name = "xgboost"
-version = "1.7.6"
+version = "2.0.3"
 description = "XGBoost Python Package"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "xgboost-1.7.6-py3-none-macosx_10_15_x86_64.macosx_11_0_x86_64.macosx_12_0_x86_64.whl", hash = "sha256:4c34675b4d2678c624ddde5d45361e7e16046923e362e4e609b88353e6b87124"},
-    {file = "xgboost-1.7.6-py3-none-macosx_12_0_arm64.whl", hash = "sha256:59b4b366d2cafc7f645e87d897983a5b59be02876194b1d213bd8d8b811d8ce8"},
-    {file = "xgboost-1.7.6-py3-none-manylinux2014_aarch64.whl", hash = "sha256:281c3c6f4fbed2d36bf95cd02a641afa95e72e9abde70064056da5e76233e8df"},
-    {file = "xgboost-1.7.6-py3-none-manylinux2014_x86_64.whl", hash = "sha256:b1d5db49b199152d62bd9217c98760207d3de86d2b9d243260c573ffe638f80a"},
-    {file = "xgboost-1.7.6-py3-none-win_amd64.whl", hash = "sha256:127cf1f5e2ec25cd41429394c6719b87af1456ce583e89f0bffd35d02ad18bcb"},
-    {file = "xgboost-1.7.6.tar.gz", hash = "sha256:1c527554a400445e0c38186039ba1a00425dcdb4e40b37eed0e74cb39a159c47"},
+    {file = "xgboost-2.0.3-py3-none-macosx_10_15_x86_64.macosx_11_0_x86_64.macosx_12_0_x86_64.whl", hash = "sha256:b21b2bb188b162c615fce468db93e3f995f3690e6184aadc7743b58466dc7f13"},
+    {file = "xgboost-2.0.3-py3-none-macosx_12_0_arm64.whl", hash = "sha256:722d5b9351dfdf61973490dfd28abd42844db1cc469d07ed9b0cde9d1ffcdb32"},
+    {file = "xgboost-2.0.3-py3-none-manylinux2014_aarch64.whl", hash = "sha256:2315a57b1883221e2f78dd514559aa9797e6c272d995d22e45495a04adac93cc"},
+    {file = "xgboost-2.0.3-py3-none-manylinux2014_x86_64.whl", hash = "sha256:30bd5f789fad467fd49e04e5d19e04238b931682c3951a514da5c2410b3bf59c"},
+    {file = "xgboost-2.0.3-py3-none-win_amd64.whl", hash = "sha256:462f131d7bfb1bc42f67c57fa5aa3e57d2b5755b1573a6e0d2c7e8895164e0fc"},
+    {file = "xgboost-2.0.3.tar.gz", hash = "sha256:505955b5d770f8217a049beecce79e04a93787371c06dfb4b2414fec9d496bf3"},
 ]
 
 [package.dependencies]
@@ -1457,4 +1428,4 @@ scikit-learn = ["scikit-learn"]
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.11"
-content-hash = "2df5cd36174bdd680b0d4d30edfb17974c127994b4da2da2b29d7579ee731b83"
+content-hash = "1aac7d6748759f401c0e76812bd394334e67d19baf63680dbb84e37e81fadcd3"
diff --git a/pyproject.toml b/pyproject.toml
index e3b5241..25a9a65 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "impactchart"
-version = "0.1.12"
+version = "0.2.0"
 description = ""
 authors = ["vengroff <vengroff@gmail.com>"]
 readme = "README.md"
@@ -8,15 +8,9 @@ readme = "README.md"
 [tool.poetry.dependencies]
 python = "^3.11"
 logargparser = "^0.1.1"
-shap = "^0.41.0"  # shap = "^0.42.0"
-# This pin is a workaround for the fact that SHAP 0.41.0 does not work
-# with numpy 1.24.0 or newer. When there is a new release of shap that
-# works with newer numpy versions we can use it an eliminate this pin.
-numpy = "1.23.2"
-pandas = "^2.0.3"
-scikit-learn = "^1.3.0"
-xgboost = "^1.7.3"
-matplotlib = "^3.7.2"
+shap = "^0.44.1"
+xgboost = "^2.0.3"
+matplotlib = "^3.8.2"
 PyYAML = "^6.0"
 
 [tool.poetry.group.test.dependencies]


Test patch:
diff --git a/.github/workflows/unit-test.yml b/.github/workflows/unit-test.yml
index c01546e..b0dc7d7 100644
--- a/.github/workflows/unit-test.yml
+++ b/.github/workflows/unit-test.yml
@@ -23,13 +23,13 @@ jobs:
       #       check out repo
       #----------------------------------------------
       - name: Check out repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       #----------------------------------------------
       #       set up python
       #----------------------------------------------
       - name: Set up python
         id: setup-python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
       #----------------------------------------------
@@ -47,7 +47,7 @@ jobs:
       #----------------------------------------------
       - name: Load cached venv
         id: cached-poetry-dependencies
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: .venv
           key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}
@@ -75,7 +75,7 @@ jobs:
       #----------------------------------------------
       - name: Archive test artifacts
         if: always()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: test_artifacts
           path: tests/_test_artifacts
diff --git a/tests/test_model.py b/tests/test_model.py
index 5d2415e..94ebaa2 100644
--- a/tests/test_model.py
+++ b/tests/test_model.py
@@ -277,7 +277,7 @@ def _assert_impact_sum(df):
         impact_y_hat.name = "y_hat"
 
         pd.testing.assert_series_equal(
-            y_hat["y_hat"], impact_y_hat.astype("float32"), atol=0.005
+            y_hat["y_hat"], impact_y_hat.astype("float32"), atol=0.01
         )
 
     def test_impact_chart(self):