h5yaml 0.0.5__tar.gz → 0.1.1__tar.gz

h5yaml-0.1.1/.pre-commit-config.yaml

@@ -0,0 +1,11 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.12.8
+    hooks:
+      - id: ruff-check
+        args: [ --fix ]
+      - id: ruff-format
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: check-yaml

{h5yaml-0.0.5 → h5yaml-0.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: h5yaml
-Version: 0.0.5
+Version: 0.1.1
 Summary: Use YAML configuration file to generate HDF5/netCDF4 formated files.
 Project-URL: Homepage, https://github.com/rmvanhees/h5_yaml
 Project-URL: Source, https://github.com/rmvanhees/h5_yaml
@@ -9,21 +9,21 @@ Author-email: Richard van Hees <r.m.van.hees@sron.nl>
 License-Expression: BSD-3-Clause
 License-File: LICENSE
 Keywords: HDF5,YAML,netCDF4
-Classifier: Development Status :: 4 - Beta
+Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
 Classifier: Operating System :: OS Independent
 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
 Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
 Classifier: Topic :: Scientific/Engineering :: Atmospheric Science
-Requires-Python: >=3.9
-Requires-Dist: h5py>=3.13
+Requires-Python: >=3.10
+Requires-Dist: h5py>=3.11
 Requires-Dist: netcdf4>=1.7
-Requires-Dist: numpy>=2.2
+Requires-Dist: numpy>=1.26.4
 Requires-Dist: pyyaml>=6.0
 Description-Content-Type: text/markdown
 
@@ -133,10 +133,11 @@ The YAML file should be structured as follows:
    Alternatively, provide a list with names of YAML files which contain the definitions
    of the compounds.
 
+   ```
    compounds:
      - h5_nomhk_tm.yaml
      - h5_science_hk.yaml
-
+   ```
  * The 'variables' are defined by their data-type ('_dtype') and dimensions ('_dims'),
    and optionally chunk sizes ('_chunks'), compression ('_compression'), variable length
    ('_vlen'). In addition, each variable can have as many attributes as you like,

{h5yaml-0.0.5 → h5yaml-0.1.1}/README.md

@@ -104,10 +104,11 @@ The YAML file should be structured as follows:
    Alternatively, provide a list with names of YAML files which contain the definitions
    of the compounds.
 
+   ```
    compounds:
      - h5_nomhk_tm.yaml
      - h5_science_hk.yaml
-
+   ```
  * The 'variables' are defined by their data-type ('_dtype') and dimensions ('_dims'),
    and optionally chunk sizes ('_chunks'), compression ('_compression'), variable length
    ('_vlen'). In addition, each variable can have as many attributes as you like,

{h5yaml-0.0.5 → h5yaml-0.1.1}/pyproject.toml

@@ -14,18 +14,18 @@ license = "BSD-3-Clause"
 authors = [
   {name = "Richard van Hees", email = "r.m.van.hees@sron.nl"}
 ]
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 classifiers = [
-   "Development Status :: 4 - Beta",
+   "Development Status :: 5 - Production/Stable",
    "Intended Audience :: Developers",
    "Intended Audience :: Science/Research",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3 :: Only",
-   "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
+   "Programming Language :: Python :: 3.14",
    "Topic :: Scientific/Engineering :: Atmospheric Science",
 ]
 keywords = [
@@ -35,9 +35,9 @@ dynamic = [
    "version",
 ]
 dependencies = [
-   "h5py>=3.13",
+   "h5py>=3.11",
    "netCDF4>=1.7",
-   "numpy>=2.2",
+   "numpy>=1.26.4",
    "pyYAML>=6.0",
 ]
 
@@ -94,7 +94,6 @@ select = [
    "RUF",  # Ruff Specific
    "UP",   # pyupgrade
 ]
-ignore = ["D203", "D213"]
 
-[lint.pydocstyle]
+[tool.ruff.lint.pydocstyle]
 convention = "pep257"

{h5yaml-0.0.5 → h5yaml-0.1.1}/src/h5yaml/Data/h5_testing.yaml

@@ -45,7 +45,10 @@ dimensions:
 # - compound elements must have a data-type, and can have a unit and long_name 
 compounds:
   stats_dtype:
-    time: [u8, seconds since 1970-01-01T00:00:00, timestamp]
+    time:
+      - u8
+      - seconds since 1970-01-01T00:00:00
+      - timestamp
     index: [u2, '1', index]
     tbl_id: [u1, '1', binning id]
     saa: [u1, '1', saa-flag]

{h5yaml-0.0.5 → h5yaml-0.1.1}/src/h5yaml/Data/nc_testing.yaml

@@ -45,7 +45,10 @@ dimensions:
 # - compound elements must have a data-type, and can have a unit and long_name 
 compounds:
   stats_dtype:
-    time: [u8, seconds since 1970-01-01T00:00:00, timestamp]
+    time:
+      - u8
+      - seconds since 1970-01-01T00:00:00
+      - timestamp
     index: [u2, '1', index]
     tbl_id: [u1, '1', binning id]
     saa: [u1, '1', saa-flag]

{h5yaml-0.0.5 → h5yaml-0.1.1}/src/h5yaml/yaml_h5.py

@@ -23,7 +23,43 @@ import numpy as np
 from h5yaml.conf_from_yaml import conf_from_yaml
 from h5yaml.lib.chunksizes import guess_chunks
 
+
 # - helper function ------------------------------------
+def adjust_attr(attr_key: str, attr_val: np.ndarray, attr_dtype: str) -> np.ndarray:
+    """..."""
+    if attr_key in ("valid_min", "valid_max", "valid_range"):
+        match attr_dtype:
+            case "i1":
+                res = np.int8(attr_val)
+            case "i2":
+                res = np.int16(attr_val)
+            case "i4":
+                res = np.int32(attr_val)
+            case "i8":
+                res = np.int64(attr_val)
+            case "u1":
+                res = np.uint8(attr_val)
+            case "u2":
+                res = np.uint16(attr_val)
+            case "u4":
+                res = np.uint32(attr_val)
+            case "u8":
+                res = np.uint64(attr_val)
+            case "f2":
+                res = np.float16(attr_val)
+            case "f4":
+                res = np.float32(attr_val)
+            case "f8":
+                res = np.float64(attr_val)
+            case _:
+                res = attr_val
+
+        return res
+
+    if attr_key == "flag_values":
+        return np.array(attr_val, dtype="u1")
+
+    return attr_val
 
 
 # - class definition -----------------------------------
@@ -82,6 +118,8 @@ class H5Yaml:
                 )
                 if "_values" in val:
                     dset[:] = val["_values"]
+                elif "_range" in val:
+                    dset[:] = np.arange(*val["_range"], dtype=val["_dtype"])
 
             dset.make_scale(
                 Path(key).name
@@ -89,36 +127,8 @@ class H5Yaml:
                 else "This is a netCDF dimension but not a netCDF variable."
             )
             for attr, attr_val in val.items():
-                if attr.startswith("_"):
-                    continue
-                if attr in ("valid_min", "valid_max"):
-                    match val["_dtype"]:
-                        case "i1":
-                            dset.attrs[attr] = np.int8(attr_val)
-                        case "i2":
-                            dset.attrs[attr] = np.int16(attr_val)
-                        case "i4":
-                            dset.attrs[attr] = np.int32(attr_val)
-                        case "i8":
-                            dset.attrs[attr] = np.int64(attr_val)
-                        case "u1":
-                            dset.attrs[attr] = np.uint8(attr_val)
-                        case "u2":
-                            dset.attrs[attr] = np.uint16(attr_val)
-                        case "u4":
-                            dset.attrs[attr] = np.uint32(attr_val)
-                        case "u8":
-                            dset.attrs[attr] = np.uint64(attr_val)
-                        case "f2":
-                            dset.attrs[attr] = np.float16(attr_val)
-                        case "f4":
-                            dset.attrs[attr] = np.float32(attr_val)
-                        case "f8":
-                            dset.attrs[attr] = np.float64(attr_val)
-                        case _:
-                            dset.attrs[attr] = attr_val
-                else:
-                    dset.attrs[attr] = attr_val
+                if not attr.startswith("_"):
+                    dset.attrs[attr] = adjust_attr(attr, attr_val, val["_dtype"])
 
     def __compounds(self: H5Yaml, fid: h5py.File) -> dict[str, str | int | float]:
         """Add compound datatypes to HDF5 product."""
@@ -192,9 +202,8 @@ class H5Yaml:
                     fillvalue=fillvalue,
                 )
                 for attr, attr_val in val.items():
-                    if attr.startswith("_"):
-                        continue
-                    dset.attrs[attr] = attr_val
+                    if not attr.startswith("_"):
+                        dset.attrs[attr] = adjust_attr(attr, attr_val, val["_dtype"])
                 continue
 
             n_udim = 0
@@ -263,38 +272,8 @@ class H5Yaml:
                 dset.dims[ii].attach_scale(fid[coord])
 
             for attr, attr_val in val.items():
-                if attr.startswith("_"):
-                    continue
-                if attr in ("valid_min", "valid_max"):
-                    match val["_dtype"]:
-                        case "i1":
-                            dset.attrs[attr] = np.int8(attr_val)
-                        case "i2":
-                            dset.attrs[attr] = np.int16(attr_val)
-                        case "i4":
-                            dset.attrs[attr] = np.int32(attr_val)
-                        case "i8":
-                            dset.attrs[attr] = np.int64(attr_val)
-                        case "u1":
-                            dset.attrs[attr] = np.uint8(attr_val)
-                        case "u2":
-                            dset.attrs[attr] = np.uint16(attr_val)
-                        case "u4":
-                            dset.attrs[attr] = np.uint32(attr_val)
-                        case "u8":
-                            dset.attrs[attr] = np.uint64(attr_val)
-                        case "f2":
-                            dset.attrs[attr] = np.float16(attr_val)
-                        case "f4":
-                            dset.attrs[attr] = np.float32(attr_val)
-                        case "f8":
-                            dset.attrs[attr] = np.float64(attr_val)
-                        case _:
-                            dset.attrs[attr] = attr_val
-                elif attr == "flag_values":
-                    dset.attrs[attr] = np.array(attr_val, dtype="u1")
-                else:
-                    dset.attrs[attr] = attr_val
+                if not attr.startswith("_"):
+                    dset.attrs[attr] = adjust_attr(attr, attr_val, val["_dtype"])
 
             if compounds is not None and val["_dtype"] in compounds:
                 if compounds[val["_dtype"]]["units"]:
@@ -318,7 +297,8 @@ class H5Yaml:
         """
         try:
             with h5py.File(l1a_name, "w") as fid:
-                self.__groups(fid)
+                if "groups" in self.h5_def:
+                    self.__groups(fid)
                 self.__dimensions(fid)
                 self.__variables(fid, self.__compounds(fid))
         except PermissionError as exc: