echoshader 0.2.0__tar.gz

echoshader-0.2.0/.github/ISSUE_TEMPLATE/gsoc2026.yml

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+name: GSoC 2026 discussion
+description: Use this if you want to discuss anything related to GSoC 2026
+title: "[GSoC 2026] ..."
+labels: ["GSoC 2026"]
+body:
+  - type: markdown
+    attributes:
+      value: Welcome to GSoC 2026!
+  - type: textarea
+    attributes:
+      label: Discussion topic
+      description: |
+        What question do you have? What idea do you want to propose?
+        Please raise only one topic in each issue.
+      placeholder: I am wondering about ...
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Related existing issues or PRs
+      description: |
+        Take a look at the current [issues](https://github.com/OSOceanAcoustics/echoshader/issues) and [PRs](https://github.com/OSOceanAcoustics/echoshader/pulls) and link anything related here.
+      placeholder: "This topic is related to #XXX; or: I have not seen related issues/PRs"
+    validations:
+      required: true

echoshader-0.2.0/.github/dependabot.yml

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+version: 2
+updates:
+  - package-ecosystem: 'github-actions'
+    directory: '/'
+    schedule:
+      # Check for updates once a week
+      interval: 'weekly'

echoshader-0.2.0/.github/workflows/pypi.yaml

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+# Publish archives to PyPI and TestPyPI using GitHub Actions
+name: Publish to PyPI
+
+# Only run for tagged releases
+on:
+  release:
+    types:
+      - released
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+  build-artifact:
+    name: Build echoshader package
+    runs-on: ubuntu-22.04
+    if: github.repository == 'echostack-org/echoshader' && !startsWith(github.ref, 'refs/tags/example-data-')
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v7
+      with:
+        # fetch all history so that setuptools-scm works
+        fetch-depth: 0
+
+    - name: Set up Python
+      uses: actions/setup-python@v7
+      with:
+        python-version: 3.13
+
+    - name: Install dependencies
+      run: python -m pip install --upgrade pip build
+
+    # This step is only necessary for testing purposes and for TestPyPI
+    - name: Fix up version string for TestPyPI
+      if: ${{ !startsWith(github.ref, 'refs/tags') }}
+      run: |
+        # Change setuptools-scm local_scheme to "no-local-version" so the
+        # local part of the version isn't included, making the version string
+        # compatible with PyPI.
+        sed --in-place "s/node-and-date/no-local-version/g" pyproject.toml
+
+    - name: Build source and wheel distributions
+      run: |
+        python -m build
+        echo ""
+        echo "Generated files:"
+        ls -lh dist/
+    - uses: actions/upload-artifact@v7
+      with:
+        name: releases
+        path: dist
+
+  test-built-dist:
+    name: Test echoshader package
+    needs: build-artifact
+    runs-on: ubuntu-22.04
+    steps:
+    - uses: actions/setup-python@v7
+      name: Install Python
+      with:
+        python-version: 3.13
+    - uses: actions/download-artifact@v8
+      with:
+        name: releases
+        path: dist
+    - name: List contents of built dist
+      run: |
+        ls -ltrh
+        ls -ltrh dist
+    - name: Publish to Test PyPI
+      uses: pypa/gh-action-pypi-publish@v1.14.3
+      with:
+        password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+        repository-url: https://test.pypi.org/legacy/
+        verbose: true
+        skip-existing: true
+    - name: Check pypi packages
+      run: |
+        sleep 3
+        python -m pip install --upgrade pip
+
+        echo "=== Testing wheel file ==="
+        # Install wheel to get dependencies and check import
+        python -m pip install --extra-index-url https://test.pypi.org/simple --upgrade --pre echoshader
+        python -c "import echoshader; print(echoshader.__version__)"
+        echo "=== Done testing wheel file ==="
+
+        echo "=== Testing source tar file ==="
+        # Install tar gz and check import
+        python -m pip uninstall --yes echoshader
+        python -m pip install --extra-index-url https://test.pypi.org/simple --upgrade --pre --no-binary=:all: echoshader
+        python -c "import echoshader; print(echoshader.__version__)"
+        echo "=== Done testing source tar file ==="
+
+  publish-pypi:
+    name: Push echoshader to production pypi
+    needs: test-built-dist
+    if: startsWith(github.ref, 'refs/tags')
+    runs-on: ubuntu-22.04
+    steps:
+    - uses: actions/download-artifact@v8
+      with:
+        name: releases
+        path: dist
+    - name: Publish to PyPI
+      uses: pypa/gh-action-pypi-publish@v1.14.3
+      with:
+        password: ${{ secrets.PYPI_API_TOKEN }}

echoshader-0.2.0/.github/workflows/pytest.yaml

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+# .github/workflows/pytest.yml
+name: PyTest
+
+on: [push, pull_request, workflow_dispatch]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.13", "3.14"]
+
+    steps:
+      - name: Check out repository code
+        uses: actions/checkout@v7
+
+      - name: Setup Python
+        uses: actions/setup-python@v7
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e ".[dev,test]"
+          python -m pip check
+          python -c "import echopype; print('Echopype:', echopype.__version__)"
+
+      - name: Run Coverage Pytest
+        run: pytest --cov=./ --cov-report=xml
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v7
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

echoshader-0.2.0/.github/workflows/update-spec0.yml

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+name: Update dependency versions to meet SPEC 0
+
+on:
+  schedule:
+    # Day 3 of each quarter, after the quarterly SPEC 0 update
+    - cron: "0 0 3 1,4,7,10 *"
+  workflow_dispatch:
+
+permissions:
+  contents: write
+  pull-requests: write
+
+concurrency:
+  group: ${{ github.workflow }}
+  cancel-in-progress: true
+
+jobs:
+  update:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: scientific-python/spec0-action@7c875bc60508e9aab2bdb851e99bfcc53b283e94 # v1.6
+        with:
+          update_all: 2

echoshader-0.2.0/.gitignore

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+# Python
+__pycache__/
+*.py[cod]
+*.egg-info/
+.eggs/
+
+# Build outputs and generated version
+build/
+dist/
+_build/
+echoshader/_echoshader_version.py
+
+# Tests and tooling
+.pytest_cache/
+.mypy_cache/
+.ruff_cache/
+.coverage*
+coverage.xml
+htmlcov/
+
+# Local environments and editor settings
+.env
+.venv/
+venv/
+.idea/
+.vscode/
+.DS_Store
+
+# Notebook checkpoints and downloaded example data
+.ipynb_checkpoints/
+examples/notebooks/*.zarr/
+examples/notebooks/*.zip
+examples/notebooks/concatenated_MVBS.nc
+
+docs/source/element_examples.ipynb
+docs/source/echogram_vertical_coordinates.ipynb

echoshader-0.2.0/.markdownlint.yaml

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+# Example markdownlint YAML configuration with all properties set to their default value
+
+# Default state for all rules
+default: true
+
+# Path to configuration file to extend
+extends: null
+
+# MD001/heading-increment/header-increment - Heading levels should only increment by one level at a time
+MD001: true
+
+# MD002/first-heading-h1/first-header-h1 - First heading should be a top-level heading
+MD002:
+  # Heading level
+  level: 1
+
+# MD003/heading-style/header-style - Heading style
+MD003:
+  # Heading style
+  style: "consistent"
+
+# MD004/ul-style - Unordered list style
+MD004:
+  # List style
+  style: "consistent"
+
+# MD005/list-indent - Inconsistent indentation for list items at the same level
+MD005: true
+
+# MD006/ul-start-left - Consider starting bulleted lists at the beginning of the line
+MD006: true
+
+# MD007/ul-indent - Unordered list indentation
+MD007:
+  # Spaces for indent
+  indent: 2
+  # Whether to indent the first level of the list
+  start_indented: false
+  # Spaces for first level indent (when start_indented is set)
+  start_indent: 2
+
+# MD009/no-trailing-spaces - Trailing spaces
+MD009:
+  # Spaces for line break
+  br_spaces: 2
+  # Allow spaces for empty lines in list items
+  list_item_empty_lines: false
+  # Include unnecessary breaks
+  strict: false
+
+# MD010/no-hard-tabs - Hard tabs
+MD010:
+  # Include code blocks
+  code_blocks: true
+  # Number of spaces for each hard tab
+  spaces_per_tab: 1
+
+# MD011/no-reversed-links - Reversed link syntax
+MD011: true
+
+# MD012/no-multiple-blanks - Multiple consecutive blank lines
+MD012:
+  # Consecutive blank lines
+  maximum: 1
+
+# MD013/line-length - Line length
+MD013:
+  # Number of characters
+  line_length: 90
+  # Number of characters for headings
+  heading_line_length: 90
+  # Number of characters for code blocks
+  code_block_line_length: 90
+  # Include code blocks
+  code_blocks: true
+  # Include tables
+  tables: true
+  # Include headings
+  headings: true
+  # Include headings
+  headers: true
+  # Strict length checking
+  strict: false
+  # Stern length checking
+  stern: false
+
+# MD014/commands-show-output - Dollar signs used before commands without showing output
+MD014: true
+
+# MD018/no-missing-space-atx - No space after hash on atx style heading
+MD018: true
+
+# MD019/no-multiple-space-atx - Multiple spaces after hash on atx style heading
+MD019: true
+
+# MD020/no-missing-space-closed-atx - No space inside hashes on closed atx style heading
+MD020: true
+
+# MD021/no-multiple-space-closed-atx - Multiple spaces inside hashes on closed atx style heading
+MD021: true
+
+# MD022/blanks-around-headings/blanks-around-headers - Headings should be surrounded by blank lines
+MD022:
+  # Blank lines above heading
+  lines_above: 1
+  # Blank lines below heading
+  lines_below: 1
+
+# MD023/heading-start-left/header-start-left - Headings must start at the beginning of the line
+MD023: true
+
+# MD024/no-duplicate-heading/no-duplicate-header - Multiple headings with the same content
+MD024:
+  # Only check sibling headings
+  allow_different_nesting: false
+  # Only check sibling headings
+  siblings_only: false
+
+# MD025/single-title/single-h1 - Multiple top-level headings in the same document
+MD025:
+  # Heading level
+  level: 1
+  # RegExp for matching title in front matter
+  front_matter_title: "^\\s*title\\s*[:=]"
+
+# MD026/no-trailing-punctuation - Trailing punctuation in heading
+MD026:
+  # Punctuation characters
+  punctuation: ".,;:!。，；：！"
+
+# MD027/no-multiple-space-blockquote - Multiple spaces after blockquote symbol
+MD027: true
+
+# MD028/no-blanks-blockquote - Blank line inside blockquote
+MD028: true
+
+# MD029/ol-prefix - Ordered list item prefix
+MD029:
+  # List style
+  style: "one_or_ordered"
+
+# MD030/list-marker-space - Spaces after list markers
+MD030:
+  # Spaces for single-line unordered list items
+  ul_single: 1
+  # Spaces for single-line ordered list items
+  ol_single: 1
+  # Spaces for multi-line unordered list items
+  ul_multi: 1
+  # Spaces for multi-line ordered list items
+  ol_multi: 1
+
+# MD031/blanks-around-fences - Fenced code blocks should be surrounded by blank lines
+MD031:
+  # Include list items
+  list_items: true
+
+# MD032/blanks-around-lists - Lists should be surrounded by blank lines
+MD032: true
+
+# MD033/no-inline-html - Inline HTML
+MD033:
+  # Allowed elements
+  allowed_elements: []
+
+# MD034/no-bare-urls - Bare URL used
+MD034: true
+
+# MD035/hr-style - Horizontal rule style
+MD035:
+  # Horizontal rule style
+  style: "consistent"
+
+# MD036/no-emphasis-as-heading/no-emphasis-as-header - Emphasis used instead of a heading
+MD036:
+  # Punctuation characters
+  punctuation: ".,;:!?。，；：！？"
+
+# MD037/no-space-in-emphasis - Spaces inside emphasis markers
+MD037: true
+
+# MD038/no-space-in-code - Spaces inside code span elements
+MD038: true
+
+# MD039/no-space-in-links - Spaces inside link text
+MD039: true
+
+# MD040/fenced-code-language - Fenced code blocks should have a language specified
+MD040: true
+
+# MD041/first-line-heading/first-line-h1 - First line in a file should be a top-level heading
+MD041:
+  # Heading level
+  level: 1
+  # RegExp for matching title in front matter
+  front_matter_title: "^\\s*title\\s*[:=]"
+
+# MD042/no-empty-links - No empty links
+MD042: true
+
+# MD043/required-headings/required-headers - Required heading structure
+MD043:
+  # List of headings
+  headings: []
+  # List of headings
+  headers: []
+
+# MD044/proper-names - Proper names should have the correct capitalization
+MD044:
+  # List of proper names
+  names: []
+  # Include code blocks
+  code_blocks: true
+
+# MD045/no-alt-text - Images should have alternate text (alt text)
+MD045: true
+
+# MD046/code-block-style - Code block style
+MD046:
+  # Block style
+  style: "consistent"
+
+# MD047/single-trailing-newline - Files should end with a single newline character
+MD047: true
+
+# MD048/code-fence-style - Code fence style
+MD048:
+  # Code fence style
+  style: "consistent"
+
+# MD049/emphasis-style - Emphasis style should be consistent
+MD049:
+  # Emphasis style should be consistent
+  style: "consistent"
+
+# MD050/strong-style - Strong style should be consistent
+MD050:
+  # Strong style should be consistent
+  style: "consistent"

echoshader-0.2.0/.markdownlintignore

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+docs/source/proposal-template.md

echoshader-0.2.0/.pre-commit-config.yaml

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+exclude: |
+  (?x)^(
+    .github/|
+    notebooks/|
+    docs/source/conf.py
+  )
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-docstring-first
+      - id: check-json
+      - id: check-yaml
+      - id: pretty-format-json
+        args: ["--autofix", "--indent=2", "--no-sort-keys"]
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.17.2
+    hooks:
+      - id: ruff-check
+        args: ["--fix"]
+        exclude: '\.ipynb$'
+      - id: ruff-format
+        exclude: '\.ipynb$'
+
+  - repo: https://github.com/igorshubovych/markdownlint-cli
+    rev: v0.50.0
+    hooks:
+      - id: markdownlint
+        args: ["**/**/*.md", "--ignore", "docs/source/gsoc", "--enable", "MD013", "--disable", "MD043", "line_length", "--fix"]

echoshader-0.2.0/.readthedocs.yaml

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+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.13"
+
+  jobs:
+    pre_build:
+      - cp examples/notebooks/element_examples.ipynb docs/source/element_examples.ipynb
+      - cp examples/notebooks/echogram_vertical_coordinates.ipynb docs/source/echogram_vertical_coordinates.ipynb
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+  # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
+  # builder: "dirhtml"
+  # Fail on all warnings to avoid broken references
+  # fail_on_warning: true
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#    - 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:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

echoshader-0.2.0/LICENSE

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+MIT License
+
+Copyright (c) 2022 Open-Source Ocean Acoustics
+
+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.

echoshader-0.2.0/MANIFEST.in

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+include LICENSE
+include README.md