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Merged
merged 12 commits into from
Oct 17, 2025
Merged

feat: support for chunked arrays #58

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72f113b
feat: support for chunked arrays
tomsail Oct 8, 2025
1d465f7
add dask in dev dependencies
tomsail Oct 8, 2025
13dc6ee
Fix test_eager_vs_lazy
lucduron Oct 15, 2025
0fd18a6
Explicitly specify engine in io_tests.py
lucduron Oct 15, 2025
b5b644f
Add a lock for dask to avoid unexpected buffer truncation while reading
lucduron Oct 15, 2025
abc0be8
Improve code in SelafinLazyArray
lucduron Oct 15, 2025
8b7ca83
Improve maintenance of write_serafin
lucduron Oct 15, 2025
476b7fc
Update README and minor changes
lucduron Oct 16, 2025
7c79e2c
Fix header.is_2d before writing selafin
lucduron Oct 16, 2025
56c3cad
Add disable_lock argument and avoid useless ravel
lucduron Oct 16, 2025
adebd1d
Implement get_dataset_as_2d
lucduron Oct 16, 2025
99c629e
Add/correct some comment lines
lucduron Oct 16, 2025
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2 changes: 1 addition & 1 deletion .github/workflows/run_tests.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@ jobs:
fail-fast: false
matrix:
os: ["ubuntu-latest"]
python: ["3.9", "3.10", "3.11"]
python: ["3.10", "3.11", "3.12", "3.13"]
include:
- os: "macos-latest"
python: "3.10"
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61 changes: 36 additions & 25 deletions README.md
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Expand Up @@ -34,19 +34,19 @@ ds.close() # avoid a ResourceWarning (unclosed file)
```

```
<xarray.Dataset>
Dimensions: (time: 17, node: 648, plan: 21)
<xarray.Dataset> Size: 5MB
Dimensions: (time: 17, plan: 21, node: 648)
Coordinates:
x (node) float32 ...
y (node) float32 ...
* time (time) datetime64[ns] 1900-01-01 ... 1900-01-02T20:26:40
Dimensions without coordinates: node, plan
x (node) float32 3kB ...
y (node) float32 3kB ...
* time (time) datetime64[ns] 136B 1900-01-01 ... 1900-01-02T20:26:40
Dimensions without coordinates: plan, node
Data variables:
Z (time, node, plan) <class 'numpy.float64'> ...
U (time, node, plan) <class 'numpy.float64'> ...
V (time, node, plan) <class 'numpy.float64'> ...
W (time, node, plan) <class 'numpy.float64'> ...
MUD (time, node, plan) <class 'numpy.float64'> ...
Z (time, plan, node) float32 925kB ...
U (time, plan, node) float32 925kB ...
V (time, plan, node) float32 925kB ...
W (time, plan, node) float32 925kB ...
MUD (time, plan, node) float32 925kB ...
Attributes:
title: Sloped flume Rouse profile test
language: en
Expand Down Expand Up @@ -74,6 +74,12 @@ ds = ds.assign(UTIMES100=lambda x: x.U * 100) # Add a new variable
ds.drop_vars(["W"]) # Remove variable `VELOCITY W`
```

## Extracting a specific layer from a 3D DataSet

```python
ds_bottom = ds.selafin.get_dataset_as_2d(plan=0) # bottom layer
```

## Write Selafin

```python
Expand All @@ -83,9 +89,14 @@ ds.selafin.write("output_file.slf")
## DataSet content

### Dimensions
* time
* node
* plan (only in 3D)
In 2D:
1. time
2. node

in 3D:
1. time
2. plan
3. node

### Coordinates

Expand All @@ -99,14 +110,14 @@ ds.selafin.write("output_file.slf")

All attributes are optional except `ikle2`:

| Attribute | Description | Default value |
|------------|-------------------------------------------------------------------------|--------------------------|
| title | Serafin title | "" (empty string) |
| language | Language for variable detection | "en" |
| float_size | Float size | 4 (single precision) |
| endian | File endianness | ">" |
| params | Table of integer parameters | (can be rebuilt) |
| ikle2 | Connectivity table in 2D (1-indexed) | - |
| ikle3 | Connectivity table in 3D (1-indexed, only in 3D, optional) | (can be rebuilt from 2D) |
| variables | Dictionary with variable names and units (key is variable abbreviation) | - |
| date_start | Starting date with integers (year to seconds) | (from first time serie) |
| Attribute | Description | Default value |
|------------|-------------------------------------------------------------------------|--------------------------------|
| title | Serafin title | "Converted with array-serafin" |
| language | Language for variable detection | "en" |
| float_size | Float size | 4 (single precision) |
| endian | File endianness | ">" |
| params | Table of integer parameters | (can be rebuilt) |
| ikle2 | Connectivity table in 2D (1-indexed) | - |
| ikle3 | Connectivity table in 3D (1-indexed, only in 3D, optional) | (can be rebuilt from 2D) |
| variables | Dictionary with variable names and units (key is variable abbreviation) | - |
| date_start | Starting date with integers (year to seconds) | (from first time serie) |
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