[DOCS] Fix docs and certain ci builds to include pygraphviz (#19)

* Fix docs and certain ci builds for pygraphviz Signed-off-by: Adam Li <[email protected]> * Add pygraphviz Signed-off-by: Adam Li <[email protected]> * Add pygraphviz Signed-off-by: Adam Li <[email protected]> Signed-off-by: Adam Li <[email protected]>
py-why · Aug 21, 2022 · dd5d26f · dd5d26f
1 parent a67b95c
commit dd5d26f
Show file tree

Hide file tree

Showing 7 changed files with 72 additions and 44 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -48,28 +48,32 @@ jobs:
           command: |
             curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py | POETRY_UNINSTALL=1 python -
             curl -sSL https://install.python-poetry.org | python3 -
-      - python/install-packages:
-          pkg-manager: poetry
-          # args: "--extras docs"
-          cache-version: "v1" # change to clear cache
-      - run:
-          name: Check poetry package versions
-          command: |
-            poetry --version
-            poetry show
       - run:
           name: Set BASH_ENV
           command: |
             set -e
             sudo apt update
-            sudo apt install -qq graphviz optipng libxft2
+            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:"
             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"
+          cache-version: "v1" # change to clear cache
+      - run:
+          name: Check poetry package versions
+          command: |
+            poetry --version
+            poetry show
       - run:
           name: Setup pandoc
           command: sudo apt update && sudo apt install -y pandoc optipng

diff --git a/.flake8 b/.flake8
@@ -18,7 +18,7 @@ exclude =
     .circleci
     paper
     setup.py
-    docs
+    doc
 
 per-file-ignores =
     # __init__.py files are allowed to have unused imports

diff --git a/.github/workflows/circle_artifacts.yml b/.github/workflows/circle_artifacts.yml
@@ -1,13 +1,13 @@
 on: [status]
- jobs:
-   circleci_artifacts_redirector_job:
-     runs-on: ubuntu-20.04
-     name: Run CircleCI artifacts redirector
-     steps:
-       - name: GitHub Action step
-         uses: larsoner/circleci-artifacts-redirector-action@master
-         with:
-           repo-token: ${{ secrets.GITHUB_TOKEN }}
-           artifact-path: 0/dev/index.html
-           circleci-jobs: build_doc
-           job-title: Check the rendered docs here!
+jobs:
+  circleci_artifacts_redirector_job:
+    runs-on: ubuntu-20.04
+    name: Run CircleCI artifacts redirector
+    steps:
+      - name: GitHub Action step
+        uses: larsoner/circleci-artifacts-redirector-action@master
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          artifact-path: 0/dev/index.html
+          circleci-jobs: build_doc
+          job-title: Check the rendered docs here!
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -55,7 +55,8 @@ jobs:
         run: poetry run poe typecheck
 
   build:
-    timeout-minutes: 10
+    # TODO: modify back to 10 mins after we improve poetry install
+    timeout-minutes: 15
     strategy:
       fail-fast: false
       matrix:
@@ -79,11 +80,10 @@ jobs:
         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: |
           poetry install
+          pip install -e .
       - name: Test package install
         run: poetry run python -c "import dodiscover; print(dodiscover.__version__)"
       - name: Remove package install

diff --git a/README.md b/README.md
@@ -26,7 +26,12 @@ Minimally, dodiscover requires:
     * numpy
     * scipy
     * networkx
+    * pandas
+
+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
 
 For explicitly representing causal graphs, we recommend using `pywhy-graphs` package, but if you have a graph library that adheres to the graph protocols we require, then you can in principle use those graphs.
 
@@ -41,5 +46,8 @@ To install the package from github, clone the repository and then `cd` into the
 
     poetry install
 
+    # for graph functionality
+    poetry install --extras graph_func
+
     # if you would like an editable install of dodiscover for dev purposes
     pip install -e .
diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -45,6 +45,8 @@ pandas = "^1.1"
 importlib-resources = { version = "*", python = "<3.9" }
 graphs = { git = "https://github.com/py-why/graphs.git", branch = 'main', optional = true }
 pywhy-graphs = { git = "https://github.com/py-why/pywhy-graphs.git", branch = 'main', optional = true }
+# pywhy-graphs = { path = "../pywhy-graphs", develop = true }
+pygraphviz = { version = "*", optional = true }
 
 # TODO: the below needs to be refactored into separate dev-dependencies
 # https://github.com/python-poetry/poetry/is
@@ -80,6 +82,8 @@ nbsphinx = { version = "^0.8" }
 
 [tool.poetry.extras]
 graph_func = ['pywhy-graphs', 'graphs']
+viz = ['pygraphviz']
+
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]
@@ -97,7 +101,7 @@ _isort = 'isort .'
 _black_check = 'black --check dodiscover examples'
 _isort_check = 'isort --check .'
 _pydocstyle = 'pydocstyle .'
-_codespell = 'codespell dodiscover/ doc/ examples/ --ignore-words=.codespellignore --skip "**/_build/*"'
+_codespell = 'codespell dodiscover/ doc/ examples/ --ignore-words=.codespellignore --skip "**/_build/*,**/auto_examples/*"'
 _changelog = 'semversioner changelog > CHANGELOG.md'
 _apply_version = 'semversioner release'