ManifoldMap app

.vscode/extensions.json

@@ -3,6 +3,6 @@
 		"tamasfe.even-better-toml",
 		"charliermarsh.ruff",
 		"biomejs.biome",
-		"ms-python.python",
-	],
+		"ms-python.python"
+	]
 }

.vscode/settings.json

@@ -1,24 +1,23 @@
 {
 	"[json][jsonc][toml][python]": {
-		"editor.formatOnSave": true,
+		"editor.formatOnSave": true
 	},
 	"[json][jsonc]": {
-		"editor.defaultFormatter": "biomejs.biome",
+		"editor.defaultFormatter": "biomejs.biome"
 	},
 	"[toml]": {
-		"editor.defaultFormatter": "tamasfe.even-better-toml",
+		"editor.defaultFormatter": "tamasfe.even-better-toml"
 	},
 	"[python]": {
 		"editor.defaultFormatter": "charliermarsh.ruff",
 		"editor.codeActionsOnSave": {
 			"source.fixAll": "always",
-			"source.organizeImports": "always",
-		},
+			"source.organizeImports": "always"
+		}
 	},
 	"python.analysis.typeCheckingMode": "basic",
 	"python.testing.pytestArgs": ["--color=yes", "-vv"],
 	"python.testing.pytestEnabled": true,
-	// mirror settings from pyproject-fmt
 	"evenBetterToml.formatter.compactArrays": false,
-	"evenBetterToml.formatter.arrayAutoCollapse": false,
+	"evenBetterToml.formatter.arrayAutoCollapse": false
 }

biome.jsonc

@@ -1,8 +1,8 @@
 {
-	"$schema": "https://biomejs.dev/schemas/1.9.4/schema.json",
+	"$schema": "https://biomejs.dev/schemas/2.0.0-beta.1/schema.json",
 	"overrides": [
 		{
-			"include": ["./.vscode/*.json", "**/*.jsonc"],
+			"includes": ["./.vscode/*.json", "**/*.jsonc"],
 			"json": {
 				"formatter": {
 					"trailingCommas": "all",

pyproject.toml

@@ -15,7 +15,13 @@ classifiers = [
   "Programming Language :: Python :: 3.13",
 ]
 dynamic = [ "description", "version" ]
-dependencies = [ "anndata", "holoviews", "numpy" ]
+dependencies = [
+  "anndata",
+  "datashader",
+  "holoviews>=1.21.0rc0",
+  "numpy",
+  "panel",
+]
 
 [tool.hatch.metadata.hooks.docstring-description]
 [tool.hatch.version]
@@ -43,16 +49,21 @@ extra-dependencies = [
 [tool.ruff]
 lint.select = [ "ALL" ]
 lint.ignore = [
-  "B019",   # functools.cache is fine to use
-  "C408",   # dict(...) calls are good
-  "COM812", # Incompatible with formatter
-  "D203",   # 0 instead of 1 blank lines before class docstring
-  "D213",   # Multi-line docstring summary should start at the first instead of second line
-  "FIX002", # TODOs are fine
-  "ISC001", # Incompatible with formatter
-  "S603",   # We don’t want to use `subprocess.run(shell=True)`
-  "S607",   # We don’t run commands with untrusted input
-  "TD002",  # No need to assign TODOs to some person
+  "B019",    # functools.cache is fine to use
+  "C408",    # dict(...) calls are good
+  "COM812",  # Incompatible with formatter
+  "D203",    # 0 instead of 1 blank lines before class docstring
+  "D213",    # Multi-line docstring summary should start at the first instead of second line
+  "FIX002",  # TODOs are fine
+  "ISC001",  # Incompatible with formatter
+  "N",       # pep8-naming
+  "PLR0124",
+  "PLR0913", # Too many arguments in function definition
+  "S603",    # We don’t want to use `subprocess.run(shell=True)`
+  "S607",    # We don’t run commands with untrusted input
+  "SLF",
+  "TD002",   # No need to assign TODOs to some person
+  "TRY",
 ]
 lint.per-file-ignores."**/*.ipynb" = [
   "I002", # Missing `from __future__ import annotations` is fine
@@ -64,12 +75,13 @@ lint.per-file-ignores."src/hv_anndata/__main__.py" = [
   "T201", # print is fine
 ]
 lint.per-file-ignores."tests/*" = [
-  "D102",   # Missing docstring in public method
-  "D103",   # Missing docstring in public function
-  "D105",   # Missing docstring in magic method
-  "INP001", # __init__.py
-  "RUF018", # assert with := is fine
-  "S101",   # Use of assert
+  "D102",    # Missing docstring in public method
+  "D103",    # Missing docstring in public function
+  "D105",    # Missing docstring in magic method
+  "INP001",  # __init__.py
+  "PLR2004", # magic-value-comparison
+  "RUF018",  # assert with := is fine
+  "S101",    # Use of assert
 ]
 lint.allowed-confusables = [ "×", "’" ]
 lint.flake8-copyright.notice-rgx = "SPDX-License-Identifier: MPL-2\\.0"
@@ -80,7 +92,9 @@ lint.pylint.max-positional-args = 3
 
 [tool.pytest.ini_options]
 addopts = [ "--import-mode=importlib", "--strict-markers" ]
-filterwarnings = [ "error" ]
+# filterwarnings = [
+# "error",
+# ]
 
 [tool.coverage.run]
 source_pkgs = [ "hv_anndata", "tests" ]

src/hv_anndata/__init__.py

@@ -3,6 +3,13 @@
 from __future__ import annotations
 
 from .interface import AnnDataInterface, register
+from .manifoldmap import ManifoldMap, create_manifoldmap_plot
 from .plotting import Dotmap
 
-__all__ = ["AnnDataInterface", "Dotmap", "register"]
+__all__ = [
+    "AnnDataInterface",
+    "Dotmap",
+    "ManifoldMap",
+    "create_manifoldmap_plot",
+    "register",
+]