Update to ESMCI/cime-6.1.173

.claude/CLAUDE.md

@@ -0,0 +1,11 @@
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+@../AGENTS.md
+
+# Important
+This CLAUDE.md file is maintained by the project maintainers and should not be
+modified by /init or any automated process. Do not overwrite, replace, or
+regenerate this file. If asked to run /init, warn the user that it will
+overwrite the project's curated AI instructions.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -5,7 +5,7 @@ Please provide a clear and concise description of what the problem is e.g. I'm a
 
 ## Describe the solution you'd like
 <!--
-A clear and consise description of what you want to happen.
+A clear and concise description of what you want to happen.
 -->
 
 ## Describe alternative solutions

.github/pull_request_template.md

@@ -7,9 +7,9 @@
 - Closes #<ISSUE_NUMBER_HERE>
 
 ## Checklist
-- [ ] My code follows the style guidlines of this proejct (black formatting)
+- [ ] My code follows the style guidelines of this project (black formatting)
 - [ ] I have performed a self-review of my own code
 - [ ] My changes generate no new warnings
-- [ ] I have added tests that excerise my feature/fix and existing tests continue to pass
+- [ ] I have added tests that exercise my feature/fix and existing tests continue to pass
 - [ ] I have commented my code, particularly in hard-to-understand areas
 - [ ] I have made corresponding additions and changes to the documentation

.github/workflows/testing.yml

@@ -40,6 +40,8 @@ jobs:
     steps:
       - name: Checkout code
         uses: actions/checkout@v4
+        with:
+          submodules: "true"
       - name: Set up QEMU
         uses: docker/setup-qemu-action@v3
       - name: Set up Docker Buildx
@@ -62,8 +64,8 @@ jobs:
       - name: Build and push
         uses: docker/build-push-action@v6
         with:
-          target: base
-          context: docker/
+          file: docker/Dockerfile
+          context: .
           push: true
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
@@ -99,7 +101,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.10", "3.12"]
+        python-version: ["3.9", "3.10", "3.12", "3.13", "3.14"]
     steps:
       - name: Checkout model code
         uses: actions/checkout@v4
@@ -123,6 +125,8 @@ jobs:
         with:
           path: cesm/cime
           submodules: "true"
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
       - name: Run tests
         shell: bash
         working-directory: cesm/cime
@@ -132,18 +136,15 @@ jobs:
           CIME_TEST_PLATFORM: "ubuntu-latest"
           SKIP_ENTRYPOINT: "true"
         run: |
-          source /opt/conda/etc/profile.d/conda.sh
-
-          conda activate cesm
-
-          mamba install -y 'python=${{ matrix.python-version }}'
-
-          pip install -r test-requirements.txt
+          # manually run the entrypoint
+          source /entrypoint.sh
 
-          # GitHub runner home is different than container
-          cp -rf /home/cime/.cime /github/home/
+          uv python install "${{ matrix.python-version }}"
+          uv venv
+          source .venv/bin/activate
+          uv pip install -r test-requirements.txt
 
-          pytest -vvv --cov=CIME --cov-branch --cov-report=xml --machine docker CIME/tests/test_unit*
+          uv run pytest -vvv --cov=CIME --cov-branch --cov-report=xml --machine docker CIME/tests/test_unit*
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v4
         with:
@@ -212,8 +213,12 @@ jobs:
       - name: Cache inputdata
         uses: actions/cache@v3
         with:
-          path: /home/cime/inputdata
+          path: /root/storage/inputdata
           key: inputdata-2
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+        with:
+          python-version: "3.10"
       - name: Run tests
         shell: bash
         working-directory: ${{ matrix.model.name }}/cime
@@ -223,31 +228,18 @@ jobs:
           CIME_TEST_PLATFORM: ubuntu-latest
           SKIP_ENTRYPOINT: "true"
         run: |
-          source /opt/conda/etc/profile.d/conda.sh
-
-          conda activate ${{ matrix.model.name }}
-
-          pip install -r test-requirements.txt
-
+          # manually run the entrypoint
           source /entrypoint.sh
 
-          if [[ "${{ matrix.model.name }}" == "e3sm" ]]; then
-            fix_mct_makefiles ../externals/mct
-          fi
-
-          # GitHub runner home is different than container
-          cp -rf /home/cime/.cime /github/home/
-
-          if [[ "${CIME_MODEL}" == "e3sm" ]]; then
-            ln -sf /github/home/.cime/config_machines.v2.xml /github/home/.cime/config_machines.xml
-          else
-            ln -sf /github/home/.cime/config_machines.v3.xml /github/home/.cime/config_machines.xml
-          fi
+          uv python install 3.10
+          uv venv
+          source .venv/bin/activate
+          uv pip install -r test-requirements.txt
 
           git config --global user.name "${{ github.actor }}"
           git config --global user.email "${{ github.actor }}@users.noreply.github.com"
 
-          pytest -vvv --cov=CIME --cov-branch --cov-report=xml --machine docker --no-fortran-run --no-teardown CIME/tests/test_sys*
+          uv run pytest -vvv --cov=CIME --cov-branch --cov-report=xml --machine docker --no-fortran-run --no-teardown CIME/tests/test_sys*
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v4
         with:
@@ -259,7 +251,7 @@ jobs:
       - name: Create testing log archive
         if: ${{ failure() }}
         shell: bash
-        run: tar -czvf /testing-logs-${GITHUB_RUN_NUMBER}-${{ matrix.model.name }}-${{ matrix.driver }}.tar.gz /home/cime/cases /home/cime/baselines /home/cime/archive
+        run: tar -czvf /testing-logs-${GITHUB_RUN_NUMBER}-${{ matrix.model.name }}-${{ matrix.driver }}.tar.gz /root/storage/cases /root/storage/baselines /root/storage/archive
         # How to download artifacts:
         # https://docs.github.com/en/actions/managing-workflow-runs/downloading-workflow-artifacts
       - name: Upload testing logs

.gitignore

@@ -23,9 +23,16 @@ scripts/Tools/JENKINS*
 # Ignore anything that are produced under scripts "cases" directory
 /scripts/cases/
 
-#Ignore Externals
-components
-libraries
-share
+# Ignore some other files
 test_coverage/**
 *.bak
+
+# AI coding tool local state
+.gemini/
+.codex/
+
+# Special for Claude Code user config
+.claude/*
+!.claude/CLAUDE.md
+CLAUDE.md
+CLAUDE.local.md

.pre-commit-config.yaml

@@ -18,7 +18,7 @@ repos:
       - id: black
         files: CIME
   - repo: https://github.com/PyCQA/pylint
-    rev: v2.11.1
+    rev: v4.0.4
     hooks:
       - id: pylint
         args:

AGENTS.md

@@ -0,0 +1,173 @@
+# AGENTS.md
+
+This file provides guidance to AI agents when working with code in this repository.
+
+## Note to AI agents
+
+This AGENTS.md is maintained by the CIME project. Do not overwrite or
+regenerate this file with init commands.
+
+## Note to claude code users
+
+A CLAUDE.md file is in .claude directory.  It includes
+this file. Ignore tips to run init.
+
+## Project Overview
+
+CIME (Common Infrastructure for Modeling the Earth) provides a Case Control System (CCS) for configuring, compiling, and executing Earth System Models, plus a framework for system testing. CIME is a Python-based infrastructure currently used by CESM, E3SM, NorESM and other models. It does NOT contain model source code itself, but provides the infrastructure to manage model runs.
+
+## Running Tests
+
+### Unit and System Tests
+
+From the repository root, run tests using either:
+
+```bash
+# Using pytest (recommended)
+pytest CIME/tests
+
+# Run specific test file
+pytest CIME/tests/test_unit_foo.py
+
+# Run specific test class
+pytest CIME/tests/test_unit_foo.py::TestClass
+
+# Run specific test case
+pytest CIME/tests/test_unit_foo.py::TestClass::test_method
+```
+
+Test files follow a naming convention:
+- Unit tests: `test_unit_*.py`
+- System tests: `test_sys_*.py`
+
+### Pre-commit Hooks
+
+Before committing, always run:
+
+```bash
+pip install pre-commit
+pre-commit run -a
+```
+
+This runs:
+- `black` formatter on CIME code
+- `pylint` with project-specific configuration
+- XML validation on config files
+- End-of-file and trailing whitespace checks
+
+## Code Quality
+
+- Code is formatted with `black`
+- Linted with `pylint` (see `.pre-commit-config.yaml` for disabled checks)
+- Python 3.9+ required
+- Follow PEP8 style guidelines
+
+## Key Architecture Concepts
+
+### Case Control System (CCS)
+
+The heart of CIME is the `Case` class (`CIME/case/case.py`), which manages all interactions with a CIME case. The Case class coordinates between:
+
+1. **Config XML Classes** (readonly) - Located in `CIME/XML/`, these read CIME distribution config files like `config_*.xml`. Python classes are named after the XML they read (e.g., `Machines` reads machine configs).
+
+2. **Env XML Classes** (read/write) - Also in `CIME/XML/`, these manage case-specific `env_*.xml` files. Classes are named `Env*` (e.g., `EnvRun`, `EnvBuild`).
+
+The Case class contains an array of Env classes and uses Config classes to populate them during case creation/configuration.
+
+### Directory Structure
+
+```
+CIME/
+├── case/              # Case control modules (setup, run, submit, etc.)
+├── XML/               # XML parsers for config and env files
+├── SystemTests/       # System test implementations (ERS, ERT, etc.)
+├── Tools/             # Case manipulation tools (xmlchange, xmlquery, etc.)
+├── scripts/           # Top-level user-facing scripts
+├── data/              # Config files, XML schemas
+├── tests/             # Unit and system tests
+├── BuildTools/        # Build system utilities
+└── non_py/            # Non-Python components (C/Fortran)
+
+scripts/
+├── create_newcase     # Create new case
+├── create_test        # Create and run tests
+├── create_clone       # Clone existing case
+├── query_config       # Query available configurations
+└── query_testlists    # Query test lists
+
+tools/
+└── mapping/           # Grid mapping file generation tools
+```
+
+### Common Workflows
+
+**Create a case** (requires machine configuration):
+```bash
+./scripts/create_newcase --case CASENAME --compset COMPSET --res GRID [--machine MACHINE]
+```
+
+**Create and run tests**:
+```bash
+./scripts/create_test TESTNAME
+./scripts/create_test TESTNAME1 TESTNAME2 ...
+./scripts/create_test -f TESTFILE  # from file
+```
+
+**Query configurations**:
+```bash
+./scripts/query_config --compsets
+./scripts/query_config --grids
+./scripts/query_config --machines
+```
+
+### Model System Tests
+
+These are tests of properties of the model CIME is included in.
+System tests inherit from `SystemTestsCommon` base class (`CIME/SystemTests/system_tests_common.py`). Common test types:
+- **ERS**: Exact restart test
+- **ERT**: Exact restart with different threading
+- **SMS**: Smoke test
+- **SEQ**: Sequencing test
+
+Each test type has its own module in `CIME/SystemTests/`.
+
+### XML-Based Configuration
+
+CIME is heavily XML-driven. Key concepts:
+- Generic XML handling is in `CIME/XML/generic_xml.py`
+- All XML classes inherit from `GenericXML`
+- XML schemas are in `CIME/data/config/xml_schemas/`
+- Config files define machines, compsets, grids, tests
+
+### Case Management Tools
+
+Located in `CIME/Tools/`, these are executable scripts:
+- `xmlchange`: Modify case XML variables
+- `xmlquery`: Query case XML variables
+- `case.setup`: Setup case directory structure
+- `case.build`: Build the case
+- `case.submit`: Submit case to batch system
+- `preview_namelists`: Generate and preview namelists
+
+## Documentation
+
+Build Sphinx documentation:
+```bash
+cd doc
+make clean
+make api
+make html
+```
+
+Requires: `sphinx`, `sphinxcontrib-programoutput`, and custom theme (see `doc/README`).
+
+Online documentation: https://esmci.github.io/cime
+
+## Development Notes
+
+- When modifying Case env classes, changes affect the case's XML files
+- The Case class extends across multiple files using imports (see imports at end of `case.py`)
+- CIME must be integrated with host models (CESM, E3SM, NorESM) to run Model System Tests
+on a supported machine (found using `./scripts/query_config --machines`)/
+- Machine-specific configurations are in XML files, not hardcoded
+- Git submodules may need initialization: `git submodule update --init`

CIME/Servers/wget.py

@@ -26,20 +26,21 @@ def wget_login(cls, address, user="", passwd=""):
             args += "--password {} ".format(passwd)
 
         try:
-            err = run_cmd("wget {} --spider {}".format(args, address), timeout=60)[0]
-        except:
+            err, _, errstr = run_cmd(
+                "wget {} --spider {}".format(args, address), timeout=60
+            )
+        except RuntimeError:
             logger.warning(
-                "Could not connect to repo '{0}'\nThis is most likely either a proxy, or network issue .(location 1)".format(
+                "Could not connect to repo '{0}'\nThis is most likely either a proxy, or network issue .".format(
                     address
                 )
             )
             return None
-
-        if err and not "storage.neonscience.org" in address:
+        if "Connecting to " in errstr and "... connected" in errstr:
+            logger.warning("Connection established with nonzero code %s", err)
+        elif err:
             logger.warning(
-                "Could not connect to repo '{0}'\nThis is most likely either a proxy, or network issue .(location 2)".format(
-                    address
-                )
+                "Could not connect to repo '{0}'\n{1}".format(address, errstr)
             )
             return None