gdrift 0.1.0__tar.gz

gdrift-0.1.0/.github/workflows/docs.yml

@@ -0,0 +1,131 @@
+name: Deploy Documentation
+
+on:
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+# Sets permissions for GitHub Pages deployment
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow only one concurrent deployment
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  # Build and deploy documentation
+  build-and-deploy:
+    name: Build and deploy docs
+    runs-on: ubuntu-latest
+    container:
+      image: firedrakeproject/firedrake-vanilla-default:dev-main
+
+    steps:
+      - name: Install system dependencies
+        run: |
+          apt-get update
+          apt-get install -y python3-venv libgeos-dev libproj-dev proj-data
+          git config --global --add safe.directory $GITHUB_WORKSPACE
+
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up virtual environment
+        run: |
+          python3 -m venv --system-site-packages .venv
+          . .venv/bin/activate
+          pip install --upgrade pip
+
+      - name: Install gadopt
+        run: |
+          . .venv/bin/activate
+          pip install git+https://github.com/g-adopt/g-adopt.git
+
+      - name: Install gdrift and docs dependencies
+        run: |
+          . .venv/bin/activate
+          pip install -e ".[docs,examples]"
+
+      - name: Install Jupyter kernel
+        run: |
+          . .venv/bin/activate
+          python -m ipykernel install --prefix .venv --name python3
+
+      - name: Prepare demo data and notebooks
+        working-directory: examples
+        run: |
+          . $GITHUB_WORKSPACE/.venv/bin/activate
+          make all
+        env:
+          MPLBACKEND: Agg
+
+      - name: Generate thumbnails
+        run: |
+          . .venv/bin/activate
+          python scripts/generate_thumbnails.py
+        env:
+          MPLBACKEND: Agg
+
+      - name: Copy notebooks to docs
+        run: |
+          for demo in mantle_solidus anelasticity_corrections geodynamic_adiabat linearisation tomography_models temperature_to_vs gadopt_loading_field; do
+            if [ -f "examples/${demo}/demo.ipynb" ]; then
+              mkdir -p "docs/examples/${demo}"
+              cp "examples/${demo}/demo.ipynb" "docs/examples/${demo}/demo.ipynb"
+              echo "Copied ${demo}/demo.ipynb"
+            fi
+          done
+
+      - name: Generate Data Catalog
+        run: |
+          . .venv/bin/activate
+          python scripts/generate_data_catalog.py
+
+      - name: Generate Tomography Gallery
+        run: |
+          . .venv/bin/activate
+          python scripts/generate_tomography_gallery.py
+        env:
+          MPLBACKEND: Agg
+        timeout-minutes: 30
+
+      - name: Verify generated files
+        run: |
+          test -f docs/data-catalog-generated.md || { echo "FAIL: data-catalog-generated.md not found"; exit 1; }
+          test -f docs/data-catalog-incomplete.md || { echo "FAIL: data-catalog-incomplete.md not found"; exit 1; }
+          test -f docs/tomography-gallery-generated.md || { echo "FAIL: tomography-gallery-generated.md not found"; exit 1; }
+          test -d docs/assets/images/tomography || { echo "FAIL: tomography image directory not found"; exit 1; }
+          test -f docs/assets/images/tomography/reference_cross_section.png || { echo "FAIL: reference map not found"; exit 1; }
+          for demo in mantle_solidus anelasticity_corrections geodynamic_adiabat linearisation tomography_models temperature_to_vs; do
+            test -f "docs/assets/images/thumbnails/${demo}.png" || { echo "FAIL: thumbnail ${demo}.png not found"; exit 1; }
+          done
+          for demo in mantle_solidus anelasticity_corrections geodynamic_adiabat linearisation tomography_models temperature_to_vs gadopt_loading_field; do
+            test -f "docs/examples/${demo}/demo.ipynb" || { echo "FAIL: notebook ${demo}/demo.ipynb not found"; exit 1; }
+          done
+          echo "OK: All generated files present"
+
+      - name: Build documentation
+        run: |
+          . .venv/bin/activate
+          mkdocs build --strict
+        env:
+          MPLBACKEND: Agg
+
+      - name: Setup Pages
+        uses: actions/configure-pages@v4
+
+      - name: Upload Pages artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: site/
+
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

gdrift-0.1.0/.github/workflows/lint.yml

@@ -0,0 +1,25 @@
+name: Run lint
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+
+jobs:
+  linter:
+    name: "Run linter"
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+      - name: Install linter
+        run: |
+          python3 -m pip install flake8
+      - name: Lint
+        run: |
+          make lint

gdrift-0.1.0/.github/workflows/publish.yml

@@ -0,0 +1,146 @@
+name: Publish to PyPI
+
+on:
+  push:
+    tags:
+      - "v*"
+
+jobs:
+  test:
+    name: Run tests before publishing
+    runs-on: ubuntu-latest
+    container:
+      image: firedrakeproject/firedrake-vanilla-default:dev-main
+
+    env:
+      OMP_NUM_THREADS: 1
+      MPLBACKEND: Agg
+
+    steps:
+      - name: Install system dependencies
+        run: |
+          apt-get update
+          apt-get install -y python3-venv
+          git config --global --add safe.directory $GITHUB_WORKSPACE
+
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up virtual environment
+        run: |
+          python3 -m venv --system-site-packages .venv
+          . .venv/bin/activate
+          pip install --upgrade pip
+
+      - name: Install gadopt
+        run: |
+          . .venv/bin/activate
+          pip install git+https://github.com/g-adopt/g-adopt.git
+
+      - name: Install gdrift
+        run: |
+          . .venv/bin/activate
+          pip install -e .
+          pip install matplotlib pytest boto3
+
+      - name: Run unit tests
+        run: |
+          . .venv/bin/activate
+          python -m pytest tests/ -v --maxfail=5 --tb=short
+
+  build:
+    name: Build distribution
+    needs: test
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install build tools
+        run: pip install build setuptools-scm
+
+      - name: Build sdist and wheel
+        run: python -m build
+
+      - name: Verify version matches tag
+        run: |
+          TAG="${GITHUB_REF#refs/tags/v}"
+          WHEEL=$(ls dist/*.whl)
+          WHEEL_VERSION=$(python -c "import re, sys; m=re.search(r'gdrift-([^-]+)-', sys.argv[1]); print(m.group(1))" "$WHEEL")
+          echo "Tag version: $TAG"
+          echo "Wheel version: $WHEEL_VERSION"
+          if [ "$TAG" != "$WHEEL_VERSION" ]; then
+            echo "ERROR: Tag version ($TAG) does not match wheel version ($WHEEL_VERSION)"
+            exit 1
+          fi
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  publish-testpypi:
+    name: Publish to TestPyPI
+    needs: build
+    runs-on: ubuntu-latest
+    environment: testpypi
+    permissions:
+      id-token: write
+
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+          skip-existing: true
+
+  publish-pypi:
+    name: Publish to PyPI
+    needs: publish-testpypi
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+
+  github-release:
+    name: Create GitHub Release
+    needs: publish-pypi
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - name: Create release
+        env:
+          GH_TOKEN: ${{ github.token }}
+        run: |
+          gh release create "${{ github.ref_name }}" \
+            dist/* \
+            --title "${{ github.ref_name }}" \
+            --generate-notes

gdrift-0.1.0/.github/workflows/test_firedrake.yml

@@ -0,0 +1,60 @@
+name: Test with Firedrake
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+  workflow_dispatch:
+
+concurrency:
+  group: firedrake-${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    name: Unit tests and examples
+    runs-on: ubuntu-latest
+    container:
+      image: firedrakeproject/firedrake-vanilla-default:dev-main
+
+    env:
+      OMP_NUM_THREADS: 1
+      MPLBACKEND: Agg
+
+    steps:
+      - name: Install system dependencies
+        run: |
+          apt-get update
+          apt-get install -y python3-venv
+          git config --global --add safe.directory $GITHUB_WORKSPACE
+
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up virtual environment
+        run: |
+          python3 -m venv --system-site-packages .venv
+          . .venv/bin/activate
+          pip install --upgrade pip
+
+      - name: Install gadopt
+        run: |
+          . .venv/bin/activate
+          pip install git+https://github.com/g-adopt/g-adopt.git
+
+      - name: Install gdrift
+        run: |
+          . .venv/bin/activate
+          pip install -e .
+          pip install matplotlib pytest boto3
+
+      - name: Run unit tests
+        run: |
+          . .venv/bin/activate
+          python -m pytest tests/ -v --maxfail=5 --tb=short
+
+      - name: Run example demo tests
+        run: |
+          . .venv/bin/activate
+          python -m pytest examples/ -v --maxfail=5 --tb=short

gdrift-0.1.0/.gitignore

@@ -0,0 +1,187 @@
+# vs code
+.vscode
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# gdrift data directories (local cache and personal copies)
+gdrift/data/
+gdrift/data-sia/
+gdrift/data-*/
+
+# setuptools-scm generated version file
+gdrift/_version.py
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# Generated notebooks in examples directories
+examples/*/demo.ipynb
+examples/*/*.png
+examples/*/*.pdf
+
+# Auto-generated documentation (regenerated in CI)
+docs/data-catalog-generated.md
+docs/data-catalog-incomplete.md
+docs/tomography-gallery-generated.md
+docs/assets/images/tomography/
+
+# Enriched manifest (for review before committing)
+gdrift/datasets.json.enriched
+
+*.DS_Store

gdrift-0.1.0/.zenodo.json

@@ -0,0 +1,36 @@
+{
+  "title": "gdrift: Geodynamics Data Reformatting and Integration Facilitation Toolkit",
+  "description": "A Python package for loading, processing, and converting geodynamic and seismic data used in large-scale mantle convection studies.",
+  "creators": [
+    {
+      "name": "Ghelichkhan, Sia",
+      "affiliation": "Australian National University",
+      "orcid": "0000-0002-8453-964X"
+    }
+  ],
+  "license": {
+    "id": "MIT"
+  },
+  "keywords": [
+    "geodynamics",
+    "seismic tomography",
+    "mantle convection",
+    "thermodynamics",
+    "earth models",
+    "Python"
+  ],
+  "related_identifiers": [
+    {
+      "identifier": "https://github.com/g-adopt/g-drift",
+      "relation": "isSupplementTo",
+      "scheme": "url"
+    },
+    {
+      "identifier": "https://gdrift.gadopt.org",
+      "relation": "isDocumentedBy",
+      "scheme": "url"
+    }
+  ],
+  "upload_type": "software",
+  "access_right": "open"
+}

gdrift-0.1.0/CITATION.cff

@@ -0,0 +1,20 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+type: software
+title: "gdrift: Geodynamics Data Reformatting and Integration Facilitation Toolkit"
+version: "0.1.0"
+date-released: "2026-03-24"
+authors:
+  - family-names: Ghelichkhan
+    given-names: Sia
+    email: siavash.ghelichkhan@anu.edu.au
+    orcid: "https://orcid.org/0000-0002-8453-964X"
+repository-code: "https://github.com/g-adopt/g-drift"
+url: "https://gdrift.gadopt.org"
+license: MIT
+keywords:
+  - geodynamics
+  - seismic tomography
+  - mantle convection
+  - thermodynamics
+  - earth models

gdrift-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Sia Ghelichkhan
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

gdrift-0.1.0/Makefile

@@ -0,0 +1,19 @@
+.PHONY: lint test longtest longtest_output convert_demos data-catalog enrich-metadata docs
+
+lint:
+	@echo "Linting module code"
+	@python3 -m flake8 gdrift
+	@echo "Linting examples and tests"
+	@python3 -m flake8 examples tests
+
+data-catalog:
+	@echo "Generating data catalog documentation"
+	@python3 scripts/generate_data_catalog.py
+
+enrich-metadata:
+	@echo "Enriching dataset metadata from HDF5 files and web search"
+	@python3 scripts/enrich_datasets_metadata.py --web-search
+
+docs: data-catalog
+	@echo "Building documentation with MkDocs"
+	@mkdocs build --strict

gdrift-0.1.0/PKG-INFO

@@ -0,0 +1,52 @@
+Metadata-Version: 2.4
+Name: gdrift
+Version: 0.1.0
+Summary: Geodynamics Data Reformatting and Integration Facilitation Toolkit
+Author-email: Sia Ghelichkhani <siavash.ghelichkhan@anu.edu.au>
+License: MIT
+Project-URL: Homepage, https://github.com/g-adopt/g-drift
+Project-URL: Documentation, https://gdrift.gadopt.org
+Project-URL: Repository, https://github.com/g-adopt/g-drift
+Project-URL: Issues, https://github.com/g-adopt/g-drift/issues
+Keywords: geodynamics,seismic tomography,mantle convection,thermodynamics,earth models
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.20
+Requires-Dist: scipy>=1.7
+Requires-Dist: h5py>=3.0
+Requires-Dist: tqdm>=4.0
+Requires-Dist: boto3>=1.20
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: pytest-cov>=3.0; extra == "dev"
+Requires-Dist: black>=22.0; extra == "dev"
+Requires-Dist: flake8>=5.0; extra == "dev"
+Requires-Dist: mypy>=0.990; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: mkdocs>=1.5; extra == "docs"
+Requires-Dist: mkdocs-material>=9.0; extra == "docs"
+Requires-Dist: mkdocstrings[python]>=0.24; extra == "docs"
+Requires-Dist: mkdocs-jupyter<0.26,>=0.24; extra == "docs"
+Provides-Extra: examples
+Requires-Dist: matplotlib>=3.5; extra == "examples"
+Requires-Dist: jupytext>=1.15; extra == "examples"
+Requires-Dist: nbconvert>=7.0; extra == "examples"
+Requires-Dist: ipykernel>=6.0; extra == "examples"
+Requires-Dist: cartopy>=0.21; extra == "examples"
+Provides-Extra: all
+Requires-Dist: gdrift[dev,docs,examples]; extra == "all"
+Dynamic: license-file
+
+# GDRIFT — Geodynamics Data Reformatting and Integration Facilitation Toolkit
+
+GDRIFT is the data arm of the [G-ADOPT project](https://gadopt.org), designed to serve as a centralized reference for geodynamic data inputs. Many of the datasets used in large-scale mantle convection inversions and forward models exist in scattered locations, lack proper documentation, and don't follow FAIR (Findable, Accessible, Interoperable, Reusable) principles. GDRIFT aims to change that by maintaining a well-curated repository of essential geodynamic inputs—from 1D reference Earth models and seismic tomography data to thermodynamic lookup tables and solidus profiles.
+
+For detailed information about available datasets, documentation, and usage examples, visit [gdrift.gadopt.org](https://gdrift.gadopt.org).