h5yaml 0.2.0__tar.gz → 0.2.1__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (25) hide show
  1. {h5yaml-0.2.0 → h5yaml-0.2.1}/.coverage +0 -0
  2. {h5yaml-0.2.0 → h5yaml-0.2.1}/.github/workflows/python-package.yml +2 -1
  3. {h5yaml-0.2.0 → h5yaml-0.2.1}/PKG-INFO +15 -3
  4. {h5yaml-0.2.0 → h5yaml-0.2.1}/README.md +14 -2
  5. {h5yaml-0.2.0 → h5yaml-0.2.1}/coverage.xml +136 -163
  6. {h5yaml-0.2.0 → h5yaml-0.2.1}/src/h5yaml/Data/h5_testing.yaml +23 -1
  7. {h5yaml-0.2.0 → h5yaml-0.2.1}/src/h5yaml/Data/nc_testing.yaml +13 -1
  8. {h5yaml-0.2.0 → h5yaml-0.2.1}/src/h5yaml/conf_from_yaml.py +3 -3
  9. {h5yaml-0.2.0 → h5yaml-0.2.1}/src/h5yaml/yaml_h5.py +16 -18
  10. {h5yaml-0.2.0 → h5yaml-0.2.1}/src/h5yaml/yaml_nc.py +19 -16
  11. {h5yaml-0.2.0 → h5yaml-0.2.1}/tests/test_from_yaml.py +16 -1
  12. {h5yaml-0.2.0 → h5yaml-0.2.1}/tests/test_yaml_h5.py +10 -10
  13. {h5yaml-0.2.0 → h5yaml-0.2.1}/tests/test_yaml_nc.py +16 -12
  14. h5yaml-0.2.0/klad.h5 +0 -0
  15. h5yaml-0.2.0/src/h5yaml/lib/chunksizes.py +0 -73
  16. {h5yaml-0.2.0 → h5yaml-0.2.1}/.gitignore +0 -0
  17. {h5yaml-0.2.0 → h5yaml-0.2.1}/.pre-commit-config.yaml +0 -0
  18. {h5yaml-0.2.0 → h5yaml-0.2.1}/LICENSE +0 -0
  19. {h5yaml-0.2.0 → h5yaml-0.2.1}/MANIFEST.in +0 -0
  20. {h5yaml-0.2.0 → h5yaml-0.2.1}/pyproject.toml +0 -0
  21. {h5yaml-0.2.0 → h5yaml-0.2.1}/src/h5yaml/Data/h5_compound.yaml +0 -0
  22. {h5yaml-0.2.0 → h5yaml-0.2.1}/src/h5yaml/Data/h5_unsupported.yaml +0 -0
  23. {h5yaml-0.2.0 → h5yaml-0.2.1}/src/h5yaml/__init__.py +0 -0
  24. {h5yaml-0.2.0 → h5yaml-0.2.1}/src/h5yaml/lib/__init__.py +0 -0
  25. {h5yaml-0.2.0 → h5yaml-0.2.1}/src/h5yaml/lib/adjust_attr.py +0 -0
{h5yaml-0.2.0 → h5yaml-0.2.1}/.coverage RENAMED
Binary file
{h5yaml-0.2.0 → h5yaml-0.2.1}/.github/workflows/python-package.yml RENAMED
@@ -37,4 +37,5 @@ jobs:
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  flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
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  - name: Test with pytest
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  run: |
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- pytest
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+ pytest tests/test_yaml_h5.py tests/test_from_yaml.py
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+ pytest tests/test_yaml_nc.py
{h5yaml-0.2.0 → h5yaml-0.2.1}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: h5yaml
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- Version: 0.2.0
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+ Version: 0.2.1
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  Summary: Use YAML configuration file to generate HDF5/netCDF4 formated files.
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  Project-URL: Homepage, https://github.com/rmvanhees/h5_yaml
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  Project-URL: Source, https://github.com/rmvanhees/h5_yaml
@@ -61,7 +61,19 @@ However, package `netCDF4` has some limitations, which `h5py` has not, for examp
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  not allow variable-length variables to have a compound data-type.
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  ## Installation
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- Releases of the code, starting from version 0.1, will be made available via PyPI.
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+ The package `h5yaml` is available from PyPI. To install it use `pip`:
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+
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+ > $ pip install [--user] h5yaml
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+
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+ The module `h5yaml` requires Python3.10+ and Python modules: h5py (v3.14+), netCDF4 (v1.7+) and numpy (v2.0+).
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+
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+ **Note**: the packages `h5py` and `netCDF4` come with their own HDF5 libraries. If these are different then they may
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+ collide and result in a *''HDF5 error''*.
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+ If this is the case then you have to install the development packages of HDF5 and netCDF4 (or compile them from source).
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+ And reinstall `h5py` and `netCDF4` using the commands:
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+
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+ > $ pip uninstall h5py; pip install --no-binary=h5py h5py
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+ > $ pip uninstall netCDF4; pip install --no-binary=netCDF4 netCDF4
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  ## Usage
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@@ -176,7 +188,7 @@ The YAML file should be structured as follows:
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  ## Support [TBW]
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- ## Roadmap
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+ ## Road map
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  * Release v0.1 : stable API to read your YAML files and generate the HDF5/netCDF4 file
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{h5yaml-0.2.0 → h5yaml-0.2.1}/README.md RENAMED
@@ -29,7 +29,19 @@ However, package `netCDF4` has some limitations, which `h5py` has not, for examp
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  not allow variable-length variables to have a compound data-type.
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  ## Installation
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- Releases of the code, starting from version 0.1, will be made available via PyPI.
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+ The package `h5yaml` is available from PyPI. To install it use `pip`:
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+
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+ > $ pip install [--user] h5yaml
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+
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+ The module `h5yaml` requires Python3.10+ and Python modules: h5py (v3.14+), netCDF4 (v1.7+) and numpy (v2.0+).
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+
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+ **Note**: the packages `h5py` and `netCDF4` come with their own HDF5 libraries. If these are different then they may
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+ collide and result in a *''HDF5 error''*.
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+ If this is the case then you have to install the development packages of HDF5 and netCDF4 (or compile them from source).
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+ And reinstall `h5py` and `netCDF4` using the commands:
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+
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+ > $ pip uninstall h5py; pip install --no-binary=h5py h5py
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+ > $ pip uninstall netCDF4; pip install --no-binary=netCDF4 netCDF4
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  ## Usage
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@@ -144,7 +156,7 @@ The YAML file should be structured as follows:
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  ## Support [TBW]
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- ## Roadmap
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+ ## Road map
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  * Release v0.1 : stable API to read your YAML files and generate the HDF5/netCDF4 file
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{h5yaml-0.2.0 → h5yaml-0.2.1}/coverage.xml RENAMED
@@ -1,18 +1,18 @@
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  <?xml version="1.0" ?>
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- <coverage version="7.12.0" timestamp="1764021429676" lines-valid="348" lines-covered="311" line-rate="0.8937" branches-covered="0" branches-valid="0" branch-rate="0" complexity="0">
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+ <coverage version="7.12.0" timestamp="1764076997420" lines-valid="326" lines-covered="297" line-rate="0.911" branches-covered="0" branches-valid="0" branch-rate="0" complexity="0">
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  <sources>
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  <source>/home/richardh/git/h5_yaml</source>
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  </sources>
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  <packages>
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- <package name="src.h5yaml" line-rate="0.8938" branch-rate="0" complexity="0">
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+ <package name="src.h5yaml" line-rate="0.9007" branch-rate="0" complexity="0">
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  <classes>
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  <class name="__init__.py" filename="src/h5yaml/__init__.py" complexity="0" line-rate="1" branch-rate="0">
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  <methods/>
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  </class>
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- <class name="conf_from_yaml.py" filename="src/h5yaml/conf_from_yaml.py" complexity="0" line-rate="0.8" branch-rate="0">
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+ <class name="conf_from_yaml.py" filename="src/h5yaml/conf_from_yaml.py" complexity="0" line-rate="1" branch-rate="0">
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- <class name="yaml_h5.py" filename="src/h5yaml/yaml_h5.py" complexity="0" line-rate="0.9701" branch-rate="0">
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+ <class name="yaml_h5.py" filename="src/h5yaml/yaml_h5.py" complexity="0" line-rate="0.9556" branch-rate="0">
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+ <line number="135" hits="0"/>
233
+ <line number="136" hits="0"/>
234
+ <line number="137" hits="0"/>
235
+ <line number="138" hits="0"/>
236
+ <line number="139" hits="0"/>
237
+ <line number="141" hits="1"/>
239
238
  <line number="142" hits="1"/>
240
- <line number="143" hits="1"/>
241
- <line number="144" hits="1"/>
242
- <line number="145" hits="1"/>
243
- <line number="146" hits="1"/>
244
239
  <line number="148" hits="1"/>
245
240
  <line number="149" hits="1"/>
241
+ <line number="150" hits="1"/>
246
242
  <line number="151" hits="1"/>
247
- <line number="153" hits="1"/>
248
- <line number="168" hits="1"/>
249
- <line number="169" hits="1"/>
250
- <line number="170" hits="1"/>
251
- <line number="171" hits="1"/>
252
- <line number="173" hits="1"/>
243
+ <line number="152" hits="1"/>
244
+ <line number="154" hits="1"/>
245
+ <line number="155" hits="1"/>
246
+ <line number="157" hits="1"/>
247
+ <line number="159" hits="1"/>
253
248
  <line number="174" hits="1"/>
254
249
  <line number="175" hits="1"/>
250
+ <line number="176" hits="1"/>
255
251
  <line number="177" hits="1"/>
256
- <line number="178" hits="1"/>
252
+ <line number="179" hits="1"/>
257
253
  <line number="180" hits="1"/>
258
- <line number="181" hits="1"/>
259
254
  <line number="182" hits="1"/>
260
- <line number="187" hits="1"/>
261
- <line number="188" hits="1"/>
262
- <line number="194" hits="1"/>
263
- <line number="201" hits="1"/>
264
- <line number="203" hits="1"/>
265
- <line number="204" hits="1"/>
266
- <line number="206" hits="1"/>
255
+ <line number="184" hits="1"/>
256
+ <line number="185" hits="1"/>
257
+ <line number="186" hits="1"/>
258
+ <line number="191" hits="1"/>
259
+ <line number="192" hits="1"/>
260
+ <line number="198" hits="1"/>
261
+ <line number="205" hits="1"/>
267
262
  <line number="207" hits="1"/>
268
263
  <line number="208" hits="1"/>
269
264
  <line number="210" hits="1"/>
270
265
  <line number="211" hits="1"/>
271
266
  <line number="212" hits="1"/>
272
- <line number="213" hits="1"/>
273
267
  <line number="214" hits="1"/>
274
268
  <line number="215" hits="1"/>
275
269
  <line number="216" hits="1"/>
276
270
  <line number="217" hits="1"/>
277
- <line number="218" hits="0"/>
271
+ <line number="218" hits="1"/>
272
+ <line number="219" hits="1"/>
278
273
  <line number="220" hits="1"/>
279
274
  <line number="221" hits="1"/>
280
275
  <line number="222" hits="1"/>
281
- <line number="223" hits="1"/>
276
+ <line number="224" hits="1"/>
277
+ <line number="225" hits="1"/>
282
278
  <line number="226" hits="1"/>
283
- <line number="227" hits="0"/>
279
+ <line number="227" hits="1"/>
284
280
  <line number="230" hits="1"/>
285
- <line number="234" hits="1"/>
286
- <line number="235" hits="1"/>
281
+ <line number="231" hits="0"/>
282
+ <line number="233" hits="1"/>
283
+ <line number="234" hits="0"/>
287
284
  <line number="238" hits="1"/>
288
285
  <line number="239" hits="1"/>
289
- <line number="247" hits="1"/>
290
- <line number="248" hits="1"/>
291
- <line number="249" hits="0"/>
292
- <line number="250" hits="1"/>
286
+ <line number="242" hits="1"/>
287
+ <line number="243" hits="1"/>
293
288
  <line number="251" hits="1"/>
294
289
  <line number="252" hits="1"/>
295
290
  <line number="253" hits="1"/>
291
+ <line number="254" hits="1"/>
296
292
  <line number="255" hits="1"/>
297
- <line number="267" hits="1"/>
298
- <line number="275" hits="1"/>
299
- <line number="276" hits="0"/>
300
- <line number="277" hits="0"/>
301
- <line number="278" hits="0"/>
293
+ <line number="256" hits="0"/>
294
+ <line number="257" hits="1"/>
295
+ <line number="258" hits="1"/>
296
+ <line number="260" hits="1"/>
297
+ <line number="270" hits="1"/>
298
+ <line number="278" hits="1"/>
302
299
  <line number="279" hits="0"/>
303
- <line number="281" hits="1"/>
304
- <line number="282" hits="1"/>
300
+ <line number="280" hits="0"/>
301
+ <line number="281" hits="0"/>
302
+ <line number="282" hits="0"/>
305
303
  <line number="284" hits="1"/>
306
- <line number="286" hits="1"/>
307
- <line number="288" hits="1"/>
304
+ <line number="285" hits="1"/>
305
+ <line number="287" hits="1"/>
308
306
  <line number="289" hits="1"/>
309
- <line number="290" hits="1"/>
310
307
  <line number="291" hits="1"/>
311
308
  <line number="292" hits="1"/>
309
+ <line number="293" hits="1"/>
312
310
  <line number="294" hits="1"/>
313
- <line number="303" hits="1"/>
314
- <line number="304" hits="1"/>
315
- <line number="305" hits="0"/>
316
- <line number="306" hits="0"/>
317
- <line number="307" hits="0"/>
318
- <line number="308" hits="1"/>
319
- <line number="309" hits="1"/>
311
+ <line number="295" hits="1"/>
312
+ <line number="297" hits="1"/>
313
+ <line number="306" hits="1"/>
314
+ <line number="307" hits="1"/>
315
+ <line number="308" hits="0"/>
316
+ <line number="309" hits="0"/>
317
+ <line number="310" hits="0"/>
318
+ <line number="311" hits="1"/>
319
+ <line number="312" hits="1"/>
320
320
  </lines>
321
321
  </class>
322
322
  </classes>
323
323
  </package>
324
- <package name="src.h5yaml.lib" line-rate="0.8929" branch-rate="0" complexity="0">
324
+ <package name="src.h5yaml.lib" line-rate="1" branch-rate="0" complexity="0">
325
325
  <classes>
326
326
  <class name="__init__.py" filename="src/h5yaml/lib/__init__.py" complexity="0" line-rate="1" branch-rate="0">
327
327
  <methods/>
@@ -366,33 +366,6 @@
366
366
  <line number="79" hits="1"/>
367
367
  </lines>
368
368
  </class>
369
- <class name="chunksizes.py" filename="src/h5yaml/lib/chunksizes.py" complexity="0" line-rate="0.7273" branch-rate="0">
370
- <methods/>
371
- <lines>
372
- <line number="23" hits="1"/>
373
- <line number="25" hits="1"/>
374
- <line number="27" hits="1"/>
375
- <line number="33" hits="1"/>
376
- <line number="48" hits="1"/>
377
- <line number="49" hits="1"/>
378
- <line number="50" hits="1"/>
379
- <line number="51" hits="1"/>
380
- <line number="54" hits="1"/>
381
- <line number="55" hits="0"/>
382
- <line number="56" hits="0"/>
383
- <line number="58" hits="0"/>
384
- <line number="59" hits="0"/>
385
- <line number="60" hits="0"/>
386
- <line number="63" hits="1"/>
387
- <line number="64" hits="1"/>
388
- <line number="66" hits="1"/>
389
- <line number="67" hits="1"/>
390
- <line number="68" hits="1"/>
391
- <line number="69" hits="0"/>
392
- <line number="71" hits="1"/>
393
- <line number="73" hits="1"/>
394
- </lines>
395
- </class>
396
369
  </classes>
397
370
  </package>
398
371
  </packages>
{h5yaml-0.2.0 → h5yaml-0.2.1}/src/h5yaml/Data/h5_testing.yaml RENAMED
@@ -25,6 +25,8 @@ groups:
25
25
  - group_01
26
26
  - group_02
27
27
  - group_03
28
+ - processing_control
29
+ - /processing_control/input_parameters
28
30
 
29
31
  # Define dimensions
30
32
  # Note dimensions with an attribute 'long_name' will also be generated as variable
@@ -91,6 +93,26 @@ variables:
91
93
  units: '1'
92
94
  valid_min: 0
93
95
  valid_max: 65534
96
+ /group_00/detector_images_chunked:
97
+ _dtype: u2
98
+ _dims: [number_of_images, column, row]
99
+ _FillValue: 65535
100
+ _chunks: [1, 640, 512]
101
+ long_name: Detector pixel values
102
+ comment: unbinned full-frame data
103
+ units: '1'
104
+ valid_min: 0
105
+ valid_max: 65534
106
+ /group_00/detector_images_autochunk:
107
+ _dtype: u2
108
+ _dims: [number_of_images, column, row]
109
+ _chunks: True
110
+ _FillValue: 65535
111
+ long_name: Detector pixel values
112
+ comment: unbinned full-frame data
113
+ units: '1'
114
+ valid_min: 0
115
+ valid_max: 65534
94
116
  # ---------- GROUP 01 ----------
95
117
  /group_01/detector_images:
96
118
  _dtype: u2
@@ -199,7 +221,7 @@ variables:
199
221
  valid_max: 999.9
200
222
  /group_03/ds_10:
201
223
  _dtype: f4
202
- _dims: [number_of_images]
224
+ _dims: [number_of_images, /group_03/viewport]
203
225
  long_name: float dataset
204
226
  units: '1'
205
227
  valid_min: -999.9
{h5yaml-0.2.0 → h5yaml-0.2.1}/src/h5yaml/Data/nc_testing.yaml RENAMED
@@ -25,6 +25,8 @@ groups:
25
25
  - group_01
26
26
  - group_02
27
27
  - group_03
28
+ - processing_control
29
+ - /processing_control/input_parameters
28
30
 
29
31
  # Define dimensions
30
32
  # Note dimensions with an attribute 'long_name' will also be generated as variable
@@ -87,6 +89,16 @@ variables:
87
89
  units: '1'
88
90
  valid_min: 0
89
91
  valid_max: 65534
92
+ /group_00/detector_images_chunked:
93
+ _dtype: u2
94
+ _dims: [number_of_images, column, row]
95
+ _FillValue: 65535
96
+ _chunks: [1, 640, 512]
97
+ long_name: Detector pixel values
98
+ comment: unbinned full-frame data
99
+ units: '1'
100
+ valid_min: 0
101
+ valid_max: 65534
90
102
  # ---------- GROUP 01 ----------
91
103
  /group_01/detector_images:
92
104
  _dtype: u2
@@ -190,7 +202,7 @@ variables:
190
202
  # valid_max: 999.9
191
203
  /group_03/ds_10:
192
204
  _dtype: f4
193
- _dims: [number_of_images]
205
+ _dims: [number_of_images, /group_03/viewport]
194
206
  long_name: float dataset
195
207
  units: '1'
196
208
  valid_min: -999.9
{h5yaml-0.2.0 → h5yaml-0.2.1}/src/h5yaml/conf_from_yaml.py RENAMED
@@ -45,7 +45,7 @@ def conf_from_yaml(file_path: Path | str) -> dict:
45
45
 
46
46
  """
47
47
  if isinstance(file_path, str):
48
- file_path = Path(str)
48
+ file_path = Path(file_path)
49
49
 
50
50
  if not file_path.is_file():
51
51
  raise FileNotFoundError(f"{file_path} not found")
@@ -53,7 +53,7 @@ def conf_from_yaml(file_path: Path | str) -> dict:
53
53
  with file_path.open("r", encoding="ascii") as fid:
54
54
  try:
55
55
  settings = yaml.safe_load(fid)
56
- except yaml.YAMLError as exc:
57
- raise RuntimeError from exc
56
+ except yaml.parser.ParserError as exc:
57
+ raise RuntimeError(f"Failed to parse {file_path}") from exc
58
58
 
59
59
  return settings
{h5yaml-0.2.0 → h5yaml-0.2.1}/src/h5yaml/yaml_h5.py RENAMED
@@ -32,7 +32,6 @@ import numpy as np
32
32
 
33
33
  from .conf_from_yaml import conf_from_yaml
34
34
  from .lib.adjust_attr import adjust_attr
35
- from .lib.chunksizes import guess_chunks
36
35
 
37
36
 
38
37
  # - class definition -----------------------------------
@@ -41,12 +40,12 @@ class H5Yaml:
41
40
 
42
41
  Parameters
43
42
  ----------
44
- h5_yaml_fl : Path
45
- YAML files with the HDF5 format definition
43
+ h5_yaml_fl : Path | str
44
+ YAML file with the HDF5 format definition
46
45
 
47
46
  """
48
47
 
49
- def __init__(self: H5Yaml, h5_yaml_fl: Path) -> None:
48
+ def __init__(self: H5Yaml, h5_yaml_fl: Path | str) -> None:
50
49
  """Construct a H5Yaml instance."""
51
50
  self.logger = logging.getLogger("h5yaml.H5Yaml")
52
51
 
@@ -72,12 +71,14 @@ class H5Yaml:
72
71
  )
73
72
 
74
73
  if val["_size"] == 0:
75
- ds_chunk = val.get("_chunks", (50,))
74
+ ds_chunk = val.get("_chunks")
75
+ if ds_chunk is not None and not isinstance(ds_chunk, bool):
76
+ ds_chunk = tuple(ds_chunk)
76
77
  dset = fid.create_dataset(
77
78
  key,
78
79
  shape=(0,),
79
80
  dtype="T" if val["_dtype"] == "str" else val["_dtype"],
80
- chunks=ds_chunk if isinstance(ds_chunk, tuple) else tuple(ds_chunk),
81
+ chunks=ds_chunk,
81
82
  maxshape=(None,),
82
83
  fillvalue=fillvalue,
83
84
  )
@@ -153,10 +154,8 @@ class H5Yaml:
153
154
  for key, val in self.h5_def["variables"].items():
154
155
  if val["_dtype"] in fid:
155
156
  ds_dtype = fid[val["_dtype"]]
156
- dtype_size = fid[val["_dtype"]].dtype.itemsize
157
157
  else:
158
158
  ds_dtype = "T" if val["_dtype"] == "str" else val["_dtype"]
159
- dtype_size = np.dtype(val["_dtype"]).itemsize
160
159
 
161
160
  fillvalue = None
162
161
  if "_FillValue" in val:
@@ -190,15 +189,13 @@ class H5Yaml:
190
189
  if n_udim > 1:
191
190
  raise ValueError(f"{key} has more than one unlimited dimension")
192
191
 
193
- # obtain chunk-size settings
194
- ds_chunk = (
195
- val["_chunks"]
196
- if "_chunks" in val
197
- else guess_chunks(ds_shape, dtype_size)
198
- )
192
+ if None in ds_maxshape and val.get("_chunks") == "contiguous":
193
+ raise KeyError(
194
+ "you can not create a contiguous dataset with unlimited dimensions."
195
+ )
199
196
 
200
197
  # create the variable
201
- if ds_chunk == "contiguous":
198
+ if val.get("_chunks") == "contiguous":
202
199
  dset = fid.create_dataset(
203
200
  key,
204
201
  ds_shape,
@@ -208,6 +205,9 @@ class H5Yaml:
208
205
  fillvalue=fillvalue,
209
206
  )
210
207
  else:
208
+ ds_chunk = val.get("_chunks")
209
+ if ds_chunk is not None and not isinstance(ds_chunk, bool):
210
+ ds_chunk = tuple(ds_chunk)
211
211
  compression = None
212
212
  shuffle = False
213
213
  # currently only gzip compression is supported
@@ -225,14 +225,12 @@ class H5Yaml:
225
225
  fid[ds_name] = h5py.vlen_dtype(ds_dtype)
226
226
  ds_dtype = fid[ds_name]
227
227
  fillvalue = None
228
- if ds_maxshape == (None,):
229
- ds_chunk = (16,)
230
228
 
231
229
  dset = fid.create_dataset(
232
230
  key,
233
231
  ds_shape,
234
232
  dtype=ds_dtype,
235
- chunks=ds_chunk if isinstance(ds_chunk, tuple) else tuple(ds_chunk),
233
+ chunks=ds_chunk,
236
234
  maxshape=ds_maxshape,
237
235
  fillvalue=fillvalue,
238
236
  compression=compression,
{h5yaml-0.2.0 → h5yaml-0.2.1}/src/h5yaml/yaml_nc.py RENAMED
@@ -35,7 +35,6 @@ from netCDF4 import Dataset
35
35
 
36
36
  from .conf_from_yaml import conf_from_yaml
37
37
  from .lib.adjust_attr import adjust_attr
38
- from .lib.chunksizes import guess_chunks
39
38
 
40
39
  if TYPE_CHECKING:
41
40
  from pathlib import Path
@@ -43,9 +42,16 @@ if TYPE_CHECKING:
43
42
 
44
43
  # - class definition -----------------------------------
45
44
  class NcYaml:
46
- """Class to create a HDF5/netCDF4 formated file from a YAML configuration file."""
45
+ """Class to create a HDF5/netCDF4 formated file from a YAML configuration file.
47
46
 
48
- def __init__(self: NcYaml, nc_yaml_fl: Path) -> None:
47
+ Parameters
48
+ ----------
49
+ nc_yaml_fl : Path | str
50
+ YAML file with the netCDF4 format definition
51
+
52
+ """
53
+
54
+ def __init__(self: NcYaml, nc_yaml_fl: Path | str) -> None:
49
55
  """Construct a NcYaml instance."""
50
56
  self.logger = logging.getLogger("h5yaml.NcYaml")
51
57
 
@@ -172,10 +178,8 @@ class NcYaml:
172
178
 
173
179
  if val["_dtype"] in fid.cmptypes:
174
180
  ds_dtype = fid.cmptypes[val["_dtype"]].dtype
175
- sz_dtype = ds_dtype.itemsize
176
181
  else:
177
182
  ds_dtype = val["_dtype"]
178
- sz_dtype = np.dtype(val["_dtype"]).itemsize
179
183
 
180
184
  fillvalue = None
181
185
  if "_FillValue" in val:
@@ -226,16 +230,16 @@ class NcYaml:
226
230
  if n_udim > 1:
227
231
  raise ValueError("more than one unlimited dimension")
228
232
 
229
- # obtain chunk-size settings
230
- ds_chunk = (
231
- val["_chunks"] if "_chunks" in val else guess_chunks(ds_shape, sz_dtype)
232
- )
233
+ if None in ds_maxshape and val.get("_chunks") == "contiguous":
234
+ raise KeyError(
235
+ "you can not create a contiguous dataset with unlimited dimensions."
236
+ )
233
237
 
234
238
  if val["_dtype"] in fid.cmptypes:
235
239
  val["_dtype"] = fid.cmptypes[val["_dtype"]]
236
240
 
237
241
  # create the variable
238
- if ds_chunk == "contiguous":
242
+ if val.get("_chunks") == "contiguous":
239
243
  dset = var_grp.createVariable(
240
244
  var_name,
241
245
  val["_dtype"],
@@ -244,25 +248,24 @@ class NcYaml:
244
248
  contiguous=True,
245
249
  )
246
250
  else:
251
+ ds_chunk = val.get("_chunks")
252
+ if ds_chunk is not None and not isinstance(ds_chunk, bool):
253
+ ds_chunk = tuple(ds_chunk)
247
254
  if val.get("_vlen"):
248
255
  if val["_dtype"] in fid.cmptypes:
249
256
  raise ValueError("can not have vlen with compounds")
250
257
  val["_dtype"] = fid.createVLType(ds_dtype, val["_dtype"])
251
258
  fillvalue = None
252
- if ds_maxshape == (None,):
253
- ds_chunk = (16,)
254
259
 
255
260
  dset = var_grp.createVariable(
256
261
  var_name,
257
262
  str if val["_dtype"] == "str" else val["_dtype"],
258
263
  dimensions=var_dims,
259
264
  fill_value=fillvalue,
260
- contiguous=False,
261
265
  compression=compression,
262
266
  complevel=complevel,
263
- chunksizes=(
264
- ds_chunk if isinstance(ds_chunk, tuple) else tuple(ds_chunk)
265
- ),
267
+ chunksizes=ds_chunk,
268
+ contiguous=False,
266
269
  )
267
270
  dset.setncatts(
268
271
  {
{h5yaml-0.2.0 → h5yaml-0.2.1}/tests/test_from_yaml.py RENAMED
@@ -22,7 +22,22 @@
22
22
 
23
23
  from __future__ import annotations
24
24
 
25
+ from importlib.resources import files
26
+
27
+ import pytest
28
+
29
+ from h5yaml.conf_from_yaml import conf_from_yaml
30
+
25
31
 
26
32
  def test_from_yaml() -> None:
27
33
  """..."""
28
- return
34
+ with pytest.raises(FileNotFoundError, match="not found") as excinfo:
35
+ _ = conf_from_yaml(files("h5yaml.Data") / "not_existing.yaml")
36
+ assert f"{files('h5yaml.Data') / 'not_existing.yaml'} not found" in str(excinfo)
37
+
38
+ with pytest.raises(RuntimeError, match=r"Failed to parse .*") as excinfo:
39
+ _ = conf_from_yaml("README.md")
40
+ assert "Failed to parse" in str(excinfo)
41
+
42
+ res = conf_from_yaml(files("h5yaml.Data") / "nc_testing.yaml")
43
+ assert isinstance(res, dict)
{h5yaml-0.2.0 → h5yaml-0.2.1}/tests/test_yaml_h5.py RENAMED
@@ -38,21 +38,21 @@ class TestH5Yaml:
38
38
  FID = H5Yaml(files("h5yaml.Data") / "h5_testing.yaml").diskless()
39
39
 
40
40
  def test_exceptions(self: TestH5Yaml) -> None:
41
- """..."""
41
+ """Unit-test for class exeptions."""
42
42
  # tests which should raise an exception because the file can not be created
43
43
  l1a_name = "/this/folder/does/not/exists/test.h5"
44
44
  with pytest.raises(FileNotFoundError, match=r"[Errno 2] .*") as excinfo:
45
- _ = H5Yaml(files("h5yaml.Data") / "h5_testing.yaml").create(l1a_name)
45
+ H5Yaml(files("h5yaml.Data") / "h5_testing.yaml").create(l1a_name)
46
46
  assert "'No such file or directory" in str(excinfo)
47
47
 
48
48
  l1a_name = Path("/this/folder/does/not/exists/test.h5")
49
49
  with pytest.raises(FileNotFoundError, match=r"[Errno 2] .*") as excinfo:
50
- _ = H5Yaml(files("h5yaml.Data") / "h5_testing.yaml").create(l1a_name)
50
+ H5Yaml(files("h5yaml.Data") / "h5_testing.yaml").create(l1a_name)
51
51
  assert "'No such file or directory" in str(excinfo)
52
52
 
53
53
  l1a_name = "/test.h5"
54
54
  with pytest.raises(RuntimeError, match=r"failed create .*") as excinfo:
55
- _ = H5Yaml(files("h5yaml.Data") / "h5_testing.yaml").create(l1a_name)
55
+ H5Yaml(files("h5yaml.Data") / "h5_testing.yaml").create(l1a_name)
56
56
  assert f"failed create {l1a_name}" in str(excinfo.value)
57
57
 
58
58
  # tests which raise an exception because the YAML file is corrupted
@@ -62,11 +62,11 @@ class TestH5Yaml:
62
62
  assert f"{file_path} not found" in str(excinfo.value)
63
63
 
64
64
  with pytest.raises(ValueError, match=r".* unlimited dimension") as excinfo:
65
- _ = H5Yaml(files("h5yaml.Data") / "h5_unsupported.yaml").create("klad.h5")
65
+ H5Yaml(files("h5yaml.Data") / "h5_unsupported.yaml").create("klad.h5")
66
66
  assert "has more than one unlimited dimension" in str(excinfo.value)
67
67
 
68
68
  def test_groups(self: TestH5Yaml) -> None:
69
- """..."""
69
+ """Unit-test to check the groups."""
70
70
  if "groups" not in self.H5_DEF:
71
71
  return
72
72
 
@@ -74,7 +74,7 @@ class TestH5Yaml:
74
74
  assert key in self.FID
75
75
 
76
76
  def test_dimensions(self: TestH5Yaml) -> None:
77
- """..."""
77
+ """Unit-test to check the dimensions."""
78
78
  if "dimensions" not in self.H5_DEF:
79
79
  return
80
80
 
@@ -101,7 +101,7 @@ class TestH5Yaml:
101
101
  assert self.FID[key].attrs[attr] == self.H5_DEF["dimensions"][key][attr]
102
102
 
103
103
  def test_compounds(self: TestH5Yaml) -> None:
104
- """..."""
104
+ """Unit-test to check the compounds."""
105
105
  if "compounds" not in self.H5_DEF:
106
106
  return
107
107
 
@@ -109,7 +109,7 @@ class TestH5Yaml:
109
109
  assert key in self.FID
110
110
 
111
111
  def test_variables(self: TestH5Yaml) -> None:
112
- """..."""
112
+ """Unit-test to check the variables."""
113
113
  if "variables" not in self.H5_DEF:
114
114
  return
115
115
 
@@ -130,5 +130,5 @@ class TestH5Yaml:
130
130
  assert self.FID[key].attrs[attr] == dset[key][attr]
131
131
 
132
132
  def test_close(self: TestH5Yaml) -> None:
133
- """..."""
133
+ """Close the in-memory HDF5 file."""
134
134
  self.FID.close()
{h5yaml-0.2.0 → h5yaml-0.2.1}/tests/test_yaml_nc.py RENAMED
@@ -38,21 +38,21 @@ class TestNcYaml:
38
38
  FID = NcYaml(files("h5yaml.Data") / "nc_testing.yaml").diskless()
39
39
 
40
40
  def test_exceptions(self: TestNcYaml) -> None:
41
- """..."""
41
+ """Unit-test for the class exdeptions."""
42
42
  # tests which should raise an exception because the file can not be created
43
43
  l1a_name = "/this/folder/does/not/exists/test.nc"
44
44
  with pytest.raises(RuntimeError, match=r"failed to create .*") as excinfo:
45
- _ = NcYaml(files("h5yaml.Data") / "nc_testing.yaml").create(l1a_name)
45
+ NcYaml(files("h5yaml.Data") / "nc_testing.yaml").create(l1a_name)
46
46
  assert f"failed to create {l1a_name}" in str(excinfo)
47
47
 
48
48
  l1a_name = Path("/this/folder/does/not/exists/test.nc")
49
49
  with pytest.raises(RuntimeError, match=r"failed to create .*") as excinfo:
50
- _ = NcYaml(files("h5yaml.Data") / "nc_testing.yaml").create(l1a_name)
50
+ NcYaml(files("h5yaml.Data") / "nc_testing.yaml").create(l1a_name)
51
51
  assert f"failed to create {l1a_name}" in str(excinfo)
52
52
 
53
53
  l1a_name = "/test.nc"
54
54
  with pytest.raises(RuntimeError, match=r"failed to create .*") as excinfo:
55
- _ = NcYaml(files("h5yaml.Data") / "nc_testing.yaml").create(l1a_name)
55
+ NcYaml(files("h5yaml.Data") / "nc_testing.yaml").create(l1a_name)
56
56
  assert f"failed to create {l1a_name}" in str(excinfo.value)
57
57
 
58
58
  # tests which raise an exception because the YAML file is corrupted
@@ -62,15 +62,19 @@ class TestNcYaml:
62
62
  assert f"{file_path} not found" in str(excinfo.value)
63
63
 
64
64
  def test_groups(self: TestNcYaml) -> None:
65
- """..."""
65
+ """Unit-test to check the groups."""
66
66
  if "groups" not in self.NC_DEF:
67
67
  return
68
68
 
69
69
  for key in self.NC_DEF["groups"]:
70
- assert key in self.FID.groups
70
+ pkey = PurePosixPath(key)
71
+ if pkey.is_absolute():
72
+ assert pkey.name in self.FID[pkey.parent].groups
73
+ else:
74
+ assert key in self.FID.groups
71
75
 
72
76
  def test_dimensions(self: TestNcYaml) -> None:
73
- """..."""
77
+ """Unit-test to check the dimensions."""
74
78
  if "dimensions" not in self.NC_DEF:
75
79
  return
76
80
 
@@ -102,7 +106,7 @@ class TestNcYaml:
102
106
  assert getattr(nc_dim, attr) == self.NC_DEF["dimensions"][key][attr]
103
107
 
104
108
  def test_compounds(self: TestNcYaml) -> None:
105
- """..."""
109
+ """Unit-test to check the compounds."""
106
110
  if "compounds" not in self.NC_DEF:
107
111
  return
108
112
 
@@ -110,7 +114,7 @@ class TestNcYaml:
110
114
  assert key in self.FID.cmptypes
111
115
 
112
116
  def test_variables(self: TestNcYaml) -> None:
113
- """..."""
117
+ """Unit-test to check the variables."""
114
118
  if "variables" not in self.NC_DEF:
115
119
  return
116
120
 
@@ -137,6 +141,6 @@ class TestNcYaml:
137
141
  else:
138
142
  assert getattr(nc_var, attr) == self.NC_DEF["variables"][key][attr]
139
143
 
140
- # def test_close(self: TestNcYaml) -> None:
141
- # """..."""
142
- # self.FID.close()
144
+ def test_close(self: TestNcYaml) -> None:
145
+ """Close the in-memory netCDF4 file."""
146
+ self.FID.close()
h5yaml-0.2.0/klad.h5 DELETED
Binary file
h5yaml-0.2.0/src/h5yaml/lib/chunksizes.py DELETED
@@ -1,73 +0,0 @@
1
- #
2
- # This file is part of Python package: `h5yaml`
3
- #
4
- # https://github.com/rmvanhees/pyxarr.git
5
- #
6
- # Copyright (c) 2025 - R.M. van Hees (SRON)
7
- # All rights reserved.
8
- #
9
- # Licensed under the Apache License, Version 2.0 (the "License");
10
- # you may not use this file except in compliance with the License.
11
- # You may obtain a copy of the License at
12
- #
13
- # http://www.apache.org/licenses/LICENSE-2.0
14
- #
15
- # Unless required by applicable law or agreed to in writing, software
16
- # distributed under the License is distributed on an "AS IS" BASIS,
17
- # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
18
- # See the License for the specific language governing permissions and
19
- # limitations under the License.
20
- #
21
- """Obtain chunksizes for HDF5 datasets."""
22
-
23
- from __future__ import annotations
24
-
25
- __all__ = ["guess_chunks"]
26
-
27
- from typing import TYPE_CHECKING
28
-
29
- if TYPE_CHECKING:
30
- from numpy.typing import ArrayLike
31
-
32
-
33
- def guess_chunks(dims: ArrayLike[int], dtype_sz: int) -> str | tuple[int]:
34
- """Perform an educated guess for the dataset chunk sizes.
35
-
36
- Parameters
37
- ----------
38
- dims : ArrayLike[int]
39
- Dimensions of the variable
40
- dtype_sz : int
41
- The element size of the data-type of the variable
42
-
43
- Returns
44
- -------
45
- "contiguous" or tuple with chunk-sizes
46
-
47
- """
48
- fixed_size = dtype_sz
49
- if len(dims) > 1:
50
- for val in [x for x in dims[1:] if x > 0]:
51
- fixed_size *= val
52
-
53
- # first variables without an unlimited dimension
54
- if 0 not in dims:
55
- if fixed_size < 400000:
56
- return "contiguous"
57
-
58
- res = list(dims)
59
- res[0] = max(1, 2048000 // fixed_size)
60
- return tuple(res)
61
-
62
- # then variables with an unlimited dimension
63
- if len(dims) == 1:
64
- return (1024,)
65
-
66
- udim = dims.index(0)
67
- res = list(dims)
68
- if fixed_size < 400000:
69
- res[udim] = 1024
70
- else:
71
- res[udim] = max(1, 2048000 // fixed_size)
72
-
73
- return tuple(res)
{h5yaml-0.2.0 → h5yaml-0.2.1}/.gitignore RENAMED
File without changes
{h5yaml-0.2.0 → h5yaml-0.2.1}/.pre-commit-config.yaml RENAMED
File without changes
{h5yaml-0.2.0 → h5yaml-0.2.1}/LICENSE RENAMED
File without changes
{h5yaml-0.2.0 → h5yaml-0.2.1}/MANIFEST.in RENAMED
File without changes
{h5yaml-0.2.0 → h5yaml-0.2.1}/pyproject.toml RENAMED
File without changes
{h5yaml-0.2.0 → h5yaml-0.2.1}/src/h5yaml/__init__.py RENAMED
File without changes