Merge pull request #2 from NASA-Planetary-Science/workflows

Workflows and Tests

.github/workflows/pypi-publish.yml

@@ -0,0 +1,30 @@
+# This workflows will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+name: Upload Python Package PyPi
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  deploy:
+    if: github.repository_owner == 'NASA-Planetary-Science'
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.11'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flit
+    - name: Build and publish
+      env:
+        FLIT_USERNAME: '__token__'
+        FLIT_PASSWORD: ${{ secrets.PYPI_TOKEN }}
+      run: |
+        flit publish

.github/workflows/rimseval_testing.yml

@@ -0,0 +1,50 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: tests
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  # Build and test
+  build:
+    if: github.repository_owner == 'NASA-Planetary-Science'
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "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: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install nox
+        pip install .[dev,db_maintainer]
+    - name: Run nox
+      run: nox --no-error-on-missing-interpreters
+    - name: Generate coverage report
+      run: |
+        pip install codecov
+        pip install pytest-cov
+        pytest --cov=./ --cov-report=xml
+        codecov
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v3
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        directory: ./coverage/reports/
+        env_vars: OS,PYTHON
+        fail_ci_if_error: true
+        files: ./coverage.xml
+        flags: unittests
+        name: codecov-umbrella
+        verbose: true

README.md

@@ -1,3 +1,10 @@
+[![PyPi](https://img.shields.io/pypi/v/pgdtools?color=informational)](https://pypi.org/project/pgdtools/)
+[![docs](https://readthedocs.org/projects/pgdtools/badge/?version=latest)](https://pgdtools.readthedocs.io)
+[![License](https://img.shields.io/badge/License-MIT-blue.svg)](https://github.com/NASA-Planetary-Science/pgdtools/blob/main/LICENSE)
+[![tests](https://github.com/NASA-Planetary-Science/pgdtools/actions/workflows/rimseval_testing.yml/badge.svg?branch=main)](https://github.com/NASA-Planetary-Science/pgdtools/)
+[![codecov](https://codecov.io/gh/NASA-Planetary-Science/pgdtools/branch/main/graph/badge.svg?token=N0NNVEI8CX)](https://codecov.io/gh/NASA-Planetary-Science/pgdtools)
+[![Style](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+
 # Presolar grain database tools (pgdTools)
 
 Currently under development.

noxfile.py

@@ -14,7 +14,7 @@
 @nox.session(python=python_main)
 def docs(session):
     """Build the documentation."""
-    session.install("sphinx", "sphinx_rtd_theme", ".[db_maintainer]")
+    session.install("sphinx", "sphinx_rtd_theme", ".[docs]")
     session.chdir("docs")
     session.run(
         "sphinx-build", "-b", "html", ".", "_build/html/"
@@ -25,7 +25,7 @@ def docs(session):
 def lint(session):
     """Lint project using ``flake8``."""
     args = session.posargs or locations
-    session.install(".[dev, db_maintainer]")
+    session.install(".[dev]")
     session.run("flake8", *args)
 
 
@@ -39,7 +39,7 @@ def tests(session):
 @nox.session(python=python_main)
 def safety(session):
     """Safety check for all dependencies."""
-    session.install(".[dev, db_maintainer]", "safety")
+    session.install(".[dev, db_maintainer, docs]", "safety")
     session.run(
         "safety",
         "check",

pgdtools/data/__init__.py

@@ -2,7 +2,7 @@
 
 from pathlib import Path
 
-DB_FILE_URL = "https://raw.githubusercontent.com/NASA-Planetary-Science/pgdtools/main/database/db.json"
+DB_FILE_URL = "https://raw.githubusercontent.com/NASA-Planetary-Science/pgdtools/main/database/db.json"  # noqa: B950
 
 BIBFILE = Path(__file__).parent.joinpath("pgd_references.bib").absolute()
 OLAFKEYFILE = (

pgdtools/pgdtools.py

@@ -224,8 +224,10 @@ def filter_value(
         if comparator not in comp_dict.keys():
             raise ValueError(f"Comparator {comparator} is not valid.")
 
-        # evaluate
-        self.db = self.db[eval(f"self.db[hdr] {comp_dict[comparator]} {value}")]
+        # evaluate -- todo: insecure, but garbage anyway
+        self.db = self.db[
+            eval(f"self.db[hdr] {comp_dict[comparator]} {value}")  # noqa: S307
+        ]
 
     def filter_type(self, grain_type):
         """Filter grain database by grain type.

pyproject.toml

@@ -35,12 +35,12 @@ dev = [
     "requests"
 ]
 
+db_maintainer = [
+    "bibtexparser"
+]
+
 docs = [
     "sphinx",
     "sphinx_rtd_theme",
     "sphinxcontrib-mermaid"
 ]
-
-pds = [
-    "bibtexparser"
-]