Merge pull request #2328 from microbiomedata/fix-project-dependencies

Ensure dependencies are correctly classified

.github/workflows/deploy-docs.yaml

@@ -21,7 +21,7 @@ jobs:
         uses: snok/[email protected]
 
       - name: Install dependencies.
-        run: poetry install -E docs
+        run: poetry install
 
       # Replace the `0.0.0` placeholder `version` number in various files (per the config in `pyproject.toml`).
       # Reference: https://github.com/mtkennerly/poetry-dynamic-versioning/blob/master/README.md#command-line-mode

.github/workflows/main.yaml

@@ -1,6 +1,5 @@
 # Built from:
 # https://docs.github.com/en/actions/guides/building-and-testing-python
-# https://github.com/snok/install-poetry#workflows-and-tips
 
 name: Build and test nmdc-schema
 
@@ -20,34 +19,28 @@ jobs:
       #       check-out repo and set-up python
       #----------------------------------------------
       - name: Check out repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
+
+      - name: Install Poetry
+        run: pipx install poetry
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-
-      #----------------------------------------------
-      #          install & configure poetry
-      #----------------------------------------------
-      - name: Install Poetry
-        uses: snok/[email protected]
+          cache: 'poetry'
 
       #----------------------------------------------
       # install dependencies if cache does not exist 
       #----------------------------------------------
       - name: Install dependencies
-        run: poetry install --no-interaction --no-root
+        run: poetry install
 
-      #----------------------------------------------
-      #    install your root project, if required 
-      #----------------------------------------------      
-      - name: Install library
-        run: poetry install --no-interaction
+      - name: Check project dependencies
+        run: make check-dependencies
 
       #----------------------------------------------
       #              run test suite   
       #----------------------------------------------
       - name: Run tests
         run: make squeaky-clean all test
-

.github/workflows/test_pages_build.yaml

@@ -29,7 +29,7 @@ jobs:
           version: 1.3.2
 
       - name: Install dependencies
-        run: poetry install -E docs
+        run: poetry install
 
       # Replace the `0.0.0` placeholder `version` number in various files (per the config in `pyproject.toml`).
       # Reference: https://github.com/mtkennerly/poetry-dynamic-versioning/blob/master/README.md#command-line-mode

Makefile

@@ -155,6 +155,10 @@ test-python:
 lint:
 	$(RUN) linkml-lint $(SOURCE_SCHEMA_PATH) > local/lint.log
 
+.PHONY: check-dependencies
+check-dependencies:
+	$(RUN) deptry nmdc_schema --known-first-party nmdc_schema
+
 check-config:
 	@(grep my-datamodel about.yaml > /dev/null && printf "\n**Project not configured**:\n\n - Remember to edit 'about.yaml'\n\n" || exit 0)
 

nmdc_schema/nmdc_version.py

@@ -2,7 +2,9 @@
 # -*- coding: utf-8 -*-
 """Provides CLI to return versions of the NMDC Schema, meta model and pypi package."""
 
-import pkg_resources, click
+from importlib import metadata
+
+import click
 from .nmdc_data import get_nmdc_schema_definition
 
 
@@ -15,7 +17,7 @@ def get_nmdc_schema_package_version() -> str:
     str
         The version of the nmdc_schema package.
     """
-    return pkg_resources.get_distribution("nmdc_schema").version
+    return metadata.version("nmdc_schema")
 
 
 def get_nmdc_schema_version() -> str:

pyproject.toml

@@ -32,35 +32,42 @@ packages = [
 
 [tool.poetry.dependencies] # having trouble with mkdocs in docker esp on linux. addits its ecosystem here may be unnecessary
 python = "^3.9"
+click = "^8"
+click-log = "^0.4.0"
+curies = "^0.9.0"
+deprecated = "^1"
+jsonasobj2 = "^1"
+jsonschema = "^4"
 linkml = "^1.7.10"
 linkml-runtime = "^1.7.7"
-mkdocs = "^1.4.2"
-mkdocs-material = "^9.0.12"
-mkdocs-mermaid2-plugin = "^0.6.0"
-mkdocs-redirects = "^1.2.1"
 pymongo = "^4.7.2"
-ruamel-yaml = "^0.18.6"
+python-dotenv = "*"
+pyyaml = "^6"
+rdflib = "^6.2.0" # some LinkML components are not compatible with rdflib 7+ yet
+requests = "^2"
 
 [tool.poetry.group.dev.dependencies] # are some of these actually required as non-dev dependencies? # cruft for cookiecutter update could be installed with pipx?
 autopep8 = "^2.2.0"
 bandit = "^1.7.8"
 black = ">=23.1,<25.0"
-click = "^8.1.3"
-click-log = "^0.4.0"
 exhaustion-check = "^0.1.1" # for exhaustion-check, pretty-sort-yaml (also get-first-of-first)
 fastjsonschema = "^2.20.0"
 flake8 = "^7.0.0"
 isort = "^5.13.2"
+mkdocs = "^1.4.2"
+mkdocs-material = "^9.0.12"
+mkdocs-mermaid2-plugin = "^0.6.0"
+mkdocs-redirects = "^1.2.1"
 mypy = "^1.10.0"
 pydocstyle = "^6.3.0"
 pylint = "^3.2.2"
 pyroma = "^4.2"
 python-dotenv = "^0.21.0"
-rdflib = "^6.2.0" # some LinkML components are not compatible with rdflib 7+ yet
 # We use `refscan` to generate diagrams of inter-collection relationships.
 # Reference: https://github.com/microbiomedata/refscan
 refscan = "^0.2.0"
 ruff = "^0.4.7"
+ruamel-yaml = "^0.18.6"
 schemasheets = "^0.1.24" # was in main dependencies but brings in so much like pandas
 sheets_and_friends = "^0.5.0" # for do_shuttle (and possibly more)
 sparql-burger = "^1.0.2"
@@ -71,6 +78,8 @@ vulture = "^2.11"
 #oaklib = "^0.5.24"
 #pydantic = "^1.10.13"
 
+[tool.poetry.group.deps.dependencies]
+deptry = "^0.23.0"
 
 [tool.poetry-dynamic-versioning]
 # We need poetry-dynamic-versioning to update the version in the src schema file,
@@ -94,9 +103,6 @@ patterns = [
 requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning"]
 build-backend = "poetry_dynamic_versioning.backend"
 
-[tool.poetry.extras]
-docs = ["mkdocs-material"]
-
 
 # scripts should have click clis
 # click parameters/options should be written out with hyphens