From 9b21196ee265bc56b876772630591177678b7ac8 Mon Sep 17 00:00:00 2001 From: albert bou Date: Wed, 7 Aug 2024 11:09:18 +0200 Subject: [PATCH] update CI --- .github/unittest/install_dependencies.sh | 12 +++++++----- .github/unittest/install_dependencies_nightly.sh | 6 +----- .github/workflows/unit_tests.yml | 2 +- README.md | 4 ++-- 4 files changed, 11 insertions(+), 13 deletions(-) diff --git a/.github/unittest/install_dependencies.sh b/.github/unittest/install_dependencies.sh index 4988803..27ecfe6 100644 --- a/.github/unittest/install_dependencies.sh +++ b/.github/unittest/install_dependencies.sh @@ -1,11 +1,13 @@ python -m pip install --upgrade pip -python -m pip install flake8 pytest pytest-cov hydra-core tqdm torch torchvision -python -m pip install rdkit==2023.3.3 -python -m pip MolScore promptsmiles +python -m pip install flake8 pytest pytest-cov hydra-core tqdm -if [ -f requirements.txt ]; then pip install -r requirements.txt; fi +# Not using nightly torch +python -m pip install torch torchvision +# python -m pip install --pre torch --extra-index-url https://download.pytorch.org/whl/nightly/cpu --force-reinstall -pip install torchrl +python -m pip torchrl +python -m pip install rdkit==2023.3.3 +python -m pip MolScore promptsmiles cd ../acegen-open pip install -e . diff --git a/.github/unittest/install_dependencies_nightly.sh b/.github/unittest/install_dependencies_nightly.sh index 2d03bff..2d831a3 100644 --- a/.github/unittest/install_dependencies_nightly.sh +++ b/.github/unittest/install_dependencies_nightly.sh @@ -1,13 +1,9 @@ python -m pip install --upgrade pip python -m pip install flake8 pytest pytest-cov hydra-core tqdm - -# Not using nightly torch python -m pip install torch torchvision # python -m pip install --pre torch --extra-index-url https://download.pytorch.org/whl/nightly/cpu --force-reinstall - -# Not testing these dependencies for now python -m pip install rdkit==2023.3.3 -# python -m pip MolScore promptsmiles +python -m pip MolScore promptsmiles cd ../acegen-open pip install -e . diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml index 7011b9e..e434f25 100644 --- a/.github/workflows/unit_tests.yml +++ b/.github/workflows/unit_tests.yml @@ -25,7 +25,7 @@ jobs: python-version: ${{ matrix.python-version }} - name: Install dependencies run: | - bash .github/unittest/install_dependencies_nightly.sh + bash .github/unittest/install_dependencies.sh - name: Test with pytest run: | pytest tests/ --cov=acegen diff --git a/README.md b/README.md index dc5d47c..c0cc09c 100644 --- a/README.md +++ b/README.md @@ -73,7 +73,7 @@ To create the conda / mamba environment, run To install the required dependencies run the following commands. Replace `cu121` with your appropriate CUDA version (e.g., `cu118`, `cu117`, `cu102`). pip3 install torch torchvision --index-url https://download.pytorch.org/whl/cu121 - pip3 install flake8 pytest pytest-cov hydra-core tqdm wandb scipy + pip3 install flake8 pytest pytest-cov hydra-core tqdm wandb pip3 install torchrl @@ -81,7 +81,7 @@ To install the required dependencies run the following commands. Replace `cu121` Unless you intend to define your own custom scoring functions, install MolScore by running - pip3 install rdkit==2023.3.3, joblib + pip3 install rdkit==2023.3.3 pip3 install MolScore To use the scaffold decoration and fragment linking, install promptsmiles by running