# Conflicts:
#   cal_tools/cal_tools/agipdlib.py
#   cal_tools/cal_tools/agipdutils.py

Fix import * in agipdlib

See merge request detectors/pycalibration!445

 The file was heavily flaked, no other changes of logic

Fix/keep time zone info 3.1.0

See merge request detectors/pycalibration!443

Rebasing to master

Refactor 'webservice' ZMQ server

See merge request detectors/pycalibration!441

Remove unused variable and import in agipdutils.py

See merge request detectors/pycalibration!428

Feat/add badpixelff jungfrau

See merge request detectors/pycalibration!429

Fix/ Use language name instead of kernel name

See merge request detectors/pycalibration!439

Create the webservice's MyMDC client in a non-blocking thread

See merge request detectors/pycalibration!431

Use asyncio subprocess interface in webservice code

See merge request detectors/pycalibration!435

Webservice: use SQLite parameter substitution instead of string formatting

See merge request detectors/pycalibration!436

Fix/pre commit whitespace

## Description

Applies whitespace fixes for pre-commit checks so that those stop being a source of errors in the future.

Marked as WIP as this requires !417  to be merged first. I'll rebase (if needed) once that's done.

First step of #36

Ran `echo 'end-of-file-fixer trailing-whitespace mixed-line-ending' | xargs -n 1 pre-commit run --all-files`

## How Has This Been Tested?

This change only does:

- end-of-file-fixer
- trailing-whitespace
- mixed-line-ending

None of which affect the code, so no real checks were performed.

## Relevant Documents (optional)
<!-- Include any relevant screenshot, elogs, reports, if appropriate. -->

## Types of changes

Formatting fixes

## Checklist:
<!--- Go over all the following points, and uncomment all lines that apply: -->

- My code ~~follows~~ implements the code style of this project.

## Reviewers

@danilevc @ahmedk @hammerd

See merge request detectors/pycalibration!433

Fix missed mixed line endings

Feat/pre commit checks

- Added pre-commit hooks which:
  - isort on `.py` and `.ipynb`
  - flake8 on `.py` and `.ipynb`
  - nbstripout
  - rstcheck
  - check-added-large-files
  - check-ast
  - check-json
  - check-yaml
  - check-toml
  - end-of-file-fixer
  - trailing-whitespace
  - check-docstring-first
  - check-merge-conflict
  - mixed-line-ending
- Hooks run as part of the `check` stage in the CI
- Fixed some of the issues:
  - EoF
  - Trailing whitespace
  - isort (but only for .py)

I included a lot of other changes and fixes in the original MR (https://git.xfel.eu/gitlab/detectors/pycalibration/merge_requests/411) before figuring out how to get the checks to run only on changed files, which meant that the MR implementing pre-commit checks also refactored a decent chunk of code. It would be better to do that refactoring in separate MRs so I've closed the original one and opened this to replace it.

@ahmedk @danilevc @hammerd feel free to review when you have time 

TODO:

- [x] Add pre-commit to requirements.txt
- [x] ~~Don't mutate the code during pre-commit checks~~ - changed my mind about this a few times, left it to mutate the code as that is only done on staged files, so any mutations can be reverted by undoing changes anyway. Added an explanation on this to the readme instead.
- [x] Add info to the readme and to the wiki
- [x] Add explanation of what each of the checks is for in more detail
- [x] Add scripts to execute w/ diff-only (same as the CI pipeline)

See merge request detectors/pycalibration!417

Author: Robert Rosca <robert.rosca@xfel.eu>
Date:   Wed Feb 24 21:04:47 2021 +0100

    Add link to wiki dev guidelines to readme

commit 0d902b2b
Author: Robert Rosca <robert.rosca@xfel.eu>
Date:   Mon Feb 22 22:25:40 2021 +0100

    Add .git-blame-ignore-revs file preemptively

commit 9e6030a3
Author: Robert Rosca <robert.rosca@xfel.eu>
Date:   Mon Feb 22 18:55:55 2021 +0100

    Fix import order

commit d7ca8e96
Author: Robert Rosca <robert.rosca@xfel.eu>
Date:   Mon Feb 22 18:52:24 2021 +0100

    Add notes on skipping checks, set to allow failure true,  break import order again

commit a6f43240
Author: Robert Rosca <robert.rosca@xfel.eu>
Date:   Mon Feb 22 18:38:08 2021 +0100

    Fix import order

commit 2854f22b
Author: Robert Rosca <robert.rosca@xfel.eu>
Date:   Mon Feb 22 18:08:35 2021 +0100

    Add accidentally removed dependencies

commit 9ecbc83e
Author: Robert Rosca <robert.rosca@xfel.eu>
Date:   Mon Feb 22 18:06:45 2021 +0100

    Add additional details to the readme

commit 6342f2e6
Author: Robert Rosca <robert.rosca@xfel.eu>
Date:   Mon Feb 22 16:33:47 2021 +0100

    Export SHA var as it's used during pre-commit itself

commit a142df25
Author: Robert Rosca <robert.rosca@xfel.eu>
Date:   Mon Feb 22 15:50:24 2021 +0100

    Swap lines to make more sense

commit 95183eb5
Author: Robert Rosca <robert.rosca@xfel.eu>
Date:   Mon Feb 22 15:50:09 2021 +0100

    Add a script for easy execution of diff-only pre-commit checks

commit b98fed75
Author: Robert Rosca <robert.rosca@xfel.eu>
Date:   Mon Feb 22 14:11:13 2021 +0100

    Add todos, adjust headings

commit d6b83d8b
Author: Robert Rosca <robert.rosca@xfel.eu>
Date:   Mon Feb 22 13:49:16 2021 +0100

    Update README.rst

    Change to be compliant with RSTcheck
    Fix some heading orders and enumerated lists
    Update the setup instructions

commit db768d61
Author: Robert Rosca <robert.rosca@xfel.eu>
Date:   Mon Feb 22 12:12:29 2021 +0100

    Sort requirements

commit 43122cd3
Author: Robert Rosca <robert.rosca@xfel.eu>
Date:   Mon Feb 22 12:12:06 2021 +0100

    Add pre-commit to requirements

commit 797af5db
Author: Cyril Danilevski <cyril.danilevski@xfel.eu>
Date:   Tue Feb 9 11:19:30 2021 +0100

    blabla

commit 6179aaa5
Author: Robert Rosca <robert.rosca@xfel.eu>
Date:   Mon Feb 8 11:22:54 2021 +0100

    Add comments to clarify non-standard sections

commit cae49ef4
Author: Robert Rosca <robert.rosca@xfel.eu>
Date:   Mon Feb 8 11:12:19 2021 +0100

    Use consistent isort version

commit c4d550a2
Author: Robert Rosca <robert.rosca@xfel.eu>
Date:   Mon Feb 8 11:09:45 2021 +0100

    Check if MR commit SHA is set

commit aceded4b
Author: Robert Rosca <robert.rosca@xfel.eu>
Date:   Mon Feb 8 10:52:12 2021 +0100

    Add pre-commit configuration

    Pretty standard setup

    Worth mentioning that flake8 is set to only run on the diff between current
    branch and merge target

    This will not work outside of a merge request

commit c5b8d367
Author: Robert Rosca <robert.rosca@xfel.eu>
Date:   Mon Feb 8 10:50:37 2021 +0100

    Update CI to work with pre-commit

    Check stage tries to find the commit hash being merged into

    Uses that hash to get  a list of changed files

    Passes this list of files to pre-commit so that checks only run on
    modified files