Release 0.12.1 (#262)

* Limiting numpy version (#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 (#218) * adding setuptools requirement * adding setuptools requirement * update dictionaries to pass linting (#230) * Refactor/unlock numpy kl (#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 <[email protected]> * Simplifying requirements - Numpy version range (#236) * Remove python 3.6 and 3.7 support (#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 <[email protected]> --------- Co-authored-by: GabrielAz <[email protected]> Co-authored-by: Gabriel Azevedo Ferreira <[email protected]> Co-authored-by: Philip Pilgerstorfer <[email protected]> * unlocking numpy (#238) Co-authored-by: Gabriel Azevedo <[email protected]> * Release 0.11.2 (#239) Co-authored-by: Gabriel Azevedo <[email protected]> * Replacing Pygraphviz with Pyvis (#237) * Replacing Pygraphviz with Pyvis * Replacing Pygraphviz with Pyvis * Replacing Pygraphviz with Pyvis * temp (#242) * Limiting numpy version (#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 (#218) * adding setuptools requirement * adding setuptools requirement * update dictionaries to pass linting (#230) * Refactor/unlock numpy kl (#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 <[email protected]> * Simplifying requirements - Numpy version range (#236) * Remove python 3.6 and 3.7 support (#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 <[email protected]> --------- Co-authored-by: GabrielAz <[email protected]> Co-authored-by: Gabriel Azevedo Ferreira <[email protected]> Co-authored-by: Philip Pilgerstorfer <[email protected]> * unlocking numpy (#238) Co-authored-by: Gabriel Azevedo <[email protected]> * Release 0.11.2 (#239) Co-authored-by: Gabriel Azevedo <[email protected]> --------- Co-authored-by: ElisabethSesterHussQB <[email protected]> Co-authored-by: kyle_lim <[email protected]> Co-authored-by: Philip Pilgerstorfer <[email protected]> Co-authored-by: Gabriel Azevedo <[email protected]> * adding cython to config * adding cython to config * adding cython to config * adding cython to config --------- Co-authored-by: Gabriel Azevedo <[email protected]> Co-authored-by: ElisabethSesterHussQB <[email protected]> Co-authored-by: kyle_lim <[email protected]> Co-authored-by: Philip Pilgerstorfer <[email protected]> * Replace pygraphviz plotting with pyvis (#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 (#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 <[email protected]> * Update tests/test_plotting.py Co-authored-by: Richard Oentaryo <[email protected]> * 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 <[email protected]> Co-authored-by: GabrielAz <[email protected]> Co-authored-by: Gabriel Azevedo <[email protected]> Co-authored-by: Gabriel Azevedo Ferreira <[email protected]> Co-authored-by: Richard Oentaryo <[email protected]> * 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 <[email protected]> * test * Release Notes 0.12.0 (#249) * temp (#242) * Limiting numpy version (#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 (#218) * adding setuptools requirement * adding setuptools requirement * update dictionaries to pass linting (#230) * Refactor/unlock numpy kl (#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 <[email protected]> * Simplifying requirements - Numpy version range (#236) * Remove python 3.6 and 3.7 support (#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 <[email protected]> --------- Co-authored-by: GabrielAz <[email protected]> Co-authored-by: Gabriel Azevedo Ferreira <[email protected]> Co-authored-by: Philip Pilgerstorfer <[email protected]> * unlocking numpy (#238) Co-authored-by: Gabriel Azevedo <[email protected]> * Release 0.11.2 (#239) Co-authored-by: Gabriel Azevedo <[email protected]> --------- Co-authored-by: ElisabethSesterHussQB <[email protected]> Co-authored-by: kyle_lim <[email protected]> Co-authored-by: Philip Pilgerstorfer <[email protected]> Co-authored-by: Gabriel Azevedo <[email protected]> * Release Notes --------- Co-authored-by: ElisabethSesterHussQB <[email protected]> Co-authored-by: kyle_lim <[email protected]> Co-authored-by: Philip Pilgerstorfer <[email protected]> Co-authored-by: Gabriel Azevedo <[email protected]> * removing remaining Pygraphviz mentions (#254) * removing remaining Pygraphviz mentions * fixing ci * fixing ci --------- Co-authored-by: QuantumBlack Labs <[email protected]> * fix: doc_requirements.txt to reduce vulnerabilities (#259) The following vulnerabilities are fixed by pinning transitive dependencies: - https://snyk.io/vuln/SNYK-PYTHON-TORNADO-5537286 Co-authored-by: snyk-bot <[email protected]> * unlocking requirements (#257) * unlocking requirements - removing networkx * unlocking requirements - pandas * unlocking requirements - pathos * unlocking requirements - torch * unlocking requirements - removing wrapt * unlocking requirements - pgmpy * unlocking requirements - adding back torch pgmpy pathos pandas * unlocking requirements - pathos * unlocking requirements - torch --------- Co-authored-by: QuantumBlack Labs <[email protected]> * Version bump 0.12.0 -> 0.12.1 (#261) * version bump * Release noted --------- Co-authored-by: Gabriel Azevedo <[email protected]> --------- Co-authored-by: ElisabethSesterHussQB <[email protected]> Co-authored-by: kyle_lim <[email protected]> Co-authored-by: Philip Pilgerstorfer <[email protected]> Co-authored-by: Gabriel Azevedo <[email protected]> Co-authored-by: Serene Yeo <[email protected]> Co-authored-by: Richard Oentaryo <[email protected]> Co-authored-by: Leon Nallamuthu <[email protected]> Co-authored-by: snyk-bot <[email protected]> Co-authored-by: QuantumBlack Labs <[email protected]>
mckinsey · Jun 22, 2023 · 0108c92 · 0108c92
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commit 0108c92
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Showing 8 changed files with 12 additions and 13 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -2,7 +2,7 @@ version: 2
 
 images:
   python: &python
-    - image: circleci/buildpack-deps:stretch-browsers
+    - image: circleci/buildpack-deps
 
 machines:
   win-python: &win-python
@@ -62,10 +62,7 @@ utils:
       conda install -y virtualenv
       pip install -U pip setuptools wheel
       conda install -y cython
-      conda install -c anaconda graphviz=2.50.0 # to be able to import pygraphviz
       pip install -r requirements.txt -U
-      #pip install --global-option=build_ext --global-option="-IC:\Program Files\Graphviz\include" --global-option="-LC:\Program Files\Graphviz\lib" pygraphviz
-      pip install --global-option=build_ext --global-option="-IC:\tools\miniconda3\pkgs\graphviz-2.50.0-hdb8b0d4_0\Library\include" --global-option="-LC:\tools\miniconda3\pkgs\graphviz-2.50.0-hdb8b0d4_0\Library\lib" pygraphviz
       pip install -r test_requirements.txt -U
       pip install ".[pytorch]"
 

diff --git a/RELEASE.md b/RELEASE.md
@@ -1,4 +1,7 @@
 # Upcoming release
+# Release 0.12.1
+* Unlocking cap on following requirements: networkx, pathos, torch and wrapt
+
 # Release 0.12.0
 * Switch to Pyvis for graph visualisation and remove dependency on Graphviz
 

diff --git a/causalnex/__init__.py b/causalnex/__init__.py
@@ -30,6 +30,6 @@
 causalnex toolkit for causal reasoning (Bayesian Networks / Inference)
 """
 
-__version__ = "0.12.0"
+__version__ = "0.12.1"
 
 __all__ = ["structure", "discretiser", "evaluation", "inference", "network", "plots"]
diff --git a/devel-cpu.Dockerfile b/devel-cpu.Dockerfile
@@ -2,7 +2,7 @@ FROM ubuntu:20.04
 
 ENV DEBIAN_FRONTEND=noninteractive
 
-RUN apt-get update -y && apt install -y python3.8 python3-pip libgraphviz-dev graphviz
+RUN apt-get update -y && apt install -y python3.8 python3-pip
 RUN ln -s $(which python3) /usr/local/bin/python
 #COPY requirements.txt test_requirements.txt tmp/
 COPY . /tmp

diff --git a/devel-gpu.Dockerfile b/devel-gpu.Dockerfile
@@ -2,7 +2,7 @@ FROM nvidia/cuda:11.7.0-base-ubuntu20.04
 
 ENV DEBIAN_FRONTEND=noninteractive
 
-RUN apt-get update -y && apt install -y python3.8 python3-pip libgraphviz-dev graphviz
+RUN apt-get update -y && apt install -y python3.8 python3-pip
 RUN ln -s $(which python3) /usr/local/bin/python
 # Copy all files to container as intalling .[pytorch] requires setup.py, which requires other files
 COPY . /tmp

diff --git a/doc_requirements.txt b/doc_requirements.txt
@@ -11,10 +11,10 @@ nbstripout==0.3.3
 patchy>=1.5, <2.0
 pydot>=1.4, <2.0
 pygments>=2.6.1, <3.0
-pygraphviz>=1.5, <2.0
 recommonmark>=0.5.0, <1.0
 sphinx-autodoc-typehints>=1.6.0, <2.0
 sphinx-markdown-tables>=0.0.15, <1.0
 sphinx>=3.0.4, <4.0
 sphinx_copybutton>=0.2.5, <1.0
 sphinx_rtd_theme>=0.4.3, <1.0
+tornado>=6.3.2 # not directly required, pinned by Snyk to avoid a vulnerability
diff --git a/requirements.txt b/requirements.txt
@@ -1,15 +1,14 @@
 ipython>=8.10.0 # Required by Snyk
-networkx~=2.5
+networkx>=2.5
 numpy>=1.14.2, <1.24
 pandas>=1.0, <2.0
-pathos>=0.2.7, <0.3.0
+pathos>=0.2.7
 pgmpy>=0.1.14, <0.1.20
 pyvis>=0.3.2
 scikit-learn>=0.22.0, !=0.22.2.post1, !=0.24.1; python_version < '3.9'
 scikit-learn>=0.24.0, !=0.24.1; python_version == '3.9'
 scikit-learn>=0.25.0; python_version == '3.10'
 scipy>=1.7
 setuptools>=65.5.1
-torch>=1.7, <2.0
+torch>=1.7
 wheel>=0.38.0
-wrapt>=1.11.0, <1.13
diff --git a/tests/test_plotting.py b/tests/test_plotting.py
@@ -49,7 +49,7 @@ def test_all_nodes_exist(self):
         assert all(node in a_graph.get_nodes() for node in ["a", "b", "c"])
 
     def test_all_edges_exist(self):
-        """All edges in original graph should exist in pygraphviz graph"""
+        """All edges in original graph should exist in graph"""
         edges = [(str(a), str(a + b + 1)) for a in range(2) for b in range(3)]
         sm = StructureModel(edges)
         a_graph = plot_structure(sm)