From bfbbe478cb8d856ca5f3de097a03fd43425d50bf Mon Sep 17 00:00:00 2001
From: lb584 <lb584@cam.ac.uk>
Date: Tue, 16 Jan 2024 16:52:37 +0000
Subject: [PATCH] doc work, adding new tppls to docker image
---
configs/docker/build/Dockerfile | 2 +-
docs/_source/installation.rst | 17 ++++++++++++-----
docs/_static/assets/linux_clone_git.sh | 1 -
..._clone_git.batch => windows_clone_git.cmd} | 19 +++++++++----------
4 files changed, 22 insertions(+), 17 deletions(-)
rename docs/_static/assets/{windows_clone_git.batch => windows_clone_git.cmd} (54%)
diff --git a/configs/docker/build/Dockerfile b/configs/docker/build/Dockerfile
index 26242dd..bd81492 100644
--- a/configs/docker/build/Dockerfile
+++ b/configs/docker/build/Dockerfile
@@ -4,7 +4,7 @@ FROM ubuntu:24.04 as base_image
SHELL ["/bin/bash", "-c"]
#install system packages
-RUN apt-get update;apt-get install --assume-yes python-dev-is-python3 python3-dev python3.11-venv wget unzip emacs gdal-bin libgdal-dev build-essential gfortran zlib1g zlib1g-dev libbz2-dev apt-utils liblzma-dev libcurl4-openssl-dev default-jre openssh-server libfribidi-dev libfontconfig1-dev libspatialindex-dev git;
+RUN apt-get update;apt-get install --assume-yes python-dev-is-python3 python3-dev python3.11-venv wget unzip emacs gdal-bin libgdal-dev build-essential gfortran zlib1g zlib1g-dev libbz2-dev apt-utils liblzma-dev libcurl4-openssl-dev default-jre openssh-server libfribidi-dev libfontconfig1-dev libspatialindex-dev git dos2unix nano;
#sets the timezone to London
RUN DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt-get -y install tzdata
diff --git a/docs/_source/installation.rst b/docs/_source/installation.rst
index 2295c76..d32481f 100644
--- a/docs/_source/installation.rst
+++ b/docs/_source/installation.rst
@@ -64,7 +64,7 @@ cd into <install_location>/code
.. code-block:: bash
- git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-coordinator.git coordinator;git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-environmental-suitability.git environmental_suitability;git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-advisory-builder.git advisory_builder;git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-plotting.git plotting;git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-epidemiology.git epimodel;git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-source-calculation.git source_gen;git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-coordinator.git coordinator;git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-job-flagging.git flagdir;git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-met-processing.git met_extractor_v2;git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-postprocessing.git post_processing;
+ git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-coordinator.git coordinator;git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-environmental-suitability.git environmental_suitability;git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-advisory-builder.git advisory_builder;git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-plotting.git plotting;git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-epidemiology.git epimodel;git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-source-calculation.git source_gen;git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-job-flagging.git flagdir;git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-met-processing.git met_extractor_v2;git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-postprocessing.git post_processing;
or generate this string in bash:
@@ -76,7 +76,6 @@ or generate this string in bash:
ews-plotting,plotting \
ews-epidemiology,epimodel \
ews-source-calculation,source_gen \
- ews-coordinator,coordinator \
ews-job-flagging,flagdir \
ews-met-processing,met_extractor_v2 \
ews-postprocessing,post_processing;
@@ -86,7 +85,7 @@ or generate this string in bash:
printf "%s" "git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/${repo}.git ${folder};"
done
-:download:`Download .cmd file <../_static/assets/windows_clone_git.batch>`
+:download:`Download .cmd file <../_static/assets/windows_clone_git.cmd>`
:download:`Download .sh file <../_static/assets/linux_clone_git.sh>`
@@ -97,13 +96,20 @@ or generate this string in bash:
Due to the size, project resources are not included in the git repository. You will need to ask the Cambridge team
for the latest version of the resources archive.
+.. admonition:: Add resources for one region at a time
+
+ There is a seperate resources archive for each geographic region. Currently there are two regions, EastAfrica and
+ SouthAsia. The instructions below denote the different regions with <EastAfrica/SouthAsia>. We suggest you start
+ with EastAfrica and get that working before setting up other regions.
+
Once you have received an archive of ``<EastAfrica/SouthAsia>_resources_<latest_date>.tar.gz`` from Cambridge, unpack
into ``<install_location>/regions/<EastAfrica/SouthAsia>/resources``. This will place all the necessary JSON
configuration and other assets required for the pipeline to run.
+e.g.:
.. code-block:: bash
-
- tar -zxvf resources_<latest_date>.tar.gz
+ cd <install_location>/regions/EastAfrica/resources
+ tar -zxvf eastafrica_resources_<latest_date>.tar.gz
Edit the coordinator run script to fix the root paths **(not necessary if running in our docker image)**:
@@ -158,6 +164,7 @@ equivalent to place the conda dependencies in the same dir before running docker
bash build.sh
+**building docker can take a while, typically 5-10 mins**
Make a copy of the docker launch template file and edit the source dir to match that of your installation.
diff --git a/docs/_static/assets/linux_clone_git.sh b/docs/_static/assets/linux_clone_git.sh
index e97d50d..1a6c4d2 100644
--- a/docs/_static/assets/linux_clone_git.sh
+++ b/docs/_static/assets/linux_clone_git.sh
@@ -5,7 +5,6 @@ git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-advisory
git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-plotting.git plotting;
git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-epidemiology.git epimodel;
git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-source-calculation.git source_gen;
-git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-coordinator.git coordinator;
git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-job-flagging.git flagdir;
git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-met-processing.git met_extractor_v2;
git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-postprocessing.git post_processing;
\ No newline at end of file
diff --git a/docs/_static/assets/windows_clone_git.batch b/docs/_static/assets/windows_clone_git.cmd
similarity index 54%
rename from docs/_static/assets/windows_clone_git.batch
rename to docs/_static/assets/windows_clone_git.cmd
index ccb6c49..e1dbd4f 100644
--- a/docs/_static/assets/windows_clone_git.batch
+++ b/docs/_static/assets/windows_clone_git.cmd
@@ -1,11 +1,10 @@
@ECHO OFF
-git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-coordinator.git coordinator;
-git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-environmental-suitability.git environmental_suitability;
-git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-advisory-builder.git advisory_builder;
-git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-plotting.git plotting;
-git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-epidemiology.git epimodel;
-git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-source-calculation.git source_gen;
-git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-coordinator.git coordinator;
-git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-job-flagging.git flagdir;
-git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-met-processing.git met_extractor_v2;
-git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-postprocessing.git post_processing;
\ No newline at end of file
+git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-coordinator.git coordinator
+git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-environmental-suitability.git environmental_suitability
+git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-advisory-builder.git advisory_builder
+git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-plotting.git plotting
+git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-epidemiology.git epimodel
+git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-source-calculation.git source_gen
+git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-job-flagging.git flagdir
+git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-met-processing.git met_extractor_v2
+git clone git@gitlab.developers.cam.ac.uk:gilligan-epid/wheat-rusts/ews-postprocessing.git post_processing
\ No newline at end of file
--
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