updating the pipenv

configs/docker/build/requirements.txt

 contextily==1.5.0
 geopandas==0.14.2
+HTMLTestRunner-rv==1.1.2
 python-docx==1.1.0
 rioxarray==0.15.0
 Rtree==1.1.0
 scitools-iris==3.7.0
-HTMLTestRunner-rv==1.1.2
 coverage==7.4.0
\ No newline at end of file

docs/_source/installation.rst

@@ -49,6 +49,7 @@ In this example, we are using the Linux user “ewsmanager” and group “ews
 
         mkdir -p .\code regions\EastAfrica\workspace regions\SouthAsia\workspace regions\EastAfrica\resources regions\SouthAsia\resources met_inputs\metofficeupload\upload\Ethiopia\toMO\  met_inputs\metofficeupload\upload\Ethiopia\fromMO\daily_name\ web_data\Ethiopia met_inputs\metofficeupload\upload\SouthAsia\toMO\ met_inputs\metofficeupload\upload\SouthAsia\fromMO\daily_name\ web_data\SouthAsia .\logs .\envs\credentials
 
+shell scripts to perform the above operations:
 :download:`Download .cmd file <../_static/assets/windows_create_dirs.cmd>`
 :download:`Download .sh file <../_static/assets/linux_create_dirs.sh>`
 
@@ -85,6 +86,7 @@ or generate this string in bash:
      printf "%s" "git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/${repo}.git ${folder};"
    done
 
+shell scripts to perform the above operations:
 :download:`Download .cmd file <../_static/assets/windows_clone_git.cmd>`
 :download:`Download .sh file <../_static/assets/linux_clone_git.sh>`
 
@@ -107,7 +109,9 @@ into ``<install_location>/regions/<EastAfrica/SouthAsia>/resources``. This will
 configuration and other assets required for the pipeline to run.
 
 e.g.:
+
 .. code-block:: bash
+
     cd <install_location>/regions/EastAfrica/resources
     tar -zxvf eastafrica_resources_<latest_date>.tar.gz
 
@@ -156,6 +160,9 @@ following credentials**:
 
 Where the various variables are all LINUX user credentials (type the ‘id’ command to see all these values)
 
+**if you are running the ews for use on your personal computer, you can exclude the --build-arg arguments from the build
+step, note that all files written by the pipeline will be owned by the root user, rather than your user account.**
+
 Once you have edited the build.sh script, run it (or run the commands within it manually). **if you are running on
 Windows and run these commands manually, make sure you run the "cp ../../conda/conda-env-py3EWS-withbuilds.yml ."
 equivalent to place the conda dependencies in the same dir before running docker build.

tests/integration/full/convertDos2unix.sh

+# run this script within the ews docker image if you have checked out the code on a windows machine, then run the new .sh script to launch the tests
+dos2unix run_tests.sh > windows_run_tests.sh
\ No newline at end of file

tests/integration/partial/convertDos2unix.sh

+# run this script within the ews docker image if you have checked out the code on a windows machine, then run the new .sh script to launch the tests
+dos2unix run_tests.sh > windows_run_tests.sh
\ No newline at end of file

tests/integration/test_suites/depo_test_suite.py

@@ -61,10 +61,10 @@ class BaseDepoTestSuite:
         def test_standard_run_all_input_csvs_produced(self):
             east_africa_csv_path = os.path.join(IntegrationTestUtils.TEST_OUT_PATH,
                                                 IntegrationTestUtils.TEST_JOB_DIR,
-                                                "plotting", "eastafrica", "input_csvs", "*.nc")
+                                                "plotting", "eastafrica", "input_nc", "*.nc")
             ethiopia_csv_path = os.path.join(IntegrationTestUtils.TEST_OUT_PATH,
                                              IntegrationTestUtils.TEST_JOB_DIR,
-                                             "plotting", "ethiopia", "input_csvs", "*.nc")
+                                             "plotting", "ethiopia", "input_nc", "*.nc")
 
             ea_csv_count: int = IntegrationTestUtils.count_files_in_wildcard(east_africa_csv_path)
             eth_csv_count: int = IntegrationTestUtils.count_files_in_wildcard(ethiopia_csv_path)