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Commit bc38a760 authored by payno's avatar payno
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Merge branch 'master' into 'integrate_h5tonx' 

# Conflicts:
#   est/io/io.py
parents a261fd59 e3effb06
Pipeline #55917 failed with stages
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.flake8 deleted 100644 → 0
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[flake8]
ignore = E265, E501
.gitignore
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......@@ -64,3 +64,6 @@ pushworkflow
# Visual Studio Code files
.vscode/
.empty/
# sphinx files
_generated
.gitlab-ci.yml
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......@@ -16,10 +16,10 @@ check_style:
stage: style
image: docker-registry.esrf.fr/dau/est:python3.7_stretch_pyqt5_gtk3_wxpython
before_script:
- pip install black
- pip install black flake8
script:
# run black
- LC_ALL=C.UTF-8 black --check --safe .
- flake8
# build
......@@ -34,8 +34,6 @@ doc:
- python --version
- python -m pip install pip --upgrade
- python -m pip install setuptools --upgrade
- python -m pip install -r requirements.txt
- python -m pip install -r requirements-doc.txt
- python -m pip install jupyterlab
- python -m pip install pymca --upgrade --pre
- python -m pip install xraylarch
......@@ -43,7 +41,7 @@ doc:
- mkdir artifacts
script:
- python setup.py build
- python -m pip install .
- python -m pip install .[doc]
- python setup.py build_sphinx
- mv build/sphinx/html artifacts/doc
artifacts:
......@@ -68,18 +66,16 @@ doc:
- python -m pip install pip --upgrade
- python -m pip install setuptools --upgrade
- python -m pip install numpy --upgrade
- python -m pip install pytest-cov
- python -m pip install matplotlib
script:
- source ./ci/install_scripts.sh
- install_anyqt 'master'
- python -m pip install fabio --upgrade --pre
- python -m pip install silx --upgrade --pre
- python -m pip install -r requirements.txt
- python -m pip install pymca --upgrade --pre
- python -m pip install orange3==3.21
- python -m pip install -r requirements.txt
- python -m pip install .
- /usr/bin/xvfb-run --server-args="-screen 0 1024x768x24" -a est test -v
- /usr/bin/xvfb-run --server-args="-screen 0 1024x768x24" -a python -m pytest est
.build_template: &test_linux_template_larch
......@@ -96,19 +92,16 @@ doc:
- python -m pip install setuptools --upgrade
- python -m pip install numpy --upgrade
- python -m pip install matplotlib
- python -m pip install pytest-cov
script:
- source ./ci/install_scripts.sh
- install_anyqt 'master'
- python -m pip install fabio --upgrade --pre
# - python -m pip install -r requirements.txt
- python -m pip install silx --upgrade --pre
- python -m pip install -r requirements.txt
- python -m pip install packaging
- python -m pip install xraylarch
- python -m pip install orange3==3.21
- python -m pip install -r requirements.txt
- python -m pip install .
- /usr/bin/xvfb-run --server-args="-screen 0 1024x768x24" -a est test -v
- /usr/bin/xvfb-run --server-args="-screen 0 1024x768x24" -a python -m pytest est
.build_template: &test_linux_template_pymca_larch
......@@ -125,20 +118,17 @@ doc:
- python -m pip install setuptools --upgrade
- python -m pip install numpy --upgrade
- python -m pip install matplotlib
- python -m pip install pytest-cov
script:
- source ./ci/install_scripts.sh
- install_anyqt 'master'
- python -m pip install fabio --upgrade --pre
# - python -m pip install -r requirements.txt
- python -m pip install silx --upgrade --pre
- python -m pip install pymca --upgrade --pre
- python -m pip install -r requirements.txt
- python -m pip install packaging
- python -m pip install xraylarch
- python -m pip install orange3==3.21
- python -m pip install -r requirements.txt
- python -m pip install .
- /usr/bin/xvfb-run --server-args="-screen 0 1024x768x24" -a est test -v
- /usr/bin/xvfb-run --server-args="-screen 0 1024x768x24" -a python -m pytest --cov=est est
test:python3.7-stretch-pyqt5_pymca:
......@@ -174,7 +164,6 @@ test:test-est-tutorials_pymca:
- python -m pip install ipykernel
- python -m pip install pymca --upgrade --pre
- python -m pip install silx --upgrade --pre
- python -m pip install -r requirements.txt
- python -m pip install .
- ls doc/tutorials/
script:
......
CHANGELOG.rst
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Change Log
==========
0.3.0: 12/04/2021
-----------------
* version to use zoccalo on BM23
* core:
* several minor fix (see !38)
* add noise operation
* starting saving some plot as results
* use h5py 3 instead of 2
0.2.0: 13/08/2019
-----------------
......
doc/api.rst 0 → 100644
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est API
=======
.. autosummary::
:toctree: _generated
:recursive:
est
doc/conf.py
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......@@ -34,11 +34,13 @@ sys.path.append(os.path.join(os.path.dirname(os.path.abspath(__file__)), "ext"))
# ones.
extensions = [
"sphinx.ext.autodoc",
"sphinx.ext.autosummary",
"sphinx.ext.intersphinx",
"nbsphinx",
]
# Add any paths that contain templates here, relative to this directory.
templates_path = ["templates"]
templates_path = ["_templates"]
# The suffix(es) of source filenames.
# You can specify multiple suffix as a list of string:
......@@ -62,9 +64,9 @@ author = "ESRF"
# built documents.
#
# The short X.Y version.
version = "0.3"
version = "0.4"
# The full version, including alpha/beta/rc tags.
release = "0.3"
release = "0.4"
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
......@@ -283,3 +285,11 @@ texinfo_documents = [
# If true, do not generate a @detailmenu in the "Top" node's menu.
# texinfo_no_detailmenu = False
autosummary_generate = True
autodoc_default_flags = [
"members",
"undoc-members",
"show-inheritance",
]
doc/index.rst
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......@@ -18,7 +18,7 @@ An `Orange3 <https://github.com/biolab/orange3>`_ add-on is also provided by the
tutorials/index.rst
install.rst
modules/index.rst
api.rst
larch_pymca.rst
app/index.rst
......@@ -29,7 +29,7 @@ An `Orange3 <https://github.com/biolab/orange3>`_ add-on is also provided by the
:doc:`app/index`
Applications
:doc:`modules/index`
:doc:`api`
API
:doc:`tutorials/index`
......
doc/modules/core/index.rst deleted 100644 → 0
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est.core package
================
Subpackages
-----------
.. toctree::
utils/index.rst
process/index.rst
est.core.io module
------------------
.. automodule:: est.core.io
:members:
:undoc-members:
:show-inheritance:
est.core.reprocessing module
----------------------------
.. automodule:: est.core.reprocessing
:members:
:undoc-members:
:show-inheritance:
est.core.types module
---------------------
.. automodule:: est.core.types
:members:
:undoc-members:
:show-inheritance:
Module contents
---------------
.. automodule:: est.core
:members:
:undoc-members:
:show-inheritance:
.. toctree::
:maxdepth: 4
utils/index.rst
doc/modules/core/process/index.rst deleted 100644 → 0
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est.core.process package
========================
Subpackages
-----------
.. toctree::
est.core.process.larch
est.core.process.pymca
est.core.process.process module
-------------------------------
.. automodule:: est.core.process.process
:members:
:undoc-members:
:show-inheritance:
est.core.process.progress module
--------------------------------
.. automodule:: est.core.process.progress
:members:
:undoc-members:
:show-inheritance:
est.core.process.roi module
---------------------------
.. automodule:: est.core.process.roi
:members:
:undoc-members:
:show-inheritance:
est.core.process.setup module
-----------------------------
.. automodule:: est.core.process.setup
:members:
:undoc-members:
:show-inheritance:
Module contents
---------------
.. automodule:: est.core.process
:members:
:undoc-members:
:show-inheritance:
doc/modules/core/process/xas.core.process.larch.rst deleted 100644 → 0
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est.core.process.larch package
==============================
est.core.process.larch.autobk module
------------------------------------
.. automodule:: est.core.process.larch.autobk
:members:
:undoc-members:
:show-inheritance:
est.core.process.larch.mback module
-----------------------------------
.. automodule:: est.core.process.larch.mback
:members:
:undoc-members:
:show-inheritance:
est.core.process.larch.mback\_norm module
-----------------------------------------
.. automodule:: est.core.process.larch.mback_norm
:members:
:undoc-members:
:show-inheritance:
est.core.process.larch.pre\_edge module
---------------------------------------
.. automodule:: est.core.process.larch.pre_edge
:members:
:undoc-members:
:show-inheritance:
est.core.process.larch.xftf module
----------------------------------
.. automodule:: est.core.process.larch.xftf
:members:
:undoc-members:
:show-inheritance:
Module contents
---------------
.. automodule:: est.core.process.larch
:members:
:undoc-members:
:show-inheritance:
doc/modules/core/process/xas.core.process.pymca.rst deleted 100644 → 0
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est.core.process.pymca package
==============================
est.core.process.pymca.exafs module
-----------------------------------
.. automodule:: est.core.process.pymca.exafs
:members:
:undoc-members:
:show-inheritance:
est.core.process.pymca.ft module
--------------------------------
.. automodule:: est.core.process.pymca.ft
:members:
:undoc-members:
:show-inheritance:
est.core.process.pymca.k\_weight module
---------------------------------------
.. automodule:: est.core.process.pymca.k_weight
:members:
:undoc-members:
:show-inheritance:
est.core.process.pymca.normalization module
-------------------------------------------
.. automodule:: est.core.process.pymca.normalization
:members:
:undoc-members:
:show-inheritance:
est.core.process.pymca.setup module
-----------------------------------
.. automodule:: est.core.process.pymca.setup
:members:
:undoc-members:
:show-inheritance:
Module contents
---------------
.. automodule:: est.core.process.pymca
:members:
:undoc-members:
:show-inheritance:
doc/modules/core/utils/index.rst deleted 100644 → 0
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est.core.utils package
======================
est.core.utils.designpattern module
-----------------------------------
.. automodule:: est.core.utils.designpattern
:members:
:undoc-members:
:show-inheritance:
est.core.utils.spectra module
-----------------------------
.. automodule:: est.core.utils.spectra
:members:
:undoc-members:
:show-inheritance:
Module contents
---------------
.. automodule:: est.core.utils
:members:
:undoc-members:
:show-inheritance:
doc/modules/gui/index.rst deleted 100644 → 0
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est.gui package
===============
Subpackages
-----------
est.gui.XasObjectViewer module
------------------------------
.. automodule:: est.gui.XasObjectViewer
:members:
:undoc-members:
:show-inheritance:
est.gui.icons module
--------------------
.. automodule:: est.gui.icons
:members:
:undoc-members:
:show-inheritance:
est.gui.qtapplicationmanager module
-----------------------------------
.. automodule:: est.gui.qtapplicationmanager
:members:
:undoc-members:
:show-inheritance:
est.gui.roiselector module
--------------------------
.. automodule:: est.gui.roiselector
:members:
:undoc-members:
:show-inheritance:
est.gui.xas\_object\_definition module
--------------------------------------
.. automodule:: est.gui.xas_object_definition
:members:
:undoc-members:
:show-inheritance:
Module contents
---------------
.. automodule:: est.gui
:members:
:undoc-members:
:show-inheritance:
.. toctree::
:maxdepth: 4
larch/est.gui.larch.rst
doc/modules/gui/larch/xas.gui.larch.rst deleted 100644 → 0
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est.gui.larch package
=====================
est.gui.larch.autobk module
---------------------------
.. automodule:: est.gui.larch.autobk
:members:
:undoc-members:
:show-inheritance:
est.gui.larch.mback module
--------------------------
.. automodule:: est.gui.larch.mback
:members:
:undoc-members:
:show-inheritance:
est.gui.larch.pre\_edge module
------------------------------
.. automodule:: est.gui.larch.pre_edge
:members:
:undoc-members:
:show-inheritance:
est.gui.larch.utils module
--------------------------
.. automodule:: est.gui.larch.utils
:members:
:undoc-members:
:show-inheritance:
est.gui.larch.xftf module
-------------------------
.. automodule:: est.gui.larch.xftf
:members:
:undoc-members:
:show-inheritance:
Module contents
---------------
.. automodule:: est.gui.larch
:members:
:undoc-members:
:show-inheritance:
doc/modules/index.rst deleted 100644 → 0
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API
===
.. toctree::
:maxdepth: 4
core/index.rst
gui/index.rst
io/index.rst
pushworkflow/index.rst
doc/modules/io/est.io.utils.rst deleted 100644 → 0
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est.io.utils package
====================
est.io.utils.larch module
-------------------------
.. automodule:: est.io.utils.larch
:members:
:undoc-members:
:show-inheritance:
est.io.utils.pymca module
-------------------------
.. automodule:: est.io.utils.pymca
:members:
:undoc-members:
:show-inheritance:
Module contents
---------------
.. automodule:: est.io.utils
:members:
:undoc-members:
:show-inheritance:
doc/modules/io/index.rst deleted 100644 → 0
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est.io package
==============
Subpackages
-----------
.. toctree::
est.io.utils
est.io.io module
----------------
.. automodule:: est.io.io
:members:
:undoc-members:
:show-inheritance:
Module contents
---------------
.. automodule:: est.io
:members:
:undoc-members:
:show-inheritance:
est/__init__.py
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......@@ -22,6 +22,7 @@
# THE SOFTWARE.
#
# ###########################################################################*/
"""est package provides a way to create processing workflows for spectroscopy from pymca and larch libraries"""
from __future__ import absolute_import, print_function, division
......@@ -39,11 +40,8 @@ _logging.getLogger(__name__).addHandler(_logging.NullHandler())
project = _os.path.basename(_os.path.dirname(_os.path.abspath(__file__)))
try:
from ._version import __date__ as date # noqa
from ._version import version, version_info, hexversion, strictversion # noqa
except ImportError:
pass
# not raised for now because fail with pip install -e option. Something to
# look at.
# raise RuntimeError("Do NOT use %s from its sources: build it and use the built version" % project)
from .version import __date__ as date # noqa
from .version import version, version_info, hexversion, strictversion # noqa
__version__ = version
est/__main__.py
View file @ bc38a760
......@@ -36,9 +36,6 @@ __date__ = "10/12/2020"