Merge pull request #87 from PainterQubits/develop

Merge develop into main

.github/dependabot.yml

@@ -1,12 +1,12 @@
 version: 2
 updates:
-  - package-ecosystem: "pip"
+  - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
       interval: "weekly"
     target-branch: "develop"
 
-  - package-ecosystem: "github-actions"
+  - package-ecosystem: "pip"
     directory: "/"
     schedule:
       interval: "weekly"

.github/workflows/ci.yml

@@ -12,7 +12,7 @@ on:
 
 env:
   PYTHON_VERSION: "3.10"
-  POETRY_VERSION: "1.5.0"
+  POETRY_VERSION: "1.5.1"
 
 jobs:
   ci:
@@ -31,7 +31,7 @@ jobs:
           cache: poetry
 
       - name: Install dependencies
-        run: poetry install --all-extras
+        run: poetry install --all-extras --without docs
 
       - name: Check Formatting (Black)
         run: poetry run black paramdb tests --check
@@ -54,4 +54,7 @@ jobs:
         run: poetry run mypy paramdb tests
 
       - name: Test (Pytest)
-        run: poetry run pytest
+        run: poetry run pytest --cov=paramdb --cov-report=xml
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3

.github/workflows/publish.yml

@@ -0,0 +1,45 @@
+name: Publish
+
+on:
+  release:
+    types: [published]
+
+env:
+  PYTHON_VERSION: "3.10"
+  POETRY_VERSION: "1.5.1"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Install Poetry
+        run: pipx install poetry==${{ env.POETRY_VERSION }}
+
+      - name: Build package
+        run: poetry build
+
+      - name: Upload package artifact
+        uses: actions/upload-artifact@v3
+        with:
+          name: paramdb-release
+          path: dist
+
+  publish:
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/project/paramdb
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v3
+        with:
+          name: paramdb-release
+          path: dist
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.gitignore

@@ -14,7 +14,8 @@ __pycache__/
 .mypy_cache/
 .pytest_cache/
 .coverage
+coverage.xml
 
-# Data files
+# Database files
 *.db
 *.db-journal

.readthedocs.yaml

@@ -0,0 +1,15 @@
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+  jobs:
+    post_create_environment:
+      - pip install poetry==1.5.1
+      - poetry config virtualenvs.create false
+    post_install:
+      - poetry install --without dev
+
+sphinx:
+  configuration: docs/conf.py

CHANGELOG.md

@@ -2,11 +2,21 @@
 
 All notable changes to this project will be documented in this file.
 
-The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/), and this
 project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
 
+## [0.8.0] (June 9 2023)
+
+### Changed
+
+- Documentation website moved to Read the Docs.
+
+### Added
+
+- Badges for latest PyPI version, license, CI status, Codecov, and docs website build.
+
 ## [0.7.0] (May 19 2023)
 
 ### Changed
@@ -89,7 +99,8 @@ project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 - Database class `ParamDB` to store parameters in a SQLite file
 - Ability to retrieve the commit history as `CommitEntry` objects
 
-[unreleased]: https://github.com/PainterQubits/paramdb/compare/v0.7.0...main
+[unreleased]: https://github.com/PainterQubits/paramdb/compare/v0.8.0...develop
+[0.8.0]: https://github.com/PainterQubits/paramdb/releases/tag/v0.8.0
 [0.7.0]: https://github.com/PainterQubits/paramdb/releases/tag/v0.7.0
 [0.6.0]: https://github.com/PainterQubits/paramdb/releases/tag/v0.6.0
 [0.5.0]: https://github.com/PainterQubits/paramdb/releases/tag/v0.5.0

CITATION.cff

@@ -4,7 +4,6 @@ authors:
   - family-names: "Hadley"
     given-names: "Alex"
 title: "ParamDB"
-version: 0.7.0
-# doi: 10.5281/zenodo.xxxx
-date-released: 2023-05-19
+version: 0.8.0
+date-released: 2023-06-09
 url: "https://github.com/PainterQubits/paramdb"

README.md

@@ -1,8 +1,14 @@
 # ParamDB
 
+[![PyPI Latest Release](https://img.shields.io/pypi/v/paramdb)](https://pypi.org/project/paramdb/)
+[![License](https://img.shields.io/pypi/l/paramdb)](https://github.com/PainterQubits/paramdb/blob/main/LICENSE)
+[![CI](https://github.com/PainterQubits/paramdb/actions/workflows/ci.yml/badge.svg)](https://github.com/PainterQubits/paramdb/actions/workflows/ci.yml)
+[![Codecov](https://codecov.io/github/PainterQubits/paramdb/branch/main/graph/badge.svg?token=PQEJWLBTBK)](https://codecov.io/github/PainterQubits/paramdb)
+[![Documentation Status](https://readthedocs.org/projects/paramdb/badge/?version=stable)](https://paramdb.readthedocs.io/en/stable/?badge=stable)
+
 <!-- start intro -->
 
-Python library for storing and retrieving experiment parameters.
+Python package for storing and retrieving experiment parameters.
 
 <!-- end intro -->
 
@@ -13,28 +19,16 @@ Python library for storing and retrieving experiment parameters.
 Install the latest version of ParamDB using pip:
 
 ```
-pip install -U paramdb --extra-index-url https://painterqubits.github.io/paramdb/releases
+pip install -U paramdb
 ```
 
-To install along with [Astropy] for support for storing [`astropy.units.Quantity`]
+To install along with [Astropy] for support for storing scalar [`astropy.units.Quantity`]
 objects in the database, ParamDB can be installed with the `astropy` extra:
 
 ```
-pip install -U paramdb[astropy] --extra-index-url https://painterqubits.github.io/paramdb/releases
-```
-
-The `extra-index-url` parameter is needed since ParamDB is not published to PyPI yet. If
-you are using a Python package manager, add
-`https://painterqubits.github.io/paramdb/releases` as a secondary source. For example, for
-[Poetry] the command is
-
-```
-poetry source add --secondary paramdb https://painterqubits.github.io/paramdb/releases
+pip install -U paramdb[astropy]
 ```
 
-Then the package can be installed like any other (e.g. `poetry add paramdb`).
-
-[poetry]: https://python-poetry.org
 [astropy]: https://docs.astropy.org/en/stable/index.html
 [`astropy.units.quantity`]: https://docs.astropy.org/en/stable/api/astropy.units.Quantity.html#astropy.units.Quantity
 
@@ -52,6 +46,6 @@ ParamDB has two main components:
 
 See the [api reference] for more information.
 
-[**parameter data**]: https://painterqubits.github.io/paramdb/parameter-data.html
-[**database**]: https://painterqubits.github.io/paramdb/database.html
-[api reference]: https://painterqubits.github.io/paramdb/api-reference
+[**parameter data**]: https://paramdb.readthedocs.io/en/stable/parameter-data.html
+[**database**]: https://paramdb.readthedocs.io/en/stable/database.html
+[api reference]: https://paramdb.readthedocs.io/en/stable/api-reference.html

docs/conf.py

@@ -4,7 +4,7 @@
 project = "ParamDB"
 copyright = "2023, California Institute of Technology"
 author = "Alex Hadley"
-release = "0.7.0"
+release = "0.8.0"
 
 # General configuration
 extensions = [

paramdb/_database.py

@@ -165,13 +165,13 @@ def commit(self, message: str, data: T) -> int:
     @overload
     def load(
         self, commit_id: int | None = None, *, load_classes: Literal[True] = True
-    ) -> T:
+    ) -> T:  # pragma: no cover
         ...
 
     @overload
     def load(
         self, commit_id: int | None = None, *, load_classes: Literal[False]
-    ) -> dict[str, Any]:
+    ) -> dict[str, Any]:  # pragma: no cover
         ...
 
     def load(self, commit_id: int | None = None, *, load_classes: bool = True) -> Any:

paramdb/_param_data/_collections.py

@@ -61,22 +61,22 @@ def __init__(self, iterable: Iterable[T] | None = None) -> None:
                 self._add_child(item)
 
     @overload
-    def __getitem__(self, index: SupportsIndex) -> T:
+    def __getitem__(self, index: SupportsIndex) -> T:  # pragma: no cover
         ...
 
     @overload
-    def __getitem__(self, index: slice) -> list[T]:
+    def __getitem__(self, index: slice) -> list[T]:  # pragma: no cover
         ...
 
     def __getitem__(self, index: Any) -> Any:
         return self._contents[index]
 
     @overload
-    def __setitem__(self, index: SupportsIndex, value: T) -> None:
+    def __setitem__(self, index: SupportsIndex, value: T) -> None:  # pragma: no cover
         ...
 
     @overload
-    def __setitem__(self, index: slice, value: Iterable[T]) -> None:
+    def __setitem__(self, index: slice, value: Iterable[T]) -> None:  # pragma: no cover
         ...
 
     def __setitem__(self, index: SupportsIndex | slice, value: Any) -> None:

paramdb/_param_data/_dataclasses.py

@@ -29,7 +29,7 @@ def __setitem__(self, name: str, value: Any) -> None:
 
     @property
     @abstractmethod
-    def last_updated(self) -> datetime | None:
+    def last_updated(self) -> datetime | None:  # pragma: no cover
         ...
 
     def to_dict(self) -> dict[str, Any]: