8.0.4 LTS Release Prep (old)

.github/pr_label_checker.py

@@ -1,5 +1,6 @@
 import os
 import re as rgx
+from itertools import chain
 from requests import get, post
 from requests import Response
 from requests.exceptions import HTTPError, RequestException
@@ -8,12 +9,15 @@
 # Constants
 GITHUB_TOKEN=os.environ["GITHUB_TOKEN"]
 GITHUB_API_URL=os.environ["GITHUB_API_URL"]
+GITHUB_SERVER_URL=os.environ["GITHUB_SERVER_URL"]
 GITHUB_SHA=os.environ["GITHUB_SHA"]
 
-BASE_URL=f'{GITHUB_API_URL}/repos/DOI-USGS/ISIS3'
-PULLS_URL=f'{BASE_URL}/pulls'
-COMMITS_URL=f'{BASE_URL}/commits'
-ISSUES_URL=f'{BASE_URL}/issues'
+REPO_URL_PATH='DOI-USGS/ISIS3'
+API_BASE_URL=f'{GITHUB_API_URL}/repos/{REPO_URL_PATH}'
+API_PULLS_URL=f'{API_BASE_URL}/pulls'
+API_COMMITS_URL=f'{API_BASE_URL}/commits'
+API_ISSUES_URL=f'{API_BASE_URL}/issues'
+ISSUES_URL=f'{GITHUB_SERVER_URL}/{REPO_URL_PATH}/issues/'
 HEADERS = {
     "Accept": "application/vnd.github+json",
     "Authorization" : f"Bearer {GITHUB_TOKEN}",
@@ -25,7 +29,7 @@ def get_prs_associated_with_commit() -> Response:
     Get list of PRs associated with commit.
     """
     try:
-        response = get(f'{COMMITS_URL}/{GITHUB_SHA}/pulls', headers=HEADERS)
+        response = get(f'{API_COMMITS_URL}/{GITHUB_SHA}/pulls', headers=HEADERS)
         response.raise_for_status()
         return response
     except HTTPError as he:
@@ -52,16 +56,30 @@ def search_for_linked_issues(pull_body: str) -> list:
     Regex examples:
     '#1' - matches
     '#123456' - matches
+    'https://github.com/DOI-USGS/ISIS3/issues/25' - matches
     '# 123' - fails
     '#ABC' - fails
     '## ABC'- fails
     """
-    linked_issues = rgx.findall('#[^\D]\d*', pull_body)
-    issue_numbers = []
-    for linked_issue in linked_issues:
-        # Strip linked issue text of '#'
-        issue_numbers.append(linked_issue.replace('#',''))
-    return issue_numbers
+    # Split the PR body by heading 
+    pull_body_list = pull_body.split('##')
+    regex_pattern = rf'{ISSUES_URL}(\d)|(#[^\D]\d*)'
+    for section in pull_body_list:
+        # Find section with heading 'Related Issue'
+        if section != None and 'Related Issue' in section:
+            # Find items that match the regex pattern
+            matched_items = rgx.findall(regex_pattern, section)
+            # Convert list of tuples to list of all items
+            flattened_list = list(chain.from_iterable(matched_items))
+            # Remove items of empty values
+            filtered_list = list(filter(None, flattened_list))
+            # Remove '#' from items
+            issue_numbers = list(map(lambda item: item.replace('#', ''), filtered_list))
+            return issue_numbers
+    # No linked issues
+    print(False)
+    sys.exit(0)
+
 
 def get_linked_issues(issue_numbers: list) -> list:
     """
@@ -71,7 +89,7 @@ def get_linked_issues(issue_numbers: list) -> list:
     for issue_number in issue_numbers:
         # Get labels from issue
         try:
-            response = get(f'{ISSUES_URL}/{issue_number}', headers=HEADERS)
+            response = get(f'{API_ISSUES_URL}/{issue_number}', headers=HEADERS)
             response.raise_for_status()
             response_list.append(response)
         except HTTPError as he:
@@ -109,7 +127,7 @@ def update_pr_labels(pull_number: str, combined_issue_labels: list):
     # Convert label list into JSON-formatted dict
     labels_data = {"labels": combined_issue_labels}
     try:
-        response = post(f'{ISSUES_URL}/{pull_number}/labels', json=labels_data, headers=HEADERS)
+        response = post(f'{API_ISSUES_URL}/{pull_number}/labels', json=labels_data, headers=HEADERS)
         response.raise_for_status()
     except HTTPError as he:
         raise HTTPError("HTTPError in updating PR.", he)
@@ -121,7 +139,7 @@ def get_pr(pull_number: str) -> Response:
     Get pull request
     """
     try:
-        response = get(f'{PULLS_URL}/{pull_number}', headers=HEADERS)
+        response = get(f'{API_PULLS_URL}/{pull_number}', headers=HEADERS)
         response.raise_for_status()
         return response
     except HTTPError as he:

.github/pull_request_template.md

@@ -33,7 +33,8 @@
 - [ ] My change requires a change to the documentation and I have updated the documentation accordingly.
 - [ ] I have added tests to cover my changes.
 - [ ] I have added myself to the [.zenodo.json](https://github.com/USGS-Astrogeology/ISIS3/blob/dev/.zenodo.json) document.
-- [ ] I have added any user impacting changes to the [CHANGELOG.md](https://github.com/USGS-Astrogeology/ISIS3/blob/dev/CHANGELOG.md) document.
+- [ ] I have added my user impacting change to the [CHANGELOG.md](https://github.com/USGS-Astrogeology/ISIS3/blob/dev/CHANGELOG.md) document. <!--- NOTE: You can only have one changelog entry per PR, see https://github.com/DOI-USGS/ISIS3/blob/dev/CONTRIBUTING.md -->
+
 
 ## Licensing
 This project is mostly composed of free and unencumbered software released into the public domain, and we are unlikely to accept contributions that are not also released into the public domain. Somewhere near the top of each file should have these words:

.github/requirements.txt

@@ -1 +1 @@
-requests==2.28.2
+requests==2.32.0

.github/workflows/autopr_bugfix.yml

@@ -30,6 +30,7 @@ jobs:
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         GITHUB_API_URL: ${{ secrets.GITHUB_API_URL }}
+        GITHUB_SERVER_URL: ${{ secrets.GITHUB_SERVER_URL }}
         GITHUB_SHA: ${{ secrets.GITHUB_SHA }}
       run: |
         echo "result=$(python ./.github/pr_label_checker.py)" >> $GITHUB_OUTPUT

.github/workflows/gitlab-codebuild.yml

@@ -0,0 +1,45 @@
+name: Github to Gitlab CI - Run CodeBuild
+
+env:
+  PR_NUMBER: ${{ github.event.number }}
+  GITLAB_TOKEN: ${{ secrets.GITLAB_TOKEN }}
+
+on:
+  pull_request_target:
+    branches: 
+      - '**'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Run script
+        run: |
+          git config --global user.name "Github_CI"
+          git config --global user.email "project_14468_bot_3f7d8e1a392afd88ead5f3f3154e809d@noreply.gitlab.com"
+          git clone https://isis-codebuild-ci:[email protected]/astrogeology/isis-codebuild-ci.git
+          cd isis-codebuild-ci
+          git checkout -b PR_$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/gitlab-release.yml

@@ -0,0 +1,32 @@
+name: Github to Gitlab CI - Run CodeBuild
+
+env:
+  GITLAB_TOKEN: ${{ secrets.GITLAB_TOKEN }}
+  ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }} 
+
+on:
+  release:
+    types: [prereleased, released]
+  push:
+    branches:
+      - '*.*.*_RC*'
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Run script
+        env:
+          ISIS_VERSION: ${{ github.event.release.tag_name || github.ref_name }}
+        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:[email protected]/astrogeology/isis-codebuild-ci.git
+          echo $ISIS_VERSION
+          cd isis-codebuild-ci
+          git checkout -b RELEASE_$ISIS_VERSION
+          echo -e "\nenv: \n  shell: bash \n  variables: \n    ISIS_VERSION: $ISIS_VERSION \n    ANACONDA_API_TOKEN: $ANACONDA_TOKEN" >> buildspec-release.yml
+          git commit -a -m "$ISIS_VERSION"
+          git push origin RELEASE_$ISIS_VERSION --force
+

.github/workflows/stale.yml

@@ -18,8 +18,8 @@ jobs:
         repo-token: ${{ secrets.GITHUB_TOKEN }}
         days-before-stale: 180
         days-before-close: 180
-        stale-issue-message: "Thank you for your contribution!\n\nUnfortunately, this issue hasn't received much attention lately, so it is labeled as 'stale.'\n\nIf no additional action is taken, this issue will be automatically closed in 180 days."
-        stale-pr-message: "Thank you for your contribution!\n\nUnfortunately, this pull request hasn't received much attention lately, so it is labeled as 'stale.'\n\nIf no additional action is taken, this pull request will be automatically closed in 180 days."
+        stale-issue-message: "Thank you for your contribution!\n\nUnfortunately, this issue hasn't received much attention lately, so it is labeled as 'stale.'\n\nIf no additional action is taken, this issue will be automatically closed in 180 days.\n\nIf you want to participate in our support prioritization meetings or be notified when support sprints are happening, you can sign up the support sprint notification emails [here](https://public.govdelivery.com/accounts/USDOIGS/signup/39118).\n\nRead more about our support processs [here](https://astrogeology.usgs.gov/docs/how-to-guides/software-management/software-support/)"
+        stale-pr-message: "Thank you for your contribution!\n\nUnfortunately, this pull request hasn't received much attention lately, so it is labeled as 'stale.'\n\nIf no additional action is taken, this pull request will be automatically closed in 180 days.\n\nIf you want to participate in our support prioritization meetings or be notified when support sprints are happening, you can sign up the support sprint notification emails [here](https://public.govdelivery.com/accounts/USDOIGS/signup/39118).\n\n Read more about our support processs [here](https://astrogeology.usgs.gov/docs/how-to-guides/software-management/software-support/)"
         stale-issue-label: 'inactive'
         stale-pr-label: 'inactive'
 

.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 && ${{ github.event.label.name == 'bug' }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Bump version
+        run: |
+          git config --global user.name 'ProjectBot'
+          git config --global user.email '[email protected]'
+          CURRENTVERSION=$(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

.zenodo.json

@@ -336,6 +336,10 @@
     {
       "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"
@@ -437,6 +441,10 @@
     {
       "name": "Sucharski, Tracie"
     },
+    {
+      "affiliation": "University of Arizona, Lunar and Planetary Laboratory",
+      "name": "Sutton, Sarah S."
+    },
     {
       "name": "Takir, Driss"
     },

CHANGELOG.md

@@ -35,11 +35,50 @@ release.
 
 ## [Unreleased]
 
-## [8.0.3] - 2023-04-18
+## [8.0.4] - 2024-11-26
+
+### Added
+- Added HRSC support in socetlinescankeywords [#5465](https://github.com/DOI-USGS/ISIS3/issues/5465)
+
+### Changed
+- Skypt has been refactored to be callable; old Makefile tests have been removed and replaced by gtests. Issue: [#5443](https://github.com/USGS-Astrogeology/ISIS3/issues/5443)
+- 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)
+- Changed 'User Parameters' group in camstats to UserParameters for PVL compliance [#5625](https://github.com/DOI-USGS/ISIS3/issues/5625).
+
+### 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 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 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)
+- 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. [#5568](https://github.com/DOI-USGS/ISIS3/pull/5568)
+- 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)
+- Fixed dstripe parallel test failing by converting tests to gtests [#5613](https://github.com/DOI-USGS/ISIS3/issues/5613)
+- Fixed autoseed SeedDomain = SampleLine only working for first overlap [#5673](https://github.com/DOI-USGS/ISIS3/issues/5673)
+
+## [8.0.3] - 2024-04-18
 
 ### Changed
 - Disabled option to use web=true when running spiceinit with HRSC images. [#5223](https://github.com/DOI-USGS/ISIS3/issues/5223)
 - Changed the default spiceinit url to https://astrogeology.usgs.gov/apis/ale/v0.9.1/spiceserver/ and added deprecation warning for use of https://services.isis.astrogeology.usgs.gov/cgi-bin/spiceinit.cgi url. [#5327](https://github.com/USGS-Astrogeology/ISIS3/issues/5327)
+- Skypt has been refactored to be callable; old Makefile tests have been removed and replaced by gtests. Issue: [#5443](https://github.com/USGS-Astrogeology/ISIS3/issues/5443)
 
 ### Fixed
 - Fixed a bug in which capital E was problematic for OSX / Ubuntu [#5466](https://github.com/DOI-USGS/ISIS3/pull/5466)

code.json

@@ -43,6 +43,43 @@
     "date": {
       "metadataLastUpdated": "2023-02-27"
     }
+  }, {
+    "name": "ISIS3",
+    "organization": "U.S. Geological Survey",
+    "description": "GitHub code repository for the Integrated Software for Imagers and Spectrometers (ISIS)",
+    "version": "8.0.4",
+    "status": "Production",
+    "permissions": {
+      "usageType": "openSource",
+      "licenses": [
+        {
+          "name": "Public Domain, CC0-1.0",
+          "URL": "https://code.usgs.gov/astrogeology/isis/-/raw/8.0.4/LICENSE.md"
+        }
+      ]
+    },
+    "homepageURL": "https://isis.astrogeology.usgs.gov",
+    "downloadURL": "https://code.usgs.gov/astrogeology/isis/-/archive/8.0.4/isis-8.0.4.zip",
+    "disclaimerURL": "https://code.usgs.gov/astrogeology/isis/-/raw/8.0.4/DISCLAIMER.md",
+    "repositoryURL": "https://code.usgs.gov/astrogeology/isis.git",
+    "vcs": "git",
+    "laborHours": 0,
+    "tags": [
+      "Planetary",
+      "Remote Sensing",
+      "Photogrammetry",
+      "Data Processing"
+    ],
+    "languages": [
+      "C++"
+    ],
+    "contact": {
+      "name": "Christine Kim",
+      "email": "[email protected]"
+    },
+    "date": {
+      "metadataLastUpdated": "2024-11-26"
+    }
   }, {
     "name": "ISIS3",
     "organization": "U.S. Geological Survey",
@@ -78,7 +115,7 @@
       "email": "[email protected]"
     },
     "date": {
-      "metadataLastUpdated": "2023-04-18"
+      "metadataLastUpdated": "2024-04-18"
     }
   }, {
     "name": "ISIS3",