obsarray 1.0.1__tar.gz → 1.0.3__tar.gz

{obsarray-1.0.1/obsarray.egg-info → obsarray-1.0.3}/PKG-INFO

@@ -1,20 +1,14 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: obsarray
-Version: 1.0.1
+Version: 1.0.3
 Summary: Measurement data handling in Python
-Home-page: https://github.com/comet-toolkit/obsarray
-Author: CoMet Toolkit Team
-Author-email: team@comet-toolkit.org
-License: GPLv3
-Classifier: Development Status :: 2 - Pre-Alpha
-Classifier: Programming Language :: Python
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
+Author-email: CoMet Toolkit Team <team@comet-toolkit.org>
+Project-URL: Homepage, https://github.com/comet-toolkit/obsarray
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: comet_maths
-Requires-Dist: netcdf4==1.6.5
+Requires-Dist: netcdf4
 Requires-Dist: xarray
 Provides-Extra: dev
 Requires-Dist: pre-commit; extra == "dev"
@@ -24,6 +18,7 @@ Requires-Dist: sphinx_design; extra == "dev"
 Requires-Dist: sphinx_book_theme; extra == "dev"
 Requires-Dist: ipython; extra == "dev"
 Requires-Dist: sphinx_autosummary_accessors; extra == "dev"
+Dynamic: license-file
 
 # obsarray: Measurement uncertainty handling in Python
 

obsarray-1.0.3/docs/conf.py

@@ -0,0 +1,181 @@
+#!/usr/bin/env python
+#
+# obsarray documentation build configuration file, created by
+# cookiecutter
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+
+# If extensions (or modules to document with autodoc) are in another
+# directory, add these directories to sys.path here. If the directory is
+# relative to the documentation root, use os.path.abspath to make it
+# absolute, like shown here.
+
+import sphinx_autosummary_accessors
+import obsarray
+
+project_title = "obsarray".replace("_", " ").title()
+
+
+# -- General configuration ---------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Attempt to make links automatially
+default_role = "code"
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+# CFAB added napolean to support google-style docstrings
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.napoleon",
+    "IPython.sphinxext.ipython_directive",
+    "IPython.sphinxext.ipython_console_highlighting",
+    "sphinx_design",
+    "sphinx_autosummary_accessors",
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates", sphinx_autosummary_accessors.templates_path]
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = ".rst"
+
+# The master toctree document.
+master_doc = "index"
+
+# General information about the project.
+project = project_title
+copyright = "CoMet Toolkit Team"
+author = "CoMet Toolkit Team"
+
+# The version info for the project you're documenting, acts as replacement
+# for |version| and |release|, also used in various other places throughout
+# the built documents.
+#
+# The short X.Y version.
+version = obsarray.__version__
+# The full version, including alpha/beta/rc tags.
+release = obsarray.__version__
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This patterns also effect to html_static_path and html_extra_path
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = "sphinx"
+
+rst_prolog = """
+.. role:: python(code)
+    :language: python
+    :class: highlight
+"""
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = False
+
+
+# -- Options for HTML output -------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "sphinx_book_theme"
+
+# Theme options are theme-specific and customize the look and feel of a
+# theme further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+html_logo = "figs/obsarray.png"
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ["_static"]
+
+# -- Options for HTMLHelp output ---------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = "obsarraydoc"
+
+
+# -- Options for LaTeX output ------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, documentclass
+# [howto, manual, or own class]).
+latex_documents = [
+    (
+        master_doc,
+        "user_manual.tex",
+        "{} Documentation".format(project_title),
+        "CoMet Toolkit Team",
+        "manual",
+    ),
+]
+
+
+# -- Options for manual page output ------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [(master_doc, "obsarray", "obsarray Documentation", [author], 1)]
+
+
+# -- Options for Texinfo output ----------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (
+        master_doc,
+        "obsarray",
+        "obsarray Documentation",
+        author,
+        "obsarray",
+        "Extension to xarray for handling uncertainty quantified observation data",
+        "Miscellaneous",
+    ),
+]

obsarray-1.0.3/notebook/test_register_err_corr_form.py

@@ -0,0 +1,45 @@
+from obsarray.err_corr import register_err_corr_form, BaseErrCorrForm
+import xarray as xr
+import numpy as np
+import obsarray
+
+
+@register_err_corr_form("new")
+class NewForm(BaseErrCorrForm):
+
+    form = "new"
+    is_systematic = True
+
+    def build_matrix(self, idx: np.ndarray) -> np.ndarray:
+        return "abc"
+
+
+# ds = xr.open_dataset("obs_example.nc")
+#
+# ds.unc["temperature"]["u_sys_temperature"] = (
+#     ["x", "y", "time"],
+#     ds.temperature * 0.03,
+#     {
+#         "err_corr": [
+#             {
+#                 "dim": "x",
+#                 "form": "new",
+#                 "params": [],
+#             },
+#             {
+#                 "dim": "y",
+#                 "form": "systematic",
+#                 "params": [],
+#             },
+#             {
+#                 "dim": "time",
+#                 "form": "systematic",
+#                 "params": [],
+#             },
+#         ]
+#     },
+# )
+#
+# p = ds.unc["temperature"]["u_sys_temperature"]
+#
+# pass

{obsarray-1.0.1 → obsarray-1.0.3}/obsarray/__init__.py

@@ -9,6 +9,7 @@ from obsarray.err_corr import err_corr_forms
 from obsarray.templater.template_util import create_ds
 from obsarray.templater.dstemplater import DSTemplater
 from obsarray.templater.dswriter import DSWriter
+from obsarray.utils import append_names
 
 __version__ = get_versions()["version"]
 del get_versions

{obsarray-1.0.1 → obsarray-1.0.3}/obsarray/_version.py

@@ -1,5 +1,5 @@
 
-# This file was generated by 'versioneer.py' (0.18) from
+# This file was generated by 'versioneer.py' (0.29) from
 # revision-control system data, or from the parent directory name of an
 # unpacked source archive. Distribution tarballs contain a pre-generated copy
 # of this file.
@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2024-10-17T11:56:22+0100",
+ "date": "2025-06-22T11:46:36+0200",
  "dirty": false,
  "error": null,
- "full-revisionid": "e69e81f9deaa8c268e07f521788251875a87ef1a",
- "version": "v1.0.1"
+ "full-revisionid": "48598121962220e8e42df0515693a450e732585c",
+ "version": "1.0.3"
 }
 '''  # END VERSION_JSON
 

{obsarray-1.0.1 → obsarray-1.0.3}/obsarray/flag_accessor.py

@@ -194,12 +194,12 @@ class FlagVariable:
         )
 
         if flag_meaning not in flag_meanings:
-            self._obj[self._flag_var_name].attrs = (
-                DatasetUtil.add_flag_meaning_to_attrs(
-                    self._obj[self._flag_var_name].attrs,
-                    flag_meaning,
-                    self._obj[self._flag_var_name].dtype,
-                )
+            self._obj[
+                self._flag_var_name
+            ].attrs = DatasetUtil.add_flag_meaning_to_attrs(
+                self._obj[self._flag_var_name].attrs,
+                flag_meaning,
+                self._obj[self._flag_var_name].dtype,
             )
 
         self[flag_meaning][:] = flag_value

{obsarray-1.0.1 → obsarray-1.0.3}/obsarray/templater/dataset_util.py

@@ -454,15 +454,15 @@ class DatasetUtil:
         if dtype == numpy.int8:
             return numpy.int8(-127)
         if dtype == numpy.uint8:
-            return numpy.uint8(-1)
+            return numpy.iinfo(numpy.uint8).max
         elif dtype == numpy.int16:
             return numpy.int16(-32767)
         elif dtype == numpy.uint16:
-            return numpy.uint16(-1)
+            return numpy.iinfo(numpy.uint16).max
         elif dtype == numpy.int32:
             return numpy.int32(-2147483647)
         elif dtype == numpy.uint32:
-            return numpy.uint32(-1)
+            return numpy.iinfo(numpy.uint32).max
         elif dtype == numpy.int64:
             return numpy.int64(-9223372036854775806)
         elif dtype == numpy.float32:
@@ -507,7 +507,7 @@ class DatasetUtil:
             ds[flag_meaning] = DatasetUtil.create_variable(
                 list(da.shape), bool, dim_names=list(da.dims)
             )
-            ds[flag_meaning] = (da & flag_mask).astype(bool)
+            ds[flag_meaning] = (da.astype(int) & flag_mask).astype(bool)
 
         return ds
 

{obsarray-1.0.1 → obsarray-1.0.3}/obsarray/test/test_unc_accessor.py

@@ -34,7 +34,7 @@ def compare_err_corr_form(self, form, exp_form):
     self.assertCountEqual(form._unc_var_name, exp_form._unc_var_name)
 
 
-def create_ds():
+def create_ds(var_suffix="", dim_suffix="", coord_dim_suffix_extra=""):
     np.random.seed(0)
     temperature = 15 + 8 * np.random.randn(2, 2, 3)
     u_r_temperature = temperature * 0.02
@@ -47,42 +47,59 @@ def create_ds():
     reference_time = pd.Timestamp("2014-09-05")
 
     ds = xr.Dataset(
-        data_vars=dict(
-            temperature=(["x", "y", "time"], temperature, {"units": "K"}),
-        ),
-        coords=dict(
-            lon=(["x", "y"], lon),
-            lat=(["x", "y"], lat),
-            time=time,
-            reference_time=reference_time,
-        ),
+        data_vars={
+            "temperature"
+            + var_suffix: (
+                [
+                    "x" + dim_suffix,
+                    "y" + dim_suffix,
+                    "time" + dim_suffix + coord_dim_suffix_extra,
+                ],
+                temperature,
+                {"units": "K"},
+            ),
+        },
+        coords={
+            "lon" + var_suffix: (["x" + dim_suffix, "y" + dim_suffix], lon),
+            "lat" + var_suffix: (["x" + dim_suffix, "y" + dim_suffix], lat),
+            "time" + var_suffix: ("time" + dim_suffix + coord_dim_suffix_extra, time),
+            "reference_time": reference_time,
+        },
         attrs=dict(description="Weather related data."),
     )
 
-    ds.unc["temperature"]["u_ran_temperature"] = (
-        ["x", "y", "time"],
+    ds.unc["temperature" + var_suffix]["u_ran_temperature" + var_suffix] = (
+        [
+            "x" + dim_suffix,
+            "y" + dim_suffix,
+            "time" + dim_suffix + coord_dim_suffix_extra,
+        ],
         temperature * 0.05,
         {"units": "K", "pdf_shape": "gaussian"},
     )
 
-    ds.unc["temperature"]["u_sys_temperature"] = (
-        ["x", "y", "time"],
+    ds.unc["temperature" + var_suffix]["u_sys_temperature" + var_suffix] = (
+        [
+            "x" + dim_suffix,
+            "y" + dim_suffix,
+            "time" + dim_suffix + coord_dim_suffix_extra,
+        ],
         temperature * 0.03,
         {
             "units": "K",
             "err_corr": [
                 {
-                    "dim": "x",
+                    "dim": "x" + dim_suffix,
                     "form": "systematic",
                     "params": [],
                 },
                 {
-                    "dim": "y",
+                    "dim": "y" + dim_suffix,
                     "form": "systematic",
                     "params": [],
                 },
                 {
-                    "dim": "time",
+                    "dim": "time" + dim_suffix + coord_dim_suffix_extra,
                     "form": "systematic",
                     "params": [],
                 },
@@ -91,19 +108,26 @@ def create_ds():
         },
     )
 
-    ds.unc["temperature"]["u_str_temperature"] = (
-        ["x", "y", "time"],
+    ds.unc["temperature" + var_suffix]["u_str_temperature" + var_suffix] = (
+        [
+            "x" + dim_suffix,
+            "y" + dim_suffix,
+            "time" + dim_suffix + coord_dim_suffix_extra,
+        ],
         temperature * 0.1,
         {
             "units": "K",
             "err_corr": [
                 {
-                    "dim": ["x", "time"],
+                    "dim": [
+                        "x" + dim_suffix,
+                        "time" + dim_suffix + coord_dim_suffix_extra,
+                    ],
                     "form": "err_corr_matrix",
-                    "params": ["err_corr_str_temperature"],
+                    "params": ["err_corr_str_temperature" + var_suffix],
                 },
                 {
-                    "dim": "y",
+                    "dim": "y" + dim_suffix,
                     "form": "systematic",
                     "params": [],
                 },
@@ -112,8 +136,8 @@ def create_ds():
         },
     )
 
-    ds["err_corr_str_temperature"] = (
-        ["x.time", "x.time"],
+    ds["err_corr_str_temperature" + var_suffix] = (
+        ["x.time" + dim_suffix, "x.time" + dim_suffix],
         np.ones(
             (
                 temperature.shape[0] * temperature.shape[2],
@@ -740,6 +764,44 @@ class TestUncertainty(unittest.TestCase):
         exp_ecm = xr.DataArray(np.ones((12, 12)), dims=["x.y.time", "x.y.time"])
         xr.testing.assert_equal(ecm, exp_ecm)
 
+    def test_rename_vars(self):
+        var_suffix = "_test"
+        input_ds = create_ds()
+
+        ds = input_ds.unc.rename(
+            {
+                "temperature": "temperature" + var_suffix,
+                "lon": "lon" + var_suffix,
+                "lat": "lat" + var_suffix,
+                "time": "time" + var_suffix,
+                "u_ran_temperature": "u_ran_temperature" + var_suffix,
+                "u_str_temperature": "u_str_temperature" + var_suffix,
+                "u_sys_temperature": "u_sys_temperature" + var_suffix,
+                "err_corr_str_temperature": "err_corr_str_temperature" + var_suffix,
+            }
+        )
+
+        exp_ds = create_ds(var_suffix=var_suffix, coord_dim_suffix_extra=var_suffix)
+
+        xr.testing.assert_identical(ds, exp_ds)
+
+    def test_rename_dims(self):
+        dim_suffix = "_test"
+        input_ds = create_ds()
+
+        ds = input_ds.unc.rename_dims(
+            {
+                "x": "x" + dim_suffix,
+                "y": "y" + dim_suffix,
+                "time": "time" + dim_suffix,
+                "x.time": "x.time_test",
+            }
+        )
+
+        exp_ds = create_ds(dim_suffix=dim_suffix)
+
+        xr.testing.assert_identical(ds, exp_ds)
+
 
 if __name__ == "__main__":
     unittest.main()

obsarray-1.0.3/obsarray/test/test_utils.py

@@ -0,0 +1,169 @@
+"""test_utils - tests for obsarray.utils"""
+
+import unittest
+import numpy as np
+from obsarray import append_names, create_ds
+import xarray as xr
+
+__author__ = "Sam Hunt <sam.hunt@npl.co.uk>"
+__all__ = []
+
+
+def create_test_ds(suffix):
+    # define ds variables
+    template = {
+        "temperature"
+        + suffix: {
+            "dtype": np.float32,
+            "dim": ["x" + suffix, "y" + suffix, "time" + suffix],
+            "attributes": {
+                "units": "K",
+                "unc_comps": [
+                    "u_ran_temperature" + suffix,
+                    "u_sys_temperature" + suffix,
+                ],
+            },
+        },
+        "u_ran_temperature"
+        + suffix: {
+            "dtype": np.float32,
+            "dim": ["x" + suffix, "y" + suffix, "time" + suffix],
+            "attributes": {
+                "units": "K",
+                "err_corr": [
+                    {"dim": "x" + suffix, "form": "random", "params": [], "units": []},
+                    {"dim": "y" + suffix, "form": "random", "params": [], "units": []},
+                    {
+                        "dim": "time" + suffix,
+                        "form": "random",
+                        "params": [],
+                        "units": [],
+                    },
+                ],
+            },
+        },
+        "u_sys_temperature"
+        + suffix: {
+            "dtype": np.float32,
+            "dim": ["x" + suffix, "y" + suffix, "time" + suffix],
+            "attributes": {
+                "units": "K",
+                "err_corr": [
+                    {
+                        "dim": "x" + suffix,
+                        "form": "systematic",
+                        "params": [],
+                        "units": [],
+                    },
+                    {
+                        "dim": "y" + suffix,
+                        "form": "systematic",
+                        "params": [],
+                        "units": [],
+                    },
+                    {
+                        "dim": "time" + suffix,
+                        "form": "systematic",
+                        "params": [],
+                        "units": [],
+                    },
+                ],
+            },
+        },
+        "pressure"
+        + suffix: {
+            "dtype": np.float32,
+            "dim": ["x" + suffix, "y" + suffix, "time" + suffix],
+            "attributes": {"units": "Pa", "unc_comps": ["u_str_pressure" + suffix]},
+        },
+        "u_str_pressure"
+        + suffix: {
+            "dtype": np.float32,
+            "dim": ["x" + suffix, "y" + suffix, "time" + suffix],
+            "attributes": {
+                "units": "Pa",
+                "err_corr": [
+                    {"dim": "x" + suffix, "form": "random", "params": [], "units": []},
+                    {
+                        "dim": "y" + suffix,
+                        "form": "err_corr_matrix",
+                        "params": "err_corr_str_pressure_y",
+                        "units": [],
+                    },
+                    {
+                        "dim": "time" + suffix,
+                        "form": "systematic",
+                        "params": [],
+                        "units": [],
+                    },
+                ],
+            },
+        },
+        "err_corr_str_pressure_y"
+        + suffix: {
+            "dtype": np.float32,
+            "dim": ["y" + suffix, "y" + suffix],
+            "attributes": {"units": ""},
+        },
+        "n_moles"
+        + suffix: {
+            "dtype": np.float32,
+            "dim": ["x" + suffix, "y" + suffix, "time" + suffix],
+            "attributes": {"units": "", "unc_comps": ["u_ran_n_moles" + suffix]},
+        },
+        "u_ran_n_moles"
+        + suffix: {
+            "dtype": np.float32,
+            "dim": ["x" + suffix, "y" + suffix, "time" + suffix],
+            "attributes": {
+                "units": "",
+                "err_corr": [
+                    {"dim": "x" + suffix, "form": "random", "params": [], "units": []},
+                    {"dim": "y" + suffix, "form": "random", "params": [], "units": []},
+                    {
+                        "dim": "time" + suffix,
+                        "form": "random",
+                        "params": [],
+                        "units": [],
+                    },
+                ],
+            },
+        },
+    }
+
+    # define dim_size_dict to specify size of arrays
+    dim_sizes = {"x" + suffix: 20, "y" + suffix: 30, "time" + suffix: 6}
+
+    # create dataset template
+    ds = create_ds(template, dim_sizes)
+
+    # populate with example data
+    ds["temperature" + suffix].values = 293 * np.ones((20, 30, 6))
+    ds["u_ran_temperature" + suffix].values = 1 * np.ones((20, 30, 6))
+    ds["u_sys_temperature" + suffix].values = 0.4 * np.ones((20, 30, 6))
+    ds["pressure" + suffix].values = 10**5 * np.ones((20, 30, 6))
+    ds["u_str_pressure" + suffix].values = 10 * np.ones((20, 30, 6))
+    ds["err_corr_str_pressure_y" + suffix].values = 0.5 * np.ones(
+        (30, 30)
+    ) + 0.5 * np.eye(30)
+    ds["n_moles" + suffix].values = 40 * np.ones((20, 30, 6))
+    ds["u_ran_n_moles" + suffix].values = 1 * np.ones((20, 30, 6))
+
+    ds.attrs["attr" + suffix] = "val"
+
+    return ds
+
+
+class TestAppendNames(unittest.TestCase):
+    def test_append_names(self):
+
+        input_ds = create_test_ds(suffix="")
+        ds = append_names(input_ds, "_test")
+
+        exp_ds = create_test_ds(suffix="_test")
+
+        xr.testing.assert_identical(ds, exp_ds)
+
+
+if __name__ == "__main__":
+    unittest.main()