tools: update Potree wrapper to 1.2.0

.github/workflows/ci.yaml

@@ -7,7 +7,7 @@ on:
     types: [run-all-tool-tests-command]
 env:
   GALAXY_FORK: galaxyproject
-  GALAXY_BRANCH: release_25.1
+  GALAXY_BRANCH: release_26.0
   MAX_CHUNKS: 40
 jobs:
   setup:
@@ -105,7 +105,7 @@ jobs:
         repository-list: ${{ needs.setup.outputs.repository-list }}
         tool-list: ${{ needs.setup.outputs.tool-list }}
         additional-planemo-options: --biocontainers --skip version_bumped
-    - uses: actions/upload-artifact@v6
+    - uses: actions/upload-artifact@v7
       if: ${{ failure() }}
       with:
         name: 'Tool linting output'
@@ -145,7 +145,7 @@ jobs:
         path: ~/.cache/pip
         key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
     - name: Get number of CPU cores
-      uses: SimenB/github-actions-cpu-cores@v2
+      uses: SimenB/github-actions-cpu-cores@v3
       id: cpu-cores
     - name: Clean dotnet folder for space
       run: rm -Rf /usr/share/dotnet
@@ -162,7 +162,7 @@ jobs:
         galaxy-slots: ${{ steps.cpu-cores.outputs.count }}
         # Limit each test to 15 minutes
         test_timeout: 900
-    - uses: actions/upload-artifact@v6
+    - uses: actions/upload-artifact@v7
       with:
         name: 'Tool test output ${{ matrix.chunk }}'
         path: upload
@@ -181,7 +181,7 @@ jobs:
     # This job runs on Linux
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/download-artifact@v7
+    - uses: actions/download-artifact@v8
       with:
         path: artifacts
     - uses: actions/setup-python@v6
@@ -200,7 +200,7 @@ jobs:
         mode: combine
         html-report: true
         markdown-report: true
-    - uses: actions/upload-artifact@v6
+    - uses: actions/upload-artifact@v7
       with:
         name: 'All tool test results'
         path: upload

.github/workflows/pr.yaml

@@ -17,7 +17,7 @@ on:
       - '*'
 env:
   GALAXY_FORK: galaxyproject
-  GALAXY_BRANCH: release_25.1
+  GALAXY_BRANCH: release_26.0
   MAX_CHUNKS: 4
   MAX_FILE_SIZE: 1M
 concurrency:
@@ -167,7 +167,7 @@ jobs:
         repository-list: ${{ needs.setup.outputs.repository-list }}
         tool-list: ${{ needs.setup.outputs.tool-list }}
         additional-planemo-options: ${{ env.EXTRA_SKIP }}
-    - uses: actions/upload-artifact@v6
+    - uses: actions/upload-artifact@v7
       if: ${{ failure() }}
       with:
         name: 'Tool linting output'
@@ -200,7 +200,7 @@ jobs:
       run: pip install flake8 flake8-import-order
     - name: Flake8
       run: echo '${{ needs.setup.outputs.repository-list }}' | xargs -d '\n' flake8 --output-file pylint_report.txt --tee
-    - uses: actions/upload-artifact@v6
+    - uses: actions/upload-artifact@v7
       if: ${{ failure() }}
       with:
         name: 'Python linting output'
@@ -239,7 +239,7 @@ jobs:
         echo '${{ needs.setup.outputs.repository-list }}' | xargs -d '\n' -n 1 ./.github/styler.R --dry off
         git status
         git diff --exit-code | tee rlint_report.txt
-    - uses: actions/upload-artifact@v6
+    - uses: actions/upload-artifact@v7
       if: ${{ failure() }}
       with:
         name: 'R linting output'
@@ -267,7 +267,7 @@ jobs:
           cat file_size_report.txt
           exit 1
         fi
-    - uses: actions/upload-artifact@v6
+    - uses: actions/upload-artifact@v7
       if: ${{ failure() }}
       with:
         name: 'File size report'
@@ -314,7 +314,7 @@ jobs:
         path: ~/.planemo
         key: planemo_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
     - name: Get number of CPU cores
-      uses: SimenB/github-actions-cpu-cores@v2
+      uses: SimenB/github-actions-cpu-cores@v3
       id: cpu-cores
     - name: Clean dotnet folder for space
       run: rm -Rf /usr/share/dotnet
@@ -330,8 +330,8 @@ jobs:
         chunk-count: ${{ needs.setup.outputs.chunk-count }}
         galaxy-slots: ${{ steps.cpu-cores.outputs.count }}
         # Limit each test to 15 minutes
-        test_timeout: 1800
-    - uses: actions/upload-artifact@v6
+        test_timeout: 900
+    - uses: actions/upload-artifact@v7
       with:
         name: 'Tool test output ${{ matrix.chunk }}'
         path: upload
@@ -350,7 +350,7 @@ jobs:
       matrix:
         python-version: ['3.11']
     steps:
-    - uses: actions/download-artifact@v7
+    - uses: actions/download-artifact@v8
       with:
         path: artifacts
     - uses: actions/setup-python@v6
@@ -369,7 +369,7 @@ jobs:
         mode: combine
         html-report: true
         markdown-report: true
-    - uses: actions/upload-artifact@v6
+    - uses: actions/upload-artifact@v7
       with:
         name: 'All tool test results'
         path: upload
@@ -393,7 +393,6 @@ jobs:
     needs: [setup, lint, combine_outputs]
     if: ${{ (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'bgruening' }}
     runs-on: ubuntu-latest
-    environment: toolshed-deployment
     strategy:
       matrix:
         python-version: ['3.11']
@@ -429,9 +428,8 @@ jobs:
   deploy-report:
     name: Report deploy status
     needs: [deploy]
-    if: ${{ always() && (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) }}
+    if: ${{ always() && (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'bgruening' }}
     runs-on: ubuntu-latest
-    environment: toolshed-deployment
     steps:
     # report to the PR if deployment failed
     - name: Get PR object

.github/workflows/pr_without_tool_change.yaml

@@ -4,9 +4,13 @@ name: Fallback
 # see https://docs.github.com/en/repositories/configuring-branches-and-merges-in-your-repository/defining-the-mergeability-of-pull-requests/troubleshooting-required-status-checks#handling-skipped-but-required-checks
 on:
   pull_request:
+    paths:
+    - 'deprecated/**'
+    - 'docs/**'
+    - '.github/**'
+    - '*'
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: true
 jobs:
   determine-success:
     name: Check workflow success

tools/3dtrees_forestmamba/.shed.yml

@@ -0,0 +1,11 @@
+name: 3dtrees_forestmamba
+owner: bgruening
+description: Forest instance segmentation with ForestMamba.
+homepage_url: https://github.com/3dTrees-earth/3Dtrees_ForestMamba
+long_description: |
+  Performs forest instance and semantic segmentation on LAZ/LAS point clouds using the
+  ForestMamba model.
+remote_repository_url: https://github.com/bgruening/galaxytools/tree/master/tools/3dtrees_forestmamba
+type: unrestricted
+categories:
+- "Geo Science"

tools/3dtrees_forestmamba/forestmamba.xml

@@ -0,0 +1,101 @@
+<tool id="3dtrees_forestmamba" name="3Dtrees: ForestMamba" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2">
+    <description>
+        Forest instance and semantic segmentation of point clouds using the ForestMamba model.
+    </description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.0.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <requirements>
+        <container type="docker">ghcr.io/3dtrees-earth/3dtrees_forestmamba:@TOOL_VERSION@</container>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        mkdir -p output_dir work_dir &&
+        ln -s '$input' 'input.${input.ext}' &&
+        python -u /workspace/src/run.py
+            --dataset-path 'input.${input.ext}'
+            --output-dir output_dir
+            --work-dir work_dir
+            --repo-dir /workspace
+            --checkpoint /workspace/work_dirs/forestmamba_chm_radius16_qp300_2many_v6/v6_epoch_1500_fix.pth
+            --config-base /workspace/configs/ForAINetv2/forestmamba_chm_radius16_qp300_2many_v6.py
+            --preprocess-workers \${GALAXY_SLOTS:-1}
+            --chunk-size '$chunk_size'
+            --semantic-dim '$semantic_dim'
+            --instance-dim '$instance_dim'
+            --score-dim '$score_dim'
+            --bluepoint-iterations '$bluepoint_iterations'
+            #if $bluepoint_score_threshold:
+                --bluepoint-score-threshold '$bluepoint_score_threshold'
+            #end if
+            --bluepoint-second-pass-threshold '$bluepoint_second_pass_threshold'
+            --spatial-match-tolerance '$spatial_match_tolerance'
+    ]]></command>
+    <environment_variables>
+        <environment_variable name="NUMBA_CACHE_DIR">\$_GALAXY_JOB_TMP_DIR</environment_variable>
+        <environment_variable name="WANDB_MODE">disabled</environment_variable>
+    </environment_variables>
+    <inputs>
+        <param name="input" type="data" format="laz,las" label="Input LAZ/LAS point cloud" help="Point cloud to segment with ForestMamba."/>
+        <param argument="--bluepoint-iterations" type="integer" min="0" max="5" value="0" label="Bluepoint iterations" help="0 keeps standard one-pass inference. 2 enables the dense-forest first/second bluepoint pass."/>
+        <param argument="--bluepoint-score-threshold" type="float" min="0" max="1" value="" optional="true" label="Bluepoint score threshold" help="Optional model score_th override for bluepoint rounds."/>
+        <param argument="--bluepoint-second-pass-threshold" type="float" min="0" max="1" value="0.01" label="Second pass threshold" help="Run the second bluepoint pass only when more than this fraction of first-pass points are non-ground with raw instance_pred == -1. Default 0.01 = 1%."/>
+        <param argument="--spatial-match-tolerance" type="float" min="0" value="0.01" label="Spatial match tolerance" help="Maximum coordinate distance used when matching bluepoint predictions back to the input points."/>
+        <param argument="--chunk-size" type="integer" min="1" value="1000000" label="LAZ write chunk size" help="Number of points processed per streamed LAZ read/write chunk."/>
+        <param argument="--semantic-dim" type="text" value="PredSemantic_FM" label="Semantic prediction dimension" help="Output extra dimension name for ForestMamba semantic predictions.">
+            <validator type="regex" message="Only letters, numbers, and underscores are allowed">^[A-Za-z0-9_]+$</validator>
+        </param>
+        <param argument="--instance-dim" type="text" value="PredInstance_FM" label="Instance prediction dimension" help="Output extra dimension name for ForestMamba instance predictions.">
+            <validator type="regex" message="Only letters, numbers, and underscores are allowed">^[A-Za-z0-9_]+$</validator>
+        </param>
+        <param argument="--score-dim" type="text" value="PredScore_FM" label="Score prediction dimension" help="Output extra dimension name for ForestMamba confidence scores.">
+            <validator type="regex" message="Only letters, numbers, and underscores are allowed">^[A-Za-z0-9_]+$</validator>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="laz" from_work_dir="output_dir/input_forestmamba.laz" label="${tool.name} on ${on_string}: Segmented point cloud"/>
+        <data name="summary" format="json" from_work_dir="output_dir/summary.json" label="${tool.name}: summary"/>
+    </outputs>
+    <tests>
+        <!-- GitHub CI has no GPU, so this test is expected to fail there. -->
+        <test expect_failure="true">
+            <param name="input" value="mikro" ftype="laz"/>
+            <assert_stderr>
+                <has_text text="RuntimeError: No CUDA GPUs are available"/>
+            </assert_stderr>
+        </test>
+    </tests>
+    <help format="markdown">
+## What it does
+
+This tool runs ForestMamba on one LAS/LAZ point cloud and writes a segmented
+LAZ output with ForestMamba prediction dimensions.
+
+## Parameters
+
+- **Input LAZ/LAS point cloud**: the point cloud to segment.
+- **Bluepoint iterations**: `0` runs the normal one-pass prediction. `2` enables
+  the dense-forest bluepoint flow: first pass, then an optional second pass on
+  points that remained unassigned.
+- **Bluepoint score threshold**: optional model confidence threshold override
+  for bluepoint runs. Leave empty to use the model/config default.
+- **Second pass threshold**: fraction of first-pass non-ground points with raw
+  `instance_pred == -1` required before the second bluepoint pass runs. The
+  default `0.01` means more than 1%.
+
+## Outputs
+
+- Segmented LAZ with `PredSemantic_FM`, `PredInstance_FM`, and `PredScore_FM`
+  by default.
+- JSON summary of the wrapper run.
+
+Valid ForestMamba instance IDs are preserved. Raw negative instance IDs are
+written as `0` in the final LAZ.
+    </help>
+    <creator>
+        <organization name="3Dtrees-Team, University of Freiburg" url="https://github.com/3dTrees-earth"/>
+    </creator>
+    <citations>
+        <citation type="doi">10.48550/arXiv.2606.01549</citation>
+    </citations>
+</tool>