From 2130d5935c32a868fa421c818bb3b1a82b0fedea Mon Sep 17 00:00:00 2001
From: Bojun <30320251+BerginJay@users.noreply.github.com>
Date: Thu, 23 Mar 2023 05:56:07 +0800
Subject: [PATCH] Update instructions on downloadIsisData and conda install in
 README (#5159)

* Update downloadIsisData in README

The ISIS SPICE Web Service section still uses rsync, updated to downloadIsisData, and added some instructions for using downloadIsisData

* Add channel_priority setting to README

channel_priority=strict would cause package conflicts

* Update .zenodo.json

* Update CHANGELOG.md

* Update CHANGELOG.md

* Update Jenkinsfile setting channel_priority
---
 .zenodo.json |  6 +++++-
 CHANGELOG.md |  2 ++
 Jenkinsfile  |  1 +
 README.md    | 19 +++++++++++++------
 4 files changed, 21 insertions(+), 7 deletions(-)

diff --git a/.zenodo.json b/.zenodo.json
index 159a9764b8..850e38994b 100644
--- a/.zenodo.json
+++ b/.zenodo.json
@@ -465,7 +465,11 @@
     },
     {
       "name": "Young, Aaron"
-    }
+    },
+    {
+      "name": "Jia, Bojun",
+      "orcid": "0000-0001-7218-6746"
+    },
   ],
   "title": "Integrated Software for Imagers and Spectrometers",
   "description": "A software library and set of tools to support ingestion, processing, and analysis of planetary science data.",
diff --git a/CHANGELOG.md b/CHANGELOG.md
index b50be7b5dc..da4f2a30a3 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -38,8 +38,10 @@ release.
 ### Changed
 - Updated download location for Dawn source files to include updated pck from HAMO Dawn mosaic [#4001](https://github.com/USGS-Astrogeology/ISIS3/issues/4001)
 - Pinned cspice version to 67 [#5083](https://github.com/USGS-Astrogeology/ISIS3/issues/5083) 
+- Changed the `rsync` related commands in the ISIS SPICE Web Service document to `downloadIsisData` command
 
 ### Added
+- Instructions on setting `channel_priority=flexible` for isis environment manually during installation [#5158](https://github.com/DOI-USGS/ISIS3/issues/5158)
 
 ### Deprecated
 
diff --git a/Jenkinsfile b/Jenkinsfile
index 85822352b2..a467b5272c 100644
--- a/Jenkinsfile
+++ b/Jenkinsfile
@@ -29,6 +29,7 @@ pipeline {
                 
                 conda create -y -n isis
                 conda activate isis > /dev/null
+                conda config --env --set channel_priority flexible
                 conda install -c conda-forge python=3 findutils
                 mamba env update -f environment.yml --prune
                 conda activate isis
diff --git a/README.md b/README.md
index d438e5d3a4..2fb13c26c7 100644
--- a/README.md
+++ b/README.md
@@ -77,6 +77,9 @@ This installation guide is for ISIS users interested in installing ISIS (3.6.0)+
     #The order is important.  If conda-forge is before usgs-astrogeology, you will need to run:
 
     conda config --env --add channels usgs-astrogeology
+    
+    #Then set channel_priority to flexible in case there is a global channel_priority=strict setting
+    conda config --env --set channel_priority flexible
     ```
 
 1. The environment is now ready to download ISIS and its dependencies:
@@ -393,9 +396,10 @@ The ISIS Data Area is hosted on a combination of AWS S3 buckets and public http
 
 To download all ISIS data, use the following command:
 
-    downloadIsisData  all $ISISDATA
+    downloadIsisData all $ISISDATA
 
-> Note: this applicaion takes in 3 parameters in the following order \<rclone command> \<mission> \<download destination>
+> Note: this applicaion takes in 3 parameters in the following order \<mission> \<download destination> \<rclone command>  
+> For more usage, run `downloadIsisData --help` or `downloadIsisData -h`.
 
 > Note: The above command downloads all ISIS data including the required base data area and all of the optional mission data areas.
 
@@ -414,17 +418,20 @@ There are many missions supported by ISIS. If you are only working with a few mi
 
 ### ISIS SPICE Web Service
 
-ISIS can now use a service to retrieve the SPICE data for all instruments ISIS supports via the internet. To use this service instead of your local SPICE data, click the WEB check box in the spiceinit program GUI or type spiceinit web=yes at the command line. Using the ISIS SPICE Web Service will significantly reduce the size of the downloads from our data area. If you want to use this new service, without having to download all the SPICE data, add the following argument to the mission-specific rsync command:
+ISIS can now use a service to retrieve the SPICE data for all instruments ISIS supports via the internet. To use this service instead of your local SPICE data, click the WEB check box in the spiceinit program GUI or type spiceinit web=yes at the command line. Using the ISIS SPICE Web Service will significantly reduce the size of the downloads from our data area. If you want to use this new service, without having to download all the SPICE data, add the following argument to the mission-specific downloadIsisData command:
 
-    --exclude='kernels'
+    --exclude="kernels/**"
 
 For example:
 
 <pre>
-cd $ISISDATA
-rsync -azv <b>--exclude='kernels'</b> --delete --partial isisdist.astrogeology.usgs.gov::isisdata/data/cassini .
+downloadIsisData cassini $ISISDATA --exclude="kernels/**"
 </pre>
 
+You can also use `include` argument to partially download specific kernels. For example, download only cks and fks of LRO mission:
+
+    downloadIsisData lro $ISISDATA --include="{ck/**,fk/**}"
+
 **WARNING:** Some instruments require mission data to be present for radiometric calibration, which is not supported by the SPICE Web Server, and some programs that are designed to run an image from ingestion through the mapping phase do not have an option to use the SPICE Web Service. For information specific to an instrument, see the documentation for radiometric calibration programs.
 
 ### Mission Specific Data Downloads
-- 
GitLab