oceanarray 0.4.0__tar.gz → 0.5.0__tar.gz

{oceanarray-0.4.0 → oceanarray-0.5.0}/.github/workflows/docs.yml

@@ -16,12 +16,12 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
         with:
           fetch-depth: 0
 
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v2
+        uses: mamba-org/setup-micromamba@v3
         with:
           environment-file: docs/environment.yml
           init-shell: bash
@@ -41,8 +41,7 @@ jobs:
         shell: bash -l {0}
         run: |
           set -e
-          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
+          micromamba run -n oceanarray jupyter nbconvert --to notebook --execute notebooks/demo_mooring.ipynb --output=demo_mooring-output.ipynb
           mv notebooks/*output.ipynb docs/source/
           pushd docs
           micromamba run -n oceanarray make clean html

{oceanarray-0.4.0 → oceanarray-0.5.0}/.github/workflows/docs_deploy.yml

@@ -15,12 +15,12 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
         with:
           fetch-depth: 0
 
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v2
+        uses: mamba-org/setup-micromamba@v3
         with:
           environment-file: docs/environment.yml
           init-shell: bash
@@ -40,8 +40,7 @@ jobs:
         shell: bash -l {0}
         run: |
           set -e
-          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
+          micromamba run -n oceanarray jupyter nbconvert --to notebook --execute notebooks/demo_mooring.ipynb --output=demo_mooring-output.ipynb
           mv notebooks/*output.ipynb docs/source/
           pushd docs
           micromamba run -n oceanarray make clean html

{oceanarray-0.4.0 → oceanarray-0.5.0}/.github/workflows/pypi.yml

@@ -26,7 +26,7 @@ jobs:
       id-token: write
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v7
         with:
           ref: ${{ github.ref }}
           fetch-depth: 0
@@ -35,9 +35,9 @@ jobs:
         run: git clean -fxd
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v7
         with:
-          python-version: "3.x"
+          python-version: "3.13"
 
       - name: Install build tools
         run: |

{oceanarray-0.4.0 → oceanarray-0.5.0}/.github/workflows/tests.yml

@@ -13,7 +13,7 @@ concurrency:
 jobs:
   unit:
     runs-on: ${{ matrix.os }}
-    # Experimental legs (3.13) are allowed to fail without cancelling real jobs.
+    # Any leg marked experimental is allowed to fail without cancelling real jobs.
     continue-on-error: ${{ matrix.experimental == true }}
     strategy:
       fail-fast: false
@@ -21,19 +21,16 @@ jobs:
         os: [ubuntu-latest, macos-latest, windows-latest]
         python-version: ["3.11"]     # full 3-OS coverage on the primary version
         include:
-          # Verify the supported range (requires-python >=3.10; docs say 3.10–3.12),
+          # Verify the supported range (requires-python >=3.11; docs say 3.11–3.13),
           # ubuntu-only to keep the job count down.
-          - { os: ubuntu-latest, python-version: "3.10" }
           - { os: ubuntu-latest, python-version: "3.12" }
-          # 3.13: experimental (allow-failure) — deps such as numba/llvmlite
-          # (via pylablib -> seasenselib) may not have 3.13 wheels yet.
-          - { os: ubuntu-latest, python-version: "3.13", experimental: true }
+          - { os: ubuntu-latest, python-version: "3.13" }
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v7
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v7
         with:
           python-version: ${{ matrix.python-version }}
           cache: "pip"
@@ -53,10 +50,10 @@ jobs:
   integration:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v7
 
       - name: Set up Python 3.11
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v7
         with:
           python-version: "3.11"
           cache: "pip"
@@ -74,10 +71,10 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v7
 
       - name: Set up Python 3.11
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v7
         with:
           python-version: "3.11"
 

{oceanarray-0.4.0 → oceanarray-0.5.0}/CHANGELOG.md

@@ -6,6 +6,40 @@ All notable changes to oceanarray are documented here.
 
 ## [Unreleased]
 
+## [0.5.0] — 2026-10-12
+
+### Added
+
+- **Serial-uniqueness validation** ([#101](https://github.com/ocean-uhh/oceanarray/pull/101)): `validate` refuses duplicate serials within a mooring, a blank serial, and the reserved names `stack`/`grid` (which would collide the per-instrument report filenames `{mooring}_{serial}_report.html`). A trailing `*` is stripped before every check — `1234` and `1234*` on one mooring are a duplicate, a serial that is only `*` is blank — and stays a diagram-only "pay attention to this sensor" annotation, never carried into filenames or nav labels.
+
+### Changed
+
+- **Report NetCDF-inventory appendix restyled** ([#103](https://github.com/ocean-uhh/oceanarray/pull/103)): the instrument, stack and grid reports share one inventory appendix — a Coordinates table (one row per coordinate variable: type, units, standard/long name, min/max, N valid, attributes), variables grouped by dimension set, QC companions shown inline as a green `(_QC)`, and global attributes split into named groups with a Type column; the per-page variable/scalar/globals templates collapse to one shared set, and the grid page gains a coordinates table it never had. The dune2 test fixture units were canonicalised in place (14 attribute edits, data byte-identical) and the hosted dune2 example suite regenerated. `demo_mooring.ipynb` is ported to `oceanarray.processors.process` and runs on the committed fixture from a clean checkout; `demo_step1.ipynb` is removed, and five old-API demo notebooks move to `notebooks/legacy/`.
+- **Shared masthead nav** ([#100](https://github.com/ocean-uhh/oceanarray/pull/100)): the report masthead navigation is rebuilt from the shared vendored macro, and the six report-design files are re-vendored from ctdcast with a vendoring guard (`scripts/check_vendored.py`).
+- **Canonical units at every stage** ([#102](https://github.com/ocean-uhh/oceanarray/pull/102)): one canonical spelling per quantity is now written to every file — `degree_Celsius`, `mS cm-1`, `dbar`, `m`, `m s-1`, `umol kg-1`, `g kg-1`, `kg m-3`, `1` (practical salinity and turbidity). A registry-scoped pass (`oceanarray.processors.units.canonicalise_units`) runs on the way out of every stage, rewriting the reader spellings (`degC`, `mS/cm`, `meters`, `db`, `S/m`→×10) to the canonical and recording any value conversion in `units_converted_from` / `units_conversion_factor`. Temperature variables carry CF-1.11 `units_metadata = "temperature: on_scale"`. Plot labels are derived from the canonical string by `format_units` (slash form: `mS/cm`, `m/s`, `kg/m³`, `µmol/kg`, `°C`, `PSU`, `NTU`).
+
+- **Single netCDF writer** ([#98](https://github.com/ocean-uhh/oceanarray/pull/98)): the six write paths the processing stages used before now go through one `oceanarray.writers.write` seam. The files that were written uncompressed — the seasenselib-written stage files, whose compression parameters its writer silently discarded, and the bare-`to_netcdf` stage3 output — shrink 58–66% on the dune2 fixtures. The two that were already zlib level-5 compressed — the pressure-gridded and stacked outputs — grow about 1% as they move to the common level-4 setting. Decoded values, dtypes, attributes, and time encoding are unchanged; raw values are byte-identical, verified per stage against the old writer. The private `_get_netcdf_writer_params` methods are removed, including the `quantize` key, which was never a valid netCDF4 encoding parameter and never took effect.
+- **Windows log encoding** ([#98](https://github.com/ocean-uhh/oceanarray/pull/98)): `stage1/2/3` open their per-stage log file as UTF-8. On Windows the default cp1252 encoding raised on the ADCP `BEAM→ENU` log message, which aborted the instrument and silently dropped it from the output.
+- **`oceanarray.writers` exposed** ([#99](https://github.com/ocean-uhh/oceanarray/pull/99)): `import oceanarray as oa; oa.writers.write(ds, path)` now resolves after a bare import.
+- **cftime time coordinates preserved** ([#99](https://github.com/ocean-uhh/oceanarray/pull/99)): a time coordinate decoded with `use_cftime=True` (object dtype, e.g. a non-standard calendar) now keeps its `units` and `calendar` on write instead of letting xarray re-guess the epoch from the data. Numpy `datetime64` time is still pinned to the 1970 epoch; only object-dtype cftime time is affected.
+- **Python 3.13 supported** ([#99](https://github.com/ocean-uhh/oceanarray/pull/99)): added to the classifiers and promoted to a required (no longer allow-failure) CI leg.
+
+### Breaking changes
+
+- **Units spellings in output files changed** ([#102](https://github.com/ocean-uhh/oceanarray/pull/102)): every processed file now carries the canonical units spelling per quantity (above), so a reader matching the old strings (`degC`, `mS/cm`, `meters`, `S/m`, …) must adapt. An unrecognised or missing `units` on a registered variable now **stops that instrument** (`UnitsError`) rather than passing through silently — one bad instrument is logged with its file and skipped, the rest process; the stack still builds but records the omission in an `instruments_omitted` attribute and exits 1. The `dissolved_oxygen` registry entry is corrected to per-mass `umol kg-1` (standard_name `moles_of_oxygen_per_unit_mass_in_sea_water`); turbidity is dimensionless `1` (display label `NTU`). Conductivity in `S/m` is converted ×10 to `mS cm-1` by the units pass, replacing the old `conductivity_normalised_from` attribute with `units_converted_from` / `units_conversion_factor`.
+- **`process` runs stage 3 by default** ([#102](https://github.com/ocean-uhh/oceanarray/pull/102)): `oceanarray process MOORING` with no `--stage` now runs stages 1, 2 and 3 (was 1 and 2). Pass `--stage 1 2` for the old raw→trim-only behaviour. The help text already described "stages 1-3"; the code now matches it.
+- **Oxygen saturation / AOU recomputed on the correct basis** ([#102](https://github.com/ocean-uhh/oceanarray/pull/102)): `derive_oxygen_saturation` previously divided per-mass `dissolved_oxygen` by in-situ density as if it were per-volume, making `oxygen_saturation_pct` and `apparent_oxygen_utilization` ~2.5% low. It now uses a per-mass (`umol kg-1`) input directly and divides only a genuine per-volume (`umol L-1`) variable. Regenerated oxygen products change by the density factor; moorings without an oxygen sensor (the dune2 example) are unaffected.
+- **Minimum Python raised to 3.11** ([#99](https://github.com/ocean-uhh/oceanarray/pull/99)): `requires-python` is now `>=3.11`; the 3.10 classifier and CI leg are dropped. Python 3.10 reached end-of-life, and the core dependencies (xarray, pandas, numpy, matplotlib, gsw, scipy) already require 3.11 — so a 3.10 install silently resolved years-old, untested versions of the whole stack.
+
+- **Dead output helpers removed** ([#99](https://github.com/ocean-uhh/oceanarray/pull/99)): `oceanarray.tools.writers.save_dataset` and `save_OS_instrument` are deleted, and `oceanarray/tools/writers.py` with them. Neither had a working caller (only tests and a dead `if 0:` notebook cell); `save_dataset` also wrote `NETCDF4_CLASSIC`, a format nothing else produced. Use `oceanarray.writers.write`. Two legacy notebooks (`notebooks/legacy/demo_batch_instrument.ipynb`, `notebooks/legacy/demo_instrument_rdb.ipynb`) still reference `save_OS_instrument` and no longer run; they are not CI-executed and are left for the notebook refresh.
+- **`None` attributes dropped, not blanked** ([#99](https://github.com/ocean-uhh/oceanarray/pull/99)): a `None`-valued attribute (global or per-variable) is now dropped with a warning instead of written as `""`. `UNK` belongs where a value is determined, not the write seam. On the dune2 fixtures no attribute is affected (0/84 globals are empty); this is a guardrail.
+- **Time encoding pinned** ([#99](https://github.com/ocean-uhh/oceanarray/pull/99)): every datetime variable is written as `seconds since 1970-01-01` (float64, `proleptic_gregorian`) rather than xarray's per-file guess. Decoded instants change by at most 0.13 µs (float64 seconds have ~238 ns spacing at the 2026 epoch, so ≤119 ns rounding; ~0.5 µs by 2050) — negligible against clock drift, which is corrected in whole seconds. **Raw stored values change**, so a reader using `decode_times=False`/`decode_cf=False` sees different numbers. This also removes a pandas-version dependence in the units string (space vs `T`).
+
+### Known issues
+
+- **Empty-units turbidity files**: a registered variable with an empty `units` fails that one instrument at stage 1 — the handler logs `ERROR: <file>: <reason>`, skips the instrument, and the mooring completes with the others and a non-zero exit (the family rule). Six turbidity files on the drive are affected; the reader fix lands in 0.5.1.
+- **dune2 test fixture stack/grid**: the committed `_stack.nc`/`_grid.nc` fixtures reference instruments not present in the committed raw and YAML — they were built from the full mooring before the fixture was trimmed to two instruments — so running `oceanarray run` on the fixture collapses the stack to those two. A known fixture inconsistency, rebuilt in 0.5.1.
+
 ## [0.4.0] — 2026-09-08
 
 ### Added

{oceanarray-0.4.0 → oceanarray-0.5.0}/CITATION.cff

@@ -7,8 +7,8 @@ authors:
   affiliation: University of Hamburg, Bundesstraße 53, 20146 Hamburg, Germany
 title: oceanarray
 doi: 10.5281/zenodo.21890564
-version: 0.4.0
-date-released: 2026-09-08
+version: 0.5.0
+date-released: 2026-10-12
 url: https://github.com/ocean-uhh/oceanarray
 repository-code: https://github.com/ocean-uhh/oceanarray
 license: MIT

{oceanarray-0.4.0/oceanarray.egg-info → oceanarray-0.5.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: oceanarray
-Version: 0.4.0
+Version: 0.5.0
 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
@@ -35,10 +35,10 @@ 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 :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
-Requires-Python: >=3.10
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy>=1.23
@@ -102,7 +102,7 @@ uv pip install oceanarray
 
 This pulls in `seasenselib` (used to read raw instrument files in stage 1) automatically.
 
-Python 3.10–3.12 is supported. See the [installation guide](https://ocean-uhh.github.io/oceanarray/installation.html) for isolated-environment (conda / venv / uv) and from-source options.
+Python 3.11–3.13 is supported. See the [installation guide](https://ocean-uhh.github.io/oceanarray/installation.html) for isolated-environment (conda / venv / uv) and from-source options.
 
 ## Quick start
 

{oceanarray-0.4.0 → oceanarray-0.5.0}/README.md

@@ -25,7 +25,7 @@ uv pip install oceanarray
 
 This pulls in `seasenselib` (used to read raw instrument files in stage 1) automatically.
 
-Python 3.10–3.12 is supported. See the [installation guide](https://ocean-uhh.github.io/oceanarray/installation.html) for isolated-environment (conda / venv / uv) and from-source options.
+Python 3.11–3.13 is supported. See the [installation guide](https://ocean-uhh.github.io/oceanarray/installation.html) for isolated-environment (conda / venv / uv) and from-source options.
 
 ## Quick start
 

oceanarray-0.5.0/VENDORED.txt

@@ -0,0 +1,9 @@
+# sha256 of the report-design files shared across ctdcast, oceanarray and
+# glidertest; ctdcast main 1a7cd91 is the source of truth.  Never
+# hand-edit; re-vendor from ctdcast, then: python scripts/check_vendored.py --update
+0856f12f8f032f8803081e207f1e46b694e68b9a837174960c5bd6fa526370a0  oceanarray/reports/_encode.py
+6804280ebe2f25b1d958cbf01ddfb8c19b12b423f4650cb8a494a7697bfa96f4  oceanarray/reports/_css.py
+aa57d10b7891164f07b0f4c5345c716934af0a3409859d48dae2387fcce71804  oceanarray/reports/_manifest.py
+752c4d4245b7ac4b82a63ea7245707c24deae2c088d03bf9bb6ea7a325ce5f1b  oceanarray/config/report_tokens.py
+18cba25d288c74129f4e393199fb0b005f7e0c926a11a4c67aba3104f72e7f61  oceanarray/config/report.mplstyle
+ab5ee1964e0a0aebba73f28bbbaf5a4036450d2be821803d357c9d6ba294a10a  oceanarray/reports/templates/_nav.html