Albrja/mic-5834/Add resuable workflows (#488)

Albrja/mic-5834/Add resuable workflows

Add reusable pipelines for github and jenkins
- *Category*: CI
- *JIRA issue*: [MIC-5834](https://jira.ihme.washington.edu/browse/MIC-5834)

-adds reusable pipelines for github and jenkins

### Testing
<!--
Details on how code was verified, any unit tests local for the
repo, regression testing, etc. At a minimum, this should include an
integration test for a framework change. Consider: plots, images,
(small) csv file.

*** REMINDER ***
CI WILL NOT RUN ANY TESTS MARKED AS SLOW (CURRENTLY INCLUDES INTEGRATION TESTS).
MANUALLY RUN SLOW TESTS LIKE `pytest --runslow` WITH EACH PR.
-->
- [ ] all tests pass (`pytest --runslow`)

Author: albrja

.github/workflows/build.yml

@@ -7,65 +7,21 @@ on:
   push:
   pull_request:
   workflow_dispatch:
-  schedule: 
+  schedule:
     - cron: "0 8 * * *"
-
+  
 jobs:
   build:
-    runs-on: ubuntu-latest
     strategy:
       matrix:
         python-version: ["3.10", "3.11"]
-    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 $GITHUB_ENV
-      - name: Update pip
-        run: |
-          python -m pip install --upgrade pip
-      - name: Install dependencies
-        run: |
-          pip install .[dev]
-      - name: Lint
-        run: |
-          pip install black==22.3.0 isort
-          black . --check --diff
-          isort . --check --verbose --only-modified --diff
-      - name: Test
-        run: |
-          if "${{ github.event_name == 'schedule' }}"; then
-            pytest --runslow ./tests
-          else
-            pytest --limit=1 ./tests
-          fi
-      - name: Doc build
-        run: |
-          make html -C docs/ SPHINXOPTS="-W --keep-going -n"
-      - name: Doctest
-        run: |
-          make doctest -C docs/
-      - name: Send mail
-        # Notify when cron job fails
-        if: (github.event_name == 'schedule' && 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: Pseudopeople Notifications
+    uses: 
+      ihmeuw/vivarium_build_utils/.github/workflows/build.yml@main
+    with:
+      dependencies: "layered_config_tree"
+      python_version: ${{ matrix.python-version }}
+      skip_mypy: true
+    secrets:
+      notify_email: ${{ secrets.NOTIFY_EMAIL }}
+      NOTIFY_PASSWORD: ${{ secrets.NOTIFY_PASSWORD }}
+    

.readthedocs.yaml

@@ -1,7 +1,10 @@
 # This is the version for the readthedocs configuration. Version 2 ignores
 # web-based configuration and uses everything from this file.
 version: 2
-
+sphinx:
+  configuration: docs/source/conf.py
+  fail_on_warning: true
+  
 # Configure the python version and environment construction run before
 # docs are built.
 build:
@@ -16,9 +19,5 @@ python:
       extra_requirements:
         - docs
 
-# Doc builds will fail if there are any warnings
-sphinx:
-  fail_on_warning: true
-
 formats:
   - pdf

CHANGELOG.rst

@@ -1,3 +1,7 @@
+**1.2.1 - 02/05/25**
+
+ - Get python versions from python_versions.json
+
 **1.2.0 - 11/14/24**
 
  - Drop support for Python 3.9

Jenkinsfile

@@ -0,0 +1,21 @@
+/*This file uses jenkins shared library `vivarium_build_utils`,
+found at https://github.com/ihmeuw/vivarium_build_utils
+Due to Jenkins convention, importable modules must be stored
+in the 'vars' folder.
+Jenkins needs to be configured globally to use the correct branch.
+To configure the repo/branch go to:
+* Manage Jenkins
+  * Configure System
+    * Global Pipeline Libraries section
+      * Library subsection
+        * Name: The Name for the lib
+        * Version: The branch you want to use. Throws an error
+                   for nonexistent branches.
+        * Project Repository: Url to the shared lib
+        * Credentials: SSH key to access the repo
+
+Updating the shared repo will take affect on the next pipeline invocation.
+The "_" denotes that all modules will be imported from the shared library.
+*/ 
+@Library("vivarium_build_utils") _
+reusable_pipeline(scheduled_branches: ["main", "release-candidate/v.orange.rebased"], upstream_repos: ["layered_config_tree"])

Makefile

@@ -0,0 +1,15 @@
+# Check if we're running in Jenkins
+ifdef JENKINS_URL
+	# Files are already in workspace from shared library
+	MAKE_INCLUDES := .
+else
+	# For local dev, search in parent directory
+	MAKE_INCLUDES := ../vivarium_build_utils/resources/makefiles
+endif
+
+PACKAGE_NAME = pseudopeople
+
+# Include makefiles from vivarium_build_utils
+include $(MAKE_INCLUDES)/base.mk
+include $(MAKE_INCLUDES)/test.mk
+

python_versions.json

@@ -0,0 +1 @@
+["3.10", "3.11"]

setup.py

@@ -1,13 +1,17 @@
+import json
 import sys
 from pathlib import Path
 
 from packaging.version import parse
 from setuptools import find_packages, setup
 
-min_version, max_version = ("3.10", "3.11")
+with open("python_versions.json", "r") as f:
+    supported_python_versions = json.load(f)
+
+python_versions = [parse(v) for v in supported_python_versions]
+min_version = min(python_versions)
+max_version = max(python_versions)
 
-min_version = parse(min_version)
-max_version = parse(max_version)
 
 if not (
     min_version <= parse(".".join([str(v) for v in sys.version_info[:2]])) <= max_version
@@ -56,12 +60,13 @@
 
     test_requirements = [
         "pytest",
+        "pytest-cov",
         "pytest-mock",
     ] + dask_requirements
 
     lint_requirements = [
         "black==22.3.0",
-        "isort",
+        "isort==5.13.2",
     ]
 
     doc_requirements = [