vivarium-public-health 2.3.3__tar.gz → 3.0.1__tar.gz

vivarium_public_health-3.0.1/.bandit

@@ -0,0 +1,2 @@
+[bandit]
+exclude: tests

vivarium_public_health-3.0.1/.flake8

@@ -0,0 +1,46 @@
+[flake8]
+# Use the following flake8 plugins:
+# ANN   : flake8-annotations
+# B,B9  : flake8-bugbear
+# BLK   : flake8-black
+# C     : mccabe code complexity
+# D     : flake8-docstrings
+# DAR   : darglint. Not currently in use because it was too slow.
+# F     : pyflakes
+# I     : flake8-isort
+# S     : flake8-bandit
+# W,E   : pycodestyle (pep8) warnings and errors
+select = ANN,B,B9,BLK,C,D,E,F,I,S,W
+
+# Ignore these flake8 errors across the board.
+extend-ignore =
+    # Missing type annotation for self
+    ANN101,
+    # Missing type annotation for cls
+    ANN102,
+    # Missing type annotation for special method
+    ANN204,
+    # Missing docstring in public module
+    D100,
+    # Missing docstring in public package
+    D104,
+    # Colons should not have whitespace before them (needed for black)
+    E203,
+    # Line break before binary operator (needed for black)
+    W503,
+
+# Only use strict docstring linting in the api/ or cli/ directory. Unfortunately it's not
+# possible to enable only those directories, so instead we disable strict docstring linting
+# everywhere else.
+# Also allow unused imports in __init__ files.
+per-file-ignores =
+    tests/**:D105,D106,D107,D205,D207,D208,D212,D214,D215,D301,D4,S101,E266
+    src/vivarium/lib/**:D105,D106,D107,D205,D207,D208,D212,D214,D215,D301,D4
+    **/__init__.py:F401
+
+# Function complexity and line length
+max-complexity = 10
+max-line-length = 95
+
+# Docstrings
+docstring-convention = google

{vivarium_public_health-2.3.3 → vivarium_public_health-3.0.1}/.github/workflows/build.yml

@@ -21,6 +21,8 @@ jobs:
         shell: bash -le {0}
     steps:
       - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4
         with:
@@ -32,35 +34,33 @@ jobs:
           else
             echo "branch_name=${GITHUB_REF_NAME}" >> $GITHUB_ENV
           fi
+      - name: Update pip
+        run: |
+          python -m pip install --upgrade pip
+      - name: Install dependencies
+        run: |
+          pip install .[dev]
+          git checkout ${branch_name}
       - name: check for upstream branch
         run: |
-          if git ls-remote --exit-code --heads https://github.com/ihmeuw/vivarium.git ${branch_name} == "0"; then
-            echo "upstream_exist=true" >> $GITHUB_ENV
-          else
-            echo "upstream_exist=false" >> $GITHUB_ENV
-          fi
+          sh get_upstream_branch.sh ${branch_name}
       - name: print environment values
         run: |
           cat $GITHUB_ENV
-      - name: Update pip
-        run: |
-          python -m pip install --upgrade pip
-      - name: Retrieve upstream branch if exists
-        if: env.upstream_exist == 'true'
+      - name: Retrieve vivarium branch
+        if: env.vivarium_branch_name != 'main'
         run: |
-          echo "Cloning upstream branch: ${branch_name}"
-          git clone --branch=${branch_name} https://github.com/ihmeuw/vivarium.git
+          echo "Cloning upstream branch: ${vivarium_branch_name}"
+          pushd ..
+          git clone --branch=${vivarium_branch_name} https://github.com/ihmeuw/vivarium.git
           pushd vivarium
           pip install .
-          popd
-      - name: Install dependencies
-        run: |
-          pip install .[dev]
+          popd && popd
       - name: Lint
         run: |
           pip install black==22.3.0 isort
-          black . --check --diff
           isort . --check --verbose --only-modified --diff
+          black . --check --diff
       - name: Test
         run: |
           if "${{ github.event_name == 'schedule' }}"; then

{vivarium_public_health-2.3.3 → vivarium_public_health-3.0.1}/.gitignore

@@ -109,3 +109,6 @@ venv.bak/
 
 # Version file
 src/vivarium_public_health/_version.py
+
+# FuzzyChecker diagnostics csv
+tests/proportion_test_diagnostics.csv

{vivarium_public_health-2.3.3 → vivarium_public_health-3.0.1}/CHANGELOG.rst

@@ -1,3 +1,28 @@
+**3.0.1 - 08/19/24**
+
+ - Fix bug in build script when the upstream vivarium branch should be main
+
+**3.0.0 - 08/13/24**
+
+Breaking changes:
+  - Update components to use new Vivarium lookup table configuration
+  - Update Observers to use new Vivarium results interface classes and methods
+  - Change the "all_causes" disability weight pipeline from "disability_weight" to "all_causes.disability_weight"
+
+Major changes:
+  - Refactor risk components to standardize/simplify risk exposure distributions
+  - Enable the setting of CSMR using a causes configuration parser
+  - Implement a PublicHealthObserver to help enforce the existence of "measure", "entity_type", "sub_entity", and "entity" columns in the results
+  - Refactor Risk component to create exposure column in state table
+  - Add support for non-loglinear relative risks
+
+Other changes:
+  - Use external layered-config-tree package instead of Vivarium ConfigTree class
+  - Install matching upstream branches in github builds
+  - Stop writing seed and draw columns to the results
+  - Automatically run Jenkins builds on push or pull request
+  - Various other minor updates
+
 **2.3.3 - 06/17/24**
 
  - Hotfix pin numpy below 2.0

vivarium_public_health-3.0.1/Jenkinsfile

@@ -0,0 +1,229 @@
+pipeline_name="vivarium_public_health"
+conda_env_name="${pipeline_name}-${BUILD_NUMBER}"
+conda_env_path="/tmp/${conda_env_name}"
+// defaults for conda and pip are a local directory /svc-simsci for improved speed.
+// In the past, we used /ihme/code/* on the NFS (which is slower)
+shared_path="/svc-simsci"
+
+
+pipeline {
+  // This agent runs as svc-simsci on node simsci-slurm-sbuild-p01.
+  // It has access to standard IHME filesystems and singularity
+  agent { label "svc-simsci" }
+
+  options {
+    // Keep 100 old builds.
+    buildDiscarder logRotator(numToKeepStr: "100")
+
+    // Wait 60 seconds before starting the build.
+    // If another commit enters the build queue in this time, the first build will be discarded.
+    quietPeriod(60)
+
+    // Fail immediately if any part of a parallel stage fails
+    parallelsAlwaysFailFast()
+  }
+
+  parameters {
+    booleanParam(
+      name: "DEPLOY_OVERRIDE",
+      defaultValue: false,
+      description: "Whether to deploy despite building a non-default branch. Builds of the default branch are always deployed."
+    )
+    booleanParam(
+      name: "IS_CRON",
+      defaultValue: true,
+      description: "Indicates a recurring build. Used to skip deployment steps."
+    )
+    string(
+      name: "SLACK_TO",
+      defaultValue: "simsci-ci-status",
+      description: "The Slack channel to send messages to."
+    )
+    booleanParam(
+      name: "DEBUG",
+      defaultValue: false,
+      description: "Used as needed for debugging purposes."
+    )
+  }
+
+  stages {
+    stage("Initialization") {
+      steps {
+        script {
+          // Use the name of the branch in the build name
+          currentBuild.displayName = "#${BUILD_NUMBER} ${GIT_BRANCH}"
+
+          // Tell BitBucket that a build has started.
+          notifyBitbucket()
+        }
+      }
+    }
+
+    stage("Python version matrix") {
+      // we don't want to go to deployment if any of the matrix branches fail
+      failFast true
+      matrix {
+        // customWorkspace setting must be ran within a node
+        agent {
+          node {
+              label "svc-simsci"
+          }
+        }
+        axes {
+          axis {
+              // parallelize by python minor version
+              name 'PYTHON_VERSION'
+              values "3.10", "3.11"
+          }
+        }
+
+        environment {
+            // Get the branch being built and strip everything but the text after the last "/"
+            BRANCH = sh(script: "echo ${GIT_BRANCH} | rev | cut -d '/' -f1 | rev", returnStdout: true).trim()
+            TIMESTAMP = sh(script: 'date', returnStdout: true)
+            // Specify the path to the .condarc file via environment variable.
+            // This file configures the shared conda package cache.
+            CONDARC = "${shared_path}/miniconda3/.condarc"
+            CONDA_BIN_PATH = "${shared_path}/miniconda3/bin"
+            // Specify conda env by build number so that we don't have collisions if builds from
+            // different branches happen concurrently.
+            PYTHON_DEPLOY_VERSION = "3.11"
+            CONDA_ENV_NAME = "${conda_env_name}"
+            CONDA_ENV_PATH = "${conda_env_path}_${PYTHON_VERSION}"
+            // Set the Pip cache.
+            XDG_CACHE_HOME = "${shared_path}/pip-cache"
+            // Jenkins commands run in separate processes, so need to activate the environment every
+            // time we run pip, poetry, etc.
+            ACTIVATE = "source ${CONDA_BIN_PATH}/activate ${CONDA_ENV_PATH} &> /dev/null"
+        }
+
+        stages {
+            stage("Debug Info") {
+              steps {
+                echo "Jenkins pipeline run timestamp: ${TIMESTAMP}"
+                // Display parameters used.
+                echo """Parameters:
+                DEPLOY_OVERRIDE: ${params.DEPLOY_OVERRIDE}"""
+
+                // Display environment variables from Jenkins.
+                echo """Environment:
+                ACTIVATE:       '${ACTIVATE}'
+                BUILD_NUMBER:   '${BUILD_NUMBER}'
+                BRANCH:         '${BRANCH}'
+                CONDARC:        '${CONDARC}'
+                CONDA_BIN_PATH: '${CONDA_BIN_PATH}'
+                CONDA_ENV_NAME: '${CONDA_ENV_NAME}'
+                CONDA_ENV_PATH: '${CONDA_ENV_PATH}'
+                GIT_BRANCH:     '${GIT_BRANCH}'
+                JOB_NAME:       '${JOB_NAME}'
+                WORKSPACE:      '${WORKSPACE}'
+                XDG_CACHE_HOME: '${XDG_CACHE_HOME}'"""
+              }
+            }
+
+            stage("Build Environment") {
+              environment {
+                // Command for activating the base environment. Activating the base environment sets
+                // the correct path to the conda binary which is used to create a new conda env.
+                ACTIVATE_BASE = "source ${CONDA_BIN_PATH}/activate &> /dev/null"
+              }
+              steps {
+                // The env should have been cleaned out after the last build, but delete it again
+                // here just to be safe.
+                sh "rm -rf ${CONDA_ENV_PATH}"
+                sh "${ACTIVATE_BASE} && make build-env PYTHON_VERSION=${PYTHON_VERSION}"
+                // open permissions for test users to create file in workspace
+                sh "chmod 777 ${WORKSPACE}"
+              }
+            }
+
+            stage("Install Package") {
+              steps {
+                sh "${ACTIVATE} && make install \"ARGS=${GIT_BRANCH}\""
+              }
+            }
+
+            // Quality Checks
+            stage("Format") {
+              steps {
+                sh "${ACTIVATE} && make format"
+              }
+            }
+
+            // stage("Lint") {
+            //   steps {
+            //     sh "${ACTIVATE} && make lint"
+            //   }
+            // }
+
+            // Tests
+            // removable, if passwords can be exported to env. securely without bash indirection
+            stage("Run Integration Tests") {
+              steps {
+                sh "${ACTIVATE} && make integration"
+                publishHTML([
+                  allowMissing: true,
+                  alwaysLinkToLastBuild: false,
+                  keepAll: true,
+                  reportDir: "output/htmlcov_integration",
+                  reportFiles: "index.html",
+                  reportName: "Coverage Report - Integration tests",
+                  reportTitles: ''
+                ])
+              }
+            }
+
+            // Build
+            stage('Build and Deploy') {
+              when {
+                expression { "${PYTHON_DEPLOY_VERSION}" == "${PYTHON_VERSION}" }
+              }
+              stages {
+                stage("Build Docs") {
+                  steps {
+                    sh "${ACTIVATE} && make build-doc"
+                  }
+                }
+                stage("Build Package") {
+                  steps {
+                    sh "${ACTIVATE} && make build-package"
+                  }
+                }
+              } // stages within build and deploy
+            } // build and deploy stage
+        } // stages bracket within Python matrix
+        post {
+            always {
+              sh "${ACTIVATE} && make clean"
+              sh "rm -rf ${CONDA_ENV_PATH}"
+              // Delete the workspace directory.
+              deleteDir()
+              // Tell BitBucket whether the build succeeded or failed.
+              script {
+                notifyBitbucket()
+              }
+            }
+            failure {
+              slackSend channel: "#${params.SLACK_TO}",
+                        message: ":x: JOB FAILURE: $JOB_NAME - $BUILD_ID\n\n${BUILD_URL}console\n\n<!channel>",
+                        teamDomain: "ihme",
+                        tokenCredentialId: "slack"
+            }
+            success {
+              script {
+                if (params.DEBUG) {
+                  echo 'Debug is enabled. Sending a success message to Slack.'
+                  slackSend channel: "#${params.SLACK_TO}",
+                            message: ":white_check_mark: (debugging) JOB SUCCESS: $JOB_NAME - $BUILD_ID\n\n${BUILD_URL}console",
+                            teamDomain: "ihme",
+                            tokenCredentialId: "slack"
+                } else {
+                  echo 'Debug is not enabled. No success message will be sent to Slack.'
+                }
+              }
+            }
+        } // post bracket
+      } // Python matrix bracket
+    } // Python matrix stage bracket
+  } // stages bracket
+}

vivarium_public_health-3.0.1/Makefile

@@ -0,0 +1,93 @@
+SHELL := /bin/bash
+this_makefile := $(lastword $(MAKEFILE_LIST)) # Used to automatically list targets
+.DEFAULT_GOAL := list # If someone runs "make", run "make list"
+
+# Source files to format, lint, and type check.
+LOCATIONS=src tests
+
+# Unless overridden, build conda environment using the package name.
+PACKAGE_NAME = vivarium_public_health
+SAFE_NAME = $(shell python -c "from pkg_resources import safe_name; print(safe_name(\"$(PACKAGE_NAME)\"))")
+
+setup_file   = $(shell find -name setup.py)
+version_line = $(shell grep "version = " ${setup_file})
+PACKAGE_VERSION = $(shell echo ${version_line} | cut -d "=" -f 2 | xargs)
+
+# Use this URL to pull IHME Python packages and deploy this package to PyPi.
+IHME_PYPI := https://artifactory.ihme.washington.edu/artifactory/api/pypi/pypi-shared/
+
+# If CONDA_ENV_PATH is set (from a Jenkins build), use the -p flag when making Conda env in
+# order to make env at specific path. Otherwise, make a named env at the default path using
+# the -n flag.
+PYTHON_VERSION ?= 3.11
+CONDA_ENV_NAME ?= ${PACKAGE_NAME}_py${PYTHON_VERSION}
+CONDA_ENV_CREATION_FLAG = $(if $(CONDA_ENV_PATH),-p ${CONDA_ENV_PATH},-n ${CONDA_ENV_NAME})
+
+# These are the doc and source code files in this repo.
+# When one of these files changes, it means that Make targets need to run again.
+MAKE_SOURCES := $(shell find . -type d -name "*" ! -path "./.git*" ! -path "./.vscode" ! -path "./output" ! -path "./output/*" ! -path "./archive" ! -path "./dist" ! -path "./output/htmlcov*" ! -path "**/.pytest_cache*" ! -path "**/__pycache__" ! -path "./output/docs_build*" ! -path "./.pytype*" ! -path "." ! -path "./src/${PACKAGE_NAME}/legacy*" ! -path ./.history ! -path "./.history/*" ! -path "./src/${PACKAGE_NAME}.egg-info" ! -path ./.idea ! -path "./.idea/*" )
+
+
+# Phony targets don't produce artifacts.
+.PHONY: .list-targets build-env clean debug deploy-doc deploy-package full help install list quick
+
+# List of Make targets is generated dynamically. To add description of target, use a # on the target definition.
+list help: debug .list-targets
+
+.list-targets: # Print available Make targets
+	@echo
+	@echo "Make targets:"
+	@grep -i "^[a-zA-Z][a-zA-Z0-9_ \.\-]*: .*[#].*" ${this_makefile} | sort | sed 's/:.*#/ : /g' | column -t -s:
+	@echo
+
+debug: # Print debug information (environment variables)
+	@echo "'make' invoked with these environment variables:"
+	@echo "CONDA_ENV_NAME:                   ${CONDA_ENV_NAME}"
+	@echo "IHME_PYPI:                        ${IHME_PYPI}"
+	@echo "LOCATIONS:                        ${LOCATIONS}"
+	@echo "PACKAGE_NAME:                     ${PACKAGE_NAME}"
+	@echo "PACKAGE_VERSION:                  ${PACKAGE_VERSION}"
+	@echo "PYPI_ARTIFACTORY_CREDENTIALS_USR: ${PYPI_ARTIFACTORY_CREDENTIALS_USR} "
+	@echo "Make sources:                     ${MAKE_SOURCES}"
+
+build-env: # Make a new conda environment
+	@[ "${CONDA_ENV_NAME}" ] && echo "" > /dev/null || ( echo "CONDA_ENV_NAME is not set"; exit 1 )
+	conda create ${CONDA_ENV_CREATION_FLAG} python=${PYTHON_VERSION} --yes
+
+install: # Install setuptools, install this package in editable mode
+	pip install --upgrade pip setuptools
+	pip install -e .[DEV]
+	@echo "Checking if the vivarium repository has the branch $(GIT_BRANCH)..."
+	@$(eval BRANCH_EXISTS=$(shell curl -s https://api.github.com/repos/ihmeuw/vivarium/branches | grep -q '"name": "$(GIT_BRANCH)"' && echo "yes" || echo "no"))
+	@if [ "$(BRANCH_EXISTS)" = "yes" ]; then \
+		pip install git+https://github.com/ihmeuw/vivarium@${GIT_BRANCH}; \
+	fi
+
+format: setup.py pyproject.toml $(MAKE_SOURCES) # Run the code formatter and import sorter
+	black $(LOCATIONS)
+	isort $(LOCATIONS)
+	@echo "Ignore, Created by Makefile, `date`" > $@
+
+lint: .flake8 .bandit $(MAKE_SOURCES) # Run the code linter and package security vulnerability checker
+	-flake8 $(LOCATIONS)
+	-safety check
+	@echo "Ignore, Created by Makefile, `date`" > $@
+
+integration: $(MAKE_SOURCES) # Run the end-to-end tests
+	export COVERAGE_FILE=./output/.coverage.integration
+	pytest --runslow tests --cov --cov-report term --cov-report html:./output/htmlcov_integration
+	@echo "Ignore, Created by Makefile, `date`" > $@
+
+build-doc: $(MAKE_SOURCES) # Build the Sphinx docs
+	$(MAKE) -C docs/ html
+	@echo "Ignore, Created by Makefile, `date`" > $@
+
+build-package: $(MAKE_SOURCES) # Build the package as a pip wheel
+	pip install build
+	python -m build
+	@echo "Ignore, Created by Makefile, `date`" > $@
+
+clean: # Delete build artifacts and do any custom cleanup such as spinning down services
+	@rm -rf format lint build-doc build-package integration .pytest_cache
+	@rm -rf dist output
+	$(shell find . -type f -name '*py[co]' -delete -o -type d -name __pycache__ -delete)

{vivarium_public_health-2.3.3 → vivarium_public_health-3.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: vivarium_public_health
-Version: 2.3.3
+Version: 3.0.1
 Summary: Components for modelling diseases, risks, and interventions with ``vivarium``
 Home-page: https://github.com/ihmeuw/vivarium_public_health
 Author: The vivarium developers
@@ -26,21 +26,26 @@ Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
 Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Software Development :: Libraries
 License-File: LICENSE.txt
-Requires-Dist: vivarium>=2.0.0
+Requires-Dist: vivarium>=3.0.0
+Requires-Dist: layered_config_tree>=1.0.1
 Requires-Dist: loguru
 Requires-Dist: numpy<2.0.0
 Requires-Dist: pandas
 Requires-Dist: scipy
 Requires-Dist: tables
 Requires-Dist: risk_distributions>=2.0.11
+Requires-Dist: pyarrow
 Provides-Extra: docs
 Requires-Dist: sphinx<7.0; extra == "docs"
 Requires-Dist: sphinx-rtd-theme; extra == "docs"
 Requires-Dist: sphinx-click; extra == "docs"
+Requires-Dist: sphinx-autodoc-typehints; extra == "docs"
 Requires-Dist: IPython; extra == "docs"
 Requires-Dist: matplotlib; extra == "docs"
 Provides-Extra: test
+Requires-Dist: vivarium_testing_utils; extra == "test"
 Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
 Requires-Dist: pytest-mock; extra == "test"
 Requires-Dist: hypothesis; extra == "test"
 Requires-Dist: pyyaml; extra == "test"
@@ -48,12 +53,17 @@ Provides-Extra: dev
 Requires-Dist: sphinx<7.0; extra == "dev"
 Requires-Dist: sphinx-rtd-theme; extra == "dev"
 Requires-Dist: sphinx-click; extra == "dev"
+Requires-Dist: sphinx-autodoc-typehints; extra == "dev"
 Requires-Dist: IPython; extra == "dev"
 Requires-Dist: matplotlib; extra == "dev"
+Requires-Dist: vivarium_testing_utils; extra == "dev"
 Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
 Requires-Dist: pytest-mock; extra == "dev"
 Requires-Dist: hypothesis; extra == "dev"
 Requires-Dist: pyyaml; extra == "dev"
+Requires-Dist: black==22.3.0; extra == "dev"
+Requires-Dist: isort; extra == "dev"
 
 Vivarium Public Health
 ======================

{vivarium_public_health-2.3.3 → vivarium_public_health-3.0.1}/docs/nitpick-exceptions

@@ -9,13 +9,17 @@ py:class pandas._libs.interval.Interval
 py:class pandas.core.frame.DataFrame
 py:class pandas.core.series.Series
 py:class pandas.core.generic.PandasObject
+# layered-config-tree
+py:class layered_config_tree.main.LayeredConfigTree
 
-# TODO: Need to revisit this. Nitpicking here to avoid failing builds on 3.8 and 3.9 in LBWSGRisk
+# TODO: Need to revisit this. Nitpicking here to avoid failing builds on 3.9 in LBWSGRisk
 py:class PopulationView
 py:class Logger
+py:class pd.DataFrame
+py:class LayeredConfigTree
 # TODO: Need to revisit this. Nitpicking here to avoid failing everywhere
 py:class Builder
 py:class SimulantData
 py:class Event
 py:class LookupTable
-py:class Pipeline
+py:class Pipeline

vivarium_public_health-3.0.1/docs/source/api_reference/results/disability.rst

@@ -0,0 +1 @@
+.. automodule:: vivarium_public_health.results.disability

vivarium_public_health-3.0.1/docs/source/api_reference/results/disease.rst

@@ -0,0 +1 @@
+.. automodule:: vivarium_public_health.results.disease

{vivarium_public_health-2.3.3/docs/source/api_reference/metrics → vivarium_public_health-3.0.1/docs/source/api_reference/results}/index.rst

@@ -1,8 +1,8 @@
 ================================
-Simulation Observers and Metrics
+Simulation Observers and Results
 ================================
 
-.. automodule:: vivarium_public_health.metrics
+.. automodule:: vivarium_public_health.results
 
 .. toctree::
    :maxdepth: 2

vivarium_public_health-3.0.1/docs/source/api_reference/results/mortality.rst

@@ -0,0 +1 @@
+.. automodule:: vivarium_public_health.results.mortality

vivarium_public_health-3.0.1/docs/source/api_reference/results/observer.rst

@@ -0,0 +1 @@
+.. automodule:: vivarium_public_health.results.observer

vivarium_public_health-3.0.1/docs/source/api_reference/results/risk.rst

@@ -0,0 +1 @@
+.. automodule:: vivarium_public_health.results.risk

vivarium_public_health-3.0.1/docs/source/api_reference/results/stratification.rst

@@ -0,0 +1 @@
+.. automodule:: vivarium_public_health.results.stratification

{vivarium_public_health-2.3.3 → vivarium_public_health-3.0.1}/docs/source/conf.py

@@ -61,6 +61,7 @@ extensions = [
     "sphinx.ext.napoleon",
     "sphinx.ext.viewcode",
     "sphinx_click.ext",
+    "sphinx_autodoc_typehints",
     "matplotlib.sphinxext.plot_directive",
 ]
 

vivarium_public_health-3.0.1/get_upstream_branch.sh

@@ -0,0 +1,40 @@
+#!/bin/bash
+
+# Define variables
+branch_name=$1
+
+vivarium_branch_name='main'
+branch_name_to_check=${branch_name}
+iterations=0
+
+while [ "$branch_name_to_check" != "$vivarium_branch_name" ] && [ $iterations -lt 20 ]
+do
+  echo "Checking for vivarium branch: '${branch_name_to_check}'"
+  if
+    git ls-remote --exit-code \
+    --heads https://github.com/ihmeuw/vivarium.git ${branch_name_to_check} == "0"
+  then
+    vivarium_branch_name=${branch_name_to_check}
+    echo "Found matching branch: ${vivarium_branch_name}"
+  else
+    echo "Could not find upstream branch '${branch_name_to_check}'. Finding parent branch."
+    branch_name_to_check="$( \
+      git show-branch -a \
+      | grep '\*' \
+      | grep -v `git rev-parse --abbrev-ref HEAD` \
+      | head -n1 \
+      | sed 's/[^\[]*//' \
+      | awk 'match($0, /\[[a-zA-Z0-9\/.-]+\]/) { print substr( $0, RSTART+1, RLENGTH-2 )}' \
+      | sed 's/^origin\///' \
+    )"
+    if [ -z "$branch_name_to_check" ]; then
+      echo "Could not find upstream branch. Will use released version."
+      branch_name_to_check="main"
+    fi
+    echo "Checking out branch: ${branch_name_to_check}"
+    git checkout ${branch_name_to_check}
+    iterations=$((iterations+1))
+  fi
+  done
+  echo "vivarium_branch_name=${vivarium_branch_name}" >> $GITHUB_ENV
+  git checkout ${branch_name}

vivarium_public_health-3.0.1/pyproject.toml

@@ -0,0 +1,21 @@
+[tool.black]
+line_length = 94
+
+[tool.isort]
+line_length = 94
+profile = "black"
+known_third_party = ["vivarium"]
+multi_line_output = 3 # Vertical Hanging Indent, see https://pypi.org/project/isort/
+
+[tool.pytest.ini_options]
+testpaths = ["tests/"]
+
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[tool.coverage.run]
+source = ["vivarium_public_health"]
+
+[tool.coverage.report]
+show_missing = true