Repair python docker and ensure GHA actions run on docker updates

.github/workflows/docker-drop-seq_java.yaml

@@ -19,6 +19,7 @@ on:
       - '.github/workflows/docker-drop-seq_java.yaml'
       - 'src/java/**'
       - 'src/tests/java/**'
+      - 'src/docker/java/**'
   workflow_dispatch:
 
 jobs:

.github/workflows/docker-drop-seq_python.yaml

@@ -18,6 +18,7 @@ on:
       - '.github/workflows/docker-drop-seq_reusable.yaml'
       - '.github/workflows/docker-drop-seq_python.yaml'
       - 'src/python/**'
+      - 'src/docker/python/**'
   workflow_dispatch:
 
 jobs:

.github/workflows/docker-drop-seq_r.yaml

@@ -18,6 +18,7 @@ on:
       - '.github/workflows/docker-drop-seq_reusable.yaml'
       - '.github/workflows/docker-drop-seq_r.yaml'
       - 'src/R/**'
+      - 'src/docker/R/**'
   workflow_dispatch:
 
 jobs:

src/docker/python/build/install.sh

@@ -51,7 +51,7 @@ export PATH=$PATH:$uv_dir:$BASEDIR
 
 # Install prerequisites
 echo "Installing prerequisites..."
-apt-get -qq update && apt-get -qq install curl
+apt-get -qq update && apt-get -qq install curl build-essential cmake
 
 # Install uv
 curl -LsSf https://astral.sh/uv/install.sh | env UV_UNMANAGED_INSTALL=$uv_dir sh
@@ -60,5 +60,10 @@ curl -LsSf https://astral.sh/uv/install.sh | env UV_UNMANAGED_INSTALL=$uv_dir sh
 for pyproject_toml in "$envs_dir"/pyproject.toml; do
   env_name=dropseq
   echo "Building $env_name"
-  uv tool install "$envs_dir"
+  # Limit python version to <3.14 until numba issue resolved.
+  # Note that pyproject.toml upper bounds are not respected by uv, so install.sh also needs to be updated too.
+  # See also:
+  #   - https://github.com/numba/numba/issues/9957
+  #   - https://github.com/astral-sh/uv/issues/11506
+  uv tool install --python ">=3.12,<3.14" "$envs_dir"
 done

src/python/pyproject.toml

@@ -25,7 +25,12 @@ authors = [
 ]
 description = "Drop-seq command-line tools and python libraries."
 readme = "README.md"
-requires-python = ">=3.12"
+# Limit python version to <3.14 until numba issue resolved.
+# Note that pyproject.toml upper bounds are not respected by uv, so install.sh also needs to be updated too.
+# See also:
+#   - https://github.com/numba/numba/issues/9957
+#   - https://github.com/astral-sh/uv/issues/11506
+requires-python = ">=3.12,<3.14"
 classifiers = [
     "Programming Language :: Python :: 3",
     "License :: OSI Approved :: MIT License",
@@ -54,5 +59,3 @@ aggregate_filter_adata = "dropseq.hdf5.aggregate_filter_adata:main"
 metacells_from_h5ad = "dropseq.hdf5.metacells_from_h5ad:main"
 kmeans_cluster_effects = "dropseq.effect_clustering.kmeans_effect_clustering:main"
 dropseq_terra_utils = "dropseq.terra_utils.cli:main"
-
-