Chore/update deps (#72)

* chore: Update pre-commits

* chore: Update tables, update Python to >=3.9,<3.13, update pyproject dev config

* chore: Install with all extras

* docs: Coverage badge

* docs: Update changelog

* chore: Github CI Python version in matrix

* fix: Typos in package name

* chore: Update CI

* chore: Update lock file

* chore: Python <3.12

* chore: Remove coverage files after testing

* chore: Update lock file

* fix: Do not use pipe types, to ensure backwards compatibility

.github/workflows/ci.yml

@@ -2,25 +2,31 @@ name: CI
 
 on:
   pull_request:
+    types:
+      - opened
+      - synchronize
+      - reopened
+      - ready_for_review
     branches:
       - main
 
 jobs:
-
   lint:
+    if: github.event.pull_request.draft == false
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
-      - uses: jpetrucciani/black-check@master
+      - uses: jpetrucciani/ruff-check@main
 
-  pytest:
+  pytest-linux:
+    if: github.event.pull_request.draft == false
     strategy:
         matrix:
-            os: [ubuntu-latest]
-            python-version: ["3.8", "3.9", "3.10", "3.11"]
-    runs-on: ${{ matrix.os }}
+            python-version: ["3.9", "3.10", "3.11"]
+
+    runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Install Poetry
         run: pipx install poetry
@@ -31,13 +37,10 @@ jobs:
           python-version: ${{ matrix.python-version }}
           cache: "poetry"
 
-      - name: Install HDF5
-        run: sudo apt install --fix-missing libhdf5-serial-dev
-
       - name: Install Dependencies
         run: |
           poetry env use "${{ matrix.python-version }}"
-          poetry install
+          poetry install --extras all
 
       - name: Test with pytest
-        run: poetry run pytest --dist no -n 0
+        run: poetry run pytest

.github/workflows/docs.yml

@@ -15,23 +15,25 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Install Poetry
         run: pipx install poetry
 
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: "3.10"
+          python-version: "3.11"
           cache: "poetry"
 
       - name: Install Dependencies
-        run: poetry install
+        run: |
+          poetry env use "${{ matrix.python-version }}"
+          poetry install --extras all
 
       - name: Build documentation
         run: |
-          poetry env use "3.10"
+          poetry env use "3.11"
           poetry run pdoc --docformat google src/doubt -o docs
 
       - name: Compress documentation

.pre-commit-config.yaml

@@ -1,23 +1,28 @@
 repos:
--   repo: https://github.com/ambv/black
-    rev: 23.3.0
+-   repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0
     hooks:
-    - id: black
--   repo: https://github.com/timothycrosley/isort
-    rev: 5.12.0
+      - id: python-use-type-annotations
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
     hooks:
-    -   id: isort
--   repo: https://github.com/pycqa/flake8
-    rev: 6.0.0
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: debug-statements
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.3.2
     hooks:
-    - id: flake8
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+        types_or: [python, pyi, jupyter]
+      - id: ruff-format
+        types_or: [python, pyi, jupyter]
 -   repo: https://github.com/kynan/nbstripout
-    rev: 0.6.0
+    rev: 0.7.1
     hooks:
     -   id: nbstripout
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.4.1
+    rev: v1.9.0
     hooks:
     -   id: mypy
         args: [--install-types, --non-interactive, --ignore-missing-imports, --show-error-codes]
-

CHANGELOG.md

@@ -8,6 +8,12 @@ and this project adheres to
 [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
 
+## [Unreleased]
+### Changed
+- Updated `tables` dependency to v3.9.x, which fixes issues with installation of the
+  package. This requires Python 3.9 or above, however, so we require that here as well.
+
+
 ## [v5.1.0] - 2023-10-31
 ### Added
 - The `Boot` class now has `save` and `load` methods, which uses `joblib` under the

README.md

@@ -7,7 +7,7 @@ ______________________________________________________________________
 [![Documentation](https://img.shields.io/badge/docs-passing-green)](https://saattrupdan.github.io/doubt/doubt.html)
 [![License](https://img.shields.io/github/license/saattrupdan/doubt)](https://github.com/saattrupdan/doubt/blob/main/LICENSE)
 [![LastCommit](https://img.shields.io/github/last-commit/saattrupdan/doubt)](https://github.com/saattrupdan/doubt/commits/main)
-[![Code Coverage](https://img.shields.io/badge/Coverage-67%25-yellow.svg)](https://github.com/saattrupdan/doubt/tree/dev/tests)
+[![Code Coverage](https://img.shields.io/badge/Coverage-66%25-yellow.svg)](https://github.com/saattrupdan/doubt/tree/dev/tests)
 [![Conference](https://img.shields.io/badge/Conference-AAAI23-blue)](https://doi.org/10.1609/aaai.v37i12.26755)
 
 A Python package to include prediction intervals in the predictions of machine

makefile

@@ -44,7 +44,7 @@ install: ## Install dependencies
 	@$(MAKE) setup-git
 
 setup-poetry:
-	@poetry env use python3.10 && poetry install
+	@poetry env use python3.10 && poetry install --extras all
 
 setup-environment-variables:
 	@poetry run python3.10 -m src.scripts.fix_dot_env_file
@@ -109,7 +109,7 @@ publish-minor: bump-minor publish  ## Publish a minor version
 publish-patch: bump-patch publish  ## Publish a patch version
 
 test:  ## Run tests
-	@poetry run pytest && readme-cov
+	@poetry run pytest && readme-cov && rm .coverage*
 
 tree:  ## Print directory tree
 	@tree -a \