From 4817712c23b2736b8c0616eef5c3795a238ada2c Mon Sep 17 00:00:00 2001 From: Sam Bessey Date: Thu, 30 May 2024 15:00:43 -0400 Subject: [PATCH] Atlanta latino (#239) (#241) * feat: create new setting for atlanta with latinos * upgrade python version in github actions --- poetry.lock | 729 +++++++++--------- pyproject.toml | 2 +- titan/settings/atlanta-latino/assort_mix.yml | 26 + titan/settings/atlanta-latino/calibration.yml | 8 + .../settings/atlanta-latino/demographics.yml | 146 ++++ titan/settings/atlanta-latino/model.yml | 53 ++ titan/settings/atlanta-latino/outputs.yml | 3 + titan/settings/atlanta-latino/partnership.yml | 44 ++ titan/settings/atlanta-latino/prep.yml | 3 + .../atlanta-latino/timeline_scaling.yml | 92 +++ 10 files changed, 758 insertions(+), 348 deletions(-) create mode 100644 titan/settings/atlanta-latino/assort_mix.yml create mode 100644 titan/settings/atlanta-latino/calibration.yml create mode 100644 titan/settings/atlanta-latino/demographics.yml create mode 100644 titan/settings/atlanta-latino/model.yml create mode 100644 titan/settings/atlanta-latino/outputs.yml create mode 100644 titan/settings/atlanta-latino/partnership.yml create mode 100644 titan/settings/atlanta-latino/prep.yml create mode 100644 titan/settings/atlanta-latino/timeline_scaling.yml diff --git a/poetry.lock b/poetry.lock index 4afcce2c..e1e0f51c 100644 --- a/poetry.lock +++ b/poetry.lock @@ -20,27 +20,27 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "attrs" -version = "22.2.0" +version = "23.2.0" description = "Classes Without Boilerplate" category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.extras] -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]"] +cov = ["attrs[tests]", "coverage[toml] (>=5.3)"] +dev = ["attrs[tests]", "pre-commit"] +docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"] +tests = ["attrs[tests-no-zope]", "zope-interface"] +tests-mypy = ["mypy (>=1.6)", "pytest-mypy-plugins"] +tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist[psutil]"] [[package]] name = "black" -version = "23.1.0" +version = "23.12.1" description = "The uncompromising code formatter." category = "main" optional = true -python-versions = ">=3.7" +python-versions = ">=3.8" [package.dependencies] click = ">=8.0.0" @@ -49,17 +49,17 @@ 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\""} +typing-extensions = {version = ">=4.0.1", markers = "python_version < \"3.11\""} [package.extras] colorama = ["colorama (>=0.4.3)"] -d = ["aiohttp (>=3.7.4)"] +d = ["aiohttp (>=3.7.4)", "aiohttp (>=3.7.4,!=3.9.0)"] jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"] uvloop = ["uvloop (>=0.15.2)"] [[package]] name = "click" -version = "8.1.3" +version = "8.1.7" description = "Composable command line interface toolkit" category = "main" optional = true @@ -78,11 +78,11 @@ python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7 [[package]] name = "coverage" -version = "7.1.0" +version = "7.5.1" description = "Code coverage measurement for Python" category = "dev" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [package.extras] toml = ["tomli"] @@ -116,19 +116,19 @@ dev = ["flake8", "markdown", "twine", "wheel"] [[package]] name = "importlib-metadata" -version = "6.0.0" +version = "7.1.0" description = "Read metadata from Python packages" category = "main" optional = true -python-versions = ">=3.7" +python-versions = ">=3.8" [package.dependencies] zipp = ">=0.5" [package.extras] -docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +docs = ["furo", "jaraco.packaging (>=9.3)", "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)", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-perf (>=0.9.2)", "pytest-ruff (>=0.2.1)"] [[package]] name = "iniconfig" @@ -140,7 +140,7 @@ python-versions = ">=3.7" [[package]] name = "Jinja2" -version = "3.1.2" +version = "3.1.4" description = "A very fast and expressive template engine." category = "main" optional = true @@ -154,21 +154,22 @@ i18n = ["Babel (>=2.7)"] [[package]] name = "Markdown" -version = "3.4.1" -description = "Python implementation of Markdown." +version = "3.6" +description = "Python implementation of John Gruber's Markdown." category = "main" optional = true -python-versions = ">=3.7" +python-versions = ">=3.8" [package.dependencies] importlib-metadata = {version = ">=4.4", markers = "python_version < \"3.10\""} [package.extras] +docs = ["mdx-gh-links (>=0.2)", "mkdocs (>=1.5)", "mkdocs-gen-files", "mkdocs-literate-nav", "mkdocs-nature (>=0.6)", "mkdocs-section-index", "mkdocstrings[python]"] testing = ["coverage", "pyyaml"] [[package]] name = "MarkupSafe" -version = "2.1.2" +version = "2.1.5" description = "Safely add untrusted strings to HTML/XML markup." category = "main" optional = true @@ -192,26 +193,31 @@ python-versions = ">=3.6" [[package]] name = "mkdocs" -version = "1.3.0" +version = "1.6.0" description = "Project documentation with Markdown." category = "main" optional = true -python-versions = ">=3.6" +python-versions = ">=3.8" [package.dependencies] -click = ">=3.3" +click = ">=7.0" +colorama = {version = ">=0.4", markers = "platform_system == \"Windows\""} ghp-import = ">=1.0" -importlib-metadata = ">=4.3" -Jinja2 = ">=2.10.2" -Markdown = ">=3.2.1" +importlib-metadata = {version = ">=4.4", markers = "python_version < \"3.10\""} +jinja2 = ">=2.11.1" +markdown = ">=3.3.6" +markupsafe = ">=2.0.1" mergedeep = ">=1.3.4" +mkdocs-get-deps = ">=0.2.0" packaging = ">=20.5" -PyYAML = ">=3.10" +pathspec = ">=0.11.1" +pyyaml = ">=5.1" pyyaml-env-tag = ">=0.1" watchdog = ">=2.0" [package.extras] i18n = ["babel (>=2.9.0)"] +min-versions = ["babel (==2.9.0)", "click (==7.0)", "colorama (==0.4)", "ghp-import (==1.0)", "importlib-metadata (==4.4)", "jinja2 (==2.11.1)", "markdown (==3.3.6)", "markupsafe (==2.0.1)", "mergedeep (==1.3.4)", "mkdocs-get-deps (==0.2.0)", "packaging (==20.5)", "pathspec (==0.11.1)", "pyyaml (==5.1)", "pyyaml-env-tag (==0.1)", "watchdog (==2.0)"] [[package]] name = "mkdocs-autorefs" @@ -225,6 +231,20 @@ python-versions = ">=3.6,<4.0" Markdown = ">=3.3,<4.0" mkdocs = ">=1.1,<2.0" +[[package]] +name = "mkdocs-get-deps" +version = "0.2.0" +description = "MkDocs extension that lists all dependencies according to a mkdocs.yml file" +category = "main" +optional = true +python-versions = ">=3.8" + +[package.dependencies] +importlib-metadata = {version = ">=4.3", markers = "python_version < \"3.10\""} +mergedeep = ">=1.3.4" +platformdirs = ">=2.2.0" +pyyaml = ">=5.1" + [[package]] name = "mkdocs-material" version = "7.3.0" @@ -242,11 +262,11 @@ pymdown-extensions = ">=7.0" [[package]] name = "mkdocs-material-extensions" -version = "1.1.1" +version = "1.3.1" description = "Extension pack for Python Markdown and MkDocs Material." category = "main" optional = true -python-versions = ">=3.7" +python-versions = ">=3.8" [[package]] name = "mkdocstrings" @@ -267,21 +287,21 @@ pytkdocs = ">=0.2.0,<0.12.0" [[package]] name = "mypy" -version = "1.0.0" +version = "1.10.0" description = "Optional static typing for Python" category = "main" optional = true -python-versions = ">=3.7" +python-versions = ">=3.8" [package.dependencies] -mypy-extensions = ">=0.4.3" +mypy-extensions = ">=1.0.0" tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""} -typing-extensions = ">=3.10" +typing-extensions = ">=4.1.0" [package.extras] dmypy = ["psutil (>=4.0)"] install-types = ["pip"] -python2 = ["typed-ast (>=1.4.0,<2)"] +mypyc = ["setuptools (>=50)"] reports = ["lxml"] [[package]] @@ -317,7 +337,7 @@ test = ["codecov (>=2.1)", "pytest (>=7.2)", "pytest-cov (>=4.0)"] [[package]] name = "numpy" -version = "1.24.2" +version = "1.24.4" description = "Fundamental package for array computing in Python" category = "main" optional = false @@ -336,7 +356,7 @@ pyyaml = "*" [[package]] name = "packaging" -version = "23.0" +version = "24.0" description = "Core utilities for Python packages" category = "main" optional = false @@ -355,31 +375,32 @@ oyaml = ">=1.0,<2.0" [[package]] name = "pathspec" -version = "0.11.0" +version = "0.12.1" description = "Utility library for gitignore style pattern matching of file paths." category = "main" optional = true -python-versions = ">=3.7" +python-versions = ">=3.8" [[package]] name = "platformdirs" -version = "3.0.0" -description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." +version = "4.2.2" +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" +python-versions = ">=3.8" [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)"] +docs = ["furo (>=2023.9.10)", "proselint (>=0.13)", "sphinx (>=7.2.6)", "sphinx-autodoc-typehints (>=1.25.2)"] +test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4.3)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)"] +type = ["mypy (>=1.8)"] [[package]] name = "pluggy" -version = "1.0.0" +version = "1.5.0" description = "plugin and hook calling mechanisms for python" category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.8" [package.extras] dev = ["pre-commit", "tox"] @@ -411,14 +432,14 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "Pygments" -version = "2.14.0" +version = "2.18.0" description = "Pygments is a syntax highlighting package written in Python." category = "main" optional = true -python-versions = ">=3.6" +python-versions = ">=3.8" [package.extras] -plugins = ["importlib-metadata"] +windows-terminal = ["colorama (>=0.4.6)"] [[package]] name = "pymdown-extensions" @@ -470,7 +491,7 @@ testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtuale [[package]] name = "python-dateutil" -version = "2.8.2" +version = "2.9.0.post0" description = "Extensions to the standard Python datetime module" category = "main" optional = true @@ -495,7 +516,7 @@ numpy-style = ["docstring_parser (>=0.7.3,<0.8.0)"] [[package]] name = "PyYAML" -version = "6.0" +version = "6.0.1" description = "YAML parser and emitter for Python" category = "main" optional = false @@ -538,45 +559,45 @@ python-versions = ">=3.7" [[package]] name = "typing-extensions" -version = "4.5.0" -description = 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100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,7 +12,7 @@ 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" diff --git a/titan/settings/atlanta-latino/assort_mix.yml b/titan/settings/atlanta-latino/assort_mix.yml new file mode 100644 index 00000000..81e0dd10 --- /dev/null +++ b/titan/settings/atlanta-latino/assort_mix.yml @@ -0,0 +1,26 @@ +assort_mix: + assort_white: + attribute: race + agent_value: white + partner_values: + white: 0.722 + __other__: 0.278 + assort_black: + attribute: race + agent_value: black + partner_values: + black: 0.765 + __other__: 0.235 + assort_receptive: + attribute: sex_role + agent_value: receptive + partner_values: + receptive: 0.00 + __other__: 1.00 + assort_insertive: + attribute: sex_role + agent_value: insertive + partner_values: + insertive: 0.0 + __other__: 1.00 + diff --git a/titan/settings/atlanta-latino/calibration.yml b/titan/settings/atlanta-latino/calibration.yml new file mode 100644 index 00000000..1da3504d --- /dev/null +++ b/titan/settings/atlanta-latino/calibration.yml @@ -0,0 +1,8 @@ +calibration: + sex: + act: 1.0 + partner: 1.0 + test_frequency: 1.00 + haart: + coverage: 0.50 + acquisition: 0.50 diff --git a/titan/settings/atlanta-latino/demographics.yml b/titan/settings/atlanta-latino/demographics.yml new file mode 100644 index 00000000..48674d00 --- /dev/null +++ b/titan/settings/atlanta-latino/demographics.yml @@ -0,0 +1,146 @@ +demographics: + black: + ppl: 0.38235 + hiv: + transmission: 3.75 + sex_type: + MSM: + ppl: 1.0 + sex_role: + init: + versatile: 0.437 + insertive: 0.242 + receptive: 0.321 + safe_sex: + Sex: + prob: 0.688 + prep: + discontinue: 0.0 + adherence: 0.568 + cap: 0.0 + init: 0.0 + drug_type: + None: + ppl: 1.0 + num_partners: + Sex: + dist_type: poisson + vars: + 1: + value: 7.0 + value_type: float + hiv: + init: 0.434 + dx: + init: 0.655 + prob: 0.0256 + aids: + init: 0.232 + exit: + death: + base: 8.6 + hiv: 17.2 + aids: 34.4 + haart: + init: 0.625 + cap: 0.35 + adherence: + init: 0.885 + prob: 0.885 + discontinue: 0.10 + latino: + ppl: 0.14388 + hiv: + transmission: 3.75 + sex_type: + MSM: + ppl: 1.0 + sex_role: + init: + versatile: 0.437 + insertive: 0.242 + receptive: 0.321 + safe_sex: + Sex: + prob: 0.811 + prep: + discontinue: 0.048 + adherence: 0.568 + cap: 0.01210742 + init: 0.01210742 + drug_type: + None: + ppl: 1.0 + num_partners: + Sex: + dist_type: poisson + vars: + 1: + value: 2.8 + value_type: float + hiv: + init: 0.175 + dx: + init: 0.818 + prob: 0.0256 + aids: + init: 0.167 + exit: + death: + base: 8.6 + hiv: 17.2 + aids: 34.4 + haart: + init: 0.585 + cap: 0.65 + adherence: + init: 0.851 + prob: 0.851 + discontinue: 0.062 + white: + ppl: 0.47377 + sex_type: + MSM: + ppl: 1.0 + sex_role: + init: + versatile: 0.544 + insertive: 0.228 + receptive: 0.228 + safe_sex: + Sex: + prob: 0.528 + 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timeline_scaling: true + +prep: + target_model: + - Racial + +hiv: + aids: + prob: 0.05 + +classes: + bond_types: + Sex: + acts_allowed: + - sex + sex_types: + MSM: + gender: M + cis_trans: cis + sleeps_with: + - MSM + drug_types: + - None + races: + white: + hispanic: false + black: + hispanic: false + latino: + hispanic: false diff --git a/titan/settings/atlanta-latino/outputs.yml b/titan/settings/atlanta-latino/outputs.yml new file mode 100644 index 00000000..bdb4564d --- /dev/null +++ b/titan/settings/atlanta-latino/outputs.yml @@ -0,0 +1,3 @@ +outputs: + reports: + - basicReport \ No newline at end of file diff --git a/titan/settings/atlanta-latino/partnership.yml b/titan/settings/atlanta-latino/partnership.yml new file mode 100644 index 00000000..5a479b6d --- /dev/null +++ b/titan/settings/atlanta-latino/partnership.yml @@ -0,0 +1,44 @@ +partnership: + duration: + Sex: + white: &partnership_duration + type: bins + bins: + 1: + prob: 0.456 + min: 1 + max: 3 + 2: + prob: 0.756 + min: 3 + max: 12 + 3: + prob: 1.0 + min: 13 + max: 24 + black: *partnership_duration + sex: + frequency: + Sex: + bins: + 1: + prob: 0.244 + min: 1 + max: 2 + 2: + prob: 0.737 + min: 3 + max: 4 + 3: + prob: 0.86 + min: 5 + max: 12 + 4: + prob: 1.0 + min: 13 + max: 20 + acquisition: + MSM: + insertive: 0.0011 + receptive: 0.0138 + versatile: 0.00745 diff --git a/titan/settings/atlanta-latino/prep.yml b/titan/settings/atlanta-latino/prep.yml new file mode 100644 index 00000000..1bf8890c --- /dev/null +++ b/titan/settings/atlanta-latino/prep.yml @@ -0,0 +1,3 @@ +prep: + target_model: + - Racial diff --git a/titan/settings/atlanta-latino/timeline_scaling.yml b/titan/settings/atlanta-latino/timeline_scaling.yml new file mode 100644 index 00000000..03fd250a --- /dev/null +++ b/titan/settings/atlanta-latino/timeline_scaling.yml @@ -0,0 +1,92 @@ +timeline_scaling: + timeline: + white_1: + parameter: demographics|white|sex_type|MSM|prep|cap + start_time: 12 + stop_time: 24 + scalar: 2.397 + white_2: + parameter: demographics|white|sex_type|MSM|prep|cap + start_time: 24 + stop_time: 36 + scalar: 3.648 + white_3: + parameter: demographics|white|sex_type|MSM|prep|cap + start_time: 36 + stop_time: 48 + scalar: 4.912 + white_4: + parameter: demographics|white|sex_type|MSM|prep|cap + start_time: 48 + stop_time: 60 + scalar: 5.514 + white_5: + parameter: demographics|white|sex_type|MSM|prep|cap + start_time: 60 + stop_time: 72 + scalar: 5.802 + white_6: + parameter: demographics|white|sex_type|MSM|prep|cap + start_time: 72 + stop_time: 999 + scalar: 5.939 + black_1: + parameter: demographics|black|sex_type|MSM|prep|cap + start_time: 12 + stop_time: 24 + scalar: 2.393 + black_2: + parameter: demographics|black|sex_type|MSM|prep|cap + start_time: 24 + stop_time: 36 + scalar: 3.562 + black_3: + parameter: demographics|black|sex_type|MSM|prep|cap + start_time: 36 + stop_time: 48 + scalar: 4.755 + black_4: + parameter: demographics|black|sex_type|MSM|prep|cap + start_time: 48 + stop_time: 60 + scalar: 5.291 + black_5: + parameter: demographics|black|sex_type|MSM|prep|cap + start_time: 60 + stop_time: 72 + scalar: 5.528 + black_6: + parameter: demographics|black|sex_type|MSM|prep|cap + start_time: 72 + stop_time: 999 + scalar: 5.631 + latino_1: + parameter: demographics|latino|sex_type|MSM|prep|cap + start_time: 12 + stop_time: 24 + scalar: 2.405 + latino_2: + parameter: demographics|latino|sex_type|MSM|prep|cap + start_time: 24 + stop_time: 36 + scalar: 3.660 + latino_3: + parameter: demographics|latino|sex_type|MSM|prep|cap + start_time: 36 + stop_time: 48 + scalar: 4.957 + latino_4: + parameter: demographics|latino|sex_type|MSM|prep|cap + start_time: 48 + stop_time: 60 + scalar: 5.593 + latino_5: + parameter: demographics|latino|sex_type|MSM|prep|cap + start_time: 60 + stop_time: 72 + scalar: 5.905 + latino_6: + parameter: demographics|latino|sex_type|MSM|prep|cap + start_time: 72 + stop_time: 999 + scalar: 6.057