Assign gis to non-default status

Author: davenquinn

.github/workflows/format-code.yml

@@ -9,8 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v5
-        with:
-          ref: ${{ github.head_ref }}
+
       - name: "Set up Python"
         uses: actions/setup-python@v6
         with:
@@ -26,6 +25,7 @@ jobs:
 
       - name: Run formatting commands
         run: make format
+
       - name: Commit changes
         uses: stefanzweifel/git-auto-commit-action@v5
         with:

Makefile

@@ -1,6 +1,12 @@
 all:
 	# Install all dependencies
-	uv sync --all-groups # Install all optional dependency groups (dev, gis, etc)
+	# Install all optional dependency groups (dev, gis, etc)
+	uv sync
+
+gis:
+	# Install GIS dependencies
+	uv pip install "GDAL==$(shell gdal-config --version)"
+	uv sync --group gis
 
 install:
 	ln -sf $(shell pwd)/bin/macrostrat /usr/local/bin/macrostrat
@@ -13,13 +19,6 @@ test:
 	# These tests may fail due to an older GDAL version in use.
 	# We need to figure out how to bundle GDAL or run in a Docker context
 	uv run macrostrat test all --skip-env -x -s
-	#	poetry run pytest -s -x \
-	#		--ignore=runtime-tests \
-	#		--ignore=services \
-	#		--ignore=v2-transition \
-	#		--ignore=submodules \
-	#		--skip-env \
-	#		.
 
 test-ci:
 	# We need a fairly recent version of GDAL (3.10) for map integration tests to pass.

cli/pyproject.toml

@@ -52,16 +52,19 @@ dependencies = [
 [project.scripts]
 macrostrat = "macrostrat.cli:main"
 
+[project.optional-dependencies]
+gis = [
+    "macrostrat.map-integration[gis]"
+]
+
 [dependency-groups]
-gis = ["macrostrat.map-integration[gis]"]
 dev = [
     "snakeviz>=2.2.0,<3",
     "macrostrat.package_tools>=1.1.0,<2",
 ]
 
 [tool.uv]
 default-groups = [
-    "gis",
     "dev",
 ]
 

map-integration/pyproject.toml

@@ -21,16 +21,18 @@ dependencies = [
     "python-magic>=0.4.27,<0.5",
     "pyyaml~=6.0",
     "shapely>=2.0.1,<3",
+    "macrostrat.core",
 ]
 
 [project.scripts]
 macrostrat-maps = "macrostrat.map_integration:app"
 
-[dependency-groups]
+[project.optional-dependencies]
 gis = [
     "GDAL>=3.10.0,<4",
-    "macrostrat.core",
 ]
+
+[dependency-groups]
 dev = [
     "bandit>=1.7.7,<2",
     "black~=24.2",
@@ -41,7 +43,6 @@ dev = [
 
 [tool.uv]
 default-groups = [
-    "gis",
     "dev",
 ]
 

pyproject.toml

@@ -4,7 +4,7 @@
 [project]
 name = "macrostrat-system"
 version = "0.1.0"
-requires-python = ">=3.11,<4"
+requires-python = ">=3.11,<3.13"
 dependencies = [
     "setuptools>=75.8.2,<76",
     "macrostrat.cli",
@@ -21,7 +21,6 @@ dev = [
 [tool.uv]
 package = false
 default-groups = [
-    "gis",
     "dev",
 ]
 

services/legacy-tileserver/Dockerfile

@@ -73,7 +73,6 @@ WORKDIR /services/main
 RUN --mount=type=cache,target=/root/.cache/uv \
     --mount=type=bind,source=uv.lock,target=uv.lock \
     --mount=type=bind,source=pyproject.toml,target=pyproject.toml \
-    --mount=type=bind,source=deps,target=deps \
     uv sync --locked --no-install-project --no-editable --active
 
 # Add source files to project