Fix dependency specifications for recent uv, avoiding nested workspaces

softboiler · Jan 16, 2025 · 9d552a4 · 9d552a4
1 parent 59ff04d
commit 9d552a4
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Showing 8 changed files with 576 additions and 617 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -2,6 +2,7 @@ exclude: |
   (?x)^(
     \.copier-answers\.yml
     |changelog/towncrier_template\.md\.jinja
+    |lock.*\.json
   )$
 ci:
   skip:
@@ -96,9 +97,16 @@ repos:
             docs/.*\.ipynb
           )$
   - repo: "https://github.com/pre-commit/pre-commit-hooks"
-    rev: "v4.6.0"
+    rev: "v5.0.0"
     hooks:
+      - id: "check-illegal-windows-names"
+      - id: "check-merge-conflict"
+      - id: "destroyed-symlinks"
+      - id: "detect-private-key"
       - id: "end-of-file-fixer"
+      - id: "mixed-line-ending"
+      - id: "trailing-whitespace"
+        args: [--markdown-linebreak-ext=md]
       - id: "trailing-whitespace"
   - repo: "https://github.com/iterative/dvc"
     rev: "3.51.2"
@@ -130,11 +138,11 @@ repos:
   - repo: "https://github.com/rbubley/mirrors-prettier"
     rev: "v3.3.3"
     hooks:
-      - id: "prettier"
+      - id: prettier
   - repo: https://github.com/ComPWA/taplo-pre-commit
-    rev: "v0.9.3"
+    rev: v0.9.3
     hooks:
-      - id: "taplo-format"
+      - id: taplo-format
   - repo: "https://github.com/charliermarsh/ruff-pre-commit"
     rev: "v0.5.1"
     hooks:

diff --git a/.uv-version b/.uv-version
@@ -1 +1 @@
-0.5.2
+0.5.20
diff --git a/justfile b/justfile
@@ -1,18 +1,16 @@
 set shell := ['pwsh', '-Command']
 set dotenv-load
 
+dev := '. ./dev.ps1; '
 pipeline := 'boilercv_pipeline'
 devpy := 'dev'
 
-dev:
-  . ./dev.ps1
-
 boilercv-preview-write file $BOILERCV_PREVIEW='true' $BOILERCV_WRITE='true':
-  iuv python {{file}}
+  {{dev}} iuv python {{file}}
 boilercv-debug-preview-write file $BOILERCV_DEBUG='true' $BOILERCV_PREVIEW='true' $BOILERCV_WRITE='true':
-  iuv python {{file}}
+  {{dev}} iuv python {{file}}
 boilercv-preview preview $BOILERCV_PREVIEW='true':
-  python -m {{pipeline}}.previews.{{preview}}
+  {{dev}} python -m {{pipeline}}.previews.{{preview}}
 
 update-binder:
   (uv pip compile --config-file requirements/binder_uv.toml \
@@ -22,29 +20,29 @@ update-binder:
     requirements/binder.in \
   ) -Replace 'opencv-python', 'opencv-python-headless' | Set-Content requirements.txt
 
-dvc-dag: dev
-  (iuv dvc dag --md) -Replace 'mermaid', '{mermaid}' | Set-Content 'docs/_static/dag.md'
+dvc-dag:
+  {{dev}} (iuv dvc dag --md) -Replace 'mermaid', '{mermaid}' | Set-Content 'docs/_static/dag.md' ;\
   markdownlint-cli2 'docs/_static/dag.md'
 
-generate-correlations file correlations: dev
-  iuv python {{file}} {{correlations}}
-generate-correlation-docs: dev
-  iuv -m boilercv_pipeline.equations.make_docs
+generate-correlations file correlations:
+  {{dev}} iuv python {{file}} {{correlations}}
+generate-correlation-docs:
+  {{dev}} iuv -m boilercv_pipeline.equations.make_docs
 
-hide-notebook-inputs: dev
-  iuv -m {{devpy}}.docs.patch_nbs
+hide-notebook-inputs:
+  {{dev}} iuv -m {{devpy}}.docs.patch_nbs
 
-pipeline-sync-dvc: dev
-  iuv -m {{pipeline}} sync-dvc
+pipeline-sync-dvc:
+  {{dev}} iuv -m {{pipeline}} sync-dvc
 
 remove-empty-data-folders:
   Get-ChildItem -Path './data', 'docs/data' -Recurse -Directory | \
     Where-Object { \
       ( Get-ChildItem -Path $_ -Recurse -File | Measure-Object ).Count -eq 0 \
     } | Remove-Item -Recurse -Force
 
-sync-contrib: dev
-  iuv -Sync -Update
+sync-contrib:
+  {{dev}} iuv -Sync -Update
 
-sync-local-dev-configs: dev
-  {{devpy}} sync-local-dev-configs
+sync-local-dev-configs:
+  {{dev}} {{devpy}} sync-local-dev-configs
diff --git a/packages/_dev/pyproject.toml b/packages/_dev/pyproject.toml
@@ -7,55 +7,49 @@ name = "dev"
 version = "0.0.0"
 description = "Dev"
 dependencies = [
-  # ? Dev
   "cyclopts>=2.9.3",
   "dulwich>=0.22.1",
   "pydantic-settings>=2.5.2",
   "pydantic>=2.9.1",
   "python-dotenv>=1.0.1",
-  # ? Docs
+]
+[project.scripts]
+"dev" = "dev.tools.__main__:main"
+[project.optional-dependencies]
+docs = [
+  "devtools>=0.12.2",
   "docutils>=0.21.2",
+  "geopandas>=0.14.3",
+  "ipython>=8.26.0",
+  "matplotlib>=3.7.2",
   "more-itertools>=10.4.0",
   "myst-parser>=3.0.1",
   "nbformat>=5.10.4",
-  "numpydoc>=1.7.0",
-  "ruamel-yaml>=0.18.6",
-  "sphinx>=7.3.7",
-  # ? Other docs
-  "devtools>=0.12.2",
-  "geopandas>=0.14.3",
-  "ipykernel>=6.29.4",
-  "matplotlib>=3.7.2",
   "numpy>=1.24.4",
+  "numpydoc>=1.7.0",
   "pandas[hdf5,performance]>=2.2.2",
+  "ruamel-yaml>=0.18.6",
   "seaborn>=0.13.2",
   "shapely>=2.0.3",
+  "sphinx>=7.3.7",
   "sympy>=1.12",
   "trackpy>=0.6.2",
-  # ? Tests
-  "pytest-harvest>=1.10.5",
-  "pytest>=8.2.2",
 ]
-[project.scripts]
-"dev" = "dev.tools.__main__:main"
+tests = ["pytest-harvest>=1.10.5", "pytest>=8.2.2"]
 
 [tool.fawltydeps]
 deps = ["packages/_dev/pyproject.toml"]
 code = ["packages/_dev", "docs", "tests"]
 ignore_undeclared = [
-  # ? This project
-  "boilercv",
   # TODO
   "pycine @ git+https://github.com/ottomatic-io/pycine@815cfca06cafc50745a43b2cd0168982225c6dca",
-  # ? Workspaces
-  "dev",
-  "boilercv_pipeline",
+  "boilercv",
   "boilercine",
   "boilercore",
-  "context_models",
-  # ? Path-sourced deps
+  "boilercv_pipeline",
   "cachier",
+  "context_models",
+  "dev",
 ]
 [tool.fawltydeps.custom_mapping]
-ipykernel = ["IPython"]
 ruamel-yaml = ["ruamel"]
diff --git a/packages/pipeline/pyproject.toml b/packages/pipeline/pyproject.toml
@@ -14,7 +14,7 @@ dependencies = [
   "cyclopts>=2.6.1",
   "dvc>=3.55.2",
   "imageio[pyav]>=2.34.1",
-  "ipykernel>=6.29.4",
+  "ipython>=8.26.0",
   "loguru>=0.7.0",
   "matplotlib>=3.7.2",
   "more-itertools>=10.4.0",
@@ -51,21 +51,16 @@ cv = ["opencv-python>=4.10.0.84"]
 deps = ["packages/pipeline/pyproject.toml"]
 code = ["packages/pipeline/boilercv_pipeline"]
 ignore_undeclared = [
-  # ? This project
-  "boilercv",
   # TODO
   "pycine @ git+https://github.com/ottomatic-io/pycine@815cfca06cafc50745a43b2cd0168982225c6dca",
-  # ? Workspaces
-  "dev",
-  "boilercv_pipeline",
+  "boilercv",
   "boilercine",
   "boilercore",
-  "context_models",
-  # ? Path-sourced deps
+  "boilercv_pipeline",
   "cachier",
+  "context_models",
+  "dev",
 ]
 ignore_unused = [
   "pyarrow", # Used in `boilercv_pipeline.__init__`
 ]
-[tool.fawltydeps.custom_mapping]
-ipykernel = ["IPython"]
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,9 +1,13 @@
 [build-system]
-requires = ["flit_core==3.9.0"]
+requires = ["flit-core==3.9.0"]
 build-backend = "flit_core.buildapi"
 
 [project]
 name = "boilercv"
+authors = [
+  { name = "Blake Naccarato", email = "[email protected]" },
+  { name = "Kwang Jin Kim" },
+]
 version = "2024.1.3"
 description = "Computer vision routines suitable for nucleate pool boiling bubble analysis"
 readme = "README.md"
@@ -18,7 +22,6 @@ classifiers = [
   # "Programming Language :: Python :: 3.14",  # ? Not yet beta (https://peps.python.org/pep-0745)
 ]
 dependencies = [
-  # TODO
   "context-models>=0.0.1",
   "matplotlib>=3.7.2",
   "numpy>=1.24.4",
@@ -33,58 +36,50 @@ dependencies = [
   "netcdf4>=1.6.5",
   "netcdf4!=1.7.1.post1 ; sys_platform == 'linux'",
 ]
-[project.optional-dependencies]
-# * Minimal CV flavor needed, but allow `boilercv` to coexist with different flavors
-cv = ["opencv-python>=4.10.0.84"]
 [project.urls]
 Changes = "https://softboiler.github.io/boilercv/changelog.html"
 Docs = "https://softboiler.github.io/boilercv"
 Home = "https://github.com/softboiler/boilercv"
 Tracker = "https://github.com/softboiler/boilercv/issues"
-[[project.authors]]
-name = "Blake Naccarato, Kwang Jin Kim"
-email = "[email protected]"
-
-[tool.uv]
-override-dependencies = ["cachier @ ${PROJECT_ROOT}/packages/cachier"]
-constraint-dependencies = [
-  # ? Security
-  "fiona>=1.10.1",
-  "setuptools>=70.0.0",
-  # ? https://nvd.nist.gov/vuln/detail/CVE-2024-37891
-  # ? via sphinx
-  "urllib3>=2.2.2",
+[project.optional-dependencies]
+# * Minimal CV flavor needed, but allow `boilercv` to coexist with different flavors
+cv = ["opencv-python>=4.10.0.84"]
+[dependency-groups]
+all = [
+  { include-group = "packages" },
+  { include-group = "dev" },
+  { include-group = "docs" },
+  { include-group = "tests" },
 ]
-dev-dependencies = [
-  # TODO
-  "pycine @ git+https://github.com/ottomatic-io/pycine@815cfca06cafc50745a43b2cd0168982225c6dca",
-  # ? Workspaces
+packages = [
   "boilercine",
   "boilercore",
-  "boilercv_pipeline",
-  "context_models",
-  "dev",
-  # ? Path-sourced deps
+  "boilercv-pipeline",
+  "dev[docs,tests]",
   "cachier",
-  # ? Dev
+  "context-models",
+]
+dev = [
+  # TODO
+  "pycine @ git+https://github.com/ottomatic-io/pycine@815cfca06cafc50745a43b2cd0168982225c6dca",
   "debugpy>=1.8.2",
   "dvc[gs]>=3.55.2",
   "fawltydeps>=0.16.0",
-  "ipython>=8.26.0",
+  "ipykernel>=6.29.4",
   "pandas-stubs~=2.2.2",
   "pipdeptree>=2.23.0",
   "pipx>=1.6.0",
-  "pre-commit>=3.7.1",
+  "pre-commit>=4.0.1",
   "pyright>=1.1.371",
   "ruff>=0.5.1",
   "rust-just>=1.36.0",
   "snakeviz>=2.2.0",
   "sourcery>=1.21.0",
   "towncrier>=23.11.0",
-  # ? Docs
+]
+docs = [
   "linkify-it-py>=2.0.3",
   "myst-nb>=1.1.1",
-  "myst-parser>=3.0.1",
   "sphinx-autobuild>=2024.4.16",
   "sphinx-autodoc2>=0.5.0",
   "sphinx-book-theme>=1.1.3",
@@ -95,30 +90,40 @@ dev-dependencies = [
   "sphinxcontrib-bibtex>=2.6.2",
   "sphinxcontrib-mermaid>=0.9.2",
   "sphinxcontrib-towncrier>=0.4.0a0",
-  # ? Tests
+]
+tests = [
   "pytest-cov>=5.0.0",
   "pytest-custom-exit-code>=0.3.0",
   "pytest-github-actions-annotate-failures>=0.2.0",
   "pytest-plt>=1.1.1",
   "pytest-xdist[psutil,setproctitle]>=3.6.1",
 ]
+
+[tool.uv]
+default-groups = ["all"]
+constraint-dependencies = [
+  # ? Security
+  "fiona>=1.10.1",
+  "setuptools>=70.0.0",
+  # ? https://nvd.nist.gov/vuln/detail/CVE-2024-37891
+  # ? via sphinx
+  "urllib3>=2.2.2",
+]
+override-dependencies = ["cachier @ ${PROJECT_ROOT}/packages/cachier"]
 [tool.uv.pip]
 python-version = "3.11"
 all-extras = true
-[tool.uv.workspace]
-members = ["packages/*"]
-exclude = ["packages/cachier"]
 [tool.uv.sources]
+boilercine = { path = "packages/boilercine", editable = true }
+dev = { path = "packages/_dev", editable = true }
+boilercore = { path = "packages/boilercore", editable = true }
+boilercv-pipeline = { path = "packages/pipeline", editable = true }
 cachier = { path = "packages/cachier", editable = true }
-dev = { workspace = true }
-boilercine = { workspace = true }
-boilercore = { workspace = true }
-boilercv_pipeline = { workspace = true }
-context_models = { workspace = true }
+context-models = { path = "packages/context_models", editable = true }
 
 [tool.coverage.run]
 branch = true
-source = ["boilercv", "boilercv_pipeline", "dev", "tests"]
+source = ["dev", "boilercv-pipeline", "boilercv", "tests"]
 
 [tool.dev.env]
 COVERAGE_CORE = "sysmon"