From 0afdfee060a4c884797baea4779d9a4cc128c8c6 Mon Sep 17 00:00:00 2001 From: Leif Denby Date: Mon, 13 May 2024 18:48:06 +0200 Subject: [PATCH 01/40] wip on simplifying pre-commit setup --- .flake8 | 3 ++ .github/workflows/pre-commit.yml | 5 ++- .pre-commit-config.yaml | 58 ++++++++++++++++---------------- requirements.txt | 6 +--- 4 files changed, 35 insertions(+), 37 deletions(-) create mode 100644 .flake8 diff --git a/.flake8 b/.flake8 new file mode 100644 index 00000000..b02dd545 --- /dev/null +++ b/.flake8 @@ -0,0 +1,3 @@ +[flake8] +max-line-length = 88 +ignore = E203, F811, I002, W503 diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml index a6ad84f1..4828afc9 100644 --- a/.github/workflows/pre-commit.yml +++ b/.github/workflows/pre-commit.yml @@ -28,6 +28,5 @@ jobs: pip install pyg-lib==0.2.0 torch-scatter==2.1.1 torch-sparse==0.6.17 \ torch-cluster==1.6.1 torch-geometric==2.3.1 \ -f https://pytorch-geometric.com/whl/torch-2.0.1+cpu.html - - name: Run pre-commit hooks - run: | - pre-commit run --all-files + - uses: pre-commit/action@v2.0.3 + diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index f48eca67..106cb64b 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,51 +1,51 @@ repos: -- repo: https://github.com/pre-commit/pre-commit-hooks + - repo: https://github.com/pre-commit/pre-commit-hooks rev: v4.5.0 hooks: - - id: check-ast - - id: check-case-conflict - - id: check-docstring-first - - id: check-symlinks - - id: check-toml - - id: check-yaml - - id: debug-statements - - id: end-of-file-fixer - - id: trailing-whitespace -- repo: local + - id: check-ast + - id: check-case-conflict + - id: check-docstring-first + - id: check-symlinks + - id: check-toml + - id: check-yaml + - id: debug-statements + - id: end-of-file-fixer + - id: trailing-whitespace + + - repo: https://github.com/codespell-project/codespell + rev: 2.0.0 hooks: - - id: codespell - name: codespell + - id: codespell description: Check for spelling errors language: system - entry: codespell -- repo: local + + - repo: https://github.com/psf/black + rev: 22.3.0 hooks: - - id: black - name: black + - id: black description: Format Python code language: system - entry: black types_or: [python, pyi] -- repo: local + + - repo: https://github.com/PyCQA/isort + rev: 5.12.0 hooks: - - id: isort - name: isort + - id: isort description: Group and sort Python imports language: system - entry: isort types_or: [python, pyi, cython] -- repo: local + + - repo: https://github.com/PyCQA/flake8 + rev: 6.1.0 hooks: - - id: flake8 - name: flake8 + - id: flake8 description: Check Python code for correctness, consistency and adherence to best practices language: system - entry: flake8 --max-line-length=80 --ignore=E203,F811,I002,W503 types: [python] -- repo: local + + - repo: https://github.com/pylint-dev/pylint hooks: - - id: pylint - name: pylint + - id: pylint entry: pylint -rn -sn language: system types: [python] diff --git a/requirements.txt b/requirements.txt index 5a2111b2..f381d54f 100644 --- a/requirements.txt +++ b/requirements.txt @@ -10,10 +10,6 @@ Cartopy>=0.22.0 pyproj>=3.4.1 tueplots>=0.0.8 plotly>=5.15.0 + # for dev -codespell>=2.0.0 -black>=21.9b0 -isort>=5.9.3 -flake8>=4.0.1 -pylint>=3.0.3 pre-commit>=2.15.0 From 28118a6e82775a4cb6d0d3d7e89e50c86541d320 Mon Sep 17 00:00:00 2001 From: Leif Denby Date: Mon, 13 May 2024 18:51:46 +0200 Subject: [PATCH 02/40] setup pylint version --- .pre-commit-config.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 106cb64b..28cd91b9 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -44,6 +44,7 @@ repos: types: [python] - repo: https://github.com/pylint-dev/pylint + rev: 2.0.0 hooks: - id: pylint entry: pylint -rn -sn From 3da310860f209bcaec6387fbebc0468505aa6331 Mon Sep 17 00:00:00 2001 From: Leif Denby Date: Mon, 13 May 2024 19:09:09 +0200 Subject: [PATCH 03/40] remove external deps install in cicd linting --- .github/workflows/pre-commit.yml | 11 ----------- 1 file changed, 11 deletions(-) diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml index 4828afc9..0ff792a3 100644 --- a/.github/workflows/pre-commit.yml +++ b/.github/workflows/pre-commit.yml @@ -11,22 +11,11 @@ on: jobs: pre-commit-job: runs-on: ubuntu-latest - defaults: - run: - shell: bash -l {0} steps: - uses: actions/checkout@v2 - name: Set up Python uses: actions/setup-python@v2 with: python-version: 3.9 - - name: Install pre-commit hooks - run: | - pip install torch==2.0.1 torchvision==0.15.2 torchaudio==2.0.2 \ - --index-url https://download.pytorch.org/whl/cpu - pip install -r requirements.txt - pip install pyg-lib==0.2.0 torch-scatter==2.1.1 torch-sparse==0.6.17 \ - torch-cluster==1.6.1 torch-geometric==2.3.1 \ - -f https://pytorch-geometric.com/whl/torch-2.0.1+cpu.html - uses: pre-commit/action@v2.0.3 From ea64309bf9215ba900fb3bcfdf4ea17219be7ef0 Mon Sep 17 00:00:00 2001 From: Leif Denby Date: Mon, 13 May 2024 19:31:34 +0200 Subject: [PATCH 04/40] create project --- .gitignore | 3 ++ README.md | 38 +++++++++---------- .../create_grid_features.py | 0 create_mesh.py => neural_lam/create_mesh.py | 0 .../create_parameter_weights.py | 0 train_model.py => neural_lam/train_model.py | 0 pyproject.toml | 36 ++++++++++++++++++ requirements.txt | 15 -------- tests/__init__.py | 5 +++ 9 files changed, 63 insertions(+), 34 deletions(-) rename create_grid_features.py => neural_lam/create_grid_features.py (100%) rename create_mesh.py => neural_lam/create_mesh.py (100%) rename create_parameter_weights.py => neural_lam/create_parameter_weights.py (100%) rename train_model.py => neural_lam/train_model.py (100%) delete mode 100644 requirements.txt create mode 100644 tests/__init__.py diff --git a/.gitignore b/.gitignore index 7bb826a2..cd447c4e 100644 --- a/.gitignore +++ b/.gitignore @@ -72,3 +72,6 @@ tags # Coc configuration directory .vim + +# pdm +.pdm-python diff --git a/README.md b/README.md index 67d9d9b1..e59bf3f5 100644 --- a/README.md +++ b/README.md @@ -45,7 +45,7 @@ Still, some restrictions are inevitable: ## A note on the limited area setting Currently we are using these models on a limited area covering the Nordic region, the so called MEPS area (see [paper](https://arxiv.org/abs/2309.17370)). There are still some parts of the code that is quite specific for the MEPS area use case. -This is in particular true for the mesh graph creation (`create_mesh.py`) and some of the constants used (`neural_lam/constants.py`). +This is in particular true for the mesh graph creation (`neural_lam.create_mesh`) and some of the constants used (`neural_lam.constants`). If there is interest to use Neural-LAM for other areas it is not a substantial undertaking to refactor the code to be fully area-agnostic. We would be happy to support such enhancements. See the issues https://github.com/joeloskarsson/neural-lam/issues/2, https://github.com/joeloskarsson/neural-lam/issues/3 and https://github.com/joeloskarsson/neural-lam/issues/4 for some initial ideas on how this could be done. @@ -77,7 +77,7 @@ See the [repository format section](#format-of-data-directory) for details on th The full MEPS dataset can be shared with other researchers on request, contact us for this. A tiny subset of the data (named `meps_example`) is available in `example_data.zip`, which can be downloaded from [here](https://liuonline-my.sharepoint.com/:f:/g/personal/joeos82_liu_se/EuiUuiGzFIFHruPWpfxfUmYBSjhqMUjNExlJi9W6ULMZ1w?e=97pnGX). Download the file and unzip in the neural-lam directory. -All graphs used in the paper are also available for download at the same link (but can as easily be re-generated using `create_mesh.py`). +All graphs used in the paper are also available for download at the same link (but can as easily be re-generated using `python -m neural_lam.create_mesh`). Note that this is far too little data to train any useful models, but all scripts can be ran with it. It should thus be useful to make sure that your python environment is set up correctly and that all the code can be ran without any issues. @@ -86,31 +86,31 @@ An overview of how the different scripts and files depend on each other is given

-In order to start training models at least three pre-processing scripts have to be ran: +In order to start training models at least three pre-processing scripts have to be run: -* `create_mesh.py` -* `create_grid_features.py` -* `create_parameter_weights.py` +* `python -m neural_lam.create_mesh` +* `python -m neural_lam.create_grid_features` +* `python -m neural_lam.create_parameter_weights` ### Create graph -Run `create_mesh.py` with suitable options to generate the graph you want to use (see `python create_mesh.py --help` for a list of options). +Run `python -m neural_lam.create_mesh` with suitable options to generate the graph you want to use (see `python neural_lam.create_mesh --help` for a list of options). The graphs used for the different models in the [paper](https://arxiv.org/abs/2309.17370) can be created as: -* **GC-LAM**: `python create_mesh.py --graph multiscale` -* **Hi-LAM**: `python create_mesh.py --graph hierarchical --hierarchical 1` (also works for Hi-LAM-Parallel) -* **L1-LAM**: `python create_mesh.py --graph 1level --levels 1` +* **GC-LAM**: `python -m neural_lam.create_mesh --graph multiscale` +* **Hi-LAM**: `python -m neural_lam.create_mesh --graph hierarchical --hierarchical 1` (also works for Hi-LAM-Parallel) +* **L1-LAM**: `python -m neural_lam.create_mesh --graph 1level --levels 1` The graph-related files are stored in a directory called `graphs`. ### Create remaining static features -To create the remaining static files run the scripts `create_grid_features.py` and `create_parameter_weights.py`. +To create the remaining static files run the scripts `python -m neural_lam.create_grid_features` and `python -m neural_lam.create_parameter_weights`. The main option to set for these is just which dataset to use. ## Weights & Biases Integration The project is fully integrated with [Weights & Biases](https://www.wandb.ai/) (W&B) for logging and visualization, but can just as easily be used without it. When W&B is used, training configuration, training/test statistics and plots are sent to the W&B servers and made available in an interactive web interface. If W&B is turned off, logging instead saves everything locally to a directory like `wandb/dryrun...`. -The W&B project name is set to `neural-lam`, but this can be changed in `neural_lam/constants.py`. +The W&B project name is set to `neural-lam`, but this can be changed in `neural_lam.constants`. See the [W&B documentation](https://docs.wandb.ai/) for details. If you would like to login and use W&B, run: @@ -123,8 +123,8 @@ wandb off ``` ## Train Models -Models can be trained using `train_model.py`. -Run `python train_model.py --help` for a full list of training options. +Models can be trained using `python -m neural_lam.train_model`. +Run `python neural_lam.train_model --help` for a full list of training options. A few of the key ones are outlined below: * `--dataset`: Which data to train on @@ -143,12 +143,12 @@ This model class is used both for the L1-LAM and GC-LAM models from the [paper]( To train 1L-LAM use ``` -python train_model.py --model graph_lam --graph 1level ... +python -m neural_lam.train_model --model graph_lam --graph 1level ... ``` To train GC-LAM use ``` -python train_model.py --model graph_lam --graph multiscale ... +python -m neural_lam.train_model --model graph_lam --graph multiscale ... ``` ### Hi-LAM @@ -156,7 +156,7 @@ A version of Graph-LAM that uses a hierarchical mesh graph and performs sequenti To train Hi-LAM use ``` -python train_model.py --model hi_lam --graph hierarchical ... +python -m neural_lam.train_model --model hi_lam --graph hierarchical ... ``` ### Hi-LAM-Parallel @@ -165,13 +165,13 @@ Not included in the paper as initial experiments showed worse results than Hi-LA To train Hi-LAM-Parallel use ``` -python train_model.py --model hi_lam_parallel --graph hierarchical ... +python -m neural_lam.train_model --model hi_lam_parallel --graph hierarchical ... ``` Checkpoint files for our models trained on the MEPS data are available upon request. ## Evaluate Models -Evaluation is also done using `train_model.py`, but using the `--eval` option. +Evaluation is also done using `python -m neural_lam.train_model`, but using the `--eval` option. Use `--eval val` to evaluate the model on the validation set and `--eval test` to evaluate on test data. Most of the training options are also relevant for evaluation (not `ar_steps`, evaluation always unrolls full forecasts). Some options specifically important for evaluation are: diff --git a/create_grid_features.py b/neural_lam/create_grid_features.py similarity index 100% rename from create_grid_features.py rename to neural_lam/create_grid_features.py diff --git a/create_mesh.py b/neural_lam/create_mesh.py similarity index 100% rename from create_mesh.py rename to neural_lam/create_mesh.py diff --git a/create_parameter_weights.py b/neural_lam/create_parameter_weights.py similarity index 100% rename from create_parameter_weights.py rename to neural_lam/create_parameter_weights.py diff --git a/train_model.py b/neural_lam/train_model.py similarity index 100% rename from train_model.py rename to neural_lam/train_model.py diff --git a/pyproject.toml b/pyproject.toml index b513a258..ccc8953f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,3 +1,32 @@ +[project] +# PEP 621 project metadata +# See https://www.python.org/dev/peps/pep-0621/ +dependencies = [ + "numpy>=1.24.2", + "wandb>=0.13.10", + "matplotlib>=3.7.0", + "scipy>=1.10.0", + "pytorch-lightning>=2.0.3", + "shapely>=2.0.1", + "networkx>=3.0", + "Cartopy>=0.22.0", + "pyproj>=3.4.1", + "tueplots>=0.0.8", + "plotly>=5.15.0", + "pre-commit>=2.15.0", +] +requires-python = ">=3.10" +name = "neural-lam" +version = "0.1.0" +description = "Neural Weather Prediction for Limited Area Modeling" +authors = [ + {name = "Joel Oskarsson", email = "joel.oskarsson@liu.se"}, + {name = "Simon Adamov", email = "simon.adamov@meteoswiss.ch"}, + {name = "Leif Denby", email = "lcd@dmi.dk"}, +] +readme = "README.md" +license = {text = "MIT"} + [tool.black] line-length = 80 @@ -63,3 +92,10 @@ max-statements=100 # Allow for some more involved functions allow-any-import-level="neural_lam" [tool.pylint.SIMILARITIES] min-similarity-lines=10 + + +[tool.pdm] +distribution = true +[build-system] +requires = ["pdm-backend"] +build-backend = "pdm.backend" diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index f381d54f..00000000 --- a/requirements.txt +++ /dev/null @@ -1,15 +0,0 @@ -# for all -numpy>=1.24.2 -wandb>=0.13.10 -matplotlib>=3.7.0 -scipy>=1.10.0 -pytorch-lightning>=2.0.3 -shapely>=2.0.1 -networkx>=3.0 -Cartopy>=0.22.0 -pyproj>=3.4.1 -tueplots>=0.0.8 -plotly>=5.15.0 - -# for dev -pre-commit>=2.15.0 diff --git a/tests/__init__.py b/tests/__init__.py new file mode 100644 index 00000000..2f88fa16 --- /dev/null +++ b/tests/__init__.py @@ -0,0 +1,5 @@ +import neural_lam + + +def test_import(): + assert neural_lam is not None From 0c68537b1bb8f2e73334fe87e3a4cb220091250f Mon Sep 17 00:00:00 2001 From: Leif Denby Date: Mon, 13 May 2024 19:34:48 +0200 Subject: [PATCH 05/40] replace absolute imports with relative --- neural_lam/create_parameter_weights.py | 4 ++-- neural_lam/interaction_net.py | 2 +- neural_lam/models/ar_model.py | 2 +- neural_lam/models/base_graph_model.py | 6 +++--- neural_lam/models/base_hi_graph_model.py | 6 +++--- neural_lam/models/graph_lam.py | 6 +++--- neural_lam/models/hi_lam.py | 4 ++-- neural_lam/models/hi_lam_parallel.py | 4 ++-- neural_lam/train_model.py | 10 +++++----- neural_lam/utils.py | 2 +- neural_lam/vis.py | 2 +- neural_lam/weather_dataset.py | 2 +- 12 files changed, 25 insertions(+), 25 deletions(-) diff --git a/neural_lam/create_parameter_weights.py b/neural_lam/create_parameter_weights.py index 494a5e81..ff420adf 100644 --- a/neural_lam/create_parameter_weights.py +++ b/neural_lam/create_parameter_weights.py @@ -8,8 +8,8 @@ from tqdm import tqdm # First-party -from neural_lam import constants -from neural_lam.weather_dataset import WeatherDataset +from . import constants +from .weather_dataset import WeatherDataset def main(): diff --git a/neural_lam/interaction_net.py b/neural_lam/interaction_net.py index 663f27e4..a81a3ab4 100644 --- a/neural_lam/interaction_net.py +++ b/neural_lam/interaction_net.py @@ -4,7 +4,7 @@ from torch import nn # First-party -from neural_lam import utils +from . import utils class InteractionNet(pyg.nn.MessagePassing): diff --git a/neural_lam/models/ar_model.py b/neural_lam/models/ar_model.py index 7d0a8320..3da353a8 100644 --- a/neural_lam/models/ar_model.py +++ b/neural_lam/models/ar_model.py @@ -9,7 +9,7 @@ import wandb # First-party -from neural_lam import constants, metrics, utils, vis +from .. import constants, metrics, utils, vis class ARModel(pl.LightningModule): diff --git a/neural_lam/models/base_graph_model.py b/neural_lam/models/base_graph_model.py index 256d4adc..77be82eb 100644 --- a/neural_lam/models/base_graph_model.py +++ b/neural_lam/models/base_graph_model.py @@ -2,9 +2,9 @@ import torch # First-party -from neural_lam import utils -from neural_lam.interaction_net import InteractionNet -from neural_lam.models.ar_model import ARModel +from .. import utils +from ..interaction_net import InteractionNet +from .ar_model import ARModel class BaseGraphModel(ARModel): diff --git a/neural_lam/models/base_hi_graph_model.py b/neural_lam/models/base_hi_graph_model.py index 8ce87030..92533f86 100644 --- a/neural_lam/models/base_hi_graph_model.py +++ b/neural_lam/models/base_hi_graph_model.py @@ -2,9 +2,9 @@ from torch import nn # First-party -from neural_lam import utils -from neural_lam.interaction_net import InteractionNet -from neural_lam.models.base_graph_model import BaseGraphModel +from .. import utils +from ..interaction_net import InteractionNet +from .base_graph_model import BaseGraphModel class BaseHiGraphModel(BaseGraphModel): diff --git a/neural_lam/models/graph_lam.py b/neural_lam/models/graph_lam.py index f767fba0..6bbe83cc 100644 --- a/neural_lam/models/graph_lam.py +++ b/neural_lam/models/graph_lam.py @@ -2,9 +2,9 @@ import torch_geometric as pyg # First-party -from neural_lam import utils -from neural_lam.interaction_net import InteractionNet -from neural_lam.models.base_graph_model import BaseGraphModel +from . import utils +from ..interaction_net import InteractionNet +from .base_graph_model import BaseGraphModel class GraphLAM(BaseGraphModel): diff --git a/neural_lam/models/hi_lam.py b/neural_lam/models/hi_lam.py index 4d7eb94c..df9d3cbb 100644 --- a/neural_lam/models/hi_lam.py +++ b/neural_lam/models/hi_lam.py @@ -2,8 +2,8 @@ from torch import nn # First-party -from neural_lam.interaction_net import InteractionNet -from neural_lam.models.base_hi_graph_model import BaseHiGraphModel +from ..interaction_net import InteractionNet +from .base_hi_graph_model import BaseHiGraphModel class HiLAM(BaseHiGraphModel): diff --git a/neural_lam/models/hi_lam_parallel.py b/neural_lam/models/hi_lam_parallel.py index 740824e1..d6dc27ee 100644 --- a/neural_lam/models/hi_lam_parallel.py +++ b/neural_lam/models/hi_lam_parallel.py @@ -3,8 +3,8 @@ import torch_geometric as pyg # First-party -from neural_lam.interaction_net import InteractionNet -from neural_lam.models.base_hi_graph_model import BaseHiGraphModel +from ..interaction_net import InteractionNet +from .base_hi_graph_model import BaseHiGraphModel class HiLAMParallel(BaseHiGraphModel): diff --git a/neural_lam/train_model.py b/neural_lam/train_model.py index 96d21a3f..9120cd4b 100644 --- a/neural_lam/train_model.py +++ b/neural_lam/train_model.py @@ -9,11 +9,11 @@ from lightning_fabric.utilities import seed # First-party -from neural_lam import constants, utils -from neural_lam.models.graph_lam import GraphLAM -from neural_lam.models.hi_lam import HiLAM -from neural_lam.models.hi_lam_parallel import HiLAMParallel -from neural_lam.weather_dataset import WeatherDataset +from . import constants, utils +from .models.graph_lam import GraphLAM +from .models.hi_lam import HiLAM +from .models.hi_lam_parallel import HiLAMParallel +from .weather_dataset import WeatherDataset MODELS = { "graph_lam": GraphLAM, diff --git a/neural_lam/utils.py b/neural_lam/utils.py index 31715502..29d638fa 100644 --- a/neural_lam/utils.py +++ b/neural_lam/utils.py @@ -8,7 +8,7 @@ from tueplots import bundles, figsizes # First-party -from neural_lam import constants +from . import constants def load_dataset_stats(dataset_name, device="cpu"): diff --git a/neural_lam/vis.py b/neural_lam/vis.py index cef34a84..80616e3b 100644 --- a/neural_lam/vis.py +++ b/neural_lam/vis.py @@ -4,7 +4,7 @@ import numpy as np # First-party -from neural_lam import constants, utils +from . import constants, utils @matplotlib.rc_context(utils.fractional_plot_bundle(1)) diff --git a/neural_lam/weather_dataset.py b/neural_lam/weather_dataset.py index eeefc313..1c2f8fde 100644 --- a/neural_lam/weather_dataset.py +++ b/neural_lam/weather_dataset.py @@ -8,7 +8,7 @@ import torch # First-party -from neural_lam import constants, utils +from . import constants, utils class WeatherDataset(torch.utils.data.Dataset): From 4b77be6cf0a74084c6f6f76d1e168ee421240292 Mon Sep 17 00:00:00 2001 From: Leif Denby Date: Mon, 13 May 2024 19:35:45 +0200 Subject: [PATCH 06/40] simplify black config --- pyproject.toml | 18 ------------------ 1 file changed, 18 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index ccc8953f..0224dbeb 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -31,25 +31,7 @@ license = {text = "MIT"} line-length = 80 [tool.isort] -default_section = "THIRDPARTY" profile = "black" -# Headings -import_heading_stdlib = "Standard library" -import_heading_thirdparty = "Third-party" -import_heading_firstparty = "First-party" -import_heading_localfolder = "Local" -# Known modules to avoid misclassification -known_standard_library = [ - # Add standard library modules that may be misclassified by isort -] -known_third_party = [ - # Add third-party modules that may be misclassified by isort - "wandb", -] -known_first_party = [ - # Add first-party modules that may be misclassified by isort - "neural_lam", -] [tool.flake8] max-line-length = 80 From f2bae03e3a1ffb537aad45aa1cc678b86573daea Mon Sep 17 00:00:00 2001 From: Leif Denby Date: Mon, 13 May 2024 19:39:32 +0200 Subject: [PATCH 07/40] headers for import sections no longer needed --- pyproject.toml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 0224dbeb..02213b0c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -52,13 +52,13 @@ skip = "requirements/*" ignore = [ "create_mesh.py", # Disable linting for now, as major rework is planned/expected ] -# Temporary fix for import neural_lam statements until set up as proper package -init-hook='import sys; sys.path.append(".")' + [tool.pylint.TYPECHECK] generated-members = [ "numpy.*", "torch.*", ] + [tool.pylint.'MESSAGES CONTROL'] disable = [ "C0114", # 'missing-module-docstring', Do not require module docstrings From 1d12b0d917e87cf0d834dc603da00a727f72c332 Mon Sep 17 00:00:00 2001 From: Leif Denby Date: Mon, 13 May 2024 21:38:49 +0200 Subject: [PATCH 08/40] minor fixes --- .github/workflows/pre-commit.yml | 1 - .pre-commit-config.yaml | 17 +---------------- neural_lam/models/base_hi_graph_model.py | 12 ++++++------ plot_graph.py | 6 +----- 4 files changed, 8 insertions(+), 28 deletions(-) diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml index 0ff792a3..29203557 100644 --- a/.github/workflows/pre-commit.yml +++ b/.github/workflows/pre-commit.yml @@ -18,4 +18,3 @@ jobs: with: python-version: 3.9 - uses: pre-commit/action@v2.0.3 - diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 28cd91b9..0547c6b9 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -13,40 +13,25 @@ repos: - id: trailing-whitespace - repo: https://github.com/codespell-project/codespell - rev: 2.0.0 + rev: v2.2.6 hooks: - id: codespell description: Check for spelling errors - language: system - repo: https://github.com/psf/black rev: 22.3.0 hooks: - id: black description: Format Python code - language: system - types_or: [python, pyi] - repo: https://github.com/PyCQA/isort rev: 5.12.0 hooks: - id: isort description: Group and sort Python imports - language: system - types_or: [python, pyi, cython] - repo: https://github.com/PyCQA/flake8 rev: 6.1.0 hooks: - id: flake8 description: Check Python code for correctness, consistency and adherence to best practices - language: system - types: [python] - - - repo: https://github.com/pylint-dev/pylint - rev: 2.0.0 - hooks: - - id: pylint - entry: pylint -rn -sn - language: system - types: [python] diff --git a/neural_lam/models/base_hi_graph_model.py b/neural_lam/models/base_hi_graph_model.py index 8ce87030..d9a4c676 100644 --- a/neural_lam/models/base_hi_graph_model.py +++ b/neural_lam/models/base_hi_graph_model.py @@ -179,9 +179,9 @@ def process_step(self, mesh_rep): ) # Update node and edge vectors in lists - mesh_rep_levels[level_l] = ( - new_node_rep # (B, num_mesh_nodes[l], d_h) - ) + mesh_rep_levels[ + level_l + ] = new_node_rep # (B, num_mesh_nodes[l], d_h) mesh_up_rep[level_l - 1] = new_edge_rep # (B, M_up[l-1], d_h) # - PROCESSOR - @@ -207,9 +207,9 @@ def process_step(self, mesh_rep): new_node_rep = gnn(send_node_rep, rec_node_rep, edge_rep) # Update node and edge vectors in lists - mesh_rep_levels[level_l] = ( - new_node_rep # (B, num_mesh_nodes[l], d_h) - ) + mesh_rep_levels[ + level_l + ] = new_node_rep # (B, num_mesh_nodes[l], d_h) # Return only bottom level representation return mesh_rep_levels[0] # (B, num_mesh_nodes[0], d_h) diff --git a/plot_graph.py b/plot_graph.py index 48427d5c..27e230e7 100644 --- a/plot_graph.py +++ b/plot_graph.py @@ -47,11 +47,7 @@ def main(): # Load graph data hierarchical, graph_ldict = utils.load_graph(args.graph) - ( - g2m_edge_index, - m2g_edge_index, - m2m_edge_index, - ) = ( + (g2m_edge_index, m2g_edge_index, m2m_edge_index,) = ( graph_ldict["g2m_edge_index"], graph_ldict["m2g_edge_index"], graph_ldict["m2m_edge_index"], From ad0accc6dafc1bcdbbb7833654b707d997553071 Mon Sep 17 00:00:00 2001 From: Leif Denby Date: Mon, 13 May 2024 21:41:49 +0200 Subject: [PATCH 09/40] run on all branch pushes --- .github/workflows/pre-commit.yml | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git 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name: Set up Python 3.10 + uses: actions/setup-python@v2 + with: + python-version: 3.10 + + - name: Install pdm + run: | + python -m pip install pdm + pdm --version + + - name: Install torch + run: | + python -m pip install torch==1.8.1+cpu -f https://download.pytorch.org/whl/torch_stable.html + + - name: Install package (including dev dependencies) + run: | + pdm install + pdm install --dev + + - name: Run tests + run: | + pdm run pytest diff --git a/tests/test_base.py b/tests/test_base.py new file mode 100644 index 00000000..c3a89171 --- /dev/null +++ b/tests/test_base.py @@ -0,0 +1,7 @@ +import neural_lam +import neural_lam.train_model + + +def test_import(): + assert neural_lam is not None + assert neural_lam.train_model is not None From 5ad02302de98267950aac271c91bf2b46a0f9ce5 Mon Sep 17 00:00:00 2001 From: Leif Denby Date: Mon, 13 May 2024 23:36:34 +0200 Subject: [PATCH 12/40] py version must be quoted --- .github/workflows/ci-tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml index 4b43f60d..09f049c3 100644 --- a/.github/workflows/ci-tests.yml +++ b/.github/workflows/ci-tests.yml @@ -16,7 +16,7 @@ jobs: - name: Set up Python 3.10 uses: actions/setup-python@v2 with: - python-version: 3.10 + python-version: "3.10" - name: Install pdm run: | From 35987e577be70107192c5c0da4f483d64acb13c3 Mon Sep 17 00:00:00 2001 From: Leif Denby Date: Mon, 13 May 2024 23:38:43 +0200 Subject: [PATCH 13/40] fix torch install url --- .github/workflows/ci-tests.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml index 09f049c3..47d15f5e 100644 --- a/.github/workflows/ci-tests.yml +++ b/.github/workflows/ci-tests.yml @@ -23,9 +23,9 @@ jobs: python -m pip install pdm pdm --version - - name: Install torch + - name: Install torch (CPU) run: | - python -m pip install torch==1.8.1+cpu -f https://download.pytorch.org/whl/torch_stable.html + python -m pip install torch --index-url https://download.pytorch.org/whl/cpu - name: Install package (including dev dependencies) run: | From 148d7f6a6421a27e0e3865aa1886a318634ff4eb Mon Sep 17 00:00:00 2001 From: Leif Denby Date: Mon, 13 May 2024 23:40:45 +0200 Subject: [PATCH 14/40] use pdm in ci/cd --- .github/workflows/ci-tests.yml | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml index 47d15f5e..34ae6d93 100644 --- a/.github/workflows/ci-tests.yml +++ b/.github/workflows/ci-tests.yml @@ -13,15 +13,11 @@ jobs: - name: Checkout uses: actions/checkout@v2 - - name: Set up Python 3.10 - uses: actions/setup-python@v2 + - name: Install pdm + uses: pdm-project/setup-pdm@v4 with: python-version: "3.10" - - - name: Install pdm - run: | - python -m pip install pdm - pdm --version + cache: true - name: Install torch (CPU) run: | From 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[ + {file = "pluggy-1.5.0-py3-none-any.whl", hash = "sha256:44e1ad92c8ca002de6377e165f3e0f1be63266ab4d554740532335b9d75ea669"}, + {file = "pluggy-1.5.0.tar.gz", hash = "sha256:2cffa88e94fdc978c4c574f15f9e59b7f4201d439195c3715ca9e2486f1d0cf1"}, +] + [[package]] name = "pre-commit" version = "3.7.1" @@ -1208,6 +1242,25 @@ files = [ {file = "pyshp-2.3.1.tar.gz", hash = "sha256:4caec82fd8dd096feba8217858068bacb2a3b5950f43c048c6dc32a3489d5af1"}, ] +[[package]] +name = "pytest" +version = "8.2.0" +requires_python = ">=3.8" +summary = "pytest: simple powerful testing with Python" +groups = ["dev"] +dependencies = [ + "colorama; sys_platform == \"win32\"", + "exceptiongroup>=1.0.0rc8; python_version < \"3.11\"", + "iniconfig", + "packaging", + "pluggy<2.0,>=1.5", + "tomli>=1; python_version < \"3.11\"", +] +files = [ + {file = "pytest-8.2.0-py3-none-any.whl", hash = "sha256:1733f0620f6cda4095bbf0d9ff8022486e91892245bb9e7d5542c018f612f233"}, + {file = "pytest-8.2.0.tar.gz", hash = "sha256:d507d4482197eac0ba2bae2e9babf0672eb333017bcedaa5fb1a3d42c1174b3f"}, +] + [[package]] name = "python-dateutil" version = "2.9.0.post0" @@ -1507,6 +1560,18 @@ files = [ {file = "tenacity-8.3.0.tar.gz", hash = "sha256:953d4e6ad24357bceffbc9707bc74349aca9d245f68eb65419cf0c249a1949a2"}, ] +[[package]] +name = "tomli" +version = "2.0.1" +requires_python = ">=3.7" +summary = "A lil' TOML parser" +groups = ["dev"] +marker = "python_version < \"3.11\"" +files = [ + {file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"}, + {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"}, +] + [[package]] name = "torch" version = "2.3.0" diff --git a/pyproject.toml b/pyproject.toml index 02213b0c..d9eb14dd 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -78,6 +78,11 @@ min-similarity-lines=10 [tool.pdm] distribution = true + +[tool.pdm.dev-dependencies] +dev = [ + "pytest>=8.2.0", +] [build-system] requires = ["pdm-backend"] build-backend = "pdm.backend" From 1af15760b01ad37b52494ebae0bf2e0c63b1f8ae Mon Sep 17 00:00:00 2001 From: Leif Denby Date: Mon, 13 May 2024 23:47:33 +0200 Subject: [PATCH 18/40] cache in cicd --- .github/workflows/ci-tests.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml index 0fff9f06..9b73f298 100644 --- a/.github/workflows/ci-tests.yml +++ b/.github/workflows/ci-tests.yml @@ -2,7 +2,7 @@ # needs to first install pdm, then install torch cpu manually and then install the package # then run the tests -name: tests +name: tests (cpu) on: [push, pull_request] @@ -17,6 +17,7 @@ jobs: uses: pdm-project/setup-pdm@v4 with: python-version: "3.10" + cache: true - name: Install torch (CPU) run: | From 7ed7c9765f451f7645cb201ecc2b4afd89c8c1be Mon Sep 17 00:00:00 2001 From: Leif Denby Date: Mon, 13 May 2024 23:50:22 +0200 Subject: [PATCH 19/40] add torch-geometric to deps --- pdm.lock | 78 +++++++++++++++++++++++++++++++++++++++++++++++++- pyproject.toml | 1 + 2 files changed, 78 insertions(+), 1 deletion(-) diff --git a/pdm.lock b/pdm.lock index 6f5e16bf..21467c0d 100644 --- a/pdm.lock +++ b/pdm.lock @@ -5,7 +5,7 @@ groups = ["default", "dev"] strategy = ["cross_platform", "inherit_metadata"] lock_version = "4.4.1" -content_hash = "sha256:042137fa24b1870b761e5e8242a9d8fcad3d4b1a95b3b89d5e280667b9ca2069" +content_hash = "sha256:c6c346f14a001266b5cc8a2eafb2081b9bcba755c41eb0f44525436548a09fde" [[package]] name = "aiohttp" @@ -550,6 +550,17 @@ files = [ {file = "jinja2-3.1.4.tar.gz", hash = "sha256:4a3aee7acbbe7303aede8e9648d13b8bf88a429282aa6122a993f0ac800cb369"}, ] +[[package]] +name = "joblib" +version = "1.4.2" +requires_python = ">=3.8" +summary = "Lightweight pipelining with Python functions" +groups = ["default"] +files = [ + {file = "joblib-1.4.2-py3-none-any.whl", hash = "sha256:06d478d5674cbc267e7496a410ee875abd68e4340feff4490bcb7afb88060ae6"}, + {file = "joblib-1.4.2.tar.gz", hash = "sha256:2382c5816b2636fbd20a09e0f4e9dad4736765fdfb7dca582943b9c1366b3f0e"}, +] + [[package]] name = "kiwisolver" version = "1.4.5" @@ -1347,6 +1358,37 @@ files = [ {file = "requests-2.31.0.tar.gz", hash = "sha256:942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1"}, ] +[[package]] +name = "scikit-learn" +version = "1.4.2" +requires_python = ">=3.9" +summary = "A set of python modules for machine learning and data mining" +groups = ["default"] +dependencies = [ + "joblib>=1.2.0", + "numpy>=1.19.5", + "scipy>=1.6.0", + "threadpoolctl>=2.0.0", +] +files = [ + {file = "scikit-learn-1.4.2.tar.gz", hash = "sha256:daa1c471d95bad080c6e44b4946c9390a4842adc3082572c20e4f8884e39e959"}, + {file = "scikit_learn-1.4.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:8539a41b3d6d1af82eb629f9c57f37428ff1481c1e34dddb3b9d7af8ede67ac5"}, + {file = 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"torch-2.3.0-cp312-none-macosx_11_0_arm64.whl", hash = "sha256:dca986214267b34065a79000cee54232e62b41dff1ec2cab9abc3fc8b3dee0ad"}, ] +[[package]] +name = "torch-geometric" +version = "2.5.3" +requires_python = ">=3.8" +summary = "Graph Neural Network Library for PyTorch" +groups = ["default"] +dependencies = [ + "aiohttp", + "fsspec", + "jinja2", + "numpy", + "psutil>=5.8.0", + "pyparsing", + "requests", + "scikit-learn", + "scipy", + "tqdm", +] +files = [ + {file = "torch_geometric-2.5.3-py3-none-any.whl", hash = "sha256:8277abfc12600b0e8047e0c3ea2d55cc43f08c1448e73e924de827c15d0b5f85"}, + {file = "torch_geometric-2.5.3.tar.gz", hash = "sha256:ad0761650c8fa56cdc46ee61c564fd4995f07f079965fe732b3a76d109fd3edc"}, +] + [[package]] name = "torchmetrics" version = "1.4.0" diff --git a/pyproject.toml b/pyproject.toml index d9eb14dd..b2461c42 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -14,6 +14,7 @@ dependencies = [ "tueplots>=0.0.8", "plotly>=5.15.0", "pre-commit>=2.15.0", + "torch-geometric>=2.5.3", ] requires-python = ">=3.10" name = "neural-lam" From 286995202ac9534eb2ef3bbb621ed8c798fa8e9a Mon Sep 17 00:00:00 2001 From: Leif Denby Date: Tue, 14 May 2024 00:08:58 +0200 Subject: [PATCH 20/40] fix import and more tests --- neural_lam/models/graph_lam.py | 2 +- tests/test_base.py | 6 ++++++ 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/neural_lam/models/graph_lam.py b/neural_lam/models/graph_lam.py index 6bbe83cc..ff641c20 100644 --- a/neural_lam/models/graph_lam.py +++ b/neural_lam/models/graph_lam.py @@ -2,7 +2,7 @@ import torch_geometric as pyg # First-party -from . import utils +from .. import utils from ..interaction_net import InteractionNet from .base_graph_model import BaseGraphModel diff --git a/tests/test_base.py b/tests/test_base.py index c3a89171..df442614 100644 --- a/tests/test_base.py +++ b/tests/test_base.py @@ -1,7 +1,13 @@ import neural_lam +import neural_lam.create_mesh +import neural_lam.create_grid_features +import neural_lam.create_parameter_weights import neural_lam.train_model def test_import(): assert neural_lam is not None + assert neural_lam.create_mesh is not None + assert neural_lam.create_grid_features is not None + assert neural_lam.create_parameter_weights is not None assert neural_lam.train_model is not None From 358c8d6965a6b1093c4d44244ff652f5835d733b Mon Sep 17 00:00:00 2001 From: Leif Denby Date: Tue, 14 May 2024 00:12:11 +0200 Subject: [PATCH 21/40] pdm to sync to requirements.txt --- .pre-commit-config.yaml | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 0547c6b9..47754c21 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -35,3 +35,12 @@ repos: hooks: - id: flake8 description: Check Python code for correctness, consistency and adherence to best practices + + # export python requirements + - repo: https://github.com/pdm-project/pdm + rev: 2.12.4 # a PDM release exposing the hook + hooks: + - id: pdm-export + # command arguments, e.g.: + args: ['-o', 'requirements.txt', '--without-hashes'] + files: ^pdm.lock$ From 6c3bdce0ca2e645220db4c19be6f20f742074079 Mon Sep 17 00:00:00 2001 From: Leif Denby Date: Tue, 14 May 2024 00:13:31 +0200 Subject: [PATCH 22/40] update requirements.txt --- requirements.txt | 93 ++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 93 insertions(+) create mode 100644 requirements.txt diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 00000000..1a87e6be --- /dev/null +++ b/requirements.txt @@ -0,0 +1,93 @@ +# This file is @generated by PDM. +# Please do not edit it manually. + +aiohttp==3.9.5 +aiosignal==1.3.1 +async-timeout==4.0.3; python_version < "3.11" +attrs==23.2.0 +cartopy==0.23.0 +certifi==2024.2.2 +cfgv==3.4.0 +charset-normalizer==3.3.2 +click==8.1.7 +colorama==0.4.6 +contourpy==1.2.1 +cycler==0.12.1 +distlib==0.3.8 +docker-pycreds==0.4.0 +exceptiongroup==1.2.1; python_version < "3.11" +filelock==3.14.0 +fonttools==4.51.0 +frozenlist==1.4.1 +fsspec==2024.3.1 +gitdb==4.0.11 +gitpython==3.1.43 +identify==2.5.36 +idna==3.7 +iniconfig==2.0.0 +intel-openmp==2021.4.0; platform_system == "Windows" +jinja2==3.1.4 +joblib==1.4.2 +kiwisolver==1.4.5 +lightning-utilities==0.11.2 +markupsafe==2.1.5 +matplotlib==3.8.4 +mkl==2021.4.0; platform_system == "Windows" +mpmath==1.3.0 +multidict==6.0.5 +networkx==3.3 +nodeenv==1.8.0 +numpy==1.26.4 +nvidia-cublas-cu12==12.1.3.1; platform_system == "Linux" and platform_machine == "x86_64" +nvidia-cuda-cupti-cu12==12.1.105; platform_system == "Linux" and platform_machine == "x86_64" +nvidia-cuda-nvrtc-cu12==12.1.105; platform_system == "Linux" and platform_machine == "x86_64" +nvidia-cuda-runtime-cu12==12.1.105; platform_system == "Linux" and platform_machine == "x86_64" +nvidia-cudnn-cu12==8.9.2.26; platform_system == "Linux" and platform_machine == "x86_64" +nvidia-cufft-cu12==11.0.2.54; platform_system == "Linux" and platform_machine == "x86_64" +nvidia-curand-cu12==10.3.2.106; platform_system == "Linux" and platform_machine == "x86_64" +nvidia-cusolver-cu12==11.4.5.107; platform_system == "Linux" and platform_machine == "x86_64" +nvidia-cusparse-cu12==12.1.0.106; platform_system == "Linux" and platform_machine == "x86_64" +nvidia-nccl-cu12==2.20.5; platform_system == "Linux" and platform_machine == "x86_64" +nvidia-nvjitlink-cu12==12.4.127; platform_system == "Linux" and platform_machine == "x86_64" +nvidia-nvtx-cu12==12.1.105; platform_system == "Linux" and platform_machine == "x86_64" +packaging==24.0 +pillow==10.3.0 +platformdirs==4.2.1 +plotly==5.22.0 +pluggy==1.5.0 +pre-commit==3.7.1 +pretty-errors==1.2.25 +protobuf==4.25.3; python_version > "3.9" or sys_platform != "linux" +psutil==5.9.8 +pyparsing==3.1.2 +pyproj==3.6.1 +pyshp==2.3.1 +pytest==8.2.0 +python-dateutil==2.9.0.post0 +pytorch-lightning==2.2.4 +pyyaml==6.0.1 +requests==2.31.0 +scikit-learn==1.4.2 +scipy==1.13.0 +sentry-sdk==2.1.1 +setproctitle==1.3.3 +setuptools==69.5.1 +shapely==2.0.4 +six==1.16.0 +smmap==5.0.1 +sympy==1.12 +tbb==2021.12.0; platform_system == "Windows" +tenacity==8.3.0 +threadpoolctl==3.5.0 +tomli==2.0.1; python_version < "3.11" +torch==2.3.0 +torch-geometric==2.5.3 +torchmetrics==1.4.0 +tqdm==4.66.4 +triton==2.3.0; platform_system == "Linux" and platform_machine == "x86_64" and python_version < "3.12" +tueplots==0.0.15 +typing-extensions==4.11.0 +urllib3==2.2.1 +virtualenv==20.26.1 +wandb==0.17.0 +yarl==1.9.4 From fbd6a2b6351d1fc7a8f00a6990a6a1bb9e20c2a1 Mon Sep 17 00:00:00 2001 From: Leif Denby Date: Tue, 14 May 2024 00:13:43 +0200 Subject: [PATCH 23/40] more import tests --- tests/test_base.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_base.py b/tests/test_base.py index df442614..27228cfb 100644 --- a/tests/test_base.py +++ b/tests/test_base.py @@ -1,6 +1,6 @@ import neural_lam -import neural_lam.create_mesh import neural_lam.create_grid_features +import neural_lam.create_mesh import neural_lam.create_parameter_weights import neural_lam.train_model From 095fdbcb30ced795285c851e3e8e84757b87c467 Mon Sep 17 00:00:00 2001 From: Leif Denby Date: Tue, 16 Jul 2024 23:08:32 +0200 Subject: [PATCH 24/40] turn meps testdata download into pytest fixture --- tests/test_mllam_dataset.py | 23 ++++++++++++++--------- 1 file changed, 14 insertions(+), 9 deletions(-) diff --git a/tests/test_mllam_dataset.py b/tests/test_mllam_dataset.py index f91170c9..cb992db5 100644 --- a/tests/test_mllam_dataset.py +++ b/tests/test_mllam_dataset.py @@ -1,15 +1,18 @@ # Standard library import os +from pathlib import Path # Third-party import pooch +import pytest -# First-party -from create_mesh import main as create_mesh from neural_lam.config import Config + +# First-party +from neural_lam.create_mesh import main as create_mesh +from neural_lam.train_model import main as train_model from neural_lam.utils import load_static_data from neural_lam.weather_dataset import WeatherDataset -from train_model import main as train_model # Disable weights and biases to avoid unnecessary logging # and to avoid having to deal with authentication @@ -25,7 +28,8 @@ ) -def test_retrieve_data_ewc(): +@pytest.fixture +def meps_example_reduced_filepath(): # Download and unzip test data into data/meps_example_reduced pooch.retrieve( url=S3_FULL_PATH, @@ -34,16 +38,17 @@ def test_retrieve_data_ewc(): path="data", fname="meps_example_reduced.zip", ) + return Path("data/meps_example_reduced") -def test_load_reduced_meps_dataset(): +def test_load_reduced_meps_dataset(meps_example_reduced_filepath): # The data_config.yaml file is downloaded and extracted in # test_retrieve_data_ewc together with the dataset itself - data_config_file = "data/meps_example_reduced/data_config.yaml" - dataset_name = "meps_example_reduced" + data_config_file = meps_example_reduced_filepath / "data_config.yaml" + dataset_name = meps_example_reduced_filepath.name - dataset = WeatherDataset(dataset_name="meps_example_reduced") - config = Config.from_file(data_config_file) + dataset = WeatherDataset(dataset_name=dataset_name) + config = Config.from_file(str(data_config_file)) var_names = config.values["dataset"]["var_names"] var_units = config.values["dataset"]["var_units"] From 49e9bfef051a0cb04a1bf4ff6371a5a117a74af8 Mon Sep 17 00:00:00 2001 From: Leif Denby Date: Tue, 16 Jul 2024 23:13:31 +0200 Subject: [PATCH 25/40] adapt README for package --- README.md | 54 +++++++++++++++++++++++++++--------------------------- 1 file changed, 27 insertions(+), 27 deletions(-) diff --git a/README.md b/README.md index 50bb0af0..00562f22 100644 --- a/README.md +++ b/README.md @@ -48,7 +48,7 @@ Still, some restrictions are inevitable: ## A note on the limited area setting Currently we are using these models on a limited area covering the Nordic region, the so called MEPS area (see [paper](https://arxiv.org/abs/2309.17370)). There are still some parts of the code that is quite specific for the MEPS area use case. -This is in particular true for the mesh graph creation (`create_mesh.py`) and some of the constants set in a `data_config.yaml` file (path specified in `train_model.py --data_config` ). +This is in particular true for the mesh graph creation (`python -m neural_lam.create_mesh`) and some of the constants set in a `data_config.yaml` file (path specified in `python -m neural_lam.train_model --data_config ` ). If there is interest to use Neural-LAM for other areas it is not a substantial undertaking to refactor the code to be fully area-agnostic. We would be happy to support such enhancements. See the issues https://github.com/joeloskarsson/neural-lam/issues/2, https://github.com/joeloskarsson/neural-lam/issues/3 and https://github.com/joeloskarsson/neural-lam/issues/4 for some initial ideas on how this could be done. @@ -81,15 +81,15 @@ The full MEPS dataset can be shared with other researchers on request, contact u A tiny subset of the data (named `meps_example`) is available in `example_data.zip`, which can be downloaded from [here](https://liuonline-my.sharepoint.com/:f:/g/personal/joeos82_liu_se/EuiUuiGzFIFHruPWpfxfUmYBSjhqMUjNExlJi9W6ULMZ1w?e=97pnGX). Download the file and unzip in the neural-lam directory. All graphs used in the paper are also available for download at the same link (but can as easily be re-generated using `python -m neural_lam.create_mesh`). -Note that this is far too little data to train any useful models, but all scripts can be ran with it. +Note that this is far too little data to train any useful models, but all pre-processing and training steps can be run with it. It should thus be useful to make sure that your python environment is set up correctly and that all the code can be ran without any issues. ## Pre-processing -An overview of how the different scripts and files depend on each other is given in this figure: +An overview of how the different pre-processing steps, training and files depend on each other is given in this figure:

-In order to start training models at least three pre-processing scripts have to be run: +In order to start training models at least three pre-processing steps have to be run: * `python -m neural_lam.create_mesh` * `python -m neural_lam.create_grid_features` @@ -106,13 +106,13 @@ The graphs used for the different models in the [paper](https://arxiv.org/abs/23 The graph-related files are stored in a directory called `graphs`. ### Create remaining static features -To create the remaining static files run the scripts `create_grid_features.py` and `create_parameter_weights.py`. +To create the remaining static files run `python -m neural_lam.create_grid_features` and `python -m neural_lam.create_parameter_weights`. ## Weights & Biases Integration The project is fully integrated with [Weights & Biases](https://www.wandb.ai/) (W&B) for logging and visualization, but can just as easily be used without it. When W&B is used, training configuration, training/test statistics and plots are sent to the W&B servers and made available in an interactive web interface. If W&B is turned off, logging instead saves everything locally to a directory like `wandb/dryrun...`. -The W&B project name is set to `neural-lam`, but this can be changed in the flags of `train_model.py` (using argsparse). +The W&B project name is set to `neural-lam`, but this can be changed in the flags of `python -m neural_lam.train_model` (using argsparse). See the [W&B documentation](https://docs.wandb.ai/) for details. If you would like to login and use W&B, run: @@ -216,13 +216,13 @@ data ā”‚ ā”œā”€ā”€ nwp_xy.npy - Coordinates of grid nodes (part of dataset) ā”‚ ā”œā”€ā”€ surface_geopotential.npy - Geopotential at surface of grid nodes (part of dataset) ā”‚ ā”œā”€ā”€ border_mask.npy - Mask with True for grid nodes that are part of border (part of dataset) -ā”‚ ā”œā”€ā”€ grid_features.pt - Static features of grid nodes (create_grid_features.py) -ā”‚ ā”œā”€ā”€ parameter_mean.pt - Means of state parameters (create_parameter_weights.py) -ā”‚ ā”œā”€ā”€ parameter_std.pt - Std.-dev. of state parameters (create_parameter_weights.py) -ā”‚ ā”œā”€ā”€ diff_mean.pt - Means of one-step differences (create_parameter_weights.py) -ā”‚ ā”œā”€ā”€ diff_std.pt - Std.-dev. of one-step differences (create_parameter_weights.py) -ā”‚ ā”œā”€ā”€ flux_stats.pt - Mean and std.-dev. of solar flux forcing (create_parameter_weights.py) -ā”‚ ā””ā”€ā”€ parameter_weights.npy - Loss weights for different state parameters (create_parameter_weights.py) +ā”‚ ā”œā”€ā”€ grid_features.pt - Static features of grid nodes (neural_lam.create_grid_features) +ā”‚ ā”œā”€ā”€ parameter_mean.pt - Means of state parameters (neural_lam.create_parameter_weights) +ā”‚ ā”œā”€ā”€ parameter_std.pt - Std.-dev. of state parameters (neural_lam.create_parameter_weights) +ā”‚ ā”œā”€ā”€ diff_mean.pt - Means of one-step differences (neural_lam.create_parameter_weights) +ā”‚ ā”œā”€ā”€ diff_std.pt - Std.-dev. of one-step differences (neural_lam.create_parameter_weights) +ā”‚ ā”œā”€ā”€ flux_stats.pt - Mean and std.-dev. of solar flux forcing (neural_lam.create_parameter_weights) +ā”‚ ā””ā”€ā”€ parameter_weights.npy - Loss weights for different state parameters (neural_lam.create_parameter_weights) ā”œā”€ā”€ dataset2 ā”œā”€ā”€ ... ā””ā”€ā”€ datasetN @@ -234,13 +234,13 @@ The structure is shown with examples below: ``` graphs ā”œā”€ā”€ graph1 - Directory with a graph definition -ā”‚ ā”œā”€ā”€ m2m_edge_index.pt - Edges in mesh graph (create_mesh.py) -ā”‚ ā”œā”€ā”€ g2m_edge_index.pt - Edges from grid to mesh (create_mesh.py) -ā”‚ ā”œā”€ā”€ m2g_edge_index.pt - Edges from mesh to grid (create_mesh.py) -ā”‚ ā”œā”€ā”€ m2m_features.pt - Static features of mesh edges (create_mesh.py) -ā”‚ ā”œā”€ā”€ g2m_features.pt - Static features of grid to mesh edges (create_mesh.py) -ā”‚ ā”œā”€ā”€ m2g_features.pt - Static features of mesh to grid edges (create_mesh.py) -ā”‚ ā””ā”€ā”€ mesh_features.pt - Static features of mesh nodes (create_mesh.py) +ā”‚ ā”œā”€ā”€ m2m_edge_index.pt - Edges in mesh graph (neural_lam.create_mesh) +ā”‚ ā”œā”€ā”€ g2m_edge_index.pt - Edges from grid to mesh (neural_lam.create_mesh) +ā”‚ ā”œā”€ā”€ m2g_edge_index.pt - Edges from mesh to grid (neural_lam.create_mesh) +ā”‚ ā”œā”€ā”€ m2m_features.pt - Static features of mesh edges (neural_lam.create_mesh) +ā”‚ ā”œā”€ā”€ g2m_features.pt - Static features of grid to mesh edges (neural_lam.create_mesh) +ā”‚ ā”œā”€ā”€ m2g_features.pt - Static features of mesh to grid edges (neural_lam.create_mesh) +ā”‚ ā””ā”€ā”€ mesh_features.pt - Static features of mesh nodes (neural_lam.create_mesh) ā”œā”€ā”€ graph2 ā”œā”€ā”€ ... ā””ā”€ā”€ graphN @@ -250,9 +250,9 @@ graphs To keep track of levels in the mesh graph, a list format is used for the files with mesh graph information. In particular, the files ``` -ā”‚ ā”œā”€ā”€ m2m_edge_index.pt - Edges in mesh graph (create_mesh.py) -ā”‚ ā”œā”€ā”€ m2m_features.pt - Static features of mesh edges (create_mesh.py) -ā”‚ ā”œā”€ā”€ mesh_features.pt - Static features of mesh nodes (create_mesh.py) +ā”‚ ā”œā”€ā”€ m2m_edge_index.pt - Edges in mesh graph (neural_lam.create_mesh) +ā”‚ ā”œā”€ā”€ m2m_features.pt - Static features of mesh edges (neural_lam.create_mesh) +ā”‚ ā”œā”€ā”€ mesh_features.pt - Static features of mesh nodes (neural_lam.create_mesh) ``` all contain lists of length `L`, for a hierarchical mesh graph with `L` layers. For non-hierarchical graphs `L == 1` and these are all just singly-entry lists. @@ -263,10 +263,10 @@ In addition, hierarchical mesh graphs (`L > 1`) feature a few additional files w ``` ā”œā”€ā”€ graph1 ā”‚ ā”œā”€ā”€ ... -ā”‚ ā”œā”€ā”€ mesh_down_edge_index.pt - Downward edges in mesh graph (create_mesh.py) -ā”‚ ā”œā”€ā”€ mesh_up_edge_index.pt - Upward edges in mesh graph (create_mesh.py) -ā”‚ ā”œā”€ā”€ mesh_down_features.pt - Static features of downward mesh edges (create_mesh.py) -ā”‚ ā”œā”€ā”€ mesh_up_features.pt - Static features of upward mesh edges (create_mesh.py) +ā”‚ ā”œā”€ā”€ mesh_down_edge_index.pt - Downward edges in mesh graph (neural_lam.create_mesh) +ā”‚ ā”œā”€ā”€ mesh_up_edge_index.pt - Upward edges in mesh graph (neural_lam.create_mesh) +ā”‚ ā”œā”€ā”€ mesh_down_features.pt - Static features of downward mesh edges (neural_lam.create_mesh) +ā”‚ ā”œā”€ā”€ mesh_up_features.pt - Static features of upward mesh edges (neural_lam.create_mesh) ā”‚ ā”œā”€ā”€ ... ``` These files have the same list format as the ones above, but each list has length `L-1` (as these edges describe connections between levels). 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https://www.python.org/dev/peps/pep-0621/ -dependencies = [ - "numpy>=1.24.2", - "wandb>=0.13.10", - "matplotlib>=3.7.0", - "scipy>=1.10.0", - "pytorch-lightning>=2.0.3", - "shapely>=2.0.1", - "networkx>=3.0", - "Cartopy>=0.22.0", - "pyproj>=3.4.1", - "tueplots>=0.0.8", - "plotly>=5.15.0", - "pre-commit>=2.15.0", - "torch-geometric>=2.5.3", -] -requires-python = ">=3.10" -name = "neural-lam" -version = "0.1.0" -description = "Neural Weather Prediction for Limited Area Modeling" -authors = [ - {name = "Joel Oskarsson", email = "joel.oskarsson@liu.se"}, - {name = "Simon Adamov", email = "simon.adamov@meteoswiss.ch"}, - {name = "Leif Denby", email = "lcd@dmi.dk"}, -] -readme = "README.md" -license = {text = "MIT"} - -[tool.black] -line-length = 80 - -[tool.isort] -profile = "black" - -[tool.flake8] -max-line-length = 80 -ignore = [ - "E203", # Allow whitespace before ':' (https://github.com/PyCQA/pycodestyle/issues/373) - "I002", # Don't check for isort configuration - "W503", # Allow line break before binary operator (PEP 8-compatible) -] -per-file-ignores = [ - "__init__.py: F401", # Allow unused imports -] - -[tool.codespell] -skip = "requirements/*" - -# Pylint config -[tool.pylint] -ignore = [ - "create_mesh.py", # Disable linting for now, as major rework is planned/expected -] - -[tool.pylint.TYPECHECK] -generated-members = [ - "numpy.*", - "torch.*", -] - -[tool.pylint.'MESSAGES CONTROL'] -disable = [ - "C0114", # 'missing-module-docstring', Do not require module docstrings - "R0901", # 'too-many-ancestors', Allow many layers of sub-classing - "R0902", # 'too-many-instance-attribtes', Allow many attributes - "R0913", # 'too-many-arguments', Allow many function arguments - "R0914", # 'too-many-locals', Allow many local variables - "W0223", # 'abstract-method', Subclasses do not have to override all abstract methods -] -[tool.pylint.DESIGN] -max-statements=100 # Allow for some more involved functions -[tool.pylint.IMPORTS] -allow-any-import-level="neural_lam" -[tool.pylint.SIMILARITIES] -min-similarity-lines=10 - - -[tool.pdm] -distribution = true - -[tool.pdm.dev-dependencies] -dev = [ - "pytest>=8.2.0", -] -[build-system] -requires = ["pdm-backend"] -build-backend = "pdm.backend" From a91eaaa32c54cf6d753f6d4011837b141b931ee3 Mon Sep 17 00:00:00 2001 From: Leif Denby Date: Tue, 16 Jul 2024 23:17:52 +0200 Subject: [PATCH 29/40] add pyproject.toml from main --- pyproject.toml | 65 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 pyproject.toml diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 00000000..b513a258 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,65 @@ +[tool.black] +line-length = 80 + +[tool.isort] +default_section = "THIRDPARTY" +profile = "black" +# Headings +import_heading_stdlib = "Standard library" +import_heading_thirdparty = "Third-party" +import_heading_firstparty = "First-party" +import_heading_localfolder = "Local" +# Known modules to avoid misclassification +known_standard_library = [ + # Add standard library modules that may be misclassified by isort +] +known_third_party = [ + # Add third-party modules that may be misclassified by isort + "wandb", +] +known_first_party = [ + # Add first-party modules that may be misclassified by isort + "neural_lam", +] + +[tool.flake8] +max-line-length = 80 +ignore = [ + "E203", # Allow whitespace before ':' (https://github.com/PyCQA/pycodestyle/issues/373) + "I002", # Don't check for isort configuration + "W503", # Allow line break before binary operator (PEP 8-compatible) +] +per-file-ignores = [ + "__init__.py: F401", # Allow unused imports +] + +[tool.codespell] +skip = "requirements/*" + +# Pylint config +[tool.pylint] +ignore = [ + "create_mesh.py", # Disable linting for now, as major rework is planned/expected +] +# Temporary fix for import neural_lam statements until set up as proper package +init-hook='import sys; sys.path.append(".")' +[tool.pylint.TYPECHECK] +generated-members = [ + "numpy.*", + "torch.*", +] +[tool.pylint.'MESSAGES CONTROL'] +disable = [ + "C0114", # 'missing-module-docstring', Do not require module docstrings + "R0901", # 'too-many-ancestors', Allow many layers of sub-classing + "R0902", # 'too-many-instance-attribtes', Allow many attributes + "R0913", # 'too-many-arguments', Allow many function arguments + "R0914", # 'too-many-locals', Allow many local variables + "W0223", # 'abstract-method', Subclasses do not have to override all abstract methods +] +[tool.pylint.DESIGN] +max-statements=100 # Allow for some more involved functions +[tool.pylint.IMPORTS] +allow-any-import-level="neural_lam" +[tool.pylint.SIMILARITIES] +min-similarity-lines=10 From 5508ceabf0bb6c8c86bd51aebee80c30d09f51c4 Mon Sep 17 00:00:00 2001 From: Leif Denby Date: Tue, 16 Jul 2024 23:19:03 +0200 Subject: [PATCH 30/40] clean out tests --- tests/__init__.py | 5 ----- tests/test_base.py | 13 ------------- 2 files changed, 18 deletions(-) delete mode 100644 tests/__init__.py delete mode 100644 tests/test_base.py diff --git a/tests/__init__.py b/tests/__init__.py deleted file mode 100644 index 2f88fa16..00000000 --- a/tests/__init__.py +++ /dev/null @@ -1,5 +0,0 @@ -import neural_lam - - -def test_import(): - assert neural_lam is not None diff --git a/tests/test_base.py b/tests/test_base.py deleted file mode 100644 index 27228cfb..00000000 --- a/tests/test_base.py +++ /dev/null @@ -1,13 +0,0 @@ -import neural_lam -import neural_lam.create_grid_features -import neural_lam.create_mesh -import neural_lam.create_parameter_weights -import neural_lam.train_model - - -def test_import(): - assert neural_lam is not None - assert neural_lam.create_mesh is not None - assert neural_lam.create_grid_features is not None - assert neural_lam.create_parameter_weights is not None - assert neural_lam.train_model is not None From 5c623c315724cd14a60d7f7d11ef640d5ba21c5e Mon Sep 17 00:00:00 2001 From: Leif Denby Date: Tue, 16 Jul 2024 23:20:00 +0200 Subject: [PATCH 31/40] fix linting --- neural_lam/create_grid_features.py | 2 +- neural_lam/create_mesh.py | 2 +- neural_lam/create_parameter_weights.py | 2 +- neural_lam/interaction_net.py | 2 +- neural_lam/models/ar_model.py | 2 +- neural_lam/models/base_graph_model.py | 2 +- neural_lam/models/base_hi_graph_model.py | 2 +- neural_lam/models/graph_lam.py | 2 +- neural_lam/models/hi_lam.py | 2 +- neural_lam/models/hi_lam_parallel.py | 2 +- neural_lam/train_model.py | 2 +- neural_lam/vis.py | 2 +- neural_lam/weather_dataset.py | 2 +- tests/test_mllam_dataset.py | 3 +-- 14 files changed, 14 insertions(+), 15 deletions(-) diff --git a/neural_lam/create_grid_features.py b/neural_lam/create_grid_features.py index 4d62fab2..adabd9dc 100644 --- a/neural_lam/create_grid_features.py +++ b/neural_lam/create_grid_features.py @@ -6,7 +6,7 @@ import numpy as np import torch -# First-party +# Local from . import config diff --git a/neural_lam/create_mesh.py b/neural_lam/create_mesh.py index 1dbbf90f..40f7ba0e 100644 --- a/neural_lam/create_mesh.py +++ b/neural_lam/create_mesh.py @@ -12,7 +12,7 @@ import torch_geometric as pyg from torch_geometric.utils.convert import from_networkx -# First-party +# Local from . import config diff --git a/neural_lam/create_parameter_weights.py b/neural_lam/create_parameter_weights.py index c109c5b2..a33b56b2 100644 --- a/neural_lam/create_parameter_weights.py +++ b/neural_lam/create_parameter_weights.py @@ -10,7 +10,7 @@ from torch.utils.data.distributed import DistributedSampler from tqdm import tqdm -# First-party +# Local from . import config from .weather_dataset import WeatherDataset diff --git a/neural_lam/interaction_net.py b/neural_lam/interaction_net.py index a81a3ab4..2f45b03f 100644 --- a/neural_lam/interaction_net.py +++ b/neural_lam/interaction_net.py @@ -3,7 +3,7 @@ import torch_geometric as pyg from torch import nn -# First-party +# Local from . import utils diff --git a/neural_lam/models/ar_model.py b/neural_lam/models/ar_model.py index 53949fb6..e94de8c6 100644 --- a/neural_lam/models/ar_model.py +++ b/neural_lam/models/ar_model.py @@ -8,7 +8,7 @@ import torch import wandb -# First-party +# Local from .. import config, metrics, utils, vis diff --git a/neural_lam/models/base_graph_model.py b/neural_lam/models/base_graph_model.py index 77be82eb..99629073 100644 --- a/neural_lam/models/base_graph_model.py +++ b/neural_lam/models/base_graph_model.py @@ -1,7 +1,7 @@ # Third-party import torch -# First-party +# Local from .. import utils from ..interaction_net import InteractionNet from .ar_model import ARModel diff --git a/neural_lam/models/base_hi_graph_model.py b/neural_lam/models/base_hi_graph_model.py index 5529ed4b..a2ebcc1b 100644 --- a/neural_lam/models/base_hi_graph_model.py +++ b/neural_lam/models/base_hi_graph_model.py @@ -1,7 +1,7 @@ # Third-party from torch import nn -# First-party +# Local from .. import utils from ..interaction_net import InteractionNet from .base_graph_model import BaseGraphModel diff --git a/neural_lam/models/graph_lam.py b/neural_lam/models/graph_lam.py index ff641c20..d73f7ad8 100644 --- a/neural_lam/models/graph_lam.py +++ b/neural_lam/models/graph_lam.py @@ -1,7 +1,7 @@ # Third-party import torch_geometric as pyg -# First-party +# Local from .. import utils from ..interaction_net import InteractionNet from .base_graph_model import BaseGraphModel diff --git a/neural_lam/models/hi_lam.py b/neural_lam/models/hi_lam.py index df9d3cbb..4f3aec05 100644 --- a/neural_lam/models/hi_lam.py +++ b/neural_lam/models/hi_lam.py @@ -1,7 +1,7 @@ # Third-party from torch import nn -# First-party +# Local from ..interaction_net import InteractionNet from .base_hi_graph_model import BaseHiGraphModel diff --git a/neural_lam/models/hi_lam_parallel.py b/neural_lam/models/hi_lam_parallel.py index d6dc27ee..b40a9424 100644 --- a/neural_lam/models/hi_lam_parallel.py +++ b/neural_lam/models/hi_lam_parallel.py @@ -2,7 +2,7 @@ import torch import torch_geometric as pyg -# First-party +# Local from ..interaction_net import InteractionNet from .base_hi_graph_model import BaseHiGraphModel diff --git a/neural_lam/train_model.py b/neural_lam/train_model.py index eaf675ed..dd1ad313 100644 --- a/neural_lam/train_model.py +++ b/neural_lam/train_model.py @@ -9,7 +9,7 @@ import torch from lightning_fabric.utilities import seed -# First-party +# Local from . import config, utils from .models.graph_lam import GraphLAM from .models.hi_lam import HiLAM diff --git a/neural_lam/vis.py b/neural_lam/vis.py index fb4bba96..2f22bef1 100644 --- a/neural_lam/vis.py +++ b/neural_lam/vis.py @@ -3,7 +3,7 @@ import matplotlib.pyplot as plt import numpy as np -# First-party +# Local from . import utils diff --git a/neural_lam/weather_dataset.py b/neural_lam/weather_dataset.py index 8f30407e..29977789 100644 --- a/neural_lam/weather_dataset.py +++ b/neural_lam/weather_dataset.py @@ -7,7 +7,7 @@ import numpy as np import torch -# First-party +# Local from . import utils diff --git a/tests/test_mllam_dataset.py b/tests/test_mllam_dataset.py index cb992db5..3edf4198 100644 --- a/tests/test_mllam_dataset.py +++ b/tests/test_mllam_dataset.py @@ -6,9 +6,8 @@ import pooch import pytest -from neural_lam.config import Config - # First-party +from neural_lam.config import Config from neural_lam.create_mesh import main as create_mesh from neural_lam.train_model import main as train_model from neural_lam.utils import load_static_data From 08ec168c52d6a62774ef84797db70c018f7642f0 Mon Sep 17 00:00:00 2001 From: Leif Denby Date: Tue, 16 Jul 2024 23:22:03 +0200 Subject: [PATCH 32/40] add cli entrypoints import test --- tests/test_cli.py | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 tests/test_cli.py diff --git a/tests/test_cli.py b/tests/test_cli.py new file mode 100644 index 00000000..e90daa04 --- /dev/null +++ b/tests/test_cli.py @@ -0,0 +1,18 @@ +# First-party +import neural_lam +import neural_lam.create_grid_features +import neural_lam.create_mesh +import neural_lam.create_parameter_weights +import neural_lam.train_model + + +def test_import(): + """ + This test just ensures that each cli entry-point can be imported for now, + eventually we should test their execution too + """ + assert neural_lam is not None + assert neural_lam.create_mesh is not None + assert neural_lam.create_grid_features is not None + assert neural_lam.create_parameter_weights is not None + assert neural_lam.train_model is not None From 3954f04f4c734fe324bca387a68f49f25d4f919a Mon Sep 17 00:00:00 2001 From: Leif Denby Date: Tue, 16 Jul 2024 23:51:07 +0200 Subject: [PATCH 33/40] tweak cicd pytest execution --- .github/workflows/run_tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml index 4c677908..810f2b2c 100644 --- a/.github/workflows/run_tests.yml +++ b/.github/workflows/run_tests.yml @@ -35,7 +35,7 @@ jobs: ${{ runner.os }}-meps-reduced-example-data-v0.1.0 - name: Test with pytest run: | - pytest -v -s + python -m pytest -v -s tests/ - name: Save cache data uses: actions/cache/save@v4 with: From db9d96f8379b8c1c053fbf808c522b17e64b5fef Mon Sep 17 00:00:00 2001 From: Leif Denby Date: Wed, 17 Jul 2024 10:37:42 +0200 Subject: [PATCH 34/40] Update tests/test_mllam_dataset.py Co-authored-by: SimonKamuk <43374850+SimonKamuk@users.noreply.github.com> --- tests/test_mllam_dataset.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_mllam_dataset.py b/tests/test_mllam_dataset.py index 3edf4198..e12a57ae 100644 --- a/tests/test_mllam_dataset.py +++ b/tests/test_mllam_dataset.py @@ -27,7 +27,7 @@ ) -@pytest.fixture +@pytest.fixture(scope="module") def meps_example_reduced_filepath(): # Download and unzip test data into data/meps_example_reduced pooch.retrieve( From 2a6796c2900017a4ee4f69c372669a1719d58543 Mon Sep 17 00:00:00 2001 From: joeloskarsson Date: Wed, 24 Jul 2024 14:51:41 +0200 Subject: [PATCH 35/40] Add init files to expose classes in editable package --- neural_lam/__init__.py | 8 ++++++++ neural_lam/models/__init__.py | 5 +++++ neural_lam/train_model.py | 9 ++++----- pyproject.toml | 7 +++++++ 4 files changed, 24 insertions(+), 5 deletions(-) create mode 100644 neural_lam/__init__.py create mode 100644 neural_lam/models/__init__.py diff --git a/neural_lam/__init__.py b/neural_lam/__init__.py new file mode 100644 index 00000000..9aff809f --- /dev/null +++ b/neural_lam/__init__.py @@ -0,0 +1,8 @@ +import neural_lam.config +import neural_lam.interaction_net +import neural_lam.metrics +import neural_lam.models +import neural_lam.utils +import neural_lam.vis +from .weather_dataset import WeatherDataset + diff --git a/neural_lam/models/__init__.py b/neural_lam/models/__init__.py new file mode 100644 index 00000000..f7c1b94f --- /dev/null +++ b/neural_lam/models/__init__.py @@ -0,0 +1,5 @@ +from .graph_lam import GraphLAM +from .hi_lam import HiLAM +from .hi_lam_parallel import HiLAMParallel +from .base_graph_model import BaseGraphModel +from .base_hi_graph_model import BaseHiGraphModel diff --git a/neural_lam/train_model.py b/neural_lam/train_model.py index dd1ad313..6c81213d 100644 --- a/neural_lam/train_model.py +++ b/neural_lam/train_model.py @@ -10,11 +10,10 @@ from lightning_fabric.utilities import seed # Local -from . import config, utils -from .models.graph_lam import GraphLAM -from .models.hi_lam import HiLAM -from .models.hi_lam_parallel import HiLAMParallel -from .weather_dataset import WeatherDataset +from . import config, utils, WeatherDataset +from .models import GraphLAM +from .models import HiLAM +from .models import HiLAMParallel MODELS = { "graph_lam": GraphLAM, diff --git a/pyproject.toml b/pyproject.toml index b513a258..c482abc9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,3 +1,10 @@ +[project] +name = "neural-lam" +version = "0.1.0" + +[tool.setuptools] +py-modules = ["neural_lam"] + [tool.black] line-length = 80 From 8f4e0e05015e8186d03c04295ae7cf4a155497f1 Mon Sep 17 00:00:00 2001 From: joeloskarsson Date: Wed, 24 Jul 2024 15:27:05 +0200 Subject: [PATCH 36/40] Linting --- neural_lam/__init__.py | 4 +++- neural_lam/create_parameter_weights.py | 3 +-- neural_lam/models/__init__.py | 5 +++-- neural_lam/train_model.py | 6 ++---- 4 files changed, 9 insertions(+), 9 deletions(-) diff --git a/neural_lam/__init__.py b/neural_lam/__init__.py index 9aff809f..dd565a26 100644 --- a/neural_lam/__init__.py +++ b/neural_lam/__init__.py @@ -1,8 +1,10 @@ +# First-party import neural_lam.config import neural_lam.interaction_net import neural_lam.metrics import neural_lam.models import neural_lam.utils import neural_lam.vis -from .weather_dataset import WeatherDataset +# Local +from .weather_dataset import WeatherDataset diff --git a/neural_lam/create_parameter_weights.py b/neural_lam/create_parameter_weights.py index a33b56b2..74058d38 100644 --- a/neural_lam/create_parameter_weights.py +++ b/neural_lam/create_parameter_weights.py @@ -11,8 +11,7 @@ from tqdm import tqdm # Local -from . import config -from .weather_dataset import WeatherDataset +from . import WeatherDataset, config class PaddedWeatherDataset(torch.utils.data.Dataset): diff --git a/neural_lam/models/__init__.py b/neural_lam/models/__init__.py index f7c1b94f..f65387ab 100644 --- a/neural_lam/models/__init__.py +++ b/neural_lam/models/__init__.py @@ -1,5 +1,6 @@ +# Local +from .base_graph_model import BaseGraphModel +from .base_hi_graph_model import BaseHiGraphModel from .graph_lam import GraphLAM from .hi_lam import HiLAM from .hi_lam_parallel import HiLAMParallel -from .base_graph_model import BaseGraphModel -from .base_hi_graph_model import BaseHiGraphModel diff --git a/neural_lam/train_model.py b/neural_lam/train_model.py index 6c81213d..39f7aecd 100644 --- a/neural_lam/train_model.py +++ b/neural_lam/train_model.py @@ -10,10 +10,8 @@ from lightning_fabric.utilities import seed # Local -from . import config, utils, WeatherDataset -from .models import GraphLAM -from .models import HiLAM -from .models import HiLAMParallel +from . import WeatherDataset, config, utils +from .models import GraphLAM, HiLAM, HiLAMParallel MODELS = { "graph_lam": GraphLAM, From 0b72e9d1b9831804b56926c68bf2a3e3f1fbb491 Mon Sep 17 00:00:00 2001 From: Leif Denby Date: Wed, 14 Aug 2024 07:51:09 +0000 Subject: [PATCH 37/40] add pyproject-flake8 to precommit config --- .pre-commit-config.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 815a92e1..7f16cbee 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -35,3 +35,4 @@ repos: hooks: - id: flake8 description: Check Python code for correctness, consistency and adherence to best practices + additional_dependencies: [pyproject-flake8] From 190d1de713a658e717d24f7d8c65323becd22f7a Mon Sep 17 00:00:00 2001 From: Leif Denby Date: Wed, 14 Aug 2024 07:51:59 +0000 Subject: [PATCH 38/40] use Flake8-pyproject instead --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 7f16cbee..dfbf8b60 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -35,4 +35,4 @@ repos: hooks: - id: flake8 description: Check Python code for correctness, consistency and adherence to best practices - additional_dependencies: [pyproject-flake8] + additional_dependencies: [Flake8-pyproject] From 791af0a8028bd9e60d2c620f383e80c2ae2227b4 Mon Sep 17 00:00:00 2001 From: Leif Denby Date: Wed, 14 Aug 2024 07:58:09 +0000 Subject: [PATCH 39/40] update README --- README.md | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index 00562f22..ce8daf69 100644 --- a/README.md +++ b/README.md @@ -62,16 +62,10 @@ Follow the steps below to create the necessary python environment. 1. Install GEOS for your system. For example with `sudo apt-get install libgeos-dev`. This is necessary for the Cartopy requirement. 2. Use python 3.9. 3. Install version 2.0.1 of PyTorch. Follow instructions on the [PyTorch webpage](https://pytorch.org/get-started/previous-versions/) for how to set this up with GPU support on your system. -4. Install required packages specified in `requirements.txt`. -5. Install PyTorch Geometric version 2.2.0. This can be done by running +4. Install `neural-lam` with pip: ``` -TORCH="2.0.1" -CUDA="cu117" - -pip install pyg-lib==0.2.0 torch-scatter==2.1.1 torch-sparse==0.6.17 torch-cluster==1.6.1\ - torch-geometric==2.3.1 -f https://pytorch-geometric.com/whl/torch-${TORCH}+${CUDA}.html +pip install -e . ``` -You will have to adjust the `CUDA` variable to match the CUDA version on your system or to run on CPU. See the [installation webpage](https://pytorch-geometric.readthedocs.io/en/latest/install/installation.html) for more information. ## Data Datasets should be stored in a directory called `data`. From 47c1f44c27c2801e80eb25845a98f4e4b3d6045a Mon Sep 17 00:00:00 2001 From: Leif Denby Date: Mon, 19 Aug 2024 15:34:26 +0200 Subject: [PATCH 40/40] update changelog --- CHANGELOG.md | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 69140a11..e0df8480 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -88,6 +88,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 [\#52](https://github.com/mllam/neural-lam/pull/52) @joeloskarsson +- turn `neural-lam` into a python package by moving all `*.py`-files into the + `neural_lam/` source directory and updating imports accordingly. This means + all cli functions are now invoke through the package name, e.g. `python -m + neural_lam.train_model` instead of `python train_model.py` (and can be done + anywhere once the package has been installed). + [\#32](https://github.com/mllam/neural-lam/pull/32), @leifdenby + ## [v0.1.0](https://github.com/joeloskarsson/neural-lam/releases/tag/v0.1.0) First tagged release of `neural-lam`, matching Oskarsson et al 2023 publication