conversion from poetry to pdm

.gitignore

@@ -162,4 +162,6 @@ cython_debug/
 nwb.schema.json
 __tmp__
 prof
-jupyter_execute
+jupyter_execute
+
+.pdm-python

.readthedocs.yaml

@@ -9,18 +9,24 @@ version: 2
 sphinx:
    configuration: docs/conf.py
 
+python:
+  install:
+    - method: pip
+      path: docs
+
+
 build:
  os: ubuntu-22.04
  tools:
    python: "3.11"
- jobs:
+# jobs:
-   post_create_environment:
+#   post_create_environment:
-     - pip install poetry
+#     - pip install poetry
-     - pip install poetry-kernel
+#     - pip install poetry-kernel
-     - poetry config virtualenvs.create false
+#     - poetry config virtualenvs.create false
-   post_install:
+#   post_install:
-     - poetry install --no-root
+#     - poetry install --no-root
-     #- poetry run python -m ipykernel install --name nwb-linkml_docs
+#     #- poetry run python -m ipykernel install --name nwb-linkml_docs
 
 # Optionally build your docs in additional formats such as PDF and ePub
 # formats:

docs/pyproject.toml

@@ -0,0 +1,39 @@
+[project]
+name = "nwb-linkml-docs"
+version = "0.1.0"
+description = "Dependency management to build nwb-linkml docs, see individual packages for actual package deps"
+authors = [
+    {name = "sneakers-the-rat", email = "JLSaunders987@gmail.com"},
+]
+license = {text = "AGPL-3.0"}
+requires-python = "<3.13,>=3.10"
+dependencies = [
+#    "nwb-linkml",
+#    "nwb-schema-language",
+    "sphinx<8.0.0,>=7.2.5",
+    "furo>=2023.8.19",
+    "myst-parser>=2.0.0",
+    "autodoc-pydantic>=2.0.1",
+    "nptyping>=2.5.0",
+    "sphinx-autobuild>=2021.3.14",
+    "nwb-linkml @ file:///${PROJECT_ROOT}/nwb_linkml",
+    "nwb-schema-language @ file:///${PROJECT_ROOT}/nwb_schema_language",
+    "sphinx-design>=0.5.0",
+    "sphinx-togglebutton>=0.3.2",
+    "myst-nb @ git+https://github.com/executablebooks/MyST-NB.git",
+    "ipykernel>=6.25.2",
+    "ipywidgets>=8.1.1",
+]
+
+[build-system]
+requires = ["pdm-backend"]
+build-backend = "pdm.backend"
+
+[tool.codespell]
+# Ref: https://github.com/codespell-project/codespell#using-a-config-file
+skip = '.git*,*.lock,*.css,./nwb_linkml/src/nwb_linkml/models,./nwb_linkml/src/nwb_linkml/schema'
+check-hidden = true
+# ignore-regex = ''
+# ignore-words-list = ''
+
+

nwb_linkml/pyproject.toml

@@ -1,80 +1,57 @@
-[tool.poetry]
+[project]
 name = "nwb-linkml"
-version = "0.1.0"
 description = "Translating NWB schema language to LinkML"
-authors = ["sneakers-the-rat <JLSaunders987@gmail.com>"]
+version = "0.1.0"
-license = "GPL-3.0"
+authors = [
+    {name = "sneakers-the-rat", email = "sneakers-the-rat@protonmail.me"},
+]
+license = {text = "AGPL-3.0"}
 readme = "README.md"
+requires-python = "<3.13,>=3.10"
+dependencies = [
+    "pyyaml>=6.0",
+    "linkml-runtime>=1.7.7",
+    "nwb-schema-language>=0.1.3",
+    "rich>=13.5.2",
+    "linkml>=1.7.10",
+    "nptyping>=2.5.0",
+    "pydantic>=2.3.0",
+    "h5py>=3.9.0",
+    "pydantic-settings>=2.0.3",
+    "dask>=2023.9.2",
+    "blosc2>=2.2.7",
+    "tqdm>=4.66.1",
+]
+
+[project.urls]
 homepage = "https://nwb-linkml.readthedocs.io"
 repository = "https://github.com/p2p-ld/nwb-linkml/"
 documentation = "https://nwb-linkml.readthedocs.io"
-packages = [
+
-    {include = "nwb_linkml", from="src"},
+[project.optional-dependencies]
-    #{include = "nwb_schema_language", from="../nwb_schema_language/src"}
+plot = [
+    "dash<3.0.0,>=2.12.1",
+    "dash-cytoscape<1.0.0,>=0.3.0",
 ]
-include = [
-    'src/nwb_linkml/schema/**/*'
-]
-
-
-[tool.poetry.dependencies]
-python = ">=3.11,<3.13"
-pyyaml = "^6.0"
-linkml-runtime = "^1.6.0"
-nwb_schema_language = "^0.1.3"
-rich = "^13.5.2"
-linkml = "^1.6.1"
-nptyping = "^2.5.0"
-pydantic = "^2.3.0"
-h5py = "^3.9.0"
-pydantic-settings = "^2.0.3"
-dask = "^2023.9.2"
-blosc2 = "^2.2.7"
-tqdm = "^4.66.1"
-dash = {version="^2.12.1", optional=true}
-dash-cytoscape = {version="^0.3.0", optional=true}
-pytest = { version="^7.4.0", optional=true}
-pytest-depends = {version="^1.0.1", optional=true}
-coverage = {version = "^6.1.1", optional = true}
-pytest-md = {version = "^0.2.0", optional = true}
-pytest-cov = {version = "^4.1.0", optional = true}
-coveralls = {version = "^3.3.1", optional = true}
-pytest-profiling = {version = "^1.7.0", optional = true}
-sybil = {version = "^5.0.3", optional = true}
-
-
-[tool.poetry.extras]
 tests = [
-    "pytest",       "pytest-depends", "coverage",         "pytest-md",
+    "pytest<8.0.0,>=7.4.0",
-    "pytest-cov",   "coveralls",      "pytest-profiling", "sybil"
+    "pytest-depends<2.0.0,>=1.0.1",
+    "coverage<7.0.0,>=6.1.1",
+    "pytest-md<1.0.0,>=0.2.0",
+    "pytest-cov<5.0.0,>=4.1.0",
+    "coveralls<4.0.0,>=3.3.1",
+    "pytest-profiling<2.0.0,>=1.7.0",
+    "sybil<6.0.0,>=5.0.3",
 ]
-plot = ["dash", "dash-cytoscape"]
 
+[tool.pdm]
+distribution = true
 
-[tool.poetry.group.tests]
+[tool.pdm.build]
-optional = true
+includes = ["src/nwb_linkml", "src/nwb_linkml/schema/**/*"]
-
-[tool.poetry.group.tests.dependencies]
-pytest = "^7.4.0"
-pytest-depends = "^1.0.1"
-coverage = "^6.1.1"
-pytest-md = "^0.2.0"
-pytest-cov = "^4.1.0"
-coveralls = "^3.3.1"
-pytest-profiling = "^1.7.0"
-sybil = "^5.0.3"
-
-[tool.poetry.group.plot]
-optional = true
-
-[tool.poetry.group.plot.dependencies]
-dash = "^2.12.1"
-dash-cytoscape = "^0.3.0"
-
 [build-system]
-requires = ["poetry-core"]
+requires = ["pdm-backend"]
-build-backend = "poetry.core.masonry.api"
+build-backend = "pdm.backend"
-
 
 [tool.pytest.ini_options]
 addopts = [
@@ -93,4 +70,4 @@ doctest_optionflags = "NORMALIZE_WHITESPACE"
 filterwarnings = [
     "ignore::DeprecationWarning",
     "ignore:parse_obj:pydantic.PydanticDeprecatedSince20"
-]
+]

nwb_schema_language/pyproject.toml

@@ -1,36 +1,39 @@
-[tool.poetry]
+[project]
-name = "nwb_schema_language"
+name = "nwb-schema-language"
+authors = [
+    {name = "Jonny Saunders", email = "j@nny.fyi"},
+]
+license = {text = "AGPL-3.0"}
+requires-python = "<3.13,>=3.10"
+dependencies = [
+    "linkml-runtime>=1.7.7",
+    "pydantic>=2.3.0",
+]
 version = "0.1.3"
 description = "Translation of the nwb-schema-language to LinkML"
-authors = ["Jonny Saunders <j@nny.fyi>"]
-license = "GNU GPL v3.0"
 readme = "README.md"
+
+[project.urls]
 homepage = "https://nwb-linkml.readthedocs.io"
 repository = "https://github.com/p2p-ld/nwb-linkml/"
 documentation = "https://nwb-linkml.readthedocs.io"
-packages = [
+
-    { include = "nwb_schema_language", from="src"}
+[project.scripts]
+run_patches = "nwb_schema_language.patches:main"
+
+[tool.pdm]
+[tool.pdm.dev-dependencies]
+dev = [
+    "linkml<2.0.0,>=1.3.5",
+    "mkdocs-material<9.0.0,>=8.2.8",
+    "mkdocs-mermaid2-plugin<1.0.0,>=0.6.0",
+    "schemasheets<1.0.0,>=0.1.14",
 ]
-include = ["README.md", "src/nwb_schema_language/schema", "project"]
 
-[tool.poetry.dependencies]
+[tool.pdm.build]
-python = "^3.9"
+includes = ["src/nwb_schema_language", "README.md", "src/nwb_schema_language/schema", "project"]
-linkml-runtime = "^1.1.24"
-pydantic = "^2.3.0"
-
-
-[tool.poetry.dev-dependencies]
-linkml = "^1.3.5"
-mkdocs-material = "^8.2.8"
-mkdocs-mermaid2-plugin = "^0.6.0"
-schemasheets = "^0.1.14"
-
-[tool.poetry.scripts]
-run_patches = 'nwb_schema_language.patches:main'
 
 [build-system]
-requires = ["poetry-core>=1.0.0"]
+requires = ["pdm-backend"]
-build-backend = "poetry.core.masonry.api"
+build-backend = "pdm.backend"
 
-[tool.poetry.extras]
-docs = ["linkml", "mkdocs-material"]

pyproject.toml

@@ -1,39 +1,11 @@
-[tool.poetry]
+[project]
-name = "nwb-linkml-docs"
+description = "Monorepo root for nwb-linkml"
-version = "0.1.0"
+dependencies = []
-description = "Dependency management to build nwb-linkml docs, see individual packages for actual package deps"
+requires-python = "<3.13,>=3.10"
-authors = ["sneakers-the-rat <JLSaunders987@gmail.com>"]
-license = "AGPL-3.0"
-readme = "README.md"
-packages = [
-    {include = "nwb_linkml", from="nwb_linkml/src"},
-    {include = "nwb_schema_language", from="nwb_schema_language/src"}
-]
 
-[tool.poetry.dependencies]
+[tool.pdm.dev-dependencies]
-python = ">=3.11,<3.13"
+dev = [
-sphinx = "^7.2.5"
+    '-e nwb-linkml @ file:///${PROJECT_ROOT}/nwb_linkml',
-furo = "^2023.8.19"
+    '-e nwb-schema-language @ file:///${PROJECT_ROOT}/nwb_schema_language',
-myst-parser = "^2.0.0"
+    '-e docs @ file:///${PROJECT_ROOT}/docs',
-autodoc-pydantic = "^2.0.1"
+]
-nptyping = "^2.5.0"
-sphinx-autobuild = "^2021.3.14"
-nwb-linkml = { path = './nwb_linkml', develop = true }
-nwb_schema_language = { path = './nwb_schema_language', develop = true }
-sphinx-design = "^0.5.0"
-sphinx-togglebutton = "^0.3.2"
-myst-nb = { git = "https://github.com/executablebooks/MyST-NB.git" }
-ipykernel = "^6.25.2"
-ipywidgets = "^8.1.1"
-
-
-[build-system]
-requires = ["poetry-core"]
-build-backend = "poetry.core.masonry.api"
-
-[tool.codespell]
-# Ref: https://github.com/codespell-project/codespell#using-a-config-file
-skip = '.git*,*.lock,*.css,./nwb_linkml/src/nwb_linkml/models,./nwb_linkml/src/nwb_linkml/schema'
-check-hidden = true
-# ignore-regex = ''
-# ignore-words-list = ''