fix imports etc

JoranAngevaare · JoranAngevaare · commit 224f5e4feaaf · 2021-12-03T10:39:12.000+01:00
diff --git a/.github/workflows/code_style.yml b/.github/workflows/code_style.yml
@@ -1,7 +1,7 @@
 name: Python style
 on:
   pull_request:
-    types: [opened]
+    types: [ opened ]
 jobs:
   qa:
     name: Quality check
@@ -14,7 +14,7 @@ jobs:
           python-version: 3.8
       - name: Change __all__ exports for pyflake
         run: |
-             bash .github/scripts/pre_pyflakes.sh
+          bash .github/scripts/pre_pyflakes.sh
       - name: Wemake Python Stylguide
         uses: wemake-services/wemake-python-styleguide@0.15.3
         continue-on-error: true
diff --git a/.github/workflows/pypi_install.yml b/.github/workflows/pypi_install.yml
@@ -5,7 +5,7 @@ name: Pipy
 on:
   workflow_dispatch:
   release:
-    types: [created]
+    types: [ created ]
 
 jobs:
   build:
@@ -28,5 +28,5 @@ jobs:
         # if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
         uses: pypa/gh-action-pypi-publish@master
         with:
-          user:  ${{ secrets.token }}
+          user: ${{ secrets.token }}
           password: ${{ secrets.pypi_password }}
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -4,7 +4,7 @@ name: Test package
 on:
   workflow_dispatch:
   release:
-    types: [created]
+    types: [ created ]
   pull_request:
   push:
     branches:
@@ -18,8 +18,8 @@ jobs:
     strategy:
       fail-fast: False
       matrix:
-        python-version: [3.7, 3.8, 3.9]
-        test: ['coveralls', 'pytest']
+        python-version: [ 3.7, 3.8, 3.9 ]
+        test: [ 'coveralls', 'pytest' ]
         # Only run coverage / no_database on py3.8
         exclude:
           - python-version: 3.7
diff --git a/.github/workflows/test_install.yml b/.github/workflows/test_install.yml
@@ -3,7 +3,7 @@ name: Installation test
 on:
   workflow_dispatch:
   release:
-    types: [created]
+    types: [ created ]
   pull_request:
     branches:
       - master
@@ -19,7 +19,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.8]
+        python-version: [ 3.8 ]
     steps:
       - name: Setup python
         uses: actions/setup-python@v2
diff --git a/HISTORY.md b/HISTORY.md
@@ -1,16 +1,17 @@
 1.0.0 / 2021-12-02
 ------------------
- - Add badges to Amstrax and update readme (#23)
- - Plugin, context and package structure (#24)
- - Fix autoprocessing scripts (#25)
- - Delete bootstrax (#26)
- - remove notebooks (#27)
- - Add documentation
- 
- 
+
+- Add badges to Amstrax and update readme (#23)
+- Plugin, context and package structure (#24)
+- Fix autoprocessing scripts (#25)
+- Delete bootstrax (#26)
+- remove notebooks (#27)
+- Add documentation
+
 0.1.0 / 2021-12-02
 --------------------
- -  Add testing and restructure amstrax (#13)
+
+- Add testing and restructure amstrax (#13)
 
 0.0.1 / <2021-12-01
 --------------------
diff --git a/README.md b/README.md
@@ -1,25 +1,33 @@
 # Amstrax
+
 [![Coverage Status](https://coveralls.io/repos/github/XAMS-nikhef/amstrax/badge.svg?branch=master)](https://coveralls.io/github/XAMS-nikhef/amstrax?branch=master)
 [![CodeFactor](https://www.codefactor.io/repository/github/xams-nikhef/amstrax/badge)](https://www.codefactor.io/repository/github/xams-nikhef/amstrax)
 [![PyPI version shields.io](https://img.shields.io/pypi/v/amstrax.svg)](https://pypi.python.org/pypi/amstrax/)
 [![PyPI downloads](https://img.shields.io/pypi/dm/amstrax.svg)](https://pypistats.org/packages/amstrax)
 [![DOI](https://zenodo.org/badge/263576054.svg)](https://zenodo.org/badge/latestdoi/263576054)
 
 ## Documentation
+
 [![Documentation Status](https://readthedocs.org/projects/amstrax/badge/?version=latest)](https://amstrax.readthedocs.io/en/latest/?badge=latest)
 
 Amsterdam Strax
 
-Amstrax is the analysis framework for XAMS, built on top of the generic [strax framework](https://github.com/AxFoundation/strax). 
+Amstrax is the analysis framework for XAMS, built on top of the
+generic [strax framework](https://github.com/AxFoundation/strax).
 
 # Installation
+
 For installing the package do the regular install-packages-from-github tricks:
+
 ```
 pip install amstrax
 ```
+
 All required dependencies will be installed for you.
 
 # Usage
-First you'll need to get some data. For this you'll need to either run somewhere where nikhef's /data/xenon/xams is available or have data downloaded.
-Either strax processed data or pax raw data is fine.
-Once you have data you can try running the Tutorial notebook (although it's in Dutch), just make sure to change the output_folder to where you have data
+
+First you'll need to get some data. For this you'll need to either run somewhere where nikhef's
+/data/xenon/xams is available or have data downloaded. Either strax processed data or pax raw data
+is fine. Once you have data you can try running the Tutorial notebook (although it's in Dutch), just
+make sure to change the output_folder to where you have data
diff --git a/amstrax/SiPMdata.py b/amstrax/SiPMdata.py
@@ -1,16 +1,11 @@
-from iminuit import Minuit
+import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
-
-from copy import deepcopy
-
-import matplotlib
-import matplotlib.pyplot as plt
+from IPython.display import clear_output
+from iminuit import Minuit
 from matplotlib.colors import BoundaryNorm
 from matplotlib.ticker import MaxNLocator
 
-from IPython.display import clear_output
-
 np.random.seed(12345)
 inch = 25.4  # mm
 
diff --git a/amstrax/__init__.py b/amstrax/__init__.py
@@ -1,15 +1,12 @@
 __version__ = '0.1.0'
 
+from . import auto_processing
 from . import hitfinder_thresholds
-from .hitfinder_thresholds import *
-
+from . import plugins
 from .common import *
-from .itp_map import *
-from .rundb import *
+from .contexts import *
 from .hitfinder_thresholds import *
-
-from . import plugins
+from .hitfinder_thresholds import *
+from .itp_map import *
 from .plugins import *
-
-from .contexts import *
-from . import auto_processing
+from .rundb import *
diff --git a/amstrax/auto_processing/__init__.py b/amstrax/auto_processing/__init__.py
@@ -1,5 +1,4 @@
 from . import amstraxer
-from . import submit_stbc
-
 from . import auto_processing
 from . import process_run
+from . import submit_stbc
diff --git a/amstrax/auto_processing/amstraxer.py b/amstrax/auto_processing/amstraxer.py
@@ -4,14 +4,15 @@
 """
 import argparse
 import datetime
+import json
 import logging
-import time
 import os
 import os.path as osp
 import platform
-import psutil
 import sys
-import json
+import time
+
+import psutil
 
 
 def parse_args():
diff --git a/amstrax/auto_processing/auto_processing.py b/amstrax/auto_processing/auto_processing.py
@@ -1,5 +1,5 @@
-import time
 import argparse
+import time
 
 
 def parse_args():
diff --git a/amstrax/auto_processing/submit_stbc.py b/amstrax/auto_processing/submit_stbc.py
@@ -1,5 +1,6 @@
-import os
 import argparse
+import os
+
 from amstrax import amstrax_dir
 
 script_template = """#!/bin/bash
diff --git a/amstrax/common.py b/amstrax/common.py
@@ -1,14 +1,11 @@
-import socket
-import sys
-import os.path as osp
-import os
 import inspect
-import urllib.request
-import tarfile
 import io
+import os
+import tarfile
+
 import numpy as np
-import straxen
 import strax
+import straxen
 
 export, __all__ = strax.exporter()
 __all__ += ['amstrax_dir', 'to_pe']
diff --git a/amstrax/contexts.py b/amstrax/contexts.py
@@ -1,9 +1,11 @@
 import os
 from datetime import timezone
+
 import strax
-import amstrax as ax
 from immutabledict import immutabledict
 
+import amstrax as ax
+
 common_opts = dict(
     # register_all=[ax.pulse_processing,
     #               ax.peak_processing,
diff --git a/amstrax/hitfinder_thresholds.py b/amstrax/hitfinder_thresholds.py
@@ -1,6 +1,6 @@
 import numpy as np
-
 import strax
+
 import amstrax
 
 export, __all__ = strax.exporter()
diff --git a/amstrax/itp_map.py b/amstrax/itp_map.py
@@ -1,12 +1,11 @@
-import logging
 import gzip
 import json
+import logging
 import re
 
 import numpy as np
-from scipy.spatial import cKDTree
-
 import strax
+from scipy.spatial import cKDTree
 
 export, __all__ = strax.exporter()
 
diff --git a/amstrax/plugins/__init__.py b/amstrax/plugins/__init__.py
@@ -1,20 +1,14 @@
 from . import daqreader
-from .daqreader import *
-
+from . import event_processing
+from . import pax_interface
+from . import peak_processing
 from . import peak_processing
-from .peak_processing import *
-
 from . import pulse_processing
-from .pulse_processing import *
-
 from . import pulse_processing_alt_baseline
-from .pulse_processing_alt_baseline import *
-
-from . import peak_processing
-from .peak_processing import *
-
-from . import event_processing
+from .daqreader import *
 from .event_processing import *
-
-from . import pax_interface
 from .pax_interface import *
+from .peak_processing import *
+from .peak_processing import *
+from .pulse_processing import *
+from .pulse_processing_alt_baseline import *
diff --git a/amstrax/plugins/daqreader.py b/amstrax/plugins/daqreader.py
@@ -1,9 +1,10 @@
 import glob
 import warnings
-from immutabledict import immutabledict
+
 import numpy as np
 import strax
 import straxen
+from immutabledict import immutabledict
 from straxen.plugins.daqreader import split_channel_ranges
 
 export, __all__ = strax.exporter()
diff --git a/amstrax/plugins/event_processing.py b/amstrax/plugins/event_processing.py
@@ -1,5 +1,5 @@
-import strax
 import numpy as np
+import strax
 from amstrax.SiPMdata import *
 
 export, __all__ = strax.exporter()
diff --git a/amstrax/plugins/pax_interface.py b/amstrax/plugins/pax_interface.py
@@ -1,11 +1,12 @@
 """Convert pax .zip files to flat records format
 """
-import numpy as np
-import os
 import glob
+import os
+
 import numba
-from straxen.plugins.pax_interface import records_needed
+import numpy as np
 import strax
+from straxen.plugins.pax_interface import records_needed
 
 export, __all__ = strax.exporter()
 
diff --git a/amstrax/plugins/peak_processing.py b/amstrax/plugins/peak_processing.py
@@ -1,8 +1,7 @@
-import numpy as np
 import numba
-from amstrax.SiPMdata import *
-
+import numpy as np
 import strax
+from amstrax.SiPMdata import *
 
 export, __all__ = strax.exporter()
 
diff --git a/amstrax/plugins/pulse_processing.py b/amstrax/plugins/pulse_processing.py
@@ -1,8 +1,8 @@
-from immutabledict import immutabledict
 import numba
 import numpy as np
-
 import strax
+from immutabledict import immutabledict
+
 import amstrax
 
 export, __all__ = strax.exporter()
diff --git a/amstrax/rundb.py b/amstrax/rundb.py
@@ -1,12 +1,12 @@
 import os
 import re
-import typing
 import socket
-from sshtunnel import SSHTunnelForwarder
-from tqdm import tqdm
-import pymongo
+import typing
 
+import pymongo
 import strax
+from sshtunnel import SSHTunnelForwarder
+from tqdm import tqdm
 
 export, __all__ = strax.exporter()
 
@@ -107,7 +107,7 @@ def __init__(self,
         self.local_only = local_only
         self.new_data_path = new_data_path
         self.reader_ini_name_is_mode = reader_ini_name_is_mode
-        self.readonly=readonly
+        self.readonly = readonly
         if self.new_data_path is None:
             self.readonly = True
 
diff --git a/docs/source/build_data_structure_doc.py b/docs/source/build_data_structure_doc.py
diff --git a/setup.cfg b/setup.cfg
diff --git a/tests/test_autoprocessing.py b/tests/test_autoprocessing.py
diff --git a/tests/test_basics.py b/tests/test_basics.py
diff --git a/tests/test_help_of_scripts.py b/tests/test_help_of_scripts.py
