Merge branch 'master' into dev/depman

.github/workflows/ci.yml

@@ -24,7 +24,7 @@ jobs:
 
     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:
 
@@ -71,7 +71,7 @@ jobs:
 
     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:
 
@@ -93,7 +93,7 @@ jobs:
         python -m venv pygraphistry
         source pygraphistry/bin/activate
         python -m pip install --upgrade pip
-        python -m pip install -e .[docs,test,build,bolt,igraph,networkx,gremlin,nodexl,jupyter]
+        python -m pip install -e .[test,build,bolt,igraph,networkx,gremlin,nodexl,jupyter]
 
     - name: Lint
       run: |
@@ -110,6 +110,47 @@ jobs:
         source pygraphistry/bin/activate
         ./bin/test.sh
 
+  test-graphviz:
+
+    needs: [ test-minimal-python ]
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: [3.8, 3.9, '3.10', 3.11, 3.12]
+
+    steps:
+
+    - name: Checkout repo
+      uses: actions/checkout@v3
+      with:
+        lfs: true
+
+    - name: Checkout LFS objects
+      run: git lfs pull
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install test dependencies
+      run: |
+        python -m venv pygraphistry
+        source pygraphistry/bin/activate
+        sudo apt-get install graphviz graphviz-dev
+        python -m pip install --upgrade pip
+        python -m pip install -e .[test,pygraphviz]
+
+    - name: Type check
+      run: |
+        source pygraphistry/bin/activate
+        ./bin/typecheck.sh
+
+    - name: Graphviz tests
+      run: |
+        source pygraphistry/bin/activate
+        ./bin/test-graphviz.sh
 
   test-core-umap:
 
@@ -118,6 +159,7 @@ jobs:
 
     strategy:
       matrix:
+        #python-version: [3.8, 3.9, '3.10', 3.11, 3.12]
         python-version: [3.8, 3.9]
 
     steps:
@@ -165,6 +207,10 @@ jobs:
     strategy:
       matrix:
         python-version: [3.8, 3.9]
+        #python-version: [3.8, 3.9, '3.10', 3.11, 3.12]
+        #include:
+        #  - python-version: 3.12
+        #    continue-on-error: true
 
     steps:
 
@@ -284,7 +330,7 @@ jobs:
 
     - name: Test building docs
       run: |
-        cd docs && ./docker.sh
+        cd docs && ./ci.sh
 
   
   test-readme:

.gitignore

@@ -61,6 +61,8 @@ coverage.xml
 
 # Sphinx documentation
 docs/_build/
+docs/doctrees/
+docs/source/demos/
 
 # PyBuilder
 target/
@@ -87,3 +89,4 @@ demos/data/BIOGRID-IDENTIFIERS-3.3.123.tab.txt
 
 # local jupyter dev
 jupyter_dev/
+docs/source/demos

.readthedocs.yml

@@ -5,24 +5,53 @@
 # Required
 version: 2
 
-# Build documentation in the docs/ directory with Sphinx
-sphinx:
-   configuration: docs/source/conf.py
-
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.8"
+    python: "3.12"
+  apt_packages:
+    # More closely mirror https://github.com/sphinx-doc/sphinx-docker-images
+    - graphviz
+    - imagemagick
+    - make
+    - pandoc
+    - texlive-latex-base
+    - texlive-latex-recommended
+    - texlive-latex-extra
+    - texlive-fonts-recommended
+  commands:
+
+    # setup
+    - pip install ".[docs]"
+    - cp -r demos docs/source/demos
+    - cp README.md docs/source/README.md
+    - cp ARCHITECTURE.md docs/source/ARCHITECTURE.md
+    - cp CONTRIBUTE.md docs/source/CONTRIBUTE.md
+    - cp DEVELOP.md docs/source/DEVELOP.md
+
+    # build html
+    - sphinx-build -b html -d docs/doctrees docs/source $READTHEDOCS_OUTPUT/html/
+
+    # build epub
+    - sphinx-build -b epub -d docs/doctrees docs/source docs/_build/latexpdf
+    - mkdir -p $READTHEDOCS_OUTPUT/epub
+    - cp docs/_build/latexpdf/PyGraphistry.epub $READTHEDOCS_OUTPUT/epub/PyGraphistry.epub
 
-# Optionally build your docs in additional formats such as PDF
+    # build pdf
+    - sphinx-build -b latex -d docs/doctrees docs/source docs/_build/latexpdf
+    - cd docs/_build/latexpdf && pdflatex -file-line-error -interaction=nonstopmode PyGraphistry.tex && pdflatex -file-line-error  -interaction=nonstopmode PyGraphistry.tex && echo ok || { echo fail && exit 1 ; }
+    - mkdir -p $READTHEDOCS_OUTPUT/pdf 
+    - cp docs/_build/latexpdf/PyGraphistry.pdf $READTHEDOCS_OUTPUT/pdf/PyGraphistry.pdf
+
+#for nav links?
 formats:
   - pdf
-  - htmlzip
   - epub
+  - htmlzip
 
 python:
   install:
     - method: pip
       path: .
       extra_requirements:
-        - dev
+        - docs

CHANGELOG.md

@@ -7,6 +7,155 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 ## [Development]
 
+## [0.34.16 - 2024-10-13]
+
+### Docs
+
+* Update and streamline readme.md
+* Add quicksheet for overall
+* More crosslinking
+
+### Infra
+
+* Add markdown support to docsite
+* ReadTheDocs homepage reuses github README.md
+* Docs pip install caches
+* Drop SVGs and external images during latexpdf generation
+
+### Changed
+
+* Treemap import `squarify` deferred to use to allow core import without squarify installed, such as in `--no-deps`
+
+## [0.34.15 - 2024-10-11]
+
+### Docs
+
+* Improve GFQL translation doc
+* Add examples and API links: Shaping, Hypergraphs, AI & ML
+* Add performance docs
+* Add AI examples
+
+## [0.34.14 - 2024-10-09]
+
+### Added
+
+* HTTP responses with error status codes log an `logging.ERROR`-level message of the status code and response body
+
+## [0.34.13 - 2024-10-07]
+
+### Docs
+
+* Add more GFQL cross-references
+
+## [0.34.12 - 2024-10-07]
+
+### Docs
+
+* Fix ipynb examples in ReadTheDocs distribution
+
+## [0.34.11 - 2024-10-07]
+
+### Fix
+
+* Types
+
+### Infra
+
+* Enable more Python version checks
+
+## [0.34.10 - 2024-10-07]
+
+### Fix
+
+* Docs: Notebook builds
+
+### Docs
+
+* More links, especially around plugins
+* Update color theme to match Graphistry branding
+
+## [0.34.9 - 2024-10-07]
+
+### Fix
+
+* Docs: 10 Minutes to PyGraphistry links
+
+## [0.34.8 - 2024-10-06]
+
+### Fix
+
+* Docs: PDF support
+* Docs: Links
+
+### Docs
+
+* More accessible theme
+
+## [0.34.7 - 2024-10-06]
+
+### Docs
+
+* RTD: Added notebook tutorials 
+* RTD: Added various guides
+* RTD: Added cross-references
+* RTD: Cleaner navigation
+
+### Infra
+
+* Python: Add Python 12 to CI and document support
+* Docs: Udated dependencies - Sphinx 8, Python 12, and various related
+* Docs: Added nbsphinx - hub url grounding, ...
+* Docs: Redo as a docker compose flow with incremental builds (docker, sphinx)
+* Docs: Updated instructions for new flow
+
+### Fix
+
+* Docs: 2024
+* Notebooks: Compatibility with nbsphinx - exactly one title heading, no uncommented `!`, correct references, ...
+
+## [0.34.6 - 2024-10-04]
+
+### Added
+
+* Plugins: graphviz bindings, such as `g.layout_graphviz("dot")`
+
+### Docs
+
+* Reorganized readthedocs
+* Added intro tutorials: `10 Minutes to PyGraphistry`, `10 Minutes to GFQL`, `Login and Sharing`
+
+## [0.34.5 - 2024-09-23]
+
+### Fixed
+
+* GFQL: Fix `chain()` regression around an incorrectly disabled check manifesting as https://github.com/graphistry/pygraphistry/issues/583
+* GFQL: Fix `chain()`, `hop()` traverse filtering logic for a multi-hop edge scenarios
+* GFQL: Fix `hop()` predicate handling in multihop scenarios
+
+### Infra
+
+* GFQL: Expand test suite around multihop edge predicates in `hop()` and `chain()`
+
+## [0.34.4 - 2024-09-20]
+
+### Added
+
+* UMAP: Optional kwargs passthrough to umap library constructor, fit, and transform methods: `g.umap(..., umap_kwargs={...}, umap_fit_kwargs={...}, umap_transform_kwargs={...})`
+* Additional GPU support in featurize paths
+
+### Changed
+
+* Replace `verbose` with `logging`
+
+### Refactor
+
+* Narrow `use_scaler` and `use_scaler_target` typing to `ScalerType` (`Literal[...]`) vs `str`
+* Rename `featurize_or_get_nodes_dataframe_if_X_is_None` (and edges variant) as non-private due to being shared
+
+### Fixed
+
+* get_indegrees: Fix warning https://github.com/graphistry/pygraphistry/issues/587
+
 ## [0.34.3 - 2024-08-03]
 
 ### Added