Add omega support for time-variant sphere transport flows

.github/copilot-instructions.md

@@ -0,0 +1,12 @@
+# Polaris Copilot Instructions
+
+Follow the repository's automated style configuration in
+`pyproject.toml` and `.pre-commit-config.yaml`.
+
+- Keep changes consistent with existing Polaris patterns.
+- For Python, follow the path-specific instructions in
+  `.github/instructions/python.instructions.md`.
+- For documentation in `docs/`, follow the path-specific instructions in
+  `.github/instructions/docs.instructions.md`.
+- Prefer changes that pass the configured pre-commit hooks without
+  adding ignores or suppressions.

.github/instructions/docs.instructions.md

@@ -0,0 +1,13 @@
+---
+applyTo: "docs/**/*.md"
+---
+
+# Documentation Instructions
+
+- When writing documentation for component tasks, follow the relevant
+  `template.md` format and inline instructions whenever a component
+  task template is available.
+- Prefer starting from the existing template instead of writing
+  component task documentation pages from scratch.
+- Keep new component task documentation consistent with neighboring
+  pages in the same component.

.github/instructions/python.instructions.md

@@ -0,0 +1,15 @@
+---
+applyTo: "**/*.py"
+---
+
+# Python Instructions
+
+- Keep lines at 79 characters or fewer whenever possible.
+- Adhere to `ruff format` formatting.
+- Keep imports at module scope whenever possible. Avoid local imports
+  unless they are needed for circular-import avoidance, lazy loading, or
+  optional dependencies.
+- Avoid nested functions whenever possible.
+- Prefer public functions before private helper functions whenever
+  practical.
+- Prefer private module-level helper functions over nested helpers.

AGENTS.md

@@ -0,0 +1,40 @@
+# Polaris Agent Instructions
+
+These instructions apply to the whole repository unless a deeper
+`AGENTS.md` overrides them.
+
+## Source of truth
+
+- Follow the repo's automated style and lint configuration in
+  `pyproject.toml` and `.pre-commit-config.yaml`.
+- If an instruction here conflicts with automated tooling, follow the
+  automated tooling.
+
+## Python style
+
+- Keep Python lines at 79 characters or fewer whenever possible.
+- Use `ruff format` style. Do not preserve manual formatting that Ruff
+  would rewrite.
+- Keep imports at module scope whenever possible. Avoid local imports
+  unless they are needed to prevent circular imports, defer expensive
+  dependencies, or avoid optional dependency failures.
+- Avoid nested functions whenever possible. Prefer private module-level
+  helpers instead.
+- Put public functions before private helper functions whenever
+  practical.
+- Name private helper functions with a leading underscore when that fits
+  existing repo conventions.
+
+## Documentation
+
+- When writing documentation for component tasks, follow the relevant
+  `template.md` format and its inline instructions whenever a component
+  task template is available.
+- Prefer starting from the existing template instead of creating task
+  documentation pages from scratch.
+
+## Validation
+
+- Run relevant pre-commit hooks on changed files before finishing when
+  practical.
+- Prefer fixing lint and formatting issues rather than suppressing them.

deploy/cli_spec.json

@@ -1,7 +1,7 @@
 {
   "meta": {
     "software": "polaris",
-    "mache_version": "3.2.0",
+    "mache_version": "3.3.0",
     "description": "Deploy polaris environment"
   },
   "arguments": [
@@ -18,9 +18,9 @@
       "route": ["deploy", "bootstrap", "run"]
     },
     {
-      "flags": ["--prefix"],
-      "dest": "prefix",
-      "help": "Install the environment into this prefix (directory). Overrides deploy/config.yaml.j2.",
+      "flags": ["--pixi-path", "--prefix"],
+      "dest": "pixi_path",
+      "help": "Install the pixi environment at this path (directory). Overrides deploy/config.yaml.j2. `--prefix` is deprecated.",
       "route": ["deploy", "bootstrap", "run"]
     },
     {

deploy/pins.cfg

@@ -3,7 +3,7 @@
 bootstrap_python = 3.14
 python = 3.14
 geometric_features = 1.6.1
-mache = 3.2.0
+mache = 3.3.0
 mpas_tools = 1.4.0
 otps = 2021.10
 parallelio = 2.6.9

docs/design_docs/index.md

@@ -6,5 +6,6 @@
 :titlesonly: true
 
 shared_steps
+vector_reconstruction
 template
 ```