added deps so a pip install will (mostly) set everything up. we still…

… depend on a few strange packages that require conda -- TBD if this can be fixed.

README.md

@@ -6,10 +6,30 @@ This repository implements GFlowNets, generative flow networks for probabilistic
 
 ### pip
 
+Prereqs: install `fftw3`:
+
+```bash
+brew install fftw  # OSX
+sudo apt-get install fftw  # Ubuntu
+```
+
+To setup the environment with all dependencies, first install the pytorch `>=2.0.1` version appropriate to your system and some other dependencies more easily handled using Conda, and then pip install the package and remaining dependencies itself:
+
 ```bash
+conda install xtb-python -c conda-forge -y
+conda install pytorch torchvision torchaudio -c pytorch -y # Use the version appropriate to your environment.
+conda install pyshtools  -c conda-forge -y
+
 python -m pip install --upgrade https://github.com/alexhernandezgarcia/gflownet/archive/main.zip
 ```
 
+Note, to install the package with developer tools, do instead 
+
+```bash
+cd /path/to/gflownet
+pip install -e .[dev]
+```.
+
 ## How to train a GFlowNet model
 
 To train a GFlowNet model with the default configuration, simply run

pyproject.toml

@@ -8,3 +8,46 @@ readme = "README.md"
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"
+
+[tool.poetry.dependencies]
+hydra-core = ">=1.3.2"
+pandas = ">=2.1.1"
+plotly = ">=5.17.0"
+pymatgen = ">=2023.9.25"
+pyxtal = ">=0.6.0"
+rdkit = "*"
+scikit-learn = ">=1.3.1"
+scipy = ">=1.11.2"
+six = ">=1.16.0"
+#torch = ">=2.0.1"
+torch-geometric = ">=2.3.1"
+torch-scatter = ">=2.1.1"
+torchani = "*"
+torchtyping = ">=0.1.4"
+tqdm = "*"
+wandb = ">=0.15.11"
+# dglgo
+# pip install dgl -f https://data.dgl.ai/wheels/repo.html
+#gdown
+
+# dev dependencies.
+black = { version = ">=23.9.1", optional = true }
+flake8 = { version = ">=6.1.0", optional = true }
+isort = { version = ">=5.12.0", optional = true }
+pylint = { version = ">=2.17.6", optional = true }
+ipdb = { version = ">=0.13.13", optional = true }
+jupyter = { version = ">=1.0.0", optional = true }
+pytest = { version = ">=7.4.2", optional = true }
+pytest-repeat = { version = ">=0.9.1", optional = true }
+
+[tool.poetry.extras]
+dev = [
+    "black",
+    "flake8",
+    "isort",
+    "pylint",
+    "ipdb",
+    "jupyter",
+    "pytest",
+    "pytest-repeat",
+]