From 449a96e1ad937c716ed2b616758d6c560e098247 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 25 Sep 2025 13:07:54 +0000
Subject: [PATCH 1/4] Initial plan


From c51e6d54ec6269d326004ef251866d6462cced1f Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 25 Sep 2025 13:16:01 +0000
Subject: [PATCH 2/4] Fix Black formatting and CI dependencies issues

Co-authored-by: Ritesh313 <36135489+Ritesh313@users.noreply.github.com>
---
 .github/workflows/ci.yml   | 4 ++--
 scripts/get_dataloaders.py | 4 +---
 2 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 5f8ee83..02a5a1c 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -12,7 +12,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.10', '3.11', '3.12']
 
     steps:
     - uses: actions/checkout@v4
@@ -27,7 +27,7 @@ jobs:
 
     - name: Install dependencies
       run: |
-        uv sync --all-extras
+        uv sync --extra dev --extra logging
 
     - name: Test imports
       run: |
diff --git a/scripts/get_dataloaders.py b/scripts/get_dataloaders.py
index 1e0a0c5..9c87aa4 100644
--- a/scripts/get_dataloaders.py
+++ b/scripts/get_dataloaders.py
@@ -37,9 +37,7 @@
 from neon_tree_classification.core.dataset import NeonCrownDataset
 
 
-DATASET_URL = (
-    "https://www.dropbox.com/scl/fi/v49xi6d7wtetctqphebx0/neon_tree_classification_dataset.zip?rlkey=fb7bz6kd0ckip4u0qd5xdor58&st=dvjyd5ry&dl=1"  
-)
+DATASET_URL = "https://www.dropbox.com/scl/fi/v49xi6d7wtetctqphebx0/neon_tree_classification_dataset.zip?rlkey=fb7bz6kd0ckip4u0qd5xdor58&st=dvjyd5ry&dl=1"
 
 
 def _dataset_exists(dataset_dir: Path) -> bool:

From 6fd54a74755c00b1fa1113b0537319202e7af7d5 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 25 Sep 2025 13:17:45 +0000
Subject: [PATCH 3/4] Add comprehensive CI with processing dependencies and
 update Python requirements

Co-authored-by: Ritesh313 <36135489+Ritesh313@users.noreply.github.com>
---
 .github/workflows/ci.yml | 35 +++++++++++++++++++++++++++++++++++
 pyproject.toml           |  7 +++----
 2 files changed, 38 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 02a5a1c..1b5bc4e 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -41,6 +41,41 @@ jobs:
     - name: Run tests
       run: uv run pytest tests/ -v --tb=short
 
+  test-with-processing:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.11'
+
+    - name: Install R
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y r-base r-base-dev
+
+    - name: Install uv
+      run: pip install uv
+
+    - name: Install all dependencies including processing
+      run: |
+        uv sync --all-extras
+
+    - name: Test processing imports
+      run: |
+        uv run python -c "
+        import neon_tree_classification
+        from neon_tree_classification import NeonCrownDataset
+        print('Core imports successful!')
+        try:
+          import rpy2
+          print('Processing dependencies (rpy2) available!')
+        except ImportError as e:
+          print(f'Processing dependencies not available: {e}')
+        "
+
   lint:
     runs-on: ubuntu-latest
     steps:
diff --git a/pyproject.toml b/pyproject.toml
index 630bdc6..a6c658f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -11,7 +11,7 @@ authors = [
 ]
 license = {text = "MIT"}
 readme = "README.md"
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 keywords = ["neon", "tree-species", "classification", "remote-sensing", "hyperspectral", "lidar", "pytorch-lightning"]
 classifiers = [
     "Development Status :: 4 - Beta",
@@ -19,7 +19,6 @@ classifiers = [
     "License :: OSI Approved :: MIT License",
     "Operating System :: OS Independent",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
@@ -88,7 +87,7 @@ include = ["neon_tree_classification*"]
 
 [tool.black]
 line-length = 88
-target-version = ['py39', 'py310', 'py311', 'py312']
+target-version = ['py310', 'py311', 'py312']
 include = '\.pyi?$'
 extend-exclude = '''
 /(
@@ -118,7 +117,7 @@ filterwarnings = [
 ]
 
 [tool.ruff]
-target-version = "py39"
+target-version = "py310"
 line-length = 88
 select = [
     "E",  # pycodestyle errors

From aab92c81086b50bf73c4f05ce54d96426265218b Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 25 Sep 2025 13:26:27 +0000
Subject: [PATCH 4/4] Fix rpy2 build issue by adding libtirpc-dev dependency

Co-authored-by: Ritesh313 <36135489+Ritesh313@users.noreply.github.com>
---
 .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 1b5bc4e..287bece 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -51,10 +51,10 @@ jobs:
       with:
         python-version: '3.11'
 
-    - name: Install R
+    - name: Install R and development dependencies
       run: |
         sudo apt-get update
-        sudo apt-get install -y r-base r-base-dev
+        sudo apt-get install -y r-base r-base-dev libtirpc-dev
 
     - name: Install uv
       run: pip install uv