Release 0.12.0 (#248)

* Limiting numpy version (mckinsey#217) * adding line on yml - no effect * adding line on yml - no effect * changing req.txt * changing req.txt * changing req.txt * adding setuptools requirement (mckinsey#218) * adding setuptools requirement * adding setuptools requirement * update dictionaries to pass linting (mckinsey#230) * Refactor/unlock numpy kl (mckinsey#235) * unlocking numpy * unlocking numpy * unlocking numpy * dependency fixes for docs and linters * requirement fixes : numpy <1.24 for all python versions --------- Co-authored-by: kyle_lim <kyle_lim@mckinsey.com> * Simplifying requirements - Numpy version range (mckinsey#236) * Remove python 3.6 and 3.7 support (mckinsey#234) * remove python 3.6 and 3.7 support * update documentation * remove comment regarding ignoring a warning when running `make build-docs` * removing ipython from test requiremnets * Update README.md Co-authored-by: Philip Pilgerstorfer <34248114+qbphilip@users.noreply.github.com> --------- Co-authored-by: GabrielAz <gabriel.azevedoferreira@quantumblack.com> Co-authored-by: Gabriel Azevedo Ferreira <57528979+GabrielAzevedoFerreiraQB@users.noreply.github.com> Co-authored-by: Philip Pilgerstorfer <34248114+qbphilip@users.noreply.github.com> * unlocking numpy (mckinsey#238) Co-authored-by: Gabriel Azevedo <gabriel_azevedo_ferreira@mckinsey.com> * Release 0.11.2 (mckinsey#239) Co-authored-by: Gabriel Azevedo <gabriel_azevedo_ferreira@mckinsey.com> * Replacing Pygraphviz with Pyvis (mckinsey#237) * Replacing Pygraphviz with Pyvis * Replacing Pygraphviz with Pyvis * Replacing Pygraphviz with Pyvis * temp (#242) * Limiting numpy version (mckinsey#217) * adding line on yml - no effect * adding line on yml - no effect * changing req.txt * changing req.txt * changing req.txt * adding setuptools requirement (mckinsey#218) * adding setuptools requirement * adding setuptools requirement * update dictionaries to pass linting (mckinsey#230) * Refactor/unlock numpy kl (mckinsey#235) * unlocking numpy * unlocking numpy * unlocking numpy * dependency fixes for docs and linters * requirement fixes : numpy <1.24 for all python versions --------- Co-authored-by: kyle_lim <kyle_lim@mckinsey.com> * Simplifying requirements - Numpy version range (mckinsey#236) * Remove python 3.6 and 3.7 support (mckinsey#234) * remove python 3.6 and 3.7 support * update documentation * remove comment regarding ignoring a warning when running `make build-docs` * removing ipython from test requiremnets * Update README.md Co-authored-by: Philip Pilgerstorfer <34248114+qbphilip@users.noreply.github.com> --------- Co-authored-by: GabrielAz <gabriel.azevedoferreira@quantumblack.com> Co-authored-by: Gabriel Azevedo Ferreira <57528979+GabrielAzevedoFerreiraQB@users.noreply.github.com> Co-authored-by: Philip Pilgerstorfer <34248114+qbphilip@users.noreply.github.com> * unlocking numpy (mckinsey#238) Co-authored-by: Gabriel Azevedo <gabriel_azevedo_ferreira@mckinsey.com> * Release 0.11.2 (mckinsey#239) Co-authored-by: Gabriel Azevedo <gabriel_azevedo_ferreira@mckinsey.com> --------- Co-authored-by: ElisabethSesterHussQB <92664441+ElisabethSesterHussQB@users.noreply.github.com> Co-authored-by: kyle_lim <kyle_lim@mckinsey.com> Co-authored-by: Philip Pilgerstorfer <34248114+qbphilip@users.noreply.github.com> Co-authored-by: Gabriel Azevedo <gabriel_azevedo_ferreira@mckinsey.com> * adding cython to config * adding cython to config * adding cython to config * adding cython to config --------- Co-authored-by: Gabriel Azevedo <gabriel_azevedo_ferreira@mckinsey.com> Co-authored-by: ElisabethSesterHussQB <92664441+ElisabethSesterHussQB@users.noreply.github.com> Co-authored-by: kyle_lim <kyle_lim@mckinsey.com> Co-authored-by: Philip Pilgerstorfer <34248114+qbphilip@users.noreply.github.com> * Replace pygraphviz plotting with pyvis (mckinsey#228) * initial draft for pyvis plotting * modify edge length and mass for strong style and return pyvis object * add pytests and fix sklearn plotting function * update to include pyvis in requirements * add in notebook check tests for test_plot_dag * downgrade pyvis for compatibility * update to latest plotting functions * update requirements to exclude pygraphviz * upgrading ipython * moving ipython as main requirement * simplify plot_structure function * remove unused code and add test cases when needed * reset pyvis version to see if .show() is working on v0.3.1 * set ipython and python versions * undo previous change (ipython version change) * remove ipython version from requirements * re-add ipython version to requirements * change ipython+python version * undo change ipython+python version * check for different ipython versions * add quotation marks in requirements.txt * revert back to ipython>=8.10.0 * try out ipython requirements from kedro * revert back to ipython>=8.10 * change ipython requirements to successfully create environments * Updated pyvis tutorials (mckinsey#232) * update tutorials and adjust default values to improve output * allow user to change layout in plot_dag function before calling .show() * display df without dataframe_image * fix dataframe_image No such file or directory * remove one cell beacause unused * incorporate windows solution from Kyle * fix typo * change plot_structure documentation * change plot_dag documentation * check and correct all notebooks * remove python 3.6 and 3.7 support * update documentation * remove comment regarding ignoring a warning when running `make build-docs` * removing ipython from test requiremnets * refactoring plot syntax and changing logic in plot_dag * addressing Gabriel's comments * removing unused IPython conditional import * refactoring code to use display * Docs - update 01-tutorial * updating first tutotiral * updating plotting tutorial * updating plotting tutorial * updating display api * fixing bug - displau * fixing notebooks * fixing notebooks * fixing notebooks * fixing notebooks * Replacing Pygraphviz with Pyvis * Replacing Pygraphviz with Pyvis * Replacing Pygraphviz with Pyvis * updating pyvis version * updating notebook * Richard Comments - batch 1 * Update tests/test_plotting.py Co-authored-by: Richard Oentaryo <oentaryorj@users.noreply.github.com> * Update tests/test_plotting.py Co-authored-by: Richard Oentaryo <oentaryorj@users.noreply.github.com> * Richard Comments - batch 2 * adjust node color test to include background color * docs * docs * test * fixing mdlp with cython * fixing mdlp with cython * test * removing cython from requirements * adding cython to config --------- Co-authored-by: ElisabethSesterHussQB <92664441+ElisabethSesterHussQB@users.noreply.github.com> Co-authored-by: GabrielAz <gabriel.azevedoferreira@quantumblack.com> Co-authored-by: Gabriel Azevedo <gabriel_azevedo_ferreira@mckinsey.com> Co-authored-by: Gabriel Azevedo Ferreira <57528979+GabrielAzevedoFerreiraQB@users.noreply.github.com> Co-authored-by: Richard Oentaryo <oentaryorj@users.noreply.github.com> * fix: requirements.txt to reduce vulnerabilities (#247) The following vulnerabilities are fixed by pinning transitive dependencies: - https://snyk.io/vuln/SNYK-PYTHON-IPYTHON-3318382 Co-authored-by: snyk-bot <snyk-bot@snyk.io> * test * Release Notes 0.12.0 (#249) * temp (#242) * Limiting numpy version (mckinsey#217) * adding line on yml - no effect * adding line on yml - no effect * changing req.txt * changing req.txt * changing req.txt * adding setuptools requirement (mckinsey#218) * adding setuptools requirement * adding setuptools requirement * update dictionaries to pass linting (mckinsey#230) * Refactor/unlock numpy kl (mckinsey#235) * unlocking numpy * unlocking numpy * unlocking numpy * dependency fixes for docs and linters * requirement fixes : numpy <1.24 for all python versions --------- Co-authored-by: kyle_lim <kyle_lim@mckinsey.com> * Simplifying requirements - Numpy version range (mckinsey#236) * Remove python 3.6 and 3.7 support (mckinsey#234) * remove python 3.6 and 3.7 support * update documentation * remove comment regarding ignoring a warning when running `make build-docs` * removing ipython from test requiremnets * Update README.md Co-authored-by: Philip Pilgerstorfer <34248114+qbphilip@users.noreply.github.com> --------- Co-authored-by: GabrielAz <gabriel.azevedoferreira@quantumblack.com> Co-authored-by: Gabriel Azevedo Ferreira <57528979+GabrielAzevedoFerreiraQB@users.noreply.github.com> Co-authored-by: Philip Pilgerstorfer <34248114+qbphilip@users.noreply.github.com> * unlocking numpy (mckinsey#238) Co-authored-by: Gabriel Azevedo <gabriel_azevedo_ferreira@mckinsey.com> * Release 0.11.2 (mckinsey#239) Co-authored-by: Gabriel Azevedo <gabriel_azevedo_ferreira@mckinsey.com> --------- Co-authored-by: ElisabethSesterHussQB <92664441+ElisabethSesterHussQB@users.noreply.github.com> Co-authored-by: kyle_lim <kyle_lim@mckinsey.com> Co-authored-by: Philip Pilgerstorfer <34248114+qbphilip@users.noreply.github.com> Co-authored-by: Gabriel Azevedo <gabriel_azevedo_ferreira@mckinsey.com> * Release Notes --------- Co-authored-by: ElisabethSesterHussQB <92664441+ElisabethSesterHussQB@users.noreply.github.com> Co-authored-by: kyle_lim <kyle_lim@mckinsey.com> Co-authored-by: Philip Pilgerstorfer <34248114+qbphilip@users.noreply.github.com> Co-authored-by: Gabriel Azevedo <gabriel_azevedo_ferreira@mckinsey.com> --------- Co-authored-by: ElisabethSesterHussQB <92664441+ElisabethSesterHussQB@users.noreply.github.com> Co-authored-by: kyle_lim <kyle_lim@mckinsey.com> Co-authored-by: Philip Pilgerstorfer <34248114+qbphilip@users.noreply.github.com> Co-authored-by: Gabriel Azevedo <gabriel_azevedo_ferreira@mckinsey.com> Co-authored-by: Serene Yeo <118331898+SereneYeo@users.noreply.github.com> Co-authored-by: Richard Oentaryo <oentaryorj@users.noreply.github.com> Co-authored-by: Leon Nallamuthu <38660312+leonnallamuthu@users.noreply.github.com> Co-authored-by: snyk-bot <snyk-bot@snyk.io>
Jimmy-INL · Apr 20, 2023 · b84e7cf · b84e7cf
1 parent 843b54a
commit b84e7cf
Show file tree

Hide file tree

Showing 46 changed files with 13,108 additions and 1,621 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -24,6 +24,7 @@ utils:
       conda create --name=causalnex_env python=${PYTHON_VERSION} -y
       conda activate causalnex_env
       conda install -y virtualenv
+      pip install cython
       pip install -U pip setuptools wheel
       sudo apt-get install graphviz
 
@@ -182,6 +183,7 @@ jobs:
           name: Success!
           command: echo "All checks passed"
 
+
 ###############################################################################
 workflows:
   version: 2

diff --git a/README.md b/README.md
@@ -52,14 +52,7 @@ CausalNex is a Python package. To install it, simply run:
 pip install causalnex
 ```
 
-Since pygraphviz can be difficult to install, esp. on Windows machines, the requirement is optional.
-If you want to use the causalnex native plotting tools, you can use
-```bash
-pip install "causalnex[plot]"
-```
-Alternatively, you can use the `networkx` drawing functionality for visualisations with fewer dependencies.
-
-Use `all` for a full installation of dependencies (only the plotting right now):
+Use `all` for a full installation of dependencies:
 ```bash
 pip install "causalnex[all]"
 ```

diff --git a/RELEASE.md b/RELEASE.md
@@ -1,4 +1,8 @@
 # Upcoming release
+# Release 0.12.0
+* Switch to Pyvis for graph visualisation and remove dependency on Graphviz
+
+# Release 0.11.2
 * Support newer version of Numpy
 * Support newer version of Scikit-learn
 * Remove python 3.6, 3.7 support

diff --git a/causalnex/__init__.py b/causalnex/__init__.py
@@ -30,6 +30,6 @@
 causalnex toolkit for causal reasoning (Bayesian Networks / Inference)
 """
 
-__version__ = "0.11.2"
+__version__ = "0.12.0"
 
 __all__ = ["structure", "discretiser", "evaluation", "inference", "network", "plots"]
diff --git a/causalnex/plots/__init__.py b/causalnex/plots/__init__.py
@@ -29,22 +29,13 @@
 """
 ``causalnex.plots`` provides functionality to visualise structure models.
 """
-
 __all__ = [
     "plot_structure",
     "NODE_STYLE",
     "EDGE_STYLE",
     "GRAPH_STYLE",
-    "color_gradient_string",
     "display_plot_ipython",
-    "display_plot_mpl",
 ]
 
-from .display import display_plot_ipython, display_plot_mpl
-from .plots import (
-    EDGE_STYLE,
-    GRAPH_STYLE,
-    NODE_STYLE,
-    color_gradient_string,
-    plot_structure,
-)
+from .display import display_plot_ipython
+from .plots import EDGE_STYLE, GRAPH_STYLE, NODE_STYLE, plot_structure
diff --git a/causalnex/plots/display.py b/causalnex/plots/display.py
@@ -25,97 +25,54 @@
 #
 # See the License for the specific language governing permissions and
 # limitations under the License.
-"""Methods to display styled pygraphgiz plots."""
+"""Methods to display styled pyvis plots."""
+import json
+from html import escape
+from typing import Dict
 
-import io
-from typing import Any, Tuple
+from IPython.lib.display import IFrame
+from pyvis.network import Network
 
-try:
-    from pygraphviz.agraph import AGraph
-except ImportError:
-    AGraph = Any
 
-try:
-    from IPython.display import Image
-except ImportError:
-    Image = Any
-
-try:
-    import matplotlib.pyplot as plt
-    from matplotlib.axes import Axes
-    from matplotlib.figure import Figure
-except ImportError:
-    Axes = Any
-    Figure = Any
-
-
-def display_plot_ipython(viz: AGraph, prog: str = "neato") -> Image:
+def display_plot_ipython(
+    viz: Network,
+    output_filename: str,
+    layout_kwargs: Dict[str, Dict] = None,
+) -> IFrame:
     """
-    Displays a pygraphviz object using ipython.
-
+    Displays a PyVis object using ipython.
     Args:
-        viz: pygraphviz object to render.
-
-        prog: The graph layout. Avaliable are:
-        dot, neato, fdp, sfdp, twopi and circo
-
+        viz: pyvis object to render.
+        output_filename: write html to a given path, e.g. "./plot.html". File as to end in ".html"
+        layout_kwargs: Dictionary to set the `layout` and `physics` of the graph.
+            Example:
+            ::
+                >>> layout_kwargs = {
+                        "physics": {
+                            "solver": "repulsion"
+                            },
+                        "layout": {
+                            "hierarchical": {
+                                "enabled": True
+                                }
+                            }
+                        }
     Returns:
-        IPython Image object. Renders in a notebook.
-
+        IPython IFrame object. Renders in a notebook.
     Raises:
         ImportError: if IPython is not installed (optional dependency).
     """
+    layout_kwargs = layout_kwargs or {}
+    viz.set_options(options=json.dumps(layout_kwargs))
 
-    if Image is Any:
-        raise ImportError("display_plot_ipython method requires IPython installed.")
-
-    return Image(viz.draw(format="png", prog=prog))
-
-
-def display_plot_mpl(
-    viz: AGraph,
-    prog: str = "neato",
-    ax: Axes = None,
-    pixel_size_in: float = 0.01,
-) -> Tuple[Figure, Axes]:
-    """
-    Displays a pygraphviz object using matplotlib.
-
-    Args:
-        viz: pygraphviz object to render.
-
-        prog: The graph layout. Avaliable are:
-        dot, neato, fdp, sfdp, twopi and circo
-
-        ax: Optional matplotlib axes to plot on.
-
-        pixel_size_in: Scaling multiple for the plot.
-
-    Returns:
-        IPython Image object. Renders in a notebook.
-
-    Raises:
-        ImportError: if matplotlib is not installed (optional dependency).
-    """
-
-    if Figure is Any:
-        raise ImportError("display_plot_mpl method requires matplotlib installed.")
-
-    # bytes:
-    s = viz.draw(format="png", prog=prog)
-    # convert to numpy array
-    array = plt.imread(io.BytesIO(s))
-    x_dim, y_dim, _ = array.shape
+    html = viz.generate_html()
 
-    # handle passed axis
-    if ax is not None:
-        ax.imshow(array)
-        ax.axis("off")
-        return None, ax
+    with open(output_filename, mode="w", encoding="UTF-8") as f:
+        f.write(html)
 
-    # handle new axis
-    f, ax = plt.subplots(1, 1, figsize=(y_dim * pixel_size_in, x_dim * pixel_size_in))
-    ax.imshow(array)
-    ax.axis("off")
-    f.tight_layout(pad=0.0)
-    return f, ax
+    return IFrame(
+        src=output_filename,
+        width=viz.width,
+        height=viz.height,
+        extras=[f"srcdoc='{escape(viz.generate_html(notebook=False))}'"],
+    )