[CI] Fix CI and update networkx dependency (#99)

* Remove python3.8 support

---------

Signed-off-by: Adam Li <adam2392@gmail.com>

Author: adam2392

.circleci/config.yml

@@ -5,7 +5,9 @@ orbs:
 
 jobs:
   build_doc:
-    executor: python/default
+    executor:
+      name: python/default
+      tag: "3.10"
     steps:
       - restore_cache:
           name: Restore .git
@@ -46,7 +48,8 @@ jobs:
       - run:
           name: Install the latest version of Poetry
           command: |
-            curl -sSL https://install.python-poetry.org | python3 - --version 1.5.0
+            curl -sSL https://install.python-poetry.org | python3 - --version 1.6.1
+            python --version
             poetry --version
       - run:
           name: Set BASH_ENV
@@ -65,30 +68,37 @@ jobs:
           name: Install pysal dependencies
           command: |
             sudo apt install libspatialindex-dev xdg-utils shared-mime-info desktop-file-utils
-      - run:
-          name: Setup torch for pgmpy
-          command: |
-            sudo apt-get install nvidia-cuda-toolkit nvidia-cuda-toolkit-gcc
-
       - run:
           name: Setup pandoc
           command: sudo apt update && sudo apt install -y pandoc optipng
 
       - python/install-packages:
           pkg-manager: poetry
-          cache-version: "v1" # change to clear cache
+          cache-version: "v2"  # change to clear cache
           args: "--with docs --extras viz --extras sims"
       - run:
           name: Check poetry package versions
           command: |
             poetry --version
             poetry show
+
+      - run:
+          name: Setup torch for pgmpy
+          command: |
+            sudo apt-get install nvidia-cuda-toolkit nvidia-cuda-toolkit-gcc
       - run:
           name: Check installation
           command: |
             poetry run python -c "import pywhy_graphs;"
             poetry run python -c "import numpy; numpy.show_config()"
             LIBGL_DEBUG=verbose poetry run python -c "import matplotlib.pyplot as plt; plt.figure()"
+
+      # dowhy currently requires an older version of numpy
+      - run:
+          name: Temporary Hack for numpy
+          command: |
+            poetry run python -m pip install numpy==1.22.0
+
       - run:
           name: Build documentation
           command: |
@@ -152,7 +162,7 @@ jobs:
             cat $BASH_ENV
       - python/install-packages:
           pkg-manager: poetry
-          cache-version: "v1" # change to clear cache
+          cache-version: "v1"  # change to clear cache
           args: "--with docs"
       - run:
           name: make linkcheck
@@ -256,4 +266,4 @@ workflows:
           filters:
             branches:
               only:
-                - main
+                - main

.github/workflows/main.yml

@@ -5,13 +5,15 @@ concurrency:
 on:
   pull_request:
     paths:
-      - '**.py'
+      - "**.py"
+      - "**.yml"
+      - "**.toml"
   push:
     branches: [main]
     paths:
-      - '**.py'
+      - "**.py"
     tags:
-      - 'v*.*.*'
+      - "v*.*.*"
   workflow_dispatch:
 
 jobs:
@@ -20,25 +22,25 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-          poetry-version: [1.5.1]
+        poetry-version: [1.6.1]
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
       - name: Setup Python 3.9
         uses: actions/setup-python@v4
         with:
-          python-version: '3.9'
-          architecture: 'x64'
+          python-version: "3.9"
+          architecture: "x64"
       - name: Install Poetry ${{ matrix.poetry-version }}
         uses: abatilo/actions-poetry@v2.3.0
         with:
           poetry-version: ${{ matrix.poetry-version }}
       - name: Install Poetry Dynamic Versioning Plugin
         run: pip install poetry-dynamic-versioning
-      
+
       - name: Install dependencies
         run: poetry install --only style
-      
+
       # check formatting of the code style
       - name: Check code formatting
         run: poetry run poe format_check
@@ -57,7 +59,7 @@ jobs:
       matrix:
         os: [ubuntu, macos, windows]
         python-version: [3.9, "3.10", "3.11"]
-        poetry-version: [1.5.1]
+        poetry-version: [1.6.1]
     name: build ${{ matrix.os }} - py${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}-latest
     defaults:
@@ -70,7 +72,7 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
-          architecture: 'x64'
+          architecture: "x64"
       - name: Install Poetry ${{ matrix.poetry-version }}
         uses: abatilo/actions-poetry@v2.3.0
         with:
@@ -113,9 +115,12 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu, macos, windows]
-        python-version: [3.9, "3.11"]  # oldest and newest supported versions
-        poetry-version: [1.5.1]
+        python-version: [3.9, "3.11"] # oldest and newest supported versions
+        poetry-version: [1.6.1]
         networkx: [stable, main]
+        exclude:
+          - python-version: 3.9
+            networkx: main
     name: Unit-test ${{ matrix.os }} - py${{ matrix.python-version }} - Networkx ${{ matrix.networkx }}
     runs-on: ${{ matrix.os }}-latest
     defaults:
@@ -128,29 +133,34 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
-          architecture: 'x64'
+          architecture: "x64"
       - name: Install Poetry ${{ matrix.poetry-version }}
         uses: abatilo/actions-poetry@v2.3.0
         with:
           poetry-version: ${{ matrix.poetry-version }}
       - name: Install Poetry Dynamic Versioning Plugin
-        run: pip install poetry-dynamic-versioning
+        run: |
+          pip install --upgrade pip
+          pip install poetry-dynamic-versioning
       - name: Install packages via poetry
         run: |
           poetry install --with test
       - name: Install Networkx (main)
         if: "matrix.networkx == 'main'"
         run: |
           pip uninstall -yq networkx
-          pip install --progress-bar off git+https://github.com/networkx/networkx
-      
+          git clone https://github.com/networkx/networkx.git
+          cd networkx
+          pip install .[default]
+          # pip install --progress-bar off git+https://github.com/networkx/networkx
+
       - name: Setup torch for pgmpy
         if: "matrix.os == 'ubuntu'"
         shell: bash
         run: |
           sudo apt-get install nvidia-cuda-toolkit nvidia-cuda-toolkit-gcc
-  
-      - name: Run pytest  # headless via Xvfb on linux
+
+      - name: Run pytest # headless via Xvfb on linux
         run: poetry run poe unit_test
       - name: Upload coverage stats to codecov
         if: ${{ matrix.os == 'ubuntu' && matrix.python-version == '3.11' && matrix.networkx == 'stable' }}
@@ -173,7 +183,7 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: 3.9
-          architecture: 'x64'
+          architecture: "x64"
       - name: Install dependencies
         run: |
           python -m pip install --progress-bar off --upgrade pip setuptools wheel

.pre-commit-config.yaml

@@ -3,10 +3,10 @@
 
 repos:
   - repo: https://github.com/floatingpurr/sync_with_poetry
-    rev: "0.4.0" # the revision or tag to clone at
+    rev: "0.4.0"  # the revision or tag to clone at
     hooks:
       - id: sync_with_poetry
-        args: ["--all"] # optional args
+        args: ["--all"]  # optional args
   - repo: https://github.com/psf/black
     rev: 22.12.0
     hooks:
@@ -27,18 +27,17 @@ repos:
     rev: "6.0.0"
     hooks:
       - id: flake8
-  - repo: https://github.com/pre-commit/mirrors-mypy 
+  - repo: https://github.com/pre-commit/mirrors-mypy
     rev: "v0.971"
     hooks:
       - id: mypy
         name: mypy (dodiscover)
         args: ["--config-file", "pyproject.toml"]
         files: ^dodiscover/
-  - repo: https://github.com/pre-commit/mirrors-mypy 
+  - repo: https://github.com/pre-commit/mirrors-mypy
     rev: "v0.971"
     hooks:
       - id: mypy
         name: mypy (tests)
         args: ["--config-file", "pyproject.toml"]
         files: ^tests/
-

.yamllint.yaml

@@ -0,0 +1,7 @@
+extends: default
+
+rules:
+  line-length: disable
+  document-start: disable
+  truthy: disable
+  comments: disable

doc/reference/functional/index.rst

@@ -13,7 +13,7 @@ model. Currently, we only support linear models, but we plan to support non-line
 and we also do not support latent confounders yet.
 
 To add a latent confounder, one can add a confounder explicitly, generate the data
-and then drop the confounder varialble in the final dataset. In the roadmap of this submodule,
+and then drop the confounder variable in the final dataset. In the roadmap of this submodule,
 the plan is to represent any bidirected edge as a uniformly randomly distributed variable
 that has an additive noise effect on both variables simultaneously.
 

doc/whats_new/v0.2.rst

@@ -28,6 +28,7 @@ Changelog
 - |Feature| Implement and test functions to validate an MAG and check the presence of almost directed cycles, by `Aryan Roy`_ (:pr:`91`)
 - |Feature| Implement and test functions to convert a DAG to MAG, by `Aryan Roy`_ (:pr:`96`)
 - |Feature| Implement and test functions to convert a PAG to MAG, by `Aryan Roy`_ (:pr:`93`)
+- |API| Remove support for Python 3.8 by `Adam Li`_ (:pr:`99`)
 
 Code and Documentation Contributors
 -----------------------------------