From eeb97a692ec949187d9856e5e6521c072f18c8bb Mon Sep 17 00:00:00 2001
From: caron <j.caron@fz-juelich.de>
Date: Wed, 11 Mar 2020 13:42:16 +0100
Subject: [PATCH] Added stuff to docs, try to make it work correctly
---
.gitlab-ci.yml | 2 +-
README.rst | 13 +++++-----
docs/api/empyre.fields.rst | 38 ---------------------------
docs/api/empyre.io.rst | 10 -------
docs/api/empyre.models.rst | 10 -------
docs/api/empyre.reconstruct.rst | 10 -------
docs/api/empyre.rst | 33 -----------------------
docs/api/empyre.vis.rst | 46 ---------------------------------
docs/api/modules.rst | 7 -----
docs/fields.rst | 18 +++++++++++++
src/empyre/fields/field.py | 26 +++++++++----------
11 files changed, 38 insertions(+), 175 deletions(-)
delete mode 100644 docs/api/empyre.fields.rst
delete mode 100644 docs/api/empyre.io.rst
delete mode 100644 docs/api/empyre.models.rst
delete mode 100644 docs/api/empyre.reconstruct.rst
delete mode 100644 docs/api/empyre.rst
delete mode 100644 docs/api/empyre.vis.rst
delete mode 100644 docs/api/modules.rst
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 4606f9f..58f8e3e 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -17,7 +17,7 @@ test_style:
image: continuumio/miniconda3:latest
script:
# -m: only run tests marked with "flake8"
- - pyroma . --min=9 # Checks setup.py for cheese! # TODO: Set to maxium cheese (10)!
+ - pyroma . --min=10 # Checks setup.py for cheese! Maxium cheese 10!
- python setup.py test --addopts "--flake8 -m flake8"
test_function:
diff --git a/README.rst b/README.rst
index 425b097..a5d5429 100644
--- a/README.rst
+++ b/README.rst
@@ -28,16 +28,16 @@ EMPyRe is available on the `Python Package Index <http://pypi.python.org/pypi>`_
Per default, only the strictly required libraries are installed, but there are a few additional dependencies that will unlock additional capabilites of EMPYRE.
* ``io`` will install the `HyperSpy <https://hyperspy.org/>`_ package that is used for loading and saving additional file formats.
-
+
.. warning::
- Due to this `issue <https://github.com/hyperspy/hyperspy/issues/2315>`_, a pip install of hyperspy is currently not possible. Please use
+ Due to this `issue <https://github.com/hyperspy/hyperspy/issues/2315>`_, a pip install of hyperspy is currently not possible. Please use
`conda <https://docs.conda.io/en/latest/>`_ to install HyperSpy, instead.
-
+
* ``fftw`` will install `PyFFTW <https://github.com/pyFFTW/pyFFTW>`_ to speed up Fourier transforms used in some forward models.
* ``colors`` will install the `cmocean <https://matplotlib.org/cmocean/>`_, whose ``balance`` color map is used as a default for the ``imshow`` commmand, if available.
-
+
* ``all`` will install all of the dependencies listed above.
@@ -53,8 +53,7 @@ Structure
EMPyRe has several dedicated submodules which are fully documented `here <https://empyre.iffgit.fz-juelich.de/empyre/>`_!
-
-* The ``fields`` submodule provides the ``Field`` container class for multidimensional scalar or vector fields and is the fundamental data structure used in EMPyRe.
+* The ``fields`` submodule provides the ``Field`` container class for multidimensional scalar or vector fields and is the fundamental data structure used in EMPyRe.
* The ``vis`` submodule enables the plotting of ``Field`` objects, based on and similar in syntax to the commonly known `matplotlib <https://matplotlib.org/>`_ framework.
@@ -68,4 +67,4 @@ EMPyRe has several dedicated submodules which are fully documented `here <https:
License
-------
-EMPyRe is licensed under `GPLv3 <https://iffgit.fz-juelich.de/empyre/empyre/-/blob/master/LICENSE>`_.
+EMPyRe is licensed under `GPLv3 <https://iffgit.fz-juelich.de/empyre/empyre/-/blob/master/LICENSE>`_.
diff --git a/docs/api/empyre.fields.rst b/docs/api/empyre.fields.rst
deleted file mode 100644
index 4669873..0000000
--- a/docs/api/empyre.fields.rst
+++ /dev/null
@@ -1,38 +0,0 @@
-empyre.fields package
-=====================
-
-Submodules
-----------
-
-empyre.fields.field module
---------------------------
-
-.. automodule:: empyre.fields.field
- :members:
- :undoc-members:
- :show-inheritance:
-
-empyre.fields.shapes module
----------------------------
-
-.. automodule:: empyre.fields.shapes
- :members:
- :undoc-members:
- :show-inheritance:
-
-empyre.fields.vectors module
-----------------------------
-
-.. automodule:: empyre.fields.vectors
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: empyre.fields
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/docs/api/empyre.io.rst b/docs/api/empyre.io.rst
deleted file mode 100644
index b90f22c..0000000
--- a/docs/api/empyre.io.rst
+++ /dev/null
@@ -1,10 +0,0 @@
-empyre.io package
-=================
-
-Module contents
----------------
-
-.. automodule:: empyre.io
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/docs/api/empyre.models.rst b/docs/api/empyre.models.rst
deleted file mode 100644
index 084117e..0000000
--- a/docs/api/empyre.models.rst
+++ /dev/null
@@ -1,10 +0,0 @@
-empyre.models package
-=====================
-
-Module contents
----------------
-
-.. automodule:: empyre.models
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/docs/api/empyre.reconstruct.rst b/docs/api/empyre.reconstruct.rst
deleted file mode 100644
index 4824387..0000000
--- a/docs/api/empyre.reconstruct.rst
+++ /dev/null
@@ -1,10 +0,0 @@
-empyre.reconstruct package
-==========================
-
-Module contents
----------------
-
-.. automodule:: empyre.reconstruct
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/docs/api/empyre.rst b/docs/api/empyre.rst
deleted file mode 100644
index a935d59..0000000
--- a/docs/api/empyre.rst
+++ /dev/null
@@ -1,33 +0,0 @@
-empyre package
-==============
-
-Subpackages
------------
-
-.. toctree::
-
- empyre.fields
- empyre.io
- empyre.models
- empyre.reconstruct
- empyre.vis
-
-Submodules
-----------
-
-empyre.version module
----------------------
-
-.. automodule:: empyre.version
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: empyre
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/docs/api/empyre.vis.rst b/docs/api/empyre.vis.rst
deleted file mode 100644
index 0a08bbc..0000000
--- a/docs/api/empyre.vis.rst
+++ /dev/null
@@ -1,46 +0,0 @@
-empyre.vis package
-==================
-
-Submodules
-----------
-
-empyre.vis.colors module
-------------------------
-
-.. automodule:: empyre.vis.colors
- :members:
- :undoc-members:
- :show-inheritance:
-
-empyre.vis.decorators module
-----------------------------
-
-.. automodule:: empyre.vis.decorators
- :members:
- :undoc-members:
- :show-inheritance:
-
-empyre.vis.plot2d module
-------------------------
-
-.. automodule:: empyre.vis.plot2d
- :members:
- :undoc-members:
- :show-inheritance:
-
-empyre.vis.tools module
------------------------
-
-.. automodule:: empyre.vis.tools
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: empyre.vis
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/docs/api/modules.rst b/docs/api/modules.rst
deleted file mode 100644
index aab6102..0000000
--- a/docs/api/modules.rst
+++ /dev/null
@@ -1,7 +0,0 @@
-empyre
-======
-
-.. toctree::
- :maxdepth: 4
-
- empyre
diff --git a/docs/fields.rst b/docs/fields.rst
index 68bd3b1..f464c05 100644
--- a/docs/fields.rst
+++ b/docs/fields.rst
@@ -2,3 +2,21 @@ The Field container class
=========================
Field docu here!
+
+
+Submodules
+----------
+
+.. toctree::
+
+ empyre.fields.field
+ empyre.fields.shapes
+ empyre.fields.vectors
+
+Module contents
+---------------
+
+.. automodule:: empyre.fields
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/src/empyre/fields/field.py b/src/empyre/fields/field.py
index ce74b76..b94f32f 100644
--- a/src/empyre/fields/field.py
+++ b/src/empyre/fields/field.py
@@ -438,7 +438,7 @@ class Field(NDArrayOperatorsMixin):
The calculation depends on the input:
3 dimensions, 3 components: Calculates the full 3D rotational vector field!
2 dimensions, 2 components: Calculates the out-of-plane component of the curl as a 2D scalar field!
- 2 dimensions, scalar: Calculates the planar rotatio as a 2D vector field!
+ 2 dimensions, scalar: Calculates the planar rotation as a 2D vector field!
"""
self._log.debug('Calling curl')
@@ -447,12 +447,12 @@ class Field(NDArrayOperatorsMixin):
if squeezed_field.ncomp == 3: # 3 component vector field (standard case):
self._log.debug('input: 3 dimensions, 3 components!')
field_x, field_y, field_z = squeezed_field.comp
- grad_xx, grad_xy, grad_xz = field_x.gradient().comp
- grad_yx, grad_yy, grad_yz = field_y.gradient().comp
- grad_zx, grad_zy, grad_zz = field_z.gradient().comp
- curl_x = grad_zy - grad_yz
- curl_y = grad_xz - grad_zx
- curl_z = grad_yx - grad_xy
+ gradx_x, grady_x, gradz_x = field_x.gradient().comp
+ gradx_y, grady_y, gradz_y = field_y.gradient().comp
+ gradx_z, grady_z, gradz_z = field_z.gradient().comp
+ curl_x = grady_z - gradz_y
+ curl_y = gradz_x - gradx_z
+ curl_z = gradx_y - grady_x
return Field.from_scalar_fields([curl_x, curl_y, curl_z])
else:
raise AssertionError('Can only handle 3 component vector fields in 3D!')
@@ -460,14 +460,14 @@ class Field(NDArrayOperatorsMixin):
if squeezed_field.ncomp == 2: # 2 component vector field (return perpendicular component as scalar field):
self._log.debug('input: 2 dimensions, 2 components!')
field_x, field_y = squeezed_field.comp
- grad_xx, grad_xy = field_x.gradient().comp
- grad_yx, grad_yy = field_y.gradient().comp
- return grad_yx - grad_xy
+ gradx_x, grady_x = field_x.gradient().comp
+ gradx_y, grady_y = field_y.gradient().comp
+ return gradx_y - grady_x
elif not squeezed_field.vector: # scalar field (return planar components as 2D vector field):
self._log.debug('input: 3 dimensions, scalar field!')
- grad_x, grad_y = squeezed_field.gradient().comp
- curl_x = grad_y
- curl_y = -grad_x
+ gradx, grady = squeezed_field.gradient().comp
+ curl_x = grady
+ curl_y = -gradx
return Field.from_scalar_fields([curl_x, curl_y])
else:
raise AssertionError('Can only handle 3 component vector or scalar fields in 2D!')
--
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