Modernize build system (#42)

* Modernize build system

Fixes #28. Also updating GitHub workflows, README/CONTRIBUTING, etc.

* Switch to using syrupy

pytest-snapshottest uses imp, which was deprecated in 3.11 and gone now.
They don't look like moving
syrusakbary/snapshottest#166

Conflicts:
	.github/workflows/python-build-test.yml

.github/workflows/python-build-test.yml

@@ -14,7 +14,8 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
@@ -24,12 +25,9 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install .
-        pip install -r test_requirements.txt
+        python -m pip install .[dev,test]
     - name: Lint with flake8 and black
       run: |
-        pip install flake8
-        pip install black
         # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # test remaining issues
@@ -38,7 +36,6 @@ jobs:
     - name: Test
       run: |
         pytest .
-
     - name: Run Examples
       run: |
         open_petro_elastic --data-file examples/example1.csv examples/example1.yaml

.github/workflows/python-publish.yml

@@ -2,7 +2,7 @@ name: Publish to PyPI
 
 on:
   release:
-    types: [created]
+    types: [published]
 
 jobs:
   deploy:
@@ -16,11 +16,11 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install setuptools wheel twine
-    - name: Build and publish
-      env:
-        TWINE_USERNAME: __token__
-        TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
-      run: |
-        python setup.py sdist bdist_wheel
-        twine upload dist/*
+        python -m pip install .[dev]
+    - name: Build package
+      run: python -m build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@v1
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_TOKEN }}

.github/workflows/python-sphinx-doc.yml

@@ -14,12 +14,11 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: '3.x'
+        python-version: '3.11'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install .
-        pip install -r doc_requirements.txt
+        python -m pip install .[docs]
     - name: Generate documentation
       run: |
         sphinx-build docs docs_out/

CONTRIBUTING.md

@@ -37,7 +37,7 @@ We expect commit messages to follow the style described [here](https://chris.bea
 You can build the documentation after installation by running:
 
 ```bash
-pip install -r dev-requirements.txt
+python -m pip install .[docs]
 sphinx-build -n -v -E -W ./docs ./tmp/ope_docs
 ```
 

README.md

@@ -9,7 +9,7 @@ A Python library for petro-elastic modelling. It contains a `Material` class for
 pip install open_petro_elastic
 ```
 
-Developers and contributors can download the repository and do `pip install .` to install the package.
+Developers and contributors can download the repository and do `pip install ".[dev,test,docs]"` to install the package with all its dependencies for development, testing, and building the docs.
 
 
 ## Usage

pyproject.toml

@@ -0,0 +1,90 @@
+[build-system]
+requires = ["setuptools>=68", "setuptools-scm>=8"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name="open_petro_elastic"
+dynamic = ["version"]
+requires-python = ">=3.8"
+authors = [{ name="Equinor", email="fg_sib-scout@equinor.com" },]
+description="Utility for calculating elastic properties of rocks and fluids."
+license = {file = "LICENSE"}
+readme = "README.md"
+keywords = ["geophysics", "rock physics", "materials science"]
+classifiers=[
+    "Development Status :: 3 - Alpha",
+    "License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+)",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Hydrology",
+    "Topic :: Scientific/Engineering :: Physics",
+    "Natural Language :: English",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+]
+dependencies = [
+    "numpy<2",
+    "scipy",
+    "pyyaml",
+    "pandas",
+    "pydantic",
+    "sympy",
+    "typing_extensions",
+]
+
+[project.optional-dependencies]
+test = [
+    "pytest",
+    "syrupy",
+    "hypothesis",
+    "matplotlib",
+    "pillow>=10.0.0",   # Not directly required, pinned by Snyk to avoid a vulnerability
+    "Flake8-pyproject", # Work around Flake8 incompatibility with pyproject.toml
+]
+docs = [
+    "sphinx",
+    "sphinx-rtd-theme",
+    "sphinx-argparse",
+    "matplotlib",
+    "recommonmark",
+    "pygments-csv-lexer",
+]
+dev = [
+    "build",
+    "setuptools",
+    "flake8",
+    "black",
+    "isort",
+    "mypy",
+]
+
+[project.urls]
+"documentation" = "https://equinor.github.io/open_petro_elastic"
+"repository" = "https://github.com/equinor/open_petro_elastic"
+
+[project.scripts]
+open_petro_elastic = "open_petro_elastic.__main__:main"
+
+[project.entry-points."open_petro_elastic.fluid_model_providers"]
+batzle_wang = "open_petro_elastic.config.fluid_model_providers:BatzleWangFluidModelProvider"
+span_wagner = "open_petro_elastic.config.fluid_model_providers:SpanWagnerFluidModelProvider"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+open_petro_elastic = ["tutorial_config/*"]
+"open_petro_elastic.material.span_wagner.tables" = [
+            "material/span_wagner/tables/carbon_dioxide_density.npz"
+]
+
+[tool.flake8]
+max-line-length = 88
+ignore = ["E302", "W503", "E501", "E741", "E203", "F405"]
+per-file-ignores = [
+    "__init__.py:F401,F403",
+    "conftest.py: F401,F403",
+]

tests/__snapshots__/test_config_fluids.ambr

@@ -0,0 +1,4 @@
+# serializer version: 1
+# name: test_fluids_vectorized
+  Material(shear_modulus=0, bulk_modulus=[1.64734606e+08 1.83184882e+08], primary_velocity=[1144.72360384 1021.36998928], secondary_velocity=[0. 0.], density=[125.71397711 175.59956795])
+# ---

tests/__snapshots__/test_depth_trend.ambr

@@ -0,0 +1,7 @@
+# serializer version: 1
+# name: test_dryrock_depthtrend_k_my
+  Material(shear_modulus=[12.], bulk_modulus=[20.], primary_velocity=[0.1165543], secondary_velocity=[0.06729266], density=[2650.])
+# ---
+# name: test_dryrock_depthtrend_vp_vs
+  Material(shear_modulus=[12.], bulk_modulus=[20.], primary_velocity=[0.1165543], secondary_velocity=[0.06729266], density=[2650.])
+# ---

tests/__snapshots__/test_dryrock.ambr

@@ -0,0 +1,13 @@
+# serializer version: 1
+# name: test_dryrock_phi_fitted_vp_vs
+  tuple(
+    Material(shear_modulus=[7.6585e+09], bulk_modulus=[1.20751667e+10], primary_velocity=[2900.], secondary_velocity=[1700.], density=[2650.]),
+    Material(shear_modulus=44.0, bulk_modulus=36.8, primary_velocity=0.18980294316133353, secondary_velocity=0.128855630784633, density=2650.0),
+  )
+# ---
+# name: test_dryrock_phi_k_my
+  tuple(
+    Material(shear_modulus=[12.], bulk_modulus=[20.], primary_velocity=[0.1165543], secondary_velocity=[0.06729266], density=[2650.]),
+    Material(shear_modulus=44.0, bulk_modulus=36.8, primary_velocity=0.18980294316133353, secondary_velocity=0.128855630784633, density=2650.0),
+  )
+# ---

tests/__snapshots__/test_fluid_substitution.ambr

@@ -0,0 +1,4 @@
+# serializer version: 1
+# name: test_fluid_substitution
+  Material(shear_modulus=[1.], bulk_modulus=[1.94708995], primary_velocity=[1.28070748], secondary_velocity=[0.70710678], density=[2.])
+# ---

tests/__snapshots__/test_murphy_coordination_number.ambr

@@ -0,0 +1,4 @@
+# serializer version: 1
+# name: test_murphy_coordination_number
+  17.555560500000002
+# ---

tests/__snapshots__/test_pressure.ambr

@@ -0,0 +1,10 @@
+# serializer version: 1
+# name: test_pressure_dependency_no_pressure_exp_fit
+  Material(shear_modulus=1.0, bulk_modulus=0.9999999999999998, primary_velocity=1.5275252316519465, secondary_velocity=1.0, density=1.0)
+# ---
+# name: test_pressure_dependency_no_pressure_poly_fit
+  Material(shear_modulus=1.0, bulk_modulus=0.9999999999999998, primary_velocity=1.5275252316519465, secondary_velocity=1.0, density=1.0)
+# ---
+# name: test_pressure_dependency_no_pressure_power_fit
+  Material(shear_modulus=1.0, bulk_modulus=0.9999999999999998, primary_velocity=1.5275252316519465, secondary_velocity=1.0, density=1.0)
+# ---