oceanarray 0.1.0__tar.gz

oceanarray-0.1.0/.github/ISSUE_TEMPLATE.md

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+---
+name: "🐛 Bug Report / 💡 Feature Request"
+about: "Report a bug or suggest an improvement for the amocarray project"
+title: "[Bug] <brief description>" or "[Feature] <brief description>"
+labels: []
+assignees: []
+---
+
+## Description
+
+Please describe the bug or feature request clearly and concisely.
+
+**For bugs:**
+- What did you expect to happen?
+- What actually happened?
+- If applicable, include error messages or stack traces.
+
+**For features:**
+- What problem does this feature solve?
+- How would this feature improve the project?
+
+
+## Reproduction (for bugs)
+
+Please provide steps to reproduce the issue, if possible:
+
+1. Go to '...'
+2. Run '...'
+3. Observe '...'
+
+If you can, include a minimal, reproducible example or link to a failing test.
+
+
+## Environment
+
+- OS: [e.g., macOS 13.3, Ubuntu 22.04, etc.]
+- Python version: [e.g., 3.11]
+- amocarray version: [if applicable]
+- Virtualenv / Conda / System Python?: [env type]
+
+
+## Checklist
+
+- [ ] I have checked the existing [issues](https://github.com/AMOCcommunity/amocarray/issues) to avoid duplicates.
+- [ ] I have included steps to reproduce the issue, if it's a bug.
+- [ ] I have described the motivation clearly, if it's a feature request.
+
+
+## Additional context
+
+Add any other context or screenshots about the problem or feature request here.
+
+---
+
+*This issue template was prepared with assistance from ChatGPT to support clear and collaborative development.*
+

oceanarray-0.1.0/.github/PULL_REQUEST_TEMPLATE.md

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+You can delete unused sections.
+
+## PR Title Convention
+
+Please prefix your pull request title with one of the following tags for clarity:
+
+- `[DOC]` for documentation updates
+- `[FIX]` for bug fixes
+- `[FEAT]` for new features
+- `[REFACTOR]` for code improvements
+- `[TEST]` for tests
+- `[CI]` for CI/CD or automation updates
+- `[CLEANUP]` for general maintenance
+
+Example:
+> `[FIX] Correct dimension handling in OSNAP reader`
+
+**Description:**
+
+Please describe your changes clearly and concisely.
+
+- What is the purpose of this pull request?
+- What issue(s) does it address? Please link them (e.g., closes #12).
+- Briefly explain the approach taken.
+
+**Checklist:**
+
+- [ ] I have followed the [coding conventions](https://amoccommunity.github.io/amocarray/conventions.html).
+- [ ] I have updated or added tests to cover my changes.
+- [ ] I have updated the documentation if needed.
+- [ ] I have run `pytest` to check that all tests pass.
+- [ ] I have run `pre-commit run --all-files` to lint and format the code.
+
+**Related Issues / Pull Requests:**
+
+Link any related issues, pull requests, or discussions:
+- Fixes #
+- Related to #
+
+**Additional Notes:**
+
+Include any additional information reviewers might need:
+
+- Screenshots (if UI/outputs are affected)
+- Design decisions or trade-offs
+- Anything reviewers should look at closely
+

oceanarray-0.1.0/.github/dependabot.yml

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+version: 2
+updates:
+  # Python dependencies
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+      day-of-month: "1"
+      time: "09:00"
+      timezone: "UTC"
+    open-pull-requests-limit: 10
+    commit-message:
+      prefix: "[DEPS]"
+      include: "scope"
+    reviewers:
+      - "eleanorfrajka"
+    assignees:
+      - "eleanorfrajka"
+    labels:
+      - "dependencies"
+      - "automated"
+    groups:
+      minor-and-patch:
+        patterns:
+          - "*"
+        update-types:
+          - "minor"
+          - "patch"
+
+  # GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+      day-of-month: "1"
+      time: "09:00"
+      timezone: "UTC"
+    open-pull-requests-limit: 5
+    commit-message:
+      prefix: "[CI]"
+      include: "scope"
+    reviewers:
+      - "eleanorfrajka"
+    assignees:
+      - "eleanorfrajka"
+    labels:
+      - "github-actions"
+      - "automated"

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

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+name: Test documentation build
+
+on:
+  pull_request:
+    paths:
+      - '**.py'
+      - '**.ipynb'
+      - '**.rst'
+      - '**.md'
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Setup Micromamba
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-file: environment.yml
+          init-shell: bash
+          condarc: |
+            channels:
+              - conda-forge
+            channel_priority: strict
+          cache-environment: true
+
+      - name: Install package (editable)
+        shell: bash -l {0}
+        run: |
+          micromamba run -n TEST python -m pip install --upgrade pip
+          micromamba run -n TEST python -m pip install -e . --no-deps --force-reinstall
+
+      - name: Build documentation
+        shell: bash -l {0}
+        run: |
+          set -e
+          micromamba run -n TEST jupyter nbconvert --to notebook --execute notebooks/demo_instrument.ipynb --output=demo_instrument-output.ipynb --ExecutePreprocessor.allow_errors=True
+          micromamba run -n TEST jupyter nbconvert --to notebook --execute notebooks/demo_mooring.ipynb --output=demo_mooring-output.ipynb --ExecutePreprocessor.allow_errors=True
+          mv notebooks/*output.ipynb docs/source/
+          pushd docs
+          micromamba run -n TEST make clean html
+          popd

oceanarray-0.1.0/.github/workflows/docs_deploy.yml

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+name: Deploy Documentation
+
+on:
+  push:
+    branches:
+      - main
+  # Optional: manual trigger
+  workflow_dispatch:
+
+jobs:
+  deploy-docs:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Setup Micromamba
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-file: environment.yml
+          init-shell: bash
+          condarc: |
+            channels:
+              - conda-forge
+            channel_priority: strict
+          cache-environment: true
+
+      - name: Install package (editable)
+        shell: bash -l {0}
+        run: |
+          micromamba run -n TEST python -m pip install --upgrade pip
+          micromamba run -n TEST python -m pip install -e . --no-deps --force-reinstall
+
+      - name: Build documentation
+        shell: bash -l {0}
+        run: |
+          set -e
+          micromamba run -n TEST jupyter nbconvert --to notebook --execute notebooks/demo_instrument.ipynb --output=demo_instrument-output.ipynb --ExecutePreprocessor.allow_errors=True
+          micromamba run -n TEST jupyter nbconvert --to notebook --execute notebooks/demo_mooring.ipynb --output=demo_mooring-output.ipynb --ExecutePreprocessor.allow_errors=True
+          mv notebooks/*output.ipynb docs/source/
+          pushd docs
+          micromamba run -n TEST make clean html
+          popd
+
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: docs/build/html
+          # Optional: publish_branch: gh-pages
+          # Optional: cname: docs.example.org

oceanarray-0.1.0/.github/workflows/pypi.yml

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+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+# GitHub recommends pinning actions to a commit SHA.
+# To get a newer version, you will need to update the SHA.
+# You can also reference a tag or branch, but the action may change without warning.
+
+# See also https://docs.github.com/en/actions/use-cases-and-examples/building-and-testing/building-and-testing-python
+name: Publish to PyPI
+
+on:
+  release:
+    types:
+      - published
+
+permissions:
+  contents: read
+
+jobs:
+  release-build:
+    runs-on: ubuntu-latest
+    environment: test
+    permissions:
+      id-token: write
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          ref: ${{ github.ref }}
+          fetch-depth: 0
+
+      - name: Clean repository before build
+        run: git clean -fxd
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: Install build tools
+        run: |
+          python -m pip install --upgrade pip wheel setuptools setuptools_scm build twine
+
+      - name: Build package
+        run: python -m build --sdist --wheel . --outdir dist
+
+      - name: Check built distributions
+        run: python -m twine check dist/*
+
+      - name: Publish to PyPI
+        if: success() && github.event_name == 'release'
+        uses: pypa/gh-action-pypi-publish@release/v1

oceanarray-0.1.0/.github/workflows/tests.yml

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+name: Run unit tests
+
+on:
+  push:
+    branches: ["**"]
+  pull_request:
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: ["3.11"]
+      fail-fast: true
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements-dev.txt
+
+      - name: Install oceanarray
+        run: pip install -e . --no-deps --force-reinstall
+
+      - name: Run unit tests
+        run: pytest tests/unit -m "not slow and not local and not needs_seasenselib" -q

oceanarray-0.1.0/.gitignore

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+setup.sh
+*/_version.py
+
+# Data files — not stored in the repository
+# Anchored to repo root so oceanarray/logsheets/data/ (package data) is NOT excluded.
+/data/
+outputs/
+
+# Legacy individual exclusions (superseded by data/ above)
+data/temp.nc
+*_use.nc
+*_raw.nc
+data/moor/raw/odb_2026/*
+
+
+# Legacy reference scripts — originals kept locally, not tracked
+oceanarray/legacy/02_aqdp_ploter.py
+
+# Caldip prototype and dev scripts (superseded by ../caldip/ package)
+oceanarray/caldip.py
+debug_caldip.py
+example_caldip_usage.py
+simple_caldip_plot.py
+plot_calibration_data.py
+test_caldip.py
+test_caldip_simple.py
+data/moor/proc_calib/
+calibration_data_plot.png
+calibration_dip_comparison.png
+matlab_calibration/
+
+logs/*log
+
+# Claude Code configuration
+.claude/
+
+# VSCode settings
+.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/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# 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/
+
+# 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/
+data/DSE18_SBE37SM_RS232_03707518_2018_08_26efw1.cnv
+data/moor/proc/dsE_1_2018/microcat/dsE_1_2018_microcat_7518_temperature_raw.png
+data/moor/raw/msm76_2018/rbrsolo/DSE18_101651_20180827_1541.mat
+data/moor/proc/dsE_1_2018/rbrsolo/dsE_1_2018_101646_raw.nc
+.gitignore
+data/moor/raw/msm76_2018/sbe56/DSE18_SBE05606363_2018_08_27.cnv
+data/moor/raw/msm76_2018/sbe56/DSE18_SBE05606364_2018_08_27.cnv
+data/moor/raw/msm76_2018/sbe56/DSE18_SBE05606365_2018_08_27.cnv
+data/moor/raw/msm76_2018/sbe56/DSE18_SBE05606366_2018_08_27.cnv
+data/moor/raw/msm76_2018/sbe56/DSE18_SBE05606370_2018_08_27.cnv
+data/moor/raw/msm76_2018/sbe56/DSE18_SBE05606394_2018_08_27.cnv
+data/moor/raw/msm76_2018/sbe56/DSE18_SBE05606397_2018_08_27.cnv
+data/moor/raw/msm76_2018/sbe56/DSE18_SBE05606401_2018_08_27.cnv
+data/moor/raw/msm76_2018/sbe56/DSE18_SBE05606402_2018_08_27.cnv
+data/moor/raw/msm76_2018/sbe56/DSE18_SBE05606409_2018_08_27.cnv

oceanarray-0.1.0/.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/psf/black
+    rev: 24.3.0
+    hooks:
+      - id: black
+        language_version: python3
+        files: \.(py|ipynb)$
+        exclude: ^data/
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.6  # Check for the latest version
+    hooks:
+      - id: codespell
+        args: ["--ignore-words-list", "nd"]  # Optional: ignore some false positives
+
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+        language_version: python3
+        files: \.(py|ipynb)$
+        exclude: ^data/
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: end-of-file-fixer
+        files: \.(py|yaml|yml|ipynb)$
+        exclude: ^data/
+      - id: trailing-whitespace
+        files: \.(py|yaml|yml|ipynb)$
+        exclude: ^data/
+      - id: check-yaml
+        files: \.(yaml|yml)$
+        exclude: ^data/
+      - id: check-added-large-files
+
+  - repo: local
+    hooks:
+      - id: pytest
+        name: pytest
+        entry: pytest -q
+        language: system
+        types: [python]
+        exclude: ^data/
+
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.3.0
+    hooks:
+      - id: ruff
+        args: [
+          "--fix",
+          "--exit-zero",
+          "--select",
+          "E,F,W,C90,ANN,B,BLE,TRY,ARG,SLF",
+        ]
+        exclude: ^data/

oceanarray-0.1.0/.vscode/settings.json

@@ -0,0 +1,37 @@
+{
+    // === Python Environment ===
+    "python.defaultInterpreterPath": "${workspaceFolder}/venv/bin/python",
+    "python.pythonPath": "${workspaceFolder}/venv/bin/python",
+    // === Formatting ===
+    "python.formatting.provider": "black",
+    "editor.formatOnSave": true,
+    "editor.codeActionsOnSave": {
+        "source.organizeImports": "explicit",
+        "source.fixAll": "explicit"
+    },
+    // === Linting ===
+    "python.linting.enabled": true,
+    "python.linting.pylintEnabled": false,
+    "ruff.enable": true,
+    "ruff.lintOnSave": true,
+    "ruff.path": [
+        "${workspaceFolder}/venv/bin/ruff"
+    ],
+    "pre-commit.executablePath": "${workspaceFolder}/venv/bin/pre-commit",
+    "terminal.integrated.env.osx": {
+        "PATH": "${workspaceFolder}/venv/bin:${env:PATH}:/opt/homebrew/bin:/opt/homebrew/opt/tcl-tk@8/bin:$HOME/.pyenv/bin"
+    },
+    "git.terminalAuthentication": true,
+    "git.useGitUserTerminal": true,
+    // === VSCode experience ===
+    "files.trimTrailingWhitespace": true,
+    "files.insertFinalNewline": true,
+    "files.autoSave": "onFocusChange",
+    // === Jupyter support (optional) ===
+    "jupyter.jupyterServerType": "local",
+    "python.testing.pytestArgs": [
+        "tests"
+    ],
+    "python.testing.unittestEnabled": false,
+    "python.testing.pytestEnabled": true,
+}

oceanarray-0.1.0/.vscode/tasks.json

@@ -0,0 +1,22 @@
+{
+    "version": "2.0.0",
+    "tasks": [
+        {
+            "label": "Pre-commit: run all hooks",
+            "type": "shell",
+            "command": "source ./venv/bin/activate && pre-commit run --all-files",
+            "problemMatcher": [],
+            "group": {
+                "kind": "build",
+                "isDefault": true
+            },
+            "presentation": {
+                "reveal": "always",
+                "panel": "dedicated"
+            },
+            "runOptions": {
+                "runOn": "folderOpen"
+            }
+        }
+    ]
+}