Add proper configuration for building (#47)

* create pyproject.toml from setup and requirements

* exclude python >3.10

* update readme

* pin specific jax version

* add python 3.9 * 3.10 variant to datagen extra

* pin torch versions for datagen extra (for compatibility reasons with JAX)

Author: leiterrl

README.md

@@ -29,29 +29,40 @@ DOIs
 
 ## Installation
 
-    pip install .
-
-## Requirements
-
 ### Using pip
+
+Locally:
 ```bash
-python3 -m venv ./venv --prompt pde_benchmark --system-site-packages 
-. ./venv/bin/activate
 pip install --upgrade pip wheel
-pip install -r requirements.txt
+pip install .
 ```
 
-The minimum required packages to train and run the baseline ML models are listed in [requirements.txt](./requirements.txt).
+From PyPI:
+```bash
+pip install pdebench
+```
+
+To include dependencies for data generation:
+```bash
+pip install "pdebench[datagen310]"
+pip install ".[datagen310]" # locally
+```
+or
+```bash
+pip install "pdebench[datagen39]"
+pip install ".[datagen39]" # locally
+```
 
-To run the data generation scripts, the complete package requirements are listed in [requirements_datagen.txt](./requirements_datagen.txt)
+### GPU Support
 
 For GPU support there are additional platform-specific instructions:
 
 For PyTorch, [see here](https://pytorch.org/get-started/locally/).
 
 For JAX, which is approximately 6 times faster for simulations than PyTorch in our tests, [see here](https://github.com/google/jax#installation)
 
-### Using conda:
+
+## Installation using conda:
 
 If you like you can also install dependencies using anaconda. We suggest using [miniforge](https://github.com/conda-forge/miniforge) (and possibly mamba) as distribution. Otherwise you may have to __enable the conda-forge__ channel for the following commands.
 
@@ -79,11 +90,6 @@ Optional dependencies for data generation:
 conda install clawpack jax jaxlib python-dotenv
 ```
 
-Optional dependencies for data downloading:
-```
-pip install pyDarus~=1.0.5
-```
-
 ## Configuring DeepXDE
 In our tests we used PyTorch as backend for DeepXDE. Please [follow the documentation](https://deepxde.readthedocs.io/en/latest/user/installation.html#working-with-different-backends) to enable this.
 

pyproject.toml

@@ -0,0 +1,65 @@
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[project]
+requires-python = ">=3.9,<3.11"
+dynamic = ["readme"]
+name = "pdebench"
+version = "0.1.0"
+description = "PDEBench: An Extensive Benchmark for Scientific Machine Learning"
+authors = [
+    {name = "Makoto Takamoto", email = "Makoto.Takamoto@neclab.eu"},
+    {name = "Timothy Praditia", email = "timothy.praditia@iws.uni-stuttgart.de"},
+    {name = "Raphael Leiteritz", email = "raphael.leiteritz@ipvs.uni-stuttgart.de"},
+    {name = "Dan MacKinlay"},
+    {name = "Francesco Alesiani"},
+    {name = "Dirk Pflüger"},
+    {name = "Mathias Niepert"},
+]
+license = {file = "LICENSE.txt"}
+dependencies = [
+    "scipy",                   
+    "matplotlib",              
+    "h5py",                    
+    "pandas",                  
+    "python-dotenv",          
+    "hydra-core",              
+    "torch~=1.13.0",
+    "torchvision~=0.14.1",             
+    "deepxde~=1.1.3",                 
+    "pyro-ppl",                       
+    "tqdm",
+]
+
+[project.urls]
+Homepage = "https://github.com/pdebench/PDEBenchm"
+Documentation = "https://github.com/pdebench/PDEBench"
+Repository = "https://github.com/pdebench/PDEBench"
+
+[project.optional-dependencies]
+datagen310 = [
+    "clawpack@git+https://github.com/clawpack/clawpack.git@d619d6835ce128a0421aa52d70d2a6c9d9d1ce93",
+    "dash",
+    "phiflow",
+    "imageio",
+    "einops",
+    "torch @ https://download.pytorch.org/whl/cu117/torch-1.13.1%2Bcu117-cp310-cp310-linux_x86_64.whl",
+    "torchvision @ https://download.pytorch.org/whl/cu117/torchvision-0.14.1%2Bcu117-cp310-cp310-linux_x86_64.whl",
+    "jax==0.4.11",
+    "jaxlib @ https://storage.googleapis.com/jax-releases/cuda11/jaxlib-0.4.11+cuda11.cudnn86-cp310-cp310-manylinux2014_x86_64.whl",
+]
+datagen39 = [
+    "clawpack@git+https://github.com/clawpack/clawpack.git@d619d6835ce128a0421aa52d70d2a6c9d9d1ce93",
+    "dash",
+    "phiflow",
+    "imageio",
+    "einops",
+    "torch @ https://download.pytorch.org/whl/cu117/torch-1.13.1%2Bcu117-cp39-cp39-linux_x86_64.whl",
+    "torchvision @ https://download.pytorch.org/whl/cu117/torchvision-0.14.1%2Bcu117-cp39-cp39-linux_x86_64.whl",
+    "jax==0.4.11",
+    "jaxlib @ https://storage.googleapis.com/jax-releases/cuda11/jaxlib-0.4.11+cuda11.cudnn86-cp39-cp39-manylinux2014_x86_64.whl"
+]
+
+[tool.setuptools.dynamic]
+readme = {file = ["README.md"], content-type = "text/markdown"}