From a47223e7b64ec61aa980af37a8e487f21534ce39 Mon Sep 17 00:00:00 2001
From: Rafael Gort <rafael.gort@xfel.eu>
Date: Mon, 27 Apr 2020 16:17:50 +0200
Subject: [PATCH] test packaging
---
README.rst | 14 ++
__init__.py | 10 --
setup.py | 23 +++
toolbox/__init__.py | 10 ++
DSSC.py => toolbox/detectors/DSSC.py | 0
.../detectors/DSSC1module.py | 0
FastCCD.py => toolbox/detectors/FastCCD.py | 0
toolbox/detectors/__init__.py | 11 ++
Load.py => toolbox/load.py | 0
toolbox/misc/__init__.py | 31 ++++
.../misc/azimuthal_integrator.py | 2 +-
.../misc/bunch_pattern.py | 0
.../misc/bunch_pattern_external.py | 0
Laser_utils.py => toolbox/misc/laser_utils.py | 0
toolbox/plot/plot_dssc.py | 0
XAS.py => toolbox/routines/XAS.py | 0
.../routines/knife_edge.py | 0
xgm.py => toolbox/routines/xgm.py | 0
.../test_package_demo-checkpoint.ipynb | 151 ++++++++++++++++++
toolbox/test/__init__.py | 1 +
toolbox/test/test_top_level.py | 79 +++++++++
21 files changed, 321 insertions(+), 11 deletions(-)
create mode 100644 README.rst
delete mode 100644 __init__.py
create mode 100644 setup.py
create mode 100644 toolbox/__init__.py
rename DSSC.py => toolbox/detectors/DSSC.py (100%)
rename DSSC1module.py => toolbox/detectors/DSSC1module.py (100%)
rename FastCCD.py => toolbox/detectors/FastCCD.py (100%)
create mode 100644 toolbox/detectors/__init__.py
rename Load.py => toolbox/load.py (100%)
create mode 100644 toolbox/misc/__init__.py
rename azimuthal_integrator.py => toolbox/misc/azimuthal_integrator.py (98%)
rename bunch_pattern.py => toolbox/misc/bunch_pattern.py (100%)
rename bunch_pattern_external.py => toolbox/misc/bunch_pattern_external.py (100%)
rename Laser_utils.py => toolbox/misc/laser_utils.py (100%)
create mode 100644 toolbox/plot/plot_dssc.py
rename XAS.py => toolbox/routines/XAS.py (100%)
rename knife_edge.py => toolbox/routines/knife_edge.py (100%)
rename xgm.py => toolbox/routines/xgm.py (100%)
create mode 100644 toolbox/test/.ipynb_checkpoints/test_package_demo-checkpoint.ipynb
create mode 100644 toolbox/test/__init__.py
create mode 100644 toolbox/test/test_top_level.py
diff --git a/README.rst b/README.rst
new file mode 100644
index 0000000..1db37f5
--- /dev/null
+++ b/README.rst
@@ -0,0 +1,14 @@
+###########
+SCS ToolBox
+###########
+
+Kernel
+######
+
+The SCS ToolBox is design to work in the exfel_anaconda3 environement. This can
+be selected on the online cluster by:
+
+`module load exfel exfel_anaconda3`
+
+before launching the jupyter-notebook or on max-jhub by selecting the 'xfel'
+kernel instead of the 'Python 3' anaconda environement maintained by DESY.
\ No newline at end of file
diff --git a/__init__.py b/__init__.py
deleted file mode 100644
index ee34d75..0000000
--- a/__init__.py
+++ /dev/null
@@ -1,10 +0,0 @@
-from ToolBox.Load import *
-from ToolBox.xgm import *
-from ToolBox.XAS import *
-from ToolBox.knife_edge import *
-from ToolBox.Laser_utils import *
-from ToolBox.DSSC import DSSC
-from ToolBox.azimuthal_integrator import *
-from ToolBox.DSSC1module import *
-from ToolBox.bunch_pattern import *
-from ToolBox.FastCCD import *
diff --git a/setup.py b/setup.py
new file mode 100644
index 0000000..34a3af7
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,23 @@
+from setuptools import setup, find_packages
+
+with open('README.rst') as f:
+ readme = f.read()
+
+# _get_version() # get current version from release tag
+# ......
+
+setup(name='toolbox_scs',
+ # to be replaced by _get_version()
+ version='1.0.0-a1',
+ description="A collection of code, often used at the SCS beamline",
+ long_description=readme,
+ author='Loic Le Guyader, Laurent Mercadier, ....',
+ url="https://git.xfel.eu/gitlab/SCS/ToolBox.git",
+ keywords='XAS, xgm, DSSC, FCCD, PPL',
+ packages=['toolbox'],
+ install_requires=[
+ 'xarray', 'numpy', 'matplotlib',
+ 'pandas', 'bisect', 'scipy', 'h5py',
+ 'extra_data', 'euxfel_bunch_pattern',
+ ],
+ )
diff --git a/toolbox/__init__.py b/toolbox/__init__.py
new file mode 100644
index 0000000..b27904a
--- /dev/null
+++ b/toolbox/__init__.py
@@ -0,0 +1,10 @@
+from .load import mnemonics, load, concatenateRuns
+
+__all__ = (
+ # Top level functions
+ "load",
+ "concatenateRuns",
+ # Classes
+ # Variables
+ "mnemonics",
+)
diff --git a/DSSC.py b/toolbox/detectors/DSSC.py
similarity index 100%
rename from DSSC.py
rename to toolbox/detectors/DSSC.py
diff --git a/DSSC1module.py b/toolbox/detectors/DSSC1module.py
similarity index 100%
rename from DSSC1module.py
rename to toolbox/detectors/DSSC1module.py
diff --git a/FastCCD.py b/toolbox/detectors/FastCCD.py
similarity index 100%
rename from FastCCD.py
rename to toolbox/detectors/FastCCD.py
diff --git a/toolbox/detectors/__init__.py b/toolbox/detectors/__init__.py
new file mode 100644
index 0000000..e0f177e
--- /dev/null
+++ b/toolbox/detectors/__init__.py
@@ -0,0 +1,11 @@
+from .detectors import (
+ DSSC, process_one_module,
+ )
+
+__all__ = (
+ # Functions
+ "process_one_module",
+ # Classes
+ "DSSC",
+ # Variables
+)
diff --git a/Load.py b/toolbox/load.py
similarity index 100%
rename from Load.py
rename to toolbox/load.py
diff --git a/toolbox/misc/__init__.py b/toolbox/misc/__init__.py
new file mode 100644
index 0000000..7ed9d39
--- /dev/null
+++ b/toolbox/misc/__init__.py
@@ -0,0 +1,31 @@
+from .bunch_pattern import (
+ extractBunchPattern, pulsePatternInfo, repRate, sortBAMdata,
+ )
+from .bunch_pattern_external import (
+ is_sase_3, is_sase_1, is_ppl, get_index_ppl, get_index_sase1,
+ get_index_sase3,
+ )
+from .laser_utils import (
+ positionToDelay, degToRelPower,
+ )
+from . azimuthal_integrator import (
+ AzimutalIntegrator,
+
+__all__ = (
+ # Functions
+ "extractBunchPattern",
+ "pulsePatternInfo",
+ "repRate",
+ "sortBAMdata",
+ "is_sase_3",
+ "is_sase_1",
+ "is_ppl",
+ "get_index_ppl",
+ "get_index_sase1",
+ "get_index_sase3",
+ "positionToDelay",
+ "degToRelPower",
+ # Classes
+ "AzimutalIntegrator",
+ # Variables
+)
diff --git a/azimuthal_integrator.py b/toolbox/misc/azimuthal_integrator.py
similarity index 98%
rename from azimuthal_integrator.py
rename to toolbox/misc/azimuthal_integrator.py
index b84df6c..e682281 100644
--- a/azimuthal_integrator.py
+++ b/toolbox/misc/azimuthal_integrator.py
@@ -1,6 +1,6 @@
import numpy as np
-class azimuthal_integrator(object):
+class AzimutalIntegrator(object):
def __init__(self, imageshape, center, polar_range, dr=2, aspect=204/236):
'''
Create a reusable integrator for repeated azimuthal integration of similar
diff --git a/bunch_pattern.py b/toolbox/misc/bunch_pattern.py
similarity index 100%
rename from bunch_pattern.py
rename to toolbox/misc/bunch_pattern.py
diff --git a/bunch_pattern_external.py b/toolbox/misc/bunch_pattern_external.py
similarity index 100%
rename from bunch_pattern_external.py
rename to toolbox/misc/bunch_pattern_external.py
diff --git a/Laser_utils.py b/toolbox/misc/laser_utils.py
similarity index 100%
rename from Laser_utils.py
rename to toolbox/misc/laser_utils.py
diff --git a/toolbox/plot/plot_dssc.py b/toolbox/plot/plot_dssc.py
new file mode 100644
index 0000000..e69de29
diff --git a/XAS.py b/toolbox/routines/XAS.py
similarity index 100%
rename from XAS.py
rename to toolbox/routines/XAS.py
diff --git a/knife_edge.py b/toolbox/routines/knife_edge.py
similarity index 100%
rename from knife_edge.py
rename to toolbox/routines/knife_edge.py
diff --git a/xgm.py b/toolbox/routines/xgm.py
similarity index 100%
rename from xgm.py
rename to toolbox/routines/xgm.py
diff --git a/toolbox/test/.ipynb_checkpoints/test_package_demo-checkpoint.ipynb b/toolbox/test/.ipynb_checkpoints/test_package_demo-checkpoint.ipynb
new file mode 100644
index 0000000..da2d5f2
--- /dev/null
+++ b/toolbox/test/.ipynb_checkpoints/test_package_demo-checkpoint.ipynb
@@ -0,0 +1,151 @@
+{
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "# Boltzmann Modules\n",
+ "\n",
+ "### This notebook is part of the repository for demonstration purposes."
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "The code below should be run from the command line in the directory: scs_simulations/test.\n",
+ "\n",
+ "The test suites directly import the scs_simulation package. The idea is to notice problems related to packaging immediately (changing folder structure, breaking relative dependencies between the subpackages ....).\n",
+ "\n",
+ "During development, use the -e flag when installing the module via pip. This makes changes effective immediately, without having to reinstall the package."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "usage: test_boltzmann_simulation.py [-h] [--list-suites]\n",
+ " [--test-suites S [S ...]]\n",
+ "\n",
+ "optional arguments:\n",
+ " -h, --help show this help message and exit\n",
+ " --list-suites list possible test suites\n",
+ " --test-suites S [S ...]\n",
+ " a list of valid test suites\n"
+ ]
+ }
+ ],
+ "source": [
+ "%run test_boltzmann_simulation.py --help"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "metadata": {
+ "scrolled": true
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "\n",
+ "Possible test suites:\n",
+ "-------------------------\n",
+ "boltzmann-imports\n",
+ "boltzmann-manipulations\n",
+ "-------------------------\n",
+ "\n"
+ ]
+ }
+ ],
+ "source": [
+ "%run test_boltzmann_simulation.py --list-suites"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "test_adddos (__main__.BoltzmannData) ... DEBUG:scs_simulations.boltzmann_data.data_manipulation:Try to append parabolic bs at high-energy DOS.\n",
+ "DEBUG:scs_simulations.boltzmann_data.data_manipulation:dataframe has been extended\n",
+ "ok\n",
+ "test_electronsholes (__main__.BoltzmannData) ... DEBUG:scs_simulations.boltzmann_data.data_manipulation:Try to add electrons and holes\n",
+ "DEBUG:scs_simulations.boltzmann_data.data_manipulation:Added columns for electrons and holes\n",
+ "ok\n",
+ "\n",
+ "----------------------------------------------------------------------\n",
+ "Ran 2 tests in 0.068s\n",
+ "\n",
+ "OK\n"
+ ]
+ }
+ ],
+ "source": [
+ "%run test_boltzmann_simulation.py --test-suites boltzmann-manipulations"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {
+ "scrolled": true
+ },
+ "outputs": [],
+ "source": []
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "py38-scs",
+ "language": "python",
+ "name": "py38-scs"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.8.0"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 1
+}
diff --git a/toolbox/test/__init__.py b/toolbox/test/__init__.py
new file mode 100644
index 0000000..8b13789
--- /dev/null
+++ b/toolbox/test/__init__.py
@@ -0,0 +1 @@
+
diff --git a/toolbox/test/test_top_level.py b/toolbox/test/test_top_level.py
new file mode 100644
index 0000000..5703c30
--- /dev/null
+++ b/toolbox/test/test_top_level.py
@@ -0,0 +1,79 @@
+import unittest
+import logging
+import os
+import sys
+import argparse
+
+
+import toolbox_scs as tb
+
+suites = {"suite-1": (
+ "test_load",
+ "test_load"
+ )
+ }
+
+
+def list_suites():
+ print("""\nPossible test suites:\n-------------------------""")
+ for key in suites:
+ print(key)
+ print("-------------------------\n")
+
+
+class TemplateTest(unittest.TestCase):
+ def setUp(self):
+ pass
+
+ def tearDown(self):
+ pass
+
+ def test_load(self):
+ #tb.load(....)
+ pass
+
+
+def suite(*tests):
+ suite = unittest.TestSuite()
+ for test in tests:
+ suite.addTest(TemplateTest(test))
+ return suite
+
+
+def main(*cliargs):
+ logging.basicConfig(level=logging.DEBUG)
+ log_root = logging.getLogger(__name__)
+ try:
+ for test_suite in cliargs:
+ if test_suite in suites:
+ runner = unittest.TextTestRunner(verbosity=2)
+ runner.run(suite(*suites[test_suite]))
+ else:
+ log_root.warning(
+ "Unknown suite: '{}'".format(test_suite))
+ pass
+ except Exception as err:
+ log_root.error("Unecpected error: {}".format(err),
+ exc_info=True)
+ pass
+
+
+
+
+
+
+if __name__ == '__main__':
+ parser = argparse.ArgumentParser()
+ parser.add_argument('--list-suites',
+ action='store_true',
+ help='list possible test suites')
+ parser.add_argument('--test-suites', metavar='S',
+ nargs='+', action='store',
+ help='a list of valid test suites')
+ args = parser.parse_args()
+
+ if args.list_suites:
+ list_suites()
+
+ if args.test_suites:
+ main(*args.test_suites)
--
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