From f0349c935af8526b787351d980f93b0e7ab664c5 Mon Sep 17 00:00:00 2001
From: Daniel Fink <danfink@mit.edu>
Date: Thu, 6 Jul 2023 15:13:52 +1000
Subject: [PATCH] remove pygraphviz dep

---
 poetry.lock    | 800 ++++++++++++++++++++++++-------------------------
 pyproject.toml |   1 -
 2 files changed, 388 insertions(+), 413 deletions(-)
 mode change 100755 => 100644 poetry.lock

diff --git a/poetry.lock b/poetry.lock
old mode 100755
new mode 100644
index a6cb5d4..bf5f9f5
--- a/poetry.lock
+++ b/poetry.lock
@@ -16,14 +16,14 @@ pygments = ">=1.5"
 
 [[package]]
 name = "aenum"
-version = "3.1.12"
+version = "3.1.15"
 description = "Advanced Enumerations (compatible with Python's stdlib Enum), NamedTuples, and NamedConstants"
 optional = false
 python-versions = "*"
 files = [
-    {file = "aenum-3.1.12-py2-none-any.whl", hash = "sha256:8d79c9e3ec997220e355b96b322e672fb56a53e61744138ed838407e3a07b610"},
-    {file = "aenum-3.1.12-py3-none-any.whl", hash = "sha256:2d544ef7323c088d68abf9a84b9f3f6db0d516fec685e15678b5f84fdb7b8ba0"},
-    {file = "aenum-3.1.12.tar.gz", hash = "sha256:3e531c91860a81f885f7e6e97d219ae9772cb899580084788935dad7d9742ef0"},
+    {file = "aenum-3.1.15-py2-none-any.whl", hash = "sha256:27b1710b9d084de6e2e695dab78fe9f269de924b51ae2850170ee7e1ca6288a5"},
+    {file = "aenum-3.1.15-py3-none-any.whl", hash = "sha256:e0dfaeea4c2bd362144b87377e2c61d91958c5ed0b4daf89cb6f45ae23af6288"},
+    {file = "aenum-3.1.15.tar.gz", hash = "sha256:8cbd76cd18c4f870ff39b24284d3ea028fbe8731a58df3aa581e434c575b9559"},
 ]
 
 [[package]]
@@ -39,13 +39,13 @@ files = [
 
 [[package]]
 name = "anyio"
-version = "3.7.0"
+version = "3.7.1"
 description = "High level compatibility layer for multiple asynchronous event loop implementations"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "anyio-3.7.0-py3-none-any.whl", hash = "sha256:eddca883c4175f14df8aedce21054bfca3adb70ffe76a9f607aef9d7fa2ea7f0"},
-    {file = "anyio-3.7.0.tar.gz", hash = "sha256:275d9973793619a5374e1c89a4f4ad3f4b0a5510a2b5b939444bee8f4c4d37ce"},
+    {file = "anyio-3.7.1-py3-none-any.whl", hash = "sha256:91dee416e570e92c64041bd18b900d1d6fa78dff7048769ce5ac5ddad004fbb5"},
+    {file = "anyio-3.7.1.tar.gz", hash = "sha256:44a3c9aba0f5defa43261a8b3efb97891f2bd7d804e0e1f56419befa1adfc780"},
 ]
 
 [package.dependencies]
@@ -54,7 +54,7 @@ idna = ">=2.8"
 sniffio = ">=1.1"
 
 [package.extras]
-doc = ["Sphinx (>=6.1.0)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme", "sphinxcontrib-jquery"]
+doc = ["Sphinx", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme (>=1.2.2)", "sphinxcontrib-jquery"]
 test = ["anyio[trio]", "coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "mock (>=4)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"]
 trio = ["trio (<0.22)"]
 
@@ -645,13 +645,13 @@ files = [
 
 [[package]]
 name = "exceptiongroup"
-version = "1.1.1"
+version = "1.1.2"
 description = "Backport of PEP 654 (exception groups)"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "exceptiongroup-1.1.1-py3-none-any.whl", hash = "sha256:232c37c63e4f682982c8b6459f33a8981039e5fb8756b2074364e5055c498c9e"},
-    {file = "exceptiongroup-1.1.1.tar.gz", hash = "sha256:d484c3090ba2889ae2928419117447a14daf3c1231d5e30d0aae34f354f01785"},
+    {file = "exceptiongroup-1.1.2-py3-none-any.whl", hash = "sha256:e346e69d186172ca7cf029c8c1d16235aa0e04035e5750b4b95039e65204328f"},
+    {file = "exceptiongroup-1.1.2.tar.gz", hash = "sha256:12c3e887d6485d16943a309616de20ae5582633e0a2eda17f4e10fd61c1e8af5"},
 ]
 
 [package.extras]
@@ -901,13 +901,13 @@ files = [
 
 [[package]]
 name = "importlib-metadata"
-version = "6.6.0"
+version = "6.7.0"
 description = "Read metadata from Python packages"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "importlib_metadata-6.6.0-py3-none-any.whl", hash = "sha256:43dd286a2cd8995d5eaef7fee2066340423b818ed3fd70adf0bad5f1fac53fed"},
-    {file = "importlib_metadata-6.6.0.tar.gz", hash = "sha256:92501cdf9cc66ebd3e612f1b4f0c0765dfa42f0fa38ffb319b6bd84dd675d705"},
+    {file = "importlib_metadata-6.7.0-py3-none-any.whl", hash = "sha256:cb52082e659e97afc5dac71e79de97d8681de3aa07ff18578330904a9d18e5b5"},
+    {file = "importlib_metadata-6.7.0.tar.gz", hash = "sha256:1aaf550d4f73e5d6783e7acb77aec43d49da8017410afae93822cc9cca98c4d4"},
 ]
 
 [package.dependencies]
@@ -916,7 +916,7 @@ zipp = ">=0.5"
 [package.extras]
 docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
 perf = ["ipython"]
-testing = ["flake8 (<5)", "flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)"]
+testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)", "pytest-ruff"]
 
 [[package]]
 name = "importlib-resources"
@@ -949,13 +949,13 @@ files = [
 
 [[package]]
 name = "ipykernel"
-version = "6.23.2"
+version = "6.24.0"
 description = "IPython Kernel for Jupyter"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "ipykernel-6.23.2-py3-none-any.whl", hash = "sha256:7ccb6e2d32fd958c21453db494c914f3474908a2fdefd99ab548a5375b548d1f"},
-    {file = "ipykernel-6.23.2.tar.gz", hash = "sha256:fcfb67c5b504aa1bfcda1c5b3716636239e0f7b9290958f1c558c79b4c0e7ed5"},
+    {file = "ipykernel-6.24.0-py3-none-any.whl", hash = "sha256:2f5fffc7ad8f1fd5aadb4e171ba9129d9668dbafa374732cf9511ada52d6547f"},
+    {file = "ipykernel-6.24.0.tar.gz", hash = "sha256:29cea0a716b1176d002a61d0b0c851f34536495bc4ef7dd0222c88b41b816123"},
 ]
 
 [package.dependencies]
@@ -1032,13 +1032,13 @@ files = [
 
 [[package]]
 name = "ipywidgets"
-version = "8.0.6"
+version = "8.0.7"
 description = "Jupyter interactive widgets"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "ipywidgets-8.0.6-py3-none-any.whl", hash = "sha256:a60bf8d2528997e05ac83fd19ea2fbe65f2e79fbe1b2b35779bdfc46c2941dcc"},
-    {file = "ipywidgets-8.0.6.tar.gz", hash = "sha256:de7d779f2045d60de9f6c25f653fdae2dba57898e6a1284494b3ba20b6893bb8"},
+    {file = "ipywidgets-8.0.7-py3-none-any.whl", hash = "sha256:e0aed0c95a1e55b6a123f64305245578bdc09e52965a34941c2b6a578b8c64a0"},
+    {file = "ipywidgets-8.0.7.tar.gz", hash = "sha256:50ace0a8886e9a0d68b980db82f94c25d55d21ff2340ed36f802dd9365e94acf"},
 ]
 
 [package.dependencies]
@@ -1133,13 +1133,13 @@ testing-libs = ["simplejson", "ujson"]
 
 [[package]]
 name = "jsonpointer"
-version = "2.3"
+version = "2.4"
 description = "Identify specific nodes in a JSON document (RFC 6901)"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*"
 files = [
-    {file = "jsonpointer-2.3-py2.py3-none-any.whl", hash = "sha256:51801e558539b4e9cd268638c078c6c5746c9ac96bc38152d443400e4f3793e9"},
-    {file = "jsonpointer-2.3.tar.gz", hash = "sha256:97cba51526c829282218feb99dab1b1e6bdf8efd1c43dc9d57be093c0d69c99a"},
+    {file = "jsonpointer-2.4-py2.py3-none-any.whl", hash = "sha256:15d51bba20eea3165644553647711d150376234112651b4f1811022aecad7d7a"},
+    {file = "jsonpointer-2.4.tar.gz", hash = "sha256:585cee82b70211fa9e6043b7bb89db6e1aa49524340dde8ad6b63206ea689d88"},
 ]
 
 [[package]]
@@ -1255,13 +1255,13 @@ testing = ["coverage", "ipykernel", "jupytext", "matplotlib", "nbdime", "nbforma
 
 [[package]]
 name = "jupyter-client"
-version = "8.2.0"
+version = "8.3.0"
 description = "Jupyter protocol implementation and client libraries"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jupyter_client-8.2.0-py3-none-any.whl", hash = "sha256:b18219aa695d39e2ad570533e0d71fb7881d35a873051054a84ee2a17c4b7389"},
-    {file = "jupyter_client-8.2.0.tar.gz", hash = "sha256:9fe233834edd0e6c0aa5f05ca2ab4bdea1842bfd2d8a932878212fc5301ddaf0"},
+    {file = "jupyter_client-8.3.0-py3-none-any.whl", hash = "sha256:7441af0c0672edc5d28035e92ba5e32fadcfa8a4e608a434c228836a89df6158"},
+    {file = "jupyter_client-8.3.0.tar.gz", hash = "sha256:3af69921fe99617be1670399a0b857ad67275eefcfa291e2c81a160b7b650f5f"},
 ]
 
 [package.dependencies]
@@ -1361,13 +1361,13 @@ jupyter-server = ">=1.1.2"
 
 [[package]]
 name = "jupyter-server"
-version = "2.6.0"
+version = "2.7.0"
 description = "The backend—i.e. core services, APIs, and REST endpoints—to Jupyter web applications."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jupyter_server-2.6.0-py3-none-any.whl", hash = "sha256:19525a1515b5999618a91b3e99ec9f6869aa8c5ba73e0b6279fcda918b54ba36"},
-    {file = "jupyter_server-2.6.0.tar.gz", hash = "sha256:ae4af349f030ed08dd78cb7ac1a03a92d886000380c9ea6283f3c542a81f4b06"},
+    {file = "jupyter_server-2.7.0-py3-none-any.whl", hash = "sha256:6a77912aff643e53fa14bdb2634884b52b784a4be77ce8e93f7283faed0f0849"},
+    {file = "jupyter_server-2.7.0.tar.gz", hash = "sha256:36da0a266d31a41ac335a366c88933c17dfa5bb817a48f5c02c16d303bc9477f"},
 ]
 
 [package.dependencies]
@@ -1393,7 +1393,7 @@ websocket-client = "*"
 
 [package.extras]
 docs = ["ipykernel", "jinja2", "jupyter-client", "jupyter-server", "myst-parser", "nbformat", "prometheus-client", "pydata-sphinx-theme", "send2trash", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-openapi (>=0.8.0)", "sphinxcontrib-spelling", "sphinxemoji", "tornado", "typing-extensions"]
-test = ["ipykernel", "pre-commit", "pytest (>=7.0)", "pytest-console-scripts", "pytest-jupyter[server] (>=0.4)", "pytest-timeout", "requests"]
+test = ["flaky", "ipykernel", "pre-commit", "pytest (>=7.0)", "pytest-console-scripts", "pytest-jupyter[server] (>=0.4)", "pytest-timeout", "requests"]
 
 [[package]]
 name = "jupyter-server-terminals"
@@ -1485,13 +1485,13 @@ test = ["hatch", "ipykernel", "jupyterlab-server[openapi]", "openapi-spec-valida
 
 [[package]]
 name = "jupyterlab-widgets"
-version = "3.0.7"
+version = "3.0.8"
 description = "Jupyter interactive widgets for JupyterLab"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "jupyterlab_widgets-3.0.7-py3-none-any.whl", hash = "sha256:c73f8370338ec19f1bec47254752d6505b03601cbd5a67e6a0b184532f73a459"},
-    {file = "jupyterlab_widgets-3.0.7.tar.gz", hash = "sha256:c3a50ed5bf528a0c7a869096503af54702f86dda1db469aee1c92dc0c01b43ca"},
+    {file = "jupyterlab_widgets-3.0.8-py3-none-any.whl", hash = "sha256:4715912d6ceab839c9db35953c764b3214ebbc9161c809f6e0510168845dfdf5"},
+    {file = "jupyterlab_widgets-3.0.8.tar.gz", hash = "sha256:d428ab97b8d87cc7c54cbf37644d6e0f0e662f23876e05fa460a73ec3257252a"},
 ]
 
 [[package]]
@@ -1607,35 +1607,35 @@ test = ["coverage", "pytest", "pytest-cov"]
 
 [[package]]
 name = "llvmlite"
-version = "0.40.0"
+version = "0.40.1"
 description = "lightweight wrapper around basic LLVM functionality"
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.dependencies]
@@ -1780,7 +1780,7 @@ kiwisolver = ">=1.0.1"
 numpy = ">=1.20"
 packaging = ">=20.0"
 pillow = ">=6.2.0"
-pyparsing = ">=2.3.1"
+pyparsing = ">=2.3.1,<3.1"
 python-dateutil = ">=2.7"
 
 [[package]]
@@ -1829,13 +1829,13 @@ files = [
 
 [[package]]
 name = "mistune"
-version = "2.0.5"
-description = "A sane Markdown parser with useful plugins and renderers"
+version = "3.0.1"
+description = "A sane and fast Markdown parser with useful plugins and renderers"
 optional = false
-python-versions = "*"
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 files = [
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 [[package]]
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 [[package]]
 name = "nbconvert"
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+version = "7.6.0"
 description = "Converting Jupyter Notebooks"
 optional = false
 python-versions = ">=3.7"
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 [package.dependencies]
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 jupyterlab-pygments = "*"
 markupsafe = ">=2.0"
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 nbclient = ">=0.5.0"
 nbformat = ">=5.7"
 packaging = "*"
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 [package.dependencies]
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 [[package]]
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 [package.dependencies]
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 [[package]]
@@ -3400,13 +3376,13 @@ win32 = ["pywin32"]
 
 [[package]]
 name = "setuptools"
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+version = "68.0.0"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
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 python-versions = ">=3.7"
 files = [
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 [package.extras]
@@ -3460,13 +3436,13 @@ files = [
 
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 python-versions = ">=3.7.2,<4.0"
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 files = [
-    {file = "websocket-client-1.5.3.tar.gz", hash = "sha256:b96f3bce3e54e3486ebe6504bc22bd4c140392bd2eb71764db29be8f2639aa65"},
-    {file = "websocket_client-1.5.3-py3-none-any.whl", hash = "sha256:3566f8467cd350874c4913816355642a4942f6c1ed1e9406e3d42fae6d6c072a"},
+    {file = "websocket-client-1.6.1.tar.gz", hash = "sha256:c951af98631d24f8df89ab1019fc365f2227c0892f12fd150e935607c79dd0dd"},
+    {file = "websocket_client-1.6.1-py3-none-any.whl", hash = "sha256:f1f9f2ad5291f0225a49efad77abf9e700b6fef553900623060dad6e26503b9d"},
 ]
 
 [package.extras]
@@ -4352,13 +4328,13 @@ test = ["pytest (>=6.0.0)"]
 
 [[package]]
 name = "widgetsnbextension"
-version = "4.0.7"
+version = "4.0.8"
 description = "Jupyter interactive widgets for Jupyter Notebook"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "widgetsnbextension-4.0.7-py3-none-any.whl", hash = "sha256:be3228a73bbab189a16be2d4a3cd89ecbd4e31948bfdc64edac17dcdee3cd99c"},
-    {file = "widgetsnbextension-4.0.7.tar.gz", hash = "sha256:ea67c17a7cd4ae358f8f46c3b304c40698bc0423732e3f273321ee141232c8be"},
+    {file = "widgetsnbextension-4.0.8-py3-none-any.whl", hash = "sha256:2e37f0ce9da11651056280c7efe96f2db052fe8fc269508e3724f5cbd6c93018"},
+    {file = "widgetsnbextension-4.0.8.tar.gz", hash = "sha256:9ec291ba87c2dfad42c3d5b6f68713fa18be1acd7476569516b2431682315c17"},
 ]
 
 [[package]]
@@ -4550,4 +4526,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9, <3.11"
-content-hash = "d78b1e157cda2b6d6dd07208c0bbfde6bc9b83f3ae91c59f404b7bb189ac1a63"
+content-hash = "31a6ed7bd483e58c888e6021f3a164adf6f27ca948897102eac59c39e20f1383"
diff --git a/pyproject.toml b/pyproject.toml
index 386b529..28558c6 100755
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -30,7 +30,6 @@ multiprocess = "^0.70.14"
 seaborn = "^0.12.2"
 jupyter-book = "^0.15.1"
 sphinx-rtd-theme = "^1.2.0"
-pygraphviz = "^1.11"
 pyvis = "^0.3.2"
 plotly = "^5.15.0"
 pyppeteer = "^1.0.2"