From 0c0d6f03558c9f10d27805d6c7ca64b313ab1ca8 Mon Sep 17 00:00:00 2001
From: Cyril Danilevski <cyril.danilevski@xfel.eu>
Date: Thu, 28 Jan 2021 11:22:56 +0100
Subject: [PATCH] Add CI config
---
.gitlab-ci.yml | 12 +++++
cal_tools/cal_tools/agipdlib.py | 8 ++--
cal_tools/cal_tools/agipdutils.py | 5 +--
cal_tools/cal_tools/agipdutils_ff.py | 3 +-
cal_tools/cal_tools/ana_tools.py | 2 +-
cal_tools/cal_tools/lpdlib.py | 2 +-
cal_tools/cal_tools/metrology.py | 6 ++-
cal_tools/cal_tools/plotting.py | 7 ++-
cal_tools/cal_tools/step_timing.py | 1 +
cal_tools/cal_tools/tools.py | 15 ++++---
cal_tools/cython/agipdalgs.pyx | 4 +-
docs/source/conf.py | 23 +++++-----
notebooks/LPD/playground/metroLib.py | 8 +++-
notebooks/pnCCD/frm6reader.py | 6 ++-
reportservice/automatic_run.py | 4 +-
reportservice/report_service.py | 5 +--
setup.py | 13 +++---
...test.suite._ErrorHolder-20210125191730.xml | 23 ++++++++++
.../AGIPDOfflineCorrection.pdf | Bin
.../CORR-R0412-AGIPD00-S00000.h5.checksum | Bin
.../CORR-R0412-AGIPD00-S00000.h5.hist.npz | Bin
.../CORR-R0412-AGIPD01-S00000.h5.checksum | Bin
.../CORR-R0412-AGIPD01-S00000.h5.hist.npz | Bin
.../CORR-R0412-AGIPD02-S00000.h5.checksum | Bin
.../CORR-R0412-AGIPD02-S00000.h5.hist.npz | Bin
.../CORR-R0412-AGIPD03-S00000.h5.checksum | Bin
.../CORR-R0412-AGIPD03-S00000.h5.hist.npz | Bin
.../CORR-R0412-AGIPD04-S00000.h5.checksum | Bin
.../CORR-R0412-AGIPD04-S00000.h5.hist.npz | Bin
.../CORR-R0412-AGIPD05-S00000.h5.checksum | Bin
.../CORR-R0412-AGIPD05-S00000.h5.hist.npz | Bin
.../CORR-R0412-AGIPD06-S00000.h5.checksum | Bin
.../CORR-R0412-AGIPD06-S00000.h5.hist.npz | Bin
.../CORR-R0412-AGIPD07-S00000.h5.checksum | Bin
.../CORR-R0412-AGIPD07-S00000.h5.hist.npz | Bin
.../CORR-R0412-AGIPD08-S00000.h5.checksum | Bin
.../CORR-R0412-AGIPD08-S00000.h5.hist.npz | Bin
.../CORR-R0412-AGIPD09-S00000.h5.checksum | Bin
.../CORR-R0412-AGIPD09-S00000.h5.hist.npz | Bin
.../CORR-R0412-AGIPD10-S00000.h5.checksum | Bin
.../CORR-R0412-AGIPD10-S00000.h5.hist.npz | Bin
.../CORR-R0412-AGIPD11-S00000.h5.checksum | Bin
.../CORR-R0412-AGIPD11-S00000.h5.hist.npz | Bin
.../CORR-R0412-AGIPD12-S00000.h5.checksum | Bin
.../CORR-R0412-AGIPD12-S00000.h5.hist.npz | Bin
.../CORR-R0412-AGIPD13-S00000.h5.checksum | Bin
.../CORR-R0412-AGIPD13-S00000.h5.hist.npz | Bin
.../CORR-R0412-AGIPD14-S00000.h5.checksum | Bin
.../CORR-R0412-AGIPD14-S00000.h5.hist.npz | Bin
.../CORR-R0412-AGIPD15-S00000.h5.checksum | Bin
.../CORR-R0412-AGIPD15-S00000.h5.hist.npz | Bin
...EST-TestAGIPDCorrection-20181116185424.xml | 0
.../TestAGIPDCorrection_G/karabo.data | Bin
.../CORR-R0154-LPD00-S00000.h5.checksum | Bin
.../CORR-R0154-LPD01-S00000.h5.checksum | Bin
.../CORR-R0154-LPD01-S00000.h5.hist.npz | Bin
.../CORR-R0154-LPD02-S00000.h5.checksum | Bin
.../CORR-R0154-LPD02-S00000.h5.hist.npz | Bin
.../CORR-R0154-LPD03-S00000.h5.checksum | Bin
.../CORR-R0154-LPD03-S00000.h5.hist.npz | Bin
.../CORR-R0154-LPD04-S00000.h5.checksum | Bin
.../CORR-R0154-LPD04-S00000.h5.hist.npz | Bin
.../CORR-R0154-LPD05-S00000.h5.checksum | Bin
.../CORR-R0154-LPD06-S00000.h5.checksum | Bin
.../CORR-R0154-LPD06-S00000.h5.hist.npz | Bin
.../CORR-R0154-LPD07-S00000.h5.checksum | Bin
.../CORR-R0154-LPD07-S00000.h5.hist.npz | Bin
.../CORR-R0154-LPD08-S00000.h5.checksum | Bin
.../CORR-R0154-LPD08-S00000.h5.hist.npz | Bin
.../CORR-R0154-LPD09-S00000.h5.checksum | Bin
.../CORR-R0154-LPD09-S00000.h5.hist.npz | Bin
.../CORR-R0154-LPD10-S00000.h5.checksum | Bin
.../CORR-R0154-LPD11-S00000.h5.checksum | Bin
.../CORR-R0154-LPD11-S00000.h5.hist.npz | Bin
.../CORR-R0154-LPD12-S00000.h5.checksum | Bin
.../CORR-R0154-LPD12-S00000.h5.hist.npz | Bin
.../CORR-R0154-LPD13-S00000.h5.checksum | Bin
.../CORR-R0154-LPD13-S00000.h5.hist.npz | Bin
.../CORR-R0154-LPD14-S00000.h5.checksum | Bin
.../CORR-R0154-LPD14-S00000.h5.hist.npz | Bin
.../CORR-R0154-LPD15-S00000.h5.checksum | Bin
.../CORR-R0154-LPD15-S00000.h5.hist.npz | Bin
.../LPDOfflineCorrection.pdf | Bin
.../TEST-TestLPDCorrection-20181116190907.xml | 0
.../TestLPDCorrection_G/karabo.data | Bin
tests/{ => legacy}/correction_base.py | 0
tests/legacy/readme.md | 7 +++
tests/{ => legacy}/test_agipd.py | 3 +-
tests/{ => legacy}/test_lpd.py | 3 +-
tests/test_cal_tools.py | 12 +++--
webservice/manual_launch.py | 41 ++++++++----------
webservice/serve_overview.py | 1 +
webservice/sqlite_view.py | 2 -
webservice/update_config.py | 1 -
webservice/update_mdc.py | 2 -
webservice/webservice.py | 7 ++-
xfel_calibrate/calibrate.py | 23 +++++-----
xfel_calibrate/finalize.py | 3 +-
98 files changed, 148 insertions(+), 104 deletions(-)
create mode 100644 .gitlab-ci.yml
create mode 100644 tests/legacy/artefacts/9088fa11013afe7bb5d4231fd4170c96e34db520/TestAGIPDCorrection_T/TEST-unittest.suite._ErrorHolder-20210125191730.xml
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestAGIPDCorrection_G/AGIPDOfflineCorrection.pdf (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestAGIPDCorrection_G/CORR-R0412-AGIPD00-S00000.h5.checksum (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestAGIPDCorrection_G/CORR-R0412-AGIPD00-S00000.h5.hist.npz (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestAGIPDCorrection_G/CORR-R0412-AGIPD01-S00000.h5.checksum (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestAGIPDCorrection_G/CORR-R0412-AGIPD01-S00000.h5.hist.npz (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestAGIPDCorrection_G/CORR-R0412-AGIPD02-S00000.h5.checksum (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestAGIPDCorrection_G/CORR-R0412-AGIPD02-S00000.h5.hist.npz (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestAGIPDCorrection_G/CORR-R0412-AGIPD03-S00000.h5.checksum (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestAGIPDCorrection_G/CORR-R0412-AGIPD03-S00000.h5.hist.npz (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestAGIPDCorrection_G/CORR-R0412-AGIPD04-S00000.h5.checksum (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestAGIPDCorrection_G/CORR-R0412-AGIPD04-S00000.h5.hist.npz (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestAGIPDCorrection_G/CORR-R0412-AGIPD05-S00000.h5.checksum (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestAGIPDCorrection_G/CORR-R0412-AGIPD05-S00000.h5.hist.npz (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestAGIPDCorrection_G/CORR-R0412-AGIPD06-S00000.h5.checksum (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestAGIPDCorrection_G/CORR-R0412-AGIPD06-S00000.h5.hist.npz (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestAGIPDCorrection_G/CORR-R0412-AGIPD07-S00000.h5.checksum (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestAGIPDCorrection_G/CORR-R0412-AGIPD07-S00000.h5.hist.npz (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestAGIPDCorrection_G/CORR-R0412-AGIPD08-S00000.h5.checksum (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestAGIPDCorrection_G/CORR-R0412-AGIPD08-S00000.h5.hist.npz (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestAGIPDCorrection_G/CORR-R0412-AGIPD09-S00000.h5.checksum (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestAGIPDCorrection_G/CORR-R0412-AGIPD09-S00000.h5.hist.npz (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestAGIPDCorrection_G/CORR-R0412-AGIPD10-S00000.h5.checksum (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestAGIPDCorrection_G/CORR-R0412-AGIPD10-S00000.h5.hist.npz (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestAGIPDCorrection_G/CORR-R0412-AGIPD11-S00000.h5.checksum (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestAGIPDCorrection_G/CORR-R0412-AGIPD11-S00000.h5.hist.npz (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestAGIPDCorrection_G/CORR-R0412-AGIPD12-S00000.h5.checksum (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestAGIPDCorrection_G/CORR-R0412-AGIPD12-S00000.h5.hist.npz (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestAGIPDCorrection_G/CORR-R0412-AGIPD13-S00000.h5.checksum (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestAGIPDCorrection_G/CORR-R0412-AGIPD13-S00000.h5.hist.npz (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestAGIPDCorrection_G/CORR-R0412-AGIPD14-S00000.h5.checksum (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestAGIPDCorrection_G/CORR-R0412-AGIPD14-S00000.h5.hist.npz (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestAGIPDCorrection_G/CORR-R0412-AGIPD15-S00000.h5.checksum (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestAGIPDCorrection_G/CORR-R0412-AGIPD15-S00000.h5.hist.npz (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestAGIPDCorrection_G/TEST-TestAGIPDCorrection-20181116185424.xml (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestAGIPDCorrection_G/karabo.data (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestLPDCorrection_G/CORR-R0154-LPD00-S00000.h5.checksum (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestLPDCorrection_G/CORR-R0154-LPD01-S00000.h5.checksum (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestLPDCorrection_G/CORR-R0154-LPD01-S00000.h5.hist.npz (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestLPDCorrection_G/CORR-R0154-LPD02-S00000.h5.checksum (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestLPDCorrection_G/CORR-R0154-LPD02-S00000.h5.hist.npz (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestLPDCorrection_G/CORR-R0154-LPD03-S00000.h5.checksum (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestLPDCorrection_G/CORR-R0154-LPD03-S00000.h5.hist.npz (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestLPDCorrection_G/CORR-R0154-LPD04-S00000.h5.checksum (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestLPDCorrection_G/CORR-R0154-LPD04-S00000.h5.hist.npz (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestLPDCorrection_G/CORR-R0154-LPD05-S00000.h5.checksum (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestLPDCorrection_G/CORR-R0154-LPD06-S00000.h5.checksum (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestLPDCorrection_G/CORR-R0154-LPD06-S00000.h5.hist.npz (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestLPDCorrection_G/CORR-R0154-LPD07-S00000.h5.checksum (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestLPDCorrection_G/CORR-R0154-LPD07-S00000.h5.hist.npz (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestLPDCorrection_G/CORR-R0154-LPD08-S00000.h5.checksum (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestLPDCorrection_G/CORR-R0154-LPD08-S00000.h5.hist.npz (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestLPDCorrection_G/CORR-R0154-LPD09-S00000.h5.checksum (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestLPDCorrection_G/CORR-R0154-LPD09-S00000.h5.hist.npz (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestLPDCorrection_G/CORR-R0154-LPD10-S00000.h5.checksum (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestLPDCorrection_G/CORR-R0154-LPD11-S00000.h5.checksum (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestLPDCorrection_G/CORR-R0154-LPD11-S00000.h5.hist.npz (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestLPDCorrection_G/CORR-R0154-LPD12-S00000.h5.checksum (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestLPDCorrection_G/CORR-R0154-LPD12-S00000.h5.hist.npz (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestLPDCorrection_G/CORR-R0154-LPD13-S00000.h5.checksum (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestLPDCorrection_G/CORR-R0154-LPD13-S00000.h5.hist.npz (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestLPDCorrection_G/CORR-R0154-LPD14-S00000.h5.checksum (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestLPDCorrection_G/CORR-R0154-LPD14-S00000.h5.hist.npz (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestLPDCorrection_G/CORR-R0154-LPD15-S00000.h5.checksum (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestLPDCorrection_G/CORR-R0154-LPD15-S00000.h5.hist.npz (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestLPDCorrection_G/LPDOfflineCorrection.pdf (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestLPDCorrection_G/TEST-TestLPDCorrection-20181116190907.xml (100%)
rename tests/{ => legacy}/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestLPDCorrection_G/karabo.data (100%)
rename tests/{ => legacy}/correction_base.py (100%)
create mode 100644 tests/legacy/readme.md
rename tests/{ => legacy}/test_agipd.py (99%)
rename tests/{ => legacy}/test_lpd.py (99%)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
new file mode 100644
index 000000000..687b779fc
--- /dev/null
+++ b/.gitlab-ci.yml
@@ -0,0 +1,12 @@
+isort:
+ stage: test
+ script:
+ - python3 -m pip install --user isort==5.6.4
+ - isort --diff **/*.py && isort -c **/*.py
+
+pytest:
+ stage: test
+ script:
+ - python3 -m pip install --user -r requirements.txt
+ - python3 -m pip install --user pytest
+ - pytest -vv tests/test_*
diff --git a/cal_tools/cal_tools/agipdlib.py b/cal_tools/cal_tools/agipdlib.py
index 54afabdc2..e52ed7435 100644
--- a/cal_tools/cal_tools/agipdlib.py
+++ b/cal_tools/cal_tools/agipdlib.py
@@ -1,16 +1,16 @@
+import traceback
from pathlib import Path
from typing import Optional, Tuple
import h5py
import numpy as np
import sharedmem
-import traceback
-
from cal_tools.agipdutils import *
-from cal_tools.cython import agipdalgs as calgs
from cal_tools.enums import BadPixels, SnowResolution
from cal_tools.tools import get_constant_from_db_and_time
-from iCalibrationDB import Constants, Conditions, Detectors
+from iCalibrationDB import Conditions, Constants, Detectors
+
+from cal_tools.cython import agipdalgs as calgs
def get_num_cells(fname, loc, module):
diff --git a/cal_tools/cal_tools/agipdutils.py b/cal_tools/cal_tools/agipdutils.py
index e217c04da..9533a6571 100644
--- a/cal_tools/cal_tools/agipdutils.py
+++ b/cal_tools/cal_tools/agipdutils.py
@@ -1,12 +1,11 @@
import copy
import numpy as np
-from scipy.signal import cwt, ricker, find_peaks_cwt
+from cal_tools.enums import BadPixels, SnowResolution
+from scipy.signal import cwt, find_peaks_cwt, ricker
from sklearn.mixture import GaussianMixture
from sklearn.preprocessing import StandardScaler
-from cal_tools.enums import BadPixels, SnowResolution
-
def assemble_constant_dict(corr_bools, pc_bools, memory_cells, bias_voltage,
gain_setting, acquisition_rate,
diff --git a/cal_tools/cal_tools/agipdutils_ff.py b/cal_tools/cal_tools/agipdutils_ff.py
index 65ff91866..97d38ce87 100644
--- a/cal_tools/cal_tools/agipdutils_ff.py
+++ b/cal_tools/cal_tools/agipdutils_ff.py
@@ -1,9 +1,8 @@
from typing import Any, Dict, List, Optional, Tuple
-from iminuit import Minuit
import numpy as np
-
from cal_tools.enums import BadPixelsFF
+from iminuit import Minuit
def any_in(mask: np.ndarray, bits: int) -> bool:
diff --git a/cal_tools/cal_tools/ana_tools.py b/cal_tools/cal_tools/ana_tools.py
index 907c1682d..b9074e118 100644
--- a/cal_tools/cal_tools/ana_tools.py
+++ b/cal_tools/cal_tools/ana_tools.py
@@ -1,6 +1,6 @@
-from enum import Enum
import datetime
import glob
+from enum import Enum
import dateutil.parser
import h5py
diff --git a/cal_tools/cal_tools/lpdlib.py b/cal_tools/cal_tools/lpdlib.py
index 47392acdc..054cebb74 100644
--- a/cal_tools/cal_tools/lpdlib.py
+++ b/cal_tools/cal_tools/lpdlib.py
@@ -4,7 +4,7 @@ import h5py
import numpy as np
from cal_tools.enums import BadPixels
from cal_tools.tools import get_constant_from_db, get_constant_from_db_and_time
-from iCalibrationDB import Constants, Conditions, Detectors
+from iCalibrationDB import Conditions, Constants, Detectors
class LpdCorrections:
diff --git a/cal_tools/cal_tools/metrology.py b/cal_tools/cal_tools/metrology.py
index bbaededce..8a6c0affc 100644
--- a/cal_tools/cal_tools/metrology.py
+++ b/cal_tools/cal_tools/metrology.py
@@ -1,6 +1,8 @@
-import numpy as np
-import h5py, os, re
+import os
+import re
+import h5py
+import numpy as np
from matplotlib import pylab as plt
diff --git a/cal_tools/cal_tools/plotting.py b/cal_tools/cal_tools/plotting.py
index a84463efa..7329e7b7e 100644
--- a/cal_tools/cal_tools/plotting.py
+++ b/cal_tools/cal_tools/plotting.py
@@ -3,13 +3,12 @@ from typing import Any, Dict, Optional
import matplotlib.pyplot as plt
import numpy as np
-from matplotlib import colors
-from matplotlib.patches import Patch
-from mpl_toolkits.axes_grid1 import AxesGrid
-
from extra_geom import (AGIPD_1MGeometry, AGIPD_500K2GGeometry,
DSSC_1MGeometry, LPD_1MGeometry)
from extra_geom import tests as eg_tests
+from matplotlib import colors
+from matplotlib.patches import Patch
+from mpl_toolkits.axes_grid1 import AxesGrid
def show_overview(d, cell_to_preview, gain_to_preview, out_folder=None, infix=None):
diff --git a/cal_tools/cal_tools/step_timing.py b/cal_tools/cal_tools/step_timing.py
index 8ae6e17a9..576f52844 100644
--- a/cal_tools/cal_tools/step_timing.py
+++ b/cal_tools/cal_tools/step_timing.py
@@ -3,6 +3,7 @@ from time import perf_counter
import numpy as np
+
class StepTimer:
def __init__(self):
self.steps = defaultdict(list)
diff --git a/cal_tools/cal_tools/tools.py b/cal_tools/cal_tools/tools.py
index 8e485f273..e4e3f44b5 100644
--- a/cal_tools/cal_tools/tools.py
+++ b/cal_tools/cal_tools/tools.py
@@ -1,12 +1,12 @@
-from collections import OrderedDict
import datetime
-from glob import glob
import json
+import re
+from collections import OrderedDict
+from glob import glob
from os import environ, listdir, path
from os.path import isfile
from pathlib import Path
from queue import Queue
-import re
from time import sleep
from typing import Optional
from urllib.parse import urljoin
@@ -14,15 +14,16 @@ from urllib.parse import urljoin
import dateutil.parser
import h5py
import ipykernel
-from metadata_client.metadata_client import MetadataClient
-from notebook.notebookapp import list_running_servers
import numpy as np
import requests
+import zmq
+from iCalibrationDB import ConstantMetaData, Versions
+from metadata_client.metadata_client import MetadataClient
+from notebook.notebookapp import list_running_servers
from .ana_tools import save_dict_to_hdf5
-from iCalibrationDB import ConstantMetaData, Versions
from .mdc_config import MDC_config
-import zmq
+
def parse_runs(runs, return_type=str):
pruns = []
diff --git a/cal_tools/cython/agipdalgs.pyx b/cal_tools/cython/agipdalgs.pyx
index 25a71e098..e5457aef1 100644
--- a/cal_tools/cython/agipdalgs.pyx
+++ b/cal_tools/cython/agipdalgs.pyx
@@ -1,6 +1,8 @@
import numpy as np
-cimport numpy as cnp
+
cimport cython
+cimport numpy as cnp
+
@cython.boundscheck(False)
@cython.wraparound(False)
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 350328d4f..23c008eba 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -40,11 +40,10 @@ extensions = [
]
import glob
-import sys
import os
+import sys
from subprocess import Popen
-
sys.path.append(os.path.abspath("../pycalibration/"))
p = Popen(["./makeAllDocs.sh"])
p.communicate()
@@ -375,13 +374,16 @@ except:
check_call(["wget", pandoc_url])
check_call(["dpkg", "-i", pandoc_pack])
-# generate the list of available notebooks
-from xfel_calibrate import notebooks
+import os
from subprocess import check_output
from textwrap import dedent, indent
-from nbconvert import RSTExporter
-import os
+
import nbformat
+from nbconvert import RSTExporter
+
+# generate the list of available notebooks
+from xfel_calibrate import notebooks
+
rst_exporter = RSTExporter()
with open("available_notebooks.rst", "w") as f:
@@ -440,14 +442,15 @@ with open("available_notebooks.rst", "w") as f:
# add test results
test_artefact_dir = os.path.realpath("../../tests/artefacts")
-from datetime import datetime
-from dateutil.parser import parse
-from lxml import etree
import shutil
-import tabulate
import textwrap
+from datetime import datetime
from uuid import uuid4
+import tabulate
+from dateutil.parser import parse
+from lxml import etree
+
def xml_to_rst_report(xml, git_tag, reports=[]):
e = etree.fromstring(xml.encode())
diff --git a/notebooks/LPD/playground/metroLib.py b/notebooks/LPD/playground/metroLib.py
index b3a4cd8b0..0ef031095 100644
--- a/notebooks/LPD/playground/metroLib.py
+++ b/notebooks/LPD/playground/metroLib.py
@@ -1,6 +1,8 @@
-import numpy as np
-import h5py, os, re
+import os
+import re
+import h5py
+import numpy as np
from matplotlib import pylab as plt
@@ -346,6 +348,8 @@ def returnPositioned2(geometry_file, modules, dquads):
return out
import re
+
+
def positionFileList(filelist, datapath, geometry_file, quad_pos, nImages='all'):
import glob
detector = "LPD" if "LPD" in datapath else "AGIPD"
diff --git a/notebooks/pnCCD/frm6reader.py b/notebooks/pnCCD/frm6reader.py
index 35ffc923c..a0539603f 100644
--- a/notebooks/pnCCD/frm6reader.py
+++ b/notebooks/pnCCD/frm6reader.py
@@ -1,7 +1,9 @@
-import os, struct
-import numpy as np
+import os
+import struct
from collections import OrderedDict
+import numpy as np
+
class Frms6Reader(object):
""" This class allows to access frm6 files
diff --git a/reportservice/automatic_run.py b/reportservice/automatic_run.py
index a85fa0b29..708037153 100644
--- a/reportservice/automatic_run.py
+++ b/reportservice/automatic_run.py
@@ -1,12 +1,12 @@
import argparse
import asyncio
-from datetime import datetime, timedelta
import logging
+from datetime import datetime, timedelta
-from dateutil import parser, tz
import yaml
import zmq
import zmq.asyncio
+from dateutil import parser, tz
async def auto_run(cfg, timeout=3000):
diff --git a/reportservice/report_service.py b/reportservice/report_service.py
index c21babe2c..03d24a9a6 100644
--- a/reportservice/report_service.py
+++ b/reportservice/report_service.py
@@ -1,17 +1,16 @@
import argparse
import asyncio
-from asyncio.subprocess import PIPE
import copy
import glob
import logging
import os
import subprocess
+from asyncio.subprocess import PIPE
-from git import Repo, InvalidGitRepositoryError
import yaml
import zmq
import zmq.asyncio
-
+from git import InvalidGitRepositoryError, Repo
from messages import Errors
loop = asyncio.get_event_loop()
diff --git a/setup.py b/setup.py
index 8213e937d..58b1c9ce1 100644
--- a/setup.py
+++ b/setup.py
@@ -1,12 +1,12 @@
-from setuptools import setup
-from setuptools.command.install import install
-from subprocess import check_call, check_output
+import sys
from distutils.command.build import build
-
-from Cython.Distutils import build_ext
from distutils.extension import Extension
-import sys
+from subprocess import check_call, check_output
+
import numpy
+from Cython.Distutils import build_ext
+from setuptools import setup
+from setuptools.command.install import install
extensions = [Extension("cal_tools.cython.agipdalgs",
['cal_tools/cython/agipdalgs.pyx'],
@@ -48,6 +48,7 @@ class PreInstallCommand(build):
from xfel_calibrate.notebooks import notebooks
+
data_files = []
for ctypes in notebooks.values():
for nb in ctypes.values():
diff --git a/tests/legacy/artefacts/9088fa11013afe7bb5d4231fd4170c96e34db520/TestAGIPDCorrection_T/TEST-unittest.suite._ErrorHolder-20210125191730.xml b/tests/legacy/artefacts/9088fa11013afe7bb5d4231fd4170c96e34db520/TestAGIPDCorrection_T/TEST-unittest.suite._ErrorHolder-20210125191730.xml
new file mode 100644
index 000000000..533ecad66
--- /dev/null
+++ b/tests/legacy/artefacts/9088fa11013afe7bb5d4231fd4170c96e34db520/TestAGIPDCorrection_T/TEST-unittest.suite._ErrorHolder-20210125191730.xml
@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<testsuite errors="1" failures="0" file="unittest/suite.py" name="unittest.suite._ErrorHolder-20210125191730" skipped="0" tests="1" time="0.000" timestamp="0001-01-01T00:00:00">
+ <testcase classname="setUpClass (__main__" name="TestAGIPDCorrection)" time="0.000" timestamp="0001-01-01T00:00:00">
+ <error message="Command '['xfel-calibrate', 'AGIPD', 'CORRECT', '--in-folder', '/gpfs/exfel/exp/XMPL/201750/p700001/raw/AGIPD', '--run', '412', '--out-folder', '/gpfs/exfel/exp/XMPL/201750/p700001/scratch/AGIPD', '--calfile', '/gpfs/exfel/exp/XMPL/201750/p700001/usr/agipd_store.h5', '--sequences', '0']' returned non-zero exit status 2." type="CalledProcessError">
+<![CDATA[Traceback (most recent call last):
+ File "/home/danilevc/calibration/pycalibration/tests/correction_base.py", line 295, in setUpClass
+ out = sp.check_output(cmd)
+ File "/software/anaconda3/5.2/lib/python3.6/subprocess.py", line 336, in check_output
+ **kwargs).stdout
+ File "/software/anaconda3/5.2/lib/python3.6/subprocess.py", line 418, in run
+ output=stdout, stderr=stderr)
+subprocess.CalledProcessError: Command '['xfel-calibrate', 'AGIPD', 'CORRECT', '--in-folder', '/gpfs/exfel/exp/XMPL/201750/p700001/raw/AGIPD', '--run', '412', '--out-folder', '/gpfs/exfel/exp/XMPL/201750/p700001/scratch/AGIPD', '--calfile', '/gpfs/exfel/exp/XMPL/201750/p700001/usr/agipd_store.h5', '--sequences', '0']' returned non-zero exit status 2.
+]]> </error>
+ <system-out>
+<![CDATA[Executing xfel-calibrate AGIPD CORRECT --in-folder /gpfs/exfel/exp/XMPL/201750/p700001/raw/AGIPD --run 412 --out-folder /gpfs/exfel/exp/XMPL/201750/p700001/scratch/AGIPD --calfile /gpfs/exfel/exp/XMPL/201750/p700001/usr/agipd_store.h5 --sequences 0
+Creating data paths for artefacts
+Last git commit is: 9088fa11013afe7bb5d4231fd4170c96e34db520
+artefacts will be placed in: /home/danilevc/calibration/pycalibration/tests/artefacts/9088fa11013afe7bb5d4231fd4170c96e34db520/TestAGIPDCorrection_T
+]]> </system-out>
+ <system-err>
+<![CDATA[]]> </system-err>
+ </testcase>
+</testsuite>
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diff --git a/tests/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestLPDCorrection_G/LPDOfflineCorrection.pdf b/tests/legacy/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestLPDCorrection_G/LPDOfflineCorrection.pdf
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diff --git a/tests/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestLPDCorrection_G/TEST-TestLPDCorrection-20181116190907.xml b/tests/legacy/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestLPDCorrection_G/TEST-TestLPDCorrection-20181116190907.xml
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diff --git a/tests/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestLPDCorrection_G/karabo.data b/tests/legacy/artefacts/ca3b513c64c05a29ae0f530c91b04349417c4fa0/TestLPDCorrection_G/karabo.data
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diff --git a/tests/correction_base.py b/tests/legacy/correction_base.py
similarity index 100%
rename from tests/correction_base.py
rename to tests/legacy/correction_base.py
diff --git a/tests/legacy/readme.md b/tests/legacy/readme.md
new file mode 100644
index 000000000..060f98982
--- /dev/null
+++ b/tests/legacy/readme.md
@@ -0,0 +1,7 @@
+These tests were historically part of pycalibration.
+
+They are broken and haven't been looked at. Some may be fixed, some are deprecated due to heavy changes since they were implemented.
+This directory is excluded from the CI runner.
+
+It does not mean that they can be freely deleted. Each test file should be assayed and fixed, if possible!
+
diff --git a/tests/test_agipd.py b/tests/legacy/test_agipd.py
similarity index 99%
rename from tests/test_agipd.py
rename to tests/legacy/test_agipd.py
index 814dfbff6..1f6aa646b 100644
--- a/tests/test_agipd.py
+++ b/tests/legacy/test_agipd.py
@@ -3,7 +3,6 @@ import unittest
import numpy as np
import xmlrunner
-
from correction_base import CorrectionTestBase, args, get_artefact_dir
@@ -45,7 +44,7 @@ class TestAGIPDCorrection(CorrectionTestBase, unittest.TestCase):
'header.pulseCount', 'trailer.status',
'detector.trainId',
'trailer.trainId']
-
+
expected_reports = ['AGIPDOfflineCorrection.pdf']
def _output_to_path(self):
diff --git a/tests/test_lpd.py b/tests/legacy/test_lpd.py
similarity index 99%
rename from tests/test_lpd.py
rename to tests/legacy/test_lpd.py
index 9119d506f..b72a211f1 100644
--- a/tests/test_lpd.py
+++ b/tests/legacy/test_lpd.py
@@ -3,7 +3,6 @@ import unittest
import numpy as np
import xmlrunner
-
from correction_base import CorrectionTestBase, args, get_artefact_dir
np.warnings.filterwarnings('ignore')
@@ -47,7 +46,7 @@ class TestLPDCorrection(CorrectionTestBase, unittest.TestCase):
'header.pulseCount', 'trailer.status',
'detector.trainId',
'trailer.trainId']
-
+
expected_reports = ['LPDOfflineCorrection.pdf']
def _output_to_path(self):
diff --git a/tests/test_cal_tools.py b/tests/test_cal_tools.py
index 803eba3b1..208066682 100644
--- a/tests/test_cal_tools.py
+++ b/tests/test_cal_tools.py
@@ -16,19 +16,17 @@ def test_show_processed_modules():
def test_dir_creation_date():
- folder = '/gpfs/exfel/exp/DETLAB/202031/p900172/raw'
+ folder = '/gpfs/exfel/exp/CALLAB/202031/p900113/raw'
- date = get_dir_creation_date(folder, 10)
+ date = get_dir_creation_date(folder, 9983)
assert isinstance(date, datetime)
- assert str(date) == '2020-07-20 10:39:03'
+ assert str(date) == '2020-09-23 13:30:50'
with pytest.raises(ValueError) as e:
get_dir_creation_date(folder, 4)
assert e.value.args[1] == Path(folder) / 'r0004'
# The following data predates the addition of creation_time in metadata
- folder = '/gpfs/exfel/exp/SQS/201930/p900075/raw/'
-
- date = get_dir_creation_date(folder, 365)
+ date = get_dir_creation_date(folder, 9999)
assert isinstance(date, datetime)
- assert str(date) == '2019-07-04 11:02:41.280000'
+ assert str(date) == '2021-01-25 20:30:52.818820'
diff --git a/webservice/manual_launch.py b/webservice/manual_launch.py
index bf07427f2..b467d89f0 100644
--- a/webservice/manual_launch.py
+++ b/webservice/manual_launch.py
@@ -1,28 +1,25 @@
-import argparse
-from datetime import datetime
-import sys
-from time import sleep
-import urllib.parse
import zmq
-parser = argparse.ArgumentParser(
- description='Request dark characterization. Will wait on data transfers to complete first!')
-parser.add_argument('--proposal', type=str, help='The proposal number, without leading p, but with leading zeros')
-parser.add_argument('--instrument', type=str, choices=["SPB", "MID", "FXE", "SCS", "SQS", "HED", "DETLAB", "CALLAB"], help='The instrument')
-parser.add_argument('--cycle', type=str, help='The facility cycle')
-parser.add_argument('--run', type=int, help='Run number as an integer')
-parser.add_argument('--mdc-id', type=int, help='Run id from MDC')
-parser.add_argument('--priority', type=int, help='Priority to launch', choices=[1,2], default=2)
-
-args = vars(parser.parse_args())
-
con = zmq.Context()
socket = con.socket(zmq.REQ)
-con = socket.connect("tcp://max-exfl016:5555")
-msg = "','".join(["correct", str(args["mdc_id"]), "SASEX", args["instrument"], args["cycle"], args["proposal"], str(args["run"]), str(args["priority"])])
-socket.send("['{}']".format(msg).encode())
-resp = socket.recv_multipart()[0]
-print(resp.decode())
+con = socket.connect("tcp://max-exfl017:5555")
-
+action = 'dark_request'
+dark_run_id = '182'
+sase = 'sase1'
+instrument = 'CALLAB'
+cycle = '202031'
+proposal = '900113'
+detector_id = 'SPB_DET_AGIPD1M-1'
+pdu_physical_names = '["AGIPD00 (Q1M1)"', '"AGIPD01 (Q1M2)"', '"AGIPD02 (Q1M3)"', '"AGIPD03 (Q1M4)"', '"AGIPD04 (Q2M1)"', '"AGIPD05 (Q2M2)"', '"AGIPD06 (Q2M3)"', '"AGIPD07 (Q2M4)"', '"AGIPD08 (Q3M1)"', '"AGIPD09 (Q3M2)"', '"AGIPD10 (Q3M3)"', '"AGIPD11 (Q3M4)"', '"AGIPD12 (Q4M1)"', '"AGIPD13 (Q4M2)"', '"AGIPD14 (Q4M3)"', '"AGIPD15 (Q4M4)"]' # noqa
+pdu_karabo_das = '["AGIPD00"', ' "AGIPD01"', ' "AGIPD02"', ' "AGIPD03"', ' "AGIPD04"', ' "AGIPD05"', ' "AGIPD06"', ' "AGIPD07"', ' "AGIPD08"', ' "AGIPD09"', ' "AGIPD10"', ' "AGIPD11"', ' "AGIPD12"', ' "AGIPD13"', ' "AGIPD14"', ' "AGIPD15"]' # noqa
+operation_mode = 'FIXED_GAIN'
+run_numbers = '[9985,]'
+
+data = [action, dark_run_id, sase, instrument, cycle, proposal, detector_id,
+ operation_mode, *pdu_physical_names, *pdu_karabo_das, run_numbers]
+
+socket.send(str(data).encode())
+resp = socket.recv_multipart()[0]
+print(resp.decode())
diff --git a/webservice/serve_overview.py b/webservice/serve_overview.py
index dd7780202..b8c6c5593 100644
--- a/webservice/serve_overview.py
+++ b/webservice/serve_overview.py
@@ -10,6 +10,7 @@ from uuid import uuid4
import yaml
from jinja2 import Template
+
from xfel_calibrate.settings import (free_nodes_cmd, preempt_nodes_cmd,
reservation)
diff --git a/webservice/sqlite_view.py b/webservice/sqlite_view.py
index 854cc3149..c16727213 100644
--- a/webservice/sqlite_view.py
+++ b/webservice/sqlite_view.py
@@ -1,8 +1,6 @@
import argparse
-
import sqlite3
-
parser = argparse.ArgumentParser(
description='Update run status at MDC for a given run id.')
parser.add_argument('--sqlite-fpath', type=str, help='Path to sqlite file path',
diff --git a/webservice/update_config.py b/webservice/update_config.py
index 0d3cf58f1..c79474236 100644
--- a/webservice/update_config.py
+++ b/webservice/update_config.py
@@ -5,7 +5,6 @@ import sys
import yaml
import zmq
-
# Defining available options
agipd_options = {
"force-hg-if-below": {'typ': int},
diff --git a/webservice/update_mdc.py b/webservice/update_mdc.py
index 56da834f6..fd8d09e89 100644
--- a/webservice/update_mdc.py
+++ b/webservice/update_mdc.py
@@ -1,10 +1,8 @@
import argparse
import yaml
-
from metadata_client.metadata_client import MetadataClient
-
parser = argparse.ArgumentParser(
description='Update run status at MDC for a given run id.')
parser.add_argument('--conf-file', type=str, help='Path to webservice config',
diff --git a/webservice/webservice.py b/webservice/webservice.py
index dbf53cf55..0249a7e44 100644
--- a/webservice/webservice.py
+++ b/webservice/webservice.py
@@ -8,17 +8,16 @@ import logging
import os
import sqlite3
import subprocess
+import traceback
import urllib.parse
from datetime import datetime
-import traceback
import yaml
import zmq
import zmq.asyncio
import zmq.auth.thread
-from dateutil import parser as timeparser
-from git import Repo, InvalidGitRepositoryError
-from messages import Errors, Success, MDC
+from git import InvalidGitRepositoryError, Repo
+from messages import MDC, Errors, Success
from metadata_client.metadata_client import MetadataClient
diff --git a/xfel_calibrate/calibrate.py b/xfel_calibrate/calibrate.py
index a1572c7b9..03242466e 100755
--- a/xfel_calibrate/calibrate.py
+++ b/xfel_calibrate/calibrate.py
@@ -1,26 +1,26 @@
#!/usr/bin/env python
import argparse
-from datetime import datetime
import inspect
-import nbconvert
-import nbformat
-from nbparameterise import (
- extract_parameters, replace_definitions, parameter_values
-)
import os
import pprint
import re
-from subprocess import check_output, DEVNULL
+import stat
import sys
+import textwrap
import warnings
-from .settings import *
-from .notebooks import notebooks
+from datetime import datetime
+from subprocess import DEVNULL, check_output
+
+import nbconvert
+import nbformat
from jinja2 import Template
-import stat
-import textwrap
+from nbparameterise import (extract_parameters, parameter_values,
+ replace_definitions)
from .finalize import tex_escape
+from .notebooks import notebooks
+from .settings import *
PKG_DIR = os.path.dirname(os.path.abspath(__file__))
@@ -271,6 +271,7 @@ def balance_sequences(in_folder, run, sequences, sequences_per_node,
:return: Balanced list of list of sequences
"""
import glob
+
import numpy as np
if sequences[0] == -1:
path = os.path.join(in_folder, f"r{run:04d}", f"*{path_inset}-S*.h5")
diff --git a/xfel_calibrate/finalize.py b/xfel_calibrate/finalize.py
index 6bdc1117c..199024679 100644
--- a/xfel_calibrate/finalize.py
+++ b/xfel_calibrate/finalize.py
@@ -1,9 +1,9 @@
+import re
from datetime import datetime
from glob import glob
from importlib.machinery import SourceFileLoader
from os import chdir, listdir, makedirs, path, remove, stat
from os.path import isdir, isfile, splitext
-import re
from shutil import copy, copytree, move, rmtree
from subprocess import CalledProcessError, check_call, check_output
from textwrap import dedent
@@ -14,6 +14,7 @@ from jinja2 import Template
from .settings import *
+
def atoi(text):
"""
Convert string to integer is possible
--
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