Public release, 2025-07

.github/workflows/docs.yaml

@@ -13,25 +13,32 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
+      - name: Set environment variables
+        run: |
+          echo "CURRENT_WEEK=$(date +'%Y-%U')" >> $GITHUB_ENV
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.10"
+          python-version: "3.11"
       - uses: actions/cache@v4
         with:
           path: ${{ env.pythonLocation }}
-          key: ${{ env.pythonLocation }}-${{ hashFiles('fme/requirements.txt') }}-${{ hashFiles('fme/docs/requirements.txt') }}-${{ hashFiles('fme/constraints.txt') }}
+          key: v1-${{ env.CURRENT_WEEK }}-${{ env.pythonLocation }}-${{ hashFiles('requirements.txt') }}-${{ hashFiles('docs/requirements.txt') }}-${{ hashFiles('requirements-healpix.txt') }}-${{ hashFiles('constraints.txt') }}
       - name: Install dependencies
         run: |
-          python -m pip install uv==0.2.5
-          uv pip install --system -c constraints.txt -e fme[docs]
+          python -m pip install uv
+          # can't use --system here because it doesn't work with --no-build-isolation and a healpix dependency
+          uv venv --python 3.11
+          uv pip install -c constraints.txt -e .[docs]
+          uv pip install --no-build-isolation -c constraints.txt -e .[docs,healpix]
       - name: Build docs
         run: |
-          cd fme/docs && make doctest html
+          source .venv/bin/activate
+          cd docs && make doctest html
       - name: Deploy to GitHub Pages
         uses: peaceiris/actions-gh-pages@v3
         if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
         with:
           publish_branch: gh-pages
           github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: fme/docs/_build/
+          publish_dir: docs/_build/
           force_orphan: true

.github/workflows/pre-commit.yml

@@ -18,7 +18,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Install dependencies
         run: |

.github/workflows/tests.yaml

@@ -18,19 +18,23 @@ jobs:
           echo "CURRENT_WEEK=$(date +'%Y-%U')" >> $GITHUB_ENV
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.10"
+          python-version: "3.11"
       - uses: actions/cache@v4
         with:
           path: ${{ env.pythonLocation }}
-          key: ${{ env.CURRENT_WEEK }}-${{ env.pythonLocation }}-${{ hashFiles('fme/requirements.txt') }}-${{ hashFiles('fme/dev-requirements.txt') }}-${{ hashFiles('constraints.txt') }}
+          key: v1-${{ env.CURRENT_WEEK }}-${{ env.pythonLocation }}-${{ hashFiles('requirements.txt') }}-${{ hashFiles('requirements-dev.txt') }}-${{ hashFiles('requirements-healpix.txt') }}-${{ hashFiles('constraints.txt') }}
       - name: Install dependencies
         run: |
           python -m pip install uv
-          uv pip install --system -c constraints.txt -e ./fme[dev]
-      - name: Run pytest
+          # can't use --system here because it doesn't work with --no-build-isolation and a healpix dependency
+          uv venv --python 3.11
+          uv pip install -c constraints.txt -e .[dev]
+          uv pip install --no-build-isolation -c constraints.txt -e .[dev,healpix]
+      - name: Run pytest with code coverage
         run: |
-          make test
-  cpu-very-fast:
+          source .venv/bin/activate
+          make test_cov
+  cpu-very-fast-no-healpix:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
@@ -39,15 +43,15 @@ jobs:
           echo "CURRENT_WEEK=$(date +'%Y-%U')" >> $GITHUB_ENV
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.10"
+          python-version: "3.11"
       - uses: actions/cache@v4
         with:
           path: ${{ env.pythonLocation }}
-          key: ${{ env.CURRENT_WEEK }}-${{ env.pythonLocation }}-${{ hashFiles('fme/requirements.txt') }}-${{ hashFiles('fme/dev-requirements.txt') }}-${{ hashFiles('constraints.txt') }}
+          key: v1-${{ env.CURRENT_WEEK }}-${{ env.pythonLocation }}-${{ hashFiles('requirements.txt') }}-${{ hashFiles('requirements-dev.txt') }}-${{ hashFiles('constraints.txt') }}
       - name: Install dependencies
         run: |
           python -m pip install uv
-          uv pip install --system -c constraints.txt -e ./fme[dev]
+          uv pip install --system -c constraints.txt -e .[dev]
       - name: Run pytest
         run: |
           make test_very_fast

.gitignore

@@ -1,5 +1,5 @@
-fme/docs/available_modules.rst
-fme/docs/_build
+docs/available_modules.rst
+docs/_build
 
 .vscode
 

.pre-commit-config.yaml

@@ -3,22 +3,29 @@ repos:
   rev: v0.8.1
   hooks:
     - id: ruff
-      args: ["--fix", "--config", "fme/pyproject.toml"]
+      args: ["--fix", "--config", "pyproject.toml"]
     - id: ruff-format
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0
     hooks:
     - id: check-added-large-files
       args: [--maxkb=250]
     - id: trailing-whitespace
+    - id: file-contents-sorter
+      files: |
+            (?x)^(
+                ^.*requirements.*\.txt|
+                constraints.txt|
+                analysis-deps.txt
+            )$
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.2.0
+    rev: v1.15.0
     hooks:
     - id: mypy
-      additional_dependencies: ["types-PyYaml==5.4.3"]
+      additional_dependencies: ["types-PyYaml==5.4.3", "wandb==0.19.0"]
       args: ["--ignore-missing-imports", "--check-untyped-defs"]
       exclude: |
         (?x)^(
         .+/conf.py |
-        .+/conftest.py
+        .+/conftest.py |
         )$

.readthedocs.yaml

@@ -17,7 +17,7 @@ build:
 
 # Build documentation in the "docs/" directory with Sphinx
 sphinx:
-  configuration: fme/docs/conf.py
+  configuration: docs/conf.py
 
 # Optionally build your docs in additional formats such as PDF and ePub
 # formats:
@@ -29,5 +29,5 @@ sphinx:
 # See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
 python:
    install:
-   - requirements: fme/docs/requirements.txt
-   - requirements: fme/requirements.txt
+   - requirements: docs/requirements.txt
+   - requirements: requirements.txt

Makefile

@@ -3,22 +3,34 @@ IMAGE ?= fme
 ENVIRONMENT_NAME ?= fme
 DEPLOY_TARGET ?= pypi
 
+ifeq ($(shell uname), Linux)
+	CONDA_PACKAGES=gxx_linux-64 pip
+else
+	CONDA_PACKAGES=pip
+endif
+
 build_docker_image:
-	docker build --platform=linux/amd64 -f docker/Dockerfile -t $(IMAGE):$(VERSION) .
+	DOCKER_BUILDKIT=1 docker build --platform=linux/amd64 -f docker/Dockerfile -t $(IMAGE):$(VERSION) --target production .
 
 enter_docker_image: build_docker_image
 	docker run -it --rm $(IMAGE):$(VERSION) bash
 
+
 # recommended to deactivate current conda environment before running this
 create_environment:
-	conda create -n $(ENVIRONMENT_NAME) python=3.10 pip
+	conda create -n $(ENVIRONMENT_NAME) python=3.11 $(CONDA_PACKAGES)
 	conda run --no-capture-output -n $(ENVIRONMENT_NAME) python -m pip install uv
-	conda run --no-capture-output -n $(ENVIRONMENT_NAME) uv pip install -c constraints.txt -e ./fme[dev,docs]
+	conda run --no-capture-output -n $(ENVIRONMENT_NAME) uv pip install -c constraints.txt -e .[dev,docs]
+	conda run --no-capture-output -n $(ENVIRONMENT_NAME) uv pip install --no-build-isolation -c constraints.txt -e .[dev,docs,healpix]
 	conda run --no-capture-output -n $(ENVIRONMENT_NAME) uv pip install -r analysis-deps.txt
 
 test:
 	pytest --durations 40 .
 
+# --cov must come  after pytest args to use the sources defined by config
+test_cov:
+	pytest --durations 40 --cov --cov-report=term-missing:skip-covered --cov-config=pyproject.toml .
+
 test_fast:
 	pytest --durations 40 --fast .
 
@@ -29,11 +41,11 @@ test_very_fast:
 # requires fme[deploy] to be installed
 
 build_pypi:
-	rm -rf fme/dist
-	cd fme && python -m build
+	rm -rf dist
+	python -m build
 
 deploy_pypi: build_pypi
-	cd fme && twine upload --repository $(DEPLOY_TARGET) dist/*
+	twine upload --repository $(DEPLOY_TARGET) dist/*
 
 deploy_test_pypi: DEPLOY_TARGET = testpypi
 deploy_test_pypi: deploy_pypi

fme/README.md → PACKAGE_README.md

@@ -2,11 +2,7 @@
 [![PyPI](https://img.shields.io/pypi/v/fme.svg)](https://pypi.org/project/fme/)
 
 # FME: Weather/Climate Model Emulation
-This package contains code to train and evaluate weather/climate model emulators as seen in
-"ACE: A fast, skillful learned global atmospheric model for climate prediction" ([arxiv:2310.02074](https://arxiv.org/abs/2310.02074))
-and "Application of the Ai2 Climate Emulator to E3SMv2's global atmosphere model, with a focus on precipitation fidelity"
-([JGR-ML](https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2024JH000136)).
-
+This package contains code to train and evaluate weather/climate model emulators.
 
 ## Installation
 

README.md

@@ -7,11 +7,12 @@
 
 Ai2 Climate Emulator (ACE) is a fast machine learning model that simulates global atmospheric variability in a changing climate over time scales ranging from hours to centuries.
 
-This repo contains code accompanying four papers describing ACE models:
+This repo contains code accompanying five papers describing ACE models:
 - "ACE: A fast, skillful learned global atmospheric model for climate prediction" ([link](https://arxiv.org/abs/2310.02074))
 - "Application of the Ai2 Climate Emulator to E3SMv2's global atmosphere model, with a focus on precipitation fidelity" ([link](https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2024JH000136))
-- "ACE2: Accurately learning subseasonal to decadal atmospheric variability and forced responses" ([link](https://arxiv.org/abs/2411.11268))
+- "ACE2: Accurately learning subseasonal to decadal atmospheric variability and forced responses" ([link](https://www.nature.com/articles/s41612-025-01090-0))
 - "ACE2-SOM: Coupling to a slab ocean and learning the sensitivity of climate to changes in CO2" ([link](https://arxiv.org/abs/2412.04418))
+- "Applying the ACE2 Emulator to SST Green's Functions for the E3SMv3 Global Atmosphere Model" ([link](https://arxiv.org/abs/2505.08742))
 
 ## Installation
 
@@ -25,25 +26,4 @@ See complete documentation [here](https://ai2-climate-emulator.readthedocs.io/en
 
 ## Model checkpoints
 
-Pretrained model checkpoints are available in the [ACE Hugging Face](https://huggingface.co/collections/allenai/ace-67327d822f0f0d8e0e5e6ca4) collection.
-
-## Available datasets
-Two versions of the complete dataset described in [arxiv:2310.02074](https://arxiv.org/abs/2310.02074)
-are available on a [requester pays](https://cloud.google.com/storage/docs/requester-pays) Google Cloud Storage bucket:
-```
-gs://ai2cm-public-requester-pays/2023-11-29-ai2-climate-emulator-v1/data/repeating-climSST-1deg-zarrs
-gs://ai2cm-public-requester-pays/2023-11-29-ai2-climate-emulator-v1/data/repeating-climSST-1deg-netCDFs
-```
-The `zarr` format is convenient for ad-hoc analysis. The netCDF version contains our
-train/validation split which was used for training and inference.
-
-The datasets used in the [ACE2 paper](https://arxiv.org/abs/2411.11268) are available at:
-```
-gs://ai2cm-public-requester-pays/2024-11-13-ai2-climate-emulator-v2-amip/data/c96-1deg-shield/
-gs://ai2cm-public-requester-pays/2024-11-13-ai2-climate-emulator-v2-amip/data/era5-1deg-1940-2022.zarr/
-```
-
-The dataset used in the [ACE2-SOM paper](https://arxiv.org/abs/2412.04418) is available at:
-```
-gs://ai2cm-public-requester-pays/2024-12-05-ai2-climate-emulator-v2-som/SHiELD-SOM-C96
-```
+Pretrained model checkpoints, and datasets to run them, are available in the [ACE Hugging Face](https://huggingface.co/collections/allenai/ace-67327d822f0f0d8e0e5e6ca4) collection.

analysis-deps.txt

@@ -1,13 +1,9 @@
-# these are some packages which are convenient to have installed for ad-hoc analysis
-# but which are not requirements of the "fme" package. We do not relist the fme
-# dependencies here.
-beaker-py
+# these are convenient to have installed for ad-hoc analysis but are not requirements of the "fme" package
 Bottleneck
-cartopy>=0.22.0
+bokeh>=3.1.0
 dask[distributed]
 ipywidgets
-nc-time-axis
 jupyterlab
+nc-time-axis
 pyproj<3.7
 seaborn
-bokeh>=3.1.0