From 5471d49d2c779043de24d021902b7f194b24f955 Mon Sep 17 00:00:00 2001
From: Austin Sanders <arsanders@usgs.gov>
Date: Fri, 22 Sep 2023 13:51:29 -0600
Subject: [PATCH 01/52] Added initial CI workflow

---
 .github/workflows/ci.yml | 55 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 55 insertions(+)
 create mode 100644 .github/workflows/ci.yml

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
new file mode 100644
index 0000000000..1c65d11f16
--- /dev/null
+++ b/.github/workflows/ci.yml
@@ -0,0 +1,55 @@
+name: CI
+
+on:
+  pull_request:
+    branches:
+      - dev
+  push:
+    branches:
+      - dev
+
+jobs:
+  Build-and-Test-LinuxOsx:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+       os: [ubuntu-latest, macos-latest]
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
+        with:
+          submodules: true
+      - uses: conda-incubator/setup-miniconda@3b0f2504dd76ef23b6d31f291f4913fb60ab5ff3
+        with:
+          miniconda-version: "latest"
+          activate-environment: isis
+          environment-file: environment.yml
+          auto-activate-base: false
+          auto-update-conda: true
+      - name: Check build environment
+        run: |
+          conda list
+      - name: Download ISIS data
+        run: |
+          mkdir isis_data
+          mkdir isis_testData
+          rclone sync asc_s3://asc-isisdata/usgs_data isis_data --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf --transfers=20 --dry-run
+          rclone sync asc_s3://asc-isisdata/isis_testData isis_testData --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf --transfers=20 --dry-run
+      - name: Build ISIS
+        run: |
+          mkdir -p build
+          cd build
+          cmake -DisisData=${GITHUB_WORKSPACE}/isis_data -DisisTestData=${GITHUB_WORKSPACE}/isis_testData -DJP2KFLAG=OFF -DCMAKE_BUILD_TYPE=RELEASE -Wdeprecated -GNinja ../isis
+          ninja
+      - name: Run ISIS tests
+        run: |
+          export ISISDATA=${GITHUB_WORKSPACE}/isis_data
+          export ISISTESTDATA=${GITHUB_WORKSPACE}/isis_testData
+          export ISISROOT=${GITHUB_WORKSPACE}/build/
+          export PATH=$PATH:${GITHUB_WORKSPACE}/build/bin/
+          cd build
+          ctest -VV
+

From f72b6d6cac1f955957967ae6ef94bb6a289752c4 Mon Sep 17 00:00:00 2001
From: Austin Sanders <arsanders@usgs.gov>
Date: Mon, 25 Sep 2023 16:28:41 -0600
Subject: [PATCH 02/52] Copy preferences to ISISROOT

---
 .github/workflows/ci.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 1c65d11f16..20da81c0bb 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -41,6 +41,7 @@ jobs:
       - name: Build ISIS
         run: |
           mkdir -p build
+          cp ${GITHUB_WORKSPACE}/isis/IsisPreferences ${GITHUB_WORKSPACES}/build/
           cd build
           cmake -DisisData=${GITHUB_WORKSPACE}/isis_data -DisisTestData=${GITHUB_WORKSPACE}/isis_testData -DJP2KFLAG=OFF -DCMAKE_BUILD_TYPE=RELEASE -Wdeprecated -GNinja ../isis
           ninja

From 832ad83a8e2f88fb26d3f58fa1a4892de25b8887 Mon Sep 17 00:00:00 2001
From: Austin Sanders <arsanders@usgs.gov>
Date: Mon, 25 Sep 2023 17:50:43 -0600
Subject: [PATCH 03/52] Fixed typo in workspace

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 20da81c0bb..a3e43df75a 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -41,7 +41,7 @@ jobs:
       - name: Build ISIS
         run: |
           mkdir -p build
-          cp ${GITHUB_WORKSPACE}/isis/IsisPreferences ${GITHUB_WORKSPACES}/build/
+          cp ${GITHUB_WORKSPACE}/isis/IsisPreferences ${GITHUB_WORKSPACE}/build/
           cd build
           cmake -DisisData=${GITHUB_WORKSPACE}/isis_data -DisisTestData=${GITHUB_WORKSPACE}/isis_testData -DJP2KFLAG=OFF -DCMAKE_BUILD_TYPE=RELEASE -Wdeprecated -GNinja ../isis
           ninja

From 457cdc02cd5ba177b6504c74e8751f905389cc5f Mon Sep 17 00:00:00 2001
From: Austin Sanders <arsanders@usgs.gov>
Date: Mon, 25 Sep 2023 18:29:13 -0600
Subject: [PATCH 04/52] Moved exports

---
 .github/workflows/ci.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index a3e43df75a..2209bd0ede 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -42,15 +42,15 @@ jobs:
         run: |
           mkdir -p build
           cp ${GITHUB_WORKSPACE}/isis/IsisPreferences ${GITHUB_WORKSPACE}/build/
+          export ISISDATA=${GITHUB_WORKSPACE}/isis_data
+          export ISISTESTDATA=${GITHUB_WORKSPACE}/isis_testData
+          export ISISROOT=${GITHUB_WORKSPACE}/build/
+          export PATH=$PATH:${GITHUB_WORKSPACE}/build/bin/
           cd build
           cmake -DisisData=${GITHUB_WORKSPACE}/isis_data -DisisTestData=${GITHUB_WORKSPACE}/isis_testData -DJP2KFLAG=OFF -DCMAKE_BUILD_TYPE=RELEASE -Wdeprecated -GNinja ../isis
           ninja
       - name: Run ISIS tests
         run: |
-          export ISISDATA=${GITHUB_WORKSPACE}/isis_data
-          export ISISTESTDATA=${GITHUB_WORKSPACE}/isis_testData
-          export ISISROOT=${GITHUB_WORKSPACE}/build/
-          export PATH=$PATH:${GITHUB_WORKSPACE}/build/bin/
           cd build
           ctest -VV
 

From bcdf2145421b30f3535e0288d1e19ce871335809 Mon Sep 17 00:00:00 2001
From: Austin Sanders <arsanders@usgs.gov>
Date: Tue, 26 Sep 2023 12:48:35 -0600
Subject: [PATCH 05/52] Added swig path to cmake call

---
 .github/workflows/ci.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 2209bd0ede..cafb83d6b5 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -22,6 +22,7 @@ jobs:
       - uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
         with:
           submodules: true
+          ref: dev
       - uses: conda-incubator/setup-miniconda@3b0f2504dd76ef23b6d31f291f4913fb60ab5ff3
         with:
           miniconda-version: "latest"
@@ -47,7 +48,7 @@ jobs:
           export ISISROOT=${GITHUB_WORKSPACE}/build/
           export PATH=$PATH:${GITHUB_WORKSPACE}/build/bin/
           cd build
-          cmake -DisisData=${GITHUB_WORKSPACE}/isis_data -DisisTestData=${GITHUB_WORKSPACE}/isis_testData -DJP2KFLAG=OFF -DCMAKE_BUILD_TYPE=RELEASE -Wdeprecated -GNinja ../isis
+          cmake -DisisData=${GITHUB_WORKSPACE}/isis_data -DisisTestData=${GITHUB_WORKSPACE}/isis_testData -DSWIG_DIR=$CONDA_PREFIX/bin/swig -DJP2KFLAG=OFF -DCMAKE_BUILD_TYPE=RELEASE -Wdeprecated -GNinja ../isis
           ninja
       - name: Run ISIS tests
         run: |

From b8ca65478b758688b9ca3b475095e42884c5d15a Mon Sep 17 00:00:00 2001
From: Austin Sanders <arsanders@usgs.gov>
Date: Tue, 26 Sep 2023 14:40:16 -0600
Subject: [PATCH 06/52] Copied env variables to test step

---
 .github/workflows/ci.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index cafb83d6b5..99b64ec8f6 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -53,5 +53,9 @@ jobs:
       - name: Run ISIS tests
         run: |
           cd build
+          export ISISDATA=${GITHUB_WORKSPACE}/isis_data
+          export ISISTESTDATA=${GITHUB_WORKSPACE}/isis_testData
+          export ISISROOT=${GITHUB_WORKSPACE}/build/
+          export PATH=$PATH:${GITHUB_WORKSPACE}/build/bin/
           ctest -VV
 

From 1fdaff26082638aecc7bb06e8d434c8de82fa74d Mon Sep 17 00:00:00 2001
From: Austin Sanders <arsanders@usgs.gov>
Date: Wed, 27 Sep 2023 11:13:30 -0600
Subject: [PATCH 07/52] Switched from rclone sync to mount

---
 .github/workflows/ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 99b64ec8f6..1c738146d7 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -37,8 +37,8 @@ jobs:
         run: |
           mkdir isis_data
           mkdir isis_testData
-          rclone sync asc_s3://asc-isisdata/usgs_data isis_data --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf --transfers=20 --dry-run
-          rclone sync asc_s3://asc-isisdata/isis_testData isis_testData --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf --transfers=20 --dry-run
+          rclone mount asc_s3://asc-isisdata/usgs_data isis_data --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf 
+          rclone mount asc_s3://asc-isisdata/isis_testData isis_testData --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf
       - name: Build ISIS
         run: |
           mkdir -p build

From acd1b9d77d0fd9df4160727dafc4fdbfbb5fdf6f Mon Sep 17 00:00:00 2001
From: Austin Sanders <arsanders@usgs.gov>
Date: Wed, 27 Sep 2023 12:23:33 -0600
Subject: [PATCH 08/52] Update rclone version to include mount command on osx

---
 .github/workflows/ci.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 1c738146d7..cc39908d65 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -37,6 +37,7 @@ jobs:
         run: |
           mkdir isis_data
           mkdir isis_testData
+          rclone selfupdate
           rclone mount asc_s3://asc-isisdata/usgs_data isis_data --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf 
           rclone mount asc_s3://asc-isisdata/isis_testData isis_testData --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf
       - name: Build ISIS

From f48fecc5a74e1ad1d6ea87f122f715797cd74b2d Mon Sep 17 00:00:00 2001
From: Austin Sanders <arsanders@usgs.gov>
Date: Wed, 27 Sep 2023 13:01:51 -0600
Subject: [PATCH 09/52] Enable verbose output for debugging

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index cc39908d65..74c6b30d37 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -37,7 +37,7 @@ jobs:
         run: |
           mkdir isis_data
           mkdir isis_testData
-          rclone selfupdate
+          rclone -VV selfupdate
           rclone mount asc_s3://asc-isisdata/usgs_data isis_data --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf 
           rclone mount asc_s3://asc-isisdata/isis_testData isis_testData --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf
       - name: Build ISIS

From 8dd8146288909ed7ec8e0f029dbac3c7633f6be6 Mon Sep 17 00:00:00 2001
From: Austin Sanders <arsanders@usgs.gov>
Date: Wed, 27 Sep 2023 13:28:51 -0600
Subject: [PATCH 10/52] More debug attempts

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 74c6b30d37..503ee07091 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -37,7 +37,7 @@ jobs:
         run: |
           mkdir isis_data
           mkdir isis_testData
-          rclone -VV selfupdate
+          which rclone
           rclone mount asc_s3://asc-isisdata/usgs_data isis_data --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf 
           rclone mount asc_s3://asc-isisdata/isis_testData isis_testData --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf
       - name: Build ISIS

From e915065d9663ad5a83002c3f1e668461448d7a72 Mon Sep 17 00:00:00 2001
From: Austin Sanders <arsanders@usgs.gov>
Date: Wed, 27 Sep 2023 17:10:38 -0600
Subject: [PATCH 11/52] Verbose mount command

---
 .github/workflows/ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 503ee07091..1792c1eca5 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -38,8 +38,8 @@ jobs:
           mkdir isis_data
           mkdir isis_testData
           which rclone
-          rclone mount asc_s3://asc-isisdata/usgs_data isis_data --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf 
-          rclone mount asc_s3://asc-isisdata/isis_testData isis_testData --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf
+          rclone mount -vv asc_s3://asc-isisdata/usgs_data isis_data --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf 
+          rclone mount -vv asc_s3://asc-isisdata/isis_testData isis_testData --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf
       - name: Build ISIS
         run: |
           mkdir -p build

From dda84f9b498f820bb967442556290ce23305602e Mon Sep 17 00:00:00 2001
From: Austin Sanders <arsanders@usgs.gov>
Date: Thu, 28 Sep 2023 09:05:02 -0600
Subject: [PATCH 12/52] Run mount in daemon mode

---
 .github/workflows/ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 1792c1eca5..aff4ad6120 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -38,8 +38,8 @@ jobs:
           mkdir isis_data
           mkdir isis_testData
           which rclone
-          rclone mount -vv asc_s3://asc-isisdata/usgs_data isis_data --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf 
-          rclone mount -vv asc_s3://asc-isisdata/isis_testData isis_testData --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf
+          rclone mount asc_s3://asc-isisdata/usgs_data isis_data --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf --daemon
+          rclone mount asc_s3://asc-isisdata/isis_testData isis_testData --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf --daemon
       - name: Build ISIS
         run: |
           mkdir -p build

From de8dfeb2ee220292dd02131b9b228e1dac614dae Mon Sep 17 00:00:00 2001
From: Austin Sanders <arsanders@usgs.gov>
Date: Thu, 28 Sep 2023 14:06:34 -0600
Subject: [PATCH 13/52] ls data area

---
 .github/workflows/ci.yml | 39 +++++++++++++++++++++------------------
 1 file changed, 21 insertions(+), 18 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index aff4ad6120..d7cb46abcb 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -40,23 +40,26 @@ jobs:
           which rclone
           rclone mount asc_s3://asc-isisdata/usgs_data isis_data --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf --daemon
           rclone mount asc_s3://asc-isisdata/isis_testData isis_testData --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf --daemon
-      - name: Build ISIS
+      - name: LS
         run: |
-          mkdir -p build
-          cp ${GITHUB_WORKSPACE}/isis/IsisPreferences ${GITHUB_WORKSPACE}/build/
-          export ISISDATA=${GITHUB_WORKSPACE}/isis_data
-          export ISISTESTDATA=${GITHUB_WORKSPACE}/isis_testData
-          export ISISROOT=${GITHUB_WORKSPACE}/build/
-          export PATH=$PATH:${GITHUB_WORKSPACE}/build/bin/
-          cd build
-          cmake -DisisData=${GITHUB_WORKSPACE}/isis_data -DisisTestData=${GITHUB_WORKSPACE}/isis_testData -DSWIG_DIR=$CONDA_PREFIX/bin/swig -DJP2KFLAG=OFF -DCMAKE_BUILD_TYPE=RELEASE -Wdeprecated -GNinja ../isis
-          ninja
-      - name: Run ISIS tests
-        run: |
-          cd build
-          export ISISDATA=${GITHUB_WORKSPACE}/isis_data
-          export ISISTESTDATA=${GITHUB_WORKSPACE}/isis_testData
-          export ISISROOT=${GITHUB_WORKSPACE}/build/
-          export PATH=$PATH:${GITHUB_WORKSPACE}/build/bin/
-          ctest -VV
+          ls ${GITHUB_WORKSPACE}/isis_data 
+#      - name: Build ISIS
+        #run: |
+          #mkdir -p build
+          #cp ${GITHUB_WORKSPACE}/isis/IsisPreferences ${GITHUB_WORKSPACE}/build/
+          #export ISISDATA=${GITHUB_WORKSPACE}/isis_data
+          #export ISISTESTDATA=${GITHUB_WORKSPACE}/isis_testData
+          #export ISISROOT=${GITHUB_WORKSPACE}/build/
+          #export PATH=$PATH:${GITHUB_WORKSPACE}/build/bin/
+          #cd build
+          #cmake -DisisData=${GITHUB_WORKSPACE}/isis_data -DisisTestData=${GITHUB_WORKSPACE}/isis_testData -DSWIG_DIR=$CONDA_PREFIX/bin/swig -DJP2KFLAG=OFF -DCMAKE_BUILD_TYPE=RELEASE -Wdeprecated -GNinja ../isis
+          #ninja
+      #- name: Run ISIS tests
+        #run: |
+          #cd build
+          #export ISISDATA=${GITHUB_WORKSPACE}/isis_data
+          #export ISISTESTDATA=${GITHUB_WORKSPACE}/isis_testData
+          #export ISISROOT=${GITHUB_WORKSPACE}/build/
+          #export PATH=$PATH:${GITHUB_WORKSPACE}/build/bin/
+          #ctest -VV
 

From 9c578d0905250e58766856528a6128f8f09f87bc Mon Sep 17 00:00:00 2001
From: Austin Sanders <arsanders@usgs.gov>
Date: Thu, 28 Sep 2023 14:07:05 -0600
Subject: [PATCH 14/52] Remove steps for debugging

---
 .github/workflows/ci.yml | 19 -------------------
 1 file changed, 19 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index d7cb46abcb..290394ba8d 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -43,23 +43,4 @@ jobs:
       - name: LS
         run: |
           ls ${GITHUB_WORKSPACE}/isis_data 
-#      - name: Build ISIS
-        #run: |
-          #mkdir -p build
-          #cp ${GITHUB_WORKSPACE}/isis/IsisPreferences ${GITHUB_WORKSPACE}/build/
-          #export ISISDATA=${GITHUB_WORKSPACE}/isis_data
-          #export ISISTESTDATA=${GITHUB_WORKSPACE}/isis_testData
-          #export ISISROOT=${GITHUB_WORKSPACE}/build/
-          #export PATH=$PATH:${GITHUB_WORKSPACE}/build/bin/
-          #cd build
-          #cmake -DisisData=${GITHUB_WORKSPACE}/isis_data -DisisTestData=${GITHUB_WORKSPACE}/isis_testData -DSWIG_DIR=$CONDA_PREFIX/bin/swig -DJP2KFLAG=OFF -DCMAKE_BUILD_TYPE=RELEASE -Wdeprecated -GNinja ../isis
-          #ninja
-      #- name: Run ISIS tests
-        #run: |
-          #cd build
-          #export ISISDATA=${GITHUB_WORKSPACE}/isis_data
-          #export ISISTESTDATA=${GITHUB_WORKSPACE}/isis_testData
-          #export ISISROOT=${GITHUB_WORKSPACE}/build/
-          #export PATH=$PATH:${GITHUB_WORKSPACE}/build/bin/
-          #ctest -VV
 

From fb662369488f0d918832cc2c722b0e0136c4d5fb Mon Sep 17 00:00:00 2001
From: Austin Sanders <arsanders@usgs.gov>
Date: Thu, 28 Sep 2023 14:53:36 -0600
Subject: [PATCH 15/52] undo previous commit

---
 .github/workflows/ci.yml | 20 ++++++++++++++++++--
 1 file changed, 18 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 290394ba8d..aff4ad6120 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -40,7 +40,23 @@ jobs:
           which rclone
           rclone mount asc_s3://asc-isisdata/usgs_data isis_data --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf --daemon
           rclone mount asc_s3://asc-isisdata/isis_testData isis_testData --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf --daemon
-      - name: LS
+      - name: Build ISIS
         run: |
-          ls ${GITHUB_WORKSPACE}/isis_data 
+          mkdir -p build
+          cp ${GITHUB_WORKSPACE}/isis/IsisPreferences ${GITHUB_WORKSPACE}/build/
+          export ISISDATA=${GITHUB_WORKSPACE}/isis_data
+          export ISISTESTDATA=${GITHUB_WORKSPACE}/isis_testData
+          export ISISROOT=${GITHUB_WORKSPACE}/build/
+          export PATH=$PATH:${GITHUB_WORKSPACE}/build/bin/
+          cd build
+          cmake -DisisData=${GITHUB_WORKSPACE}/isis_data -DisisTestData=${GITHUB_WORKSPACE}/isis_testData -DSWIG_DIR=$CONDA_PREFIX/bin/swig -DJP2KFLAG=OFF -DCMAKE_BUILD_TYPE=RELEASE -Wdeprecated -GNinja ../isis
+          ninja
+      - name: Run ISIS tests
+        run: |
+          cd build
+          export ISISDATA=${GITHUB_WORKSPACE}/isis_data
+          export ISISTESTDATA=${GITHUB_WORKSPACE}/isis_testData
+          export ISISROOT=${GITHUB_WORKSPACE}/build/
+          export PATH=$PATH:${GITHUB_WORKSPACE}/build/bin/
+          ctest -VV
 

From 8ed75d8639fc2885ed3e6dabdd9346a6f0359488 Mon Sep 17 00:00:00 2001
From: Austin Sanders <arsanders@usgs.gov>
Date: Fri, 29 Sep 2023 11:39:24 -0600
Subject: [PATCH 16/52] export conda env

---
 .github/workflows/ci.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index aff4ad6120..d140d72eaf 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -33,6 +33,7 @@ jobs:
       - name: Check build environment
         run: |
           conda list
+          conda env export
       - name: Download ISIS data
         run: |
           mkdir isis_data

From dba96f0034b7308edcca55462c218afd350a48cd Mon Sep 17 00:00:00 2001
From: Kelvin <krodriguez@usgs.gov>
Date: Wed, 4 Oct 2023 12:20:35 -0700
Subject: [PATCH 17/52] removed swig flag

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index d140d72eaf..bd89073165 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -50,7 +50,7 @@ jobs:
           export ISISROOT=${GITHUB_WORKSPACE}/build/
           export PATH=$PATH:${GITHUB_WORKSPACE}/build/bin/
           cd build
-          cmake -DisisData=${GITHUB_WORKSPACE}/isis_data -DisisTestData=${GITHUB_WORKSPACE}/isis_testData -DSWIG_DIR=$CONDA_PREFIX/bin/swig -DJP2KFLAG=OFF -DCMAKE_BUILD_TYPE=RELEASE -Wdeprecated -GNinja ../isis
+          cmake -DisisData=${GITHUB_WORKSPACE}/isis_data -DisisTestData=${GITHUB_WORKSPACE}/isis_testData -DJP2KFLAG=OFF -DCMAKE_BUILD_TYPE=RELEASE -Wdeprecated -GNinja ../isis
           ninja
       - name: Run ISIS tests
         run: |

From 6a6fcd546966fa6a724a72a297126e5e0a0afbb9 Mon Sep 17 00:00:00 2001
From: Kelvin <krodriguez@usgs.gov>
Date: Wed, 4 Oct 2023 14:27:49 -0700
Subject: [PATCH 18/52] tweaking cmake

---
 isis/python_bindings/CMakeLists.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/isis/python_bindings/CMakeLists.txt b/isis/python_bindings/CMakeLists.txt
index f07cb8c230..0348a43bdd 100644
--- a/isis/python_bindings/CMakeLists.txt
+++ b/isis/python_bindings/CMakeLists.txt
@@ -9,6 +9,7 @@ list(APPEND CMAKE_SWIG_FLAGS "-py3;-DPY3")
 message(STATUS "SWIG flags: " ${CMAKE_SWIG_FLAGS} )
 
 # Setup for Python linking
+list(APPEND CMAKE_PREFIX_PATH $ENV{CONDA_PREFIX})
 find_package(Python3 REQUIRED COMPONENTS Interpreter Development)
 
 # Setup for wrapper library

From 00ec1fdbec6a7ce4ca753958aa97dac6beb3f028 Mon Sep 17 00:00:00 2001
From: Kelvin <krodriguez@usgs.gov>
Date: Wed, 4 Oct 2023 14:45:31 -0700
Subject: [PATCH 19/52] tweaking cmake w/ prepend

---
 isis/python_bindings/CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/isis/python_bindings/CMakeLists.txt b/isis/python_bindings/CMakeLists.txt
index 0348a43bdd..7a01e6690f 100644
--- a/isis/python_bindings/CMakeLists.txt
+++ b/isis/python_bindings/CMakeLists.txt
@@ -9,7 +9,7 @@ list(APPEND CMAKE_SWIG_FLAGS "-py3;-DPY3")
 message(STATUS "SWIG flags: " ${CMAKE_SWIG_FLAGS} )
 
 # Setup for Python linking
-list(APPEND CMAKE_PREFIX_PATH $ENV{CONDA_PREFIX})
+list(TRANSFORM CMAKE_PREFIX_PATH PREPEND $ENV{CONDA_PREFIX})
 find_package(Python3 REQUIRED COMPONENTS Interpreter Development)
 
 # Setup for wrapper library

From 60c73493a67519c864ff12abbe0e819c7b5ea255 Mon Sep 17 00:00:00 2001
From: Kelvin <krodriguez@usgs.gov>
Date: Wed, 4 Oct 2023 15:05:38 -0700
Subject: [PATCH 20/52] tweaking cmake w/ prepend

---
 isis/python_bindings/CMakeLists.txt | 1 -
 1 file changed, 1 deletion(-)

diff --git a/isis/python_bindings/CMakeLists.txt b/isis/python_bindings/CMakeLists.txt
index 7a01e6690f..f07cb8c230 100644
--- a/isis/python_bindings/CMakeLists.txt
+++ b/isis/python_bindings/CMakeLists.txt
@@ -9,7 +9,6 @@ list(APPEND CMAKE_SWIG_FLAGS "-py3;-DPY3")
 message(STATUS "SWIG flags: " ${CMAKE_SWIG_FLAGS} )
 
 # Setup for Python linking
-list(TRANSFORM CMAKE_PREFIX_PATH PREPEND $ENV{CONDA_PREFIX})
 find_package(Python3 REQUIRED COMPONENTS Interpreter Development)
 
 # Setup for wrapper library

From 8f8177de93124b674904384eb2dcf96a81e0fe3a Mon Sep 17 00:00:00 2001
From: Kelvin <krodriguez@usgs.gov>
Date: Wed, 4 Oct 2023 15:16:20 -0700
Subject: [PATCH 21/52] trying to remove python

---
 .github/workflows/ci.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index bd89073165..dedc1c5cd9 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -43,6 +43,7 @@ jobs:
           rclone mount asc_s3://asc-isisdata/isis_testData isis_testData --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf --daemon
       - name: Build ISIS
         run: |
+          sudo apt autoremove python3 -y
           mkdir -p build
           cp ${GITHUB_WORKSPACE}/isis/IsisPreferences ${GITHUB_WORKSPACE}/build/
           export ISISDATA=${GITHUB_WORKSPACE}/isis_data

From d896c824cb832361a210e40f76837f2b1399db1b Mon Sep 17 00:00:00 2001
From: Kelvin <krodriguez@usgs.gov>
Date: Thu, 5 Oct 2023 13:01:02 -0700
Subject: [PATCH 22/52] trying xlarge

---
 .github/workflows/ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index dedc1c5cd9..f3f69ecc44 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -14,7 +14,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-       os: [ubuntu-latest, macos-latest]
+       os: [ubuntu-latest-xlarge, macos-latest-xlarge]
     defaults:
       run:
         shell: bash -l {0}
@@ -60,5 +60,5 @@ jobs:
           export ISISTESTDATA=${GITHUB_WORKSPACE}/isis_testData
           export ISISROOT=${GITHUB_WORKSPACE}/build/
           export PATH=$PATH:${GITHUB_WORKSPACE}/build/bin/
-          ctest -VV
+          ctest -VV -j8
 

From 492c39f4469db73e5833166812207f0a29e821ee Mon Sep 17 00:00:00 2001
From: Kelvin <krodriguez@usgs.gov>
Date: Thu, 5 Oct 2023 13:08:59 -0700
Subject: [PATCH 23/52] trying xlarge

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index f3f69ecc44..f82ff721e2 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -14,7 +14,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-       os: [ubuntu-latest-xlarge, macos-latest-xlarge]
+       os: [ubuntu-latest, macos-latest-large]
     defaults:
       run:
         shell: bash -l {0}

From 72114b383ef49b2cea300ebb549441925cdc6fa5 Mon Sep 17 00:00:00 2001
From: Kelvin <krodriguez@usgs.gov>
Date: Tue, 10 Oct 2023 09:53:41 -0700
Subject: [PATCH 24/52] trying to limit parallel jobs, checking ISISDATA

---
 .github/workflows/ci.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index f82ff721e2..e6418cefa6 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -51,8 +51,9 @@ jobs:
           export ISISROOT=${GITHUB_WORKSPACE}/build/
           export PATH=$PATH:${GITHUB_WORKSPACE}/build/bin/
           cd build
+          ls ${GITHUB_WORKSPACE}/isis_data 
           cmake -DisisData=${GITHUB_WORKSPACE}/isis_data -DisisTestData=${GITHUB_WORKSPACE}/isis_testData -DJP2KFLAG=OFF -DCMAKE_BUILD_TYPE=RELEASE -Wdeprecated -GNinja ../isis
-          ninja
+          ninja -j8
       - name: Run ISIS tests
         run: |
           cd build
@@ -60,5 +61,5 @@ jobs:
           export ISISTESTDATA=${GITHUB_WORKSPACE}/isis_testData
           export ISISROOT=${GITHUB_WORKSPACE}/build/
           export PATH=$PATH:${GITHUB_WORKSPACE}/build/bin/
-          ctest -VV -j8
+          ctest -VV 
 

From aa27f5acd53c0d1c27737a667fdba11c09fe3137 Mon Sep 17 00:00:00 2001
From: Kelvin <krodriguez@usgs.gov>
Date: Mon, 24 Jun 2024 08:22:07 -0700
Subject: [PATCH 25/52] added line to only run ctests

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index e6418cefa6..bd9c07881d 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -61,5 +61,5 @@ jobs:
           export ISISTESTDATA=${GITHUB_WORKSPACE}/isis_testData
           export ISISROOT=${GITHUB_WORKSPACE}/build/
           export PATH=$PATH:${GITHUB_WORKSPACE}/build/bin/
-          ctest -VV 
+          ctest -R '.' -E '(_app_|_unit_|_module_)' -j 8 --output-on-failure --timeout 10000
 

From a316d73a7a3ce2bc37d22572ffe314c18656df0a Mon Sep 17 00:00:00 2001
From: Kelvin <krodriguez@usgs.gov>
Date: Mon, 24 Jun 2024 08:38:06 -0700
Subject: [PATCH 26/52] added ls for cholmod

---
 .github/workflows/ci.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index bd9c07881d..d445f246a4 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -52,6 +52,7 @@ jobs:
           export PATH=$PATH:${GITHUB_WORKSPACE}/build/bin/
           cd build
           ls ${GITHUB_WORKSPACE}/isis_data 
+          ls ${CONDA_PREFIX}/include/cholmod*
           cmake -DisisData=${GITHUB_WORKSPACE}/isis_data -DisisTestData=${GITHUB_WORKSPACE}/isis_testData -DJP2KFLAG=OFF -DCMAKE_BUILD_TYPE=RELEASE -Wdeprecated -GNinja ../isis
           ninja -j8
       - name: Run ISIS tests

From a02823a448b685a3aba4f3e4583b60eaead95866 Mon Sep 17 00:00:00 2001
From: Kelvin <krodriguez@usgs.gov>
Date: Mon, 24 Jun 2024 10:12:53 -0700
Subject: [PATCH 27/52] changed OS names

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index d445f246a4..65b88ea610 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -14,7 +14,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-       os: [ubuntu-latest, macos-latest-large]
+       os: [ubuntu, macos-latest]
     defaults:
       run:
         shell: bash -l {0}

From 1149c7359ca4ece1bd627a0908088851572e0226 Mon Sep 17 00:00:00 2001
From: Kelvin <krodriguez@usgs.gov>
Date: Mon, 24 Jun 2024 10:38:22 -0700
Subject: [PATCH 28/52] trying fedora

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 65b88ea610..4f2ab8c4a1 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -14,7 +14,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-       os: [ubuntu, macos-latest]
+       os: [fedora-latest, macos-latest]
     defaults:
       run:
         shell: bash -l {0}

From 3745ea846e58ba9772217e442562bd59a70d6da2 Mon Sep 17 00:00:00 2001
From: Kelvin <krodriguez@usgs.gov>
Date: Mon, 24 Jun 2024 12:21:50 -0700
Subject: [PATCH 29/52] trying fedora

---
 .github/workflows/ci.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 4f2ab8c4a1..b39ae609c6 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -14,10 +14,12 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-       os: [fedora-latest, macos-latest]
+       os: [ubuntu-latest, macos-latest]
     defaults:
       run:
         shell: bash -l {0}
+    container:
+      image: ubuntu:24.04
     steps:
       - uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
         with:

From 06a9b11a98165d0eb8e6a7410ffaf78bc93e28b1 Mon Sep 17 00:00:00 2001
From: Kelvin <krodriguez@usgs.gov>
Date: Mon, 24 Jun 2024 13:32:05 -0700
Subject: [PATCH 30/52] using 20.04

---
 .github/workflows/ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index b39ae609c6..7c2294d791 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -14,12 +14,12 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-       os: [ubuntu-latest, macos-latest]
+       os: [ubuntu-latest]
     defaults:
       run:
         shell: bash -l {0}
     container:
-      image: ubuntu:24.04
+      image: ubuntu:20.04
     steps:
       - uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
         with:

From 732e9610e1994de3faa790a715c5b39eadd1b546 Mon Sep 17 00:00:00 2001
From: Kelvin <krodriguez@usgs.gov>
Date: Mon, 24 Jun 2024 13:50:43 -0700
Subject: [PATCH 31/52] using 22.04

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 7c2294d791..b037f3f51c 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -19,7 +19,7 @@ jobs:
       run:
         shell: bash -l {0}
     container:
-      image: ubuntu:20.04
+      image: ubuntu:22.04
     steps:
       - uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
         with:

From f82067840599ee300022a475d849d484f765be4d Mon Sep 17 00:00:00 2001
From: Kelvin <krodriguez@usgs.gov>
Date: Mon, 24 Jun 2024 14:12:13 -0700
Subject: [PATCH 32/52] updated git

---
 .github/workflows/ci.yml | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index b037f3f51c..22c25bf00f 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -19,8 +19,15 @@ jobs:
       run:
         shell: bash -l {0}
     container:
-      image: ubuntu:22.04
+      image: ubuntu:20.04
     steps:
+      - name: update git 
+        run: | 
+          sudo add-apt-repository ppa:git-core/ppa -y
+          sudo apt-key adv --recv-keys --keyserver keyserver.ubuntu.com A1715D88E1DF1F24 40976EAF437D05B5 3B4FE6ACC0B21F32 A6616109451BBBF2
+          sudo apt-get update
+          sudo apt-get install git -y
+          git --version
       - uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
         with:
           submodules: true

From d725384879bc2745c76750e2acd07eec09cf67eb Mon Sep 17 00:00:00 2001
From: Kelvin <krodriguez@usgs.gov>
Date: Mon, 24 Jun 2024 14:48:27 -0700
Subject: [PATCH 33/52] updated git

---
 .github/workflows/ci.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 22c25bf00f..09cb466b7d 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -23,10 +23,10 @@ jobs:
     steps:
       - name: update git 
         run: | 
-          sudo add-apt-repository ppa:git-core/ppa -y
-          sudo apt-key adv --recv-keys --keyserver keyserver.ubuntu.com A1715D88E1DF1F24 40976EAF437D05B5 3B4FE6ACC0B21F32 A6616109451BBBF2
-          sudo apt-get update
-          sudo apt-get install git -y
+          add-apt-repository ppa:git-core/ppa -y
+          apt-key adv --recv-keys --keyserver keyserver.ubuntu.com A1715D88E1DF1F24 40976EAF437D05B5 3B4FE6ACC0B21F32 A6616109451BBBF2
+          apt-get update
+          apt-get install git -y
           git --version
       - uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
         with:

From db6dbc3f7627668aed91f1e7ed092682f0702949 Mon Sep 17 00:00:00 2001
From: Kelvin <krodriguez@usgs.gov>
Date: Mon, 24 Jun 2024 15:05:55 -0700
Subject: [PATCH 34/52] removed mount command

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 09cb466b7d..1443af449e 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -49,7 +49,7 @@ jobs:
           mkdir isis_testData
           which rclone
           rclone mount asc_s3://asc-isisdata/usgs_data isis_data --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf --daemon
-          rclone mount asc_s3://asc-isisdata/isis_testData isis_testData --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf --daemon
+          # rclone mount asc_s3://asc-isisdata/isis_testData isis_testData --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf --daemon
       - name: Build ISIS
         run: |
           sudo apt autoremove python3 -y

From 31f1d9b7224ea1d42ead95a31db60f0db5fc0c46 Mon Sep 17 00:00:00 2001
From: Kelvin <krodriguez@usgs.gov>
Date: Mon, 24 Jun 2024 15:12:31 -0700
Subject: [PATCH 35/52] removed mount command

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 1443af449e..ca9ee411df 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -48,7 +48,7 @@ jobs:
           mkdir isis_data
           mkdir isis_testData
           which rclone
-          rclone mount asc_s3://asc-isisdata/usgs_data isis_data --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf --daemon
+          # rclone mount asc_s3://asc-isisdata/usgs_data isis_data --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf --daemon
           # rclone mount asc_s3://asc-isisdata/isis_testData isis_testData --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf --daemon
       - name: Build ISIS
         run: |

From bca576d55ca0e7d538bf4425d6fe5461cc12fd14 Mon Sep 17 00:00:00 2001
From: Kelvin <krodriguez@usgs.gov>
Date: Mon, 24 Jun 2024 15:15:48 -0700
Subject: [PATCH 36/52] removed mount command

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index ca9ee411df..f68d18f968 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -52,7 +52,7 @@ jobs:
           # rclone mount asc_s3://asc-isisdata/isis_testData isis_testData --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf --daemon
       - name: Build ISIS
         run: |
-          sudo apt autoremove python3 -y
+          # apt autoremove python3 -y
           mkdir -p build
           cp ${GITHUB_WORKSPACE}/isis/IsisPreferences ${GITHUB_WORKSPACE}/build/
           export ISISDATA=${GITHUB_WORKSPACE}/isis_data

From 979180f9807df88c007bfaa655a31f29032b2452 Mon Sep 17 00:00:00 2001
From: Kelvin <krodriguez@usgs.gov>
Date: Tue, 25 Jun 2024 07:12:48 -0700
Subject: [PATCH 37/52] installing libgl

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index f68d18f968..906b5144c8 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -26,7 +26,7 @@ jobs:
           add-apt-repository ppa:git-core/ppa -y
           apt-key adv --recv-keys --keyserver keyserver.ubuntu.com A1715D88E1DF1F24 40976EAF437D05B5 3B4FE6ACC0B21F32 A6616109451BBBF2
           apt-get update
-          apt-get install git -y
+          apt-get install git libgl1-mesa-glx -y
           git --version
       - uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
         with:

From fc94236bf3f4ee268c8348d55624420105cc169a Mon Sep 17 00:00:00 2001
From: Kelvin <krodriguez@usgs.gov>
Date: Wed, 26 Jun 2024 08:51:11 -0700
Subject: [PATCH 38/52] mac only

---
 .github/workflows/ci.yml | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 906b5144c8..382971df59 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -14,20 +14,20 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-       os: [ubuntu-latest]
+       os: [macos-latest]
     defaults:
       run:
         shell: bash -l {0}
     container:
       image: ubuntu:20.04
     steps:
-      - name: update git 
-        run: | 
-          add-apt-repository ppa:git-core/ppa -y
-          apt-key adv --recv-keys --keyserver keyserver.ubuntu.com A1715D88E1DF1F24 40976EAF437D05B5 3B4FE6ACC0B21F32 A6616109451BBBF2
-          apt-get update
-          apt-get install git libgl1-mesa-glx -y
-          git --version
+      # - name: update git 
+      #   run: | 
+      #     add-apt-repository ppa:git-core/ppa -y
+      #     apt-key adv --recv-keys --keyserver keyserver.ubuntu.com A1715D88E1DF1F24 40976EAF437D05B5 3B4FE6ACC0B21F32 A6616109451BBBF2
+      #     apt-get update
+      #     apt-get install git libgl1-mesa-glx -y
+      #     git --version
       - uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
         with:
           submodules: true

From 78c76adc720d8efee0bc3c72134e6682339a8713 Mon Sep 17 00:00:00 2001
From: Kelvin <krodriguez@usgs.gov>
Date: Thu, 27 Jun 2024 06:55:14 -0700
Subject: [PATCH 39/52] j1

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 382971df59..4018a5890a 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -63,7 +63,7 @@ jobs:
           ls ${GITHUB_WORKSPACE}/isis_data 
           ls ${CONDA_PREFIX}/include/cholmod*
           cmake -DisisData=${GITHUB_WORKSPACE}/isis_data -DisisTestData=${GITHUB_WORKSPACE}/isis_testData -DJP2KFLAG=OFF -DCMAKE_BUILD_TYPE=RELEASE -Wdeprecated -GNinja ../isis
-          ninja -j8
+          ninja -j1
       - name: Run ISIS tests
         run: |
           cd build

From 61aa0557d374adcbaad26b748a1cb4db4b8d335d Mon Sep 17 00:00:00 2001
From: Kelvin <krodriguez@usgs.gov>
Date: Thu, 27 Jun 2024 06:56:05 -0700
Subject: [PATCH 40/52] j1

---
 .github/workflows/ci.yml | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 4018a5890a..b6d66153bb 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -14,20 +14,20 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-       os: [macos-latest]
+       os: [ubuntu-latest]
     defaults:
       run:
         shell: bash -l {0}
     container:
       image: ubuntu:20.04
     steps:
-      # - name: update git 
-      #   run: | 
-      #     add-apt-repository ppa:git-core/ppa -y
-      #     apt-key adv --recv-keys --keyserver keyserver.ubuntu.com A1715D88E1DF1F24 40976EAF437D05B5 3B4FE6ACC0B21F32 A6616109451BBBF2
-      #     apt-get update
-      #     apt-get install git libgl1-mesa-glx -y
-      #     git --version
+      - name: update git 
+        run: | 
+          add-apt-repository ppa:git-core/ppa -y
+          apt-key adv --recv-keys --keyserver keyserver.ubuntu.com A1715D88E1DF1F24 40976EAF437D05B5 3B4FE6ACC0B21F32 A6616109451BBBF2
+          apt-get update
+          apt-get install git libgl1-mesa-glx -y
+          git --version
       - uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
         with:
           submodules: true

From 49364cc5eafd09ffb98198249cd4860802d0a73e Mon Sep 17 00:00:00 2001
From: Kelvin <krodriguez@usgs.gov>
Date: Thu, 27 Jun 2024 12:48:32 -0700
Subject: [PATCH 41/52] pinned CXX

---
 .github/workflows/ci.yml | 2 --
 environment.yml          | 2 +-
 2 files changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index b6d66153bb..3c7a8b3a48 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -18,8 +18,6 @@ jobs:
     defaults:
       run:
         shell: bash -l {0}
-    container:
-      image: ubuntu:20.04
     steps:
       - name: update git 
         run: | 
diff --git a/environment.yml b/environment.yml
index 95f6012fce..940ebeab73 100644
--- a/environment.yml
+++ b/environment.yml
@@ -15,7 +15,7 @@ dependencies:
   - cspice=67
   - csm>=3.0.3,<3.0.4
   - curl>=8.3.0,<9.0a0
-  - cxx-compiler>=1.1.2
+  - cxx-compiler=1.1.2
   - doxygen
   - eigen>=3, <4
   - embree>=3, <4

From 8ba8ce4445d271678e533a92d0947b0078d17425 Mon Sep 17 00:00:00 2001
From: Kelvin <krodriguez@usgs.gov>
Date: Thu, 27 Jun 2024 12:48:43 -0700
Subject: [PATCH 42/52] pinned CXX

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 3c7a8b3a48..45c278d8e8 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -14,7 +14,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-       os: [ubuntu-latest]
+       os: [ubuntu-latest, macos-latest]
     defaults:
       run:
         shell: bash -l {0}

From d519d9c63e4806540c8b4d2c9c286bc7ac20312a Mon Sep 17 00:00:00 2001
From: Kelvin <krodriguez@usgs.gov>
Date: Fri, 28 Jun 2024 13:25:46 -0700
Subject: [PATCH 43/52] removed mac

---
 .github/workflows/ci.yml | 2 +-
 environment.yml          | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 45c278d8e8..3c7a8b3a48 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -14,7 +14,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-       os: [ubuntu-latest, macos-latest]
+       os: [ubuntu-latest]
     defaults:
       run:
         shell: bash -l {0}
diff --git a/environment.yml b/environment.yml
index 940ebeab73..95f6012fce 100644
--- a/environment.yml
+++ b/environment.yml
@@ -15,7 +15,7 @@ dependencies:
   - cspice=67
   - csm>=3.0.3,<3.0.4
   - curl>=8.3.0,<9.0a0
-  - cxx-compiler=1.1.2
+  - cxx-compiler>=1.1.2
   - doxygen
   - eigen>=3, <4
   - embree>=3, <4

From 9eb014d1a21002abf9df638ecd72695f976f18de Mon Sep 17 00:00:00 2001
From: Kelvin <krodriguez@usgs.gov>
Date: Fri, 28 Jun 2024 13:26:30 -0700
Subject: [PATCH 44/52] added mounts back

---
 .github/workflows/ci.yml | 12 +++++-------
 1 file changed, 5 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 3c7a8b3a48..57be1cd9a5 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -41,13 +41,6 @@ jobs:
         run: |
           conda list
           conda env export
-      - name: Download ISIS data
-        run: |
-          mkdir isis_data
-          mkdir isis_testData
-          which rclone
-          # rclone mount asc_s3://asc-isisdata/usgs_data isis_data --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf --daemon
-          # rclone mount asc_s3://asc-isisdata/isis_testData isis_testData --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf --daemon
       - name: Build ISIS
         run: |
           # apt autoremove python3 -y
@@ -64,6 +57,11 @@ jobs:
           ninja -j1
       - name: Run ISIS tests
         run: |
+          mkdir isis_data
+          mkdir isis_testData
+          which rclone
+          rclone mount asc_s3://asc-isisdata/usgs_data isis_data --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf --daemon
+          rclone mount asc_s3://asc-isisdata/isis_testData isis_testData --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf --daemon
           cd build
           export ISISDATA=${GITHUB_WORKSPACE}/isis_data
           export ISISTESTDATA=${GITHUB_WORKSPACE}/isis_testData

From 41385c6807697e85422984423962dbf111f71c58 Mon Sep 17 00:00:00 2001
From: Kelvin <krodriguez@usgs.gov>
Date: Mon, 1 Jul 2024 07:11:33 -0700
Subject: [PATCH 45/52] removed ls's

---
 .github/workflows/ci.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 57be1cd9a5..fe30f92d0e 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -50,9 +50,7 @@ jobs:
           export ISISTESTDATA=${GITHUB_WORKSPACE}/isis_testData
           export ISISROOT=${GITHUB_WORKSPACE}/build/
           export PATH=$PATH:${GITHUB_WORKSPACE}/build/bin/
-          cd build
-          ls ${GITHUB_WORKSPACE}/isis_data 
-          ls ${CONDA_PREFIX}/include/cholmod*
+          cd build 
           cmake -DisisData=${GITHUB_WORKSPACE}/isis_data -DisisTestData=${GITHUB_WORKSPACE}/isis_testData -DJP2KFLAG=OFF -DCMAKE_BUILD_TYPE=RELEASE -Wdeprecated -GNinja ../isis
           ninja -j1
       - name: Run ISIS tests

From 4af04cc5c3bfce0c7f784528d7087da3409744a3 Mon Sep 17 00:00:00 2001
From: Kelvin <krodriguez@usgs.gov>
Date: Mon, 1 Jul 2024 10:44:09 -0700
Subject: [PATCH 46/52] download?

---
 .github/workflows/ci.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index fe30f92d0e..62d0208b66 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -58,8 +58,10 @@ jobs:
           mkdir isis_data
           mkdir isis_testData
           which rclone
-          rclone mount asc_s3://asc-isisdata/usgs_data isis_data --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf --daemon
-          rclone mount asc_s3://asc-isisdata/isis_testData isis_testData --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf --daemon
+          downloadIsisData base isis_data/ --exclude "dems/" 
+          ls isis_data/ 
+          # rclone mount asc_s3://asc-isisdata/usgs_data isis_data --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf --daemon
+          # rclone mount asc_s3://asc-isisdata/isis_testData isis_testData --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf --daemon
           cd build
           export ISISDATA=${GITHUB_WORKSPACE}/isis_data
           export ISISTESTDATA=${GITHUB_WORKSPACE}/isis_testData

From 084847945138cd5a6512e6a6575340e2c2f8e1ff Mon Sep 17 00:00:00 2001
From: Kelvin <krodriguez@usgs.gov>
Date: Mon, 1 Jul 2024 14:07:56 -0700
Subject: [PATCH 47/52] download?

---
 .github/workflows/ci.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 62d0208b66..f81ebe1842 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -50,16 +50,16 @@ jobs:
           export ISISTESTDATA=${GITHUB_WORKSPACE}/isis_testData
           export ISISROOT=${GITHUB_WORKSPACE}/build/
           export PATH=$PATH:${GITHUB_WORKSPACE}/build/bin/
+
+          mkdir isis_data
+          mkdir isis_testData
+          downloadIsisData base isis_data/ --exclude "dems/" 
+          ls isis_data/ 
           cd build 
           cmake -DisisData=${GITHUB_WORKSPACE}/isis_data -DisisTestData=${GITHUB_WORKSPACE}/isis_testData -DJP2KFLAG=OFF -DCMAKE_BUILD_TYPE=RELEASE -Wdeprecated -GNinja ../isis
           ninja -j1
       - name: Run ISIS tests
         run: |
-          mkdir isis_data
-          mkdir isis_testData
-          which rclone
-          downloadIsisData base isis_data/ --exclude "dems/" 
-          ls isis_data/ 
           # rclone mount asc_s3://asc-isisdata/usgs_data isis_data --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf --daemon
           # rclone mount asc_s3://asc-isisdata/isis_testData isis_testData --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf --daemon
           cd build

From 812ebdae5eab65cc7122c6b22fbc3633672c39ff Mon Sep 17 00:00:00 2001
From: Kelvin <krodriguez@usgs.gov>
Date: Tue, 2 Jul 2024 09:17:03 -0700
Subject: [PATCH 48/52] downloadIsisData

---
 .github/workflows/ci.yml | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index f81ebe1842..3f051a81f3 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -51,10 +51,6 @@ jobs:
           export ISISROOT=${GITHUB_WORKSPACE}/build/
           export PATH=$PATH:${GITHUB_WORKSPACE}/build/bin/
 
-          mkdir isis_data
-          mkdir isis_testData
-          downloadIsisData base isis_data/ --exclude "dems/" 
-          ls isis_data/ 
           cd build 
           cmake -DisisData=${GITHUB_WORKSPACE}/isis_data -DisisTestData=${GITHUB_WORKSPACE}/isis_testData -DJP2KFLAG=OFF -DCMAKE_BUILD_TYPE=RELEASE -Wdeprecated -GNinja ../isis
           ninja -j1
@@ -62,6 +58,12 @@ jobs:
         run: |
           # rclone mount asc_s3://asc-isisdata/usgs_data isis_data --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf --daemon
           # rclone mount asc_s3://asc-isisdata/isis_testData isis_testData --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf --daemon
+          
+          mkdir isis_data
+          mkdir isis_testData
+          ./build/scripts/downloadIsisData base isis_data/ --exclude "dems/" 
+          ls isis_data/ 
+          
           cd build
           export ISISDATA=${GITHUB_WORKSPACE}/isis_data
           export ISISTESTDATA=${GITHUB_WORKSPACE}/isis_testData

From fee36219d459dbd13e51edba439e971baab6e397 Mon Sep 17 00:00:00 2001
From: Kelvin <krodriguez@usgs.gov>
Date: Tue, 2 Jul 2024 11:59:51 -0700
Subject: [PATCH 49/52] downloadIsisData

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 3f051a81f3..ab74e8e7b1 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -61,7 +61,7 @@ jobs:
           
           mkdir isis_data
           mkdir isis_testData
-          ./build/scripts/downloadIsisData base isis_data/ --exclude "dems/" 
+          ./build/scripts/downloadIsisData base isis_data/ --exclude "dems/" --config ${GITHUB_WORKSPACE}/isis/config/rclone.conf
           ls isis_data/ 
           
           cd build

From 08514422b7d66c4f08301a593f8a014d35c5ba74 Mon Sep 17 00:00:00 2001
From: Kelvin <krodriguez@usgs.gov>
Date: Fri, 5 Jul 2024 11:24:04 -0700
Subject: [PATCH 50/52] args moved

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index ab74e8e7b1..b9603c2f54 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -61,7 +61,7 @@ jobs:
           
           mkdir isis_data
           mkdir isis_testData
-          ./build/scripts/downloadIsisData base isis_data/ --exclude "dems/" --config ${GITHUB_WORKSPACE}/isis/config/rclone.conf
+          ./build/scripts/downloadIsisData --exclude "dems/" --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf base isis_data/ 
           ls isis_data/ 
           
           cd build

From ec83683b83fb8a546c7bc296e170ddc19ab0c4b5 Mon Sep 17 00:00:00 2001
From: Kelvin <krodriguez@usgs.gov>
Date: Fri, 5 Jul 2024 14:25:40 -0700
Subject: [PATCH 51/52] args moved

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index b9603c2f54..80a465bbad 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -61,7 +61,7 @@ jobs:
           
           mkdir isis_data
           mkdir isis_testData
-          ./build/scripts/downloadIsisData --exclude "dems/" --config=${GITHUB_WORKSPACE}/isis/config/rclone.conf base isis_data/ 
+          ./build/scripts/downloadIsisData --config isis/config/rclone.conf base isis_data/ 
           ls isis_data/ 
           
           cd build

From f8d24597c2446d463eaf326ded5a4d77c615967c Mon Sep 17 00:00:00 2001
From: Kelvin <krodriguez@usgs.gov>
Date: Fri, 5 Jul 2024 16:47:29 -0700
Subject: [PATCH 52/52] args moved

---
 .github/workflows/ci.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 80a465bbad..bbfe8c8fc6 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -61,7 +61,8 @@ jobs:
           
           mkdir isis_data
           mkdir isis_testData
-          ./build/scripts/downloadIsisData --config isis/config/rclone.conf base isis_data/ 
+          cp ${GITHUB_WORKSPACE}/isis/config/rclone.conf  . 
+          ./build/scripts/downloadIsisData --exclude "dems/"  base isis_data/ 
           ls isis_data/ 
           
           cd build