Sparrow Version 4

.gitignore

@@ -12,4 +12,7 @@ _docker
 .venv/
 
 # Ignore files present on other branches
-backend/shared-modules
+backend/shared-modules
+
+# IDE files
+.idea

.gitmodules

@@ -1,9 +1,6 @@
 [submodule "deps/sadisplay"]
 	path = deps/sadisplay
 	url = https://github.com/davenquinn/sadisplay.git
-[submodule "backend/python-tools"]
-	path = backend/shared-modules
-	url = https://github.com/UW-Macrostrat/python-tools.git
 [submodule "deps/postgis-tile-utils"]
 	path = backend/deps/postgis-tile-utils
 	url = https://github.com/UW-Macrostrat/postgis-tile-utils.git

_cli/pyproject.toml

@@ -16,21 +16,18 @@ envbash = "*"
 pytest = "*"
 pyyaml = "^6.0.1"
 pydantic = "^1.9.0"
-# The below pin of 'docker' ensures that we don't encounter
-# https://github.com/docker/compose/issues/8499
-# It should be deleted when docker-compose dependency is upgraded.
-docker = "^6.0.1"
+docker = "^7.1.0"
 
 click-default-group = "^1.2.2"
 keepachangelog = "2.0.0.dev2"
 packaging = "^23.2"
 
 # Utility functions (we would move this to a separate folder, ideally)
-"macrostrat.utils" = { path = "../backend/shared-modules/utils", develop = true }
+"macrostrat.utils" = "^1.2.1"
 
 # Database backup and schema migration functionality
-"macrostrat.dinosaur" = {path = "../backend/shared-modules/dinosaur", develop = true }
-"macrostrat.database" = {path = "../backend/shared-modules/database", develop = true }
+"macrostrat.dinosaur" = "^3.1.0"
+"macrostrat.database" = "^3.3.1"
 chardet = "^5.1.0"
 charset-normalizer = "2.1.0"
 
@@ -41,4 +38,4 @@ sparrow = "sparrow_cli:cli"
 [tool.black]
 line-length = 88
 skip-magic-trailing-comma = true
-target-version = ['py38']
+target-version = ['py38']

backend/Dockerfile

@@ -12,11 +12,6 @@ WORKDIR /app
 # For shared modules, first copy only requirements to install their dependencies.
 # Poetry must see them as a set of modules.
 COPY poetry.lock pyproject.toml /app/
-COPY __docker/dummy-shared-module-tree /app/shared-modules
-COPY shared-modules/database/pyproject.toml  /app/shared-modules/database/
-COPY shared-modules/dinosaur/pyproject.toml /app/shared-modules/dinosaur/
-COPY shared-modules/utils/pyproject.toml /app/shared-modules/utils/
-COPY shared-modules/pyproject.toml /app/shared-modules/pyproject.toml
 
 RUN mkdir -p /app/loader/sparrow/loader && touch /app/loader/sparrow/loader/__init__.py
 COPY loader/pyproject.toml /app/loader/
@@ -42,7 +37,7 @@ COPY ./docker-scripts/* /bin/
 ## Copy app core
 COPY ./ /app/
 
-RUN poetry install --no-interaction --no-ansi 
+RUN poetry install --no-interaction --no-ansi
 
 # Copy command-line options to a place where they can be easily accessed
 # by the wrapper CLI.

backend/loader/pyproject.toml

@@ -13,13 +13,11 @@ python = "^3.9"
 marshmallow = "^3.20.1"
 marshmallow-sqlalchemy = "^0.29.0"
 marshmallow-jsonschema = "^0.13.0"
-GeoAlchemy2 = "^0.9.4"
-SQLAlchemy = "^1.4.41"
-"macrostrat.database" = "^2.0.1"
+"macrostrat.database" = "^3.3.1"
 stringcase = "^1.2.0"
 shapely = "^1"
 typer = "^0.6.1"
-rich = "^12.6.0"
+rich = "^13"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.1.3"