cerbere/datamodel/abstractfeature.py

@@ -158,7 +158,7 @@ class AbstractFeature(cerbere.feature.feature.Feature):
         for field, values in content.items():
             if field not in GEOCOORDINATES:
                 if isinstance(values, Field):
-                    data_vars[values.name] = values.xarray()
+                    data_vars[values.name] = values.to_dataarray()
                 elif isinstance(values, (xr.DataArray, numpy.ndarray)):
                     data_vars[field] = (('lon', 'lat',), values)
                 else:
@@ -656,7 +656,7 @@ class AbstractFeature(cerbere.feature.feature.Feature):
                 * a :class:`xarray.DataArray`
         """
         if isinstance(values, Field):
-            xrdata = values.xarray()
+            xrdata = values.to_dataarray()
 
         elif isinstance(values, xr.DataArray):
             xrdata = values

cerbere/datamodel/field.py

@@ -185,7 +185,7 @@ class Field(newfield.Field):
         """
         return Field(data=xrdata)
 
-    def xarray(self):
+    def to_dataarray(self):
         """Return the field values a xarray DataArray"""
         if self.mapper is None:
             return self.array

cerbere/dataset/dataset.py

@@ -258,7 +258,7 @@ class Dataset(ABC):
             if isinstance(self._url, list) and mode in [WRITE_NEW, READ_WRITE]:
                 raise ValueError("A list of files is read only")
 
-            self.open(**kwargs)
+            self._open(**kwargs)
 
         elif isinstance(dataset, xr.Dataset):
             self.dataset = dataset
@@ -307,16 +307,16 @@ class Dataset(ABC):
 
         for var in data.keys():
             if isinstance(data[var], Field):
-                data[var] = to_dict(data[var].xarray)
+                data[var] = to_dict(data[var].to_dataarray)
 
         if 'coords' in data.keys():
             for var, value in data['coords'].items():
                 if isinstance(value, Field):
-                    data[var] = to_dict(value.xarray)
+                    data[var] = to_dict(value.to_dataarray)
         if 'data_vars' in data.keys():
             for var, value in data['data_vars'].items():
                 if isinstance(value, Field):
-                    data[var] = to_dict(value.xarray)
+                    data[var] = to_dict(value.to_dataarray)
 
         # create a dataset
         self.dataset = xr.Dataset.from_dict(data)
@@ -359,7 +359,7 @@ class Dataset(ABC):
         raise NotImplementedError
 
     @classmethod
-    def exists(cls, url):
+    def exists(cls, url: str) -> bool:
         """tests if `url` is an existing resource"""
         try:
             result = urlparse(url)
@@ -509,7 +509,7 @@ class Dataset(ABC):
         else:
             return xr.Dataset()
 
-    def open(self, **kwargs):
+    def _open(self, **kwargs):
         if self.is_opened():
             logging.warning("A file is already opened : {}".format(
                 self._url)
@@ -653,35 +653,26 @@ class Dataset(ABC):
         return tuple(self.get_field_dims(fieldname).values())
 
     @property
-    def _varnames(self):
-        """Returns the names of all the fields of the dataset.
-
-        Returns:
-            list<string>: list of field names
+    def _varnames(self) -> List[str]:
+        """List names of all the fields (including coordinates) of the dataset.
         """
         if isinstance(self.dataset, Dataset):
            return self.dataset._varnames
         return list(self.dataset.variables.keys())
 
     @property
-    def coordnames(self):
-        """Returns the names of the coordinate fields of the dataset.
-
-        Returns:
-            list<string>: list of field names
-        """
+    def coordnames(self) -> List[str]:
+        """List of names of the coordinate fields of the dataset."""
         if isinstance(self.dataset, Dataset):
            return self.dataset._coordnames
         return list(self.dataset.coords.keys())
 
 
     @property
-    def geocoords(self):
-        """
-        Return the geolocation fields
-        """
+    def geocoords(self) -> List['xarray.DataArray']:
+        """List of geolocation coordinates (as DataArray)"""
         if isinstance(self.dataset, Dataset):
-           return self.dataset.geocoords
+            return self.dataset.geocoords
         return [
             _ for _ in self.dataset.coords if _ in GEOCOORDINATES
         ]
@@ -736,7 +727,7 @@ class Dataset(ABC):
                 .format(field.name)
             )
         self.dataset = self.dataset.assign(
-            {field.name: field.xarray}
+            {field.name: field.to_dataarray}
         )
         field._attach_dataset(self)
 

cerbere/dataset/ghrsstncdataset.py

@@ -46,9 +46,9 @@ class GHRSSTNCDataset(NCDataset):
 
         self.__collection_id = None
 
-    def open(self, **kwargs):
+    def _open(self, **kwargs):
         # url needs to be opened first in order to guess default datamodel
-        super().open(**kwargs)
+        super()._open(**kwargs)
 
         if self._mode != 'w':
 

cerbere/feature/feature.py

@@ -82,7 +82,7 @@ class Feature(Dataset):
                 * a :class:`xarray.DataArray`
         """
         if isinstance(values, Field):
-            xrdata = values.xarray()
+            xrdata = values.to_dataarray()
 
         elif isinstance(values, xr.DataArray):
             xrdata = values

cerbere/mapper/ecmwf05ncfile.py

@@ -43,11 +43,11 @@ class ECMWF05NCFile(NCFile):
         super(ECMWF05NCFile, self).__init__(url=url,center_on_greenwhich=True, **kwargs)
         return
     
-    def open(self,
-             view=None,
-             datamodel=None,
-             datamodel_geolocation_dims=None):
-        handler = super(ECMWF05NCFile, self).open(view=view,datamodel='Grid',datamodel_geolocation_dims=datamodel_geolocation_dims)
+    def _open(self,
+              view=None,
+              datamodel=None,
+              datamodel_geolocation_dims=None):
+        handler = super(ECMWF05NCFile, self)._open(view=view, datamodel='Grid', datamodel_geolocation_dims=datamodel_geolocation_dims)
         return handler
     
     def get_fieldnames(self):

cerbere/mapper/ghrsstncfile.py

@@ -44,9 +44,9 @@ class GHRSSTNCFile(Dataset):
 
         self.__collection_id = None
 
-    def open(self, **kwargs):
+    def _open(self, **kwargs):
         # url needs to be opened first in order to guess default datamodel
-        super().open(**kwargs)
+        super()._open(**kwargs)
 
         # recompose and unpack time variable if required
         self._unsplit_time_coord(split_time=('time', 'sst_dtime'), unpack=True)

cerbere/mapper/gribfile.py

@@ -78,7 +78,7 @@ class GribFile(AbstractMapper):
         logging.debug("opening in mode : %s", self._mode)
         logging.debug("url : %s", url)
 #         print "START", url
-        self._handler = pygrib.open(url)
+        self._handler = pygrib._open(url)
 #         print "OPEN"
         # get list of fields
         self._handler.seek(0)

cerbere/mapper/gribfile_test.py

@@ -82,7 +82,7 @@ class GribFile(AbstractMapper):
         logging.debug("opening in mode : %s", self._mode)
         logging.debug("url : %s", url)
 #         print "START", url
-        self._handler = pygrib.open(url)
+        self._handler = pygrib._open(url)
 #         print "OPEN"
         # get list of fields
         self._handler.seek(0)

cerbere/mapper/test/checker.py

@@ -48,7 +48,7 @@ logging.info("")
 
 logging.info("Open file")
 f = classreader(url=infile)
-f.open()
+f._open()
 logging.info("OK")
 logging.info("")
 

cerbere/mapper/test/test_lecture_cfsr_grib.py

@@ -61,7 +61,7 @@ def test_lonlat(hh):
 # sensinle_heat = hh.read_values('shtfl')
 
 def recup_var_names_with_pygrib(ff):
-    grbs=pygrib.open(ff)
+    grbs=pygrib._open(ff)
     print dir(grbs)
     grbs.message(6).data()[1].shape
     for dodo in range(grbs.messages):

cerbere/mapper/test/test_safeolfile.py

@@ -22,7 +22,7 @@ elif 'S3A_OL_2_WRR' in fname or 'S3A_OL_2_WFR' in fname:
 ncf = SAFEOLFile(url=fname)
 
 print 'OPEN'
-ncf.open()
+ncf._open()
 
 print '\n\nFIELDS :'
 fields = ncf.get_fieldnames()

cerbere/mapper/test/test_safeslfile.py

@@ -61,7 +61,7 @@ else:
 
 
 print 'OPEN'
-ncf.open()
+ncf._open()
 
 print '\n\nFIELDS :'
 fields = ncf.get_fieldnames()

docs/api/index.rst → docs/api.rst

@@ -8,30 +8,68 @@ This page provides a summary of cerbere's API. For more details
 and examples, refer to the relevant chapters in the main part of the
 documentation.
 
-See also: :ref:`public api`
 
 Dataset
 =======
 
+The base class for ``Dataset`` objects, than can be imported from
+``cerbere.dataset.dataset`` module. All other classes in ``cerbere.dataset``
+package are derived from this class.
+
 Creating a dataset
 ------------------
+.. currentmodule:: cerbere.dataset.dataset
 
 .. autosummary::
    :toctree: generated/
 
-   Dataset
+    Dataset
 
 Attributes
 ----------
+.. autosummary::
+    :toctree: generated
+
+    Dataset.dims
+    Dataset.sizes
+    Dataset.geocoords
+    Dataset.coordnames
+    Dataset.attrs
+
+Other built-in datasets
+-----------------------
+.. currentmodule:: cerbere.dataset
 
 .. autosummary::
    :toctree: generated/
 
-   Dataset.dims
-   Dataset.sizes
-   Dataset.coords
-   Dataset.attrs
+    ncdataset.NCDataset
+    ghrsstncdataset.GHRSSTNCDataset
+
+Field
+=======
+
+Creating a field
+----------------
+.. currentmodule:: cerbere.dataset.field
 
+.. autosummary::
+    :toctree: generated
+
+   dataset.field.Field
 
 Feature
 =======
+
+Creating a feature
+------------------
+.. currentmodule:: cerbere.feature
+
+.. autosummary::
+    :toctree: generated
+
+    feature.Feature
+    trajectory.Trajectory
+    grid.Grid
+    swath.Swath
+    pointcollection.PointCollection

docs/api/Makefile

-# Makefile for Sphinx documentation
-#
-
-# You can set these variables from the command line.
-SPHINXOPTS    =
-SPHINXBUILD   = sphinx-build
-PAPER         =
-BUILDDIR      = _build
-
-# User-friendly check for sphinx-build
-ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
-$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
-endif
-
-# Internal variables.
-PAPEROPT_a4     = -D latex_paper_size=a4
-PAPEROPT_letter = -D latex_paper_size=letter
-ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
-# the i18n builder cannot share the environment and doctrees with the others
-I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
-
-.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
-
-help:
-	@echo "Please use \`make <target>' where <target> is one of"
-	@echo "  html       to make standalone HTML files"
-	@echo "  dirhtml    to make HTML files named index.html in directories"
-	@echo "  singlehtml to make a single large HTML file"
-	@echo "  pickle     to make pickle files"
-	@echo "  json       to make JSON files"
-	@echo "  htmlhelp   to make HTML files and a HTML help project"
-	@echo "  qthelp     to make HTML files and a qthelp project"
-	@echo "  devhelp    to make HTML files and a Devhelp project"
-	@echo "  epub       to make an epub"
-	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
-	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
-	@echo "  latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
-	@echo "  text       to make text files"
-	@echo "  man        to make manual pages"
-	@echo "  texinfo    to make Texinfo files"
-	@echo "  info       to make Texinfo files and run them through makeinfo"
-	@echo "  gettext    to make PO message catalogs"
-	@echo "  changes    to make an overview of all changed/added/deprecated items"
-	@echo "  xml        to make Docutils-native XML files"
-	@echo "  pseudoxml  to make pseudoxml-XML files for display purposes"
-	@echo "  linkcheck  to check all external links for integrity"
-	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
-
-clean:
-	rm -rf $(BUILDDIR)/*
-
-html:
-	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
-	@echo
-	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
-
-dirhtml:
-	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
-	@echo
-	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
-
-singlehtml:
-	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
-	@echo
-	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
-
-pickle:
-	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
-	@echo
-	@echo "Build finished; now you can process the pickle files."
-
-json:
-	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
-	@echo
-	@echo "Build finished; now you can process the JSON files."
-
-htmlhelp:
-	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
-	@echo
-	@echo "Build finished; now you can run HTML Help Workshop with the" \
-	      ".hhp project file in $(BUILDDIR)/htmlhelp."
-
-qthelp:
-	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
-	@echo
-	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
-	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
-	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/cerbere.qhcp"
-	@echo "To view the help file:"
-	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/cerbere.qhc"
-
-devhelp:
-	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
-	@echo
-	@echo "Build finished."
-	@echo "To view the help file:"
-	@echo "# mkdir -p $$HOME/.local/share/devhelp/cerbere"
-	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/cerbere"
-	@echo "# devhelp"
-
-epub:
-	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
-	@echo
-	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
-
-latex:
-	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
-	@echo
-	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
-	@echo "Run \`make' in that directory to run these through (pdf)latex" \
-	      "(use \`make latexpdf' here to do that automatically)."
-
-latexpdf:
-	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
-	@echo "Running LaTeX files through pdflatex..."
-	$(MAKE) -C $(BUILDDIR)/latex all-pdf
-	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
-
-latexpdfja:
-	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
-	@echo "Running LaTeX files through platex and dvipdfmx..."
-	$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
-	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
-
-text:
-	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
-	@echo
-	@echo "Build finished. The text files are in $(BUILDDIR)/text."
-
-man:
-	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
-	@echo
-	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
-
-texinfo:
-	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
-	@echo
-	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
-	@echo "Run \`make' in that directory to run these through makeinfo" \
-	      "(use \`make info' here to do that automatically)."
-
-info:
-	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
-	@echo "Running Texinfo files through makeinfo..."
-	make -C $(BUILDDIR)/texinfo info
-	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
-
-gettext:
-	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
-	@echo
-	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
-
-changes:
-	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
-	@echo
-	@echo "The overview file is in $(BUILDDIR)/changes."
-
-linkcheck:
-	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
-	@echo
-	@echo "Link check complete; look for any errors in the above output " \
-	      "or in $(BUILDDIR)/linkcheck/output.txt."
-
-doctest:
-	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
-	@echo "Testing of doctests in the sources finished, look at the " \
-	      "results in $(BUILDDIR)/doctest/output.txt."
-
-xml:
-	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
-	@echo
-	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
-
-pseudoxml:
-	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
-	@echo
-	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."

docs/api/cerbere.dataset.rst

-cerbere.dataset
-===============
-
-.. rubric:: Description
-
-.. automodule:: cerbere.dataset
-
-.. currentmodule:: cerbere.dataset
-
-
-
-

docs/api/cerbere.feature.rst

-cerbere.feature
-===============
-
-.. rubric:: Description
-
-.. automodule:: cerbere.feature
-
-.. currentmodule:: cerbere.feature
-
-
-
-

docs/api/index.rst~

-.. cerbere documentation master file, created by
-   sphinx-quickstart on Tue Dec 10 15:47:17 2013.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
-Welcome to cerbere's reference documentation!
-=============================================
-
-Contents:
-
-.. toctree::
-   :maxdepth: 4
-
-   cerbere
-   setup
-
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
-

docs/api/make.bat

-@ECHO OFF
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
-	set SPHINXBUILD=sphinx-build
-)
-set BUILDDIR=_build
-set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% .
-set I18NSPHINXOPTS=%SPHINXOPTS% .
-if NOT "%PAPER%" == "" (
-	set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS%
-	set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS%
-)
-
-if "%1" == "" goto help
-
-if "%1" == "help" (
-	:help
-	echo.Please use `make ^<target^>` where ^<target^> is one of
-	echo.  html       to make standalone HTML files
-	echo.  dirhtml    to make HTML files named index.html in directories
-	echo.  singlehtml to make a single large HTML file
-	echo.  pickle     to make pickle files
-	echo.  json       to make JSON files
-	echo.  htmlhelp   to make HTML files and a HTML help project
-	echo.  qthelp     to make HTML files and a qthelp project
-	echo.  devhelp    to make HTML files and a Devhelp project
-	echo.  epub       to make an epub
-	echo.  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter
-	echo.  text       to make text files
-	echo.  man        to make manual pages
-	echo.  texinfo    to make Texinfo files
-	echo.  gettext    to make PO message catalogs
-	echo.  changes    to make an overview over all changed/added/deprecated items
-	echo.  xml        to make Docutils-native XML files
-	echo.  pseudoxml  to make pseudoxml-XML files for display purposes
-	echo.  linkcheck  to check all external links for integrity
-	echo.  doctest    to run all doctests embedded in the documentation if enabled
-	goto end
-)
-
-if "%1" == "clean" (
-	for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i
-	del /q /s %BUILDDIR%\*
-	goto end
-)
-
-
-%SPHINXBUILD% 2> nul
-if errorlevel 9009 (
-	echo.
-	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
-	echo.installed, then set the SPHINXBUILD environment variable to point
-	echo.to the full path of the 'sphinx-build' executable. Alternatively you
-	echo.may add the Sphinx directory to PATH.
-	echo.
-	echo.If you don't have Sphinx installed, grab it from
-	echo.http://sphinx-doc.org/
-	exit /b 1
-)
-
-if "%1" == "html" (
-	%SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html
-	if errorlevel 1 exit /b 1
-	echo.
-	echo.Build finished. The HTML pages are in %BUILDDIR%/html.
-	goto end
-)
-
-if "%1" == "dirhtml" (
-	%SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml
-	if errorlevel 1 exit /b 1
-	echo.
-	echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml.
-	goto end
-)
-
-if "%1" == "singlehtml" (
-	%SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml
-	if errorlevel 1 exit /b 1
-	echo.
-	echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml.
-	goto end
-)
-
-if "%1" == "pickle" (
-	%SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle
-	if errorlevel 1 exit /b 1
-	echo.
-	echo.Build finished; now you can process the pickle files.
-	goto end
-)
-
-if "%1" == "json" (
-	%SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json
-	if errorlevel 1 exit /b 1
-	echo.
-	echo.Build finished; now you can process the JSON files.
-	goto end
-)
-
-if "%1" == "htmlhelp" (
-	%SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp
-	if errorlevel 1 exit /b 1
-	echo.
-	echo.Build finished; now you can run HTML Help Workshop with the ^
-.hhp project file in %BUILDDIR%/htmlhelp.
-	goto end
-)
-
-if "%1" == "qthelp" (
-	%SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp
-	if errorlevel 1 exit /b 1
-	echo.
-	echo.Build finished; now you can run "qcollectiongenerator" with the ^
-.qhcp project file in %BUILDDIR%/qthelp, like this:
-	echo.^> qcollectiongenerator %BUILDDIR%\qthelp\cerbere.qhcp
-	echo.To view the help file:
-	echo.^> assistant -collectionFile %BUILDDIR%\qthelp\cerbere.ghc
-	goto end
-)
-
-if "%1" == "devhelp" (
-	%SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp
-	if errorlevel 1 exit /b 1
-	echo.
-	echo.Build finished.
-	goto end
-)
-
-if "%1" == "epub" (
-	%SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub
-	if errorlevel 1 exit /b 1
-	echo.
-	echo.Build finished. The epub file is in %BUILDDIR%/epub.
-	goto end
-)
-
-if "%1" == "latex" (
-	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
-	if errorlevel 1 exit /b 1
-	echo.
-	echo.Build finished; the LaTeX files are in %BUILDDIR%/latex.
-	goto end
-)
-
-if "%1" == "latexpdf" (
-	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
-	cd %BUILDDIR%/latex
-	make all-pdf
-	cd %BUILDDIR%/..
-	echo.
-	echo.Build finished; the PDF files are in %BUILDDIR%/latex.
-	goto end
-)
-
-if "%1" == "latexpdfja" (
-	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
-	cd %BUILDDIR%/latex
-	make all-pdf-ja
-	cd %BUILDDIR%/..
-	echo.
-	echo.Build finished; the PDF files are in %BUILDDIR%/latex.
-	goto end
-)
-
-if "%1" == "text" (
-	%SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text
-	if errorlevel 1 exit /b 1
-	echo.
-	echo.Build finished. The text files are in %BUILDDIR%/text.
-	goto end
-)
-
-if "%1" == "man" (
-	%SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man
-	if errorlevel 1 exit /b 1
-	echo.
-	echo.Build finished. The manual pages are in %BUILDDIR%/man.
-	goto end
-)
-
-if "%1" == "texinfo" (
-	%SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo
-	if errorlevel 1 exit /b 1
-	echo.
-	echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo.
-	goto end
-)
-
-if "%1" == "gettext" (
-	%SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale
-	if errorlevel 1 exit /b 1
-	echo.
-	echo.Build finished. The message catalogs are in %BUILDDIR%/locale.
-	goto end
-)
-
-if "%1" == "changes" (
-	%SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes
-	if errorlevel 1 exit /b 1
-	echo.
-	echo.The overview file is in %BUILDDIR%/changes.
-	goto end
-)
-
-if "%1" == "linkcheck" (
-	%SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck
-	if errorlevel 1 exit /b 1
-	echo.
-	echo.Link check complete; look for any errors in the above output ^
-or in %BUILDDIR%/linkcheck/output.txt.
-	goto end
-)
-
-if "%1" == "doctest" (
-	%SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest
-	if errorlevel 1 exit /b 1
-	echo.
-	echo.Testing of doctests in the sources finished, look at the ^
-results in %BUILDDIR%/doctest/output.txt.
-	goto end
-)
-
-if "%1" == "xml" (
-	%SPHINXBUILD% -b xml %ALLSPHINXOPTS% %BUILDDIR%/xml
-	if errorlevel 1 exit /b 1
-	echo.
-	echo.Build finished. The XML files are in %BUILDDIR%/xml.
-	goto end
-)
-
-if "%1" == "pseudoxml" (
-	%SPHINXBUILD% -b pseudoxml %ALLSPHINXOPTS% %BUILDDIR%/pseudoxml
-	if errorlevel 1 exit /b 1
-	echo.
-	echo.Build finished. The pseudo-XML files are in %BUILDDIR%/pseudoxml.
-	goto end
-)
-
-:end

docs/conf.py

@@ -11,9 +11,23 @@
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
 import os
+import pathlib
 import sys
-sys.path.insert(0, os.path.abspath('..'))
 
+#sys.path.insert(0, os.path.abspath('..'))
+
+# make sure the source version is preferred (#3567)
+root = pathlib.Path(__file__).absolute().parent.parent
+os.environ["PYTHONPATH"] = str(root)
+sys.path.insert(0, str(root))
+
+import cerbere  # isort:skip
+
+allowed_failures = set()
+
+print("python exec:", sys.executable)
+print("sys.path:", sys.path)
+print("PYTHONPATH:", os.environ["PYTHONPATH"])
 
 # -- Project information -----------------------------------------------------
 
@@ -27,21 +41,37 @@ release = '2'
 
 # -- General configuration ---------------------------------------------------
 autoclass_content = "both"  # include both class docstring and __init__
-autodoc_default_flags = [
-         # Make sure that any autodoc declarations show the right members
-         "members",
-         "inherited-members",
-         "show-inheritance",
-]
+autodoc_default_options = {
+    # Make sure that any autodoc declarations show the right members
+    "members": True,
+    "inherited-members": True,
+    "show-inheritance": True,
+}
+autodoc_typehints = "signature"
+
 autosummary_generate = True  # Make _autosummary files and include them
 napoleon_numpy_docstring = False  # Force consistency, leave only Google
 napoleon_use_rtype = False  # More legible
 
+numpydoc_class_members_toctree = True
+numpydoc_show_class_members = False
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.autosummary', 'sphinx.ext.doctest', 'sphinx.ext.todo', 'sphinx.ext.coverage', 'sphinx.ext.ifconfig', 'sphinx.ext.viewcode', 'sphinx.ext.graphviz', 'sphinx.ext.napoleon', 'sphinx_autodoc_typehints']
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.doctest',
+    'sphinx.ext.todo',
+    'sphinx.ext.coverage',
+    'sphinx.ext.ifconfig',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.graphviz',
+    'sphinx.ext.napoleon',
+    'sphinx_autodoc_typehints',
+    "sphinx.ext.napoleon",
+]
 
 
 
@@ -60,9 +90,23 @@ exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinxdoc'
+html_theme = 'sphinx_rtd_theme'
 
 # 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']
+
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3/", None),
+    "pandas": ("https://pandas.pydata.org/pandas-docs/stable", None),
+    "numpy": ("https://docs.scipy.org/doc/numpy", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy/reference", None),
+    "numba": ("https://numba.pydata.org/numba-doc/latest", None),
+    "matplotlib": ("https://matplotlib.org", None),
+    "dask": ("https://docs.dask.org/en/latest", None),
+    "cftime": ("https://unidata.github.io/cftime", None),
+    "xarray": ("http://xarray.pydata.org/en/stable", None),
+}
\ No newline at end of file

docs/index.rst

@@ -6,9 +6,11 @@ This is the home of **cerbere** package.  The objective of **cerbere** is to
 provide different free and open source python modules for the reading,
 interpretation, and writing of (ocean by designer's tropism but any other) earth observation data.
 
-It is now based on **xarray** but extends it to read more data formats and adds
+It is now based on xarray_ but extends it to read more data formats and adds
 a typology of observation objects (called **features**).
 
+.. _NumPy: http://www.numpy.org
+.. _xarray: http://xarray.pydata.org
 
 Contents
 ========
@@ -50,7 +52,7 @@ Reference
 .. toctree::
    :maxdepth: 1
 
-   ./api/index.rst
+   api
 
 Recipes
 =======
@@ -66,3 +68,9 @@ Indices and tables
 * :ref:`modindex`
 * :ref:`search`
 
+License
+-------
+
+cerbere is available under the open source `GPL License`__.
+
+__ https://www.gnu.org/licenses/gpl-3.0.en.html
\ No newline at end of file

tests/test_grib.py

@@ -10,7 +10,7 @@ f = '/home/cerdata/provider/ncep/model/cfsr/monthly/1999/03/pgbhnl.gdas.199903.g
 
 gribm = mapper.gribfile.GribFile(url=f)
 
-gribm.open()
+gribm._open()
 
 attrs = gribm.read_field_attributes('msl')
 for k in attrs:

tests/test_xarray_dataset.py

@@ -278,8 +278,8 @@ class TestXArrayDataset(unittest.TestCase):
             subset.get_values('test_var').shape, (360, 160)
         )
         self.assertIsNot(
-            subset.get_field('test_var').xarray,
-            dst.get_field('test_var').xarray
+            subset.get_field('test_var').to_dataarray,
+            dst.get_field('test_var').to_dataarray
         )
 
     def test_extract_as_view(self):
@@ -290,8 +290,8 @@ class TestXArrayDataset(unittest.TestCase):
             subset.get_values('test_var').shape, (360, 160)
         )
         self.assertIs(
-            subset.get_field('test_var').xarray,
-            dst.get_field('test_var').xarray
+            subset.get_field('test_var').to_dataarray,
+            dst.get_field('test_var').to_dataarray
         )
 
     def test_extract_rename(self):
@@ -302,8 +302,8 @@ class TestXArrayDataset(unittest.TestCase):
             subset.get_values('new_test_var').shape, (360, 160)
         )
         self.assertIsNot(
-            subset.get_field('new_test_var').xarray,
-            dst.get_field('test_var').xarray
+            subset.get_field('new_test_var').to_dataarray,
+            dst.get_field('test_var').to_dataarray
         )
 
     def test_extract_subset(self):
@@ -316,8 +316,8 @@ class TestXArrayDataset(unittest.TestCase):
             subset.get_values('test_var').shape, (5, 10)
         )
         self.assertIsNot(
-            subset.get_field('test_var').xarray,
-            dst.get_field('test_var').xarray
+            subset.get_field('test_var').to_dataarray,
+            dst.get_field('test_var').to_dataarray
         )
 
     def test_extract_subset_padding(self):
@@ -332,8 +332,8 @@ class TestXArrayDataset(unittest.TestCase):
             subset.get_values('test_var').shape, (10, 10)
         )
         self.assertIsNot(
-            subset.get_field('test_var').xarray,
-            dst.get_field('test_var').xarray
+            subset.get_field('test_var').to_dataarray,
+            dst.get_field('test_var').to_dataarray
         )
         self.assertEqual(subset.get_values('test_var').count(), 50)
         self.assertEqual(subset.get_values('test_var').size, 100)
\ No newline at end of file

tests/test_xarray_field.py

@@ -25,6 +25,20 @@ class TestField(unittest.TestCase):
         data = np.ma.zeros((100, 200))
         return Field(data, name='test', dims=('x', 'y'))
 
+    def test_create_field_from_numpy2(self):
+        data = np.ma.zeros((100, 200))
+        field = Field(data=(), name='test')
+        print("TEST2", field)
+        print("TOTO")
+        self.assertIsInstance(field, Field)
+
+    def test_create_field_from_numpy2(self):
+        data = np.ma.zeros((100, 200))
+        field = Field(data=xr.DataArray(data), name='test')
+        print("TEST2", field)
+        print("TOTO")
+        self.assertIsInstance(field, Field)
+
     def test_create_field(self):
         field = self.create_field_from_numpy()
         self.assertIsInstance(field, Field)
@@ -32,7 +46,7 @@ class TestField(unittest.TestCase):
 
     def test_get_xarray(self):
         field = self.create_field_from_numpy()
-        xarr = field.xarray
+        xarr = field.to_dataarray
         self.assertIsInstance(xarr, xr.DataArray)
         print(xarr.dims)
         self.assertTrue('x' in xarr.dims)
@@ -86,4 +100,11 @@ class TestField(unittest.TestCase):
         self.assertIsInstance(values, np.ma.MaskedArray)
         self.assertEqual(values.shape, (20, 5))
         self.assertEqual(values.count(), 50)
-        self.assertEqual(values[10:, :].count(), 0)
+        self.assertEqual(values[10:, :].count(), 0)
\ No newline at end of file
+
+    def test_apply_func(self):
+        field1 = self.create_field_from_numpy()
+        field2 = self.create_field_from_numpy()
+        np.ma.multiply(field1.get_values(), field2.get_values())
+        fsum = Field.compute(np.ma.multiply, field1, field2)
+        print("SUM ", fsum)
\ No newline at end of file