From 63e1c6fd7761a7c0dbcaad21f599caf70d26fd31 Mon Sep 17 00:00:00 2001
From: Cammille Carinan <cammille.carinan@xfel.eu>
Date: Wed, 26 May 2021 09:33:20 +0200
Subject: [PATCH] Refactor packaging
---
doc/getting_started.rst | 4 +-
setup.py | 21 ++--
src/toolbox_scs/__init__.py | 53 ++++------
src/toolbox_scs/constants.py | 5 +
src/toolbox_scs/detectors/__init__.py | 97 ++++---------------
.../detectors/azimuthal_integrator.py | 5 +
src/toolbox_scs/detectors/bam_detectors.py | 3 +
src/toolbox_scs/detectors/digitizers.py | 8 ++
src/toolbox_scs/detectors/dssc.py | 5 +-
src/toolbox_scs/detectors/dssc_data.py | 7 ++
src/toolbox_scs/detectors/dssc_misc.py | 8 ++
src/toolbox_scs/detectors/dssc_processing.py | 4 +
src/toolbox_scs/detectors/fccd.py | 3 +-
src/toolbox_scs/detectors/pes.py | 6 ++
src/toolbox_scs/detectors/xgm.py | 5 +
src/toolbox_scs/load.py | 7 ++
src/toolbox_scs/misc/__init__.py | 28 ++----
src/toolbox_scs/misc/bunch_pattern.py | 6 ++
.../misc/bunch_pattern_external.py | 7 ++
src/toolbox_scs/misc/laser_utils.py | 6 ++
src/toolbox_scs/mnemonics_machinery.py | 4 +
src/toolbox_scs/routines/XAS.py | 5 +
src/toolbox_scs/routines/__init__.py | 33 ++-----
src/toolbox_scs/routines/knife_edge.py | 4 +
24 files changed, 161 insertions(+), 173 deletions(-)
diff --git a/doc/getting_started.rst b/doc/getting_started.rst
index 05e2d9f..f90b9d6 100644
--- a/doc/getting_started.rst
+++ b/doc/getting_started.rst
@@ -15,10 +15,10 @@ If the toolbox has been installed in your home directory previously, everything
.. code:: bash
- pip install --user .
+ pip install --user ".[maxwell]"
Alternatively, use the -e flag for installation to install the package in development mode.
.. code:: bash
- pip install --user -e .
+ pip install --user -e ".[maxwell]"
diff --git a/setup.py b/setup.py
index 9076e91..fc1c33f 100644
--- a/setup.py
+++ b/setup.py
@@ -8,6 +8,13 @@ with open('VERSION') as f:
_version = _version.strip("\n")
+basic_analysis_reqs = ['numpy', 'scipy',] # and is readily available in Karabo
+advanced_analysis_reqs = [
+ 'pandas', 'imageio', 'xarray>=0.13.0', 'h5py', 'h5netcdf',]
+interactive_reqs = ['ipykernel', 'matplotlib', 'tqdm',]
+maxwell_reqs = ['joblib', 'extra_data', 'euxfel_bunch_pattern>=0.6']
+
+
setup(name='toolbox_scs',
version=_version,
description="A collection of code for the SCS beamline",
@@ -20,9 +27,11 @@ setup(name='toolbox_scs',
package_dir={'': 'src'},
packages=find_packages('src'),
package_data={},
- install_requires=[
- 'xarray>=0.13.0', 'numpy', 'matplotlib',
- 'pandas', 'scipy', 'h5py', 'h5netcdf',
- 'extra_data', 'euxfel_bunch_pattern>=0.6',
- ],
- )
+ install_requires=basic_analysis_reqs,
+ extras_require={
+ 'advanced': advanced_analysis_reqs,
+ 'interactive': interactive_reqs,
+ 'maxwell': advanced_analysis_reqs + interactive_reqs + maxwell_reqs,
+ 'test': ['pytest']
+ }
+)
diff --git a/src/toolbox_scs/__init__.py b/src/toolbox_scs/__init__.py
index f1acd89..a1d290a 100644
--- a/src/toolbox_scs/__init__.py
+++ b/src/toolbox_scs/__init__.py
@@ -1,39 +1,22 @@
-from .load import (load, concatenateRuns, get_array, run_by_path)
-from .constants import mnemonics
-from .mnemonics_machinery import mnemonics_for_run
-
-__all__ = (
- # functions
- "load",
- "concatenateRuns",
- "get_array",
- "run_by_path",
- "mnemonics_for_run",
- # Classes
- # Variables
- "mnemonics",
-)
+from .constants import *
+from .detectors import *
+# Module name is the same as a child function, we use alias to avoid conflict
+import toolbox_scs.load as load_module
+from .load import *
-# ------------------------------------------------------------------------------
-# Clean namespace
-# clean_ns is a collection of undesired items in the namespace
-# ------------------------------------------------------------------------------
+from .misc import *
+from .mnemonics_machinery import *
+from .routines import *
-clean_ns = [
- # filenames
- 'constants',
- 'mnemonics_machinery'
- # folders
- 'misc',
- 'util',
- 'detectors',
- 'routines',
- ]
-
-for name in dir():
- if name in clean_ns:
- del globals()[name]
+__all__ = (
+ # top-level modules
+ constants.__all__
+ + load_module.__all__
+ + mnemonics_machinery.__all__
-del globals()['clean_ns']
-del globals()['name']
+ # submodules
+ + detectors.__all__
+ + misc.__all__
+ + routines.__all__
+)
diff --git a/src/toolbox_scs/constants.py b/src/toolbox_scs/constants.py
index 28587b5..09784e7 100644
--- a/src/toolbox_scs/constants.py
+++ b/src/toolbox_scs/constants.py
@@ -1,3 +1,8 @@
+__all__ = [
+ 'mnemonics'
+]
+
+
mnemonics = {
# Machine
"sase3": ({'source': 'SCS_RR_UTC/MDL/BUNCH_DECODER',
diff --git a/src/toolbox_scs/detectors/__init__.py b/src/toolbox_scs/detectors/__init__.py
index a34b0b9..da11c8f 100644
--- a/src/toolbox_scs/detectors/__init__.py
+++ b/src/toolbox_scs/detectors/__init__.py
@@ -1,82 +1,21 @@
-from .xgm import (
- get_xgm, calibrate_xgm)
-from .digitizers import (
- get_peaks, get_tim_peaks, get_laser_peaks, get_digitizer_peaks,
- check_peak_params)
-from .bam_detectors import get_bam
-from .pes import get_pes_tof, get_pes_params
-from .dssc_data import (
- save_xarray, load_xarray, get_data_formatted, save_attributes_h5)
-from .dssc_misc import (
- load_dssc_info, create_dssc_bins, quickmask_DSSC_ASIC,
- get_xgm_formatted, load_mask)
-from .dssc_processing import (
- process_dssc_data)
-from .dssc import (
- DSSCBinner, DSSCFormatter)
-from .azimuthal_integrator import (
- AzimuthalIntegrator, AzimuthalIntegratorDSSC)
+from .azimuthal_integrator import *
+from .bam_detectors import *
+from .digitizers import *
+from .dssc import *
+from .dssc_data import *
+from .dssc_misc import *
+from .dssc_processing import *
+from .pes import *
+from .xgm import *
__all__ = (
- # Functions
- "get_xgm",
- "calibrate_xgm",
- "get_peaks",
- "get_tim_peaks",
- "get_laser_peaks",
- "get_digitizer_peaks",
- "check_peak_params",
- "get_bam",
- "get_pes_tof",
- "get_pes_params",
- "save_xarray",
- "load_xarray",
- "get_data_formatted",
- "save_attributes_h5",
- "load_dssc_info",
- "create_dssc_bins",
- "quickmask_DSSC_ASIC",
- "get_xgm_formatted",
- "load_mask",
- "calc_xgm_frame_indices",
- "process_dssc_data",
- # Classes
- "DSSCBinner",
- "DSSCFormatter",
- "AzimuthalIntegrator",
- "AzimuthalIntegratorDSSC",
- # Variables
+ azimuthal_integrator.__all__
+ + bam_detectors.__all__
+ + digitizers.__all__
+ + dssc.__all__
+ + dssc_data.__all__
+ + dssc_misc.__all__
+ + dssc_processing.__all__
+ + pes.__all__
+ + xgm.__all__
)
-
-
-# -----------------------------------------------------------------------------
-# Clean namespace
-# -> certain filenames we dont need in the namespace. Especially not those
-# that are marked as private by using an underscore (_<filename>.py).
-# -----------------------------------------------------------------------------
-
-clean_ns = [
- # filenames
- 'DSSC_bkp',
- 'DSSC1module',
- 'dssc',
- 'dssc_routines',
- 'dssc_processing',
- 'dssc_data',
- 'dssc_misc',
- 'dssc_plot',
- 'azimuthal_integrator',
- 'FastCCD',
- 'xgm',
- 'digitizers',
- 'bam_detectors',
- 'pes'
- ]
-
-
-for name in dir():
- if name in clean_ns:
- del globals()[name]
-
-del globals()['clean_ns']
-del globals()['name']
diff --git a/src/toolbox_scs/detectors/azimuthal_integrator.py b/src/toolbox_scs/detectors/azimuthal_integrator.py
index d6326df..235c958 100644
--- a/src/toolbox_scs/detectors/azimuthal_integrator.py
+++ b/src/toolbox_scs/detectors/azimuthal_integrator.py
@@ -1,6 +1,11 @@
import logging
import numpy as np
+__all__ = [
+ 'AzimuthalIntegrator',
+ 'AzimuthalIntegratorDSSC'
+]
+
log = logging.getLogger(__name__)
diff --git a/src/toolbox_scs/detectors/bam_detectors.py b/src/toolbox_scs/detectors/bam_detectors.py
index 12d6ef1..667d20a 100644
--- a/src/toolbox_scs/detectors/bam_detectors.py
+++ b/src/toolbox_scs/detectors/bam_detectors.py
@@ -15,6 +15,9 @@ from ..misc.bunch_pattern_external import is_pulse_at
from ..mnemonics_machinery import (mnemonics_to_process,
mnemonics_for_run)
+__all__ = [
+ 'get_bam',
+]
log = logging.getLogger(__name__)
diff --git a/src/toolbox_scs/detectors/digitizers.py b/src/toolbox_scs/detectors/digitizers.py
index b677323..339d17a 100644
--- a/src/toolbox_scs/detectors/digitizers.py
+++ b/src/toolbox_scs/detectors/digitizers.py
@@ -18,6 +18,14 @@ from ..util.exceptions import ToolBoxValueError
from ..mnemonics_machinery import (mnemonics_to_process,
mnemonics_for_run)
+__all__ = [
+ 'check_peak_params',
+ 'get_digitizer_peaks',
+ 'get_laser_peaks',
+ 'get_peaks',
+ 'get_tim_peaks',
+]
+
log = logging.getLogger(__name__)
diff --git a/src/toolbox_scs/detectors/dssc.py b/src/toolbox_scs/detectors/dssc.py
index aaa80bf..7aa93a9 100644
--- a/src/toolbox_scs/detectors/dssc.py
+++ b/src/toolbox_scs/detectors/dssc.py
@@ -29,7 +29,10 @@ from .dssc_misc import (
from .dssc_processing import (
process_dssc_data, create_empty_dataset)
-__all__ = ["DSSCBinner", "DSSCFormatter"]
+__all__ = [
+ "DSSCBinner",
+ "DSSCFormatter"]
+
log = logging.getLogger(__name__)
diff --git a/src/toolbox_scs/detectors/dssc_data.py b/src/toolbox_scs/detectors/dssc_data.py
index 0781177..94b2336 100644
--- a/src/toolbox_scs/detectors/dssc_data.py
+++ b/src/toolbox_scs/detectors/dssc_data.py
@@ -6,6 +6,13 @@ import xarray as xr
from ..util.exceptions import ToolBoxFileError
+__all__ = [
+ 'get_data_formatted',
+ 'load_xarray',
+ 'save_attributes_h5',
+ 'save_xarray',
+]
+
log = logging.getLogger(__name__)
diff --git a/src/toolbox_scs/detectors/dssc_misc.py b/src/toolbox_scs/detectors/dssc_misc.py
index 96f5254..db89aa7 100644
--- a/src/toolbox_scs/detectors/dssc_misc.py
+++ b/src/toolbox_scs/detectors/dssc_misc.py
@@ -14,6 +14,14 @@ import extra_data as ed
from .xgm import get_xgm
from .digitizers import get_tim_peaks
+__all__ = [
+ 'create_dssc_bins',
+ 'get_xgm_formatted',
+ 'load_dssc_info',
+ 'load_mask',
+ 'quickmask_DSSC_ASIC',
+]
+
log = logging.getLogger(__name__)
diff --git a/src/toolbox_scs/detectors/dssc_processing.py b/src/toolbox_scs/detectors/dssc_processing.py
index 2858308..a95607d 100644
--- a/src/toolbox_scs/detectors/dssc_processing.py
+++ b/src/toolbox_scs/detectors/dssc_processing.py
@@ -15,6 +15,10 @@ import extra_data as ed
from ..mnemonics_machinery import mnemonics_for_run
from .dssc_data import save_xarray
+__all__ = [
+ 'process_dssc_data'
+]
+
log = logging.getLogger(__name__)
diff --git a/src/toolbox_scs/detectors/fccd.py b/src/toolbox_scs/detectors/fccd.py
index 0396df5..f0cb5de 100644
--- a/src/toolbox_scs/detectors/fccd.py
+++ b/src/toolbox_scs/detectors/fccd.py
@@ -1,6 +1,5 @@
from joblib import Parallel, delayed, parallel_backend
from time import strftime
-import tempfile
import shutil
from tqdm.auto import tqdm
import os
@@ -17,11 +16,11 @@ import h5py
from glob import glob
from imageio import imread
-import ToolBox as tb
from ..constants import mnemonics as _mnemonics
from .azimuthal_integrator import AzimuthalIntegrator
from ..misc.laser_utils import positionToDelay
+
class FastCCD:
def __init__(self, proposal, distance=1, raw=False):
diff --git a/src/toolbox_scs/detectors/pes.py b/src/toolbox_scs/detectors/pes.py
index 49d73f7..cb36e49 100644
--- a/src/toolbox_scs/detectors/pes.py
+++ b/src/toolbox_scs/detectors/pes.py
@@ -16,6 +16,12 @@ from ..mnemonics_machinery import (mnemonics_to_process,
mnemonics_for_run)
+__all__ = [
+ 'get_pes_params',
+ 'get_pes_tof',
+]
+
+
log = logging.getLogger(__name__)
diff --git a/src/toolbox_scs/detectors/xgm.py b/src/toolbox_scs/detectors/xgm.py
index cdb84dc..944dcc5 100644
--- a/src/toolbox_scs/detectors/xgm.py
+++ b/src/toolbox_scs/detectors/xgm.py
@@ -16,6 +16,11 @@ from ..misc.bunch_pattern_external import is_sase_1, is_sase_3
from ..mnemonics_machinery import (mnemonics_to_process,
mnemonics_for_run)
+__all__ = [
+ 'calibrate_xgm',
+ 'get_xgm',
+]
+
log = logging.getLogger(__name__)
diff --git a/src/toolbox_scs/load.py b/src/toolbox_scs/load.py
index 48360c7..d51b5b1 100644
--- a/src/toolbox_scs/load.py
+++ b/src/toolbox_scs/load.py
@@ -21,6 +21,13 @@ from .mnemonics_machinery import mnemonics_for_run
from .util.exceptions import ToolBoxValueError
import toolbox_scs.detectors as tbdet
+__all__ = [
+ 'concatenateRuns',
+ 'get_array',
+ 'load',
+ 'run_by_path',
+]
+
log = logging.getLogger(__name__)
diff --git a/src/toolbox_scs/misc/__init__.py b/src/toolbox_scs/misc/__init__.py
index 0f4edde..3ff302d 100644
--- a/src/toolbox_scs/misc/__init__.py
+++ b/src/toolbox_scs/misc/__init__.py
@@ -1,25 +1,9 @@
-from .bunch_pattern import (extractBunchPattern, pulsePatternInfo,
- repRate)
-from .bunch_pattern_external import (is_sase_3, is_sase_1,
- is_ppl, is_pulse_at)
-from .laser_utils import positionToDelay, degToRelPower
-
+from .bunch_pattern import *
+from .bunch_pattern_external import *
+from .laser_utils import *
__all__ = (
- # Functions
- "extractBunchPattern",
- "pulsePatternInfo",
- "repRate",
- "sortBAMdata",
- "is_sase_3",
- "is_sase_1",
- "is_ppl",
- "is_pulse_at",
- "get_index_ppl",
- "get_index_sase1",
- "get_index_sase3",
- "positionToDelay",
- "degToRelPower",
- # Classes
- # Variables
+ bunch_pattern.__all__
+ + bunch_pattern_external.__all__
+ + laser_utils.__all__
)
diff --git a/src/toolbox_scs/misc/bunch_pattern.py b/src/toolbox_scs/misc/bunch_pattern.py
index 3f5939b..852f9ed 100644
--- a/src/toolbox_scs/misc/bunch_pattern.py
+++ b/src/toolbox_scs/misc/bunch_pattern.py
@@ -16,6 +16,12 @@ from extra_data import RunDirectory
# import and hide variable, such that it does not alter namespace.
from ..constants import mnemonics as _mnemonics_bp
+__all__ = [
+ 'extractBunchPattern',
+ 'pulsePatternInfo',
+ 'repRate'
+]
+
def extractBunchPattern(bp_table=None, key='sase3', runDir=None):
''' generate the bunch pattern and number of pulses of a source directly from the
diff --git a/src/toolbox_scs/misc/bunch_pattern_external.py b/src/toolbox_scs/misc/bunch_pattern_external.py
index 993b584..70d6afc 100644
--- a/src/toolbox_scs/misc/bunch_pattern_external.py
+++ b/src/toolbox_scs/misc/bunch_pattern_external.py
@@ -11,6 +11,13 @@ import logging
import euxfel_bunch_pattern as ebp
+__all__ = [
+ 'is_sase_3',
+ 'is_sase_1',
+ 'is_ppl',
+ 'is_pulse_at',
+]
+
PPL_SCS = ebp.LASER_SEED6
log = logging.getLogger(__name__)
diff --git a/src/toolbox_scs/misc/laser_utils.py b/src/toolbox_scs/misc/laser_utils.py
index 55e44a3..b284999 100644
--- a/src/toolbox_scs/misc/laser_utils.py
+++ b/src/toolbox_scs/misc/laser_utils.py
@@ -1,3 +1,9 @@
+__all__ = [
+ 'degToRelPower',
+ 'positionToDelay',
+]
+
+
def positionToDelay(pos, origin=0, invert = False, reflections=1):
''' converts a motor position in mm into optical delay in picosecond
Inputs:
diff --git a/src/toolbox_scs/mnemonics_machinery.py b/src/toolbox_scs/mnemonics_machinery.py
index f09e14b..a3aa8f0 100644
--- a/src/toolbox_scs/mnemonics_machinery.py
+++ b/src/toolbox_scs/mnemonics_machinery.py
@@ -10,6 +10,10 @@ import logging
from .constants import mnemonics as _mnemonics
+__all__ = [
+ 'mnemonics_for_run'
+]
+
log = logging.getLogger(__name__)
diff --git a/src/toolbox_scs/routines/XAS.py b/src/toolbox_scs/routines/XAS.py
index 1c9ca17..3bf52a5 100644
--- a/src/toolbox_scs/routines/XAS.py
+++ b/src/toolbox_scs/routines/XAS.py
@@ -14,6 +14,11 @@ import matplotlib.gridspec as gridspec
import matplotlib.pyplot as plt
import re
+__all__ = [
+ 'xas',
+ 'xasxmcd',
+]
+
def absorption(T, Io, fluorescence=False):
""" Compute the absorption A = -ln(T/Io) (or A = T/Io
diff --git a/src/toolbox_scs/routines/__init__.py b/src/toolbox_scs/routines/__init__.py
index de3ef38..d8fbb26 100644
--- a/src/toolbox_scs/routines/__init__.py
+++ b/src/toolbox_scs/routines/__init__.py
@@ -1,29 +1,10 @@
-from .XAS import (
- xas, xasxmcd)
-from .knife_edge import knife_edge
+from .XAS import *
+
+# Module name is the same as a child function, we use alias to avoid conflict
+import toolbox_scs.routines.knife_edge as knife_edge_module
+from .knife_edge import *
__all__ = (
- # Functions
- "xas",
- "xasxmcd",
- "knife_edge"
+ knife_edge_module.__all__
+ + XAS.__all__
)
-
-# -----------------------------------------------------------------------------
-# Clean namespace
-# -> certain filenames we dont need in the namespace. Especially not those
-# that are marked as private by using an underscore (_<filename>.py).
-# -----------------------------------------------------------------------------
-
-clean_ns = [
- # filenames
- 'XAS',
- ]
-
-
-for name in dir():
- if name in clean_ns:
- del globals()[name]
-
-del globals()['clean_ns']
-del globals()['name']
diff --git a/src/toolbox_scs/routines/knife_edge.py b/src/toolbox_scs/routines/knife_edge.py
index 191213d..fccc153 100644
--- a/src/toolbox_scs/routines/knife_edge.py
+++ b/src/toolbox_scs/routines/knife_edge.py
@@ -11,6 +11,10 @@ from scipy.special import erfc
from scipy.optimize import curve_fit
import bisect
+__all__ = [
+ 'knife_edge'
+]
+
def knife_edge(ds, axisKey='scannerX',
signalKey='FastADC4peaks',
--
GitLab