Normalize files (#2334)

* Make python-flake8.yml a general lint workflow

* Add a lint check to prevent crlf endings in git

* Set text=auto and renormalize files

* Add a lint check to prevent whitespace issues

Whitespace issues as understood by git (by default) are trailing
whitespace at EOL, whitespace on an otherwise empty line, a space
character immediately followed by a tab character in the indentation of
a line, and multiple newlines at EOF.

References:
- https://git-scm.com/docs/git-diff#Documentation/git-diff.txt---check
- https://peter.eisentraut.org/blog/2014/11/04/checking-whitespace-with-git

* Fix trailing whitespace issues

* Fix issues with multiple newlines at EOF

* Ignore conflict marker warning in rst files

.coveragerc

@@ -1,7 +1,7 @@
 [run]
-omit = 
+omit =
      _tests/*
-     */_tests/* 
+     */_tests/*
      mslib/msui/qt5/*
      docs/*
      /tmp/*

.gitattributes

@@ -0,0 +1 @@
+* text=auto

.github/workflows/build_docs_gallery.yml

@@ -1,6 +1,6 @@
 name: Build Gallery
 
-on: 
+on:
    pull_request:
      inputs:
         branch_name:

.github/workflows/lint.yml

@@ -0,0 +1,57 @@
+name: lint
+
+on:
+  push:
+    branches:
+    - develop
+    - stable
+  pull_request:
+    branches:
+    - develop
+    - stable
+
+jobs:
+  flake8:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v3
+      with:
+        python-version: 3.8
+    - name: Lint with flake8
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8
+        flake8 --count --statistics mslib tests
+
+  no-crlf-in-git:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    steps:
+    - uses: actions/checkout@v4
+    - name: Check for CRLF in the repository
+      run: |
+        files_with_crlf="$(git ls-files --eol | awk '$1 ~ "crlf"')"
+        echo "$files_with_crlf"
+        [ "$files_with_crlf" == "" ] || exit 1
+
+  no-whitespace-issues-in-git:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    steps:
+    - uses: actions/checkout@v4
+    - name: Check for whitespace issues in the repository
+      # The two example.txt files need to be excluded because whitespace at EOL is part
+      # of their format and they fail to parse otherwise.
+      # The leftover conflict marker warning is ignored for all rst files because
+      # section headings consisting of 7 "=" characters are mistaken to be part of a
+      # conflict marker.
+      run: |
+        issues="$(
+          git diff --check $(git hash-object -t tree /dev/null) HEAD :^tests/data/example.txt :^docs/samples/flight-tracks/example.txt |
+            { grep -v '^.*\.rst:.*leftover conflict marker$' || true; }
+        )"
+        echo "$issues"
+        [ "$issues" == "" ] || exit 1

.github/workflows/testing-develop.yml

@@ -9,24 +9,23 @@ on:
     branches:
     - develop
 
-jobs:     
+jobs:
   test-develop:
-    uses: 
+    uses:
       ./.github/workflows/testing.yml
     with:
       xdist: no
       branch_name: develop
       event_name: ${{ github.event_name }}
-    secrets: 
+    secrets:
       PAT: ${{ secrets.PAT }}
 
   test-develop-xdist:
-    uses: 
+    uses:
       ./.github/workflows/testing.yml
     with:
       xdist: yes
       branch_name: develop
       event_name: ${{ github.event_name }}
     secrets:
       PAT: ${{ secrets.PAT }}
-

.github/workflows/testing-scheduled.yml

@@ -2,12 +2,12 @@ name: new dependency test (scheduled)
 
 on:
   schedule:
-    - cron: '30 5 * * 1' 
+    - cron: '30 5 * * 1'
 
 
-jobs:     
+jobs:
   test-stable-scheduled:
-    uses: 
+    uses:
       ./.github/workflows/testing.yml
     with:
       xdist: no
@@ -17,14 +17,11 @@ jobs:
       PAT: ${{ secrets.PAT }}
 
   test-develop-scheduled:
-    uses: 
+    uses:
       ./.github/workflows/testing.yml
     with:
       xdist: no
       branch_name: develop
       event_name: ${{ github.event_name }}
     secrets:
       PAT: ${{ secrets.PAT }}
-
-
-

.github/workflows/testing-stable.yml

@@ -9,9 +9,9 @@ on:
     - stable
   workflow_dispatch:
 
-jobs:     
+jobs:
   test-stable:
-    uses: 
+    uses:
       ./.github/workflows/testing.yml
     with:
       xdist: no
@@ -21,13 +21,11 @@ jobs:
       PAT: ${{ secrets.PAT }}
 
   test-stable-xdist:
-    uses: 
+    uses:
       ./.github/workflows/testing.yml
     with:
       xdist: yes
       branch_name: stable
       event_name: ${{ github.event_name }}
     secrets:
       PAT: ${{ secrets.PAT }}
-
-

.gitignore

@@ -24,4 +24,3 @@ build/
 mss.egg-info/
 tutorials/recordings
 tutorials/cursor_image.png
-

CHANGES.rst

@@ -253,7 +253,7 @@ Version 6.2.0
 
 This release includes the use of the new basemap-1.3.3 release and enables packaging for python 3.10.x.
 We added the possibility of flight level as vertical coordinate.
-A user can now leave on his own an operation. 
+A user can now leave on his own an operation.
 
 
 All changes:
@@ -804,7 +804,7 @@ Bug Fixes:
   - mswms crashes on a wms server when the request object is None, #339, #342
   - data_dir not used for default filepicker, #337
   - post_link.sh update on conda-forge, #334
- 
+
 
 Version 1.7.2
 -------------
@@ -1126,7 +1126,7 @@ New Features:
  - Suggest standard name for saving plots, #13
  - KML Overlay introduced for overplot of flight region borders, #61, #97
  - implemented demodata for standalone server and py.test, #80
- - simplified server setup, added demodata. 
+ - simplified server setup, added demodata.
  - Always provide simplified aircraft range estimates in TableView. #85
  - server data needs standard_name in data, #87
  - plugin infrastructure introduced for supporting file formats for flight track saving/loading, #69, #88
@@ -1176,7 +1176,7 @@ Other Changes:
 
 
 
-Version 1.2.2 
+Version 1.2.2
 -------------
 
 Bug Fixes:
@@ -1190,7 +1190,7 @@ New Features:
 Other Changes:
  - installation with conda-forge described#63
 
-Version 1.2.1 
+Version 1.2.1
 -------------
 
 Bug Fixes:
@@ -1223,17 +1223,17 @@ Other Changes:
  - improved documentations
 
 
-Version 1.1.0 
+Version 1.1.0
 -------------
 
 New Features:
  - Vertical section styles supported in standalone server, #10
  - More formats for exchanging flight paths implemented, #7
- - Reverse flight path, #11 
+ - Reverse flight path, #11
  - Displaying model data from CLaMS, #4
  - Visualisation of gravity wave forecasts, #14
  - Improved labels in plots, #8
-   
+
 Bug Fixes:
  - Improved debugging in standalone server, #9
  - Fix for Labels accumulate in plots upon saving, #5
@@ -1243,7 +1243,6 @@ Bug Fixes:
 Other Changes:
  - Namespace refactored, all modules dependend to mslib #24
  - Sphinx documentation introduced, #25, #26
- - Documentation on http://mss.rtfd.io 
- - Installation recipes based on conda  
+ - Documentation on http://mss.rtfd.io
+ - Installation recipes based on conda
  - First public release on June 28, 2016
-

CITATION.cff

@@ -1,5 +1,5 @@
 cff-version: "1.2.0"
-contact: 
+contact:
     - website: https://github.com/Open-MSS/MSS/wiki/Contact
       name: "MSS community"
 license: "Apache-2.0"
@@ -19,7 +19,7 @@ authors:
     email: "j.ungermann@fz-juelich.de"
     orcid:  "https://orcid.org/0000-0001-9095-8332"
   - affiliation: "Forschungszentrum Jülich GmbH"
-    family-names: "Grooß" 
+    family-names: "Grooß"
     given-names: "Jens-Uwe"
     email: "j.-u.grooss@fz-juelich.de"
     orcid: "https://orcid.org/0000-0002-9485-866X"

CONTRIBUTING.md

@@ -1,17 +1,17 @@
 # Contributing
 
 When contributing to this repository, please first discuss the change you wish to make via issue,
-email, or any other method with the owners of this repository before making a change. 
+email, or any other method with the owners of this repository before making a change.
 
 Please note we have a code of conduct, please follow it in all your interactions with the project.
 
 ## Pull Request Process
 
-1. Ensure any install or build dependencies are removed before the end of the layer when doing a 
+1. Ensure any install or build dependencies are removed before the end of the layer when doing a
    build.
-2. Update the README.md with details of changes to the interface, this includes new environment 
+2. Update the README.md with details of changes to the interface, this includes new environment
    variables, exposed ports, useful file locations and container parameters.
 3. Increase the version numbers in any examples files and the README.md to the new version that this
    Pull Request would represent. The versioning scheme we use is [SemVer](http://semver.org/).
-4. You may merge the Pull Request in once you have the sign-off of two other developers, or if you 
+4. You may merge the Pull Request in once you have the sign-off of two other developers, or if you
    do not have permission to do that, you may request the second reviewer to merge it for you.

LICENSE

@@ -206,7 +206,7 @@
 ***************************************************************************
 ***************************************************************************
 
-MISSION SUPPORT SYSTEM THIRD PARTY COMPONENTS: 
+MISSION SUPPORT SYSTEM THIRD PARTY COMPONENTS:
 
 The Mission Support System includes a number of components with
 separate copyright notices and license terms. Your use of the source

NOTICE

@@ -39,11 +39,11 @@ Package for working with OGC map, feature, and coverage services.
 Obtained from SVN (http://svn.gispython.org/svn/gispy/OWSLib/trunk),
 revision 1672, on 2010/08/11.
 
-NOTE: The file "wms.py" has been modified for the MSS. Changes are marked 
+NOTE: The file "wms.py" has been modified for the MSS. Changes are marked
 with "(mss)". We renamed it to "ogcwms.py" (2017-04-28)
 
 We also did a PEP8 review of the ogcwms.py and adopted it to the recent 0.14 version
-https://pypi.python.org/pypi/OWSLib/0.14.0 
+https://pypi.python.org/pypi/OWSLib/0.14.0
 
 
 NETCDF4-PYTHON
@@ -62,7 +62,7 @@ https://code.google.com/p/netcdf4-python/
 KML Examples
 -------------
 
-Below are links from where certain KML Files have been obtained, which are used 
+Below are links from where certain KML Files have been obtained, which are used
 as Test Samples in MSS (mss/docs/samples/kml/):
 
 World_Map.kml (mss/docs/samples/kml/World_Map.kml)

README.md

@@ -26,7 +26,7 @@ Automatically
 Manually
 --------
 
-As **Beginner** start with an installation of Mambaforge 
+As **Beginner** start with an installation of Mambaforge
 Get [mambaforge](https://github.com/conda-forge/miniforge#mambaforge) for your Operation System
 
 
@@ -42,7 +42,7 @@ to leave out the 'source' here and below).
 For updating an existing MSS installation to the current version, it is
 best to install it into a new environment. If an existing environment
 shall be updated, it is important to update all packages in this
-environment. 
+environment.
 
 ```
   $ mamba activate mssenv
@@ -74,7 +74,7 @@ Current release info
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6572620.svg)](https://doi.org/10.5281/zenodo.6572620)
 [![Conda Platforms](https://img.shields.io/conda/pn/conda-forge/mss.svg)](https://anaconda.org/conda-forge/mss)
 [![DOCS](https://img.shields.io/badge/%F0%9F%95%AE-docs-green.svg)](http://mss.rtd.io)
-[![Conda Recipe](https://img.shields.io/badge/recipe-mss-green.svg)](https://anaconda.org/conda-forge/mss) 
+[![Conda Recipe](https://img.shields.io/badge/recipe-mss-green.svg)](https://anaconda.org/conda-forge/mss)
 [![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/mss.svg)](https://anaconda.org/conda-forge/mss)
 [![Coverage Status](https://coveralls.io/repos/github/Open-MSS/MSS/badge.svg?branch=develop)](https://coveralls.io/github/Open-MSS/MSS?branch=develop)
 
@@ -100,11 +100,8 @@ application. The documents are available at:
 
 For copyright information, please see the files NOTICE and LICENSE, located
 in the same directory as this README file.
-   
+
 
    When using this software, please be so kind and acknowledge its use by
    citing the above mentioned reference documentation in publications,
    presentations, reports, etc. that you create. Thank you very much.
-
-
-

conftest.py

@@ -145,7 +145,7 @@ class mscolab_settings(object):
 
     # used to generate the password token
     SECURITY_PASSWORD_SALT = secrets.token_urlsafe(16)
-    
+
     # looks for a given category for an operation ending with GROUP_POSTFIX
     # e.g. category = Tex will look for TexGroup
     # all users in that Group are set to the operations of that category