From b1b6bb1aa0bf371f7406deb8d0492355a4817434 Mon Sep 17 00:00:00 2001
From: Sam Bessey <sam_bessey@brown.edu>
Date: Wed, 15 Feb 2023 13:49:39 -0500
Subject: [PATCH 1/7] change numpy version

---
 .github/workflows/deploy_pypi.yml | 2 +-
 pyproject.toml                    | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/deploy_pypi.yml b/.github/workflows/deploy_pypi.yml
index 3668459b..2a5f405c 100644
--- a/.github/workflows/deploy_pypi.yml
+++ b/.github/workflows/deploy_pypi.yml
@@ -13,7 +13,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: 3.7
+          python-version: 3.8
 
       - name: Set up Poetry
         run: |
diff --git a/pyproject.toml b/pyproject.toml
index 49192653..a99ea9ff 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -12,11 +12,11 @@ classifiers = ["Operating System :: OS Independent"]
 packages = [{ include = "titan" }]
 
 [tool.poetry.dependencies]
-python = "^3.6"
+python = "^3.8"
 paraml= "^0.1"
 networkx = "^2.4"
 nanoid = "^2.0"
-numpy = "^1.18"
+numpy = "^1.21"
 black = {version = "^20.8b1", optional = true}
 flake8 = {version = "^3.8", optional = true}
 mypy = {version = "^0.812", optional = true}

From ba9d5e27f2014577c12497f76478bb07361c6004 Mon Sep 17 00:00:00 2001
From: Sam Bessey <sam_bessey@brown.edu>
Date: Wed, 15 Feb 2023 13:51:58 -0500
Subject: [PATCH 2/7] update more stuff

---
 .github/workflows/unit-tests.yml |  18 +--
 poetry.lock                      | 181 ++++++++++++++++---------------
 pyproject.toml                   |   2 +-
 3 files changed, 104 insertions(+), 97 deletions(-)

diff --git a/.github/workflows/unit-tests.yml b/.github/workflows/unit-tests.yml
index 6135ee18..7ab8b56c 100644
--- a/.github/workflows/unit-tests.yml
+++ b/.github/workflows/unit-tests.yml
@@ -12,7 +12,7 @@ jobs:
     - name: Set up Python for linting, formatting, type checking
       uses: actions/setup-python@v2
       with:
-        python-version: '3.6'
+        python-version: '3.8'
     - name: Set up Poetry for linting, formatting, type checking
       run: |
         pip install poetry
@@ -21,7 +21,7 @@ jobs:
       uses: actions/cache@v2
       with:
         path: .venv
-        key: venv-lint-python3.6-${{ hashFiles('**/poetry.lock') }}
+        key: venv-lint-python3.8-${{ hashFiles('**/poetry.lock') }}
     - name: Install dependencies
       run: poetry install -E linting --no-dev
     - name: Lint with flake8
@@ -43,7 +43,7 @@ jobs:
     - name: Set up Python for testing
       uses: actions/setup-python@v2
       with:
-        python-version: '3.6'
+        python-version: '3.8'
     - name: Set up Poetry for testing
       run: |
         pip install poetry
@@ -52,7 +52,7 @@ jobs:
       uses: actions/cache@v2
       with:
         path: .venv
-        key: venv-python3.6-${{ hashFiles('**/poetry.lock') }}
+        key: venv-python3.8-${{ hashFiles('**/poetry.lock') }}
     - name: Install dependencies
       run: poetry install
     - name: Unit Test with pytest
@@ -71,7 +71,7 @@ jobs:
     - name: Set up Python for testing
       uses: actions/setup-python@v2
       with:
-        python-version: '3.6'
+        python-version: '3.8'
     - name: Set up Poetry for testing
       run: |
         pip install poetry
@@ -80,7 +80,7 @@ jobs:
       uses: actions/cache@v2
       with:
         path: .venv
-        key: venv-python3.6-${{ hashFiles('**/poetry.lock') }}
+        key: venv-python3.8-${{ hashFiles('**/poetry.lock') }}
     - name: Install dependencies
       run: poetry install
     - name: Integration Test with pytest
@@ -99,7 +99,7 @@ jobs:
     - name: Set up Python for testing
       uses: actions/setup-python@v2
       with:
-        python-version: '3.6'
+        python-version: '3.8'
     - name: Set up Poetry for testing
       run: |
         pip install poetry
@@ -136,7 +136,7 @@ jobs:
     - name: Set up pypy for testing
       uses: actions/setup-python@v2
       with:
-        python-version: pypy-3.6
+        python-version: pypy-3.8
     - name: Set up Poetry for testing
       run: |
         pip install poetry
@@ -145,7 +145,7 @@ jobs:
       uses: actions/cache@v2
       with:
         path: .venv
-        key: venv-pypy3.6-${{ hashFiles('**/poetry.lock') }}
+        key: venv-pypy3.8-${{ hashFiles('**/poetry.lock') }}
     - name: Install dependencies
       run: poetry install --no-dev
 
diff --git a/poetry.lock b/poetry.lock
index 4127c042..582d5777 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -16,6 +16,7 @@ python-versions = "*"
 
 [package.dependencies]
 six = ">=1.6.1,<2.0"
+wheel = ">=0.23.0,<1.0"
 
 [[package]]
 name = "atomicwrites"
@@ -34,10 +35,10 @@ optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [package.extras]
-dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit"]
-docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"]
-tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface"]
-tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins"]
+dev = ["coverage[toml] (>=5.0.2)", "furo", "hypothesis", "mypy", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "six", "sphinx", "sphinx-notfound-page", "zope.interface"]
+docs = ["furo", "sphinx", "sphinx-notfound-page", "zope.interface"]
+tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "mypy", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "six", "zope.interface"]
+tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "mypy", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "six"]
 
 [[package]]
 name = "black"
@@ -50,7 +51,6 @@ python-versions = ">=3.6"
 [package.dependencies]
 appdirs = "*"
 click = ">=7.1.2"
-dataclasses = {version = ">=0.6", markers = "python_version < \"3.7\""}
 mypy-extensions = ">=0.4.3"
 pathspec = ">=0.6,<1"
 regex = ">=2020.1.8"
@@ -62,14 +62,6 @@ typing-extensions = ">=3.7.4"
 colorama = ["colorama (>=0.4.3)"]
 d = ["aiohttp (>=3.3.2)", "aiohttp-cors"]
 
-[[package]]
-name = "cached-property"
-version = "1.5.2"
-description = "A decorator for caching properties in classes."
-category = "main"
-optional = true
-python-versions = "*"
-
 [[package]]
 name = "click"
 version = "8.0.3"
@@ -80,7 +72,6 @@ python-versions = ">=3.6"
 
 [package.dependencies]
 colorama = {version = "*", markers = "platform_system == \"Windows\""}
-importlib-metadata = {version = "*", markers = "python_version < \"3.8\""}
 
 [[package]]
 name = "colorama"
@@ -101,14 +92,6 @@ python-versions = ">=3.6"
 [package.extras]
 toml = ["tomli"]
 
-[[package]]
-name = "dataclasses"
-version = "0.8"
-description = "A backport of the dataclasses module for Python 3.6"
-category = "main"
-optional = true
-python-versions = ">=3.6, <3.7"
-
 [[package]]
 name = "decorator"
 version = "4.4.2"
@@ -126,7 +109,6 @@ optional = true
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
 
 [package.dependencies]
-importlib-metadata = {version = "*", markers = "python_version < \"3.8\""}
 mccabe = ">=0.6.0,<0.7.0"
 pycodestyle = ">=2.7.0,<2.8.0"
 pyflakes = ">=2.3.0,<2.4.0"
@@ -143,24 +125,23 @@ python-versions = "*"
 python-dateutil = ">=2.8.1"
 
 [package.extras]
-dev = ["twine", "markdown", "flake8", "wheel"]
+dev = ["flake8", "markdown", "twine", "wheel"]
 
 [[package]]
 name = "importlib-metadata"
 version = "4.8.2"
 description = "Read metadata from Python packages"
 category = "main"
-optional = false
+optional = true
 python-versions = ">=3.6"
 
 [package.dependencies]
-typing-extensions = {version = ">=3.6.4", markers = "python_version < \"3.8\""}
 zipp = ">=0.5"
 
 [package.extras]
-docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
+docs = ["jaraco.packaging (>=8.2)", "rst.linker (>=1.9)", "sphinx"]
 perf = ["ipython"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"]
+testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pep517", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-flake8", "pytest-mypy", "pytest-perf (>=0.9.2)"]
 
 [[package]]
 name = "iniconfig"
@@ -341,7 +322,7 @@ python-versions = ">=3.6"
 decorator = ">=4.3,<5"
 
 [package.extras]
-all = ["numpy", "scipy", "pandas", "matplotlib", "pygraphviz", "pydot", "pyyaml", "lxml", "pytest"]
+all = ["lxml", "matplotlib", "numpy", "pandas", "pydot", "pygraphviz", "pytest", "pyyaml", "scipy"]
 gdal = ["gdal"]
 lxml = ["lxml"]
 matplotlib = ["matplotlib"]
@@ -355,11 +336,11 @@ scipy = ["scipy"]
 
 [[package]]
 name = "numpy"
-version = "1.19.5"
+version = "1.21.0"
 description = "NumPy is the fundamental package for array computing with Python."
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [[package]]
 name = "oyaml"
@@ -410,9 +391,6 @@ category = "dev"
 optional = false
 python-versions = ">=3.6"
 
-[package.dependencies]
-importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""}
-
 [package.extras]
 dev = ["pre-commit", "tox"]
 testing = ["pytest", "pytest-benchmark"]
@@ -483,7 +461,6 @@ python-versions = ">=3.6"
 atomicwrites = {version = ">=1.0", markers = "sys_platform == \"win32\""}
 attrs = ">=19.2.0"
 colorama = {version = "*", markers = "sys_platform == \"win32\""}
-importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""}
 iniconfig = "*"
 packaging = "*"
 pluggy = ">=0.12,<2.0"
@@ -507,7 +484,7 @@ pytest = ">=4.6"
 toml = "*"
 
 [package.extras]
-testing = ["fields", "hunter", "process-tests", "six", "pytest-xdist", "virtualenv"]
+testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtualenv"]
 
 [[package]]
 name = "python-dateutil"
@@ -530,9 +507,6 @@ python-versions = ">=3.6,<4.0"
 
 [package.dependencies]
 astunparse = {version = ">=1.6.3,<2.0.0", markers = "python_version < \"3.9\""}
-cached-property = {version = ">=1.5.2,<2.0.0", markers = "python_version < \"3.8\""}
-dataclasses = {version = ">=0.7,<0.9", markers = "python_version == \"3.6\""}
-typing-extensions = {version = ">=3.7.4.3,<4.0.0.0", markers = "python_version < \"3.8\""}
 
 [package.extras]
 numpy-style = ["docstring_parser (>=0.7.3,<0.8.0)"]
@@ -593,7 +567,7 @@ name = "typing-extensions"
 version = "3.10.0.2"
 description = "Backported and Experimental Type Hints for Python 3.5+"
 category = "main"
-optional = false
+optional = true
 python-versions = "*"
 
 [[package]]
@@ -607,17 +581,28 @@ python-versions = ">=3.6"
 [package.extras]
 watchmedo = ["PyYAML (>=3.10)"]
 
+[[package]]
+name = "wheel"
+version = "0.38.4"
+description = "A built-package format for Python"
+category = "main"
+optional = true
+python-versions = ">=3.7"
+
+[package.extras]
+test = ["pytest (>=3.0.0)"]
+
 [[package]]
 name = "zipp"
 version = "3.6.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 category = "main"
-optional = false
+optional = true
 python-versions = ">=3.6"
 
 [package.extras]
-docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
-testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy"]
+docs = ["jaraco.packaging (>=8.2)", "rst.linker (>=1.9)", "sphinx"]
+testing = ["func-timeout", "jaraco.itertools", "pytest (>=4.6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-flake8", "pytest-mypy"]
 
 [extras]
 docs = ["mkdocs", "mkdocs-material", "mkdocstrings"]
@@ -625,8 +610,8 @@ linting = ["black", "flake8", "mypy"]
 
 [metadata]
 lock-version = "1.1"
-python-versions = "^3.6"
-content-hash = "f7e3031f0f6103045aa92f4a372fbbcc3e7fc2ae9a2e2944d18d9539f31430f9"
+python-versions = "^3.8"
+content-hash = "350123d2653219fd539911adc4798b495d9ee7600467b61be8958a079e9e4b11"
 
 [metadata.files]
 appdirs = [
@@ -648,10 +633,6 @@ attrs = [
 black = [
     {file = "black-20.8b1.tar.gz", hash = "sha256:1c02557aa099101b9d21496f8a914e9ed2222ef70336404eeeac8edba836fbea"},
 ]
-cached-property = [
-    {file = "cached-property-1.5.2.tar.gz", hash = "sha256:9fa5755838eecbb2d234c3aa390bd80fbd3ac6b6869109bfc1b499f7bd89a130"},
-    {file = "cached_property-1.5.2-py2.py3-none-any.whl", hash = "sha256:df4f613cf7ad9a588cc381aaf4a512d26265ecebd5eb9e1ba12f1319eb85a6a0"},
-]
 click = [
     {file = "click-8.0.3-py3-none-any.whl", hash = "sha256:353f466495adaeb40b6b5f592f9f91cb22372351c84caeb068132442a4518ef3"},
     {file = "click-8.0.3.tar.gz", hash = "sha256:410e932b050f5eed773c4cda94de75971c89cdb3155a72a0831139a79e5ecb5b"},
@@ -709,10 +690,6 @@ coverage = [
     {file = "coverage-6.2-pp36.pp37.pp38-none-any.whl", hash = "sha256:5829192582c0ec8ca4a2532407bc14c2f338d9878a10442f5d03804a95fac9de"},
     {file = "coverage-6.2.tar.gz", hash = "sha256:e2cad8093172b7d1595b4ad66f24270808658e11acf43a8f95b41276162eb5b8"},
 ]
-dataclasses = [
-    {file = "dataclasses-0.8-py3-none-any.whl", hash = "sha256:0201d89fa866f68c8ebd9d08ee6ff50c0b255f8ec63a71c16fda7af82bb887bf"},
-    {file = "dataclasses-0.8.tar.gz", hash = "sha256:8479067f342acf957dc82ec415d355ab5edb7e7646b90dc6e2fd1d96ad084c97"},
-]
 decorator = [
     {file = "decorator-4.4.2-py2.py3-none-any.whl", hash = "sha256:41fa54c2a0cc4ba648be4fd43cff00aedf5b9465c9bf18d64325bc225f08f760"},
     {file = "decorator-4.4.2.tar.gz", hash = "sha256:e3a62f0520172440ca0dcc823749319382e377f37f140a0b99ef45fecb84bfe7"},
@@ -877,40 +854,34 @@ networkx = [
     {file = "networkx-2.5.1.tar.gz", hash = "sha256:109cd585cac41297f71103c3c42ac6ef7379f29788eb54cb751be5a663bb235a"},
 ]
 numpy = [
-    {file = "numpy-1.19.5-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:cc6bd4fd593cb261332568485e20a0712883cf631f6f5e8e86a52caa8b2b50ff"},
-    {file = "numpy-1.19.5-cp36-cp36m-manylinux1_i686.whl", hash = "sha256:aeb9ed923be74e659984e321f609b9ba54a48354bfd168d21a2b072ed1e833ea"},
-    {file = "numpy-1.19.5-cp36-cp36m-manylinux1_x86_64.whl", hash = "sha256:8b5e972b43c8fc27d56550b4120fe6257fdc15f9301914380b27f74856299fea"},
-    {file = "numpy-1.19.5-cp36-cp36m-manylinux2010_i686.whl", hash = "sha256:43d4c81d5ffdff6bae58d66a3cd7f54a7acd9a0e7b18d97abb255defc09e3140"},
-    {file = "numpy-1.19.5-cp36-cp36m-manylinux2010_x86_64.whl", hash = "sha256:a4646724fba402aa7504cd48b4b50e783296b5e10a524c7a6da62e4a8ac9698d"},
-    {file = "numpy-1.19.5-cp36-cp36m-manylinux2014_aarch64.whl", hash = "sha256:2e55195bc1c6b705bfd8ad6f288b38b11b1af32f3c8289d6c50d47f950c12e76"},
-    {file = "numpy-1.19.5-cp36-cp36m-win32.whl", hash = "sha256:39b70c19ec771805081578cc936bbe95336798b7edf4732ed102e7a43ec5c07a"},
-    {file = "numpy-1.19.5-cp36-cp36m-win_amd64.whl", hash = "sha256:dbd18bcf4889b720ba13a27ec2f2aac1981bd41203b3a3b27ba7a33f88ae4827"},
-    {file = "numpy-1.19.5-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:603aa0706be710eea8884af807b1b3bc9fb2e49b9f4da439e76000f3b3c6ff0f"},
-    {file = "numpy-1.19.5-cp37-cp37m-manylinux1_i686.whl", hash = "sha256:cae865b1cae1ec2663d8ea56ef6ff185bad091a5e33ebbadd98de2cfa3fa668f"},
-    {file = "numpy-1.19.5-cp37-cp37m-manylinux1_x86_64.whl", hash = "sha256:36674959eed6957e61f11c912f71e78857a8d0604171dfd9ce9ad5cbf41c511c"},
-    {file = "numpy-1.19.5-cp37-cp37m-manylinux2010_i686.whl", hash = "sha256:06fab248a088e439402141ea04f0fffb203723148f6ee791e9c75b3e9e82f080"},
-    {file = "numpy-1.19.5-cp37-cp37m-manylinux2010_x86_64.whl", hash = "sha256:6149a185cece5ee78d1d196938b2a8f9d09f5a5ebfbba66969302a778d5ddd1d"},
-    {file = "numpy-1.19.5-cp37-cp37m-manylinux2014_aarch64.whl", hash = "sha256:50a4a0ad0111cc1b71fa32dedd05fa239f7fb5a43a40663269bb5dc7877cfd28"},
-    {file = "numpy-1.19.5-cp37-cp37m-win32.whl", hash = "sha256:d051ec1c64b85ecc69531e1137bb9751c6830772ee5c1c426dbcfe98ef5788d7"},
-    {file = "numpy-1.19.5-cp37-cp37m-win_amd64.whl", hash = "sha256:a12ff4c8ddfee61f90a1633a4c4afd3f7bcb32b11c52026c92a12e1325922d0d"},
-    {file = "numpy-1.19.5-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:cf2402002d3d9f91c8b01e66fbb436a4ed01c6498fffed0e4c7566da1d40ee1e"},
-    {file = "numpy-1.19.5-cp38-cp38-manylinux1_i686.whl", hash = "sha256:1ded4fce9cfaaf24e7a0ab51b7a87be9038ea1ace7f34b841fe3b6894c721d1c"},
-    {file = "numpy-1.19.5-cp38-cp38-manylinux1_x86_64.whl", hash = "sha256:012426a41bc9ab63bb158635aecccc7610e3eff5d31d1eb43bc099debc979d94"},
-    {file = "numpy-1.19.5-cp38-cp38-manylinux2010_i686.whl", hash = "sha256:759e4095edc3c1b3ac031f34d9459fa781777a93ccc633a472a5468587a190ff"},
-    {file = "numpy-1.19.5-cp38-cp38-manylinux2010_x86_64.whl", hash = "sha256:a9d17f2be3b427fbb2bce61e596cf555d6f8a56c222bd2ca148baeeb5e5c783c"},
-    {file = "numpy-1.19.5-cp38-cp38-manylinux2014_aarch64.whl", hash = "sha256:99abf4f353c3d1a0c7a5f27699482c987cf663b1eac20db59b8c7b061eabd7fc"},
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+    {file = "regex-2021.11.10-cp38-cp38-musllinux_1_1_i686.whl", hash = "sha256:a955b747d620a50408b7fdf948e04359d6e762ff8a85f5775d907ceced715129"},
+    {file = "regex-2021.11.10-cp38-cp38-musllinux_1_1_ppc64le.whl", hash = "sha256:139a23d1f5d30db2cc6c7fd9c6d6497872a672db22c4ae1910be22d4f4b2068a"},
+    {file = "regex-2021.11.10-cp38-cp38-musllinux_1_1_s390x.whl", hash = "sha256:ca49e1ab99593438b204e00f3970e7a5f70d045267051dfa6b5f4304fcfa1dbf"},
+    {file = "regex-2021.11.10-cp38-cp38-musllinux_1_1_x86_64.whl", hash = "sha256:96fc32c16ea6d60d3ca7f63397bff5c75c5a562f7db6dec7d412f7c4d2e78ec0"},
     {file = "regex-2021.11.10-cp38-cp38-win32.whl", hash = "sha256:0617383e2fe465732af4509e61648b77cbe3aee68b6ac8c0b6fe934db90be5cc"},
     {file = "regex-2021.11.10-cp38-cp38-win_amd64.whl", hash = "sha256:a3feefd5e95871872673b08636f96b61ebef62971eab044f5124fb4dea39919d"},
     {file = "regex-2021.11.10-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:f7f325be2804246a75a4f45c72d4ce80d2443ab815063cdf70ee8fb2ca59ee1b"},
@@ -1058,6 +1056,11 @@ regex = [
     {file = "regex-2021.11.10-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:962b9a917dd7ceacbe5cd424556914cb0d636001e393b43dc886ba31d2a1e449"},
     {file = "regex-2021.11.10-cp39-cp39-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:fa8c626d6441e2d04b6ee703ef2d1e17608ad44c7cb75258c09dd42bacdfc64b"},
     {file = "regex-2021.11.10-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:3c5fb32cc6077abad3bbf0323067636d93307c9fa93e072771cf9a64d1c0f3ef"},
+    {file = "regex-2021.11.10-cp39-cp39-musllinux_1_1_aarch64.whl", hash = "sha256:cd410a1cbb2d297c67d8521759ab2ee3f1d66206d2e4328502a487589a2cb21b"},
+    {file = "regex-2021.11.10-cp39-cp39-musllinux_1_1_i686.whl", hash = "sha256:e6096b0688e6e14af6a1b10eaad86b4ff17935c49aa774eac7c95a57a4e8c296"},
+    {file = "regex-2021.11.10-cp39-cp39-musllinux_1_1_ppc64le.whl", hash = "sha256:529801a0d58809b60b3531ee804d3e3be4b412c94b5d267daa3de7fadef00f49"},
+    {file = "regex-2021.11.10-cp39-cp39-musllinux_1_1_s390x.whl", hash = "sha256:0f594b96fe2e0821d026365f72ac7b4f0b487487fb3d4aaf10dd9d97d88a9737"},
+    {file = "regex-2021.11.10-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:2409b5c9cef7054dde93a9803156b411b677affc84fca69e908b1cb2c540025d"},
     {file = "regex-2021.11.10-cp39-cp39-win32.whl", hash = "sha256:3b5df18db1fccd66de15aa59c41e4f853b5df7550723d26aa6cb7f40e5d9da5a"},
     {file = "regex-2021.11.10-cp39-cp39-win_amd64.whl", hash = "sha256:83ee89483672b11f8952b158640d0c0ff02dc43d9cb1b70c1564b49abe92ce29"},
     {file = "regex-2021.11.10.tar.gz", hash = "sha256:f341ee2df0999bfdf7a95e448075effe0db212a59387de1a70690e4acb03d4c6"},
@@ -1132,6 +1135,10 @@ watchdog = [
     {file = "watchdog-2.1.6-py3-none-win_ia64.whl", hash = "sha256:a0f1c7edf116a12f7245be06120b1852275f9506a7d90227648b250755a03923"},
     {file = "watchdog-2.1.6.tar.gz", hash = "sha256:a36e75df6c767cbf46f61a91c70b3ba71811dfa0aca4a324d9407a06a8b7a2e7"},
 ]
+wheel = [
+    {file = "wheel-0.38.4-py3-none-any.whl", hash = "sha256:b60533f3f5d530e971d6737ca6d58681ee434818fab630c83a734bb10c083ce8"},
+    {file = "wheel-0.38.4.tar.gz", hash = "sha256:965f5259b566725405b05e7cf774052044b1ed30119b5d586b2703aafe8719ac"},
+]
 zipp = [
     {file = "zipp-3.6.0-py3-none-any.whl", hash = "sha256:9fe5ea21568a0a70e50f273397638d39b03353731e6cbbb3fd8502a33fec40bc"},
     {file = "zipp-3.6.0.tar.gz", hash = "sha256:71c644c5369f4a6e07636f0aa966270449561fcea2e3d6747b8d23efaa9d7832"},
diff --git a/pyproject.toml b/pyproject.toml
index a99ea9ff..55925c99 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "titan-model"
-version = "3.2.0"
+version = "3.2.1"
 description = "TITAN Agent Based Model"
 license = "GPL-3.0-only"
 authors = ["Sam Bessey <sam_bessey@brown.edu>", "Mary McGrath <mary_mcgrath@brown.edu>"]

From 4fbc1d85f594e1bd5e2228733b00c786f2f35ca6 Mon Sep 17 00:00:00 2001
From: Sam Bessey <sam_bessey@brown.edu>
Date: Wed, 15 Feb 2023 14:01:36 -0500
Subject: [PATCH 3/7] try this

---
 poetry.lock    | 757 +++++++++++++++++++++++--------------------------
 pyproject.toml |   2 +-
 2 files changed, 363 insertions(+), 396 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 582d5777..dc826d37 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -20,7 +20,7 @@ wheel = ">=0.23.0,<1.0"
 
 [[package]]
 name = "atomicwrites"
-version = "1.4.0"
+version = "1.4.1"
 description = "Atomic file writes."
 category = "dev"
 optional = false
@@ -28,17 +28,19 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
 name = "attrs"
-version = "21.2.0"
+version = "22.2.0"
 description = "Classes Without Boilerplate"
 category = "dev"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = ">=3.6"
 
 [package.extras]
-dev = ["coverage[toml] (>=5.0.2)", "furo", "hypothesis", "mypy", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "six", "sphinx", "sphinx-notfound-page", "zope.interface"]
-docs = ["furo", "sphinx", "sphinx-notfound-page", "zope.interface"]
-tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "mypy", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "six", "zope.interface"]
-tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "mypy", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "six"]
+cov = ["attrs[tests]", "coverage-enable-subprocess", "coverage[toml] (>=5.3)"]
+dev = ["attrs[docs,tests]"]
+docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope.interface"]
+tests = ["attrs[tests-no-zope]", "zope.interface"]
+tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=0.971,<0.990)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+tests_no_zope = ["cloudpickle", "hypothesis", "mypy (>=0.971,<0.990)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
 
 [[package]]
 name = "black"
@@ -64,42 +66,34 @@ d = ["aiohttp (>=3.3.2)", "aiohttp-cors"]
 
 [[package]]
 name = "click"
-version = "8.0.3"
+version = "8.1.3"
 description = "Composable command line interface toolkit"
 category = "main"
 optional = true
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.dependencies]
 colorama = {version = "*", markers = "platform_system == \"Windows\""}
 
 [[package]]
 name = "colorama"
-version = "0.4.4"
+version = "0.4.6"
 description = "Cross-platform colored terminal text."
 category = "main"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
 
 [[package]]
 name = "coverage"
-version = "6.2"
+version = "7.1.0"
 description = "Code coverage measurement for Python"
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.extras]
 toml = ["tomli"]
 
-[[package]]
-name = "decorator"
-version = "4.4.2"
-description = "Decorators for Humans"
-category = "main"
-optional = false
-python-versions = ">=2.6, !=3.0.*, !=3.1.*"
-
 [[package]]
 name = "flake8"
 version = "3.9.2"
@@ -115,7 +109,7 @@ pyflakes = ">=2.3.0,<2.4.0"
 
 [[package]]
 name = "ghp-import"
-version = "2.0.2"
+version = "2.1.0"
 description = "Copy your docs directly to the gh-pages branch."
 category = "main"
 optional = true
@@ -129,35 +123,35 @@ dev = ["flake8", "markdown", "twine", "wheel"]
 
 [[package]]
 name = "importlib-metadata"
-version = "4.8.2"
+version = "6.0.0"
 description = "Read metadata from Python packages"
 category = "main"
 optional = true
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.dependencies]
 zipp = ">=0.5"
 
 [package.extras]
-docs = ["jaraco.packaging (>=8.2)", "rst.linker (>=1.9)", "sphinx"]
+docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
 perf = ["ipython"]
-testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pep517", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-flake8", "pytest-mypy", "pytest-perf (>=0.9.2)"]
+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)"]
 
 [[package]]
 name = "iniconfig"
-version = "1.1.1"
-description = "iniconfig: brain-dead simple config-ini parsing"
+version = "2.0.0"
+description = "brain-dead simple config-ini parsing"
 category = "dev"
 optional = false
-python-versions = "*"
+python-versions = ">=3.7"
 
 [[package]]
-name = "jinja2"
-version = "3.0.3"
+name = "Jinja2"
+version = "3.1.2"
 description = "A very fast and expressive template engine."
 category = "main"
 optional = true
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.dependencies]
 MarkupSafe = ">=2.0"
@@ -166,12 +160,12 @@ MarkupSafe = ">=2.0"
 i18n = ["Babel (>=2.7)"]
 
 [[package]]
-name = "markdown"
-version = "3.3.6"
+name = "Markdown"
+version = "3.4.1"
 description = "Python implementation of Markdown."
 category = "main"
 optional = true
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.dependencies]
 importlib-metadata = {version = ">=4.4", markers = "python_version < \"3.10\""}
@@ -180,12 +174,12 @@ importlib-metadata = {version = ">=4.4", markers = "python_version < \"3.10\""}
 testing = ["coverage", "pyyaml"]
 
 [[package]]
-name = "markupsafe"
-version = "2.0.1"
+name = "MarkupSafe"
+version = "2.1.2"
 description = "Safely add untrusted strings to HTML/XML markup."
 category = "main"
 optional = true
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [[package]]
 name = "mccabe"
@@ -205,7 +199,7 @@ python-versions = ">=3.6"
 
 [[package]]
 name = "mkdocs"
-version = "1.2.3"
+version = "1.3.0"
 description = "Project documentation with Markdown."
 category = "main"
 optional = true
@@ -214,8 +208,8 @@ python-versions = ">=3.6"
 [package.dependencies]
 click = ">=3.3"
 ghp-import = ">=1.0"
-importlib-metadata = ">=3.10"
-Jinja2 = ">=2.10.1"
+importlib-metadata = ">=4.3"
+Jinja2 = ">=2.10.2"
 Markdown = ">=3.2.1"
 mergedeep = ">=1.3.4"
 packaging = ">=20.5"
@@ -255,11 +249,11 @@ pymdown-extensions = ">=7.0"
 
 [[package]]
 name = "mkdocs-material-extensions"
-version = "1.0.3"
-description = "Extension pack for Python Markdown."
+version = "1.1.1"
+description = "Extension pack for Python Markdown and MkDocs Material."
 category = "main"
 optional = true
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [[package]]
 name = "mkdocstrings"
@@ -296,11 +290,11 @@ dmypy = ["psutil (>=4.0)"]
 
 [[package]]
 name = "mypy-extensions"
-version = "0.4.3"
+version = "0.4.4"
 description = "Experimental type system extensions for programs checked with the mypy typechecker."
 category = "main"
 optional = true
-python-versions = "*"
+python-versions = ">=2.7"
 
 [[package]]
 name = "nanoid"
@@ -312,35 +306,26 @@ python-versions = "*"
 
 [[package]]
 name = "networkx"
-version = "2.5.1"
+version = "2.8.8"
 description = "Python package for creating and manipulating graphs and networks"
 category = "main"
 optional = false
-python-versions = ">=3.6"
-
-[package.dependencies]
-decorator = ">=4.3,<5"
+python-versions = ">=3.8"
 
 [package.extras]
-all = ["lxml", "matplotlib", "numpy", "pandas", "pydot", "pygraphviz", "pytest", "pyyaml", "scipy"]
-gdal = ["gdal"]
-lxml = ["lxml"]
-matplotlib = ["matplotlib"]
-numpy = ["numpy"]
-pandas = ["pandas"]
-pydot = ["pydot"]
-pygraphviz = ["pygraphviz"]
-pytest = ["pytest"]
-pyyaml = ["pyyaml"]
-scipy = ["scipy"]
+default = ["matplotlib (>=3.4)", "numpy (>=1.19)", "pandas (>=1.3)", "scipy (>=1.8)"]
+developer = ["mypy (>=0.982)", "pre-commit (>=2.20)"]
+doc = ["nb2plots (>=0.6)", "numpydoc (>=1.5)", "pillow (>=9.2)", "pydata-sphinx-theme (>=0.11)", "sphinx (>=5.2)", "sphinx-gallery (>=0.11)", "texext (>=0.6.6)"]
+extra = ["lxml (>=4.6)", "pydot (>=1.4.2)", "pygraphviz (>=1.9)", "sympy (>=1.10)"]
+test = ["codecov (>=2.1)", "pytest (>=7.2)", "pytest-cov (>=4.0)"]
 
 [[package]]
 name = "numpy"
-version = "1.21.0"
-description = "NumPy is the fundamental package for array computing with Python."
+version = "1.24.2"
+description = "Fundamental package for array computing in Python"
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 
 [[package]]
 name = "oyaml"
@@ -355,14 +340,11 @@ pyyaml = "*"
 
 [[package]]
 name = "packaging"
-version = "21.3"
+version = "23.0"
 description = "Core utilities for Python packages"
 category = "main"
 optional = false
-python-versions = ">=3.6"
-
-[package.dependencies]
-pyparsing = ">=2.0.2,<3.0.5 || >3.0.5"
+python-versions = ">=3.7"
 
 [[package]]
 name = "paraml"
@@ -377,11 +359,11 @@ oyaml = ">=1.0,<2.0"
 
 [[package]]
 name = "pathspec"
-version = "0.9.0"
+version = "0.11.0"
 description = "Utility library for gitignore style pattern matching of file paths."
 category = "main"
 optional = true
-python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
+python-versions = ">=3.7"
 
 [[package]]
 name = "pluggy"
@@ -420,12 +402,15 @@ optional = true
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
-name = "pygments"
-version = "2.10.0"
+name = "Pygments"
+version = "2.14.0"
 description = "Pygments is a syntax highlighting package written in Python."
 category = "main"
 optional = true
-python-versions = ">=3.5"
+python-versions = ">=3.6"
+
+[package.extras]
+plugins = ["importlib-metadata"]
 
 [[package]]
 name = "pymdown-extensions"
@@ -438,17 +423,6 @@ python-versions = ">=3.6"
 [package.dependencies]
 Markdown = ">=3.2"
 
-[[package]]
-name = "pyparsing"
-version = "3.0.6"
-description = "Python parsing module"
-category = "main"
-optional = false
-python-versions = ">=3.6"
-
-[package.extras]
-diagrams = ["jinja2", "railroad-diagrams"]
-
 [[package]]
 name = "pytest"
 version = "6.2.5"
@@ -499,11 +473,11 @@ six = ">=1.5"
 
 [[package]]
 name = "pytkdocs"
-version = "0.11.0"
+version = "0.11.1"
 description = "Load Python objects documentation."
 category = "main"
 optional = true
-python-versions = ">=3.6,<4.0"
+python-versions = ">=3.6.1,<4.0.0"
 
 [package.dependencies]
 astunparse = {version = ">=1.6.3,<2.0.0", markers = "python_version < \"3.9\""}
@@ -512,7 +486,7 @@ astunparse = {version = ">=1.6.3,<2.0.0", markers = "python_version < \"3.9\""}
 numpy-style = ["docstring_parser (>=0.7.3,<0.8.0)"]
 
 [[package]]
-name = "pyyaml"
+name = "PyYAML"
 version = "6.0"
 description = "YAML parser and emitter for Python"
 category = "main"
@@ -520,7 +494,7 @@ optional = false
 python-versions = ">=3.6"
 
 [[package]]
-name = "pyyaml-env-tag"
+name = "pyyaml_env_tag"
 version = "0.1"
 description = "A custom YAML tag for referencing environment variables in YAML files. "
 category = "main"
@@ -532,11 +506,11 @@ pyyaml = "*"
 
 [[package]]
 name = "regex"
-version = "2021.11.10"
+version = "2022.10.31"
 description = "Alternative regular expression module, to replace re."
 category = "main"
 optional = true
-python-versions = "*"
+python-versions = ">=3.6"
 
 [[package]]
 name = "six"
@@ -564,15 +538,15 @@ python-versions = "*"
 
 [[package]]
 name = "typing-extensions"
-version = "3.10.0.2"
-description = "Backported and Experimental Type Hints for Python 3.5+"
+version = "4.5.0"
+description = "Backported and Experimental Type Hints for Python 3.7+"
 category = "main"
 optional = true
-python-versions = "*"
+python-versions = ">=3.7"
 
 [[package]]
 name = "watchdog"
-version = "2.1.6"
+version = "2.2.1"
 description = "Filesystem events monitoring"
 category = "main"
 optional = true
@@ -594,15 +568,15 @@ test = ["pytest (>=3.0.0)"]
 
 [[package]]
 name = "zipp"
-version = "3.6.0"
+version = "3.13.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 category = "main"
 optional = true
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.extras]
-docs = ["jaraco.packaging (>=8.2)", "rst.linker (>=1.9)", "sphinx"]
-testing = ["func-timeout", "jaraco.itertools", "pytest (>=4.6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-flake8", "pytest-mypy"]
+docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["flake8 (<5)", "func-timeout", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
 
 [extras]
 docs = ["mkdocs", "mkdocs-material", "mkdocstrings"]
@@ -611,7 +585,7 @@ linting = ["black", "flake8", "mypy"]
 [metadata]
 lock-version = "1.1"
 python-versions = "^3.8"
-content-hash = "350123d2653219fd539911adc4798b495d9ee7600467b61be8958a079e9e4b11"
+content-hash = "9fbdf1e60fb26c936e0440b59ac831472333b38368f14d14359618a7c6c092ce"
 
 [metadata.files]
 appdirs = [
@@ -623,171 +597,151 @@ astunparse = [
     {file = "astunparse-1.6.3.tar.gz", hash = "sha256:5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872"},
 ]
 atomicwrites = [
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-    {file = "watchdog-2.1.6-py3-none-win_amd64.whl", hash = "sha256:bd9ba4f332cf57b2c1f698be0728c020399ef3040577cde2939f2e045b39c1e5"},
-    {file = "watchdog-2.1.6-py3-none-win_ia64.whl", hash = "sha256:a0f1c7edf116a12f7245be06120b1852275f9506a7d90227648b250755a03923"},
-    {file = "watchdog-2.1.6.tar.gz", hash = "sha256:a36e75df6c767cbf46f61a91c70b3ba71811dfa0aca4a324d9407a06a8b7a2e7"},
+    {file = "watchdog-2.2.1-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:a09483249d25cbdb4c268e020cb861c51baab2d1affd9a6affc68ffe6a231260"},
+    {file = "watchdog-2.2.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:5100eae58133355d3ca6c1083a33b81355c4f452afa474c2633bd2fbbba398b3"},
+    {file = "watchdog-2.2.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:e618a4863726bc7a3c64f95c218437f3349fb9d909eb9ea3a1ed3b567417c661"},
+    {file = "watchdog-2.2.1-cp311-cp311-macosx_10_9_universal2.whl", hash = "sha256:102a60093090fc3ff76c983367b19849b7cc24ec414a43c0333680106e62aae1"},
+    {file = "watchdog-2.2.1-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:748ca797ff59962e83cc8e4b233f87113f3cf247c23e6be58b8a2885c7337aa3"},
+    {file = "watchdog-2.2.1-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:6ccd8d84b9490a82b51b230740468116b8205822ea5fdc700a553d92661253a3"},
+    {file = "watchdog-2.2.1-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:6e01d699cd260d59b84da6bda019dce0a3353e3fcc774408ae767fe88ee096b7"},
+    {file = "watchdog-2.2.1-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:8586d98c494690482c963ffb24c49bf9c8c2fe0589cec4dc2f753b78d1ec301d"},
+    {file = "watchdog-2.2.1-cp38-cp38-macosx_10_9_universal2.whl", hash = "sha256:adaf2ece15f3afa33a6b45f76b333a7da9256e1360003032524d61bdb4c422ae"},
+    {file = "watchdog-2.2.1-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:83a7cead445008e880dbde833cb9e5cc7b9a0958edb697a96b936621975f15b9"},
+    {file = "watchdog-2.2.1-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:f8ac23ff2c2df4471a61af6490f847633024e5aa120567e08d07af5718c9d092"},
+    {file = "watchdog-2.2.1-cp39-cp39-macosx_10_9_universal2.whl", hash = "sha256:d0f29fd9f3f149a5277929de33b4f121a04cf84bb494634707cfa8ea8ae106a8"},
+    {file = "watchdog-2.2.1-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:967636031fa4c4955f0f3f22da3c5c418aa65d50908d31b73b3b3ffd66d60640"},
+    {file = "watchdog-2.2.1-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:96cbeb494e6cbe3ae6aacc430e678ce4b4dd3ae5125035f72b6eb4e5e9eb4f4e"},
+    {file = "watchdog-2.2.1-pp37-pypy37_pp73-macosx_10_9_x86_64.whl", hash = "sha256:61fdb8e9c57baf625e27e1420e7ca17f7d2023929cd0065eb79c83da1dfbeacd"},
+    {file = "watchdog-2.2.1-pp38-pypy38_pp73-macosx_10_9_x86_64.whl", hash = "sha256:4cb5ecc332112017fbdb19ede78d92e29a8165c46b68a0b8ccbd0a154f196d5e"},
+    {file = "watchdog-2.2.1-pp39-pypy39_pp73-macosx_10_9_x86_64.whl", hash = "sha256:a480d122740debf0afac4ddd583c6c0bb519c24f817b42ed6f850e2f6f9d64a8"},
+    {file = "watchdog-2.2.1-py3-none-manylinux2014_aarch64.whl", hash = "sha256:978a1aed55de0b807913b7482d09943b23a2d634040b112bdf31811a422f6344"},
+    {file = "watchdog-2.2.1-py3-none-manylinux2014_armv7l.whl", hash = "sha256:8c28c23972ec9c524967895ccb1954bc6f6d4a557d36e681a36e84368660c4ce"},
+    {file = "watchdog-2.2.1-py3-none-manylinux2014_i686.whl", hash = "sha256:c27d8c1535fd4474e40a4b5e01f4ba6720bac58e6751c667895cbc5c8a7af33c"},
+    {file = "watchdog-2.2.1-py3-none-manylinux2014_ppc64.whl", hash = "sha256:d6b87477752bd86ac5392ecb9eeed92b416898c30bd40c7e2dd03c3146105646"},
+    {file = "watchdog-2.2.1-py3-none-manylinux2014_ppc64le.whl", hash = "sha256:cece1aa596027ff56369f0b50a9de209920e1df9ac6d02c7f9e5d8162eb4f02b"},
+    {file = "watchdog-2.2.1-py3-none-manylinux2014_s390x.whl", hash = "sha256:8b5cde14e5c72b2df5d074774bdff69e9b55da77e102a91f36ef26ca35f9819c"},
+    {file = "watchdog-2.2.1-py3-none-manylinux2014_x86_64.whl", hash = "sha256:e038be858425c4f621900b8ff1a3a1330d9edcfeaa1c0468aeb7e330fb87693e"},
+    {file = "watchdog-2.2.1-py3-none-win32.whl", hash = "sha256:bc43c1b24d2f86b6e1cc15f68635a959388219426109233e606517ff7d0a5a73"},
+    {file = "watchdog-2.2.1-py3-none-win_amd64.whl", hash = "sha256:17f1708f7410af92ddf591e94ae71a27a13974559e72f7e9fde3ec174b26ba2e"},
+    {file = "watchdog-2.2.1-py3-none-win_ia64.whl", hash = "sha256:195ab1d9d611a4c1e5311cbf42273bc541e18ea8c32712f2fb703cfc6ff006f9"},
+    {file = "watchdog-2.2.1.tar.gz", hash = "sha256:cdcc23c9528601a8a293eb4369cbd14f6b4f34f07ae8769421252e9c22718b6f"},
 ]
 wheel = [
     {file = "wheel-0.38.4-py3-none-any.whl", hash = "sha256:b60533f3f5d530e971d6737ca6d58681ee434818fab630c83a734bb10c083ce8"},
     {file = "wheel-0.38.4.tar.gz", hash = "sha256:965f5259b566725405b05e7cf774052044b1ed30119b5d586b2703aafe8719ac"},
 ]
 zipp = [
-    {file = "zipp-3.6.0-py3-none-any.whl", hash = "sha256:9fe5ea21568a0a70e50f273397638d39b03353731e6cbbb3fd8502a33fec40bc"},
-    {file = "zipp-3.6.0.tar.gz", hash = "sha256:71c644c5369f4a6e07636f0aa966270449561fcea2e3d6747b8d23efaa9d7832"},
+    {file = "zipp-3.13.0-py3-none-any.whl", hash = "sha256:e8b2a36ea17df80ffe9e2c4fda3f693c3dad6df1697d3cd3af232db680950b0b"},
+    {file = "zipp-3.13.0.tar.gz", hash = "sha256:23f70e964bc11a34cef175bc90ba2914e1e4545ea1e3e2f67c079671883f9cb6"},
 ]
diff --git a/pyproject.toml b/pyproject.toml
index 55925c99..4d9244c6 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -16,7 +16,7 @@ python = "^3.8"
 paraml= "^0.1"
 networkx = "^2.4"
 nanoid = "^2.0"
-numpy = "^1.21"
+numpy = "^1.23"
 black = {version = "^20.8b1", optional = true}
 flake8 = {version = "^3.8", optional = true}
 mypy = {version = "^0.812", optional = true}

From 7ee569821aac065ac5849598d976c6fd1bfca6d6 Mon Sep 17 00:00:00 2001
From: Sam Bessey <sam_bessey@brown.edu>
Date: Wed, 15 Feb 2023 14:07:10 -0500
Subject: [PATCH 4/7] update black

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 4d9244c6..71681d6c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,7 +17,7 @@ paraml= "^0.1"
 networkx = "^2.4"
 nanoid = "^2.0"
 numpy = "^1.23"
-black = {version = "^20.8b1", optional = true}
+black = {version = "^22.3.0", optional = true}
 flake8 = {version = "^3.8", optional = true}
 mypy = {version = "^0.812", optional = true}
 mkdocs = {version = "^1.1", optional = true}

From 080a8d47f774d161bf12eed8ca5d2281cf1e5c9b Mon Sep 17 00:00:00 2001
From: Sam Bessey <sam_bessey@brown.edu>
Date: Wed, 15 Feb 2023 14:08:45 -0500
Subject: [PATCH 5/7] update black again

---
 poetry.lock    | 189 +++++++++++++++++--------------------------------
 pyproject.toml |   2 +-
 2 files changed, 67 insertions(+), 124 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index dc826d37..8372f4d5 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,11 +1,3 @@
-[[package]]
-name = "appdirs"
-version = "1.4.4"
-description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
-category = "main"
-optional = true
-python-versions = "*"
-
 [[package]]
 name = "astunparse"
 version = "1.6.3"
@@ -44,25 +36,26 @@ tests_no_zope = ["cloudpickle", "hypothesis", "mypy (>=0.971,<0.990)", "pympler"
 
 [[package]]
 name = "black"
-version = "20.8b1"
+version = "23.1.0"
 description = "The uncompromising code formatter."
 category = "main"
 optional = true
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.dependencies]
-appdirs = "*"
-click = ">=7.1.2"
+click = ">=8.0.0"
 mypy-extensions = ">=0.4.3"
-pathspec = ">=0.6,<1"
-regex = ">=2020.1.8"
-toml = ">=0.10.1"
-typed-ast = ">=1.4.0"
-typing-extensions = ">=3.7.4"
+packaging = ">=22.0"
+pathspec = ">=0.9.0"
+platformdirs = ">=2"
+tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
+typing-extensions = {version = ">=3.10.0.0", markers = "python_version < \"3.10\""}
 
 [package.extras]
 colorama = ["colorama (>=0.4.3)"]
-d = ["aiohttp (>=3.3.2)", "aiohttp-cors"]
+d = ["aiohttp (>=3.7.4)"]
+jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"]
+uvloop = ["uvloop (>=0.15.2)"]
 
 [[package]]
 name = "click"
@@ -365,6 +358,18 @@ category = "main"
 optional = true
 python-versions = ">=3.7"
 
+[[package]]
+name = "platformdirs"
+version = "3.0.0"
+description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+category = "main"
+optional = true
+python-versions = ">=3.7"
+
+[package.extras]
+docs = ["furo (>=2022.12.7)", "proselint (>=0.13)", "sphinx (>=6.1.3)", "sphinx-autodoc-typehints (>=1.22,!=1.23.4)"]
+test = ["appdirs (==1.4.4)", "covdefaults (>=2.2.2)", "pytest (>=7.2.1)", "pytest-cov (>=4)", "pytest-mock (>=3.10)"]
+
 [[package]]
 name = "pluggy"
 version = "1.0.0"
@@ -504,14 +509,6 @@ python-versions = ">=3.6"
 [package.dependencies]
 pyyaml = "*"
 
-[[package]]
-name = "regex"
-version = "2022.10.31"
-description = "Alternative regular expression module, to replace re."
-category = "main"
-optional = true
-python-versions = ">=3.6"
-
 [[package]]
 name = "six"
 version = "1.16.0"
@@ -524,10 +521,18 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
 name = "toml"
 version = "0.10.2"
 description = "Python Library for Tom's Obvious, Minimal Language"
-category = "main"
+category = "dev"
 optional = false
 python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
 
+[[package]]
+name = "tomli"
+version = "2.0.1"
+description = "A lil' TOML parser"
+category = "main"
+optional = true
+python-versions = ">=3.7"
+
 [[package]]
 name = "typed-ast"
 version = "1.4.3"
@@ -585,13 +590,9 @@ linting = ["black", "flake8", "mypy"]
 [metadata]
 lock-version = "1.1"
 python-versions = "^3.8"
-content-hash = "9fbdf1e60fb26c936e0440b59ac831472333b38368f14d14359618a7c6c092ce"
+content-hash = "f785e7b02acf01c43347ba82b032b9fb5504752a1e6decb58c0dfea95a9cb00b"
 
 [metadata.files]
-appdirs = [
-    {file = "appdirs-1.4.4-py2.py3-none-any.whl", hash = "sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128"},
-    {file = "appdirs-1.4.4.tar.gz", hash = "sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41"},
-]
 astunparse = [
     {file = "astunparse-1.6.3-py2.py3-none-any.whl", hash = "sha256:c2652417f2c8b5bb325c885ae329bdf3f86424075c4fd1a128674bc6fba4b8e8"},
     {file = "astunparse-1.6.3.tar.gz", hash = "sha256:5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872"},
@@ -604,7 +605,31 @@ attrs = [
     {file = "attrs-22.2.0.tar.gz", hash = "sha256:c9227bfc2f01993c03f68db37d1d15c9690188323c067c641f1a35ca58185f99"},
 ]
 black = [
-    {file = "black-20.8b1.tar.gz", hash = "sha256:1c02557aa099101b9d21496f8a914e9ed2222ef70336404eeeac8edba836fbea"},
+    {file = "black-23.1.0-cp310-cp310-macosx_10_16_arm64.whl", hash = "sha256:b6a92a41ee34b883b359998f0c8e6eb8e99803aa8bf3123bf2b2e6fec505a221"},
+    {file = "black-23.1.0-cp310-cp310-macosx_10_16_universal2.whl", hash = "sha256:57c18c5165c1dbe291d5306e53fb3988122890e57bd9b3dcb75f967f13411a26"},
+    {file = "black-23.1.0-cp310-cp310-macosx_10_16_x86_64.whl", hash = "sha256:9880d7d419bb7e709b37e28deb5e68a49227713b623c72b2b931028ea65f619b"},
+    {file = "black-23.1.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:e6663f91b6feca5d06f2ccd49a10f254f9298cc1f7f49c46e498a0771b507104"},
+    {file = "black-23.1.0-cp310-cp310-win_amd64.whl", hash = "sha256:9afd3f493666a0cd8f8df9a0200c6359ac53940cbde049dcb1a7eb6ee2dd7074"},
+    {file = "black-23.1.0-cp311-cp311-macosx_10_16_arm64.whl", hash = "sha256:bfffba28dc52a58f04492181392ee380e95262af14ee01d4bc7bb1b1c6ca8d27"},
+    {file = "black-23.1.0-cp311-cp311-macosx_10_16_universal2.whl", hash = "sha256:c1c476bc7b7d021321e7d93dc2cbd78ce103b84d5a4cf97ed535fbc0d6660648"},
+    {file = "black-23.1.0-cp311-cp311-macosx_10_16_x86_64.whl", hash = "sha256:382998821f58e5c8238d3166c492139573325287820963d2f7de4d518bd76958"},
+    {file = "black-23.1.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:2bf649fda611c8550ca9d7592b69f0637218c2369b7744694c5e4902873b2f3a"},
+    {file = "black-23.1.0-cp311-cp311-win_amd64.whl", hash = "sha256:121ca7f10b4a01fd99951234abdbd97728e1240be89fde18480ffac16503d481"},
+    {file = "black-23.1.0-cp37-cp37m-macosx_10_16_x86_64.whl", hash = "sha256:a8471939da5e824b891b25751955be52ee7f8a30a916d570a5ba8e0f2eb2ecad"},
+    {file = "black-23.1.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:8178318cb74f98bc571eef19068f6ab5613b3e59d4f47771582f04e175570ed8"},
+    {file = "black-23.1.0-cp37-cp37m-win_amd64.whl", hash = "sha256:a436e7881d33acaf2536c46a454bb964a50eff59b21b51c6ccf5a40601fbef24"},
+    {file = "black-23.1.0-cp38-cp38-macosx_10_16_arm64.whl", hash = "sha256:a59db0a2094d2259c554676403fa2fac3473ccf1354c1c63eccf7ae65aac8ab6"},
+    {file = "black-23.1.0-cp38-cp38-macosx_10_16_universal2.whl", hash = "sha256:0052dba51dec07ed029ed61b18183942043e00008ec65d5028814afaab9a22fd"},
+    {file = "black-23.1.0-cp38-cp38-macosx_10_16_x86_64.whl", hash = "sha256:49f7b39e30f326a34b5c9a4213213a6b221d7ae9d58ec70df1c4a307cf2a1580"},
+    {file = "black-23.1.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:162e37d49e93bd6eb6f1afc3e17a3d23a823042530c37c3c42eeeaf026f38468"},
+    {file = "black-23.1.0-cp38-cp38-win_amd64.whl", hash = "sha256:8b70eb40a78dfac24842458476135f9b99ab952dd3f2dab738c1881a9b38b753"},
+    {file = "black-23.1.0-cp39-cp39-macosx_10_16_arm64.whl", hash = "sha256:a29650759a6a0944e7cca036674655c2f0f63806ddecc45ed40b7b8aa314b651"},
+    {file = "black-23.1.0-cp39-cp39-macosx_10_16_universal2.whl", hash = "sha256:bb460c8561c8c1bec7824ecbc3ce085eb50005883a6203dcfb0122e95797ee06"},
+    {file = "black-23.1.0-cp39-cp39-macosx_10_16_x86_64.whl", hash = "sha256:c91dfc2c2a4e50df0026f88d2215e166616e0c80e86004d0003ece0488db2739"},
+    {file = "black-23.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:2a951cc83ab535d248c89f300eccbd625e80ab880fbcfb5ac8afb5f01a258ac9"},
+    {file = "black-23.1.0-cp39-cp39-win_amd64.whl", hash = "sha256:0680d4380db3719ebcfb2613f34e86c8e6d15ffeabcf8ec59355c5e7b85bb555"},
+    {file = "black-23.1.0-py3-none-any.whl", hash = "sha256:7a0f701d314cfa0896b9001df70a530eb2472babb76086344e688829efd97d32"},
+    {file = "black-23.1.0.tar.gz", hash = "sha256:b0bd97bea8903f5a2ba7219257a44e3f1f9d00073d6cc1add68f0beec69692ac"},
 ]
 click = [
     {file = "click-8.1.3-py3-none-any.whl", hash = "sha256:bb4d8133cb15a609f44e8213d9b391b0809795062913b383c62be0ee95b1db48"},
@@ -852,6 +877,10 @@ pathspec = [
     {file = "pathspec-0.11.0-py3-none-any.whl", hash = "sha256:3a66eb970cbac598f9e5ccb5b2cf58930cd8e3ed86d393d541eaf2d8b1705229"},
     {file = "pathspec-0.11.0.tar.gz", hash = "sha256:64d338d4e0914e91c1792321e6907b5a593f1ab1851de7fc269557a21b30ebbc"},
 ]
+platformdirs = [
+    {file = "platformdirs-3.0.0-py3-none-any.whl", hash = "sha256:b1d5eb14f221506f50d6604a561f4c5786d9e80355219694a1b244bcd96f4567"},
+    {file = "platformdirs-3.0.0.tar.gz", hash = "sha256:8a1228abb1ef82d788f74139988b137e78692984ec7b08eaa6c65f1723af28f9"},
+]
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     {file = "six-1.16.0-py2.py3-none-any.whl", hash = "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"},
     {file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"},
@@ -1036,6 +975,10 @@ toml = [
     {file = "toml-0.10.2-py2.py3-none-any.whl", hash = "sha256:806143ae5bfb6a3c6e736a764057db0e6a0e05e338b5630894a5f779cabb4f9b"},
     {file = "toml-0.10.2.tar.gz", hash = "sha256:b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f"},
 ]
+tomli = [
+    {file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"},
+    {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
+]
 typed-ast = [
     {file = "typed_ast-1.4.3-cp35-cp35m-manylinux1_i686.whl", hash = "sha256:2068531575a125b87a41802130fa7e29f26c09a2833fea68d9a40cf33902eba6"},
     {file = "typed_ast-1.4.3-cp35-cp35m-manylinux1_x86_64.whl", hash = "sha256:c907f561b1e83e93fad565bac5ba9c22d96a54e7ea0267c708bffe863cbe4075"},
diff --git a/pyproject.toml b/pyproject.toml
index 71681d6c..0ccfce32 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,7 +17,7 @@ paraml= "^0.1"
 networkx = "^2.4"
 nanoid = "^2.0"
 numpy = "^1.23"
-black = {version = "^22.3.0", optional = true}
+black = {version = "^23.1.0", optional = true}
 flake8 = {version = "^3.8", optional = true}
 mypy = {version = "^0.812", optional = true}
 mkdocs = {version = "^1.1", optional = true}

From a27b361c9d05aec981e6d8e86096f97bcf327d49 Mon Sep 17 00:00:00 2001
From: Sam Bessey <sam_bessey@brown.edu>
Date: Wed, 15 Feb 2023 14:17:40 -0500
Subject: [PATCH 6/7] format with black

---
 poetry.lock                            | 112 +++++++++----------------
 pyproject.toml                         |   2 +-
 tests/conftest.py                      |   1 +
 tests/exposures/knowledge_test.py      |   1 -
 tests/integration_test.py              |   1 +
 titan/exposures/base_exposure.py       |   1 -
 titan/exposures/hiv.py                 |   1 -
 titan/exposures/knowledge.py           |   1 -
 titan/exposures/monkeypox.py           |   1 -
 titan/features/external_exposure.py    |   1 -
 titan/features/high_risk.py            |   2 -
 titan/features/incar.py                |   1 -
 titan/features/partner_tracing.py      |   1 -
 titan/features/prep.py                 |   1 -
 titan/features/random_trial.py         |   1 -
 titan/features/syringe_services.py     |   1 -
 titan/features/vaccine.py              |   1 -
 titan/interactions/base_interaction.py |   1 -
 titan/interactions/injection.py        |   1 -
 titan/interactions/pca.py              |   1 -
 titan/interactions/sex.py              |   1 -
 titan/location.py                      |   1 -
 titan/output.py                        |   2 +-
 titan/population.py                    |   1 -
 titan/utils.py                         |   2 +-
 25 files changed, 45 insertions(+), 95 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 8372f4d5..4afcce2c 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -267,27 +267,30 @@ pytkdocs = ">=0.2.0,<0.12.0"
 
 [[package]]
 name = "mypy"
-version = "0.812"
+version = "1.0.0"
 description = "Optional static typing for Python"
 category = "main"
 optional = true
-python-versions = ">=3.5"
+python-versions = ">=3.7"
 
 [package.dependencies]
-mypy-extensions = ">=0.4.3,<0.5.0"
-typed-ast = ">=1.4.0,<1.5.0"
-typing-extensions = ">=3.7.4"
+mypy-extensions = ">=0.4.3"
+tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
+typing-extensions = ">=3.10"
 
 [package.extras]
 dmypy = ["psutil (>=4.0)"]
+install-types = ["pip"]
+python2 = ["typed-ast (>=1.4.0,<2)"]
+reports = ["lxml"]
 
 [[package]]
 name = "mypy-extensions"
-version = "0.4.4"
-description = "Experimental type system extensions for programs checked with the mypy typechecker."
+version = "1.0.0"
+description = "Type system extensions for programs checked with the mypy type checker."
 category = "main"
 optional = true
-python-versions = ">=2.7"
+python-versions = ">=3.5"
 
 [[package]]
 name = "nanoid"
@@ -533,14 +536,6 @@ category = "main"
 optional = true
 python-versions = ">=3.7"
 
-[[package]]
-name = "typed-ast"
-version = "1.4.3"
-description = "a fork of Python 2 and 3 ast modules with type comment support"
-category = "main"
-optional = true
-python-versions = "*"
-
 [[package]]
 name = "typing-extensions"
 version = "4.5.0"
@@ -590,7 +585,7 @@ linting = ["black", "flake8", "mypy"]
 [metadata]
 lock-version = "1.1"
 python-versions = "^3.8"
-content-hash = "f785e7b02acf01c43347ba82b032b9fb5504752a1e6decb58c0dfea95a9cb00b"
+content-hash = "aa9c0440f65f4b3ac2f56f39e586442e2e54098a702b1087630a0831a03d5a78"
 
 [metadata.files]
 astunparse = [
@@ -797,31 +792,36 @@ mkdocstrings = [
     {file = "mkdocstrings-0.15.2.tar.gz", hash = "sha256:c2fee9a3a644647c06eb2044fdfede1073adfd1a55bf6752005d3db10705fe73"},
 ]
 mypy = [
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-    {file = "mypy-0.812-cp35-cp35m-manylinux1_x86_64.whl", hash = "sha256:28fb5479c494b1bab244620685e2eb3c3f988d71fd5d64cc753195e8ed53df7c"},
-    {file = "mypy-0.812-cp35-cp35m-manylinux2010_x86_64.whl", hash = "sha256:9743c91088d396c1a5a3c9978354b61b0382b4e3c440ce83cf77994a43e8c521"},
-    {file = "mypy-0.812-cp35-cp35m-win_amd64.whl", hash = "sha256:d7da2e1d5f558c37d6e8c1246f1aec1e7349e4913d8fb3cb289a35de573fe2eb"},
-    {file = "mypy-0.812-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:4eec37370483331d13514c3f55f446fc5248d6373e7029a29ecb7b7494851e7a"},
-    {file = "mypy-0.812-cp36-cp36m-manylinux1_x86_64.whl", hash = "sha256:d65cc1df038ef55a99e617431f0553cd77763869eebdf9042403e16089fe746c"},
-    {file = "mypy-0.812-cp36-cp36m-manylinux2010_x86_64.whl", hash = "sha256:61a3d5b97955422964be6b3baf05ff2ce7f26f52c85dd88db11d5e03e146a3a6"},
-    {file = "mypy-0.812-cp36-cp36m-win_amd64.whl", hash = "sha256:25adde9b862f8f9aac9d2d11971f226bd4c8fbaa89fb76bdadb267ef22d10064"},
-    {file = "mypy-0.812-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:552a815579aa1e995f39fd05dde6cd378e191b063f031f2acfe73ce9fb7f9e56"},
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-    {file = "mypy-0.812-cp38-cp38-manylinux1_x86_64.whl", hash = "sha256:674e822aa665b9fd75130c6c5f5ed9564a38c6cea6a6432ce47eafb68ee578c5"},
-    {file = "mypy-0.812-cp38-cp38-manylinux2010_x86_64.whl", hash = "sha256:abf7e0c3cf117c44d9285cc6128856106183938c68fd4944763003decdcfeb66"},
-    {file = "mypy-0.812-cp38-cp38-win_amd64.whl", hash = "sha256:0d0a87c0e7e3a9becdfbe936c981d32e5ee0ccda3e0f07e1ef2c3d1a817cf73e"},
-    {file = "mypy-0.812-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:7ce3175801d0ae5fdfa79b4f0cfed08807af4d075b402b7e294e6aa72af9aa2a"},
-    {file = "mypy-0.812-cp39-cp39-manylinux1_x86_64.whl", hash = "sha256:b09669bcda124e83708f34a94606e01b614fa71931d356c1f1a5297ba11f110a"},
-    {file = "mypy-0.812-cp39-cp39-manylinux2010_x86_64.whl", hash = "sha256:33f159443db0829d16f0a8d83d94df3109bb6dd801975fe86bacb9bf71628e97"},
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-    {file = "mypy-0.812-py3-none-any.whl", hash = "sha256:2f9b3407c58347a452fc0736861593e105139b905cca7d097e413453a1d650b4"},
-    {file = "mypy-0.812.tar.gz", hash = "sha256:cd07039aa5df222037005b08fbbfd69b3ab0b0bd7a07d7906de75ae52c4e3119"},
+    {file = "mypy-1.0.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:e0626db16705ab9f7fa6c249c017c887baf20738ce7f9129da162bb3075fc1af"},
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+    {file = "mypy-1.0.0-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:0ab090d9240d6b4e99e1fa998c2d0aa5b29fc0fb06bd30e7ad6183c95fa07593"},
+    {file = "mypy-1.0.0-cp310-cp310-win_amd64.whl", hash = "sha256:7cc2c01dfc5a3cbddfa6c13f530ef3b95292f926329929001d45e124342cd6b7"},
+    {file = "mypy-1.0.0-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:14d776869a3e6c89c17eb943100f7868f677703c8a4e00b3803918f86aafbc52"},
+    {file = "mypy-1.0.0-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:bb2782a036d9eb6b5a6efcdda0986774bf798beef86a62da86cb73e2a10b423d"},
+    {file = "mypy-1.0.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:5cfca124f0ac6707747544c127880893ad72a656e136adc935c8600740b21ff5"},
+    {file = "mypy-1.0.0-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:8845125d0b7c57838a10fd8925b0f5f709d0e08568ce587cc862aacce453e3dd"},
+    {file = "mypy-1.0.0-cp311-cp311-win_amd64.whl", hash = "sha256:01b1b9e1ed40544ef486fa8ac022232ccc57109f379611633ede8e71630d07d2"},
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+    {file = "mypy-1.0.0-cp38-cp38-win_amd64.whl", hash = "sha256:50979d5efff8d4135d9db293c6cb2c42260e70fb010cbc697b1311a4d7a39ddb"},
+    {file = "mypy-1.0.0-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:3ae4c7a99e5153496243146a3baf33b9beff714464ca386b5f62daad601d87af"},
+    {file = "mypy-1.0.0-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:5e398652d005a198a7f3c132426b33c6b85d98aa7dc852137a2a3be8890c4072"},
+    {file = "mypy-1.0.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:be78077064d016bc1b639c2cbcc5be945b47b4261a4f4b7d8923f6c69c5c9457"},
+    {file = "mypy-1.0.0-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:92024447a339400ea00ac228369cd242e988dd775640755fa4ac0c126e49bb74"},
+    {file = "mypy-1.0.0-cp39-cp39-win_amd64.whl", hash = "sha256:fe523fcbd52c05040c7bee370d66fee8373c5972171e4fbc323153433198592d"},
+    {file = "mypy-1.0.0-py3-none-any.whl", hash = "sha256:2efa963bdddb27cb4a0d42545cd137a8d2b883bd181bbc4525b568ef6eca258f"},
+    {file = "mypy-1.0.0.tar.gz", hash = "sha256:f34495079c8d9da05b183f9f7daec2878280c2ad7cc81da686ef0b484cea2ecf"},
 ]
 mypy-extensions = [
-    {file = "mypy_extensions-0.4.4.tar.gz", hash = "sha256:c8b707883a96efe9b4bb3aaf0dcc07e7e217d7d8368eec4db4049ee9e142f4fd"},
+    {file = "mypy_extensions-1.0.0-py3-none-any.whl", hash = "sha256:4392f6c0eb8a5668a69e23d168ffa70f0be9ccfd32b5cc2d26a34ae5b844552d"},
+    {file = "mypy_extensions-1.0.0.tar.gz", hash = "sha256:75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782"},
 ]
 nanoid = [
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@@ -979,38 +979,6 @@ tomli = [
     {file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"},
     {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
 ]
-typed-ast = [
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-    {file = "typed_ast-1.4.3-cp38-cp38-manylinux1_x86_64.whl", hash = "sha256:7538e495704e2ccda9b234b82423a4038f324f3a10c43bc088a1636180f11a41"},
-    {file = "typed_ast-1.4.3-cp38-cp38-manylinux2014_aarch64.whl", hash = "sha256:af3d4a73793725138d6b334d9d247ce7e5f084d96284ed23f22ee626a7b88e39"},
-    {file = "typed_ast-1.4.3-cp38-cp38-win32.whl", hash = "sha256:f2362f3cb0f3172c42938946dbc5b7843c2a28aec307c49100c8b38764eb6927"},
-    {file = "typed_ast-1.4.3-cp38-cp38-win_amd64.whl", hash = "sha256:dd4a21253f42b8d2b48410cb31fe501d32f8b9fbeb1f55063ad102fe9c425e40"},
-    {file = "typed_ast-1.4.3-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:f328adcfebed9f11301eaedfa48e15bdece9b519fb27e6a8c01aa52a17ec31b3"},
-    {file = "typed_ast-1.4.3-cp39-cp39-manylinux1_i686.whl", hash = "sha256:2c726c276d09fc5c414693a2de063f521052d9ea7c240ce553316f70656c84d4"},
-    {file = "typed_ast-1.4.3-cp39-cp39-manylinux1_x86_64.whl", hash = "sha256:cae53c389825d3b46fb37538441f75d6aecc4174f615d048321b716df2757fb0"},
-    {file = "typed_ast-1.4.3-cp39-cp39-manylinux2014_aarch64.whl", hash = "sha256:b9574c6f03f685070d859e75c7f9eeca02d6933273b5e69572e5ff9d5e3931c3"},
-    {file = "typed_ast-1.4.3-cp39-cp39-win32.whl", hash = "sha256:209596a4ec71d990d71d5e0d312ac935d86930e6eecff6ccc7007fe54d703808"},
-    {file = "typed_ast-1.4.3-cp39-cp39-win_amd64.whl", hash = "sha256:9c6d1a54552b5330bc657b7ef0eae25d00ba7ffe85d9ea8ae6540d2197a3788c"},
-    {file = "typed_ast-1.4.3.tar.gz", hash = "sha256:fb1bbeac803adea29cedd70781399c99138358c26d05fcbd23c13016b7f5ec65"},
-]
 typing-extensions = [
     {file = "typing_extensions-4.5.0-py3-none-any.whl", hash = "sha256:fb33085c39dd998ac16d1431ebc293a8b3eedd00fd4a32de0ff79002c19511b4"},
     {file = "typing_extensions-4.5.0.tar.gz", hash = "sha256:5cb5f4a79139d699607b3ef622a1dedafa84e115ab0024e0d9c044a9479ca7cb"},
diff --git a/pyproject.toml b/pyproject.toml
index 0ccfce32..9a56a416 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -19,7 +19,7 @@ nanoid = "^2.0"
 numpy = "^1.23"
 black = {version = "^23.1.0", optional = true}
 flake8 = {version = "^3.8", optional = true}
-mypy = {version = "^0.812", optional = true}
+mypy = {version = "^1.0.0", optional = true}
 mkdocs = {version = "^1.1", optional = true}
 mkdocs-material = {version = "^7.0", optional = true}
 mkdocstrings = {version = "^0.15.0", optional = true}
diff --git a/tests/conftest.py b/tests/conftest.py
index 9f7d7ecb..8d8249cb 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -9,6 +9,7 @@
 from titan.agent import Agent, Relationship
 from titan.location import Location
 
+
 # helper method to generate a fake number deterministically
 class FakeRandom:
     def __init__(self, num: float, fake_choice: int = 0):
diff --git a/tests/exposures/knowledge_test.py b/tests/exposures/knowledge_test.py
index 93f6eb11..6b262db2 100644
--- a/tests/exposures/knowledge_test.py
+++ b/tests/exposures/knowledge_test.py
@@ -89,7 +89,6 @@ def test_knowledge_influence(make_model, make_agent):
 
 @pytest.mark.unit
 def test_knowledge_exposure(make_model, make_agent, params):
-
     # test update all agents for knowledge
     params.exposures.knowledge = True
     params.knowledge.prob = 0.0
diff --git a/tests/integration_test.py b/tests/integration_test.py
index 760f65c8..eb37b43f 100644
--- a/tests/integration_test.py
+++ b/tests/integration_test.py
@@ -13,6 +13,7 @@
 from titan.model import TITAN
 from titan.run_titan import script_init
 
+
 # overwrite
 @pytest.fixture
 def params_integration(tmpdir):
diff --git a/titan/exposures/base_exposure.py b/titan/exposures/base_exposure.py
index c42db438..b0459951 100644
--- a/titan/exposures/base_exposure.py
+++ b/titan/exposures/base_exposure.py
@@ -6,7 +6,6 @@
 
 
 class BaseExposure:
-
     name: str = ""
     """Name of exposure in the params file.  Also used to name the attribute in Agent"""
 
diff --git a/titan/exposures/hiv.py b/titan/exposures/hiv.py
index ce53de1e..84679790 100644
--- a/titan/exposures/hiv.py
+++ b/titan/exposures/hiv.py
@@ -8,7 +8,6 @@
 
 
 class HIV(base_exposure.BaseExposure):
-
     name: str = "hiv"
     stats: List[str] = ["hiv", "hiv_dx", "hiv_aids", "hiv_new", "hiv_dx_new"]
     """
diff --git a/titan/exposures/knowledge.py b/titan/exposures/knowledge.py
index abc3a8a5..b464e517 100644
--- a/titan/exposures/knowledge.py
+++ b/titan/exposures/knowledge.py
@@ -11,7 +11,6 @@
 
 
 class Knowledge(base_exposure.BaseExposure):
-
     name: str = "knowledge"
     stats: List[str] = ["knowledge_aware"]
     """
diff --git a/titan/exposures/monkeypox.py b/titan/exposures/monkeypox.py
index 230fd843..ae1d42ae 100644
--- a/titan/exposures/monkeypox.py
+++ b/titan/exposures/monkeypox.py
@@ -8,7 +8,6 @@
 
 
 class MonkeyPox(base_exposure.BaseExposure):
-
     name: str = "monkeypox"
     stats: List[str] = [
         "monkeypox",
diff --git a/titan/features/external_exposure.py b/titan/features/external_exposure.py
index 3f3d24ec..b0bf0f27 100644
--- a/titan/features/external_exposure.py
+++ b/titan/features/external_exposure.py
@@ -5,7 +5,6 @@
 
 
 class ExternalExposure(base_feature.BaseFeature):
-
     name = "external_exposure"
 
     def __init__(self, agent: "agent.Agent"):
diff --git a/titan/features/high_risk.py b/titan/features/high_risk.py
index 7277904d..824b052b 100644
--- a/titan/features/high_risk.py
+++ b/titan/features/high_risk.py
@@ -11,7 +11,6 @@
 
 
 class HighRisk(base_feature.BaseFeature):
-
     name = "high_risk"
     stats = [
         "high_risk_new",
@@ -76,7 +75,6 @@ def update_agent(self, model: "model.TITAN"):
 
             # incarcerated last step, evaluate agent's partners for high risk
             elif self.agent.incar.time == model.time - 1:  # type: ignore[attr-defined]
-
                 # put partners in high risk
                 for partner in self.agent.get_partners(
                     self.agent.location.params.high_risk.partnership_types
diff --git a/titan/features/incar.py b/titan/features/incar.py
index a4a6ee40..3f705956 100644
--- a/titan/features/incar.py
+++ b/titan/features/incar.py
@@ -8,7 +8,6 @@
 
 
 class Incar(base_feature.BaseFeature):
-
     name = "incar"
     stats = ["incar", "incar_hiv", "new_release", "new_release_hiv"]
     """
diff --git a/titan/features/partner_tracing.py b/titan/features/partner_tracing.py
index 5194d3f0..2f1ac74e 100644
--- a/titan/features/partner_tracing.py
+++ b/titan/features/partner_tracing.py
@@ -4,7 +4,6 @@
 
 
 class PartnerTracing(base_feature.BaseFeature):
-
     name = "partner_tracing"
 
     def __init__(self, agent: "agent.Agent"):
diff --git a/titan/features/prep.py b/titan/features/prep.py
index 6ff569c7..b4ba8574 100644
--- a/titan/features/prep.py
+++ b/titan/features/prep.py
@@ -11,7 +11,6 @@
 
 
 class Prep(base_feature.BaseFeature):
-
     name = "prep"
     stats = ["prep", "prep_new", "prep_injectable", "prep_oral"]
     """
diff --git a/titan/features/random_trial.py b/titan/features/random_trial.py
index 7928f10e..707560ff 100644
--- a/titan/features/random_trial.py
+++ b/titan/features/random_trial.py
@@ -9,7 +9,6 @@
 
 
 class RandomTrial(base_feature.BaseFeature):
-
     name = "random_trial"
     stats = [
         "random_trial",
diff --git a/titan/features/syringe_services.py b/titan/features/syringe_services.py
index 89ca25ea..fda212fe 100644
--- a/titan/features/syringe_services.py
+++ b/titan/features/syringe_services.py
@@ -6,7 +6,6 @@
 
 
 class SyringeServices(base_feature.BaseFeature):
-
     name = "syringe_services"
 
     enrolled_risk = 0.0
diff --git a/titan/features/vaccine.py b/titan/features/vaccine.py
index 0a41c6a3..b880ce15 100644
--- a/titan/features/vaccine.py
+++ b/titan/features/vaccine.py
@@ -9,7 +9,6 @@
 
 
 class Vaccine(base_feature.BaseFeature):
-
     name = "vaccine"
     stats = ["vaccine"]
     """
diff --git a/titan/interactions/base_interaction.py b/titan/interactions/base_interaction.py
index 23d14c65..ca01dda5 100644
--- a/titan/interactions/base_interaction.py
+++ b/titan/interactions/base_interaction.py
@@ -3,7 +3,6 @@
 
 
 class BaseInteraction:
-
     name: str = ""
     """Name of interaction in the params file."""
 
diff --git a/titan/interactions/injection.py b/titan/interactions/injection.py
index 909ae7a5..c3ba5fd9 100644
--- a/titan/interactions/injection.py
+++ b/titan/interactions/injection.py
@@ -6,7 +6,6 @@
 
 
 class Injection(base_interaction.BaseInteraction):
-
     name = "injection"
 
     @classmethod
diff --git a/titan/interactions/pca.py b/titan/interactions/pca.py
index 908784d7..f4a5301e 100644
--- a/titan/interactions/pca.py
+++ b/titan/interactions/pca.py
@@ -5,7 +5,6 @@
 
 
 class PCA(base_interaction.BaseInteraction):
-
     name = "pca"
 
     @classmethod
diff --git a/titan/interactions/sex.py b/titan/interactions/sex.py
index dc0a25f8..edc76c95 100644
--- a/titan/interactions/sex.py
+++ b/titan/interactions/sex.py
@@ -5,7 +5,6 @@
 
 
 class Sex(base_interaction.BaseInteraction):
-
     name = "sex"
 
     @classmethod
diff --git a/titan/location.py b/titan/location.py
index 9f6fdbae..89d50837 100644
--- a/titan/location.py
+++ b/titan/location.py
@@ -129,7 +129,6 @@ def add_weight(d, v, w):
 # * how will mobility be implemented?
 # * assorting?
 class LocationEdge:
-
     next_edge_id = 0
 
     @classmethod
diff --git a/titan/output.py b/titan/output.py
index 15f876a9..0c7e9ed4 100644
--- a/titan/output.py
+++ b/titan/output.py
@@ -301,7 +301,7 @@ def print_components(
             "\tdensity\tEffectiveSize\tdeg_cent\n"
         )
 
-    for (id, comp) in enumerate(components):
+    for id, comp in enumerate(components):
         num_nodes = comp.number_of_nodes()
 
         average_size = effective_size(comp) / num_nodes
diff --git a/titan/population.py b/titan/population.py
index b0cbeed0..8845fa31 100644
--- a/titan/population.py
+++ b/titan/population.py
@@ -411,7 +411,6 @@ def update_partner_assignments(self, t: int):
             while eligible_agents:
                 agent = eligible_agents.popleft()
                 if len(agent.partners[bond]) < agent.target_partners[bond]:
-
                     # no match
                     if self.update_agent_partners(agent, bond, network_components):
                         attempts[agent] += 1
diff --git a/titan/utils.py b/titan/utils.py
index fc35d929..757efdf5 100644
--- a/titan/utils.py
+++ b/titan/utils.py
@@ -391,7 +391,7 @@ def grid_file_to_edges(file_path: str, diagonal_neighbors: bool = False) -> Dict
                     add_edge(edges, loc, grid[i + 1][j - 1])
 
     res = {}
-    for (i, edge) in enumerate(edges):
+    for i, edge in enumerate(edges):
         res[f"edge_{i+1}"] = {"location_1": edge[0], "location_2": edge[1]}
 
     return res

From 7fa17a43cf4a5d5c2fde75e47d0857c4b4cfd8fc Mon Sep 17 00:00:00 2001
From: Sam Bessey <sam_bessey@brown.edu>
Date: Wed, 15 Feb 2023 14:24:48 -0500
Subject: [PATCH 7/7] fix mypy typing errors

---
 titan/features/high_risk.py | 2 +-
 titan/model.py              | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/titan/features/high_risk.py b/titan/features/high_risk.py
index 824b052b..8ce14054 100644
--- a/titan/features/high_risk.py
+++ b/titan/features/high_risk.py
@@ -128,7 +128,7 @@ def set_stats(self, stats: Dict[str, int], time: int):
     # ============== HELPER METHODS ================
 
     def become_high_risk(
-        self, pop: "population.Population", time: int, duration: int = None
+        self, pop: "population.Population", time: int, duration: Optional[int] = None
     ):
         """
         Mark an agent as high risk and assign a duration to their high risk period
diff --git a/titan/model.py b/titan/model.py
index 57aa2c0d..e70ad942 100644
--- a/titan/model.py
+++ b/titan/model.py
@@ -192,9 +192,9 @@ def step(self, outdir: str):
             "  STARTING HIV count:{}  Total Incarcerated:{}  HR+:{}  "
             "PrEP:{}".format(
                 len(exposures.HIV.agents),
-                sum([1 for a in self.pop.all_agents if a.incar.active]),  # type: ignore[attr-defined]
-                sum([1 for a in self.pop.all_agents if a.high_risk.active]),  # type: ignore[attr-defined]
-                sum([1 for a in self.pop.all_agents if a.prep.active]),  # type: ignore[attr-defined]
+                sum([1 for a in self.pop.all_agents if a.incar.active]),  # type: ignore[misc, attr-defined]
+                sum([1 for a in self.pop.all_agents if a.high_risk.active]),  # type: ignore[misc, attr-defined]
+                sum([1 for a in self.pop.all_agents if a.prep.active]),  # type: ignore[misc, attr-defined]
             )
         )