Updated GitLab URLs due to changes on the server side.

Signed-off-by: Daniel Scheffler <danschef@gfz-potsdam.de>

.gitlab-ci.yml

@@ -28,7 +28,7 @@ test_gms_preprocessing:
 
     # update sicor
     # - rm -rf context/sicor
-    # - git clone https://gitext.gfz-potsdam.de/EnMAP/sicor.git ./context/sicor
+    # - git clone https://git.gfz-potsdam.de/EnMAP/sicor.git ./context/sicor
     # - cd ./context/sicor
     # - make download-tables
     # - python setup.py install

CONTRIBUTING.rst

@@ -15,7 +15,7 @@ Types of Contributions
 Report Bugs
 ~~~~~~~~~~~
 
-Report bugs at https://gitext.gfz-potsdam.de/geomultisens/gms_preprocessing/issues.
+Report bugs at https://git.gfz-potsdam.de/geomultisens/gms_preprocessing/issues.
 
 If you are reporting a bug, please include:
 
@@ -45,7 +45,7 @@ articles, and such.
 Submit Feedback
 ~~~~~~~~~~~~~~~
 
-The best way to send feedback is to file an issue at https://gitext.gfz-potsdam.de/geomultisens/gms_preprocessing/issues.
+The best way to send feedback is to file an issue at https://git.gfz-potsdam.de/geomultisens/gms_preprocessing/issues.
 
 If you are proposing a feature:
 
@@ -62,7 +62,7 @@ Ready to contribute? Here's how to set up `gms_preprocessing` for local developm
 1. Fork the `gms_preprocessing` repo on GitHub.
 2. Clone your fork locally::
 
-    $ git clone https://gitext.gfz-potsdam.de/geomultisens/gms_preprocessing
+    $ git clone https://git.gfz-potsdam.de/geomultisens/gms_preprocessing
 
 3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
 

README.rst

@@ -7,8 +7,8 @@ pre-precessing pipeline for spatial and spectral fusion (i.e., homogenization)
 of multispectral satellite image data. Currently it offers compatibility to
 Landsat-5, Landsat-7, Landsat-8, Sentinel-2A and Sentinel-2B.
 
-* Free software: GNU General Public License v3 or later (GPLv3+) (`license details <https://gitext.gfz-potsdam.de/geomultisens/gms_preprocessing/blob/master/LICENSE>`_)
-* Documentation: https://geomultisens.gitext-pages.gfz-potsdam.de/gms_preprocessing/doc/
+* Free software: GNU General Public License v3 or later (GPLv3+) (`license details <https://git.gfz-potsdam.de/geomultisens/gms_preprocessing/blob/master/LICENSE>`_)
+* Documentation: https://geomultisens.git-pages.gfz-potsdam.de/gms_preprocessing/doc/
 * Code history: Release notes for the current and earlier versions of gms_preprocessing can be found `here <./HISTORY.rst>`_.
 * OS compatibility: Linux
 
@@ -16,16 +16,16 @@ Landsat-5, Landsat-7, Landsat-8, Sentinel-2A and Sentinel-2B.
 Status
 ------
 
-.. image:: https://gitext.gfz-potsdam.de/geomultisens/gms_preprocessing/badges/master/pipeline.svg
-        :target: https://gitext.gfz-potsdam.de/geomultisens/gms_preprocessing/commits/master
-.. image:: https://gitext.gfz-potsdam.de/geomultisens/gms_preprocessing/badges/master/coverage.svg
-        :target: https://geomultisens.gitext-pages.gfz-potsdam.de/gms_preprocessing/coverage/
+.. image:: https://git.gfz-potsdam.de/geomultisens/gms_preprocessing/badges/master/pipeline.svg
+        :target: https://git.gfz-potsdam.de/geomultisens/gms_preprocessing/commits/master
+.. image:: https://git.gfz-potsdam.de/geomultisens/gms_preprocessing/badges/master/coverage.svg
+        :target: https://geomultisens.git-pages.gfz-potsdam.de/gms_preprocessing/coverage/
 .. image:: https://img.shields.io/pypi/v/gms_preprocessing.svg
         :target: https://pypi.python.org/pypi/gms_preprocessing
 .. image:: https://img.shields.io/conda/vn/conda-forge/gms_preprocessing.svg
         :target: https://anaconda.org/conda-forge/gms_preprocessing
 .. image:: https://img.shields.io/pypi/l/gms_preprocessing.svg
-        :target: https://gitext.gfz-potsdam.de/danschef/gms_preprocessing/blob/master/LICENSE
+        :target: https://git.gfz-potsdam.de/danschef/gms_preprocessing/blob/master/LICENSE
 .. image:: https://img.shields.io/pypi/pyversions/gms_preprocessing.svg
         :target: https://img.shields.io/pypi/pyversions/gms_preprocessing.svg
 
@@ -39,14 +39,14 @@ Level-1 processing:
 
 * data import and  metadata homogenization (compatibility: Landsat-5/7/8, Sentinel-2A/2B)
 * equalization of acquisition- and illumination geometry
-* atmospheric correction (using `SICOR <https://gitext.gfz-potsdam.de/EnMAP/sicor>`_)
-* correction of geometric errors (using `AROSICS <https://gitext.gfz-potsdam.de/danschef/arosics>`_)
+* atmospheric correction (using `SICOR <https://git.gfz-potsdam.de/EnMAP/sicor>`_)
+* correction of geometric errors (using `AROSICS <https://git.gfz-potsdam.de/danschef/arosics>`_)
 
 Level-2 processing:
 ^^^^^^^^^^^^^^^^^^^
 
 * spatial homogenization
-* spectral homogenization (using `SpecHomo <https://gitext.gfz-potsdam.de/geomultisens/spechomo>`_)
+* spectral homogenization (using `SpecHomo <https://git.gfz-potsdam.de/geomultisens/spechomo>`_)
 * estimation of accuracy layers
 
 => application oriented analysis dataset
@@ -65,7 +65,7 @@ homogenization jobs (using gms_preprocessing) can be defined and started. All
 configuration parameters of gms_preprocessing are accessible in the UI.
 
 
-.. image:: https://gitext.gfz-potsdam.de/geomultisens/gms_preprocessing/raw/master/docs/images/webapp_screenshot_900x497.png
+.. image:: https://git.gfz-potsdam.de/geomultisens/gms_preprocessing/raw/master/docs/images/webapp_screenshot_900x497.png
     :width: 900 px
     :height: 497 px
     :scale: 100 %
@@ -76,7 +76,7 @@ Usage via console interface
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Homogenization jobs can also be created and started using the command line
-interface. Documentation can be found `here <https://geomultisens.gitext-pages.gfz-potsdam.de/gms_preprocessing/doc/usage.html#gms-preprocessing-command-line-interface>`__.
+interface. Documentation can be found `here <https://geomultisens.git-pages.gfz-potsdam.de/gms_preprocessing/doc/usage.html#gms-preprocessing-command-line-interface>`__.
 
 Here is a small example:
 
@@ -110,14 +110,14 @@ This is an example:
     PC = ProcessController(job_ID=123456, **configuration)
     PC.run_all_processors()
 
-Possible configuration arguments can be found `here <https://gitext.gfz-potsdam.de/geomultisens/gms_preprocessing/blob/master/gms_preprocessing/options/options_schema.py>`__.
+Possible configuration arguments can be found `here <https://git.gfz-potsdam.de/geomultisens/gms_preprocessing/blob/master/gms_preprocessing/options/options_schema.py>`__.
 
 
 History / Changelog
 -------------------
 
 You can find the protocol of recent changes in the gms_preprocessing package
-`here <https://gitext.gfz-potsdam.de/geomultisens/gms_preprocessing/-/blob/master/HISTORY.rst>`__.
+`here <https://git.gfz-potsdam.de/geomultisens/gms_preprocessing/-/blob/master/HISTORY.rst>`__.
 
 
 License
@@ -166,8 +166,8 @@ Survey. Sentinel-2 data have been provided by ESA.
 
 .. _Cookiecutter: https://github.com/audreyr/cookiecutter
 .. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
-.. _coverage: https://geomultisens.gitext-pages.gfz-potsdam.de/gms_preprocessing/coverage/
-.. _nosetests: https://geomultisens.gitext-pages.gfz-potsdam.de/gms_preprocessing/nosetests_reports/nosetests.html
+.. _coverage: https://geomultisens.git-pages.gfz-potsdam.de/gms_preprocessing/coverage/
+.. _nosetests: https://geomultisens.git-pages.gfz-potsdam.de/gms_preprocessing/nosetests_reports/nosetests.html
 .. _conda: https://conda.io/docs/
 .. _redis-server: https://www.rosehosting.com/blog/how-to-install-configure-and-use-redis-on-ubuntu-16-04/
-.. _gms-vis: https://gitext.gfz-potsdam.de/geomultisens/gms-vis
+.. _gms-vis: https://git.gfz-potsdam.de/geomultisens/gms-vis

bin/run_gms.py

@@ -209,7 +209,7 @@ def get_gms_argparser():
 
     gop_p('-jc', '--json_config', nargs='?', type=str,
           help='file path of a JSON file containing options. See here for an example: '
-               'https://gitext.gfz-potsdam.de/geomultisens/gms_preprocessing/'
+               'https://git.gfz-potsdam.de/geomultisens/gms_preprocessing/'
                'blob/master/gms_preprocessing/options/options_default.json')
 
     # '-exec_L1AP': dict(nargs=3, type=bool, help="L1A Processor configuration",

docs/about.rst

@@ -7,8 +7,8 @@ pre-precessing pipeline for spatial and spectral fusion (i.e., homogenization)
 of multispectral satellite image data. Currently it offers compatibility to
 Landsat-5, Landsat-7, Landsat-8, Sentinel-2A and Sentinel-2B.
 
-* Free software: GNU General Public License v3 or later (GPLv3+) (`license details <https://gitext.gfz-potsdam.de/geomultisens/gms_preprocessing/blob/master/LICENSE>`_)
-* Documentation: https://geomultisens.gitext-pages.gfz-potsdam.de/gms_preprocessing/doc/
+* Free software: GNU General Public License v3 or later (GPLv3+) (`license details <https://git.gfz-potsdam.de/geomultisens/gms_preprocessing/blob/master/LICENSE>`_)
+* Documentation: https://geomultisens.git-pages.gfz-potsdam.de/gms_preprocessing/doc/
 * Code history: Release notes for the current and earlier versions of gms_preprocessing can be found `here <./HISTORY.rst>`_.
 * OS compatibility: Linux
 
@@ -21,14 +21,14 @@ Level-1 processing:
 
 * data import and  metadata homogenization (compatibility: Landsat-5/7/8, Sentinel-2A/2B)
 * equalization of acquisition- and illumination geometry
-* atmospheric correction (using `SICOR <https://gitext.gfz-potsdam.de/EnMAP/sicor>`_)
-* correction of geometric errors (using `AROSICS <https://gitext.gfz-potsdam.de/danschef/arosics>`_)
+* atmospheric correction (using `SICOR <https://git.gfz-potsdam.de/EnMAP/sicor>`_)
+* correction of geometric errors (using `AROSICS <https://git.gfz-potsdam.de/danschef/arosics>`_)
 
 Level-2 processing:
 -------------------
 
 * spatial homogenization
-* spectral homogenization (using `SpecHomo <https://gitext.gfz-potsdam.de/geomultisens/spechomo>`_)
+* spectral homogenization (using `SpecHomo <https://git.gfz-potsdam.de/geomultisens/spechomo>`_)
 * estimation of accuracy layers
 
 => application oriented analysis dataset

docs/conf.py

@@ -136,7 +136,7 @@ def setup(app):
 
 # Add mappings for intersphinx extension (allows to link to the API reference of other sphinx documentations)
 intersphinx_mapping = {
-    'geoarray': ('https://danschef.gitext-pages.gfz-potsdam.de/geoarray/doc/', None),
+    'geoarray': ('https://danschef.git-pages.gfz-potsdam.de/geoarray/doc/', None),
     'python': ('https://docs.python.org/3', None),
 }
 

docs/history.rst

@@ -2,4 +2,4 @@ History / Changelog
 *******************
 
 You can find the protocol of recent changes in the gms_preprocessing package
-`here <https://gitext.gfz-potsdam.de/geomultisens/gms_preprocessing/-/blob/master/HISTORY.rst>`__.
+`here <https://git.gfz-potsdam.de/geomultisens/gms_preprocessing/-/blob/master/HISTORY.rst>`__.

docs/index.rst

@@ -13,7 +13,7 @@ Documentation of the gms_preprocessing package
    :caption: Contents:
 
    about
-   Source code repository <https://gitext.gfz-potsdam.de/geomultisens/gms_preprocessing>
+   Source code repository <https://git.gfz-potsdam.de/geomultisens/gms_preprocessing>
    installation
    infrastructure
    algorithm_descriptions

docs/infrastructure/ecmwf_db.rst

 ECMWF database
 ==============
 
-The atmospheric correction implemented in gms_preprocessing (`SICOR <https://gitext.gfz-potsdam.de/EnMAP/sicor>`_)
+The atmospheric correction implemented in gms_preprocessing (`SICOR <https://git.gfz-potsdam.de/EnMAP/sicor>`_)
 uses `ECMWF  <https://www.ecmwf.int/>`_ data (European Centre for Medium-Range Weather Forecasts) to model the
 atmospheric state for each scene processed.
 

docs/usage/execute_jobs.rst

@@ -19,4 +19,4 @@ This runs the job with the ID 123456 with the configuration parameters as given
 There is a default configuration file, called `options_default.json`_. options_default.json where all the available
 configuration parameters are documented.
 
-.. _`options_default.json`: https://gitext.gfz-potsdam.de/geomultisens/gms_preprocessing/blob/master/gms_preprocessing/options/options_default.json
+.. _`options_default.json`: https://git.gfz-potsdam.de/geomultisens/gms_preprocessing/blob/master/gms_preprocessing/options/options_default.json

gms_preprocessing/misc/environment.py

@@ -101,13 +101,13 @@ class GMSEnvironment(object):
                       "be processed! For Anaconda, run 'conda install --yes -c conda-forge pyhdf' to fix that!"
                 self.logger.warning(MissingNonPipLibraryWarning(msg))
 
-        # # 'sicor', # pip install git+https://gitext.gfz-potsdam.de/hollstei/sicor.git
+        # # 'sicor', # pip install git+https://git.gfz-potsdam.de/hollstei/sicor.git
         # try:
         #     # noinspection PyUnresolvedReferences
         #     import sicor  # noqa F401 unused
         # except ImportError:
         #     msg = "The library 'sicor' has not been installed automatically because installation requires login " \
-        #           "credentials. See installation instrucions here: https://gitext.gfz-potsdam.de/EnMAP/sicor"
+        #           "credentials. See installation instrucions here: https://git.gfz-potsdam.de/EnMAP/sicor"
         #     self.logger.warning(MissingNonPipLibraryWarning(msg))
 
     def check_dependencies(self):

setup.py

@@ -124,7 +124,7 @@ setup(
     scripts=["bin/run_gms.py", "bin/run_gms.sh"],
     test_suite='tests',
     tests_require=req_test,
-    url='https://gitext.gfz-potsdam.de/geomultisens/gms_preprocessing',
+    url='https://git.gfz-potsdam.de/geomultisens/gms_preprocessing',
     version=version['__version__'],
     zip_safe=False
 )

tests/CI_docker/build_testsuite_image.sh

@@ -33,7 +33,7 @@ docker run \
     gitlab/gitlab-runner:latest
 
 # register the runner at the corresponding GitLab repository via a registration-token
-echo "#### Register container at gitlab, get token here https://gitext.gfz-potsdam.de/geomultisens/gms_preprocessing/settings/ci_cd"
+echo "#### Register container at gitlab, get token here https://git.gfz-potsdam.de/geomultisens/gms_preprocessing/settings/ci_cd"
 read -p "Please enter gitlab token: " token
 echo ""
 read -p "Please enter gitlab runner name: " runner_name
@@ -46,7 +46,7 @@ gitlab-ci-multi-runner register \
   --non-interactive \
   --executor 'docker' \
   --docker-image '${tag}' \
-  --url 'https://gitext.gfz-potsdam.de/ci' \
+  --url 'https://git.gfz-potsdam.de/ci' \
   --registration-token '${token}' \
   --description '${runner_name}' \
   --tag-list gms_preprocessing_ci_client \

tests/CI_docker/context/environment_gms_preprocessing.yml

@@ -22,7 +22,7 @@ dependencies:
   - scikit-image
   - scikit-learn=0.23.2  # pinned due to spechomo classifiers created with this version
   - shapely
-  - scipy<=1.1.0  # pinned due to https://gitext.gfz-potsdam.de/EnMAP/sicor/-/issues/63
+  - scipy<=1.1.0  # pinned due to https://git.gfz-potsdam.de/EnMAP/sicor/-/issues/63
   - sicor>=0.15.2
   - spechomo