Merge remote-tracking branch 'origin/master' into aguide-convention-fix

reflectometry · Feb 21, 2025 · bb8742f · bb8742f
2 parents f6f4672 + b09d43b
commit bb8742f
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diff --git a/.github/workflows/test-webview-client.yaml b/.github/workflows/test-webview-client.yaml
@@ -56,20 +56,35 @@ jobs:
         run: bun run test:lint
 
   # test that app has no typescript errors
-#   test-types:
-#     runs-on: ubuntu-latest
-#     steps:
-#       - name: Checkout code
-#         uses: actions/checkout@v4
+  test-types:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
 
-#       - name: Set up Bun
-#         uses: oven-sh/setup-bun@v2
+      - name: Checkout bumps source
+        uses: actions/checkout@v4
+        with:
+          repository: bumps/bumps
+          sparse-checkout: 'bumps/webview/client'
+          path: bumps
 
-#       - name: Install packages
-#         run: bun install
+      - name: Set up Bun
+        uses: oven-sh/setup-bun@v2
 
-#       - name: Run test
-#         run: bun run test:types
+      - name: Install packages
+        run: bun install
+
+      - name: Use bumps code from source
+        run: |
+          cd ../../../bumps/bumps/webview/client
+          bun install
+          bun link
+          cd ../../../../refl1d/webview/client
+          bun link bumps-webview-client
+
+      - name: Run test
+        run: bun run test:types
 
   # run unit tests
 #   test-unit:

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -16,7 +16,7 @@ repos:
       # - id: end-of-file-fixer
       # - id: trailing-whitespace
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.2
+    rev: v0.8.6
     hooks:
       # - id: ruff
       #   args: [--fix, --exit-non-zero-on-fix]

diff --git a/Makefile b/Makefile
@@ -30,13 +30,30 @@ test: ## Run pytest and doc tests
 	pytest -v
 	python check_examples.py --chisq
 
+#######################
+### Dev environment ###
+#######################
+
+.PHONY: dev-backend
+dev-backend: ## Start the backend server in headless mode
+	refl1d-webview --port 8080 --headless
+
+.PHONY: dev-frontend
+dev-frontend: ## Start the frontend server in development mode
+	cd refl1d/webview/client && \
+		$(FE_CMD) run dev
+
 ##############################
 ### Linting and formatting ###
 ##############################
 
 .PHONY: lint
 lint: lint-backend lint-frontend ## Run all linters
 
+.PHONY: lint-backend-check
+lint-backend-check: ## Run ruff linting on python code
+	@ruff check bumps/ run.py test.py check_*.py
+
 .PHONY: lint-backend
 lint-backend: ## Run ruff linting on python code
 	@ruff check --fix refl1d/ tests/ setup.py

diff --git a/README.rst b/README.rst
@@ -1,7 +1,7 @@
 Refl1D
 ======
 
-Refl1D is a program for analyzing 1D reflectometry measurements made with
+Refl1D is a program for analyzing 1-D reflectometry measurements made with
 X-ray and neutron beamlines.  The 1-D models give the depth profile for
 material scattering density composed of a mixture of flat and continuously
 varying freeform layers. With polarized neutron measurements, scientists

diff --git a/pyproject.toml b/pyproject.toml
@@ -22,22 +22,24 @@ classifiers = [
 ]
 requires-python = ">=3.9"
 dependencies = [
-    "bumps>=1.0.0a11",
+    "bumps>=1.0.0a12",
     "matplotlib",
     "numba",
     "numpy",
     "periodictable",
     "scipy",
+    "orsopy"
 ]
 
 [project.optional-dependencies]
 dev = [
+    "matplotlib", # for testing
     "pre-commit",
     "pydantic",
     "pytest",
     "pytest-cov",
     "ruff",
-    "sphinx",
+    "sphinx < 8.2",
     "versioningit",
 ]
 full = ["wxpython", "ipython"]
@@ -74,13 +76,15 @@ script-files = ["bin/refl1d_cli.py", "bin/refl1d_gui.py"]
 
 [tool.setuptools.packages.find]
 where = ["."]
+include = ["refl1d*"]
 
 [project.scripts]
 refl1d = "refl1d.main:cli"
 refl1d-webview = "refl1d.webview.server.webserver:main"
 
 [tool.pytest.ini_options]
-addopts = "--doctest-modules --doctest-glob=*.rst --cov=refl1d"
+# TODO: remove --assert=plain when https://github.com/scipy/scipy/issues/22236 is resolved
+addopts = "--doctest-modules --doctest-glob=*.rst --cov=bumps --assert=plain"
 doctest_optionflags = ["ELLIPSIS", "NORMALIZE_WHITESPACE"]
 testpaths = ["refl1d", "tests", "doc/getting_started", "doc/guide"]
 norecursedirs = ["view", "mystic", "bin", "webview/client", "explore"]

diff --git a/refl1d/probe/data_loaders/load4.py b/refl1d/probe/data_loaders/load4.py
@@ -1,29 +1,50 @@
+# standard imports
 import json
 
-import numpy as np
+# third party imports
 from bumps.data import parse_multi, strip_quotes
+import numpy as np
+from orsopy.fileio.orso import load_nexus, load_orso
 
-from ...sample.reflectivity import BASE_GUIDE_ANGLE
-from ..probe import (
+# refl1d imports
+from refl1d.probe import (
     NeutronProbe,
     PolarizedNeutronProbe,
     PolarizedQProbe,
     Probe,
     QProbe,
     XrayProbe,
 )
-from ..resolution import QL2T, QT2L, FWHM2sigma, dQdL2dT, dQdT2dLoL, sigma2FWHM
+from refl1d.probe.resolution import QL2T, QT2L, FWHM2sigma, dQdL2dT, dQdT2dLoL, sigma2FWHM
+from refl1d.sample.reflectivity import BASE_GUIDE_ANGLE
 
 
-def parse_orso(filename, *args, **kwargs):
-    """load an ORSO text (.ort) or binary (.orb) file"""
+def parse_orso(filename):
+    """
+    Load an ORSO text (.ort) or binary (.orb) file containing one or more datasets
+
+    Parameters
+    ----------
+    filename : str
+        The path to the ORSO file to be loaded.
+
+    Returns
+    -------
+    list of tuple
+        A list of tuples, each containing a header dictionary and a data array derived from each loaded dataset.
+        The header dictionary contains metadata about the measurement,
+        and the data array contains the measurement data.
+
+    Notes
+    -----
+    The function supports both ORSO text (.ort) and binary (.orb) files.
+    The polarization information is converted using a predefined mapping.
+    The header dictionary includes keys for polarization, angle, angular resolution,
+    wavelength, and wavelength resolution.
+    """
     if filename.endswith(".ort"):
-        from orsopy.fileio.orso import load_orso
-
         entries = load_orso(filename)
     elif filename.endswith(".orb"):
-        from orsopy.fileio.orso import load_nexus
-
         entries = load_nexus(filename)
 
     POL_CONVERSION = {
@@ -45,6 +66,23 @@ def parse_orso(filename, *args, **kwargs):
         header_out = {"polarization": polarization}
 
         def get_key(orso_name, refl1d_name, refl1d_resolution_name):
+            """
+            Extract value and error from one of the ORSO columns. If no column corresponding
+            to entry `orso_name` is found, search in the instrument settings.
+
+            Parameters
+            ----------
+            orso_name : str
+                The name of the ORSO column or instrument setting to extract.
+            refl1d_name : str
+                The corresponding refl1d name for the value of entry `orso_name`
+            refl1d_resolution_name : str
+                The corresponding refl1d error name the error of entry `orso_name`
+
+            Notes
+            -----
+            This function requires the instrument setting `orso_name` to have a "magnitue" and "error" attribute.
+            """
             column_index = next(
                 (i for i, c in enumerate(columns) if getattr(c, "physical_quantity", None) == orso_name),
                 None,

diff --git a/refl1d/sample/layers.py b/refl1d/sample/layers.py
@@ -224,6 +224,7 @@ def __repr__(self):
 
 @dataclass(init=False)
 class Stack(Layer):
+    # TODO: Finish this docstring
     """
     Reflectometry layer stack
 

diff --git a/refl1d/webview/build_client.py b/refl1d/webview/build_client.py
@@ -34,7 +34,7 @@ def cleanup_bumps_packages():
         cleanup_bumps_packages()
         bumps_path = Path(bumps.webview.__file__).parent / "client"
         # pack it up for install...
-        os.system(f"npm pack {bumps_path}")
+        os.system(f"npm pack {bumps_path} --quiet")
         # get the package filename:
         bumps_package_file = next(client_folder.glob("bumps-webview-client*.tgz"))
         os.system(f"npm install {bumps_package_file} --no-save")

diff --git a/refl1d/webview/client/eslint.config.js b/refl1d/webview/client/eslint.config.js
@@ -1,10 +1,10 @@
+import url from "url";
+import eslintPluginPrettierRecommended from "eslint-plugin-prettier/recommended";
+import pluginVue from "eslint-plugin-vue";
 import { FlatCompat } from "@eslint/eslintrc";
 import js from "@eslint/js";
 import prettierConfig from "@vue/eslint-config-prettier";
 import vueTsEslintConfig from "@vue/eslint-config-typescript";
-import eslintPluginPrettierRecommended from "eslint-plugin-prettier/recommended";
-import pluginVue from "eslint-plugin-vue";
-import url from "url";
 
 const __dirname = url.fileURLToPath(new URL(".", import.meta.url));
 const compat = new FlatCompat({
@@ -35,6 +35,10 @@ export default [
       "prefer-const": 0,
       "@typescript-eslint/ban-ts-comment": ["error", { "ts-ignore": "allow-with-description" }],
       "@typescript-eslint/no-explicit-any": "off",
+      "@typescript-eslint/no-unused-expressions": [
+        "error",
+        { allowShortCircuit: true, allowTernary: true }, // Temporary fix for indirect dependency @typescript-eslint <= 8.15.0
+      ],
       "prettier/prettier": [
         "warn",
         {},

diff --git a/refl1d/webview/client/package.json b/refl1d/webview/client/package.json
@@ -14,37 +14,39 @@
     "preview": "vite preview --port 4173",
     "format": "prettier --write src",
     "lint": "eslint src --fix",
-    "test:lint": "eslint src"
+    "test:lint": "eslint src",
+    "test:types": "vue-tsc --noEmit --skipLibCheck -p tsconfig.json --composite false"
   },
   "dependencies": {
     "bootstrap": "^5.3.3",
     "bumps-webview-client": "^0.1.20",
     "comlink": "^4.4.2",
     "json-difference": "^1.16.1",
-    "plotly.js": "^2.35.2",
+    "plotly.js": "^2.35.3",
     "socket.io-client": "^4.8.1",
-    "uuid": "^11.0.3",
+    "uuid": "^11.0.5",
     "vue": "^3.5.13"
   },
   "devDependencies": {
-    "@ianvs/prettier-plugin-sort-imports": "^4.4.0",
-    "@types/plotly.js": "^2.35.0",
+    "@tsconfig/node22": "22.0.0",
+    "@types/plotly.js": "^2.35.1",
     "@types/uuid": "^10.0.0",
-    "@vitejs/plugin-vue": "^5.2.0",
+    "@vitejs/plugin-vue": "^5.2.1",
+    "@vue/tsconfig": "^0.7.0",
     "@vue/eslint-config-prettier": "10.1.0",
-    "@vue/eslint-config-typescript": "^14.1.3",
-    "eslint": "9.14.0",
-    "eslint-config-prettier": "^9.1.0",
+    "@vue/eslint-config-typescript": "^14.2.0",
+    "typescript": "^5.7.3",
+    "vite": "^6.0.7",
+    "vite-svg-loader": "5.1.0",
+    "vue-tsc": "^2.2.0",
+    "eslint": "^9.18.0",
+    "eslint-config-prettier": "^10.0.1",
     "eslint-plugin-prettier": "^5.2.1",
-    "eslint-plugin-vue": "^9.31.0",
+    "eslint-plugin-vue": "^9.32.0",
     "eslint-plugin-vuejs-accessibility": "^2.4.1",
-    "prettier": "^3.3.3",
+    "prettier": "^3.4.2",
     "prettier-plugin-css-order": "^2.1.2",
-    "prettier-plugin-jsdoc": "^1.3.0",
-    "vite": "^5.4.11",
-    "vite-svg-loader": "^5.1.0"
-  },
-  "trustedDependencies": [
-    "es5-ext"
-  ]
+    "prettier-plugin-jsdoc": "^1.3.2",
+    "@ianvs/prettier-plugin-sort-imports": "^4.4.1"
+  }
 }
diff --git a/refl1d/webview/client/prettier.config.js b/refl1d/webview/client/prettier.config.js
@@ -1,43 +1,24 @@
 /**
- * @see https://prettier.io/docs/en/configuration.html
  * @type {import("prettier").Config}
+ * @see https://prettier.io/docs/en/configuration.html
  */
 
-// module.exports ={
-//   "plugins": [ 
-//     "@ianvs/prettier-plugin-sort-imports",
-//     "./node_modules/prettier-plugin-jsdoc/dist/index.js",
-//     "prettier-plugin-css-order"
-//   ],
-//   "importOrder": ["^vue", "^[a-zA-Z]", "^@[a-zA-Z]", "^@/", "^./", "^../"],
-//   "cssDeclarationSorterOrder": "smacss",
-//   "jsdocCapitalizeDescription": false,
-//   "overrides": [
-//     {
-//       "files": "*.svg",
-//       "options": {
-//         "parser": "html"
-//       }
-//     }
-//   ]
-// }
-
 const config = {
-  "plugins": [ 
+  plugins: [
     "@ianvs/prettier-plugin-sort-imports",
     "./node_modules/prettier-plugin-jsdoc/dist/index.js",
-    "prettier-plugin-css-order"
+    "prettier-plugin-css-order",
   ],
-  "importOrder": ["^vue", "^[a-zA-Z]", "^@[a-zA-Z]", "^@/", "^./", "^../"],
-  "cssDeclarationSorterOrder": "smacss",
-  "jsdocCapitalizeDescription": false,
-  "overrides": [
+  importOrder: ["^vue", "^[a-zA-Z]", "^@[a-zA-Z]", "^@/", "^./", "^../"],
+  cssDeclarationSorterOrder: "smacss",
+  jsdocCapitalizeDescription: false,
+  overrides: [
     {
-      "files": "*.svg",
-      "options": {
-        "parser": "html"
-      }
-    }
+      files: "*.svg",
+      options: {
+        parser: "html",
+      },
+    },
   ],
   experimentalTernaries: true,
   printWidth: 120,