Merge branch 'dev' into application_change

.github/requirements.txt

@@ -1 +1 @@
-requests==2.31.0
+requests==2.32.0

.github/workflows/gitlab-codebuild.yml

@@ -0,0 +1,45 @@
+name: Github to Gitlab CI - Run CodeBuild
+
+env:
+  PR_NUMBER: ${{ github.event.number }}
+  GITLAB_TOKEN: ${{ secrets.GITLAB_TOKEN }}
+
+on:
+  pull_request_target:
+    branches: 
+      - '**'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Run script
+        run: |
+          git config --global user.name "Github_CI"
+          git config --global user.email "project_14468_bot_3f7d8e1a392afd88ead5f3f3154e809d@noreply.gitlab.com"
+          git clone https://isis-codebuild-ci:$GITLAB_TOKEN@code.usgs.gov/astrogeology/isis-codebuild-ci.git
+          cd isis-codebuild-ci
+          git checkout -b PR_$PR_NUMBER
+          echo -e "\nenv: \n  shell: bash \n  variables: \n    PR_NUMBER: $PR_NUMBER \n    MERGE_BRANCH: $GITHUB_BASE_REF" >> buildspec.yml
+          git commit -a -m "$PR_NUMBER"
+          git push origin PR_$PR_NUMBER --force
+          
+  comment-bot:
+      permissions: write-all
+      runs-on: [ubuntu-latest]
+      needs: [build]
+      steps:
+      - name: Check out code
+        uses: actions/checkout@v4 
+      - name: Comment PR
+        uses: thollander/actions-comment-pull-request@v2
+        with:
+          message: |
+            The build and test suite have started for your pull request. 
+            
+            To view your [build log](https://us-west-2.codebuild.aws.amazon.com/project/eyJlbmNyeXB0ZWREYXRhIjoiNDJNZ2MxbHFKTkwxV1RyQUxJekdJY3FIanNqU29rMHB4Nk1YUzk4REIrZUZDeEtEaW9HQlZ1dTZOSHpML2VUTGVDekYydmVFcU9sUHJKN20wQzd1Q0UzSzJscnB0MElDb1M3Ti9GTlJYR1RuMWJTV3V1SkJTa3NoYmc9PSIsIml2UGFyYW1ldGVyU3BlYyI6IjF3U2NTSGlDcEtCc29YVnEiLCJtYXRlcmlhbFNldFNlcmlhbCI6MX0%3D), please reference the build with source version: "PR_${{ github.event.number }}". 
+            
+            Additionally, check the latest "dev" source version to identify existing test failures. Please note that you are not responsible for the test failures that exist on both your PR and the dev branch.
+          

.github/workflows/version_bump.yml

@@ -0,0 +1,26 @@
+name: versionbump
+on:
+  pull_request:
+    branches:
+      - lts
+    types:
+      - closed
+
+jobs:
+  version_bump:
+    if: github.event.pull_request.merged && ${{ github.event.label.name == 'bug' }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Bump version
+        run: |
+          git config --global user.name 'ProjectBot'
+          git config --global user.email 'bot@users.noreply.github.com'
+          CURRENTVERSION=$(sed -n '0,/^{%[[:space:]]*set[[:space:]]*version[[:space:]]*=[[:space:]]*"\([^"]*\)"[[:space:]]*%}/s//\1/p' ${{github.workspace}}/recipe/meta.yaml)
+          CURRENTVERSION=`echo $CURRENTVERSION | awk -F. '/[0-9]+\./{$NF;print}' OFS=.`
+          NEWVERSION=`echo $CURRENTVERSION | awk -F. '/[0-9]+\./{$NF++;print}' OFS=.`
+          sed -i "0,/^{%.*version.*\"\([^\"]*\)\".*/s//{% set version = "\"${NEWVERSION}"\" %}/" ${{github.workspace}}/recipe/meta.yaml
+          sed -i "0,/set(VERSION.*/s//set(VERSION \""${NEWVERSION}"\")/" ${{github.workspace}}/isis/CMakeLists.txt          
+          git add ${{github.workspace}}/isis/CMakeLists.txt ${{github.workspace}}/recipe/meta.yaml
+          git commit -m 'auto bump version'
+          git push

.gitignore

@@ -63,6 +63,9 @@ install/
 # Unignore mosrange cube files in data area as input files require these
 !isis/tests/data/mosrange/*.cub
 
+# Unignore phocube cube files in data area as input files require these
+!isis/tests/data/phocube/*.cub
+
 # Ensure the contents of ISISDATA mockup tests are preserved
 !isis/tests/data/isisdata/mockup/**/*
 

.zenodo.json

@@ -166,6 +166,11 @@
       "affiliation": "United States Geological Survey, Astro Geology Science Center",
       "name": "Fergason, Robin"
     },
+    {
+      "affiliation": "Italian National Institute for Astrophysics (INAF), Istituto di Astrofisica e Planetologia Spaziali (IAPS), Rome, Italy",
+      "name": "Frigeri, Alessandro",
+      "orcid": "0000-0002-9140-3977"   
+    },
     {
       "name": "Gaddis, Lisa"
     },
@@ -336,6 +341,10 @@
     {
       "name": "Miller-Ribelin, Elizabeth"
     },
+    {
+      "affiliation": "Japan Aerospace Exploration Agency, Institute of Space and Astronautical Science",
+      "name": "Murakami, Shin-ya",
+      "orcid": "0000-0002-7137-4849"
     {
       "affiliation": "United States Geological Survey, Astro Geology Science Center",
       "name": "Nelson, Gavin"

AUTHORS.rst

@@ -176,4 +176,4 @@ Integrated Software for Imagers and Spectrometers Contributors
 
 -----
 This list was generated from the .zenodo.json file by running the
-isis/scripts/zenodo_to_authors.py Python program.
+isis/scripts/zenodo_to_authors.py Python program.

CHANGELOG.md

@@ -35,8 +35,61 @@ release.
 
 ## [Unreleased]
 
+### Added
+- Added TOVECT output parameter which generate a geospatial CSV file with a VRT metadata sidecar file [#5571](https://github.com/DOI-USGS/ISIS3/issues/5571)  
+- Added Vectorize to ProcessGroundPolygon library
+- Added gtest files for the app and unit test 
+- Added Chandrayaan2 template for isisimport
+
+### Changed
+- Refactored the pixel2map app
+- Updated pixel2map documentation
+
+### Fixed
+- Fixed noseam bug where a debugging output statement was inadvertently left in noseam.cpp.
+Issue: [5660](https://github.com/DOI-USGS/ISIS3/issues/5660)
+- Fixed jigsaw bugs in which RADIUS is handled incorrectly in the jigsaw gui and in the bundleout.txt
+file. Slightly modified the FunctionalTestJigsawBundleXYZ ctest accordingly. Issue: [5642](https://github.com/DOI-USGS/ISIS3/issues/5642)
+- Fixed a bug in isisminer in which bad (e.g. self-intersecting) polygon geometries were not treated properly. Added pertinent unit tests to GisGeometry and Strategy classes. Issue: [5612](https://github.com/DOI-USGS/ISIS3/issues/5612)
+- Fixed a bug in kaguyasp2isis that doesn't work for data with a detached label.
+- Fixed FunctionalTestCamstatsDefaultParameters test by increasing the runtime speed [#5459](https://github.com/DOI-USGS/ISIS3/issues/5459)
+- Fixed XmlToJson namespaced key conversion [#5652](https://github.com/DOI-USGS/ISIS3/pull/5652)
+- Fixed PHOTOMET not accepting backplanes [#5281](https://github.com/DOI-USGS/ISIS3/issues/5281)
+
+## [8.3.0] - 2024-09-30
+
+### Added
+- Added backplane options for SunIllumination and SurfaceObliqueDetectorResolution to phocube [#5467](https://github.com/DOI-USGS/ISIS3/issues/5467)
+- Added *.history to the ignore list in downloadIsisData
+
+### Changed
+- Noseam has been refactored to be callable; old Makefile test has been removed and replaced by a gtest. Issue: [#5599](https://github.com/USGS-Astrogeology/ISIS3/issues/5599)
+- Explode has been refactored to be callable; old Makefile test has been removed and replaced by a gtest. Issue: [#5557](https://github.com/USGS-Astrogeology/ISIS3/issues/5557)
+- Isisminer has been refactored to be callable; old Makefile tests have been removed and replaced by gtests. Issue: [#5516](https://github.com/USGS-Astrogeology/ISIS3/issues/5516)
+- Algebra has been refactored to be callable; old Makefile tests have been removed and replaced by gtests. Issue: [#5594](https://github.com/USGS-Astrogeology/ISIS3/issues/5594)
+- Photrim has been refactored to be callable; old Makefile tests have been removed and replaced by gtests. Issue: [#5581](https://github.com/USGS-Astrogeology/ISIS3/issues/5581)
+- Bandtrim has been refactored to be callable; old Makefile tests have been removed and replaced by gtests. Issue: [#5571](https://github.com/USGS-Astrogeology/ISIS3/issues/5571)
+- Modified kaguyasp2isis to work with new (detached) data [#5436](https://github.com/DOI-USGS/ISIS3/issues/5436)
+- Added jigsaw error message for csminit'd images without csm parameters[#5486](https://github.com/DOI-USGS/ISIS3/issues/5486)
+- Changed `qwt` dependency version to 6.2.0 or below [#5498](https://github.com/DOI-USGS/ISIS3/issues/5498)
+- Pinned `suitesparse` dependency version to maximum not including 7.7.0 [#5496](https://github.com/DOI-USGS/ISIS3/issues/5496)
+
+
 ### Fixed
+- Fixed a bug in noproj.cpp which left a persisent lbl file after running noproj. [#5577] (https://github.com/DOI-USGS/ISIS3/issues/5577)
+- Fixed a bug in QVIEW's FindTool in which camera was prioritized over projction [#5508](https://github.com/DOI-USGS/ISIS3/issues/5508)
+- Fixed a bug in PolygonTools in which the program exited before attempting to fix an invalid Polygon [#5520](https://github.com/DOI-USGS/ISIS3/issues/5520)
 - Fixed a bug in QVIEW's Stretch tool where the default min/max type was not an available option [#5289](https://github.com/DOI-USGS/ISIS3/issues/5289)
+- Fixed a bug in QVIEW where images would double load if loaded from the commandline [#5505](https://github.com/DOI-USGS/ISIS3/pull/5505)
+- Fixed qmos segfault under GEOS 3.12 [#5539](https://github.com/DOI-USGS/ISIS3/issues/5539)
+- Fixed CSMSerialNumber.trn typo [#5485](https://github.com/DOI-USGS/ISIS3/issues/5485)
+- Fixed CSMSerialNumber.trn to be PVL compliant [#5484](https://github.com/DOI-USGS/ISIS3/issues/5484)
+- Fixed hrsc2isis to support level 3 hrsc images [#5497](https://github.com/DOI-USGS/ISIS3/issues/5497)
+- Fixed gllssi2isis to support V1.1 data [#5396](https://github.com/DOI-USGS/ISIS3/issues/5396)
+
+### Added
+- Added option to save and apply bundle adjustment values in `jigsaw` [#4474](https://github.com/DOI-USGS/ISIS3/issues/4474)
+- Added versioned default values to lrowacphomap's PHOALGO and PHOPARCUBE parameters and updated lrowacphomap to handle them properly. [#5452](https://github.com/DOI-USGS/ISIS3/pull/5452)
 
 ## [8.2.0] - 2024-04-18
 
@@ -64,6 +117,10 @@ release.
 - Added new option in `ctxcal` to use monthly computed flatfield files for "Frown" removal in CTX images. [#5338](https://github.com/DOI-USGS/ISIS3/pull/5338)
 - CSMCamera can now read and use the body rotation from ALE produced ISDs [#5072](https://github.com/DOI-USGS/ISIS3/pull/5072)
 - CSMSkyMap added to CSMCamera for use with local rover projections in ISIS [#5072](https://github.com/DOI-USGS/ISIS3/pull/5072)
+
+- Cneteditor can now display point coordinates and sigmas in either lat/lon/radius or XYZ
+format. A priori coordinate sigmas can now be edited in both formats. New filters have been implemented for coordinates and sigmas in XYZ. [#5421](https://github.com/DOI-USGS/ISIS3/issues/5421)
+
 - Added new Hayabusa2 translation for `SpacecraftName` to accept `HAYABUSA2` [#5395](https://github.com/DOI-USGS/ISIS3/issues/5395)
 - Added ALLOWERROR parameter to campt [#5393](https://github.com/DOI-USGS/ISIS3/pull/5393)
 - OSIRIS-REx Tagcams instrument support, tests, and test data added [#5424](https://github.com/DOI-USGS/ISIS3/issues/5424)

README.md

@@ -500,19 +500,12 @@ ISIS is comprised of two types of tests, custom Makefile based tests, and GTest
 ### How to download the ISIS test data with rclone  
 Test data is hosted using Amazon S3 storage buckets. We recommend using rclone to pull the data into a local directory. You can download rclone using their instructions (see: https://rclone.org/downloads/) or by using an anaconda environment (see: https://docs.anaconda.com/anaconda/install/). If you already have an anaconda environment up, install rclone with: `conda install –c conda-forge rclone` 
 
-Next, you will want to configure rclone using a default S3 configuration. See: https://rclone.org/s3/ for detailed information on how to configure S3, but for the purposes of downloading the ISIS3 test data, you simply run rclone config which will start an interactive menu. Press enter through it all except for these details: 
-
-1. Set S3 as both your storage type and storage provider
-2. Set us-west-2 as both your region to connect to and as the location constraint. 
-3. Everything else, just leave as the default. 
-
-Example output: https://gist.github.com/Kelvinrr/706bbd54b1c2c30d0ce3d12f7dcaa10a
-
-Once rclone is configured, simply run: `rclone sync remote:asc-isisdata/isis_testData/ $ISISTESTDATA`
+Once rclone is installed, with `$ISISROOT` set, simply run: `rclone --config $ISISROOT/etc/isis/rclone.conf sync asc_s3:asc-isisdata/isis_testData/ $ISISTESTDATA`
 where:
-  - $ISISTESTDATA is the environment variable defining the location of the ISISTESTDATA
-  - remote: is the name of the configuration you created earlier. This can be whatever you want to name it, in this case it is named remote. 
-  - asc-isisdata/isis_testData/ is the name of the S3 bucket you’re downloading from
+  - `$ISISTESTDATA` is the environment variable defining the location of the isis test data. 
+  - `--config` overwrites the default config path, you want to use the rclone config that ships with ISIS.
+  - `asc_s3:` is the name of S3 configuration in the configuration file that ships with ISIS. This can be whatever you want to name it, in this case it is named remote. 
+  - `asc-isisdata/isis_testData/` is the name of the S3 bucket you’re downloading from
 
 $ISISTESTDATA should now contain a full clone of the ISIS test data for running Makefile based tests. 
 

code.json

@@ -55,14 +55,14 @@
       "licenses": [
         {
           "name": "Public Domain, CC0-1.0",
-          "URL": "https://code.usgs.gov/astrogeology/isis/-/raw/7.1.0/LICENSE.md"
+          "URL": "https://code.usgs.gov/astrogeology/isis/-/raw/8.0.0/LICENSE.md"
         }
       ]
     },
 
     "homepageURL": "https://isis.astrogeology.usgs.gov",
-    "downloadURL": "https://code.usgs.gov/astrogeology/isis/-/archive/7.1.0/isis-7.1.0.zip",
-    "disclaimerURL": "https://code.usgs.gov/astrogeology/isis/-/raw/7.1.0/DISCLAIMER.md",
+    "downloadURL": "https://code.usgs.gov/astrogeology/isis/-/archive/8.0.0/isis-8.0.0.zip",
+    "disclaimerURL": "https://code.usgs.gov/astrogeology/isis/-/raw/8.0.0/DISCLAIMER.md",
     "repositoryURL": "https://code.usgs.gov/astrogeology/isis.git",
     "vcs": "git",
 
@@ -91,22 +91,22 @@
     "name": "ISIS3",
     "organization": "U.S. Geological Survey",
     "description": "GitHub code repository for the Integrated Software for Imagers and Spectrometers (ISIS)",
-    "version": "8.1.0_RC2",
+    "version": "8.3.0",
     "status": "Production",
 
     "permissions": {
       "usageType": "openSource",
       "licenses": [
         {
           "name": "Public Domain, CC0-1.0",
-          "URL": "https://code.usgs.gov/astrogeology/isis/-/raw/8.1.0_RC2/LICENSE.md"
+          "URL": "https://code.usgs.gov/astrogeology/isis/-/raw/8.3.0/LICENSE.md"
         }
       ]
     },
 
     "homepageURL": "https://isis.astrogeology.usgs.gov",
-    "downloadURL": "https://code.usgs.gov/astrogeology/isis/-/archive/8.1.0_RC2/8.1.0_RC2.zip",
-    "disclaimerURL": "https://code.usgs.gov/astrogeology/isis/-/raw/8.1.0_RC2/DISCLAIMER.md",
+    "downloadURL": "https://code.usgs.gov/astrogeology/isis/-/archive/8.3.0/8.3.0.zip",
+    "disclaimerURL": "https://code.usgs.gov/astrogeology/isis/-/raw/8.3.0/DISCLAIMER.md",
     "repositoryURL": "https://code.usgs.gov/astrogeology/isis.git",
     "vcs": "git",
 
@@ -129,7 +129,7 @@
     },
 
     "date": {
-      "metadataLastUpdated": "2024-01-08"
+      "metadataLastUpdated": "2024-09-30"
     }
   }
 ]

environment.yml

@@ -3,74 +3,76 @@ channels:
   - defaults
 
 dependencies:
-  - ale>=0.10.0, <1
+  - ale =0.10.0,<1
+  - aom
   - armadillo
-  - boost>=1.72.0, <2
-  - boost-cpp>=1.72.0, <2
+  - boost >=1.78.0,<1.79
+  - boost-cpp >=1.78.0,<1.79
   - blas
   - usgs-astrogeology::bullet
   - bz2file
   - bzip2
-  - cmake >=3.15, <4
-  - cspice=67
-  - csm>=3.0.3,<3.0.4
-  - curl>=8.3.0,<9.0a0
-  - cxx-compiler>=1.1.2
+  - cmake >=3.27,<3.28
+  - cspice =67
+  - csm >=3.0.3,<3.0.4
+  - curl >=8.4.0,<8.5
+  - cxx-compiler=1.7
   - doxygen
-  - eigen>=3, <4
-  - embree>=3, <4
+  - eigen >=3, <4
+  - embree >=3, <4
   - ffmpeg
-  - geos>=3.12.1, <4
+  - geos >=3.12, <3.13
   - geotiff
   - gmp
   - graphviz
-  - gsl>=2.6
-  - hdf5>=1.14.2,<1.14.3.0a0
+  - conda-forge::gsl >=2.6, <2.7
+  - hdf5
+  - highfive
   - icu
   - inja
   - jama
   - usgs-astrogeology::kakadu==1
   - kalasiris
   - krb5
-  - libboost>=1.72.0, <2
-  - libgdal >=3.7.2,<3.8.0a0
-  - libopencv>=4.5.2, <5
-  - libpng>=1.6.34, <2
+  - libgdal >=3.7,<3.8
+  - libopencv >=4.7,<4.8
+  - libpng >=1.6.34,<1.7
   - libprotobuf
-  - libtiff>=4.0, <5
+  - libtiff >=4.5,<4.6
   - libxml2
   - make
   - mesalib
   - mysql
   - mysql-connector-c
-  - nanoflann<1.4
-  - nlohmann_json
-  - ninja>=1.7.2, <2
+  - nanoflann <1.4
+  - nlohmann_json=3.11.2
+  - ninja >=1.7.2,<1.8
   - nn
-  - opencv>=4.5.2, <5
-  - openssl>=3.1.2,<4.0a0
-  - pcl >=1.10, <2
+  - opencv >=4.7,<4.8
+  - openssl >=3.1.2,<3.2
+  - pcl >=1.13,<1.14
   - plio
   - protobuf
-  - python=3.12
-  - python_abi=3.12
+  - python >=3.10
+  - python_abi >=3.10
   - pytest
-  - qhull
-  - qt-main
-  - qwt
   - rclone
-  - sqlite>=3.43.0,<4.0a0
-  - suitesparse
+  - qhull
+  - qt-main>=5.15.8, <5.16
+  - qwt <6.3.0
+  - sqlite >=3.46.0,<3.47
+  - suitesparse <7.7.0
   - superlu
   - swig
   - texlive-core
   - tnt
+  - usgscsm
   - x264
   - xalan-c
-  - xerces-c>=3.2.4,<3.3.0a0
+  - xerces-c >=3.2.4,<3.3.0a0
   - xorg-kbproto
   - xorg-libice
   - xorg-libsm
   - xorg-libx11
   - xorg-libxi
-  - zlib>=1.2.13,<1.3.0a0
+  - zlib >=1.3,<1.4.0a0