oceanarray 0.1.0__tar.gz → 0.2.0__tar.gz

{oceanarray-0.1.0 → oceanarray-0.2.0}/.github/ISSUE_TEMPLATE.md

@@ -1,7 +1,7 @@
 ---
 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>"
+about: "Report a bug or suggest an improvement for oceanarray"
+title: "[Bug] <brief description>"
 labels: []
 assignees: []
 ---
@@ -33,24 +33,20 @@ 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.]
+- OS: [e.g., macOS 13.3, Ubuntu 22.04]
 - Python version: [e.g., 3.11]
-- amocarray version: [if applicable]
+- `oceanarray` version: [`pip show oceanarray`]
+- `seasenselib` version: [`pip show seasenselib`]
 - Virtualenv / Conda / System Python?: [env type]
 
 
 ## Checklist
 
-- [ ] I have checked the existing [issues](https://github.com/AMOCcommunity/amocarray/issues) to avoid duplicates.
+- [ ] I have checked the existing [issues](https://github.com/ocean-uhh/oceanarray/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.*
-
+Add any other context or screenshots about the problem here.

{oceanarray-0.1.0 → oceanarray-0.2.0}/.github/PULL_REQUEST_TEMPLATE.md

@@ -2,7 +2,7 @@ You can delete unused sections.
 
 ## PR Title Convention
 
-Please prefix your pull request title with one of the following tags for clarity:
+Please prefix your pull request title with one of the following tags:
 
 - `[DOC]` for documentation updates
 - `[FIX]` for bug fixes
@@ -13,7 +13,7 @@ Please prefix your pull request title with one of the following tags for clarity
 - `[CLEANUP]` for general maintenance
 
 Example:
-> `[FIX] Correct dimension handling in OSNAP reader`
+> `[FIX] Correct dimension handling in RBR reader`
 
 **Description:**
 
@@ -25,11 +25,10 @@ Please describe your changes clearly and concisely.
 
 **Checklist:**
 
-- [ ] I have followed the [coding conventions](https://amoccommunity.github.io/amocarray/conventions.html).
+- [ ] I have followed the [code conventions](CONTRIBUTING.md).
 - [ ] 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.
+- [ ] I have run `ruff check . --fix` and `pytest` — all tests pass.
 
 **Related Issues / Pull Requests:**
 
@@ -41,7 +40,6 @@ Link any related issues, pull requests, or discussions:
 
 Include any additional information reviewers might need:
 
-- Screenshots (if UI/outputs are affected)
+- Screenshots (if outputs are affected)
 - Design decisions or trade-offs
 - Anything reviewers should look at closely
-

{oceanarray-0.1.0 → oceanarray-0.2.0}/.github/workflows/docs.yml

@@ -34,16 +34,16 @@ jobs:
       - 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
+          micromamba run -n oceanarray python -m pip install --upgrade pip
+          micromamba run -n oceanarray 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
+          micromamba run -n oceanarray jupyter nbconvert --to notebook --execute notebooks/demo_instrument.ipynb --output=demo_instrument-output.ipynb --ExecutePreprocessor.allow_errors=True
+          micromamba run -n oceanarray 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
+          micromamba run -n oceanarray make clean html
           popd

{oceanarray-0.1.0 → oceanarray-0.2.0}/.github/workflows/docs_deploy.yml

@@ -33,18 +33,18 @@ jobs:
       - 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
+          micromamba run -n oceanarray python -m pip install --upgrade pip
+          micromamba run -n oceanarray 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
+          micromamba run -n oceanarray jupyter nbconvert --to notebook --execute notebooks/demo_instrument.ipynb --output=demo_instrument-output.ipynb --ExecutePreprocessor.allow_errors=True
+          micromamba run -n oceanarray 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
+          micromamba run -n oceanarray make clean html
           popd
 
       - name: Deploy to GitHub Pages

oceanarray-0.2.0/.github/workflows/tests.yml

@@ -0,0 +1,61 @@
+name: Run tests
+
+on:
+  push:
+    branches: ["**"]
+  pull_request:
+
+jobs:
+  unit:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-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
+
+  integration:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+          cache: "pip"
+
+      - name: Install dependencies
+        # requirements-test.txt = requirements-dev.txt + the PyPI seasenselib
+        # release, so the golden integration tests (stage2/stage3/grid) run for
+        # real here rather than skipping.
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements-test.txt
+
+      - name: Install oceanarray
+        run: pip install -e . --no-deps --force-reinstall
+
+      - name: Run integration tests
+        # needs_seasenselib is NOT excluded here: seasenselib is installed above.
+        run: pytest tests/integration -m "not local" -q

{oceanarray-0.1.0 → oceanarray-0.2.0}/.gitignore

@@ -31,8 +31,6 @@ matlab_calibration/
 
 logs/*log
 
-# Claude Code configuration
-.claude/
 
 # VSCode settings
 .vscode/*

oceanarray-0.2.0/CHANGELOG.md

@@ -0,0 +1,90 @@
+# Changelog
+
+All notable changes to oceanarray are documented here.
+
+---
+
+## [0.2.0] — unreleased
+
+### Breaking changes
+
+- **`--basedir` removed** ([#52](https://github.com/ocean-uhh/oceanarray/pull/52)): use `--raw-dir` and `--proc-dir` instead. See the [migration guide](https://ocean-uhh.github.io/oceanarray/migration.html).
+- **`plotter.py` retired** ([#53](https://github.com/ocean-uhh/oceanarray/pull/53)): the monolithic `oceanarray/plotter.py` and all backward-compatibility re-export shims have been removed. Import from canonical modules (`oceanarray.plotters.current`, `oceanarray.plotters.timeseries`, etc.).
+- **Subpackage reorganisation** ([#49](https://github.com/ocean-uhh/oceanarray/pull/49), [#59](https://github.com/ocean-uhh/oceanarray/pull/59)): processing modules moved from `oceanarray/instrument/` and `oceanarray/mooring/` into `oceanarray.processors.*`. Top-level `oceanarray` imports unchanged; internal paths have moved.
+
+### New features
+
+- **`--stage stack grid` in `oceanarray process`**: the `--stage` flag now accepts `stack` and `grid` in addition to `1`, `2`, `3`. Run the full pipeline as `oceanarray process MOORING --stage 1 2 3 stack grid`. New flags `--dt`, `--dp`, `--pmin`, `--pmax` added to `process` (same defaults as `oceanarray run`).
+- **`process()` public API** ([#58](https://github.com/ocean-uhh/oceanarray/pull/58)): `oceanarray.process(mooring_yaml, proc_dir, stages=…)` runs any combination of Stage 1–3, stack, and grid in a single call. `oceanarray.STAGES` is the registry of available stages.
+- **Array report** ([#48](https://github.com/ocean-uhh/oceanarray/pull/48)): `oceanarray report <array.yaml> --array` generates a multi-mooring HTML summary with smart rebuild (only re-renders sections whose NC files are newer than the existing report).
+- **Wave / frequency diagnostics** ([#47](https://github.com/ocean-uhh/oceanarray/pull/47)): rotary power spectra, near-inertial band energy, and wave diagnostics added to ADCP instrument reports.
+- **Release automation** ([#61](https://github.com/ocean-uhh/oceanarray/pull/61)): pushing a `v*` tag now auto-creates a draft GitHub release with PR-based release notes; publishing the draft triggers PyPI upload.
+
+### Bug fixes
+
+- **QC flags unified to OceanSITES table** ([#54](https://github.com/ocean-uhh/oceanarray/pull/54)): all QC flag values now use the standard OceanSITES convention (0 no QC, 1 good, 2 probably good, 3 probably bad, 4 bad, 9 missing). Previously mixed conventions caused flag collisions on merge.
+- **Plot regularisation** ([#50](https://github.com/ocean-uhh/oceanarray/pull/50)): fixed irregular time-axis sampling in instrument report figures.
+- **Turbidity `units=MISSING`** ([#61](https://github.com/ocean-uhh/oceanarray/pull/61)): stage1 now strips placeholder `units` strings (`"MISSING"`, `""`) written by the RBR RSK reader when the instrument database has no units entry, and emits a `UserWarning` so the operator can verify the sensor spec.
+
+### Deprecations
+
+- **`oceanarray stack`**: deprecated in favour of `oceanarray process MOORING --stage stack`. Emits `DeprecationWarning`. Will be removed in v0.3.0.
+- **`oceanarray grid`**: deprecated in favour of `oceanarray process MOORING --stage grid`. Emits `DeprecationWarning`. Will be removed in v0.3.0.
+- `file_type: rbr-hex-oa` remapped automatically to `rbr-hex` with a `DeprecationWarning`; update mooring YAMLs.
+- `file_type: sbe-asc` remapped automatically to `sbe-ascii`.
+
+### Refactoring
+
+- Single-source variable registries in `parameters.py`; `validation.py` derives from it ([#51](https://github.com/ocean-uhh/oceanarray/pull/51)).
+- Figure-returning shape for `report/_plots.py` ([#56](https://github.com/ocean-uhh/oceanarray/pull/56)); `draw_*` helpers relocated to `plotters/` ([#57](https://github.com/ocean-uhh/oceanarray/pull/57)).
+- Type annotations backfilled on `hydrographic.py` and `temporal.py`; two ANN per-file-ignores removed from `pyproject.toml`.
+
+### Tests
+
+- Integration chain tests (stage1 → stage2 → stage3 → stack → grid) over committed `dune2_1_2026` fixtures ([#60](https://github.com/ocean-uhh/oceanarray/pull/60)).
+- CI: integration job now installs seasenselib from PyPI; Windows and macOS unit jobs run seasenselib-free.
+
+---
+
+## [0.1.0] — 2026-07-27
+
+First public release.
+
+### Processing pipeline
+
+- **Stage 1** — raw instrument files → CF-NetCDF: Sea-Bird SBE37 MicroCAT (`sbe-cnv`, `sbe-ascii`), Nortek Aquadopp (`nortek-raw`, `nortek-ascii`, `nortek-csv`), RBR Solo/Duet (`rbr-rsk`, `rbr-dat`), RDI WorkHorse ADCP (`rdi-raw`). Nortek BEAM→XYZ transformation matrix parsed from `.hdr` file and applied at stage 1; matrix stored in output for reproducibility.
+- **Stage 2** — deployment trimming (YAML `deployment_time`/`recovery_time`) and linear clock-drift correction from recovery timestamps.
+- **Stage 3** — QARTOD gross-range and spike QC on T/C/S/P; pressure interpolation (QC flag 8) for instruments without a pressure sensor; Aquadopp XYZ→ENU rotation using heading/pitch/roll + IGRF magnetic declination (`ppigrf`); tilt QC on velocity; potential density via `gsw`.
+
+### Mooring-level commands
+
+- `oceanarray stack` — resample all instruments to a common time axis, stack into a single `(time, N_LEVELS)` dataset ordered deep-first.
+- `oceanarray grid` — linearly interpolate the stacked dataset onto a regular pressure grid (`--pmin`, `--pmax`, `--dp`).
+
+### Reporting
+
+- `oceanarray report` — self-contained HTML reports (all figures base64-embedded, offline-readable):
+  - Mooring summary: deployment metadata, instrument pipeline status, QC flag breakdown, clock corrections, knockdown figures, clock alignment check.
+  - Per-instrument pages (`--instruments`): full time series with QC markers, T-S diagram, current roses, data histograms, QC table, scalar metadata.
+  - Stack report (`--stack`): pressure/T/S/velocity time series, T-S diagram, current roses, spacing histogram.
+  - Grid report (`--grid`): T/S/density pcolormesh, N², velocity sections, T-S diagram, power spectra.
+  - Array report (`--array`): position map, summary table with clickable links to mooring reports.
+
+### CLI
+
+- `oceanarray process` — run stage 1, 2, and/or 3 for a mooring or a single instrument (`--serial`).
+- `oceanarray run` — complete pipeline in one command (process + stack + grid + report).
+- `oceanarray validate` — check mooring YAML for missing fields and unknown instrument types.
+- `oceanarray list` — print accepted `instrument:` names and `file_type:` values.
+- `oceanarray logsheet` — generate PDF logsheets from YAML instrument inventory.
+
+### Logsheets
+
+- `oceanarray logsheet` subcommand generates LaTeX-rendered PDF deployment logsheets from a cruise configuration YAML.
+
+### Notable design choices
+
+- Data provenance: all processing parameters (QC thresholds, declination value, transformation matrix) stored as NetCDF attributes so any file can be reprocessed exactly from itself.
+- Discrete colorbars throughout (≤ 20 levels, `BoundaryNorm`).
+- CF-convention variable names and standard names throughout; OceanSITES QC flag values.
+- `seasenselib` is used for raw file reading but is a separate install (`pip install seasenselib --no-deps` — see installation docs).

oceanarray-0.2.0/CITATION.cff

@@ -0,0 +1,24 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it using the metadata below."
+authors:
+- family-names: Frajka-Williams
+  given-names: Eleanor
+  orcid: https://orcid.org/0000-0001-8773-7838
+  affiliation: University of Hamburg, Bundesstraße 53, 20146 Hamburg, Germany
+title: oceanarray
+version: 0.2.0
+date-released: 2026-07-27
+url: https://github.com/ocean-uhh/oceanarray
+repository-code: https://github.com/ocean-uhh/oceanarray
+license: MIT
+abstract: >
+  Multi-stage processing pipeline for moored oceanographic array observations:
+  converts raw instrument files (Sea-Bird, RBR, Nortek, RDI) to QC-flagged,
+  CF-compliant NetCDF and generates self-contained HTML mooring recovery reports.
+keywords:
+  - oceanography
+  - mooring
+  - ADCP
+  - CTD
+  - NetCDF
+  - quality-control

oceanarray-0.2.0/CONTRIBUTING.md

@@ -0,0 +1,125 @@
+# Contributing to oceanarray
+
+Thanks for taking the time to contribute.
+
+All contributions are welcome: bug reports, feature suggestions, documentation improvements, and code.
+
+## Table of Contents
+
+- [I Have a Question](#i-have-a-question)
+- [Reporting Bugs](#reporting-bugs)
+- [Suggesting Enhancements](#suggesting-enhancements)
+- [Your First Code Contribution](#your-first-code-contribution)
+- [Improving The Documentation](#improving-the-documentation)
+
+---
+
+## I Have a Question
+
+Read the [documentation](https://ocean-uhh.github.io/oceanarray/) first.
+Then search [existing issues](https://github.com/ocean-uhh/oceanarray/issues) — your question may already be answered.
+
+If you still need help, [open an issue](https://github.com/ocean-uhh/oceanarray/issues/new) and include:
+
+- What you were trying to do and what you expected to happen.
+- A minimal reproducible example (e.g. a short script or notebook cell).
+- Your platform, Python version, and `pip show oceanarray seasenselib` output.
+
+---
+
+## Reporting Bugs
+
+Security vulnerabilities must be reported by email to [eleanorfrajka@gmail.com](mailto:eleanorfrajka@gmail.com) — do not use the public issue tracker.
+
+For all other bugs:
+
+1. Confirm you are on the latest release (`pip show oceanarray`).
+2. [Open an issue](https://github.com/ocean-uhh/oceanarray/issues/new) with:
+   - Steps to reproduce (minimal script if possible).
+   - Expected vs. actual behaviour.
+   - Full traceback.
+   - OS, Python version, `oceanarray` and `seasenselib` versions.
+
+---
+
+## Suggesting Enhancements
+
+[Open an issue](https://github.com/ocean-uhh/oceanarray/issues/new) describing:
+
+- What you want to do that is currently impossible or inconvenient.
+- Why it would be useful to other users (not just your specific cruise).
+- Whether you are willing to implement it yourself.
+
+Keep in mind that oceanarray is designed for reproducible processing of moored array data. Features that require cruise-specific raw data, add heavy new dependencies, or break the CF-NetCDF output contract are unlikely to be merged.
+
+---
+
+## Your First Code Contribution
+
+### Architecture overview
+
+| Layer | Modules | Role |
+|-------|---------|------|
+| Tier 1 | `tools/`, `utilities.py` | Pure functions, no side effects |
+| Tier 2 | `processors/stage1.py` … `processors/grid.py` | Processing orchestrators — read, transform, write CF-NetCDF |
+| Tier 3 | `cli.py` | Entry point — argument parsing, subcommand dispatch |
+| — | `plotters/`, `report/` | Visualisation and HTML report generation |
+| — | `analysis/` | Science utilities (filtering, isopycnals, QC) |
+| — | `config/` | Parameters, variable registry, YAML validation |
+
+Processing flows from raw files → Stage 1 (CF-NetCDF) → Stage 2 (trimming + clock) → Stage 3 (QC + ENU) → stack → grid.
+
+### Development setup
+
+```bash
+git clone https://github.com/ocean-uhh/oceanarray.git
+cd oceanarray
+python -m venv venv && source venv/bin/activate
+pip install -e .
+pip install -r requirements-dev.txt
+# seasenselib (needed for raw file reading):
+pip install pyrsktools pycnv
+pip install seasenselib --no-deps
+```
+
+### Workflow
+
+1. Fork the repository and create a feature branch from `main`.
+2. Make your changes, following the conventions below.
+3. Run `ruff check . --fix` and then `pytest` — all tests must pass.
+4. Open a pull request against `main`. Use a title prefixed with `[FEAT]`, `[FIX]`, `[REFACTOR]`, `[DOC]`, `[TEST]`, or `[CLEANUP]`.
+
+### Code conventions
+
+- **Docstrings**: NumPy style on every public function and class. Include `Parameters`, `Returns`, and `Raises` sections. Period at the end.
+- **Type annotations**: all public function arguments and return values.
+- **Lint**: `ruff check .` must be clean. No bare `except:`. No suppressed warnings without a comment explaining why.
+- **Units**: never strip or assume units. Use `gsw` for all seawater property calculations.
+- **Plot style**: discrete colorbars (`BoundaryNorm`, ≤ 20 levels); call `plt.style.use(str(P.MPLSTYLE))` at the start of every plot function.
+- **Data provenance**: store all processing parameters (thresholds, coefficients) in NC output attributes so any file can be reprocessed exactly from itself.
+
+### Testing
+
+Tests live in `tests/unit/` and `tests/integration/`. Run the full suite:
+
+```bash
+pytest                                                # all tests
+pytest tests/unit -m "not slow and not needs_seasenselib"  # without seasenselib
+pytest --cov=oceanarray --cov-report=term-missing -q  # with coverage
+```
+
+New or changed code must have test coverage. Integration tests use committed NetCDF fixtures in `tests/fixtures/`.
+
+---
+
+## Improving The Documentation
+
+Documentation is built with Sphinx from `docs/source/`. To build locally:
+
+```bash
+pip install -r requirements-dev.txt
+cd docs && make clean html
+open build/html/index.html
+```
+
+Docstring changes are picked up automatically. For narrative docs, edit `.rst` files in `docs/source/`. The API reference is auto-generated from docstrings via `autodoc`.

{oceanarray-0.1.0 → oceanarray-0.2.0}/MIGRATION-BASEDIR.md

@@ -1,9 +1,9 @@
 # Migrating from --basedir to --raw-dir / --proc-dir
 
-The `--basedir` flag is deprecated.  All subcommands now accept
-`--raw-dir` and `--proc-dir` instead.  `--basedir` still works and
-will continue to work indefinitely, but it prints a `DeprecationWarning`
-on every invocation.
+The `--basedir` flag has been **removed**.  All subcommands now require
+`--raw-dir` and `--proc-dir` instead.  Passing `--basedir` prints a migration
+message naming the replacement and exits without processing.  This document
+explains how to convert an old `--basedir` layout to the current one.
 
 ---
 
@@ -166,3 +166,25 @@ The old `--basedir DIR` resolved paths as:
 The new `--raw-dir`/`--proc-dir` flags give you explicit control over
 each root, support mooring-first raw layout, and put logs in a
 `processing_logs/` subdirectory.
+
+---
+
+## If you call the Python API directly (notebooks / scripts)
+
+The same removal touched the Python entry points:
+
+- **Processor constructors are keyword-only and required.** Replace
+  `MooringProcessor(basedir)` with
+  `MooringProcessor(raw_dir=RAW, proc_dir=PROC)`, and
+  `Stage2Processor(basedir)` / `Stage3Processor` / `MooringStacker` /
+  `MooringGridder` / `MooringReport` / `TimeGriddingProcessor` with
+  `proc_dir=PROC` (add `raw_dir=RAW` for stage 1 and the report). A positional
+  or `base_dir=` call now raises `TypeError`.
+- **Removed convenience functions:** `stage1_mooring`,
+  `process_multiple_moorings`, `stage2_mooring`,
+  `process_multiple_moorings_stage2`. Use the `oceanarray` CLI, or loop over
+  moorings yourself constructing the processor directly.
+- **`time_gridding_mooring(mooring, proc_dir, ...)`** and
+  `process_multiple_moorings_time_gridding` — the second positional argument is
+  now the **proc root**, not a cruise base dir. Update call sites; a positional
+  `basedir` value will be silently misused as `proc_dir`.

oceanarray-0.2.0/PKG-INFO

@@ -0,0 +1,108 @@
+Metadata-Version: 2.4
+Name: oceanarray
+Version: 0.2.0
+Summary: Multi-stage processing pipeline for moored oceanographic observations: raw instrument files to QC-flagged CF-compliant NetCDF with automated HTML reports.
+Maintainer-email: Eleanor Frajka-Williams <eleanorfrajka@gmail.com>
+License: MIT License
+        
+        Copyright (c) 2025 Eleanor Frajka-Williams
+        
+        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.
+        
+Project-URL: Documentation, https://ocean-uhh.github.io/oceanarray
+Project-URL: Homepage, https://github.com/ocean-uhh/oceanarray
+Project-URL: Repository, https://github.com/ocean-uhh/oceanarray
+Project-URL: Issue Tracker, https://github.com/ocean-uhh/oceanarray/issues
+Keywords: oceanography,mooring,ADCP,CTD,NetCDF,QC,oceanographic-data,AMOC
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Oceanography
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.23
+Requires-Dist: pandas>=2.0
+Requires-Dist: xarray>=2023.12.0
+Requires-Dist: netcdf4>=1.6
+Requires-Dist: scipy>=1.10
+Requires-Dist: matplotlib>=3.7
+Requires-Dist: gsw>=3.6.16
+Requires-Dist: ppigrf
+Requires-Dist: ioos_qc
+Requires-Dist: dolfyn
+Requires-Dist: pycwt
+Requires-Dist: jinja2>=3.0
+Requires-Dist: packaging>=21.0
+Requires-Dist: ruamel.yaml>=0.18
+Dynamic: license-file
+
+# OceanArray
+
+Python tools for processing moored oceanographic array observations from raw instrument files to quality-controlled, CF-compliant NetCDF.
+
+**Documentation**: https://ocean-uhh.github.io/oceanarray/
+
+## Installation
+
+```bash
+pip install oceanarray
+```
+
+`seasenselib` is required for reading raw instrument files (available on PyPI but needs `--no-deps`):
+
+```bash
+pip install pyrsktools pycnv
+pip install seasenselib --no-deps
+```
+
+Python 3.9–3.12 is supported.
+
+## Quick start
+
+Create a skeleton YAML, fill in the deployment metadata, then process:
+
+```bash
+oceanarray init dsG3_1_2026 --proc-dir /data/proc
+# edit /data/proc/dsG3_1_2026/dsG3_1_2026.mooring.yaml
+oceanarray validate /data/proc/dsG3_1_2026/dsG3_1_2026.mooring.yaml
+oceanarray process dsG3_1_2026 --raw-dir /data/raw --proc-dir /data/proc --stage 1 2 3 stack grid
+oceanarray report  dsG3_1_2026 --raw-dir /data/raw --proc-dir /data/proc --all
+```
+
+See the [documentation](https://ocean-uhh.github.io/oceanarray/) for the recommended first-processing workflow, YAML reference, and CLI reference.
+
+## Python API
+
+```python
+import oceanarray
+
+oceanarray.process('dsG3_1_2026', raw_dir='/data/raw', proc_dir='/data/proc')
+```
+
+See the [API reference](https://ocean-uhh.github.io/oceanarray/oceanarray.html) for the full interface.
+
+## License
+
+MIT License

oceanarray-0.2.0/README.md

@@ -0,0 +1,48 @@
+# OceanArray
+
+Python tools for processing moored oceanographic array observations from raw instrument files to quality-controlled, CF-compliant NetCDF.
+
+**Documentation**: https://ocean-uhh.github.io/oceanarray/
+
+## Installation
+
+```bash
+pip install oceanarray
+```
+
+`seasenselib` is required for reading raw instrument files (available on PyPI but needs `--no-deps`):
+
+```bash
+pip install pyrsktools pycnv
+pip install seasenselib --no-deps
+```
+
+Python 3.9–3.12 is supported.
+
+## Quick start
+
+Create a skeleton YAML, fill in the deployment metadata, then process:
+
+```bash
+oceanarray init dsG3_1_2026 --proc-dir /data/proc
+# edit /data/proc/dsG3_1_2026/dsG3_1_2026.mooring.yaml
+oceanarray validate /data/proc/dsG3_1_2026/dsG3_1_2026.mooring.yaml
+oceanarray process dsG3_1_2026 --raw-dir /data/raw --proc-dir /data/proc --stage 1 2 3 stack grid
+oceanarray report  dsG3_1_2026 --raw-dir /data/raw --proc-dir /data/proc --all
+```
+
+See the [documentation](https://ocean-uhh.github.io/oceanarray/) for the recommended first-processing workflow, YAML reference, and CLI reference.
+
+## Python API
+
+```python
+import oceanarray
+
+oceanarray.process('dsG3_1_2026', raw_dir='/data/raw', proc_dir='/data/proc')
+```
+
+See the [API reference](https://ocean-uhh.github.io/oceanarray/oceanarray.html) for the full interface.
+
+## License
+
+MIT License