obsarray 0.2.4__tar.gz → 0.2.5__tar.gz

{obsarray-0.2.4 → obsarray-0.2.5}/.gitignore

@@ -76,8 +76,8 @@ instance/
 .scrapy
 
 # Sphinx documentation
-docs/sphinx/_build/
-docs/sphinx/content/api
+docs/_build/
+docs/content/generated/
 
 # PyBuilder
 target/

{obsarray-0.2.4/obsarray.egg-info → obsarray-0.2.5}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.1
 Name: obsarray
-Version: 0.2.4
-Summary: Measurement uncertainty handling in Python
+Version: 0.2.5
+Summary: Measurement data handling in Python
 Home-page: https://github.com/comet-toolkit/obsarray
 Author: CoMet Toolkit Team
 Author-email: team@comet-toolkit.org
@@ -9,9 +9,10 @@ License: GPLv3
 Platform: UNKNOWN
 Classifier: Development Status :: 2 - Pre-Alpha
 Classifier: Programming Language :: Python
-Classifier: Programming Language :: Python :: 3.6
-Classifier: Programming Language :: Python :: 3.7
 Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
 Provides-Extra: dev
 License-File: LICENSE
 

obsarray-0.2.5/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/comet_logo.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-0.2.5/docs/index.rst

@@ -0,0 +1,66 @@
+obsarray: Measurement data handling in Python
+=============================================
+
+**obsarray** is an extension to `xarray <https://docs.xarray.dev/en/stable/>`_ to support defining, storing and interfacing with measurement data - in particular, measurement uncertainty information using standardised metadata. It is designed to work well with `netCDF <https://www.unidata.ucar.edu/software/netcdf/>`_ files and for the Earth Observation community.
+
+**obsarray** is part of the `CoMet Toolkit <https://www.comet-toolkit.org>`_ (community metrology toolkit), and can combined with the  `punpy <https://punpy.readthedocs.io/en/latest/>`_ (propagating uncertainties in python) module for very simple propagation of defined data uncertainties through arbitrary python functions.
+
+.. grid:: 2
+    :gutter: 2
+
+    .. grid-item-card::  Quickstart Guide
+        :link: content/user/quickstart
+        :link-type: doc
+
+        New to *obsarray*? Check out the quickstart guide for an introduction.
+
+    .. grid-item-card::  User Guide
+        :link: content/user/user_guide
+        :link-type: doc
+
+        The user guide provides a documentation and examples how to use **obsarray** to handle measurement data.
+
+    .. grid-item-card::  API Reference
+        :link: content/user/api
+        :link-type: doc
+
+        The API Reference contains a description the **obsarray** API.
+
+    .. grid-item-card::  Developer Guide
+        :link: content/developer/developer_guide
+        :link-type: doc
+
+        Guide for contributing to **obsarray** (under development).
+
+
+Acknowledgements
+----------------
+
+obsarray has been developed by `Sam Hunt <https://github.com/shunt16>`_.
+
+The development has been funded by:
+
+* The UK's Department for Business, Energy and Industrial Strategy's (BEIS) National Measurement System (NMS) programme
+* The IDEAS-QA4EO project funded by the European Space Agency.
+
+
+Project status
+--------------
+
+obsarray is under active development. It is beta software.
+
+.. toctree::
+   :maxdepth: 2
+   :hidden:
+   :caption: For users
+
+   Quickstart <content/user/quickstart>
+   User Guide <content/user/user_guide>
+   API Reference <content/user/api>
+
+.. toctree::
+   :maxdepth: 2
+   :hidden:
+   :caption: For developers/contributors
+
+   Developer Guide <content/developer/developer_guide>

{obsarray-0.2.4 → obsarray-0.2.5}/obsarray/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2023-03-06T21:45:43+0000",
+ "date": "2024-02-14T16:24:15+0000",
  "dirty": false,
  "error": null,
- "full-revisionid": "f73bc4314bb5f5dca1e7ee619ae4c20527ed1d87",
- "version": "v0.2.4"
+ "full-revisionid": "a4c0efeceef26dd8201830bc88caab5689f25595",
+ "version": "v0.2.5"
 }
 '''  # END VERSION_JSON
 

{obsarray-0.2.4 → obsarray-0.2.5}/obsarray/flag_accessor.py

@@ -54,7 +54,7 @@ class Flag:
         """
 
         # update slice
-        self._sli = self.expand_sli(sli)
+        self._sli = self._expand_sli(sli)
 
         return self
 
@@ -66,7 +66,7 @@ class Flag:
         :param flag_value: flag value as a single value boolean to apply to all data or boolean mask array
         """
 
-        self._sli = self.expand_sli(sli)
+        self._sli = self._expand_sli(sli)
 
         flag_meanings, flag_masks = DatasetUtil.unpack_flag_attrs(
             self._obj[self._flag_var_name].attrs
@@ -78,11 +78,11 @@ class Flag:
         # if boolean to apply to all data
         if isinstance(flag_value, bool):
             if flag_value:
-                self._obj[self._flag_var_name][self._sli].values[:] = (
+                self._obj[self._flag_var_name].values[self._sli] = (
                     self._obj[self._flag_var_name][self._sli].values | flag_mask
                 )
             else:
-                self._obj[self._flag_var_name][self._sli].values[:] = (
+                self._obj[self._flag_var_name].values[self._sli] = (
                     self._obj[self._flag_var_name][self._sli].values & ~flag_mask
                 )
 
@@ -94,15 +94,15 @@ class Flag:
             i_true = np.where(flag_value == True)
             i_false = np.where(flag_value == False)
 
-            self._obj[self._flag_var_name][self._sli].values[i_true] = (
+            self._obj[self._flag_var_name][self._sli].values[i_true] = np.array(
                 self._obj[self._flag_var_name][self._sli].values[i_true] | flag_mask
             )
 
-            self._obj[self._flag_var_name][self._sli].values[i_false] = (
+            self._obj[self._flag_var_name][self._sli].values[i_false] = np.array(
                 self._obj[self._flag_var_name][self._sli].values[i_false] & ~flag_mask
             )
 
-    def expand_sli(self, sli: Optional[tuple] = None) -> tuple:
+    def _expand_sli(self, sli: Optional[tuple] = None) -> tuple:
         """
         Function to expand the provided sli so that it always has the right number of dimensions
 
@@ -114,9 +114,12 @@ class Flag:
         if sli is None:
             out_sli = tuple([slice(None)] * self._obj[self._flag_var_name].ndim)
 
+        # Otherwise, set each : dimension to slice(None)
+        # E.g. if providing [0] for a variable with 3 dimensions, this becomes
+        # [0,slice(None),slice(None)]
         else:
             out_sli = list([slice(None)] * self._obj[self._flag_var_name].ndim)
-            sli_list = list(sli)
+            sli_list = list(sli) if isinstance(sli, tuple) else [sli]
             for i in range(len(sli_list)):
                 if not sli_list[i] == ":":
                     out_sli[i] = sli_list[i]
@@ -268,6 +271,8 @@ class FlagVariable:
 
         return flag_meanings
 
+    # todo - add return set flags - array of objects, where object is list of set flags
+
 
 @xr.register_dataset_accessor("flag")
 class FlagAccessor(object):
@@ -435,325 +440,3 @@ class FlagAccessor(object):
 
 if __name__ == "__main__":
     pass
-
-
-class DatasetUtil2:
-    @staticmethod
-    def create_flags_variable(dim_sizes, meanings, dim_names=None, attributes=None):
-        """
-        Return default empty 1d xarray flag Variable
-
-        :type dim_sizes: list
-        :param dim_sizes: dimension sizes as ints, i.e. [dim1_size, dim2_size, dim3_size] (e.g. [2,3,5])
-
-        :type attributes: dict
-        :param attributes: (optional) dictionary of variable attributes, e.g. standard_name
-
-        :type dim_names: list
-        :param dim_names: (optional) dimension names as strings, i.e. ["dim1_name", "dim2_name", "dim3_size"]
-
-        :return: Default empty flag vector variable
-        :rtype: xarray.Variable
-        """
-
-        n_masks = len(meanings)
-
-        data_type = DatasetUtil.return_flags_dtype(n_masks)
-
-        variable = DatasetUtil.create_variable(
-            dim_sizes,
-            data_type,
-            dim_names=dim_names,
-            attributes=attributes,
-        )
-
-        #initialise flags to zero (instead of fillvalue)
-        variable.values=0*variable.values
-
-        # add flag attributes
-        variable.attrs["flag_meanings"] = (
-            str(meanings)[1:-1].replace("'", "").replace(",", "")
-        )
-        variable.attrs["flag_masks"] = str([2 ** i for i in range(0, n_masks)])[1:-1]
-
-        # todo - make sure flags can't have units
-
-        return variable
-
-    @staticmethod
-    def return_flags_dtype(n_masks):
-        """
-        Return required flags array data type
-
-        :type n_masks: int
-        :param n_masks: number of masks required in flag array
-
-        :return: data type
-        :rtype: dtype
-        """
-
-        if n_masks <= 8:
-            return np.int8
-        elif n_masks <= 16:
-            return np.int16
-        elif n_masks <= 32:
-            return np.int32
-        else:
-            return np.int64
-
-    @staticmethod
-    def add_encoding(
-        variable, dtype, scale_factor=1.0, offset=0.0, fill_value=None, chunksizes=None
-    ):
-        """
-        Add encoding to xarray Variable to apply when writing netCDF files
-
-        :type variable: xarray.Variable
-        :param variable: data variable
-
-        :type dtype: type
-        :param dtype: numpy data type
-
-        :type scale_factor: float
-        :param scale_factor: variable scale factor
-
-        :type offset: float
-        :param offset: variable offset value
-
-        :type fill_value: int/float
-        :param fill_value: (optional) fill value
-
-        :type chunksizes: float
-        :param chunksizes: (optional) chucksizes
-        """
-
-        # todo - make sure flags can't have encoding added
-
-        encoding_dict = {
-            "dtype": dtype,
-            "scale_factor": scale_factor,
-            "add_offset": offset,
-        }
-
-        if chunksizes is not None:
-            encoding_dict.update({"chunksizes": chunksizes})
-
-        if fill_value is not None:
-            encoding_dict.update({"_FillValue": fill_value})
-
-        variable.encoding = encoding_dict
-
-    @staticmethod
-    def get_default_fill_value(dtype):
-        """
-        Returns default fill_value for given data type
-
-        :type dtype: type
-        :param dtype: numpy dtype
-
-        :return: CF-conforming fill value
-        :rtype: fill_value
-        """
-
-        if dtype == np.int8:
-            return np.int8(-129)
-        if dtype == np.uint8:
-            return np.uint8(-1)
-        elif dtype == np.int16:
-            return np.int16(-32769)
-        elif dtype == np.uint16:
-            return np.uint16(-1)
-        elif dtype == np.int32:
-            return np.int32(-2147483649)
-        elif dtype == np.uint32:
-            return np.uint32(-1)
-        elif dtype == np.int64:
-            return np.int64(-9223372036854775808)
-        elif dtype == np.float32:
-            return np.float32(9.96921e36)
-        elif dtype == np.float64:
-            return np.float64(9.969209968386869e36)
-
-    @staticmethod
-    def _get_flag_encoding(da):
-        """
-        Returns flag encoding for flag type data array
-        :type da: xarray.DataArray
-        :param da: data array
-        :return: flag meanings
-        :rtype: list
-        :return: flag masks
-        :rtype: list
-        """
-
-        try:
-            flag_meanings = da.attrs["flag_meanings"].split()
-            flag_masks = [int(fm) for fm in da.attrs["flag_masks"].split(",")]
-        except KeyError:
-            raise KeyError(da.name + " not a flag variable")
-
-        return flag_meanings, flag_masks
-
-    @staticmethod
-    def unpack_flags(da):
-        """
-        Breaks down flag data array into dataset of boolean masks for each flag
-        :type da: xarray.DataArray
-        :param da: dataset
-        :return: flag masks
-        :rtype: xarray.Dataset
-        """
-
-        flag_meanings, flag_masks = DatasetUtil._get_flag_encoding(da)
-
-        ds = Dataset()
-        for flag_meaning, flag_mask in zip(flag_meanings, flag_masks):
-            ds[flag_meaning] = DatasetUtil.create_variable(
-                list(da.shape), bool, dim_names=list(da.dims)
-            )
-            ds[flag_meaning] = (da & flag_mask).astype(bool)
-
-        return ds
-
-    @staticmethod
-    def get_flags_mask_or(da, flags=None):
-        """
-        Returns boolean mask for set of flags, defined as logical or of flags
-
-        :type da: xarray.DataArray
-        :param da: dataset
-
-        :type flags: list
-        :param flags: list of flags (if unset all data flags selected)
-
-        :return: flag masks
-        :rtype: numpy.ndarray
-        """
-
-        flags_ds = DatasetUtil.unpack_flags(da)
-
-        flags = flags if flags is not None else flags_ds.variables
-        mask_flags = [flags_ds[flag].values for flag in flags]
-
-        return np.logical_or.reduce(mask_flags)
-
-    @staticmethod
-    def get_flags_mask_and(da, flags=None):
-        """
-        Returns boolean mask for set of flags, defined as logical and of flags
-
-        :type da: xarray.DataArray
-        :param da: dataset
-
-        :type flags: list
-        :param flags: list of flags (if unset all data flags selected)
-
-        :return: flag masks
-        :rtype: numpy.ndarray
-        """
-
-        flags_ds = DatasetUtil.unpack_flags(da)
-
-        flags = flags if flags is not None else flags_ds.variables
-        mask_flags = [flags_ds[flag].values for flag in flags]
-
-        return np.logical_and.reduce(mask_flags)
-
-    @staticmethod
-    def set_flag(da, flag_name, error_if_set=False):
-        """
-        Sets named flag for elements in data array
-        :type da: xarray.DataArray
-        :param da: dataset
-        :type flag_name: str
-        :param flag_name: name of flag to set
-        :type error_if_set: bool
-        :param error_if_set: raises error if chosen flag is already set for any element
-        """
-
-        set_flags = DatasetUtil.unpack_flags(da)[flag_name]
-
-        if np.any(set_flags == True) and error_if_set:
-            raise ValueError(
-                "Flag " + flag_name + " already set for variable " + da.name
-            )
-
-        # Find flag mask
-        flag_meanings, flag_masks = DatasetUtil._get_flag_encoding(da)
-        flag_bit = flag_meanings.index(flag_name)
-        flag_mask = flag_masks[flag_bit]
-
-        da.values = da.values | flag_mask
-
-        return da
-
-    @staticmethod
-    def unset_flag(da, flag_name, error_if_unset=False):
-        """
-        Unsets named flag for specified index of dataset variable
-        :type da: xarray.DataArray
-        :param da: data array
-        :type flag_name: str
-        :param flag_name: name of flag to unset
-        :type error_if_unset: bool
-        :param error_if_unset: raises error if chosen flag is already set at specified index
-        """
-
-        set_flags = DatasetUtil.unpack_flags(da)[flag_name]
-
-        if np.any(set_flags == False) and error_if_unset:
-            raise ValueError(
-                "Flag " + flag_name + " already set for variable " + da.name
-            )
-
-        # Find flag mask
-        flag_meanings, flag_masks = DatasetUtil._get_flag_encoding(da)
-        flag_bit = flag_meanings.index(flag_name)
-        flag_mask = flag_masks[flag_bit]
-
-        da.values = da.values & ~flag_mask
-
-        return da
-
-    @staticmethod
-    def get_set_flags(da):
-        """
-        Return list of set flags for single element data array
-        :type da: xarray.DataArray
-        :param da: single element data array
-        :return: set flags
-        :rtype: list
-        """
-
-        if da.shape != ():
-            raise ValueError("Must pass single element data array")
-
-        flag_meanings, flag_masks = DatasetUtil._get_flag_encoding(da)
-
-        set_flags = []
-        for flag_meaning, flag_mask in zip(flag_meanings, flag_masks):
-            if da & flag_mask:
-                set_flags.append(flag_meaning)
-
-        return set_flags
-
-    @staticmethod
-    def check_flag_set(da, flag_name):
-        """
-        Returns if flag for single element data array
-        :type da: xarray.DataArray
-        :param da: single element data array
-        :type flag_name: str
-        :param flag_name: name of flag to set
-        :return: set flags
-        :rtype: list
-        """
-
-        if da.shape != ():
-            raise ValueError("Must pass single element data array")
-
-        set_flags = DatasetUtil.get_set_flags(da)
-
-        if flag_name in set_flags:
-            return True
-        return False