dolphin 0.22.0__tar.gz

dolphin-0.22.0/.dockerignore

@@ -0,0 +1,8 @@
+**/__pycache__/*
+.mypy_cache/*
+.asv
+build/
+data/
+tests/data/*
+dist/
+.nox/

dolphin-0.22.0/.flake8

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+[flake8]
+ignore=E203,E722,E402,W502,W503
+max-line-length=90

dolphin-0.22.0/.git-blame-ignore-revs

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+# Added new ruff configuration
+a7d7722b4447a8fbaaa138233864b1668fffd233

dolphin-0.22.0/.github/ISSUE_TEMPLATE/bug_report.yml

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+name: Bug Report
+description: Create a report to help us improve
+title: "[Bug]: "
+labels: ["bug", "needs triage"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        > _Thanks for filing a bug ticket. We appreciate your time and effort. Please answer a few questions._
+  - type: dropdown
+    id: checked-for-duplicates
+    attributes:
+      label: Checked for duplicates
+      description: Have you checked for duplicate issue tickets?
+      multiple: false
+      options:
+        - "Yes - I've already checked"
+        - "No - I haven't checked"
+    validations:
+      required: yes
+  - type: textarea
+    id: description
+    attributes:
+      label: Describe the bug
+      description: A clear and concise description of what the bug is. Plain-text snippets preferred but screenshots welcome.
+      placeholder: Tell us what you saw
+      value: "When I did [...] action, I noticed [...]"
+    validations:
+      required: true
+  - type: textarea
+    id: expected-behavior
+    attributes:
+      label: What did you expect?
+      description: A clear and concise description of what you expect to happen
+      placeholder: Tell us what you expected
+      value: "I expected [...]"
+    validations:
+      required: true
+  - type: textarea
+    id: reproduction
+    attributes:
+      label: Reproducible steps
+      description: "How would we reproduce this bug? Please walk us through it step by step. Plain-text snippets preferred but screenshots welcome."
+      value: |
+        1.
+        2.
+        3.
+        ...
+        If you have a `dolphin_config.yaml` that you used, you can attach that as well.
+      render: bash
+  - type: textarea
+    id: environment
+    attributes:
+      label: Environment
+      description: "What is your environment?"
+      value: |
+        Please paste the output of the following:
+        `python -c "import dolphin; print(dolphin.show_versions())"`
+        ...
+      render: bash

dolphin-0.22.0/.github/ISSUE_TEMPLATE/feature_request.yml

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+name: New Feature
+description: Submit a new feature request
+title: "[New Feature]: "
+labels: ["enhancement", "needs triage"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        > _Thanks for filing a new feature request. We appreciate your time and effort. Please answer a few questions._
+  - type: dropdown
+    id: checked-for-duplicates
+    attributes:
+      label: Checked for duplicates
+      description: Have you checked for duplicate issue tickets?
+      multiple: false
+      options:
+        - "Yes - I've already checked"
+        - "No - I haven't checked"
+    validations:
+      required: yes
+  - type: dropdown
+    id: checked-alternatives
+    attributes:
+      label: Alternatives considered
+      description: Have you considered alternative solutions to your feature request?
+      options:
+        - "Yes - and alternatives don't suffice"
+        - "No - I haven't considered"
+    validations:
+      required: yes
+  - type: textarea
+    id: related-problems
+    attributes:
+      label: Related problems
+      description: Is your feature request related to any problems? Please help us understand if so, including linking to any other issue tickets.
+      placeholder: Tell us the problems
+      value: "I'm frustrated when [...] happens as documented in issue-XYZ"
+    validations:
+      required: false
+  - type: textarea
+    id: description
+    attributes:
+      label: Describe the feature request
+      description: A clear and concise description of your request.
+      placeholder: Tell us what you want
+      value: "I need or want [...]"
+    validations:
+      required: true

dolphin-0.22.0/.github/dependabot.yml

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+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "daily"
+    groups:
+      actions:
+        patterns:
+          - "*"

dolphin-0.22.0/.github/release.yml

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+changelog:
+  exclude:
+    authors:
+      - dependabot
+      - pre-commit-ci

dolphin-0.22.0/.github/workflows/benchmark.yml

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+# Based off of scikit-image .github/workflows/benchmarks.yml
+# and tqdm .github/workflows/check.yml#L54C1-L54C1
+name: Benchmark
+
+on:
+  pull_request:
+    types: [labeled]
+  workflow_dispatch:
+
+jobs:
+  benchmark:
+    if: contains(github.event.label.name, 'benchmark') || github.event_name == 'workflow_dispatch'
+    name: Linux
+    runs-on: ubuntu-latest
+
+    steps:
+      # We need the full repo to avoid this issue
+      # https://github.com/actions/checkout/issues/23
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Setup environment
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: requirements.txt
+          environment-name: dolphin
+          condarc: |
+            channels:
+              - conda-forge
+              - nodefaults
+          create-args: >-
+            python=3.11
+            asv>=0.6
+
+      - name: Record machine info
+        shell: bash -l {0}
+        run: |
+          asv machine --yes
+      # https://github.com/tqdm/tqdm/blob/4c956c20b83be4312460fc0c4812eeb3fef5e7df/.github/workflows/check.yml#L26
+      - name: Restore previous results
+        uses: actions/cache@v4
+        with:
+          path: .asv
+          key: asv-${{ runner.os }}
+          restore-keys: |
+            asv-
+
+      - name: Run benchmarks
+        shell: bash -l {0}
+        id: benchmark
+        env:
+          OPENBLAS_NUM_THREADS: 1
+          MKL_NUM_THREADS: 1
+          OMP_NUM_THREADS: 1
+        run: |
+          set -x
+
+          echo "Baseline:  ${{ github.event.pull_request.base.sha }} (${{ github.event.pull_request.base.label }})"
+          echo "Contender: ${GITHUB_SHA} (${{ github.event.pull_request.head.label }})"
+
+          # Run benchmarks for current commit against base
+          ASV_OPTIONS="--split --show-stderr"
+          asv continuous $ASV_OPTIONS ${{ github.event.pull_request.base.sha }} ${GITHUB_SHA} \
+              | sed "/Traceback \|failed$/ s/^/::error::/" \
+              | tee benchmarks.log
+
+          # Report and export results for subsequent steps
+          if grep "Traceback \|failed" benchmarks.log > /dev/null ; then
+              exit 1
+          fi
+
+      - name: Add instructions to artifact
+        if: always()
+        run: cp benchmarks/README_CI.md benchmarks.log .asv/results/
+
+      - uses: actions/upload-artifact@v4
+        if: always()
+        with:
+          name: asv-benchmark-results-${{ runner.os }}
+          path: .asv/results
+
+# For now, we're just uploading the artifact
+# If we want to publish to github pages, may want this:
+# https://github.com/tqdm/tqdm/blob/4c956c20b83be4312460fc0c4812eeb3fef5e7df/.github/workflows/check.yml#L54C1-L54C1

dolphin-0.22.0/.github/workflows/cd.yml

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+# This workflow will build a Python Package and upload to pypi. See:
+# https://docs.pypi.org/trusted-publishers/using-a-publisher/
+# https://github.com/marketplace/actions/pypi-publish
+name: CD
+
+on:
+  workflow_dispatch:
+  release:
+    types: [created]
+
+jobs:
+  pypi-publish:
+    name: upload release to PyPI
+    runs-on: ubuntu-latest
+    environment: release
+    permissions:
+      id-token: write
+    steps:
+      # retrieve your distributions here
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.x'
+    - name: Install build dependencies and package
+      run: |
+        python -m pip install --upgrade pip setuptools_scm
+        pip install build
+    - name: Get version and Build
+      run: |
+        # Version added upon installing package
+        python -m pip install --no-deps .
+        python -m build --sdist --wheel
+    - name: Publish package distributions to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

dolphin-0.22.0/.github/workflows/test-build-push.yml

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+name: Pytest, build docker image, push to GHCR
+
+on: [pull_request, push]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref }}
+  cancel-in-progress: true
+
+env:
+  # https://github.com/pytest-dev/pytest/issues/2042#issuecomment-429289164
+  PY_IGNORE_IMPORTMISMATCH: 1
+
+jobs:
+  pytest:
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-14]
+        deps:
+          - label: Latest
+            # we can't specify `tophu` for conda, not available on mac
+            spec: >-
+              isce3
+              dask
+
+      fail-fast: true
+    name: ${{ matrix.os }} • ${{ matrix.deps.label }}
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Setup environment
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: conda-env.yml
+          environment-name: dolphin-env
+          generate-run-shell: false
+          create-args: ${{ matrix.deps.spec }}
+          condarc: |
+            channels:
+              - conda-forge
+      - name: Install
+        run: |
+          pip install --no-deps "snaphu>=0.4.0" "opera-utils>=0.4.1" git+https://github.com/isce-framework/tophu@main
+          pip install --no-deps .
+      - name: Install test dependencies
+        run: |
+          micromamba install -f tests/requirements.txt -c conda-forge
+          pip install --no-deps git+https://github.com/isce-framework/tophu@main
+      - name: Enable numba boundscheck for better error catching
+        run: |
+          echo "NUMBA_BOUNDSCHECK=1" >> $GITHUB_ENV
+          echo "TQDM_DISABLE=1" >> $GITHUB_ENV
+      - name: Test (with numba boundscheck on)
+        run: |
+          pytest -n0 -vv
+      # https://community.codecov.com/t/numba-jitted-methods-are-not-captured-by-codecov/2649
+      # - name: Coverage report
+      #   uses: codecov/codecov-action@v2
+
+  dockerize: # Based on Mintpy: https://github.com/insarlab/MintPy/blob/5ca554fef324b816f9130feec567e2cf463e41d2/.github/workflows/build-n-publish-to-pypi.yml
+    name: Build Docker image and push to GitHub Container Registry
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+      - name: Set environment variables for docker build
+        run: |
+          pip install setuptools_scm # Install setuptools_scm to get version number
+          # Save version number from CLI
+          version=$(python -m setuptools_scm)
+          sanitized_version=${version//+/-} # Replace all '+' with '-'
+          echo "DOLPHIN_VERSION=${sanitized_version}" >> $GITHUB_ENV
+
+      - name: Login to GitHub Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build, tag, and push image to Github Container Registry
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          file: ./docker/Dockerfile
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: |
+            ghcr.io/${{ github.repository }}:${{ env.DOLPHIN_VERSION }}
+          labels: |
+            org.opencontainers.image.created=${{ env.CI_JOB_TIMESTAMP }}
+            org.opencontainers.image.version=${{ env.DOLPHIN_VERSION }}
+            org.opencontainers.image.revision=${{ github.sha }}
+
+      - name: Add develop tag
+        if: github.ref == 'refs/heads/main'
+        uses: akhilerm/tag-push-action@v2.2.0
+        with:
+          src: ghcr.io/${{ github.repository }}:${{ env.DOLPHIN_VERSION }}
+          dst: ghcr.io/${{ github.repository }}:develop
+
+      - name: Add latest tag
+        if: startsWith(github.ref, 'refs/tags/v')
+        uses: akhilerm/tag-push-action@v2.2.0
+        with:
+          src: ghcr.io/${{ github.repository }}:${{ env.DOLPHIN_VERSION }}
+          dst: ghcr.io/${{ github.repository }}:latest

dolphin-0.22.0/.gitignore

@@ -0,0 +1,171 @@
+# setuptools-scm: autogenerated version, see pyproject.toml
+src/dolphin/_version.py
+
+docs/reference
+
+# airspeed cache directory
+.asv
+
+# Testing data dir
+data/
+docs/**/*.h5
+
+# MacOS
+.DS_Store
+
+# 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
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__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
+
+# VSCode project settings
+.vscode
+
+# mkdocs documentation
+site
+docs/reference
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintainted 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/

dolphin-0.22.0/.pre-commit-config.yaml

@@ -0,0 +1,41 @@
+ci:
+  autofix_prs: true
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v4.6.0"
+    hooks:
+      # https://github.com/pre-commit/pre-commit-hooks/issues/718
+      # - id: check-added-large-files  # Fails with git v1.8.3
+      - id: check-case-conflict
+      - id: check-docstring-first
+      - id: check-merge-conflict
+      - id: check-yaml
+        args: [--allow-multiple-documents]
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: file-contents-sorter
+        files: (requirements.txt)$
+      - id: mixed-line-ending
+      - id: trailing-whitespace
+
+  - repo: https://github.com/psf/black
+    rev: "24.4.2"
+    hooks:
+      - id: black
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.5.2
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix, --show-fixes]
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: "v1.10.1"
+    hooks:
+      - id: mypy
+        additional_dependencies:
+        - types-pkg_resources
+        - types-requests
+        - "pydantic>=2.4"
+        - types-markdown

dolphin-0.22.0/.readthedocs.yaml

@@ -0,0 +1,24 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+version: 2
+
+mkdocs:
+  configuration: mkdocs.yml
+
+# Conda is causing "excessive memory usage"
+# https://docs.readthedocs.io/en/stable/guides/conda.html#making-builds-faster-with-mamba
+build:
+  os: "ubuntu-20.04"
+  tools:
+    python: "mambaforge-4.10"
+
+conda:
+  environment: conda-env.yml
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs