Update circleCI and gh actions and package to python 3.9 (#137)

* Update circleCI and gh actions and package to python 3.9

---------

Signed-off-by: Adam Li <[email protected]>

.circleci/config.yml

@@ -1,17 +1,13 @@
 version: 2.1
 
-orbs:
-  python: circleci/[email protected]
-
 jobs:
   build_doc:
-    executor: python/default
+    docker:
+      - image: cimg/python:3.9
+
     steps:
-      - restore_cache:
-          name: Restore .git
-          keys:
-            - source-cache-graphs
       - checkout
+
       - run:
           name: Complete checkout
           command: |
@@ -34,61 +30,59 @@ jobs:
               echo "Skip detected, exiting job ${CIRCLE_JOB} for PR ${CIRCLE_PULL_REQUEST}."
               circleci-agent step halt;
             fi
-      - run:
-          name: Merge with upstream
-          command: |
-            echo $(git log -1 --pretty=%B) | tee gitlog.txt
-            echo ${CI_PULL_REQUEST//*pull\//} | tee merge.txt
-            if [[ $(cat merge.txt) != "" ]]; then
-              echo "Merging $(cat merge.txt)";
-              git pull --ff-only upstream "refs/pull/$(cat merge.txt)/merge";
-            fi
-      - run:
-          name: Install the latest version of Poetry
-          command: |
-            curl -sSL https://install.python-poetry.org | python3 - --version 1.3.0
-            poetry --version
+      - restore_cache:
+          keys:
+            - poetry-v1-{{ checksum "poetry.lock" }}
+            - poetry-v1-
+
       - run:
           name: Set BASH_ENV
           command: |
             set -e
             sudo apt update
             sudo apt-get update
             sudo apt install -qq graphviz optipng libxft2 graphviz-dev
-            echo "set -e" >> $BASH_ENV
-            echo "export OPENBLAS_NUM_THREADS=4" >> $BASH_ENV
-            echo "export XDG_RUNTIME_DIR=/tmp/runtime-circleci" >> $BASH_ENV
-            echo "export PATH=~/.local/bin/:$PATH" >> $BASH_ENV
-            echo "export DISPLAY=:99" >> $BASH_ENV
-            echo "BASH_ENV:"
+            echo 'set -e' >> $BASH_ENV
+            echo 'export OPENBLAS_NUM_THREADS=4' >> $BASH_ENV
+            echo 'export XDG_RUNTIME_DIR=/tmp/runtime-circleci' >> $BASH_ENV
+            echo 'export PATH=~/.local/bin/:$PATH' >> $BASH_ENV
+            echo 'export DISPLAY=:99' >> $BASH_ENV
+            echo 'BASH_ENV:'
             cat $BASH_ENV
       - run:
           name: Install pysal dependencies
           command: |
-            sudo apt install libspatialindex-dev xdg-utils
-      - python/install-packages:
-          pkg-manager: poetry
-          args: "-E graph_func -E viz --with docs"
-          cache-version: "v1" # change to clear cache
-      - run:
-          name: Check poetry package versions
-          command: |
-            poetry --version
-            poetry show
+            sudo apt install libspatialindex-dev xdg-utils shared-mime-info
+
       - run:
           name: Setup pandoc
           command: sudo apt update && sudo apt install -y pandoc optipng
+
+      - run:
+          name: Install Poetry
+          command: |
+            curl -sSL https://install.python-poetry.org | python -
+            export PATH='$HOME/.poetry/bin:$PATH'
+
+      - run:
+          name: Install Dependencies
+          command: |
+            poetry install --no-interaction --no-ansi  --with docs --extras viz --extras graph_func
+
       - run:
-          name: Check installation
+          name: Show installed versions
           command: |
-            poetry run python -c "import dodiscover;"
-            poetry run python -c "import numpy; numpy.show_config()"
-            LIBGL_DEBUG=verbose poetry run python -c "import matplotlib.pyplot as plt; plt.figure()"
+            poetry show
+
+      - save_cache:
+          paths:
+            - $HOME/.poetry
+          key: poetry-v1-{{ checksum "poetry.lock" }}
+
       - run:
-          name: Build documentation
+          name: Build Documentation
           command: |
-            cd doc
-            poetry run make html
+            poetry run poe build_docs
       # Save the example test results
       - store_test_results:
           path: doc/_build/test-results
@@ -113,53 +107,6 @@ jobs:
             - html
             - html_stable
 
-  linkcheck:
-    parameters:
-      scheduled:
-        type: string
-        default: "false"
-    executor: python/default
-    steps:
-      - restore_cache:
-          keys:
-            - source-cache-graphs
-      - checkout
-      - run:
-          name: Check-skip
-          command: |
-            export COMMIT_MESSAGE=$(git log --format=oneline -n 1);
-            if [[ "$COMMIT_MESSAGE" != *"[circle linkcheck]"* ]] && [ "<< parameters.scheduled >>" != "true" ]; then
-              echo "Skip detected, exiting job ${CIRCLE_JOB}."
-              circleci-agent step halt;
-            fi
-      - run:
-          name: Set BASH_ENV
-          command: |
-            set -e
-            echo "set -e" >> $BASH_ENV
-            echo "export PATH=~/.local/bin/:$PATH" >> $BASH_ENV
-      - python/install-packages:
-          pkg-manager: poetry
-          cache-version: "v1" # change to clear cache
-          args: "--with docs"
-      - run:
-          name: Check poetry package versions
-          command: |
-            poetry --version
-            poetry show
-      - run:
-          name: make linkcheck
-          command: |
-            make -C doc linkcheck
-      - run:
-          name: make linkcheck-grep
-          when: always
-          command: |
-            make -C doc linkcheck-grep
-      - store_artifacts:
-          path: doc/_build/linkcheck
-          destination: linkcheck
-
   deploy:
     docker:
       - image: cimg/node:lts
@@ -209,8 +156,6 @@ workflows:
     jobs:
       - build_doc:
           name: build_doc
-      - linkcheck:
-          name: linkcheck
       - deploy:
           requires:
             - build_doc
@@ -236,17 +181,3 @@ workflows:
             branches:
               only:
                 - main
-
-  weekly:
-    jobs:
-      - linkcheck:
-          name: linkcheck_weekly
-          scheduled: "true"
-    triggers:
-      - schedule:
-          # "At 00:00 on Sunday" should be often enough
-          cron: "0 0 * * 0"
-          filters:
-            branches:
-              only:
-                - main

.github/workflows/main.yml

@@ -22,7 +22,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        poetry-version: [1.3.0]
+        poetry-version: [1.5.1]
     steps:
       - name: Checkout repository
         uses: actions/checkout@v3
@@ -58,8 +58,8 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu, macos, windows]
-        python-version: [3.8, 3.9, "3.10"]
-        poetry-version: [1.3.0]
+        python-version: [3.9, "3.10", "3.11"]
+        poetry-version: [1.5.1]
     name: build ${{ matrix.os }} - py${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}-latest
     defaults:
@@ -121,8 +121,8 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu, macos, windows]
-        python-version: [3.8, "3.10"]  # oldest and newest supported versions
-        poetry-version: [1.3.0]
+        python-version: [3.9, "3.11"] # oldest and newest supported versions
+        poetry-version: [1.5.1]
         networkx: [stable, main]
     name: Unit-test ${{ matrix.os }} - py${{ matrix.python-version }} - Networkx ${{ matrix.networkx }}
     runs-on: ${{ matrix.os }}-latest
@@ -165,8 +165,8 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu]
-        python-version: ["3.10"]  # oldest and newest supported versions
-        poetry-version: [1.3.0]
+        python-version: ["3.10"] # oldest and newest supported versions
+        poetry-version: [1.5.1]
         networkx: [main]
     name: Integration test ${{ matrix.os }} - py${{ matrix.python-version }} - Networkx ${{ matrix.networkx }}
     runs-on: ${{ matrix.os }}-latest
@@ -180,17 +180,27 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
-          architecture: 'x64'
+          architecture: "x64"
       - name: Install Poetry ${{ matrix.poetry-version }}
         uses: abatilo/[email protected]
         with:
           poetry-version: ${{ matrix.poetry-version }}
+
+      - name: Install packages for Ubuntu
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y graphviz optipng libxft2 graphviz-dev
+      
+      - name: Setup torch
+        run: |
+          sudo apt-get install nvidia-cuda-toolkit nvidia-cuda-toolkit-gcc
+
       - name: Install Poetry Dynamic Versioning Plugin
         run: pip install poetry-dynamic-versioning
       - name: Install packages via poetry
         run: |
           poetry install --with test,docs --extras graph_func
-      - name: Run pytest  # headless via Xvfb on linux
+      - name: Run pytest # headless via Xvfb on linux
         run: poetry run poe integration_test
 
   # release is ran when a release is made on Github
@@ -220,7 +230,7 @@ jobs:
       - name: Build the release artifact
         run: |
           poetry-dynamic-versioning
-          poetry build      
+          poetry build
       - name: Download package distribution files
         uses: actions/download-artifact@v3
         with:

README.md

@@ -82,13 +82,13 @@ Installation is best done via `pip` or `conda`. For developers, they can also in
 
 Minimally, dodiscover requires:
 
-    * Python (>=3.8)
+    * Python (>=3.9)
     * numpy
     * scipy
     * networkx
     * pandas
 
-For explicit graph functionality for representing various causal graphs, such as ADMG, or CPDAGs, you will also need:
+We have removed support for Python 3.8 as we depend explicitly on networkx, which has deprecated Python 3.8 support. For explicit graph functionality for representing various causal graphs, such as ADMG, or CPDAGs, you will also need:
 
     * pywhy-graphs
     * graphs  # this is a development version for PRable MixedEdgeGraph to networkx

dodiscover/_version.py

@@ -1,9 +1,4 @@
 """Version number."""
-
-# TODO: Remove try/except once the minimum python requirement is bumped to 3.8
-try:
-    from importlib.metadata import version  # type: ignore
-except ImportError:
-    from importlib_metadata import version  # type: ignore
+from importlib.metadata import version  # type: ignore
 
 __version__ = version(__package__)