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Merge branch 'release_candidate' for release 0.3.0 into master
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Benders authored and Benders committed Oct 9, 2018
2 parents a1f641c + 9bfdf4a commit d22bb3f
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20 changes: 14 additions & 6 deletions .travis.yml
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Expand Up @@ -2,8 +2,7 @@ cache: apt
sudo: true
language: python
python:
- "2.7"
- "3.3"
- 2.7
before_install:
- wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh; # grab miniconda
- bash miniconda.sh -b -p $HOME/miniconda # install miniconda
Expand All @@ -13,12 +12,21 @@ before_install:
- conda install pyyaml
- conda info -a # and print the info

install:
- conda env create --file environment.yml #set up the environment thats in the file
- source activate test-environment # activate it
- python setup.py install # install ptypy
env:
- TEST_ENV_NAME=core_dependencies
- TEST_ENV_NAME=full_dependencies

install: True

script:
- conda env create --file ${TEST_ENV_NAME}.yml #set up the environment thats in the file
- source activate ${TEST_ENV_NAME} # activate it
- conda install pytest # additional dependencies for the tests
- pip install pytest-cov
- pip install coveralls
- echo $PYTHONPATH
- conda list
- python setup.py install # install ptypy
- py.test ptypy/test -v --cov ptypy --cov-report term-missing # now run the tests

after_script:
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16 changes: 16 additions & 0 deletions benchmark/model_speed.py
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@@ -0,0 +1,16 @@

from ptypy import utils as u
from ptypy.core import Ptycho, Vanilla

p = u.Param()
p.verbose_level = 3
p.io = u.Param()
p.io.home = "/tmp/ptypy/"
p.scans = u.Param()
p.scans.MF = u.Param()
p.scans.MF.data= u.Param()
p.scans.MF.name = 'Vanilla'
p.scans.MF.data.name = 'QuickScan'
p.scans.MF.data.num_frames = 50000
p.scans.MF.data.shape = 32
Ptycho(p,level=2)
8 changes: 8 additions & 0 deletions core_dependencies.yml
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@@ -0,0 +1,8 @@
name: core_dependencies
channels:
- conda-forge
dependencies:
- python=2.7
- numpy
- scipy
- h5py
7 changes: 6 additions & 1 deletion doc/Makefile
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Expand Up @@ -3,8 +3,13 @@

# You can set these variables from the command line.
SPHINXOPTS =
SPHINXBUILD = ~/.local/bin/sphinx-build

ifeq ($(SPHINXBUILD),"")
SPHINXBUILD = ~/.local/bin/sphinx-build
endif

#SPHINXBUILD = /usr/bin/sphinx-build

PAPER =
BUILDDIR = build

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66 changes: 28 additions & 38 deletions doc/conf.py
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Expand Up @@ -21,11 +21,11 @@
#sys.path.insert(0, os.path.abspath('.'))

# generate paramters.rst and other rst
execfile('parameters2rst.py')
execfile('tmp2rst.py')
execfile('version.py')
import subprocess
subprocess.call(['python', 'script2rst.py']) # We need this to have a clean sys.argv
subprocess.check_call(['python', 'script2rst.py']) # We need this to have a clean sys.argv
subprocess.check_call(['python','parameters2rst.py'])
subprocess.check_call(['python','tmp2rst.py'])
execfile('version.py')

# -- General configuration ------------------------------------------------

Expand All @@ -42,73 +42,63 @@
]


def truncate_docstring(app, what, name, obj, options, lines):
"""
Remove the Default parameter entries.
"""
if not hasattr(obj, 'DEFAULT'):
return
if any(l.strip().startswith('Defaults:') for l in lines):
while True:
if lines.pop(-1).strip().startswith('Defaults:'):
break


def remove_mod_docstring(app, what, name, obj, options, lines):
from ptypy import utils as u
import numpy as np
from ptypy import defaults_tree
u.verbose.report.headernewline='\n\n'
searchstr = ':py:data:'

def get_refs(dct,pd,depth=2, indent = ''):
if depth<0:
def get_refs(dct, pd, depth=2, indent=''):
if depth < 0:
return

for k, value in dct.iteritems():
ref = ', see :py:data:`~%s`' % pd.children[k].entry_point if pd.children.has_key(k) else ''
if hasattr(value,'items'):
if hasattr(value, 'items'):
v = str(value.__class__.__name__)
elif str(value)==value:
v='"%s"' % value
elif str(value) == value:
v = '"%s"' % value
else:
v=str(value)
v = str(value)

lines.append(indent+'* *' +k+'* = ``'+v+'``' +ref)#+'\n')
lines.append(indent + '* *' + k + '* = ``' + v + '``' + ref)

if hasattr(value,'items'):
#lines.append('\n\n')
if hasattr(value, 'items'):
lines.append("")
get_refs(value,pd.children[k],depth=depth-1, indent = indent+' ')
get_refs(value, pd.children[k], depth=depth-1, indent=indent+' ')
lines.append("")
#lines.append('\n\n')

#if name.find('DEFAULT')>=0:
if isinstance(obj, u.Param) or isinstance(obj, dict):
keys = obj.keys()
pd = None

"""
# auto_matching
for entry,pdesc in u.validator.entry_points_Param.iteritems():
chkeys = ':'.join([k.split('.')[-1] for k in pdesc.children.keys()])
#print chkeys
#print keys
matches = [key in chkeys for key in keys]
#print matches
print np.mean(matches)
if np.mean(matches)>0.8:
print 'Param match'
e=entry
print e
pd = pdesc
break
"""
for l in lines:
start = l.find(searchstr)
if start > -1:
newstr = l[start:]
newstr = newstr.split('`')[1]
newstr = newstr.replace('~', '')
#print newstr, what, name, options
pd = u.validator.entry_points_dct.get(newstr,None)
pd = defaults_tree.get(newstr)
break

if pd is not None:
#lines.append('Match with :py:data:`.%s` \n\n' %pd.entry_point)
get_refs(obj, pd, depth=2, indent='')
#print lines


def setup(app):
app.connect('autodoc-process-docstring', remove_mod_docstring)
app.connect('autodoc-process-docstring', truncate_docstring)


napoleon_use_ivar = True
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2 changes: 1 addition & 1 deletion doc/html_templates/ptypysphinx/download.html
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Expand Up @@ -32,5 +32,5 @@
<ul class="simple">
<li>I13, <a href="https://www.diamond.ac.uk">Diamond</a></li>
<li>ID16, <a href="https://www.esrf.eu">ESRF</a></li>
<li>NanoScopium, <a href="https://www.synchrotron-soleil.fr">Soleil</a></li>
<!--<li>NanoScopium, <a href="https://www.synchrotron-soleil.fr">Soleil</a></li>-->
</ul>
10 changes: 5 additions & 5 deletions doc/index.rst
Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@ Highlights
overcoming partial coherence or related phenomena.

* **On-the-fly** reconstructions (while data is being acquired) using the
the :any:`PtyScan` class in the linking mode :ref:`linking mode<case_flyscan>`
the :py:class:`PtyScan` class in the linking mode :ref:`linking mode<case_flyscan>`


Quicklinks
Expand All @@ -68,10 +68,10 @@ Quicklinks

.. rubric:: Footnotes

.. [#Enders2016] B.Enders and P.Thibault, **Proc. R. Soc. A** 472, 20160640 (2016), `doi <http://dx.doi.org/10.1098/rspa.2016.0640>`_
.. [#Enders2016] B.Enders and P.Thibault, **Proc. R. Soc. A** 472, 20160640 (2016), `doi <http://dx.doi.org/10.1098/rspa.2016.0640>`__
.. [#Thi2013] P.Thibault and A.Menzel, **Nature** 494, 68 (2013), `doi <http://dx.doi.org/10.1038/nature11806>`_
.. [#Thi2013] P.Thibault and A.Menzel, **Nature** 494, 68 (2013), `doi <http://dx.doi.org/10.1038/nature11806>`__
.. [#ml] P.Thibault and M.Guizar-Sicairos, **New J. of Phys.** 14, 6 (2012), `doi <http://dx.doi.org/10.1126/science.1158573>`_
.. [#ml] P.Thibault and M.Guizar-Sicairos, **New J. of Phys.** 14, 6 (2012), `doi <http://dx.doi.org/10.1126/science.1158573>`__
.. [#dm] P.Thibault, M.Dierolf *et al.*, **New J. of Phys. 14**, 6 (2012), `doi <http://dx.doi.org/10.1088/1367-2630/14/6/063004>`_
.. [#dm] P.Thibault, M.Dierolf *et al.*, **New J. of Phys. 14**, 6 (2012), `doi <http://dx.doi.org/10.1088/1367-2630/14/6/063004>`__
68 changes: 44 additions & 24 deletions doc/parameters2rst.py
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@

from ptypy import utils as u
from ptypy import defaults_tree

prst = open('rst/parameters.rst','w')

Expand All @@ -9,32 +9,52 @@
Header+= '************************\n\n'
prst.write(Header)

names = u.validator.parameter_descriptions
for name,desc in u.validator.parameter_descriptions.iteritems():
if name=='':
for path, desc in defaults_tree.descendants:

types = desc.type
default = desc.default
lowlim, uplim = desc.limits
is_wildcard = (desc.name == '*')

if is_wildcard:
path = path.replace('*', desc.parent.name[:-1] + '_00')

if path == '':
continue
if hasattr(desc,'children') and desc.parent is u.validator.pdroot:
prst.write('\n'+name+'\n')
prst.write('='*len(name)+'\n\n')
if hasattr(desc,'children') and desc.parent.parent is u.validator.pdroot:
prst.write('\n'+name+'\n')
prst.write('-'*len(name)+'\n\n')

prst.write('.. py:data:: '+name)
prst.write('('+', '.join([t for t in desc.type])+')')
if desc.children and desc.parent is desc.root:
prst.write('\n'+path+'\n')
prst.write('='*len(path)+'\n\n')
if desc.children and desc.parent.parent is desc.root:
prst.write('\n'+path+'\n')
prst.write('-'*len(path)+'\n\n')

prst.write('.. py:data:: '+path)

if desc.is_symlink:
tp = 'Param'
else:
tp = ', '.join([str(t) for t in types])
prst.write(' ('+tp+')')
prst.write('\n\n')
num = str(desc.ID) if hasattr(desc,'ID') else "None"
prst.write(' *('+num+')* '+desc.shortdoc+'\n\n')
prst.write(' '+desc.longdoc.replace('\n','\n ')+'\n\n')
prst.write(' *default* = ``'+str(desc.default))
if desc.lowlim is not None and desc.uplim is not None:
prst.write(' (>'+str(desc.lowlim)+', <'+str(desc.uplim)+')``\n')
elif desc.lowlim is not None and desc.uplim is None:
prst.write(' (>'+str(desc.lowlim)+')``\n')
elif desc.lowlim is None and desc.uplim is not None:
prst.write(' (<'+str(desc.uplim)+')``\n')

if is_wildcard:
prst.write(' *Wildcard*: multiple entries with arbitrary names are accepted.\n\n')

prst.write(' '+desc.help+'\n\n')
prst.write(' '+desc.doc.replace('<newline>','\n').replace('\n', '\n ')+'\n\n')

if desc.is_symlink:
prst.write(' *default* = '+':py:data:`'+desc.path+'`\n')
else:
prst.write('``\n')
prst.write(' *default* = ``'+repr(default))
if lowlim is not None and uplim is not None:
prst.write(' (>'+str(lowlim)+', <'+str(uplim)+')``\n')
elif lowlim is not None and uplim is None:
prst.write(' (>'+str(lowlim)+')``\n')
elif lowlim is None and uplim is not None:
prst.write(' (<'+str(uplim)+')``\n')
else:
prst.write('``\n')

prst.write('\n')
prst.close()
8 changes: 0 additions & 8 deletions doc/rst/ptypy.core.rst
Original file line number Diff line number Diff line change
Expand Up @@ -44,14 +44,6 @@ ptypy.core.manager module
:undoc-members:
:show-inheritance:

ptypy.core.model module
-----------------------

.. automodule:: ptypy.core.model
:members:
:undoc-members:
:show-inheritance:

ptypy.core.paths module
-----------------------

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29 changes: 29 additions & 0 deletions doc/rst/ptypy.debug.rst
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@@ -0,0 +1,29 @@
ptypy.debug package
===================

Submodules
----------

ptypy.debug.embedded_shell module
---------------------------------

.. automodule:: ptypy.debug.embedded_shell
:members:
:undoc-members:
:show-inheritance:

ptypy.debug.ipython_kernel module
---------------------------------

.. automodule:: ptypy.debug.ipython_kernel
:members:
:undoc-members:
:show-inheritance:

Module contents
---------------

.. automodule:: ptypy.debug
:members:
:undoc-members:
:show-inheritance:
1 change: 1 addition & 0 deletions doc/rst/ptypy.rst
Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@ Subpackages
ptypy.resources
ptypy.simulations
ptypy.utils
ptypy.debug

Module contents
---------------
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14 changes: 3 additions & 11 deletions doc/rst/ptypy.utils.rst
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Expand Up @@ -12,14 +12,6 @@ ptypy.utils.array_utils module
:undoc-members:
:show-inheritance:

ptypy.utils.embedded_shell module
---------------------------------

.. automodule:: ptypy.utils.embedded_shell
:members:
:undoc-members:
:show-inheritance:

ptypy.utils.math_utils module
-----------------------------

Expand Down Expand Up @@ -76,10 +68,10 @@ ptypy.utils.scripts module
:undoc-members:
:show-inheritance:

ptypy.utils.validator module
----------------------------
ptypy.utils.descriptor module
-----------------------------

.. automodule:: ptypy.utils.validator
.. automodule:: ptypy.utils.descriptor
:members:
:undoc-members:
:show-inheritance:
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