Merge pull request #37 from yoctoyotta1024/newobs

Major re-writing of Observers and Zarr Libraries :)

.gitignore

@@ -14,3 +14,4 @@ build
 bin
 docs/source/_autosummary
 examples/examplesolutions/
+roughpaper/share

docs/doxygen/doxygen.dox

@@ -949,7 +949,7 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = ../libs/runcleo/ ../libs/superdrops/
+INPUT                  = ../libs/runcleo/ ../libs/superdrops/ ../libs/zarr2/ ../libs/observers2/
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses

docs/source/conf.py

@@ -6,7 +6,7 @@
 Author: Clara Bayley (CB)
 Additional Contributors:
 -----
-Last Modified: Monday 12th February 2024
+Last Modified: Wednesday 27th March 2024
 Modified By: CB
 -----
 License: BSD 3-Clause "New" or "Revised" License
@@ -76,6 +76,8 @@
 breathe_projects = {
     "runcleo"          : "../build/doxygen/xml/",
     "superdrops"       : "../build/doxygen/xml/",
+    "zarr2"            : "../build/doxygen/xml/",
+    "observers2"        : "../build/doxygen/xml/",
 }
 
 breathe_default_project = 'proj'

docs/source/cxx/cxx.rst

@@ -19,6 +19,8 @@ a SDM coupled to a Dynamics Solver.
 
    runcleo/runcleomod
    superdrops/superdropsmod
+   zarr2/zarr2mod
+   observers2/observers2mod
 
 Indices and tables
 ------------------

docs/source/cxx/observers2/observers.rst

@@ -0,0 +1,35 @@
+Observers
+=========
+
+Header file: ``<libs/observers2/observers.hpp>``
+`[source] <https://github.com/yoctoyotta1024/CLEO/blob/main/libs/observers2/observers.hpp>`_
+
+.. doxygenconcept:: Observer
+   :project: observers2
+
+.. doxygenstruct:: CombinedObserver
+   :project: observers2
+   :private-members:
+   :protected-members:
+   :members:
+   :undoc-members:
+
+.. doxygenfunction:: operator>>(const Observer auto obs1, const Observer auto obs2)
+   :project: observers2
+
+.. doxygenstruct:: NullObserver
+   :project: observers2
+   :private-members:
+   :protected-members:
+   :members:
+   :undoc-members:
+
+.. doxygenconcept:: ObsFuncs
+   :project: observers2
+
+.. doxygenstruct:: ConstTstepObserver
+   :project: observers2
+   :private-members:
+   :protected-members:
+   :members:
+   :undoc-members:

docs/source/cxx/observers2/observers2mod.rst

@@ -0,0 +1,16 @@
+.. CLEO C++ documentation master file, created by
+   sphinx-quickstart on Mon Nov 20 12:27:54 2023.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Observers Module
+================
+
+This module of CLEO contains the all the implementation of observers for outputing data from CLEO,
+e.g. to a dataset or to a computer screen.
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Contents:
+
+   observers

docs/source/cxx/superdrops/microphysical_process.rst

@@ -14,7 +14,7 @@ Header file: ``<libs/superdrops/microphysicalprocess.hpp>``
    :members:
    :undoc-members:
 
-.. doxygenfunction:: operator>>
+.. doxygenfunction:: operator>>(const MicrophysicalProcess auto a, const MicrophysicalProcess auto b)
    :project: superdrops
 
 .. doxygenstruct:: NullMicrophysicalProcess

docs/source/cxx/zarr2/buffer.rst

@@ -0,0 +1,12 @@
+Buffer
+======
+
+Header file: ``<libs/zarr2/buffer.hpp>``
+`[source] <https://github.com/yoctoyotta1024/CLEO/blob/main/libs/zarr2/buffer.hpp>`_
+
+.. doxygenstruct:: Buffer
+   :project: zarr2
+   :private-members:
+   :protected-members:
+   :members:
+   :undoc-members:

docs/source/cxx/zarr2/chunks.rst

@@ -0,0 +1,18 @@
+Chunks
+======
+
+Header file: ``<libs/zarr2/chunks.hpp>``
+`[source] <https://github.com/yoctoyotta1024/CLEO/blob/main/libs/zarr2/chunks.hpp>`_
+
+.. doxygenfunction:: vec_product(const std::vector<size_t>& vec)
+   :project: zarr2
+
+.. doxygenfunction:: vec_product(const std::vector<size_t>& vec, const size_t aa)
+   :project: zarr2
+
+.. doxygenclass:: Chunks
+   :project: zarr2
+   :private-members:
+   :protected-members:
+   :members:
+   :undoc-members:

docs/source/cxx/zarr2/dataset.rst

@@ -0,0 +1,12 @@
+Dataset
+=======
+
+Header file: ``<libs/zarr2/dataset.hpp>``
+`[source] <https://github.com/yoctoyotta1024/CLEO/blob/main/libs/zarr2/dataset.hpp>`_
+
+.. doxygenclass:: Dataset
+   :project: zarr2
+   :private-members:
+   :protected-members:
+   :members:
+   :undoc-members:

docs/source/cxx/zarr2/fsstore.rst

@@ -0,0 +1,12 @@
+FSStore
+=======
+
+Header file: ``<libs/zarr2/fsstore.hpp>``
+`[source] <https://github.com/yoctoyotta1024/CLEO/blob/main/libs/zarr2/fsstore.hpp>`_
+
+.. doxygenclass:: FSStore
+   :project: zarr2
+   :private-members:
+   :protected-members:
+   :members:
+   :undoc-members:

docs/source/cxx/zarr2/store_accessor.rst

@@ -0,0 +1,12 @@
+StoreAccessor
+=============
+
+Header file: ``<libs/zarr2/store_accessor.hpp>``
+`[source] <https://github.com/yoctoyotta1024/CLEO/blob/main/libs/zarr2/store_accessor.hpp>`_
+
+.. doxygenstruct:: StoreAccessor
+   :project: zarr2
+   :private-members:
+   :protected-members:
+   :members:
+   :undoc-members:

docs/source/cxx/zarr2/xarray_zarr_array.rst

@@ -0,0 +1,24 @@
+XarrayZarrArray
+===============
+
+Header file: ``<libs/zarr2/xarray_zarr_array.hpp>``
+`[source] <https://github.com/yoctoyotta1024/CLEO/blob/main/libs/zarr2/xarray_zarr_array.hpp>`_
+
+.. doxygenfunction:: write_zattrs_json
+   :project: zarr2
+
+.. doxygenfunction:: reduced_arrayshape_from_dims
+   :project: zarr2
+
+.. doxygenfunction:: vecstr_to_string
+   :project: zarr2
+
+.. doxygenfunction:: make_xarray_metadata
+   :project: zarr2
+
+.. doxygenclass:: XarrayZarrArray
+   :project: zarr2
+   :private-members:
+   :protected-members:
+   :members:
+   :undoc-members:

docs/source/cxx/zarr2/zarr2mod.rst

@@ -0,0 +1,23 @@
+.. CLEO C++ documentation master file, created by
+   sphinx-quickstart on Mon Nov 20 12:27:54 2023.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Zarr Module
+===========
+
+This module of CLEO contains the all the implementation of writing Zarr arrays to a dataset in
+a store which can be Xarray and NetCDF compatible.
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Contents:
+
+   buffer
+   chunks
+   dataset
+   fsstore
+   store_accessor
+   xarray_zarr_array
+   zarr_array
+   zarr_group

docs/source/cxx/zarr2/zarr_array.rst

@@ -0,0 +1,24 @@
+ZarrArray
+=========
+
+Header file: ``<libs/zarr2/zarr_array.hpp>``
+`[source] <https://github.com/yoctoyotta1024/CLEO/blob/main/libs/zarr2/zarr_array.hpp>`_
+
+.. doxygenfunction:: good2Dchunkshape
+   :project: zarr2
+
+.. doxygenfunction:: write_zarray_json
+   :project: zarr2
+
+.. doxygenfunction:: vec_to_string
+   :project: zarr2
+
+.. doxygenfunction:: make_part_zarrmetadata
+   :project: zarr2
+
+.. doxygenclass:: ZarrArray
+   :project: zarr2
+   :private-members:
+   :protected-members:
+   :members:
+   :undoc-members:

docs/source/cxx/zarr2/zarr_group.rst

@@ -0,0 +1,12 @@
+ZarrGroup
+=========
+
+Header file: ``<libs/zarr2/zarr_group.hpp>``
+`[source] <https://github.com/yoctoyotta1024/CLEO/blob/main/libs/zarr2/zarr_group.hpp>`_
+
+.. doxygenstruct:: ZarrGroup
+   :project: zarr2
+   :private-members:
+   :protected-members:
+   :members:
+   :undoc-members:

docs/source/usage/requirements.rst

@@ -1,6 +1,8 @@
 Requirements
 ============
 
+TODO(CB) update requirements with micromambda package installer advice
+
 The following requirements ensure CLEO's build, compilation and
 execution on DKRZ's Levante HPC. If they do not work,
 please :ref:`contact us <contact>` or `open a new

environment.yml

@@ -1,4 +1,4 @@
-name: enviropy3
+name: cleoenv
 dependencies:
     - python>=3.9
     - pytest