Merge pull request #17 from enigne/change_to_lower_case_package_name

Change to lower case package name
ISSMteam · Apr 10, 2024 · 32d335b · 32d335b
2 parents d65ad00 + 33c3f14
commit 32d335b
Show file tree

Hide file tree

Showing 44 changed files with 229 additions and 67 deletions.
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -8,6 +8,8 @@ build:
 python:
   install:
     - requirements: docs/requirements.txt
+    - method: pip
+      path: .
 
 sphinx:
   configuration: docs/conf.py
diff --git a/docs/Makefile b/docs/Makefile
@@ -3,17 +3,21 @@
 
 # You can set these variables from the command line, and also
 # from the environment for the first two.
-SPHINXOPTS    ?=
-SPHINXBUILD   ?= sphinx-build
-SOURCEDIR     = source
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SOURCEDIR     = .
 BUILDDIR      = build
 
 # Put it first so that "make" without argument is like "make help".
 help:
 	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
+
 .PHONY: help Makefile
 
+html: Makefile
+	@DDE_BACKEND=tensorflow $(SPHINXBUILD) -M html "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile

diff --git a/docs/api/pinnicle.domain.rst b/docs/api/pinnicle.domain.rst
@@ -0,0 +1,10 @@
+pinnicle.domain
+===============
+
+pinnicle.domain.domain module
+-----------------------------
+
+.. automodule:: pinnicle.domain.domain
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/api/pinnicle.modeldata.rst b/docs/api/pinnicle.modeldata.rst
@@ -0,0 +1,26 @@
+pinnicle.modeldata
+==================
+
+pinnicle.modeldata.data module
+------------------------------
+
+.. automodule:: pinnicle.modeldata.data
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pinnicle.modeldata.general_mat_data module
+------------------------------------------
+
+.. automodule:: pinnicle.modeldata.general_mat_data
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pinnicle.modeldata.issm_data module
+-----------------------------------
+
+.. automodule:: pinnicle.modeldata.issm_data
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/api/pinnicle.nn.rst b/docs/api/pinnicle.nn.rst
@@ -0,0 +1,18 @@
+pinnicle.nn
+===========
+
+pinnicle.nn.nn module
+---------------------
+
+.. automodule:: pinnicle.nn.nn
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pinnicle.nn.helper module
+-------------------------
+
+.. automodule:: pinnicle.nn.helper
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/api/pinnicle.physics.rst b/docs/api/pinnicle.physics.rst
@@ -0,0 +1,42 @@
+pinnicle.physics
+================
+
+pinnicle.physics.constants module
+---------------------------------
+
+.. automodule:: pinnicle.physics.constants
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pinnicle.physics.physics module
+-------------------------------
+
+.. automodule:: pinnicle.physics.physics
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pinnicle.physics.equationbase module
+------------------------------------
+
+.. automodule:: pinnicle.physics.equationbase
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pinnicle.physics.continuity module
+----------------------------------
+
+.. automodule:: pinnicle.physics.continuity
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pinnicle.physics.stressbalance module
+-------------------------------------
+
+.. automodule:: pinnicle.physics.stressbalance
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/api/pinnicle.rst b/docs/api/pinnicle.rst
@@ -1,42 +1,19 @@
 pinnicle
-=======
+========
 
-pinnicle.domain module
-------------------------
-
-.. automodule:: pinnicle.domain
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-pinnicle.modeldata module
----------------------
-
-.. automodule:: pinnicle.modeldata
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-pinnicle.nn module
----------------------
+pinnicle.pinn module
+--------------------
 
-.. automodule:: pinnicle.nn
+.. automodule:: pinnicle.pinn
    :members:
    :undoc-members:
    :show-inheritance:
 
-pinnicle.physics module
-----------------------
-
-.. automodule:: pinnicle.physics
-   :members:
-   :undoc-members:
-   :show-inheritance:
 
-pinnicle.utils module
---------------------
+pinnicle.parameter module
+-------------------------
 
-.. automodule:: pinnicle.utils
+.. automodule:: pinnicle.parameter
    :members:
    :undoc-members:
    :show-inheritance:

diff --git a/docs/api/pinnicle.utils.rst b/docs/api/pinnicle.utils.rst
@@ -0,0 +1,34 @@
+pinnicle.utils
+==============
+
+pinnicle.utils.data_misfit module
+---------------------------------
+
+.. automodule:: pinnicle.utils.data_misfit
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pinnicle.utils.history module
+-----------------------------
+
+.. automodule:: pinnicle.utils.history
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pinnicle.utils.plotting module
+------------------------------
+
+.. automodule:: pinnicle.utils.plotting
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pinnicle.utils.helper module
+----------------------------
+
+.. automodule:: pinnicle.utils.helper
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/conf.py b/docs/conf.py
@@ -1,5 +1,5 @@
 # Configuration file for the Sphinx documentation builder.
-#from importlib.metadata import version
+from importlib.metadata import version
 
 # -- Project information
 
@@ -8,19 +8,22 @@
 author = 'Cheng Gong'
 
 # The short X.Y version
-#version = version("PINNICLE")
+version = version("pinnicle")
 version = '0.1'
 # The full version, including alpha/beta/rc tags
 release = version
 
 # -- General configuration
-
 extensions = [
     'sphinx.ext.duration',
     'sphinx.ext.doctest',
     'sphinx.ext.autodoc',
     'sphinx.ext.autosummary',
     'sphinx.ext.intersphinx',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.napoleon',
+    'sphinx_copybutton',
 ]
 
 intersphinx_mapping = {
@@ -37,3 +40,13 @@
 # -- Options for HTML output
 html_theme = 'sphinx_rtd_theme'
 
+# The suffix(es) of source filenames.
+source_suffix = ".rst"
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects 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"
diff --git a/docs/index.rst b/docs/index.rst
@@ -1,7 +1,7 @@
 PINNICLE
-===================================
+========
 
-`PINNICLE<https://github.com/enigne/PINNICLE>` is a Python library for solving ice sheet modeling problems using a unified framework with Physics Informed Neural Networks
+`PINNICLE <https://github.com/enigne/PINNICLE>`_ is a Python library for solving ice sheet modeling problems using a unified framework with Physics Informed Neural Networks
 
 
 Check out the :doc:`usage` section for further information, including
@@ -12,20 +12,25 @@ how to :ref:`installation` the project.
    This project is under active development.
 
 User guide
---------
+----------
 
 .. toctree::
    :maxdepth: 2
 
 
 API reference
---------
+-------------
 
 .. toctree::
    :maxdepth: 2
    :caption: API
 
    api/pinnicle
+   api/pinnicle.domain
+   api/pinnicle.modeldata
+   api/pinnicle.nn
+   api/pinnicle.physics
+   api/pinnicle.utils
 
 
 Indices and tables

diff --git a/docs/make.bat b/docs/make.bat
@@ -7,7 +7,7 @@ REM Command file for Sphinx documentation
 if "%SPHINXBUILD%" == "" (
 	set SPHINXBUILD=sphinx-build
 )
-set SOURCEDIR=source
+set SOURCEDIR=.
 set BUILDDIR=build
 
 if "%1" == "" goto help

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,2 +1,24 @@
+numpy
+scipy
+scikit-learn
+matplotlib
+pandas
+mat73
+deepxde
+
+# TensorFlow 1.x
+tensorflow>=2.7.0
+# TensorFlow 2.x
+tensorflow-probability>=0.10.0
+# PyTorch
+torch<2.0.0    # build fails on RTD with torch 2.0.0
+# PaddlePaddle
+# https://paddle-wheel.bj.bcebos.com/develop/linux/linux-cpu-mkl-avx/paddlepaddle-0.0.0-cp38-cp38-linux_x86_64.whl
+paddlepaddle==2.6.0
+# JAX
+jax
+flax
+optax
+
 sphinx-copybutton
 sphinx-rtd-theme
diff --git a/PINNICLE/__init__.py → pinnicle/__init__.py b/PINNICLE/__init__.py → pinnicle/__init__.py
diff --git a/PINNICLE/domain/__init__.py → pinnicle/domain/__init__.py b/PINNICLE/domain/__init__.py → pinnicle/domain/__init__.py
diff --git a/PINNICLE/domain/domain.py → pinnicle/domain/domain.py b/PINNICLE/domain/domain.py → pinnicle/domain/domain.py
diff --git a/PINNICLE/modeldata/__init__.py → pinnicle/modeldata/__init__.py b/PINNICLE/modeldata/__init__.py → pinnicle/modeldata/__init__.py
diff --git a/PINNICLE/modeldata/data.py → pinnicle/modeldata/data.py b/PINNICLE/modeldata/data.py → pinnicle/modeldata/data.py
diff --git a/PINNICLE/modeldata/general_mat_data.py → pinnicle/modeldata/general_mat_data.py b/PINNICLE/modeldata/general_mat_data.py → pinnicle/modeldata/general_mat_data.py
diff --git a/PINNICLE/modeldata/issm_data.py → pinnicle/modeldata/issm_data.py b/PINNICLE/modeldata/issm_data.py → pinnicle/modeldata/issm_data.py
@@ -65,6 +65,7 @@ def load_data(self):
 
     def plot(self, data_names=[], vranges={}, axs=None, resolution=200, **kwargs):
         """ use `utils.plot_dict_data` to plot the ISSM data
+
         Args:
             data_names (list): Names of the variables. if not specified, plot all variables in data_dict
             vranges (dict): range of the data

diff --git a/PINNICLE/nn/__init__.py → pinnicle/nn/__init__.py b/PINNICLE/nn/__init__.py → pinnicle/nn/__init__.py
diff --git a/PINNICLE/nn/helper.py → pinnicle/nn/helper.py b/PINNICLE/nn/helper.py → pinnicle/nn/helper.py
diff --git a/PINNICLE/nn/nn.py → pinnicle/nn/nn.py b/PINNICLE/nn/nn.py → pinnicle/nn/nn.py
diff --git a/PINNICLE/parameter.py → pinnicle/parameter.py b/PINNICLE/parameter.py → pinnicle/parameter.py
diff --git a/PINNICLE/physics/__init__.py → pinnicle/physics/__init__.py b/PINNICLE/physics/__init__.py → pinnicle/physics/__init__.py
diff --git a/PINNICLE/physics/constants.py → pinnicle/physics/constants.py b/PINNICLE/physics/constants.py → pinnicle/physics/constants.py
diff --git a/PINNICLE/physics/continuity.py → pinnicle/physics/continuity.py b/PINNICLE/physics/continuity.py → pinnicle/physics/continuity.py
diff --git a/PINNICLE/physics/equationbase.py → pinnicle/physics/equationbase.py b/PINNICLE/physics/equationbase.py → pinnicle/physics/equationbase.py
diff --git a/PINNICLE/physics/physics.py → pinnicle/physics/physics.py b/PINNICLE/physics/physics.py → pinnicle/physics/physics.py
@@ -54,6 +54,7 @@ def pdes(self, nn_input_var, nn_output_var):
 
     def vel_mag(self, nn_input_var, nn_output_var, X):
         """ a wrapper for PointSetOperatorBC func call
+
         Args: 
             nn_input_var:  input tensor to the nn
             nn_output_var: output tensor from the nn

diff --git a/PINNICLE/physics/stressbalance.py → pinnicle/physics/stressbalance.py b/PINNICLE/physics/stressbalance.py → pinnicle/physics/stressbalance.py
@@ -121,6 +121,7 @@ def __init__(self, parameters=EquationParameter()):
 
     def pde(self, nn_input_var, nn_output_var):
         """ residual of MOLHO 2D PDEs
+
         Args:
             nn_input_var: global input to the nn
             nn_output_var: global output from the nn

diff --git a/PINNICLE/pinn.py → pinnicle/pinn.py b/PINNICLE/pinn.py → pinnicle/pinn.py
@@ -112,6 +112,7 @@ def plot_history(self, path=""):
 
     def plot_predictions(self, path="", **kwargs):
         """ plot model predictions
+
         Args:
             path (Path, str): Path to save the figures
             X_ref (dict): Coordinates of the reference solutions, if None, then just plot the predicted solutions

diff --git a/PINNICLE/utils/__init__.py → pinnicle/utils/__init__.py b/PINNICLE/utils/__init__.py → pinnicle/utils/__init__.py
diff --git a/PINNICLE/utils/data_misfit.py → pinnicle/utils/data_misfit.py b/PINNICLE/utils/data_misfit.py → pinnicle/utils/data_misfit.py
@@ -4,12 +4,7 @@
 
 
 def surface_log_vel_misfit(v_true, v_pred):
-    """Compute SurfaceLogVelMisfit:
-    This function can only work with tensorflow backend for now, since we use tf.math.log()
-            [        vel + eps     ] 2
-       J =  | log ( -----------  ) |
-            [       vel   + eps    ]
-                       obs
+    """Compute SurfaceLogVelMisfit: This function can only work with tensorflow backend for now, since we use tf.math.log()
     """
     epsvel=2.220446049250313e-16
     return bkd.reduce_mean(bkd.square((tf.math.log((tf.abs(v_pred)+epsvel)/(tf.abs(v_true)+epsvel)))))