Update dependencies, Python 3.12 compatibility and CI workflow

- Update python dependencies
- Add compatibility with Python 3.12
- Modify CI workflow to address doc building issues
- Change time until an issue becomes inactive

Signed-off-by: Patrick Bloebaum <bloebp@amazon.com>

.github/workflows/advanced-on-demand.yml

@@ -10,7 +10,7 @@ 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"]
         poetry-version: [1.5.1]
         test-group: [1, 2, 3, 4]
 
@@ -54,6 +54,12 @@ jobs:
         with:
           poetry-version: ${{ matrix.poetry-version }}
 
+      - name: Install LLVM and Clang
+        uses: KyleMayes/install-llvm-action@v2
+        with:
+          version: "14.0"
+          directory: ${{ runner.temp }}/llvm
+
       - name: Install graphviz
         run: |
           sudo apt install graphviz libgraphviz-dev graphviz-dev pkg-config

.github/workflows/ci-install.yml

@@ -26,7 +26,7 @@ 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"]
 
     steps:
     - uses: actions/checkout@v4
@@ -36,6 +36,12 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
+    - name: Install LLVM and Clang
+      uses: KyleMayes/install-llvm-action@v2
+      with:
+        version: "14.0"
+        directory: ${{ runner.temp }}/llvm
+
     - name: Install graphviz
       run: |
         sudo apt install graphviz libgraphviz-dev graphviz-dev pkg-config

.github/workflows/ci.yml

@@ -27,7 +27,7 @@ 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"]
         poetry-version: [1.5.1]
         test-group: [1, 2, 3, 4, 5, 6]
 
@@ -44,6 +44,12 @@ jobs:
       with:
         poetry-version: ${{ matrix.poetry-version }}
 
+    - name: Install LLVM and Clang
+      uses: KyleMayes/install-llvm-action@v2.0.5
+      with:
+        version: "14.0"
+        directory: ${{ runner.temp }}/llvm
+
     - name: Install graphviz
       run: |
         sudo apt install graphviz libgraphviz-dev graphviz-dev pkg-config

.github/workflows/close-inactive-issues.yml

@@ -12,11 +12,11 @@ jobs:
     steps:
       - uses: actions/stale@v9
         with:
-          days-before-issue-stale: 14
-          days-before-issue-close: 7
+          days-before-issue-stale: 30
+          days-before-issue-close: 14
           stale-issue-label: "stale"
-          stale-issue-message: "This issue is stale because it has been open for 14 days with no activity."
-          close-issue-message: "This issue was closed because it has been inactive for 7 days since being marked as stale."
+          stale-issue-message: "This issue is stale because it has been open for 30 days with no activity."
+          close-issue-message: "This issue was closed because it has been inactive for 14 days since being marked as stale."
           # in case of issue, only process issues with any of the following labels:
           any-of-issue-labels: "question,help wanted,waiting for author"
 

.github/workflows/docs-ci.yml

@@ -12,7 +12,7 @@ on:
 
 jobs:
   docs:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     container:
       image: "ghcr.io/${{ github.repository_owner }}/dowhy-docs-generation:latest"
     steps:

.github/workflows/docs.yml

@@ -16,7 +16,7 @@ on:
 
 jobs:
   docs:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     container:
       image: "ghcr.io/${{ github.repository_owner }}/dowhy-docs-generation:latest"
     steps:

.github/workflows/nightly-tests.yml

@@ -11,7 +11,7 @@ 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"]
         poetry-version: [1.5.1]
 
     steps:
@@ -27,6 +27,12 @@ jobs:
         with:
           poetry-version: ${{ matrix.poetry-version }}
 
+      - name: Install LLVM and Clang
+        uses: KyleMayes/install-llvm-action@v2
+        with:
+          version: "14.0"
+          directory: ${{ runner.temp }}/llvm
+
       - name: Install graphviz
         run: |
           sudo apt install graphviz libgraphviz-dev graphviz-dev pkg-config

dowhy/causal_estimators/econml.py

@@ -5,7 +5,6 @@
 
 import numpy as np
 import pandas as pd
-from numpy.distutils.misc_util import is_sequence
 
 from dowhy.causal_estimator import CausalEstimate, CausalEstimator
 from dowhy.causal_identifier import IdentifiedEstimand
@@ -295,7 +294,6 @@ def shap_values(self, df: pd.DataFrame, *args, **kwargs):
     def apply_multitreatment(self, df: pd.DataFrame, fun: Callable, *args, **kwargs):
         ests = []
         assert not isinstance(self._treatment_value, str)
-        assert is_sequence(self._treatment_value)
 
         if df is None:
             filtered_df = None

pyproject.toml

@@ -19,6 +19,7 @@ classifiers = [
     'Programming Language :: Python :: 3.9',
     'Programming Language :: Python :: 3.10',
     'Programming Language :: Python :: 3.11',
+    'Programming Language :: Python :: 3.12',
 ]
 keywords = [
     'causality',
@@ -36,7 +37,7 @@ priority = "explicit"
 
 
 [build-system]
-requires = ["poetry-core>=1.0.0"]
+requires = ["poetry-core>=1.0.0", "cython<3"]
 build-backend = "poetry.core.masonry.api"
 
 [tool.poetry-dynamic-versioning]
@@ -53,25 +54,41 @@ files = ["dowhy/__init__.py"]
 # * numba (imported by econml) requires python <3.11
 #
 [tool.poetry.dependencies]
-python = ">=3.8,<3.12"
-cython = ">=0.29.32"
-scipy = ">=1.4.1"
+python = ">=3.8,<3.13"
+cython = "<3.0"
+scipy = [
+    {version = ">=1.7", python = "<3.9"},
+    {version = ">=1.10", python = ">=3.9"}
+]
 statsmodels = ">=0.13.5"
-numpy = ">=1.20"
-pandas = ">=1.4.3"
+numpy = [
+    {version = "<2.0", python = "<3.9"},
+    {version = ">1.0", python = ">=3.9"}
+]
+pandas = [
+    {version = "<2.0", python = "<3.9"},
+    {version = ">1.0", python = ">=3.9"}
+]
 networkx = ">=2.8.5"
 sympy = ">=1.10.1"
 scikit-learn = ">1.0"
 pydot = { version = "^1.4.2", optional = true }
 joblib = ">=1.1.0"
-pygraphviz = { version = "^1.9", optional = true }
-econml = { version = ">=0.14.1", optional = true }
+pygraphviz = { version = ">=1.9", optional = true }
+econml = ">=0.15.1"
 tqdm = ">=4.64.0"
 causal-learn = ">=0.1.3.0"
+numba = [
+    {version = "<0.59", python = "<3.9"},
+    {version = ">=0.59", python = ">=3.9"}
+]
 
 #Plotting Extra
 matplotlib = { version = ">=3.5.3", optional = true }
-cvxpy = "^1.2.2"
+cvxpy = [
+    {version = "<1.5.0", python = "<3.9"},
+    {version = ">=1.2.2", python = ">=3.9"}
+]
 
 [tool.poetry.extras]
 pygraphviz = ["pygraphviz"]
@@ -80,28 +97,31 @@ plotting = ["matplotlib"]
 econml = ["econml"]
 
 [tool.poetry.group.dev.dependencies]
-poethepoet = "^0.24.4"
-flake8 = "^5.0.4"
-black = { version = ">=22.6,<25.0", extras = ["jupyter"] }
-isort = "^5.10.1"
-pytest = "^7.1.2"
-pytest-cov = "^4.1.0"
-pytest-split = "^0.8.0"
-nbformat = "^5.4.0"
-jupyter = "^1.0.0"
-flaky = "^3.7.0"
-keras = "^2.9.0"
-xgboost = "^2.0.2"
-mypy = "^1.7.1"
+poethepoet = ">=0.24.4"
+flake8 = ">=5.0.4"
+black = { version = ">=22.6", extras = ["jupyter"] }
+isort = ">=5.10.1"
+pytest = ">=7.1.2"
+pytest-cov = ">=4.1.0"
+pytest-split = ">=0.8.0"
+nbformat = ">=5.4.0"
+jupyter = ">=1.0.0"
+flaky = ">=3.7.0"
+keras = ">=2.9.0"
+xgboost = ">=2.0.2"
+mypy = ">=1.7.1"
 torch = [
     {version = "<=1.99", python = ">=3.8,<3.11"},
-    {version = "^2.0", python = ">=3.11", source = "torch-cpu"}
+    {version = ">2.0", python = ">=3.11", source = "torch-cpu"}
 ]
 torchvision = [
     {version = ">=0.13.1", python = ">=3.8,<3.11"},
-    {version = ">=0.15.2", python=">=3.11"}
+    {version = ">=0.15.2", python=">=3.11", source = "torch-cpu"}
+]
+pytorch-lightning = [
+    {version = "<2.0", python = ">=3.8,<3.11"},
+    {version = ">=2.0", python=">=3.11"}
 ]
-pytorch-lightning = "<2.0"
 
 [tool.poetry.group.docs]
 optional = true
@@ -111,17 +131,16 @@ optional = true
 # Dependencies for Documentation Generation
 #
 
-sphinx_design = "^0.3.0"
-sphinx = "^5.3.0"
+sphinx_design = ">=0.3.0"
+sphinx = ">=5.3.0"
 sphinxcontrib-googleanalytics = { git = "https://github.com/sphinx-contrib/googleanalytics.git", branch = "master" }
-nbsphinx = "^0.8.9"
-sphinx-rtd-theme = "^1.0.0"
-pydata-sphinx-theme = "^0.9.0"
-ipykernel = "^6.15.1"
+nbsphinx = ">=0.8.9"
+sphinx-rtd-theme = ">=1.0.0"
+pydata-sphinx-theme = ">=0.9.0"
+ipykernel = ">=6.15.1"
 sphinx-copybutton = "0.5.0"
-seaborn = "^0.12.1"
-tensorflow = "^2.11.0"
-cdt ="^0.6.0"
+seaborn = ">=0.12.1"
+cdt =">=0.6.0"
 
 #
 # Versions defined for security reasons