Merge branch 'dev' into hackathon2024

.github/workflows/benchmark.yml

@@ -15,18 +15,15 @@ jobs:
         python-version: ['3.10']
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install pytest
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        python setup.py develop
-        pip install pytest-benchmark
+        python -m pip install .[tests]
     - name: Benchmark with pytest
       run: |
         pytest tests/test_db_benchmark.py --benchmark-json output.json

.github/workflows/codeql.yml

@@ -24,18 +24,18 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Initialize CodeQL
-        uses: github/codeql-action/init@v2
+        uses: github/codeql-action/init@v3
         with:
           languages: ${{ matrix.language }}
           queries: +security-and-quality
 
       - name: Autobuild
-        uses: github/codeql-action/autobuild@v2
+        uses: github/codeql-action/autobuild@v3
 
       - name: Perform CodeQL Analysis
-        uses: github/codeql-action/analyze@v2
+        uses: github/codeql-action/analyze@v3
         with:
           category: "/language:${{ matrix.language }}"

.github/workflows/coveralls.yml

@@ -18,17 +18,16 @@ jobs:
         python-version: ['3.10']
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install flake8 pytest
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        python -m pip install --editable .
+        python -m pip install flake8
+        python -m pip install --editable .[tests]
         cd tests/cannonsim/src; make; cd ../../..
         pip install pytest-cov
         pip install coveralls

.github/workflows/docker.yml

@@ -6,7 +6,7 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Copy Dockerfile
       run: |
         cp tutorials/kubernetes/Dockerfile .

.github/workflows/pdocs.yml

@@ -13,20 +13,20 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        python -m pip install --editable .
+        python -m pip install setuptools
+        python -m pip install --editable .[docs]
         cd tests/cannonsim/src; make; cd ../../.. 
         pip install pdoc
     - name: Checkout
-      uses: actions/checkout@v2.3.1
+      uses: actions/checkout@v3
     - name: Build
       run: |
         export PDOC_ALLOW_EXEC=1

.github/workflows/python-package.yml

@@ -18,17 +18,16 @@ jobs:
         python-version: ['3.8', '3.9', '3.10', '3.11']
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install flake8 pytest
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        python -m pip install --editable .
+        python -m pip install flake8
+        python -m pip install --editable .[tests]
         cd tests/cannonsim/src; make; cd ../../..
         pip install pytest-cov
         pip install coveralls

.github/workflows/pythonpublish.yml

@@ -13,19 +13,22 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install setuptools wheel twine
+        pip install build twine
+    - name: Build package
+      run: python -m build --sdist --wheel
+    - name: Check package
+      run: python -m twine check dist/*
     - name: Build and publish
       env:
         TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
         TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
       run: |
-        python setup.py sdist bdist_wheel
         twine upload dist/*

.gitignore

@@ -21,3 +21,4 @@ pep.sh
 *.csv
 env/
 .ipynb_checkpoints/
+easyvvuq/_version.py

.readthedocs.yaml

@@ -27,9 +27,9 @@ sphinx:
 #    - pdf
 #    - epub
 
-# Optional but recommended, declare the Python requirements required
-# to build your documentation
-# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
-# python:
-#    install:
-#    - requirements: docs/requirements.txt
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

easyvvuq/__init__.py

@@ -11,9 +11,14 @@
 from . import analysis
 from . import comparison
 
-# First make sure python version is 3.6+
-assert sys.version_info >= (3, 6), (f"Python version must be >= 3.6,"
-                                    f"found {sys.version_info}")
+from importlib.metadata import version, PackageNotFoundError
+
+try:
+    __version__ = version("easyvvuq")
+except PackageNotFoundError:
+    from setuptools_scm import get_version  # type: ignore[import]
+
+    __version__ = get_version(root="..", relative_to=__file__)
 
 __copyright__ = """
 
@@ -36,6 +41,3 @@
 
 """
 __license__ = "LGPL"
-
-from . import _version
-__version__ = _version.get_versions()['version']