Merge pull request #6 from adam2392/cpdag

[ENH] Adding cpdag class

.codespellignore

@@ -1 +1,2 @@
 raison
+GES

.github/workflows/main.yml

@@ -1,4 +1,4 @@
-name: unit-tests
+name: gh-ci-checks
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.type }}
   cancel-in-progress: true
@@ -10,12 +10,17 @@ on:
     branches: [main]
     paths:
       - '**.py'
+    tags:
+      - 'v*.*.*'
   workflow_dispatch:
 
 jobs:
   style:
     timeout-minutes: 10
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+          poetry-version: [1.1.14]
     steps:
       - name: Checkout repository
         uses: actions/checkout@v3
@@ -24,42 +29,36 @@ jobs:
         with:
           python-version: '3.9'
           architecture: 'x64'
-      - name: Install dependencies
-        run: |
-          python -m pip install --progress-bar off --upgrade pip setuptools wheel
-          python -m pip install --progress-bar off .[style]
-      - name: Run flake8
-        uses: py-actions/flake8@v2
+      - name: Install Poetry ${{ matrix.poetry-version }}
+        uses: abatilo/[email protected]
         with:
-          path: "pywhy_graphs"
-      - name: Run isort
-        uses: isort/isort-action@master
-      - name: Run black
-        uses: psf/black@stable
-        with:
-          options: "--check --verbose"
-      - name: Run codespell
-        uses: codespell-project/actions-codespell@master
-        with:
-          check_filenames: true
-          check_hidden: true
-          skip: './.git,./build,./.mypy_cache,./.pytest_cache'
-          ignore_words_file: ./.codespellignore
-      - name: Run pydocstyle
-        run: pydocstyle .
-      - name: Run mypy
-        uses: jpetrucciani/mypy-check@master
-        with:
-          path: './pywhy_graphs'
-          mypy_flags: '--config-file pyproject.toml'
+          poetry-version: ${{ matrix.poetry-version }}
+      - name: Install Poetry Dynamic Versioning Plugin
+        run: pip install poetry-dynamic-versioning
+
+      # TODO: once poetry v1.2 is release, we want to only install dev dependencies
+      - name: Install dependencies
+        run: poetry install
+
+      # check formatting of the code style
+      - name: Check code formatting
+        run: poetry run poe check_format
+
+      # this applies various linting
+      - name: Lint codebase
+        run: poetry run poe lint
+
+      - name: Typecheck
+        run: poetry run poe typecheck
 
   build:
     timeout-minutes: 10
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu, macos, windows]
-        python-version: [3.7, 3.8, 3.9, "3.10"]
+        python-version: [3.8, 3.9, "3.10"]
+        poetry-version: [1.1.14]
     name: build ${{ matrix.os }} - py${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}-latest
     defaults:
@@ -73,17 +72,25 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
           architecture: 'x64'
-      - name: Install dependencies
+      - name: Install Poetry ${{ matrix.poetry-version }}
+        uses: abatilo/[email protected]
+        with:
+          poetry-version: ${{ matrix.poetry-version }}
+      - name: Install Poetry Dynamic Versioning Plugin
+        run: pip install poetry-dynamic-versioning
+      - name: Install from source
         run: |
-          python -m pip install --progress-bar off --upgrade pip setuptools wheel
-          python -m pip install --progress-bar off .[build]
+          poetry install
       - name: Test package install
-        run: python -c "import pywhy_graphs; print(pywhy_graphs.__version__)"
+        run: poetry run python -c "import pywhy_graphs; print(pywhy_graphs.__version__)"
       - name: Remove package install
         run: python -m pip uninstall -yq pywhy_graphs
+      - name: Check poetry lock file
+        run: poetry update --dry-run
       - name: Build package
-        run: python -m build
+        run: poetry build
       - name: Upload package distribution files
+        if: ${{ matrix.os == 'ubuntu' && matrix.python-version == '3.10' }}
         uses: actions/upload-artifact@v3
         with:
           name: package
@@ -108,6 +115,7 @@ jobs:
       matrix:
         os: [ubuntu, macos, windows]
         python-version: [3.8, "3.10"]  # oldest and newest supported versions
+        poetry-version: [1.1.14]
         networkx: [stable, main]
     name: pytest ${{ matrix.os }} - py${{ matrix.python-version }} - Networkx ${{ matrix.networkx }}
     runs-on: ${{ matrix.os }}-latest
@@ -117,32 +125,27 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v3
-        with:
-          path: main  # clone repository in a sub-directory
       - name: Setup Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
           architecture: 'x64'
-      - name: Install Qt dependencies
-        if: "matrix.os == 'ubuntu'"
-        run: |
-          sudo apt update
-          sudo apt install qt5-default
-      - name: Install package
+      - name: Install Poetry ${{ matrix.poetry-version }}
+        uses: abatilo/[email protected]
+        with:
+          poetry-version: ${{ matrix.poetry-version }}
+      - name: Install Poetry Dynamic Versioning Plugin
+        run: pip install poetry-dynamic-versioning
+      - name: Install packages via poetry
         run: |
-          python -m pip install --progress-bar off --upgrade pip setuptools wheel
-          python -m pip install --progress-bar off main/.[test]
-          # TODO: remove this eventually
-          python -m pip install --progress-bar off git+https://github.com/py-why/graphs
+          poetry install
       - name: Install Networkx (main)
         if: "matrix.networkx == 'main'"
         run: |
-          python -m pip uninstall -yq networkx
+          pip uninstall -yq networkx
+          pip install --progress-bar off git+https://github.com/networkx/networkx
       - name: Run pytest  # headless via Xvfb on linux
-        uses: GabrielBB/[email protected]
-        with:
-          run: pytest main/pywhy_graphs --cov=main/pywhy_graphs --cov-report=xml --cov-config=main/pyproject.toml
+        run: poetry run poe unit_test
       - name: Upload coverage stats to codecov
         if: ${{ matrix.os == 'ubuntu' && matrix.python-version == '3.10' && matrix.networkx == 'stable' }}
         uses: codecov/codecov-action@v3
@@ -168,7 +171,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --progress-bar off --upgrade pip setuptools wheel
-          python -m pip install --progress-bar off .[build]
+          python -m pip install --progress-bar off build twine
       - name: Prepare environment
         run: |
           echo "RELEASE_VERSION=${GITHUB_REF#refs/tags/v}" >> $GITHUB_ENV

.github/workflows/pr_checks.yml

@@ -38,14 +38,14 @@ jobs:
             exit 0
           fi
           all_changelogs=$(cat ./docs/whats_new/v*.rst)
-          if [[ "$all_changelogs" =~ :gh:\`$PR_NUMBER\` ]]
+          if [[ "$all_changelogs" =~ :pr:\`$PR_NUMBER\` ]]
           then
             echo "Changelog has been updated."
             # If the pull request is milestoned check the correspondent changelog
             if exist -f ./docs/whats_new/v${TAGGED_MILESTONE:0:4}.rst
             then
               expected_changelog=$(cat ./docs/whats_new/v${TAGGED_MILESTONE:0:4}.rst)
-              if [[ "$expected_changelog" =~ :gh:\`$PR_NUMBER\` ]]
+              if [[ "$expected_changelog" =~ :pr:\`$PR_NUMBER\` ]]
               then
                 echo "Changelog and milestone correspond."
               else
@@ -63,7 +63,7 @@ jobs:
             echo "in time for the next release of pywhy-graphs."
             echo ""
             echo "Look at other entries in that file for inspiration and please"
-            echo "reference this pull request using the ':gh:' directive and"
+            echo "reference this pull request using the ':pr:' directive and"
             echo "credit yourself (and other contributors if applicable) with"
             echo "the ':user:' directive."
             echo ""

.gitignore

@@ -4,10 +4,11 @@ __pycache__/
 *$py.class
 
 .vscode
+junit-results.xml
 
 # C extensions
 *.so
-
+.DS_Store
 # Distribution / packaging
 .Python
 build/

Makefile

@@ -1,4 +1,4 @@
-# simple makefile to simplify repetetive build env management tasks under posix
+# simple makefile to simplify repetitive build env management tasks under posix
 # caution: testing won't work on windows
 
 PYTHON ?= python

docs/api.rst

@@ -23,59 +23,5 @@ graphs encountered in the literature.
 .. autosummary::
    :toctree: generated/
 
-   StructuralCausalModel
    CPDAG
    ADMG
-   PAG
-
-To see a breakdown of different inner graph functionalities,
-see the :ref:`Graph API <graph_api>` page. See 
-
-.. toctree::
-   :maxdepth: 0
-
-   graph_api
-
-
-IO for reading/writing causal graphs
-====================================
-We advocate for using our implemented causal graph classes whenever
-utilizing various packages. However, we also support transformations
-to and from popular storage classes, such as ``numpy arrays``,
-``pandas dataframes``, ``pgmpy``, ``DOT`` and ``dagitty``. Note that
-not all these are supported for all types of graphs because of
-inherent limitations in supporting mixed-edge graphs in other formats.
-
-.. currentmodule:: pywhy_graphs.io
-
-.. autosummary::
-   :toctree: generated/
-
-   load_from_networkx
-   load_from_numpy
-   load_from_pgmpy
-   to_networkx
-   to_numpy
-
-Converting Graphs
-=================
-.. currentmodule:: pywhy_graphs.algorithms
-
-.. autosummary::
-   :toctree: generated/
-
-   dag2cpdag
-   admg2pag
-
-Utility Algorithms for Causal Graphs
-====================================
-.. currentmodule:: pywhy_graphs.algorithms
-
-.. autosummary::
-   :toctree: generated/
-
-   discriminating_path
-   possibly_d_sep_sets
-   uncovered_pd_path
-   is_markov_equivalent
-   compute_v_structures