From 69075becc8bccb6c3ccfa8e4f4d0061dd75cd052 Mon Sep 17 00:00:00 2001 From: Patrick Bloebaum Date: Thu, 3 Oct 2024 17:13:17 -0700 Subject: [PATCH 1/2] Update dependencies and add Python 3.12 compatibility Signed-off-by: Patrick Bloebaum --- .github/workflows/advanced-on-demand.yml | 8 +- .github/workflows/ci-install.yml | 8 +- .github/workflows/ci.yml | 8 +- .github/workflows/docs-ci.yml | 14 + .github/workflows/docs.yml | 14 + .github/workflows/nightly-tests.yml | 8 +- dowhy/causal_estimators/econml.py | 2 - poetry.lock | 5293 ++++++++++------------ pyproject.toml | 87 +- 9 files changed, 2589 insertions(+), 2853 deletions(-) diff --git a/.github/workflows/advanced-on-demand.yml b/.github/workflows/advanced-on-demand.yml index 2f963868c7..7d28d22e8a 100644 --- a/.github/workflows/advanced-on-demand.yml +++ b/.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 diff --git a/.github/workflows/ci-install.yml b/.github/workflows/ci-install.yml index 711052ee5e..8d4a5f8aa8 100644 --- a/.github/workflows/ci-install.yml +++ b/.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 diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 09e0da7d16..7440b5463b 100644 --- a/.github/workflows/ci.yml +++ b/.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 diff --git a/.github/workflows/docs-ci.yml b/.github/workflows/docs-ci.yml index 19f0952c0f..3134af6f98 100644 --- a/.github/workflows/docs-ci.yml +++ b/.github/workflows/docs-ci.yml @@ -20,6 +20,20 @@ jobs: with: fetch-depth: 0 + - name: Install LLVM and Clang + uses: KyleMayes/install-llvm-action@v2.0.5 + with: + version: "14.0" + directory: ${{ runner.temp }}/llvm + + - name: Some cleanup for more disk space + run: | + rm -rf /usr/share/dotnet + rm -rf "$AGENT_TOOLSDIRECTORY" + apt-get autoremove -y + apt-get clean + df -h + - name: Install Python Dependencies run: poetry install -E plotting -E pydot -E pygraphviz -E econml --with docs diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index c9795ac7ba..355ec52a78 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -24,6 +24,20 @@ jobs: with: fetch-depth: 0 + - name: Install LLVM and Clang + uses: KyleMayes/install-llvm-action@v2.0.5 + with: + version: "14.0" + directory: ${{ runner.temp }}/llvm + + - name: Some cleanup for more disk space + run: | + rm -rf /usr/share/dotnet + rm -rf "$AGENT_TOOLSDIRECTORY" + apt-get autoremove -y + apt-get clean + df -h + - name: Install Python Dependencies run: poetry install -E plotting -E pydot -E pygraphviz -E econml --with docs diff --git a/.github/workflows/nightly-tests.yml b/.github/workflows/nightly-tests.yml index 32b2bfb4dc..1a9c59af2e 100644 --- a/.github/workflows/nightly-tests.yml +++ b/.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 diff --git a/dowhy/causal_estimators/econml.py b/dowhy/causal_estimators/econml.py index 6d3fda5a48..3546ff4e79 100755 --- a/dowhy/causal_estimators/econml.py +++ b/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 diff --git a/poetry.lock b/poetry.lock index 9213f65935..f2e2f7e2fa 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,110 +1,128 @@ -# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. 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= ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"] +cover = ["pytest-cov"] doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] -test = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] +enabler = ["pytest-enabler (>=2.2)"] +test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] +type = ["pytest-mypy"] [extras] econml = ["econml"] @@ -6054,5 +5721,5 @@ pygraphviz = ["pygraphviz"] [metadata] lock-version = "2.0" -python-versions = ">=3.8,<3.12" -content-hash = "3039466778b222a3e6124bc1ebc3a6d94cbaff5ece3f641ad453f303e619dca0" +python-versions = ">=3.8,<3.13" +content-hash = "14cd645747c244735975c83f5c157eaaefd16a4b1e85f37345508bce12ac09e4" diff --git a/pyproject.toml b/pyproject.toml index e82002212c..97746c0d4d 100644 --- a/pyproject.toml +++ b/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 From 589dbcfcf27125d5e3b9148049b9ef25d8870bde Mon Sep 17 00:00:00 2001 From: Patrick Bloebaum Date: Fri, 4 Oct 2024 07:10:58 -0700 Subject: [PATCH 2/2] Add step to reduce disk space when building docs --- .github/workflows/docs-ci.yml | 30 +++++++++++++++++++----------- .github/workflows/docs.yml | 30 +++++++++++++++++++----------- 2 files changed, 38 insertions(+), 22 deletions(-) diff --git a/.github/workflows/docs-ci.yml b/.github/workflows/docs-ci.yml index 3134af6f98..ac0aec2d47 100644 --- a/.github/workflows/docs-ci.yml +++ b/.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: @@ -20,18 +20,26 @@ jobs: with: fetch-depth: 0 - - name: Install LLVM and Clang - uses: KyleMayes/install-llvm-action@v2.0.5 - with: - version: "14.0" - directory: ${{ runner.temp }}/llvm - + # Following https://github.com/marketplace/actions/free-disk-space-ubuntu - name: Some cleanup for more disk space run: | - rm -rf /usr/share/dotnet - rm -rf "$AGENT_TOOLSDIRECTORY" - apt-get autoremove -y - apt-get clean + df -h + rm -rf "$AGENT_TOOLSDIRECTORY" || true + rm -rf /usr/local/lib/android || true + rm -rf /opt/ghc || true + rm -rf /usr/local/.ghcup || true + swapoff -a || true + rm -f /mnt/swapfile || true + apt-get remove -y '^aspnetcore-.*' || true + apt-get remove -y '^dotnet-.*' --fix-missing || true + apt-get remove -y 'php.*' --fix-missing || true + apt-get remove -y '^mongodb-.*' --fix-missing || true + apt-get remove -y '^mysql-.*' --fix-missing || true + apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing || true + apt-get remove -y google-cloud-sdk --fix-missing || true + apt-get remove -y google-cloud-cli --fix-missing || true + apt-get autoremove -y || true + apt-get clean || true df -h - name: Install Python Dependencies diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 355ec52a78..7239c4f750 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -16,7 +16,7 @@ on: jobs: docs: - runs-on: ubuntu-latest + runs-on: ubuntu-24.04 container: image: "ghcr.io/${{ github.repository_owner }}/dowhy-docs-generation:latest" steps: @@ -24,18 +24,26 @@ jobs: with: fetch-depth: 0 - - name: Install LLVM and Clang - uses: KyleMayes/install-llvm-action@v2.0.5 - with: - version: "14.0" - directory: ${{ runner.temp }}/llvm - + # Following https://github.com/marketplace/actions/free-disk-space-ubuntu - name: Some cleanup for more disk space run: | - rm -rf /usr/share/dotnet - rm -rf "$AGENT_TOOLSDIRECTORY" - apt-get autoremove -y - apt-get clean + df -h + rm -rf "$AGENT_TOOLSDIRECTORY" || true + rm -rf /usr/local/lib/android || true + rm -rf /opt/ghc || true + rm -rf /usr/local/.ghcup || true + swapoff -a || true + rm -f /mnt/swapfile || true + apt-get remove -y '^aspnetcore-.*' || true + apt-get remove -y '^dotnet-.*' --fix-missing || true + apt-get remove -y 'php.*' --fix-missing || true + apt-get remove -y '^mongodb-.*' --fix-missing || true + apt-get remove -y '^mysql-.*' --fix-missing || true + apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing || true + apt-get remove -y google-cloud-sdk --fix-missing || true + apt-get remove -y google-cloud-cli --fix-missing || true + apt-get autoremove -y || true + apt-get clean || true df -h - name: Install Python Dependencies