Merge pull request #922 from rickecon/tests

Update GH Actions and CodeCov

.github/workflows/build_and_test.yml

@@ -1,14 +1,25 @@
-name: Build and test [Python 3.9, 3.10, 3.11]
-
-on: [push, pull_request]
-  # paths:
-  #   - '*.py'
-  #   - 'environment.yml'
-  #   - 'requirements.txt'
-  #   - '*.pkl'
-  #   - '*.csv'
-  #   - '*.json'
-
+name: Build and test
+on:
+  push:
+    paths:
+      - '**.yml'
+      - '**.toml'
+      - '**.ini'
+      - '**.py'
+      - '**.json'
+      - '**.csv'
+      - '**.pkl'
+      - '**.pbz2'
+  pull_request:
+    paths:
+      - '**.yml'
+      - '**.toml'
+      - '**.ini'
+      - '**.py'
+      - '**.json'
+      - '**.csv'
+      - '**.pkl'
+      - '**.pbz2'
 jobs:
   build:
     runs-on: ${{ matrix.os }}
@@ -19,36 +30,34 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           persist-credentials: false
-
       - name: Setup Miniconda using Python ${{ matrix.python-version }}
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           miniforge-variant: Mambaforge
           auto-update-conda: true
           activate-environment: ogcore-dev
           environment-file: environment.yml
           python-version: ${{ matrix.python-version }}
           auto-activate-base: false
-
       - name: Build
         shell: bash -l {0}
         run: |
           pip install -e .
-          pip install pytest-cov
-          pip install pytest-pycodestyle
       - name: Test
         shell: bash -l {0}
         working-directory: ./
         run: |
-          pytest -m 'not local' --cov=./ --cov-report=xml
+          python -m pytest -m "not local" --cov=./ --cov-report=xml
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v3
+        if: matrix.os == 'ubuntu-latest'
+        uses: codecov/codecov-action@v4
         with:
           files: ./coverage.xml
           flags: unittests
           name: codecov-umbrella
+          token: ${{ secrets.CODECOV_TOKEN }}
           fail_ci_if_error: true
           verbose: true

.github/workflows/deploy_docs.yml

@@ -3,6 +3,14 @@ on:
   push:
     branches:
       - master
+    paths:
+      - './docs/**.png'
+      - './docs/book/content/theory/images/**.png'
+      - './docs/book/**.yml'
+      - './docs/book/**.bib'
+      - '**.md'
+      - './docs/book/content/api/**.rst'
+      - './ogcore/**.py'
 jobs:
   build-and-deploy:
     if: github.repository == 'PSLmodels/OG-Core'
@@ -14,21 +22,20 @@ jobs:
           persist-credentials: false
 
       - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           miniforge-variant: Mambaforge
-          activate-environment: ogusa-dev
+          activate-environment: ogcore-dev
           environment-file: environment.yml
-          python-version: "3.10"
+          python-version: "3.11"
           auto-activate-base: false
 
       - name: Build # Build Jupyter Book
         shell: bash -l {0}
         run: |
           pip install -e .
           python -m ipykernel install --user --name=ogcore-dev
-          cd docs
-          jb build ./book
+          jb build ./docs/book
 
       - name: Deploy
         uses: JamesIves/github-pages-deploy-action@v4

.github/workflows/docs_check.yml

@@ -1,28 +1,36 @@
 name: Check that docs build
-on: [push, pull_request]
+on:
+  pull_request:
+    paths:
+      - './docs/**.png'
+      - './docs/book/content/theory/images/**.png'
+      - './docs/book/**.yml'
+      - './docs/book/**.bib'
+      - '**.md'
+      - './docs/book/content/api/**.rst'
+      - './ogcore/**.py'
 
 jobs:
   build:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v4 # If you're using actions/checkout@v2 you must set persist-credentials to false in most cases for the deployment to work correctly.
+        uses: actions/checkout@v4
         with:
           persist-credentials: false
 
       - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           miniforge-variant: Mambaforge
-          activate-environment: ogusa-dev
+          activate-environment: ogcore-dev
           environment-file: environment.yml
-          python-version: "3.10"
+          python-version: "3.11"
           auto-activate-base: false
 
       - name: Build # Build Jupyter Book
         shell: bash -l {0}
         run: |
           pip install -e .
           python -m ipykernel install --user --name=ogcore-dev
-          cd docs
-          jb build ./book
+          jb build ./docs/book

.github/workflows/publish_to_pypi.yml

@@ -12,16 +12,16 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: Setup Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: "3.11"
       - name: Build package
         run: make pip-package
       - name: Publish a Python distribution to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
           user: __token__
           password: ${{ secrets.PYPI }}
-          skip_existing: true
+          skip_existing: true

CHANGELOG.md

@@ -6,6 +6,15 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 
+## [0.11.5] - 2024-04-11 12:00:00
+
+### Added
+
+- Adds a list of file change event triggers to `build_and_test.yml` so that those tests only run when one of those files is changed.
+- Updates the codecov GH Action to version 4 and adds a secret token.
+- Adds a list of file change event triggers to `deploy_docs.yml` and `docs_check.yml`, and limits `docs_check.yml` to only run on pull requests.
+
+
 ## [0.11.4] - 2024-04-03 22:00:00
 
 ### Added
@@ -210,6 +219,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Any earlier versions of OG-USA can be found in the [`OG-Core`](https://github.com/PSLmodels/OG-Core) repository [release history](https://github.com/PSLmodels/OG-Core/releases) from [v.0.6.4](https://github.com/PSLmodels/OG-Core/releases/tag/v0.6.4) (Jul. 20, 2021) or earlier.
 
 
+[0.11.5]: https://github.com/PSLmodels/OG-Core/compare/v0.11.4...v0.11.5
 [0.11.4]: https://github.com/PSLmodels/OG-Core/compare/v0.11.3...v0.11.4
 [0.11.3]: https://github.com/PSLmodels/OG-Core/compare/v0.11.2...v0.11.3
 [0.11.2]: https://github.com/PSLmodels/OG-Core/compare/v0.11.1...v0.11.2

codecov.yml

@@ -22,7 +22,4 @@ comment:
 ignore:
   - "setup.py"
   - "./ogcore/_version.py"
-  - "./cs-config/**/*"  # ignore folders and all its contents
   - "./tests/"  # ignore folders and all its contents
-  - "./ogcore/tests/"  # ignore folders and all its contents
-  - "./regression/**/*"  # ignore folders and all its contents

environment.yml

@@ -13,19 +13,20 @@ dependencies:
 - dask-core>=2.30.0
 - distributed>=2.30.1
 - paramtools>=0.15.0
-- sphinx
+- sphinx>=3.5.4
 - sphinx-argparse
 - sphinxcontrib-bibtex>=2.0.0
 - sphinx-math-dollar
 - pydata-sphinx-theme
 - jupyter-book>=0.11.3
 - jupyter
 - pytest>=6.0
+- pytest-cov
 - pytest-xdist
 - pylint
 - coverage
 - requests
-- openpyxl
+- openpyxl>=3.1.2
 - black>=24.1.1
 - pip
 - pip:

ogcore/SS.py

@@ -255,7 +255,7 @@ def inner_loop(outer_loop_vars, p, client):
         results = results = compute(
             *lazy_values,
             scheduler=dask.multiprocessing.get,
-            num_workers=p.num_workers
+            num_workers=p.num_workers,
         )
 
     for j, result in enumerate(results):

ogcore/TPI.py

@@ -743,7 +743,7 @@ def run_TPI(p, client=None):
             results = results = compute(
                 *lazy_values,
                 scheduler=dask.multiprocessing.get,
-                num_workers=p.num_workers
+                num_workers=p.num_workers,
             )
 
         for j, result in enumerate(results):

ogcore/__init__.py

@@ -20,4 +20,4 @@
 from ogcore.txfunc import *
 from ogcore.utils import *
 
-__version__ = "0.11.4"
+__version__ = "0.11.5"

ogcore/demographics.py

@@ -165,17 +165,17 @@ def get_fert(
     if graph:
         if plot_path:
             pp.plot_fert_rates(
-                fert_rates_2D,
-                start_year,
-                [start_year, end_year],
+                [fert_rates_2D],
+                start_year=start_year,
+                years_to_plot=[start_year, end_year],
                 path=plot_path,
             )
             return fert_rates_2D
         else:
             fig = pp.plot_fert_rates(
-                fert_rates_2D,
-                start_year,
-                [start_year, end_year],
+                [fert_rates_2D],
+                start_year=start_year,
+                years_to_plot=[start_year, end_year],
             )
             return fert_rates_2D, fig
     else:

pyproject.toml

@@ -1,3 +1,15 @@
 [build-system]
-requires = ["setuptools>=42"]
+requires = ["setuptools>=61.0"]
 build-backend = "setuptools.build_meta"
+
+# Configuration for Black.
+
+# NOTE: you have to use single-quoted strings in TOML for regular expressions.
+# It's the equivalent of r-strings in Python.  Multiline strings are treated as
+# verbose regular expressions by Black.  Use [ ] to denote a significant space
+# character.
+
+[tool.black]
+line-length = 79
+target-version = ["py39", "py310", "py311"]
+include = '\.pyi?$'

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="ogcore",
-    version="0.11.4",
+    version="0.11.5",
     author="Jason DeBacker and Richard W. Evans",
     license="CC0 1.0 Universal (CC0 1.0) Public Domain Dedication",
     description="A general equilibribum overlapping generations model for fiscal policy analysis",

tests/test_demographics.py

@@ -260,7 +260,7 @@ def test_infant_mort():
     mort_rates, infmort_rate = demographics.get_mort(100, 0, 99, graph=False)
     # check that infant mortality equals rate hardcoded into
     # demographics.py
-    assert infmort_rate == 0.00491958
+    assert infmort_rate == 0.00477758
 
 
 def test_pop_rebin():