easylink 0.1.0__tar.gz

easylink-0.1.0/.bandit

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

easylink-0.1.0/.flake8

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+[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 =
+    ANN101, # Missing type annotation for self
+    ANN102, # Missing type annotation for cls
+    ANN204, # Missing type annotation for special method
+    D100,   # Missing docstring in public module
+    D104,   # Missing docstring in public package
+    E203,   # Colons should not have whitespace before them (needed for black)
+    W503,   # Line break before binary operator (needed for black)
+
+# 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
+    src/vivarium_gbd_access/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

easylink-0.1.0/.github/CODEOWNERS

@@ -0,0 +1,2 @@
+# default owners
+* @aflaxman @albrja @hussain-jafari @patricktnast @rmudambi @stevebachmeier @zmbc

easylink-0.1.0/.github/pull_request_template.md

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+## Title: Summary, imperative, start upper case, don't end with a period
+<!-- Ideally, <=50 chars. 50 chars is here..: -->
+
+### Description
+<!-- For use in commit message, wrap at 72 chars. 72 chars is here: -->
+- *Category*: <!-- one of bugfix, implementation, refactor, revert,
+                   test, release, other/misc -->
+- *JIRA issue*: https://jira.ihme.washington.edu/browse/MIC-XYZ
+- *Research reference*: <!--Link to research documentation for code -->
+
+### Changes and notes
+<!-- 
+Change description – why, what, anything unexplained by the above.
+Include guidance to reviewers if changes are complex.
+--> 
+
+### Verification and Testing
+<!--
+Details on how code was verified. Consider: plots, images, (small) csv files.
+-->
+

easylink-0.1.0/.github/workflows/build.yml

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+# -----------------------------------------------------------------------------
+#   - invoked on push, pull_request, or manual trigger
+#   - test under at least 3 versions of python
+# -----------------------------------------------------------------------------
+name: build
+on: [push, pull_request, workflow_dispatch]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.11", "3.12"]
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Print environment values
+        run: |
+          python --version
+          cat $GITHUB_ENV
+      - name: Update pip
+        run: |
+          python -m pip install --upgrade pip
+      - name: Lint
+        run: |
+          pip install black==22.3.0 isort
+          black . --check --diff
+          isort . --check --verbose --only-modified --diff
+      - name: Install dependencies
+        run: |
+          pip install .[dev]
+      - name: Test
+        run: |
+          pytest ./tests

easylink-0.1.0/.github/workflows/deploy.yml

@@ -0,0 +1,50 @@
+name: deploy
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+      - name: Install dependencies
+        run: |
+          python --version
+          python -m pip install --upgrade pip
+          pip install setuptools wheel build
+      - name: Test
+        run: |
+          pip install .[test]
+          pytest ./tests
+      - name: Build
+        run: python -m build
+      - name: Publish
+        uses: pypa/gh-action-pypi-publish@release/v1
+      - name: Send mail
+        # Notify when cron job fails
+        if: failure()
+        uses: dawidd6/action-send-mail@v2
+        with:
+          # mail server settings
+          server_address: smtp.gmail.com
+          server_port: 465
+          # user credentials
+          username: ${{ secrets.NOTIFY_EMAIL }}
+          password: ${{ secrets.NOTIFY_PASSWORD }}
+          # email subject
+          subject: ${{ github.job }} job of ${{ github.repository }} has ${{ job.status }}
+          # email body as text
+          body: ${{ github.job }} job in worflow ${{ github.workflow }} of ${{ github.repository }} has ${{ job.status }}
+          # comma-separated string, send email to
+          to: uw_ihme_simulationscience@uw.edu
+          # from email name
+          from: Vivarium Notifications
+          

easylink-0.1.0/.gitignore

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+**/*.tar
+**/*.tar.gz
+**/*.sif
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+*.pyc
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pycharm project settings
+.idea/
+
+# Vscode project settings
+.vscode/
+
+# Local user jupyter notebooks directory
+notebooks/
+
+# Mac OS stuff
+.DS_Store
+
+# Version
+src/easylink/_version.py
+
+# Local specification files
+.specifications/
+
+.snakemake/

easylink-0.1.0/CHANGELOG.rst

@@ -0,0 +1,3 @@
+**0.1.0 - 11/22/24**
+
+ - Initial release

easylink-0.1.0/Jenkinsfile

@@ -0,0 +1,259 @@
+def githubUsernameToSlackName(github_author) {
+  // Add team members as necessary
+  def mapping = [
+    "Jim Albright": "albrja",
+    "Steve Bachmeier": "sbachmei",
+    "Hussain Jafari": "hjafari",
+    "Patrick Nast": "pnast",
+    "Rajan Mudambi": "rmudambi",
+  ]
+  return mapping.get(github_author, "channel")
+}
+
+pipeline_name="easylink"
+conda_env_name="${pipeline_name}-${BUILD_NUMBER}"
+// using /tmp for things is MUCH faster but not shared between nodes.
+shared_filesystem_path="/mnt/team/simulation_science/priv/engineering/tests"
+conda_env_path="${shared_filesystem_path}/venv/${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_jenkins_node_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 {
+    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."
+    )
+  }
+
+  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_jenkins_node_path}/miniconda3/.condarc"
+    CONDA_BIN_PATH = "${shared_jenkins_node_path}/miniconda3/bin"
+    // Specify conda env by build number so that we don't have collisions if builds from
+    // different branches happen concurrently.
+    CONDA_ENV_NAME = "${conda_env_name}"
+    CONDA_ENV_PATH = "${conda_env_path}"
+    // Set the Pip cache.
+    XDG_CACHE_HOME = "${shared_jenkins_node_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 ${CONDA_ENV_PATH} &> /dev/null"
+  }
+
+  stages {
+    stage("Initialization") {
+      steps {
+        script {
+          // Use the name of the branch in the build name
+          currentBuild.displayName = "#${BUILD_NUMBER} ${GIT_BRANCH}"
+          // Tell BitBucket that a build has started.
+          notifyBitbucket()
+        }
+      }
+    }
+
+    stage("Debug Info") {
+      steps {
+        echo "Jenkins pipeline run timestamp: ${TIMESTAMP}"
+        // Display environment variables from Jenkins.
+        echo """Environment:
+        ACTIVATE:       '${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}'"""
+        // display env
+        sh "env | sort"
+      }
+    }
+
+    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"
+        // open permissions for test users to create file in workspace
+        sh "chmod 777 ${WORKSPACE}"
+      }
+    }
+
+    stage("Install Package") {
+      steps {
+        // NOTE: If you're having issues with the env not being found, it's possible
+        // that 'make install' is generating symlinks. Try adding
+        // '&& pip install .' to install a second time w/ realpaths.
+        sh "${ACTIVATE} && make install && pip install ."
+      }
+    }
+
+    stage("Quality Checks") {
+      parallel {
+        stage("Format") {
+          steps {
+            sh "${ACTIVATE} && make format"
+          }
+        }
+
+        stage("Lint") {
+          steps {
+            sh "${ACTIVATE} && make lint"
+          }
+        }
+
+        stage("Type Check") {
+          steps {
+            sh "${ACTIVATE} && make typecheck"
+          }
+        }
+      }
+    }
+
+    stage("Test") {
+      parallel {
+        stage("Run End-to-End Tests") {
+          steps {
+            sh "${ACTIVATE} && make e2e"
+            publishHTML([
+              allowMissing: true,
+              alwaysLinkToLastBuild: false,
+              keepAll: true,
+              reportDir: "output/htmlcov_e2e",
+              reportFiles: "index.html",
+              reportName: "Coverage Report - E2E Tests",
+              reportTitles: ''
+            ])
+          }
+        }
+
+        stage("Run Integration Tests") {
+          steps {
+            sh "${ACTIVATE} && make integration"
+            publishHTML([
+              allowMissing: true,
+              alwaysLinkToLastBuild: false,
+              keepAll: true,
+              reportDir: "output/htmlcov_integration",
+              reportFiles: "index.html",
+              reportName: "Coverage Report - Integration Tests",
+              reportTitles: ''
+            ])
+          }
+        }
+      
+        stage("Run Unit Tests") {
+          steps {
+            sh "${ACTIVATE} && make unit"
+            publishHTML([
+              allowMissing: true,
+              alwaysLinkToLastBuild: false,
+              keepAll: true,
+              reportDir: "output/htmlcov_unit",
+              reportFiles: "index.html",
+              reportName: "Coverage Report - Unit Tests",
+              reportTitles: ''
+            ])
+          }
+        }
+      }
+    }
+  }
+
+  post {
+    always {
+      script {
+        if (env.BRANCH == "main") {
+          channelName = "simsci-ci-status"
+        } else {
+          channelName = "simsci-ci-status-test"
+        }
+        // Run git command to get the author of the last commit
+        developerID = sh(
+          script: "git log -1 --pretty=format:'%an'",
+          returnStdout: true
+        ).trim()
+        slackID = githubUsernameToSlackName(developerID)
+        slackMessage = """
+          Job: *${env.JOB_NAME}*
+          Build number: #${env.BUILD_NUMBER}
+          Build status: *${currentBuild.result}*
+          Author: @${slackID}
+          Build details: <${env.BUILD_URL}/console|See in web console>
+      """.stripIndent()
+
+      // Must be after setting up slack message
+      if (params.DEBUG) {
+          echo "Debug is enabled. Not cleaning up."
+        } else {
+          echo "Cleaning up."
+          sh "${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: slackMessage,
+                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: slackMessage,
+                    teamDomain: "ihme",
+                    tokenCredentialId: "slack"
+        }
+      }
+    }
+  }
+}

easylink-0.1.0/Makefile

@@ -0,0 +1,101 @@
+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 = easylink
+SAFE_NAME = $(shell python -c "from pkg_resources import safe_name; print(safe_name(\"$(PACKAGE_NAME)\"))")
+
+about_file   = $(shell find src -name __about__.py)
+version_file = $(shell find src -name _version.py)
+version_line = $(shell grep "__version__ = " ${version_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.
+# TODO: [MIC-4953] build w/ multiple python versions
+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
+	conda install python-graphviz
+	pip install --upgrade pip setuptools
+	pip install -e .[DEV]
+
+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`" > $@
+
+typecheck: pytype.cfg $(MAKE_SOURCES) # Run the type checker
+	-pytype --config=pytype.cfg $(LOCATIONS)
+	@echo "Ignore, Created by Makefile, `date`" > $@
+
+e2e: $(MAKE_SOURCES) # Run the e2e tests
+	export COVERAGE_FILE=./output/.coverage.e2e
+	pytest -vvv --runslow --cov --cov-report term --cov-report html:./output/htmlcov_e2e tests/e2e/
+	@echo "Ignore, Created by Makefile, `date`" > $@
+
+integration: $(MAKE_SOURCES) # Run unit tests
+	export COVERAGE_FILE=./output/.coverage.integration
+	pytest -vvv --runslow --cov --cov-report term --cov-report html:./output/htmlcov_integration tests/integration/
+	@echo "Ignore, Created by Makefile, `date`" > $@
+
+unit: $(MAKE_SOURCES) # Run unit tests
+	export COVERAGE_FILE=./output/.coverage.unit
+	pytest -vvv --runslow --cov --cov-report term --cov-report html:./output/htmlcov_unit tests/unit/
+	@echo "Ignore, Created by Makefile, `date`" > $@
+
+clean: # Delete build artifacts and do any custom cleanup such as spinning down services
+	@rm -rf format lint typecheck build-doc build-package unit e2e integration .pytest_cache .pytype
+	@rm -rf dist output
+	$(shell find . -type f -name '*py[co]' -delete -o -type d -name __pycache__ -delete)
+
+quick: # Run a "quick" build
+	$(MAKE) format lint typecheck unit build-doc
+
+full: clean # Run a "full" build
+	$(MAKE) install quick e2e build-package