doc-str update; Version bump

README.md

@@ -17,14 +17,23 @@ ogs5py is A python-API for the [OpenGeoSys 5][ogs5_link] scientific modeling pac
 
 You can install the latest version with the following command:
 
-    pip install https://github.com/GeoStat-Framework/ogs5py/archive/master.zip
+    pip install ogs5py
 
 
 ## Documentation for ogs5py
 
 You can find the documentation under [geostat-framework.readthedocs.io][doc_link].
 
 
+### Further Information
+
+- General homepage: https://www.opengeosys.org/ogs-5
+- OGS5 Repository: https://github.com/ufz/ogs5
+- Keyword documentation: https://ogs5-keywords.netlify.com
+- OGS5 Benchmarks: https://github.com/ufz/ogs5-benchmarks
+- ogs5py Benchmarks: https://github.com/GeoStat-Framework/ogs5py_benchmarks
+
+
 ### Tutorials and Examples
 
 In the following a simple transient pumping test is simulated on a radial symmetric mesh.
@@ -72,13 +81,6 @@ model.num.add_block(  # numerical solver
     PCS_TYPE='GROUNDWATER_FLOW',
     LINEAR_SOLVER=[2, 5, 1.0e-14, 1000, 1.0, 100, 4],
 )
-model.out.add_block(  # domain output
-    PCS_TYPE='GROUNDWATER_FLOW',
-    NOD_VALUES='HEAD',
-    GEO_TYPE='DOMAIN',
-    DAT_TYPE='PVD',
-    TIM_TYPE=['STEPS', 1],
-)
 model.out.add_block(  # point observation
     PCS_TYPE='GROUNDWATER_FLOW',
     NOD_VALUES='HEAD',
@@ -125,24 +127,32 @@ It comes along with a set of handy readers for almost all output formats:
 
 * VTK Domain output
 
-        ogs5py.reader.readvtk
+    ```python
+    from ogs5py.reader import readvtk
+    ```
 
 * PVD Domain output
 
-        ogs5py.reader.readpvd
+    ```python
+    from ogs5py.reader import readpvd
+    ```
 
 * TECPLOT point output
 
-        ogs5py.reader.readtec_point
+    ```python
+    from ogs5py.reader import readtec_point
+    ```
 
 * TECPLOT polyline output
 
-        ogs5py.reader.readtec_polyline
+    ```python
+    from ogs5py.reader import readtec_polyline
+    ```
 
 
 ### OGS5 executable
 
-The OGS5 executable needs to be in your sys-path under ``ogs``.
+The OGS5 executable needs to be in your sys-path under ``ogs[.exe]``.
 Otherwise you need to specify the path to the executable within the run command:
 
     ogs.run_model(ogs_root="path/to/ogs")

docs/source/conf.py

@@ -76,7 +76,7 @@ def setup(app):
 # class members have no separate file, so they are not in a toctree
 numpydoc_class_members_toctree = False
 # for the covmodels alot of classmembers show up...
-numpydoc_show_inherited_class_members = False
+numpydoc_show_inherited_class_members = True
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
 

docs/source/fileclasses.base.rst

@@ -4,6 +4,7 @@ ogs5py.fileclasses.base
 .. automodule:: ogs5py.fileclasses.base
    :members:
    :undoc-members:
+   :inherited-members:
    :show-inheritance:
 
 .. raw:: latex

docs/source/index.rst

@@ -18,9 +18,18 @@ Python and pip running.
 
 .. code-block:: none
 
-    pip install https://github.com/GeoStat-Framework/ogs5py/archive/master.zip
+    pip install ogs5py
 
 
+Further Information
+===================
+
+- General homepage: https://www.opengeosys.org/ogs-5
+- OGS5 Repository: https://github.com/ufz/ogs5
+- Keyword documentation: https://ogs5-keywords.netlify.com
+- OGS5 Benchmarks: https://github.com/ufz/ogs5-benchmarks
+- ogs5py Benchmarks: https://github.com/GeoStat-Framework/ogs5py_benchmarks
+
 
 Pumping Test Example
 ====================
@@ -71,13 +80,6 @@ The point output at the observation well is plotted afterwards.
         PCS_TYPE='GROUNDWATER_FLOW',
         LINEAR_SOLVER=[2, 5, 1.0e-14, 1000, 1.0, 100, 4],
     )
-    model.out.add_block(  # domain output
-        PCS_TYPE='GROUNDWATER_FLOW',
-        NOD_VALUES='HEAD',
-        GEO_TYPE='DOMAIN',
-        DAT_TYPE='PVD',
-        TIM_TYPE=['STEPS', 1],
-    )
     model.out.add_block(  # point observation
         PCS_TYPE='GROUNDWATER_FLOW',
         NOD_VALUES='HEAD',
@@ -135,7 +137,7 @@ It comes along with a set of handy readers for almost all output formats:
 OGS5 executable
 ===============
 
-The OGS5 executable needs to be in your sys-path under ``ogs``.
+The OGS5 executable needs to be in your sys-path under ``ogs[.exe]``.
 Otherwise you need to specify the path to the executable within the run command:
 
 .. code-block:: python

examples/01_pump_test.py

@@ -40,13 +40,6 @@
     PCS_TYPE='GROUNDWATER_FLOW',
     LINEAR_SOLVER=[2, 5, 1.0e-14, 1000, 1.0, 100, 4],
 )
-model.out.add_block(  # domain output
-    PCS_TYPE='GROUNDWATER_FLOW',
-    NOD_VALUES='HEAD',
-    GEO_TYPE='DOMAIN',
-    DAT_TYPE='PVD',
-    TIM_TYPE=['STEPS', 1],
-)
 model.out.add_block(  # point observation
     PCS_TYPE='GROUNDWATER_FLOW',
     NOD_VALUES='HEAD',

ogs5py/__init__.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 """
 Purpose
 =======

ogs5py/_version.py

@@ -1,2 +1,3 @@
+# -*- coding: utf-8 -*-
 """Provide a central version"""
-__version__ = "0.5.0"
+__version__ = "0.5.0rc1"

ogs5py/fileclasses/asc/__init__.py

@@ -1,5 +1,16 @@
+# -*- coding: utf-8 -*-
 """
-OGS5 File class
+Class for the ogs ASC file.
+
+.. currentmodule:: ogs5py.fileclasses.asc
+
+File Class
+^^^^^^^^^^
+
+.. autosummary::
+   ASC
+
+----
 """
 from __future__ import absolute_import
 

ogs5py/fileclasses/asc/core.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 """
 Class for the ogs ASC file.
 """

ogs5py/fileclasses/base.py

@@ -385,9 +385,13 @@ class BlockFile(File):
     """
 
     MKEYS = []
+    """:class:`list`: Main Keywords of this OGS-BlockFile"""
+
     SKEYS = []
+    """:class:`list`: Sub Keywords of this OGS-BlockFile"""
 
     STD = {}
+    """:class:`dict`: Standard Block OGS-BlockFile"""
 
     def __init__(
         self,

ogs5py/fileclasses/bc/__init__.py

@@ -1,5 +1,16 @@
+# -*- coding: utf-8 -*-
 """
-OGS5 File class
+Class for the ogs BOUNDARY CONDITION file.
+
+.. currentmodule:: ogs5py.fileclasses.bc
+
+File Class
+^^^^^^^^^^
+
+.. autosummary::
+   BC
+
+----
 """
 from __future__ import absolute_import
 

ogs5py/fileclasses/bc/core.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 """
 Class for the ogs BOUNDARY CONDITION file.
 """

ogs5py/fileclasses/cct/__init__.py

@@ -1,5 +1,16 @@
+# -*- coding: utf-8 -*-
 """
-OGS5 File class
+Class for the ogs COMMUNICATION TABLE file.
+
+.. currentmodule:: ogs5py.fileclasses.cct
+
+File Class
+^^^^^^^^^^
+
+.. autosummary::
+   CCT
+
+----
 """
 from __future__ import absolute_import
 

ogs5py/fileclasses/cct/core.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 """
 Class for the ogs COMMUNICATION TABLE file.
 """

ogs5py/fileclasses/ddc/__init__.py

@@ -1,5 +1,16 @@
+# -*- coding: utf-8 -*-
 """
-OGS5 File class
+Class for the ogs DOMAIN DECOMPOSITION file.
+
+.. currentmodule:: ogs5py.fileclasses.ddc
+
+File Class
+^^^^^^^^^^
+
+.. autosummary::
+   DDC
+
+----
 """
 from __future__ import absolute_import
 

ogs5py/fileclasses/ddc/core.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 """
 Class for the ogs DOMAIN DECOMPOSITION file.
 """

ogs5py/fileclasses/fct/__init__.py

@@ -1,5 +1,16 @@
+# -*- coding: utf-8 -*-
 """
-OGS5 File class
+Class for the ogs FUNCTION file.
+
+.. currentmodule:: ogs5py.fileclasses.fct
+
+File Class
+^^^^^^^^^^
+
+.. autosummary::
+   FCT
+
+----
 """
 from __future__ import absolute_import
 

ogs5py/fileclasses/fct/core.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 """
 Class for the ogs FUNCTION file.
 """

ogs5py/fileclasses/gem/__init__.py

@@ -1,5 +1,17 @@
+# -*- coding: utf-8 -*-
 """
-OGS5 File class
+Class for the ogs GEOCHEMICAL THERMODYNAMIC MODELING COUPLING file.
+
+.. currentmodule:: ogs5py.fileclasses.gem
+
+File Classes
+^^^^^^^^^^^^
+
+.. autosummary::
+   GEM
+   GEMinit
+
+----
 """
 from __future__ import absolute_import
 

ogs5py/fileclasses/gem/core.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 """
 Class for the ogs GEOCHEMICAL THERMODYNAMIC MODELING COUPLING file.
 """

ogs5py/fileclasses/gli/__init__.py

@@ -1,8 +1,29 @@
+# -*- coding: utf-8 -*-
 """
-OGS5 File class
+Class for the ogs GEOMETRY file.
+
+.. currentmodule:: ogs5py.fileclasses.gli
+
+File Classes
+^^^^^^^^^^^^
+
+.. autosummary::
+   GLI
+   GLIext
+
+Generator
+^^^^^^^^^
+
+.. autosummary::
+   rectengular
+   radial
+
+----
 """
 from __future__ import absolute_import
 
 from ogs5py.fileclasses.gli.core import GLI, GLIext
+from ogs5py.fileclasses.gli.generator import rectengular, radial
 
 __all__ = ["GLI", "GLIext"]
+__all__ += ["rectengular", "radial"]

ogs5py/fileclasses/gli/core.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 """
 core module for the ogs5py GLI file.
 Containing the classes for the OGS5 GLI files.

ogs5py/fileclasses/ic/__init__.py

@@ -1,5 +1,17 @@
+# -*- coding: utf-8 -*-
 """
-OGS5 File class
+Class for the ogs INITIAL_CONDITION file.
+
+.. currentmodule:: ogs5py.fileclasses.ic
+
+File Classes
+^^^^^^^^^^^^
+
+.. autosummary::
+   IC
+   RFR
+
+----
 """
 from __future__ import absolute_import
 

ogs5py/fileclasses/ic/core.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 """
 Class for the ogs INITIAL_CONDITION file.
 """

ogs5py/fileclasses/krc/__init__.py

@@ -1,5 +1,16 @@
+# -*- coding: utf-8 -*-
 """
-OGS5 File class
+Class for the ogs KINETRIC REACTION file.
+
+.. currentmodule:: ogs5py.fileclasses.krc
+
+File Class
+^^^^^^^^^^
+
+.. autosummary::
+   KRC
+
+----
 """
 from __future__ import absolute_import
 

ogs5py/fileclasses/krc/core.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 """
 Class for the ogs KINETRIC REACTION file.
 """