Repository: OpenSaMD/OpenSaMD (language: python)

Issue:
[Stack b.4] Fixing CI using pants
This is now passing CI again.

Docs aren't yet building, and the pyright type checker isn't yet activated again. These will come later, in a separate PR.


Discussion / hints:

Fix patch:
diff --git a/.env b/.env
new file mode 100644
index 00000000..c3a52485
--- /dev/null
+++ b/.env
@@ -0,0 +1,4 @@
+; Generated with (TODO: script this):
+; https://www.pantsbuild.org/docs/setting-up-an-ide#first-party-sources
+
+PYTHONPATH="./src/python/rai:./src/python/raicontours:$PYTHONPATH"
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 87674250..544e32a0 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -7,119 +7,61 @@ on:
   pull_request:
 
 jobs:
-  Build:
-    runs-on: ubuntu-latest
-    timeout-minutes: 60
+  build:
+    name: Perform CI Checks
 
-    defaults:
-      run:
-        working-directory: ./src/python/rai
+    runs-on: ubuntu-20.04
+    timeout-minutes: 60
 
     strategy:
       fail-fast: false
       matrix:
-        task: ["pytest", "docs", "pyright"]
+        python-version: [3.9]
 
     steps:
-      - uses: actions/checkout@v2
-
-      - name: Setup Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
-        with:
-          python-version: "3.10.6"
-
-      - name: Get full Python version
-        id: full-python-version
-        shell: bash
-        run: |
-          echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
-
-      - name: Get pip cache dir
-        id: pip-cache
-        run: |
-          python -m pip install -U pip # to ensure version > 20 to have cache dir
-          echo "::set-output name=dir::$(pip cache dir)"
+      - uses: actions/checkout@v3
 
-      - name: Pip cache
-        uses: actions/cache@v2
+      - uses: pantsbuild/actions/init-pants@v2
         with:
-          path: ${{ steps.pip-cache.outputs.dir }}
-          key: pip-${{ matrix.task }}-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}
+          pants-python-version: ${{ matrix.python-version }}
+          gha-cache-key: cache0-py${{ matrix.python-version }}
+          named-caches-hash: ${{ hashFiles('3rdparty/python/default.lock') }}
+          cache-lmdb-store: "false"
 
-      - name: Upgrade pip and setuptools
+      - name: Check BUILD files
         run: |
-          pip install --upgrade pip setuptools
-
-      - name: Install Poetry
-        uses: snok/install-poetry@v1
-        with:
-          version: 1.2.1
-          virtualenvs-create: true
+          ./pants tailor --check update-build-files --check ::
 
-      - name: Configure Poetry to not use experimental installer
+      - name: Lint and typecheck
         run: |
-          poetry config experimental.new-installer false
-
-      - name: Configure Poetry
-        run: |
-          poetry config virtualenvs.in-project true
-
-      - name: Poetry cache
-        uses: actions/cache@v3
-        id: poetry-cache
-        with:
-          path: .venv
-          key: venv-${{ matrix.task }}-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('**/poetry.lock') }}
+          ./pants lint check ::
 
-      # This is from <https://github.com/python-poetry/poetry/blob/639d5e057/.github/workflows/main.yml#L57-L60>
-      - name: Ensure cache is healthy
-        if: steps.poetry-cache.outputs.cache-hit == 'true'
-        shell: bash
+      - name: Test
         run: |
-          timeout 10s poetry run pip --version || rm -rf .venv
+          ./pants test ::
 
-      - name: Poetry install
+      - name: Package
         run: |
-          poetry install
-
-      # =======
-      # PyRight
-      # =======
-
-      - name: Run PyRight
-        if: matrix.task == 'pyright'
-        run: |
-          poetry run pyright
-
-      # ======
-      # PyTest
-      # ======
-
-      - name: Run PyTest
-        if: matrix.task == 'pytest'
-        run: |
-          poetry run pytest --pylint --doctest-modules
-
-      # ====
-      # Docs
-      # ====
-
-      - name: Build docs
-        if: matrix.task == 'docs'
-        run: |
-          [[ ! -d docs/_build/html ]]
-          poetry run rai docs
-          [[ -d docs/_build/html ]]
-
-      - name: Add GitHub Pages config files
-        if: github.event_name == 'push' && matrix.task == 'docs'
-        run: |
-          echo docs.radiotherapy.ai > docs/_build/html/CNAME
-          touch docs/_build/html/.nojekyll
-
-      - name: Deploy to gh-pages branch
-        if: github.event_name == 'push' && matrix.task == 'docs'
-        uses: JamesIves/github-pages-deploy-action@4.1.3
-        with:
-          branch: gh-pages
-          folder: docs/_build/html
+          ./pants package ::
+
+      # TODO: Add docs building back in
+
+      # - name: Build docs
+      #   if: matrix.task == 'docs'
+      #   run: |
+      #     [[ ! -d docs/_build/html ]]
+      #     poetry run rai docs
+      #     [[ -d docs/_build/html ]]
+
+      # - name: Add GitHub Pages config files
+      #   if: github.event_name == 'push' && matrix.task == 'docs'
+      #   run: |
+      #     echo docs.radiotherapy.ai > docs/_build/html/CNAME
+      #     touch docs/_build/html/.nojekyll
+
+      # - name: Deploy to gh-pages branch
+      #   if: github.event_name == 'push' && matrix.task == 'docs'
+      #   uses: JamesIves/github-pages-deploy-action@4.1.3
+      #   with:
+      #     branch: gh-pages
+      #     folder: docs/_build/html
diff --git a/.gitignore b/.gitignore
index af52fb9a..a0292f4f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -102,7 +102,6 @@ celerybeat.pid
 *.sage.py
 
 # Environments
-.env
 .venv
 env/
 venv/
diff --git a/.vscode/workspace.code-workspace b/.vscode/workspace.code-workspace
index 2a2b9e13..c1b42994 100644
--- a/.vscode/workspace.code-workspace
+++ b/.vscode/workspace.code-workspace
@@ -56,6 +56,7 @@
       "Bronchpulm",
       "Bronchpulms",
       "BRTO",
+      "buildroot",
       "capa",
       "Cartlg",
       "Cavernosum",
@@ -190,13 +191,13 @@
       "tmpl",
       "tomlkit",
       "Trachbrnchs",
+      "typecheck",
       "Unported",
       "Venacava",
       "venv",
       "virtualenvs",
       "Vomer",
       "waivable",
-      "waivable",
       "Wouter",
       "Zygomatic",
       "Zygomatics"
diff --git a/3rdparty/python/BUILD b/3rdparty/python/BUILD
new file mode 100644
index 00000000..b8519ce5
--- /dev/null
+++ b/3rdparty/python/BUILD
@@ -0,0 +1,3 @@
+python_requirements(
+    name="reqs",
+)
diff --git a/3rdparty/python/black.lock b/3rdparty/python/black.lock
new file mode 100644
index 00000000..33dfa38e
--- /dev/null
+++ b/3rdparty/python/black.lock
@@ -0,0 +1,228 @@
+// This lockfile was autogenerated by Pants. To regenerate, run:
+//
+//    ./pants generate-lockfiles --resolve=black
+//
+// --- BEGIN PANTS LOCKFILE METADATA: DO NOT EDIT OR REMOVE ---
+// {
+//   "version": 3,
+//   "valid_for_interpreter_constraints": [
+//     "CPython==3.9.15"
+//   ],
+//   "generated_with_requirements": [
+//     "black==22.6.0",
+//     "typing-extensions>=3.10.0.0; python_version < \"3.10\""
+//   ],
+//   "manylinux": "manylinux2014",
+//   "requirement_constraints": [],
+//   "only_binary": [],
+//   "no_binary": []
+// }
+// --- END PANTS LOCKFILE METADATA ---
+
+{
+  "allow_builds": true,
+  "allow_prereleases": false,
+  "allow_wheels": true,
+  "build_isolation": true,
+  "constraints": [],
+  "locked_resolves": [
+    {
+      "locked_requirements": [
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+            },
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diff --git a/3rdparty/python/default.lock b/3rdparty/python/default.lock
new file mode 100644
index 00000000..9d63e4a7
--- /dev/null
+++ b/3rdparty/python/default.lock
@@ -0,0 +1,1313 @@
+// This lockfile was autogenerated by Pants. To regenerate, run:
+//
+//    ./pants generate-lockfiles --resolve=python-default
+//
+// --- BEGIN PANTS LOCKFILE METADATA: DO NOT EDIT OR REMOVE ---
+// {
+//   "version": 3,
+//   "valid_for_interpreter_constraints": [
+//     "CPython==3.9.15"
+//   ],
+//   "generated_with_requirements": [
+//     "black",
+//     "click",
+//     "matplotlib",
+//     "numpy",
+//     "pydicom",
+//     "pylint",
+//     "scikit-image",
+//     "shapely",
+//     "tomlkit",
+//     "typing_extensions"
+//   ],
+//   "manylinux": "manylinux2014",
+//   "requirement_constraints": [],
+//   "only_binary": [],
+//   "no_binary": []
+// }
+// --- END PANTS LOCKFILE METADATA ---
+
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+  "prefer_older_binary": false,
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+  ],
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+    "==3.9.15"
+  ],
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diff --git a/3rdparty/python/requirements.txt b/3rdparty/python/requirements.txt
new file mode 100644
index 00000000..9df54fbb
--- /dev/null
+++ b/3rdparty/python/requirements.txt
@@ -0,0 +1,14 @@
+# User
+black
+click
+matplotlib
+numpy
+pydicom
+shapely
+scikit-image
+tomlkit
+typing_extensions
+
+# Dev
+# TODO: Shouldn't need this here as pants has its own location for it
+pylint
diff --git a/3rdparty/python/user_reqs.lock b/3rdparty/python/user_reqs.lock
deleted file mode 100644
index 56fdb187..00000000
--- a/3rdparty/python/user_reqs.lock
+++ /dev/null
@@ -1,42 +0,0 @@
-// This lockfile was autogenerated by Pants. To regenerate, run:
-//
-//    ./pants generate-lockfiles --resolve=python-default
-//
-// --- BEGIN PANTS LOCKFILE METADATA: DO NOT EDIT OR REMOVE ---
-// {
-//   "version": 3,
-//   "valid_for_interpreter_constraints": [
-//     "CPython==3.9.15"
-//   ],
-//   "generated_with_requirements": [],
-//   "manylinux": "manylinux2014",
-//   "requirement_constraints": [],
-//   "only_binary": [],
-//   "no_binary": []
-// }
-// --- END PANTS LOCKFILE METADATA ---
-
-{
-  "allow_builds": true,
-  "allow_prereleases": false,
-  "allow_wheels": true,
-  "build_isolation": true,
-  "constraints": [],
-  "locked_resolves": [],
-  "path_mappings": {},
-  "pex_version": "2.1.108",
-  "pip_version": "20.3.4-patched",
-  "prefer_older_binary": false,
-  "requirements": [],
-  "requires_python": [
-    "==3.9.15"
-  ],
-  "resolver_version": "pip-2020-resolver",
-  "style": "universal",
-  "target_systems": [
-    "linux",
-    "mac"
-  ],
-  "transitive": true,
-  "use_pep517": null
-}
diff --git a/pants.toml b/pants.toml
index b0042a50..f95b692f 100644
--- a/pants.toml
+++ b/pants.toml
@@ -1,16 +1,25 @@
 [GLOBAL]
 pants_version = "2.14.0"
 backend_packages = [
-  "pants.backend.shell",
   "pants.backend.python",
   "pants.backend.python.lint.black",
-  "pants.backend.python.lint.bandit",
-  "pants.backend.python.lint.docformatter",
   "pants.backend.python.lint.isort",
   "pants.backend.python.lint.pylint",
-  "pants.backend.python.typecheck.mypy",
+
+  # TODO: Include this once it lands
+  # "pants.backend.python.typecheck.pyright"
+
+  # TODO: Include the following in their own PRs later on
+  # "pants.backend.experimental.python.lint.pyupgrade",
+  # "pants.backend.python.lint.docformatter",
+  # "pants.backend.python.lint.bandit",
+  # "pants.backend.experimental.python.lint.autoflake",
+  # "pants.backend.python.lint.flake8",
 ]
 
+[GLOBAL.pants_ignore]
+add = ["records/"]
+
 [anonymous-telemetry]
 enabled = true
 repo_id = "ad4dd1f1-8c32-4d36-9bb3-71a966bbc771"
@@ -24,12 +33,26 @@ root_patterns = [
 # TODO: Propagate this from to/from .tool-versions
 interpreter_constraints = ["==3.9.15"]
 enable_resolves = true
-resolves = { python-default = "3rdparty/python/user_reqs.lock"}
+resolves = { python-default = "3rdparty/python/default.lock"}
+
+# [pyupgrade]
+# args = ["--py39-plus"]
 
 [python-infer]
 assets = true
 unowned_dependency_behavior = "error"
 
+[black]
+lockfile = "3rdparty/python/black.lock"
+
+[isort]
+args = ["--profile", "black", "-p", "rai", "-p", "raicontours"]
+lockfile = "3rdparty/python/isort.lock"
+
+[pylint]
+args = ["--ignore-patterns=.*.pyi"]
+lockfile = "3rdparty/python/pylint.lock"
+
 [pytest]
 args = ["--no-header"]
 lockfile = "3rdparty/python/pytest.lock"
@@ -44,4 +67,4 @@ add = [
 ]
 
 [python-bootstrap]
-search_path = ["<ASDF_LOCAL>"]
+search_path = ["<ASDF_LOCAL>", "<ASDF>", "<PYENV>", "<PATH>"]
diff --git a/src/python/rai/README.md b/src/python/rai/README.md
index 45a794dd..2f8eb34d 100644
--- a/src/python/rai/README.md
+++ b/src/python/rai/README.md
@@ -24,7 +24,7 @@ achieve.
 
 This open source research library is able to be installed by running:
 
-```
+```bash
 pip install rai
 ```
 
diff --git a/src/python/rai/poetry.lock b/src/python/rai/poetry.lock
deleted file mode 100644
index 4cf0c7c7..00000000
--- a/src/python/rai/poetry.lock
+++ /dev/null
@@ -1,4945 +0,0 @@
-[[package]]
-name = "absl-py"
-version = "1.3.0"
-description = "Abseil Python Common Libraries, see https://github.com/abseil/abseil-py."
-category = "main"
-optional = false
-python-versions = ">=3.6"
-
-[[package]]
-name = "alabaster"
-version = "0.7.12"
-description = "A configurable sidebar-enabled Sphinx theme"
-category = "dev"
-optional = false
-python-versions = "*"
-
-[[package]]
-name = "anyio"
-version = "3.6.2"
-description = "High level compatibility layer for multiple asynchronous event loop implementations"
-category = "dev"
-optional = false
-python-versions = ">=3.6.2"
-
-[package.dependencies]
-idna = ">=2.8"
-sniffio = ">=1.1"
-
-[package.extras]
-doc = ["packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"]
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-]
-zipp = [
-    {file = "zipp-3.11.0-py3-none-any.whl", hash = "sha256:83a28fcb75844b5c0cdaf5aa4003c2d728c77e05f5aeabe8e95e56727005fbaa"},
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diff --git a/src/python/rai/pyproject.toml b/src/python/rai/pyproject.toml
deleted file mode 100644
index 972e2c3b..00000000
--- a/src/python/rai/pyproject.toml
+++ /dev/null
@@ -1,102 +0,0 @@
-[tool.poetry]
-name = "rai"
-version = "0.2.0-dev12"
-readme = "README.md"
-description = "AI assisted treatments accessible to all"
-authors = ["Simon Biggs <simon.biggs@radiotherapy.ai>"]
-license = "AGPL-3.0-or-later"
-
-homepage = "https://radiotherapy.ai"
-repository = "https://github.com/RadiotherapyAI/rai"
-documentation = "https://docs.radiotherapy.ai"
-
-classifiers = [
-    "Development Status :: 4 - Beta",
-    "Topic :: Scientific/Engineering :: Medical Science Apps.",
-    "Topic :: Scientific/Engineering :: Physics",
-    "Intended Audience :: Science/Research",
-    "Intended Audience :: Healthcare Industry",
-]
-
-[tool.poetry.dependencies]
-# Upper pinning here is being forced on us by scipy. We don't want to do this.
-# Ideally find a way to not upper pin if possible. See the following for more
-# details:
-# https://iscinumpy.dev/post/bound-version-constraints/#pinning-the-python-version-is-special
-
-# TODO: Create a release CLI that temporarily removes these bounds prior to
-# release.
-python = ">=3.8,<3.11"
-
-# We keep all version constraints as broad as possible for the library release.
-# For the application release, all versions are pinned and tightly controlled.
-# But that is managed within the `poetry.lock` file, not here. See
-# https://iscinumpy.dev/post/app-vs-library/ and
-# https://iscinumpy.dev/post/bound-version-constraints/ for more info.
-click = "*"
-cryptography = "*"
-numba = "*"
-numpy = ">=1.23.0"
-pydicom = "*"
-scikit-image = "*"
-scipy = "*"
-shapely = "*"
-tqdm = "*"
-
-# Using directml plugin on Windows makes install nearly seamless
-tensorflow = { version = "*", markers = "platform_system != \"Windows\"" }
-tensorflow-intel = { version = "*", markers = "platform_system == \"Windows\"" }
-tensorflow-directml-plugin = { version = "*", markers = "platform_system == \"Windows\"" }
-
-# Pin while the model is likely to change significantly from one version to the
-# next, and also pinning while raicontours is utilising development releases.
-raicontours = "0.3.0-dev6"
-
-[tool.poetry.dev-dependencies]
-black = "*"
-blackdoc = "*"
-ipykernel = "*"
-jupyter-book = "*"
-matplotlib = "*"
-mypy = "*"
-pre-commit = "*"
-pylint = "*"
-pyoxidizer = "*"
-pyright = "*"
-pytest = "*"
-pytest-pylint = "*"
-tomlkit = "*"
-
-[tool.poetry.scripts]
-rai = "rai.__main__:cli"
-
-[tool.pyright]
-include = ["rai"]
-exclude = [
-    "**/node_modules",
-    "**/__pycache__",
-]
-typeCheckingMode = "strict"
-
-[tool.isort]
-multi_line_output = 3
-line_length = 88
-include_trailing_comma = true
-force_grid_wrap = 0
-use_parentheses = true
-ensure_newline_before_comments = true
-
-known_second_party = ["raicontours"]
-known_first_party = ["rai"]
-sections = [
-    "FUTURE",
-    "STDLIB",
-    "THIRDPARTY",
-    "SECOND_PARTY",
-    "FIRSTPARTY",
-    "LOCALFOLDER",
-]
-
-[build-system]
-requires = ["poetry-core>=1.0.0"]
-build-backend = "poetry.core.masonry.api"
diff --git a/src/python/rai/rai/BUILD b/src/python/rai/rai/BUILD
new file mode 100644
index 00000000..db46e8d6
--- /dev/null
+++ b/src/python/rai/rai/BUILD
@@ -0,0 +1,1 @@
+python_sources()
diff --git a/src/python/rai/rai/_cli/BUILD b/src/python/rai/rai/_cli/BUILD
new file mode 100644
index 00000000..db46e8d6
--- /dev/null
+++ b/src/python/rai/rai/_cli/BUILD
@@ -0,0 +1,1 @@
+python_sources()
diff --git a/src/python/rai/rai/_cli/propagate.py b/src/python/rai/rai/_cli/propagate.py
index bbcff4f8..7b4169f5 100644
--- a/src/python/rai/rai/_cli/propagate.py
+++ b/src/python/rai/rai/_cli/propagate.py
@@ -25,7 +25,7 @@
 import tomlkit
 from typing_extensions import Literal
 
-from rai._paths import RAICONTOURS_REPO_ROOT, REPO_ROOT
+from rai._paths import RAICONTOURS_DIR, REPO_ROOT
 
 PyProjectContents = Dict[
     Literal["tool"], Dict[Literal["poetry"], Dict[Literal["version"], str]]
@@ -41,7 +41,7 @@ def run():
     """Undergo data propagation."""
     _propagate_python_version(REPO_ROOT)
     _propagate_product_version(REPO_ROOT, update_docs=True)
-    _propagate_product_version(RAICONTOURS_REPO_ROOT, update_docs=False)
+    _propagate_product_version(RAICONTOURS_DIR, update_docs=False)
 
 
 def _propagate_python_version(repo_root: pathlib.Path):
diff --git a/src/python/rai/rai/_paths.py b/src/python/rai/rai/_paths.py
index 664c6a29..2225f5e8 100644
--- a/src/python/rai/rai/_paths.py
+++ b/src/python/rai/rai/_paths.py
@@ -18,14 +18,21 @@
 
 import pathlib
 
-HERE = pathlib.Path(__file__)
-REPO_ROOT = pathlib.Path(HERE.parents[4])
-DOCS_DIR = REPO_ROOT / "docs"
-LIBRARY_DIR = pathlib.Path(HERE.parents[1])
-
+HOME = pathlib.Path.home()
 RAI_HOME_DIR = pathlib.Path.home() / ".rai"
 RAI_DATA = RAI_HOME_DIR / "data"
 
-PYTHON_PACKAGES_DIR = pathlib.Path(HERE.parents[2])
-RAICONTOURS_REPO_ROOT = PYTHON_PACKAGES_DIR / "raicontours"
-RAICONTOURS_LIBRARY_DIR = RAICONTOURS_REPO_ROOT / "raicontours"
+# TODO: Need a robust way to get the repo directory when using pants
+
+REPO_ROOT = pathlib.Path("/home/runner/work/OpenSaMD/OpenSaMD")
+
+if not REPO_ROOT.exists():
+    REPO_ROOT = HOME / "git" / "OpenSaMD"
+
+DOCS_DIR = REPO_ROOT / "docs"
+PYTHON_PACKAGES_DIR = REPO_ROOT / "src" / "python"
+
+RAI_DIR = PYTHON_PACKAGES_DIR / "rai"
+RAICONTOURS_DIR = PYTHON_PACKAGES_DIR / "raicontours"
+
+TEST_RECORDS_DIR = REPO_ROOT / "records" / "tests" / "python"
diff --git a/src/python/rai/rai/data/BUILD b/src/python/rai/rai/data/BUILD
new file mode 100644
index 00000000..db46e8d6
--- /dev/null
+++ b/src/python/rai/rai/data/BUILD
@@ -0,0 +1,1 @@
+python_sources()
diff --git a/src/python/rai/rai/data/download.py b/src/python/rai/rai/data/download.py
index 096ce302..b2610bff 100644
--- a/src/python/rai/rai/data/download.py
+++ b/src/python/rai/rai/data/download.py
@@ -20,7 +20,7 @@
 import pathlib
 import urllib.parse
 import urllib.request
-from typing import List, Union, NamedTuple
+from typing import List, NamedTuple, Union
 
 from rai._paths import RAI_DATA
 
diff --git a/src/python/rai/rai/dicom/BUILD b/src/python/rai/rai/dicom/BUILD
new file mode 100644
index 00000000..db46e8d6
--- /dev/null
+++ b/src/python/rai/rai/dicom/BUILD
@@ -0,0 +1,1 @@
+python_sources()
diff --git a/src/python/rai/rai/mask/BUILD b/src/python/rai/rai/mask/BUILD
new file mode 100644
index 00000000..0eea8b1c
--- /dev/null
+++ b/src/python/rai/rai/mask/BUILD
@@ -0,0 +1,5 @@
+python_sources()
+
+python_tests(
+    name="tests",
+)
diff --git a/src/python/rai/rai/metrics/BUILD b/src/python/rai/rai/metrics/BUILD
new file mode 100644
index 00000000..0eea8b1c
--- /dev/null
+++ b/src/python/rai/rai/metrics/BUILD
@@ -0,0 +1,5 @@
+python_sources()
+
+python_tests(
+    name="tests",
+)
diff --git a/src/python/rai/rai/vendor/fma/BUILD b/src/python/rai/rai/vendor/fma/BUILD
new file mode 100644
index 00000000..db46e8d6
--- /dev/null
+++ b/src/python/rai/rai/vendor/fma/BUILD
@@ -0,0 +1,1 @@
+python_sources()
diff --git a/src/python/rai/typings/shapely/geometry/BUILD b/src/python/rai/typings/shapely/geometry/BUILD
new file mode 100644
index 00000000..db46e8d6
--- /dev/null
+++ b/src/python/rai/typings/shapely/geometry/BUILD
@@ -0,0 +1,1 @@
+python_sources()
diff --git a/src/python/rai/typings/shapely/geometry/polygon.pyi b/src/python/rai/typings/shapely/geometry/polygon.pyi
index adfa4200..545ce97d 100644
--- a/src/python/rai/typings/shapely/geometry/polygon.pyi
+++ b/src/python/rai/typings/shapely/geometry/polygon.pyi
@@ -1,6 +1,7 @@
-from numpy.typing import NDArray
 from typing import Any, Optional, Union
 
+from numpy.typing import NDArray
+
 from .base import BaseGeometry
 
 class Polygon(BaseGeometry):
diff --git a/src/python/rai/typings/skimage/draw/BUILD b/src/python/rai/typings/skimage/draw/BUILD
new file mode 100644
index 00000000..db46e8d6
--- /dev/null
+++ b/src/python/rai/typings/skimage/draw/BUILD
@@ -0,0 +1,1 @@
+python_sources()
diff --git a/src/python/rai/typings/skimage/measure/BUILD b/src/python/rai/typings/skimage/measure/BUILD
new file mode 100644
index 00000000..db46e8d6
--- /dev/null
+++ b/src/python/rai/typings/skimage/measure/BUILD
@@ -0,0 +1,1 @@
+python_sources()
diff --git a/src/python/raicontours/poetry.lock b/src/python/raicontours/poetry.lock
deleted file mode 100644
index 772b2e3d..00000000
--- a/src/python/raicontours/poetry.lock
+++ /dev/null
@@ -1,717 +0,0 @@
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-[package.extras]
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-[[package]]
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-zipp = [
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diff --git a/src/python/raicontours/pyproject.toml b/src/python/raicontours/pyproject.toml
deleted file mode 100644
index 5756b3b5..00000000
--- a/src/python/raicontours/pyproject.toml
+++ /dev/null
@@ -1,42 +0,0 @@
-[tool.poetry]
-name = "raicontours"
-version = "0.3.0-dev7"
-description = ""
-authors = ["Simon Biggs <simon.biggs@radiotherapy.ai>"]
-license = "AGPL-3.0-or-later"
-readme = "README.md"
-
-[tool.poetry.dependencies]
-python = ">=3.7"
-pydicom = "*"
-typing-extensions = "*"
-
-[tool.poetry.dev-dependencies]
-black = "*"
-blackdoc = "*"
-pyright = "*"
-pylint = "*"
-mypy = "*"
-pre-commit = "*"
-
-
-[tool.pyright]
-include = ["raicontours"]
-exclude = [
-    "**/node_modules",
-    "**/__pycache__",
-]
-typeCheckingMode = "strict"
-
-[tool.isort]
-multi_line_output = 3
-line_length = 88
-include_trailing_comma = true
-force_grid_wrap = 0
-use_parentheses = true
-ensure_newline_before_comments = true
-
-
-[build-system]
-requires = ["poetry-core"]
-build-backend = "poetry.core.masonry.api"
diff --git a/src/python/raicontours/raicontours/BUILD b/src/python/raicontours/raicontours/BUILD
new file mode 100644
index 00000000..db46e8d6
--- /dev/null
+++ b/src/python/raicontours/raicontours/BUILD
@@ -0,0 +1,1 @@
+python_sources()
diff --git a/src/python/raicontours/raicontours/__init__.py b/src/python/raicontours/raicontours/__init__.py
index d4d55b25..df53c632 100644
--- a/src/python/raicontours/raicontours/__init__.py
+++ b/src/python/raicontours/raicontours/__init__.py
@@ -16,6 +16,8 @@
 
 # pylint: disable = invalid-name, useless-import-alias
 
+"""RAiContours model package"""
+
 from __future__ import annotations
 
 import json
@@ -39,12 +41,16 @@
 
 
 class UtilisationRecord(str, Enum):
+    """Representation of dataset training or validation"""
+
     Training = "training"
     Validation = "validation"
     NotUsed = "not-used"
 
 
 def dicom_utilisation(ds: pydicom.Dataset):
+    """Determine the utilisation status of a given pydicom dataset"""
+
     training, validation = _training_record()
 
     study_uid = ds.StudyInstanceUID
@@ -69,15 +75,15 @@ def _training_record() -> Tuple[Set[str], Set[str]]:
     return training, validation
 
 
-class ContourOptions(TypedDict, total=False):
-    from_mask: TG263
-    mask_level: float
-    union: list[StructureName]
-    difference: list[StructureName]
-    intersection: list[StructureName]
-    # buffer: float
-    colour: str
-    display: bool
+# class ContourOptions(TypedDict, total=False):
+#     from_mask: TG263
+#     mask_level: float
+#     union: list[StructureName]
+#     difference: list[StructureName]
+#     intersection: list[StructureName]
+#     # buffer: float
+#     colour: str
+#     display: bool
 
 
 class Config(TypedDict):
@@ -98,6 +104,8 @@ class Config(TypedDict):
 
 
 def get_config():
+    """Get the raicontours configuration"""
+
     # By (re)creating cfg within a function, separate cfg instances are
     # protected from mutating each other.
     cfg: Config = {
@@ -197,6 +205,12 @@ def get_config():
 
 
 def get_mask_level(cfg: Config, structure_name: StructureName):
+    """Determine the configuration mask level for a given structure.
+
+    This defaults to cfg['mask_level'] while taking into account the
+    individual structure overrides within cfg['mask_level_overrides'].
+    """
+
     try:
         mask_level = cfg["mask_level_overrides"][structure_name]
     except KeyError:
@@ -205,9 +219,8 @@ def get_mask_level(cfg: Config, structure_name: StructureName):
     return mask_level
 
 
-# TODO: Add a "uids used for training" list and use it to verify a DICOM
-# file can be used for metric calculation.
-
+# The below is a mock up of what integrated config inheritance might
+# look like. The below approaches have not yet been implemented.
 
 # "contours": {
 #     TG263.Lens_L: {
diff --git a/src/python/raicontours/raicontours/tg263.py b/src/python/raicontours/raicontours/tg263.py
index 1252eb10..b5103ea9 100644
--- a/src/python/raicontours/raicontours/tg263.py
+++ b/src/python/raicontours/raicontours/tg263.py
@@ -14,6 +14,8 @@
 # You should have received a copy of the GNU Affero General Public License
 # along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
+"""Implementation of TG263 naming"""
+
 # pylint: disable = invalid-name,
 
 from enum import Enum


Test patch:
diff --git a/src/python/rai/rai/mask/test_figures/edge-of-mask.png b/records/tests/python/mask_test_figures/edge-of-mask.png
similarity index 99%
rename from src/python/rai/rai/mask/test_figures/edge-of-mask.png
rename to records/tests/python/mask_test_figures/edge-of-mask.png
index 0505576f..8128452b 100644
Binary files a/src/python/rai/rai/mask/test_figures/edge-of-mask.png and b/records/tests/python/mask_test_figures/edge-of-mask.png differ
diff --git a/src/python/rai/rai/mask/test_figures/offset-ellipse.png b/records/tests/python/mask_test_figures/offset-ellipse.png
similarity index 99%
rename from src/python/rai/rai/mask/test_figures/offset-ellipse.png
rename to records/tests/python/mask_test_figures/offset-ellipse.png
index 1057eed1..74475894 100644
Binary files a/src/python/rai/rai/mask/test_figures/offset-ellipse.png and b/records/tests/python/mask_test_figures/offset-ellipse.png differ
diff --git a/src/python/rai/rai/mask/test_figures/right-angle-triangle.png b/records/tests/python/mask_test_figures/right-angle-triangle.png
similarity index 99%
rename from src/python/rai/rai/mask/test_figures/right-angle-triangle.png
rename to records/tests/python/mask_test_figures/right-angle-triangle.png
index a4633182..c1a5b357 100644
Binary files a/src/python/rai/rai/mask/test_figures/right-angle-triangle.png and b/records/tests/python/mask_test_figures/right-angle-triangle.png differ
diff --git a/src/python/rai/rai/mask/test_figures/two-small-abutting-circles.png b/records/tests/python/mask_test_figures/two-small-abutting-circles.png
similarity index 99%
rename from src/python/rai/rai/mask/test_figures/two-small-abutting-circles.png
rename to records/tests/python/mask_test_figures/two-small-abutting-circles.png
index 9ba79e09..4554dd1c 100644
Binary files a/src/python/rai/rai/mask/test_figures/two-small-abutting-circles.png and b/records/tests/python/mask_test_figures/two-small-abutting-circles.png differ
diff --git a/src/python/rai/rai/mask/test_convert.py b/src/python/rai/rai/mask/test_convert.py
index 06737051..c3c6c49b 100644
--- a/src/python/rai/rai/mask/test_convert.py
+++ b/src/python/rai/rai/mask/test_convert.py
@@ -16,18 +16,17 @@
 
 """Testing the mask conversion to and from contour lines"""
 
-import pathlib
 from typing import TypedDict
 
 import matplotlib.pyplot as plt  # pyright: ignore [reportMissingTypeStubs, reportUnknownVariableType]
 import numpy as np
 
+from rai._paths import TEST_RECORDS_DIR
 from rai.metrics import dice
 
 from .convert import Contours, Grid, contours_to_mask, mask_to_contours
 
-HERE = pathlib.Path(__file__).parent
-FIGURE_DIR = HERE / "test_figures"
+FIGURE_DIR = TEST_RECORDS_DIR / "mask_test_figures"
 
 
 def test_conversion_round_trip():