diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
new file mode 100644
index 0000000000000000000000000000000000000000..687b779fc369965d8789ef9f3ebc1c56222cd1d0
--- /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 54afabdc2d78b32c0808dd4336817878fd838507..e52ed743572fb1866825e7f3f2022f743b9e1a0e 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 e217c04dafbf19c53fcb0b73bec0cd23a6bed91c..9533a65717676bef660795007a090214121847a5 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 65ff9186690cdd07a532641d7276164dac2ebeb2..97d38ce87718cc5759ac807fd5a506decdffa02d 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 907c1682d9c53f6f220a8bc582b2f04f13e44f17..b9074e1187e2316b881088a460c6e752e9f34079 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 47392acdcaf67b36137179bbf12c1dc511a80216..054cebb74170bd7651cf65419efcacf7088e1f36 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 bbaededcef42c94b60dba86c08ba91e7073dfc27..8a6c0affceb3151dc993e50e8972464cef978e57 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 a84463efaf71a6308c88f58abf4100c60e21a3d7..7329e7b7eec613497c8943ba290cfb7771ed9a90 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 8ae6e17a9e762c4cfc4ee2994f48d54430422794..576f5284493108d923d40fb0565669229f5b689e 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 8e485f2739364e29aa0349e990c75e3f113e1e22..e4e3f44b5aefac4dd7f6aa92f7a08db46c0d305e 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 25a71e0984a879bfa971e72addcd01e476a3ce3b..e5457aef11a29a81ced4538e00365cf99096c88f 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 350328d4f03abcb534f0ef4c164adac12b5f8bb8..23c008eba4f6ed9c3cf63b4d03b4cb01668b2c73 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 b3a4cd8b073961a685168926c280d952d6a99692..0ef031095e14ec7bae0cd1b1b42497635f82194a 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 35ffc923cac07d72bbebd537b72e5e3c6dd49f16..a0539603fbd1c64534475daff511d39ffc20dea7 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 a85fa0b299aa1d5ad109c3bae349035e59551006..708037153f3b84f3d821f5d0814d24973b797504 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 c21babe2c0843b3bd3788a95de299ec34607600b..03d24a9a6d0606920df0668ab4eaf8dae650e09d 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 8213e937d6d08a795d7e9ed466653a7df4ec43c3..58b1c9ce10dbb518dd11c7af2bada148433de433 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 0000000000000000000000000000000000000000..533ecad66971d102f9d68c6c6e4178d35e11a120
--- /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/legacy/readme.md b/tests/legacy/readme.md
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index 0000000000000000000000000000000000000000..060f9898283312292a14c51c6d0da0c14cc00ea5
--- /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!
+
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similarity index 99%
rename from tests/test_agipd.py
rename to tests/legacy/test_agipd.py
index 814dfbff6b39ab6db3ddea1bf087ff123ad6dbf7..1f6aa646b3de858b4391ed0a011242690ef52af6 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 9119d506f66b5ecebaf3e859b682990c6cd6120e..b72a211f1105a2761ba0a9094589df6418fb62d8 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 803eba3b12f85f80bb3d1603f47c51c9959ea297..208066682fdbb409c97df7106ce567e68a8b81a7 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 bf07427f2ba6a40c53f5884ed84234f016cab754..b467d89f0dff3d78367f13e7b6eb4c97970511dd 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 dd77802028fd28de5f4991d2ee30f520fab6d908..b8c6c5593a8a385a9ed044d9d85031e822f18f4b 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 854cc3149242b65e3356a8acfdadb787d6748003..c1672721386a0a5024b12bc9f2a5fb3247b4d630 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 0d3cf58f1f45be6e51be83eaf31b6046aac43805..c794742367810190be1e8514800af79d5464d227 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 56da834f642f769568fd0fbaf9faf3338ab5d46e..fd8d09e895490b5bbd418c9824c7e34f51285f7a 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 dbf53cf554d8f3529a35534a95ea8576eca67802..0249a7e443996cbfb9dcb8eb3af71bac4ab78807 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 a1572c7b9f82a0bb60341fed627a7478b424f55d..03242466e9d9dbb6bf4a9d95a3de67db53cac8fd 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 6bdc1117cc5eba7ce18e08300044e41ad7cd2cee..1990246790cb892841713a2de509b0aa8dc76432 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