From 1039619f184b8f3e20b3ecab367e3fc19ac435a0 Mon Sep 17 00:00:00 2001
From: lb584 <lb584@cam.ac.uk>
Date: Thu, 25 Jan 2024 16:28:14 +0000
Subject: [PATCH] updating the pipenv
---
configs/docker/build/requirements.txt | 2 +-
docs/_source/installation.rst | 7 +++++++
tests/integration/full/convertDos2unix.sh | 2 ++
tests/integration/partial/convertDos2unix.sh | 2 ++
tests/integration/test_suites/depo_test_suite.py | 4 ++--
5 files changed, 14 insertions(+), 3 deletions(-)
create mode 100644 tests/integration/full/convertDos2unix.sh
create mode 100644 tests/integration/partial/convertDos2unix.sh
diff --git a/configs/docker/build/requirements.txt b/configs/docker/build/requirements.txt
index 9b989be..23caa52 100644
--- a/configs/docker/build/requirements.txt
+++ b/configs/docker/build/requirements.txt
@@ -1,8 +1,8 @@
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
diff --git a/docs/_source/installation.rst b/docs/_source/installation.rst
index d32481f..528689e 100644
--- a/docs/_source/installation.rst
+++ b/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.
diff --git a/tests/integration/full/convertDos2unix.sh b/tests/integration/full/convertDos2unix.sh
new file mode 100644
index 0000000..9080214
--- /dev/null
+++ b/tests/integration/full/convertDos2unix.sh
@@ -0,0 +1,2 @@
+# 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
diff --git a/tests/integration/partial/convertDos2unix.sh b/tests/integration/partial/convertDos2unix.sh
new file mode 100644
index 0000000..9080214
--- /dev/null
+++ b/tests/integration/partial/convertDos2unix.sh
@@ -0,0 +1,2 @@
+# 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
diff --git a/tests/integration/test_suites/depo_test_suite.py b/tests/integration/test_suites/depo_test_suite.py
index 897462b..6065f7d 100644
--- a/tests/integration/test_suites/depo_test_suite.py
+++ b/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)
--
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