Merge pull request #20 from ihmeuw-msca/refactor/pypkg-format

Refactor/pypkg-format

.github/workflows/build.yml

@@ -0,0 +1,25 @@
+name: build
+
+on:
+  push:
+    branches:
+      - "*"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.12"
+    - name: Install dependencies
+      run: python -m pip install .[test] --upgrade pip
+    - name: Test with pytest
+      run: pytest --cov=./ --cov-report=xml
+    - name: Upload coverage reports to Codecov
+      uses: codecov/codecov-action@v4
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        slug: ihmeuw-msca/SFMA

.github/workflows/deploy.yml

@@ -0,0 +1,58 @@
+name: deploy
+
+on:
+  push:
+    tags:
+      - "v[0-9]+.[0-9]+.[0-9]+"
+
+permissions:
+  contents: write
+
+jobs:
+  pypi:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.12"
+    - name: Install dependencies
+      run: python -m pip install build . --upgrade pip
+    - name: Build package distribution
+      run: python -m build --sdist --wheel --outdir dist/ .
+    - name: Publish package distribution to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        skip_existing: true
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}
+
+  docs:
+    runs-on: ubuntu-latest
+    permissions:
+      pages: write
+      id-token: write
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - name: Install dependencies
+        run: python -m pip install .[docs] --upgrade pip
+      - name: Generate API docs & Build sphinx documentation
+        run: |
+          git fetch --tags
+          cd docs
+          python build.py
+          cd ..
+      - name: Setup Pages
+        uses: actions/configure-pages@v5
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: './docs/pages'
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.gitignore

@@ -126,13 +126,4 @@ venv.bak/
 dmypy.json
 
 # Pyre type checker
-.pyre/
-
-# pycharm
-.idea/
-
-# vscode
-.vscode/
-
-# mac store
-.DS_Store/
+.pyre/

.pre-commit-config.yaml

@@ -0,0 +1,17 @@
+repos:
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.4.2
+  hooks:
+    - id: ruff
+      args: [ --fix ]
+    - id: ruff-format
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.6.0
+  hooks:
+    - id: trailing-whitespace
+    - id: end-of-file-fixer
+- repo: https://github.com/pre-commit/mirrors-mypy
+  rev: v1.10.0
+  hooks:
+    - id: mypy
+      files: ^src

.vscode/settings.json

@@ -0,0 +1,10 @@
+{
+    "[python]": {
+        "editor.defaultFormatter": "charliermarsh.ruff",
+        "editor.formatOnSave": true,
+        "editor.codeActionsOnSave": {
+            "source.organizeImports": "explicit",
+        },
+        "editor.rulers": [80],
+    },
+}

CODE_OF_CONDUCT.md

@@ -0,0 +1,111 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our community a harassment-free experience for
+everyone, regardless of age, body size, visible or invisible disability, ethnicity, sex characteristics, gender identity
+and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, religion,
+or sexual identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes, and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of acceptable behavior and will take
+appropriate and fair corrective action in response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits,
+issues, and other contributions that are not aligned to this Code of Conduct, and will communicate reasons for
+moderation decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when an individual is officially representing
+the community in public spaces. Examples of representing our community include using an official e-mail address, posting
+via an official social media account, or acting as an appointed representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported to the community leaders responsible
+for enforcement at
+[INSERT CONTACT METHOD]. All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining the consequences for any action they deem
+in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed unprofessional or unwelcome in the
+community.
+
+**Consequence**: A private, written warning from community leaders, providing clarity around the nature of the violation
+and an explanation of why the behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No interaction with the people involved, including
+unsolicited interaction with those enforcing the Code of Conduct, for a specified period of time. This includes avoiding
+interactions in community spaces as well as external channels like social media. Violating these terms may lead to a
+temporary or permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public communication with the community for a specified
+period of time. No public or private interaction with the people involved, including unsolicited interaction with those
+enforcing the Code of Conduct, is allowed during this period. Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community standards, including sustained inappropriate
+behavior, harassment of an individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 2.0, available at
+[https://www.contributor-covenant.org/version/2/0/code_of_conduct.html][v2.0].
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
+
+For answers to common questions about this code of conduct, see the FAQ at
+[https://www.contributor-covenant.org/faq][FAQ]. Translations are available
+at [https://www.contributor-covenant.org/translations][translations].
+
+[homepage]: https://www.contributor-covenant.org
+
+[v2.0]: https://www.contributor-covenant.org/version/2/0/code_of_conduct.html
+
+[Mozilla CoC]: https://github.com/mozilla/diversity
+
+[FAQ]: https://www.contributor-covenant.org/faq
+
+[translations]: https://www.contributor-covenant.org/translations

LICENSE

@@ -1,6 +1,6 @@
 BSD 2-Clause License
 
-Copyright (c) 2021, IHME Math Sciences
+Copyright (c) 2019-2024, IHME Math Sciences
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without
@@ -22,4 +22,4 @@ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

@@ -1,3 +1,12 @@
+[![PyPI](https://img.shields.io/pypi/l/SFMA)](https://pypi.org/project/SFMA/)
+![Python](https://img.shields.io/badge/python-3.10%2B-blue.svg)
+![GitHub Workflow Status](https://img.shields.io/github/actions/workflow/status/ihmeuw-msca/SFMA/build.yml)
+[![GitHub](https://img.shields.io/github/license/ihmeuw-msca/SFMA)](./LICENSE)
+[![docs](https://img.shields.io/badge/docs-here-green)](https://ihmeuw-msca.github.io/SFMA)
+[![codecov](https://img.shields.io/codecov/c/github/ihmeuw-msca/SFMA)](https://codecov.io/gh/ihmeuw-msca/SFMA)
+[![codacy](https://img.shields.io/codacy/grade/ae72a07785f5469eac234d1f6bdf555f)](https://app.codacy.com/gh/ihmeuw-msca/SFMA/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade)
+
+
 # SFMA
 Stochastic Frontier Meta-Analysis
 

notebooks/helpers.py

@@ -5,8 +5,16 @@
 
 
 class Simulator:
-    def __init__(self, nu: int, gamma: int, sigma_min: float, sigma_max: float,
-                 x: callable, func: callable, ineff_dist: str = 'half-normal'):
+    def __init__(
+        self,
+        nu: int,
+        gamma: int,
+        sigma_min: float,
+        sigma_max: float,
+        x: callable,
+        func: callable,
+        ineff_dist: str = "half-normal",
+    ):
         """
         Simulation class for stochastic frontier meta-analysis.
 
@@ -31,17 +39,21 @@ def __init__(self, nu: int, gamma: int, sigma_min: float, sigma_max: float,
         self.x = x
         self.func = func
 
-        if ineff_dist == 'half-normal':
+        if ineff_dist == "half-normal":
             self.rvs = halfnorm.rvs
-        elif ineff_dist == 'exponential':
+        elif ineff_dist == "exponential":
             self.rvs = expon.rvs
         else:
-            raise RuntimeError("Inefficiency distribution must be half-normal or exponential")
+            raise RuntimeError(
+                "Inefficiency distribution must be half-normal or exponential"
+            )
 
     def simulate(self, n: int = 1, seed=None, **kwargs):
         if seed is not None:
             np.random.seed(seed)
-        sigma = stats.uniform.rvs(loc=self.sigma_min, scale=self.sigma_max, size=n)
+        sigma = stats.uniform.rvs(
+            loc=self.sigma_min, scale=self.sigma_max, size=n
+        )
         epsilon = stats.norm.rvs(loc=0, scale=sigma, size=n)
 
         us = stats.norm.rvs(loc=0, scale=self.gamma, size=n)

pyproject.toml

@@ -0,0 +1,33 @@
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "SFMA"
+version = "0.1.0"
+description = "Python package template"
+readme = "README.md"
+requires-python = ">=3.10"
+license = { text = "BSD-2-Clause" }
+authors = [
+    { name = "IHME Math Sciences", email = "[email protected]" },
+]
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: BSD License",
+    "Natural Language :: English",
+]
+dependencies = [
+    "anml==0.2.1",
+    "matplotlib",
+    "msca",
+    "xspline==0.0.7",
+    "numpy<2.0.0"
+]
+
+[project.optional-dependencies]
+test = ["pytest", "pytest-mock"]
+docs = ["sphinx", "sphinx-autodoc-typehints", "furo"]
+
+[project.urls]
+github = "https://github.com/ihmeuw-msca/SFMA"

ruff.toml

@@ -0,0 +1,8 @@
+line-length = 80
+src = ["src"]
+
+[format]
+docstring-code-format = true
+
+[lint.pydocstyle]
+convention = "numpy"