Merge pull request #2 from gmum/fix_minor_issues

Update the link and external setup

README.md

@@ -34,6 +34,10 @@ conda activate gflownet
 pip install torch==2.3.0 --index-url https://download.pytorch.org/whl/cu118
 pip install dgl==1.1.2 -f https://data.dgl.ai/wheels/torch-2.3/cu118/repo.html
 
+# If using CPU:
+pip install torch==2.3.0 --index-url https://download.pytorch.org/whl/cpu
+pip install dgl==1.1.2 -f https://data.dgl.ai/wheels/torch-2.3/cpu/repo.html
+
 pip install -e .
 
 pip install pre-commit
@@ -45,7 +49,7 @@ To evaluate the RetroGFN using [Syntheseus API](https://github.com/microsoft/syn
 ```sh
 sh external/setup_syntheseus.sh
 ```
-If you want to additionally evaluate the RetroGFN with round-trip accuracy, you need to download the (eval) Chemformer Forward checkpoints from [here](https://ujchmura-my.sharepoint.com/:f:/r/personal/piotr_gainski_doctoral_uj_edu_pl/Documents/feasibility_proxies/chemformer?csf=1&web=1&e=rIjzdH) into `checkpoints` directory.
+If you want to additionally evaluate the RetroGFN with round-trip accuracy, you need to download the (eval) Chemformer Forward checkpoints from [here](https://ujchmura-my.sharepoint.com/:f:/g/personal/piotr_gainski_doctoral_uj_edu_pl/EuN67EdWZ6JCs7bkhV0zJCUBRhH-tO7nNrHNSjBzdJuXVg?e=b3sgcs) into `checkpoints` directory.
 
 ### Setup RFM Proxy
 To train the RetroGFN using Reaction Feasibility Model (RFM) and evaluate it with Feasibility Thresholded Count (FTC) metric, you need to install [our RFM repository](https://github.com/panpiort8/ReactionFeasibilityModel/) with the following command:

external/setup_shared.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+# Add the `external/` directory to `PYTHONPATH` when the environment is activated.
+mkdir -p $CONDA_PREFIX/etc/conda/activate.d
+echo "export PYTHONPATH=$PWD/external:.:$PYTHONPATH" >> $CONDA_PREFIX/etc/conda/activate.d/env_vars.sh
+source $CONDA_PREFIX/etc/conda/activate.d/env_vars.sh
+
+export GITHUB_NAME="$GITHUB_ORG_NAME/$GITHUB_REPO_NAME"
+export MODEL_DIR="external/$GITHUB_REPO_DIR"
+
+echo "Setting up $GITHUB_NAME under $MODEL_DIR"
+git -C external clone "git@github.com:$GITHUB_NAME.git" $GITHUB_REPO_DIR
+git -C $MODEL_DIR checkout $GITHUB_COMMIT_ID

external/setup_syntheseus.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+# Install extra dependencies specific to Chemformer.
+pip install pytorch-lightning==1.9.4 git+https://github.com/MolecularAI/pysmilesutils.git
+
+export GITHUB_ORG_NAME=panpiort8
+export GITHUB_REPO_NAME=syntheseus
+export GITHUB_REPO_DIR=syntheseus
+export GITHUB_COMMIT_ID=e5754963e4768ceada4fe7a60199bb1c5ceed2ea
+
+source external/setup_shared.sh