oceanarray 0.1.0__py3-none-any.whl

oceanarray-0.1.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: oceanarray
+Version: 0.1.0
+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: jinja2>=3.0
+Requires-Dist: packaging>=21.0
+Dynamic: license-file
+
+# OceanArray
+
+Python tools for processing moored oceanographic array observations from raw instrument files to quality-controlled, CF-compliant NetCDF.
+
+## Overview
+
+OceanArray implements a multi-stage processing pipeline for mooring data, controlled by YAML configuration files for reproducible processing:
+
+- **Instrument-level** (Stages 1–3): convert raw files → standardise → clock-correct → QC-flag
+- **Mooring-level** (Stack + Grid): combine instruments → common time axis → pressure grid
+- **HTML report**: self-contained mooring recovery summary from YAML + processed files
+
+## Installation
+
+```bash
+pip install oceanarray
+```
+
+Then install `seasenselib` (required for reading raw instrument files; available on PyPI
+but needs `--no-deps` to avoid version conflicts):
+
+```bash
+pip install pyrsktools pycnv
+pip install seasenselib --no-deps
+```
+
+### From source (conda)
+
+```bash
+git clone https://github.com/ocean-uhh/oceanarray.git
+cd oceanarray
+conda create -n oceanarray python=3.11
+conda activate oceanarray
+pip install -r requirements-dev.txt
+pip install -e .
+pip install pyrsktools pycnv && pip install seasenselib --no-deps
+```
+
+### From source (venv)
+
+```bash
+git clone https://github.com/ocean-uhh/oceanarray.git
+cd oceanarray
+python3.11 -m venv venv
+source venv/bin/activate        # Windows: venv\Scripts\activate
+pip install -r requirements-dev.txt
+pip install -e .
+pip install pyrsktools pycnv && pip install seasenselib --no-deps
+```
+
+> **Python version**: Python 3.9–3.12 is supported. Python 3.13+ has not been
+> tested with all dependencies and is not recommended.
+
+## Quick start
+
+```bash
+RAW=/path/to/cruise/raw       # raw instrument files: $RAW/{mooring}/{instrument}/file
+PROC=/path/to/cruise/proc     # processed output root
+
+# Instrument-level: stages 1 and 2 (default)
+oceanarray process dsG3_1_2026 --raw-dir $RAW --proc-dir $PROC
+
+# All three instrument-level stages (stage 3 adds QC flags and velocity rotation)
+oceanarray process dsG3_1_2026 --raw-dir $RAW --proc-dir $PROC --stage 1 2 3
+
+# Single instrument rerun
+oceanarray process dsG3_1_2026 --raw-dir $RAW --proc-dir $PROC --stage 3 --serial 7507 --force
+
+# Mooring-level: stack all instruments onto 60 s time grid
+oceanarray stack dsG3_1_2026 --proc-dir $PROC
+
+# Mooring-level: vertically interpolate onto pressure grid
+oceanarray grid dsG3_1_2026 --proc-dir $PROC
+
+# Generate main HTML mooring report (fast — no per-instrument pages)
+oceanarray report dsG3_1_2026 --raw-dir $RAW --proc-dir $PROC
+
+# Also generate per-instrument pages (slow)
+oceanarray report dsG3_1_2026 --raw-dir $RAW --proc-dir $PROC --instruments
+
+# Also generate gridded and stacked report pages
+oceanarray report dsG3_1_2026 --raw-dir $RAW --proc-dir $PROC --grid --stack
+
+# One specific instrument page only
+oceanarray report dsG3_1_2026 --raw-dir $RAW --proc-dir $PROC --serial 7507
+
+# Validate mooring YAML configuration
+oceanarray validate dsG3_1_2026.mooring.yaml
+
+# Run the complete pipeline in one command (stages 1–3, stack, grid, all reports)
+oceanarray run dsG3_1_2026 --raw-dir $RAW --proc-dir $PROC --dp 10
+```
+
+## Recommended first-processing workflow
+
+Processing a mooring for the first time has a natural checkpoint: you need to
+verify that the deployment start and end times in the YAML are correct before
+stage 2 trims the records.  The sequence below catches problems early and
+avoids reprocessing the full mooring unnecessarily.
+
+### Step 1 — convert raw files to CF-NetCDF
+
+```bash
+oceanarray process dsG3_1_2026 --raw-dir $RAW --proc-dir $PROC --stage 1
+```
+
+Stage 1 reads each raw instrument file and writes `_stage1.nc` with no
+modifications — the full record exactly as recorded by the instrument.
+Check the console output for any read errors or missing files.
+
+### Step 2 — inspect the summary report
+
+```bash
+oceanarray report dsG3_1_2026 --raw-dir $RAW --proc-dir $PROC --instruments
+```
+
+The summary page shows which stage 1 files exist and how many records each
+instrument has.  Open the per-instrument pages to look at time series and
+check for obvious pre-deployment records (instrument left running on deck,
+depth hovering near zero) that will need to be trimmed by stage 2.
+
+### Step 3 — set deployment start/end times in the YAML
+
+Edit `dsG3_1_2026.mooring.yaml` and set `deployment_time` and `recovery_time`
+(or per-instrument `deployment_start` / `deployment_end` overrides) to the
+correct times identified from the data.  Stage 2 will trim to this window.
+
+If you are unsure about one instrument, process it alone first:
+
+```bash
+oceanarray process dsG3_1_2026 --raw-dir $RAW --proc-dir $PROC --stage 2 --serial 7507
+oceanarray report dsG3_1_2026 --raw-dir $RAW --proc-dir $PROC --serial 7507 --force
+```
+
+Iterate on the YAML until the trimmed record looks correct for each instrument.
+
+### Step 4 — complete the pipeline
+
+Once deployment times are confirmed for all instruments:
+
+```bash
+oceanarray process dsG3_1_2026 --raw-dir $RAW --proc-dir $PROC --stage 2 3
+oceanarray stack   dsG3_1_2026 --proc-dir $PROC
+oceanarray grid    dsG3_1_2026 --proc-dir $PROC --dp 10
+oceanarray report  dsG3_1_2026 --raw-dir $RAW --proc-dir $PROC --instruments --stack --grid
+```
+
+### Subsequent reruns
+
+Once settings are finalised (deployment window, QC thresholds, clock offsets)
+the full pipeline can be rerun in a single command:
+
+```bash
+oceanarray run dsG3_1_2026 --raw-dir $RAW --proc-dir $PROC --dp 10 --force
+```
+
+`oceanarray run` executes all stages in order (1 → 2 → 3 → stack → grid →
+all reports).  Each step runs regardless of earlier failures; check the exit
+code and log files in `processing_logs/` if something looks wrong.
+
+## Processing pipeline
+
+### Instrument-level
+
+| Stage | Module | Input | Output | What it does |
+|-------|--------|-------|--------|--------------|
+| 1 | `stage1.py` | raw instrument file | `_stage1.nc` | Format conversion to CF-NetCDF; normalises pressure units (`db` → `dbar`), conductivity names, ITS-90 temperature scale annotation; for Nortek Aquadopps: reads BEAM→XYZ transformation matrix from header and stores it as `nortek_transformation_matrix`; applies T-matrix to produce instrument-frame XYZ velocities |
+| 2 | `stage2.py` | `_stage1.nc` | `_stage2.nc` | Clock corrections; trim to deployment window |
+| 3 | `stage3.py` | `_stage2.nc` | `_stage3.nc` | Normalises conductivity to mS/cm; derives practical salinity via `gsw.SP_from_C`; pressure interpolation for instruments without a sensor; QARTOD gross-range + spike QC on T, C, S, P; **Aquadopp only**: XYZ → ENU rotation using heading/pitch/roll + magnetic declination (via `ppigrf`), producing `east_velocity`, `north_velocity`, `up_velocity`, `current_speed`, `current_direction`; tilt QC on velocity |
+
+Stage 3 writes `_stage3.nc` for **all** instruments. Instruments that already have pressure receive QC flags only; those lacking pressure additionally receive interpolated pressure (flagged `pressure_qc = 8`).
+
+Thresholds applied during stage 3 are stored as attributes on each `*_qc` variable (e.g. `qc_gross_range_fail_min`) so the report can display exactly what was used without re-reading the YAML.
+
+**Aquadopp coordinate transformation (stage 1 → stage 3):**
+
+Stage 1 reads the instrument-specific BEAM→XYZ transformation matrix `T` from the Nortek header and stores it as a scalar variable `nortek_transformation_matrix` (shape 3×3, flattened). It applies `T` to the raw beam velocities to produce `velocity_x/y/z` in the instrument frame (XYZ).
+
+Stage 3 then rotates XYZ → ENU using the per-sample heading, pitch, and roll recorded by the instrument:
+
+```
+ENU = H(heading, declination) @ P(pitch) @ XYZ
+```
+
+where `H` is the horizontal rotation matrix (heading − 90° + magnetic declination) and `P` is the pitch tilt matrix. Magnetic declination is computed by `ppigrf` at the deployment midpoint (lat/lon/date from YAML) and stored in `magnetic_declination` as a global attribute. If `ppigrf` is unavailable or the position is unknown, declination defaults to 0° with a warning. The resulting `east_velocity` and `north_velocity` are in true geographic (ENU) coordinates. The attribute `nortek_coordinate_system` tracks the current frame (`BEAM` → `XYZ` → `ENU`).
+
+### Mooring-level
+
+| Command | Output | What it does |
+|---------|--------|--------------|
+| `oceanarray stack` | `{mooring}_stack.nc` | Resample all instruments to a common time axis (default 60 s); stack into a single file with an `N_LEVELS` dimension ordered deep-first; compute potential density; Aquadopp velocity/orientation stored unmasked with `velocity_flag` (worst of east/north/up QC); `tilt_from_pressure` computed for each Aquadopp from the nearest reference instrument ≥10 m above |
+| `oceanarray grid` | `{mooring}_grid.nc` | Linearly interpolate stacked data onto a regular pressure grid |
+
+### Report
+
+`oceanarray report` generates self-contained HTML pages (all figures embedded as base64 PNGs — no external dependencies, open offline, printable via Ctrl+P).
+
+By default only the main mooring summary is generated (fast).  Use flags to opt in to the slower pages:
+
+| Flag | Page generated | Speed |
+|------|---------------|-------|
+| *(none)* | `{mooring}_report.html` — mooring summary | fast |
+| `--instruments` | `{mooring}_{serial}_report.html` per instrument | slow |
+| `--grid` | `{mooring}_grid_report.html` — T/S pcolormesh | moderate |
+| `--stack` | `{mooring}_stack_report.html` — pressure & T time series | moderate |
+| `--serial SN [SN ...]` | per-instrument page(s) for listed serial(s) only | moderate |
+
+**Mooring summary** (`{mooring}_report.html`):
+1. Header card (cruise, ship, deployment/recovery times, location, water depth)
+2. Mooring diagram — embedded inline if `{mooring}_diagram.pdf` is found alongside the YAML
+3. Processing pipeline badges per instrument (Raw → Read → Stage 1 → 2 → 3 → Stack → Grid)
+4. Instrument summary table (first/last sample, N records, YAML Δt, observed Δt, variable presence) — S/N links to per-instrument page
+5. Clock correction table
+6. Sensor calibration metadata (from `SENSOR_*` variables in stage 2 NC files)
+7. QC flag summary — per-instrument × per-variable percentage breakdown with colour-coded stacked bars (OceanSITES flag colours)
+
+**Gridded data report** (`{mooring}_grid_report.html`, requires `--grid`):
+- Variable coverage table
+- Temperature pcolormesh (20 discrete levels, RdYlBu_r)
+- Practical salinity pcolormesh (20 discrete levels, YlGnBu_r; blue = fresh)
+- Potential density pcolormesh and contourf (BuPu) with iso-density contour lines (default 27.7 and 27.8 kg m⁻³); depth of isopycnals over the full deployment and a 3-day zoom
+- Current speed pcolormesh (plasma) and current direction (0–360° true, hsv colormap) — requires Aquadopp ENU data from stage 3
+- Up velocity pcolormesh (RdBu_r, symmetric)
+- N² buoyancy frequency squared (log₁₀ scale)
+- T-S heat map (log₁₀ count per bin, half-page width)
+- Temperature power spectrum (Welch PSD, one line per depth level)
+
+**Stacked data report** (`{mooring}_stack_report.html`, requires `--stack`):
+- Instrument table (type, serial [linked to per-instrument page], HAB, approximate depth)
+- Pressure, temperature, salinity time series (all instruments overlaid)
+- East, north, and up velocity time series (Aquadopp instruments; velocities stored unmasked; `velocity_flag` = worst of east/north/up QC)
+- Aquadopp tilt panels — one panel per Aquadopp: time series of |pitch|, |roll|, and pressure-derived tilt (`arccos(ΔP / rope_length)` using the nearest instrument ≥10 m above with valid pressure); scatter plot of |pitch|/|roll| vs. pressure tilt with 1:1 line and 20°/30° threshold lines
+- T-S diagram (two panels: scatter coloured by pressure + 2-D count heatmap)
+- Current rose diagrams (ENU, good/suspect/bad QC split)
+- Adjacent instrument spacing histogram
+- Variable coverage table (at page end)
+
+**Per-instrument pages** (`{mooring}_{serial}_report.html`, requires `--instruments` or `--serial`):
+- Processing history (the NC `history` attribute, one row per stage)
+- Full deployment time series with QC flag markers (+ suspect/bad, · interpolated); velocity panels centred on zero
+- First 48 h and last 48 h window zooms
+- T-S diagram (two panels: scatter coloured by pressure with QC overlays, and 2-D count heatmap)
+- Current rose diagrams (ENU frame; good/suspect/bad split by QARTOD flag)
+- Data value histograms — one panel per variable; heading fixed to 0–360°; velocity panels centred on zero; battery excluded
+- QC flag breakdown table with stacked bars
+- NetCDF variable table (all time-series variables: dims, N, units, long name, standard name, QC companion flag)
+- Scalar metadata table (InstrDepth, serial_number, coordinate system, transformation matrix, etc.)
+- Global attributes table
+
+## Supported instrument types
+
+| Instrument | File types | Variables |
+|------------|------------|-----------|
+| Sea-Bird SBE37 MicroCAT | `sbe-cnv`, `sbe-asc`, `sbe-ascii` | T, C, P |
+| Nortek Aquadopp | `nortek-aqd`, `nortek-ascii`, `nortek-csv` | U, V, W, P, T |
+| RBR Solo / Duet | `rbr-rsk`, `rbr-dat` | T (Solo), T+C (Duet) |
+| RDI WorkHorse ADCP | `rdi-raw` | U, V, W (all bins) |
+
+## Configuration
+
+Each mooring is described by a `{mooring}.mooring.yaml` file placed in `proc/{mooring}/`.
+The same YAML is shared with the `moordiag` package; fields used only by `moordiag` (`year`, `status`, `label`, `image`, `clamp_id`, hardware entries without `instrument`) are silently ignored by `oceanarray`.
+
+**Required top-level fields:** `name`, `waterdepth`, `deployment_time`, `recovery_time`, `directory`
+
+**Required per-instrument fields:** `instrument` (sets subdirectory), `serial`, `file_type`, `filename`
+
+`oceanarray` processes only `clamp` entries that have an `instrument` key; hardware entries (e.g. shackles, floats) used by `moordiag` are skipped.
+
+**Location fields** — report uses the first available in priority order: `seabed_latitude/longitude` → `deployment_latitude/longitude` → `planned_latitude/longitude` → `latitude/longitude`
+
+```yaml
+name: dsG3_1_2026
+waterdepth: 992
+seabed_latitude: "65 29.84 N"       # best position (triangulated); or use deployment_ or planned_
+seabed_longitude: "029 24.60 W"
+deployment_cruise: MSM142           # used in report header; if absent, 'cruise' is used
+deployment_ship: MS Merian
+deployment_time: "2026-05-07T17:05:00"
+recovery_cruise: OdB                # if absent, deployment_cruise is repeated
+recovery_ship: Odon de Buen
+recovery_time: "2026-07-10T17:45:00"
+
+# QC overrides apply at mooring level (all instruments) or per instrument in clamp.
+# qc_ranges, qc_spike, and tilt_qc can appear at either level.
+qc_ranges:
+  temperature:
+    fail_span: [-2.5, 12.0]
+    suspect_span: [-1.0, 10.0]
+  pressure:
+    fail_span: [-5.0, 1050.0]
+    suspect_span: [-0.5, 1020.0]
+  salinity:
+    fail_span: [0.0, 50.0]
+    suspect_span: [0.0, 35.5]
+
+clamp:
+  - instrument: microcat            # sets raw file subdirectory (basedir/raw/microcat/…)
+    serial: 7507
+    hab: 412.3                      # height above bottom (m); used for depth and ordering
+    file_type: sbe-cnv
+    filename: 7507_recovery.cnv
+    sample_interval_seconds: 15     # optional; used in report
+    # clock_offset = total correction at deployment; clock_drift_seconds = total at recovery.
+    # Stage 2 ramps linearly between the two (positive = instrument was slow/behind UTC).
+    clock_offset: 0                  # instrument correctly set at deployment
+    # Option B — two timestamps at recovery give the total correction at recovery
+    computer_clock_at_recovery:  '20260710T19:12:30'   # compact ISO or "HH:MM:SS"
+    instrument_clock_at_recovery: '20260710T19:12:39'  # computer − instrument = −9 s
+
+  - instrument: aquadopp
+    serial: 14321
+    hab: 26.5
+    file_type: nortek-ascii
+    filename: 14321_recovery.dat
+    sample_interval_seconds: 120
+    qc_spike:                       # instrument-level override (also valid at mooring level)
+      east_velocity: {suspect_threshold: 0.3, fail_threshold: 1.0}
+
+  - instrument: microcat
+    serial: 5367
+    hab: 716
+    file_type: sbe-ascii
+    filename: 5367_recovery.asc
+    sample_interval_seconds: 60
+    computer_clock_at_recovery: '20260710T18:43:30'
+    instrument_clock_at_recovery: '20260710T18:44:03'
+```
+
+## QC flags (QARTOD / OceanSITES Reference Table 2)
+
+| Flag | Meaning |
+|------|---------|
+| 1 | Good data |
+| 3 | Suspect (outside `suspect_span`, spike detected, or tilt 20–30°) |
+| 4 | Bad (outside `fail_span`, or tilt > 30°) |
+| 8 | Interpolated (pressure assigned from neighbouring instrument) |
+| 9 | Missing value |
+
+Default thresholds live in `oceanarray/parameters.py` (`QC_GROSS_RANGE`, `QC_SPIKE`, `QC_TILT`). All thresholds are in the units stored in the NC variable (degC, mS/cm, PSU, dbar, m/s). Stage 3 normalises conductivity to mS/cm before applying QC, so thresholds are always compared against values in the right unit.
+
+Override priority (highest wins): **instrument-level** → **mooring-level** → **package defaults**
+
+| YAML key | Level | Purpose |
+|----------|-------|---------|
+| `qc_ranges` | mooring or instrument | Gross-range fail/suspect spans per variable |
+| `qc_spike` | mooring or instrument | Spike test thresholds per variable |
+| `tilt_qc` | mooring or instrument | Roll thresholds for Aquadopp velocity flagging |
+
+Instrument-level values override mooring-level values for that instrument only; other instruments continue to use the mooring-level setting.
+
+**Default gross-range spans** (global ocean; override per mooring or instrument via `qc_ranges`):
+
+| Variable | Suspect span | Fail span | Units | Notes |
+|----------|-------------|-----------|-------|-------|
+| `temperature` | −2 to 35 | −2.5 to 40 | °C | |
+| `conductivity` | 0 to 65 | 0 to 75 | mS/cm | stage 3 converts S/m → mS/cm first |
+| `salinity` | 2 to 40 | 0 to 40 | PSU | derived from T/C/P via gsw |
+| `pressure` | −0.5 to 7000 | −5 to 7000 | dbar | override per instrument for known depth |
+| `east/north_velocity` | −5 to 5 | −5 to 5 | m/s | |
+| `up_velocity` | −2 to 2 | −5 to 5 | m/s | |
+
+**Default spike thresholds** (60–120 s sampling; override via `qc_spike`):
+
+| Variable | Suspect | Fail | Notes |
+|----------|---------|------|-------|
+| `temperature` | 2.0 °C | 6.0 °C | |
+| `conductivity` | 2.0 mS/cm | 5.0 mS/cm | catches biofouling (fish in cell) low spikes |
+| `salinity` | 0.5 PSU | 2.0 PSU | catches T/C timing mismatches on unpumped sensors |
+| `pressure` | 10.0 dbar | 50.0 dbar | |
+| velocity | — | — | omitted: burst-mode Aquadopps produce false positives at burst boundaries |
+
+**Tilt QC (Aquadopp):** stage 3 flags all velocity variables (`east/north/up_velocity`) when pitch or roll exceeds the tilt thresholds. The primary path uses `pitch_qc` and `roll_qc` already computed by the gross-range step and merges them (worst flag wins). The fallback path (when neither `_qc` flag exists) computes `max(|pitch|, |roll|)` and compares against the thresholds. Default: suspect at 20°, bad at 30°. Override example:
+
+```yaml
+  - instrument: aquadopp
+    serial: 14321
+    hab: 26.5
+    tilt_qc:
+      suspect_threshold: 15   # degrees (applied to pitch and roll)
+      fail_threshold: 25
+```
+
+## Python API
+
+> **Note**: the CLI (`oceanarray process`, `stack`, `grid`, `report`) is the primary
+> interface and is stable.  The Python API is available but may change between minor
+> versions while the package is in beta.
+
+```python
+from oceanarray.stage1 import MooringProcessor
+from oceanarray.stage2 import Stage2Processor
+from oceanarray.stage3 import Stage3Processor
+from oceanarray.mooring_level import MooringStacker, MooringGridder
+
+base = '/path/to/data'
+mooring = 'dsG3_1_2026'
+
+MooringProcessor(base).process_mooring(mooring)
+Stage2Processor(base).process_mooring(mooring)
+Stage3Processor(base).process_mooring(mooring)
+MooringStacker(base).stack(mooring)
+MooringGridder(base).grid(mooring)
+```
+
+## Project structure
+
+```
+oceanarray/
+├── oceanarray/
+│   ├── stage1.py          # Raw → CF-NetCDF conversion
+│   ├── stage2.py          # Clock corrections + deployment trim
+│   ├── stage3.py          # Pressure interpolation + QARTOD QC
+│   ├── mooring_level.py   # Stack (N_LEVELS×time) and Grid (pressure×time)
+│   ├── report.py          # HTML mooring recovery report generator
+│   ├── parameters.py      # Package defaults (QC thresholds, colormaps, …)
+│   ├── plotters.py        # Visualisation
+│   ├── clock_offset.py    # Clock drift analysis
+│   ├── time_gridding.py   # Multi-instrument time gridding
+│   ├── readers.py         # Low-level format readers
+│   ├── writers.py         # NetCDF writers
+│   ├── logger.py          # Processing log system
+│   └── validation.py      # YAML and file format validation
+├── tests/
+├── notebooks/
+└── docs/
+```
+
+## Testing
+
+```bash
+pytest                    # full suite
+pytest tests/test_stage1.py -v
+pytest --cov=oceanarray   # with coverage
+```
+
+## Documentation
+
+```bash
+cd docs && make html
+```
+
+## License
+
+MIT License

oceanarray-0.1.0.dist-info/RECORD

@@ -0,0 +1,76 @@
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+oceanarray-0.1.0.dist-info/licenses/LICENSE,sha256=Mas8UNj-qZ0qpZpfCtA1_mp434PAB0jDSmo_IFO2p0M,1080
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+oceanarray-0.1.0.dist-info/RECORD,,

oceanarray-0.1.0.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: setuptools (83.0.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

oceanarray-0.1.0.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+oceanarray = oceanarray.cli:main

oceanarray-0.1.0.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+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.

oceanarray-0.1.0.dist-info/top_level.txt

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+oceanarray