diff --git a/docs/installation.rst b/docs/installation.rst index f6da8943..7af20cce 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -34,7 +34,7 @@ We have a `yaml` file on our repo for easily installing BABS and its dependencie wget https://raw.githubusercontent.com/PennLINC/babs/refs/heads/main/environment_hpc.yml # Install into a new environment called babs: - mamba create -f evironment_hpc.yml + mamba create -f environment_hpc.yml # Activate the environment: mamba activate babs diff --git a/environment_hpc.yml b/environment_hpc.yml index 7226d653..c335bf1e 100644 --- a/environment_hpc.yml +++ b/environment_hpc.yml @@ -2,30 +2,33 @@ name: babs channels: - conda-forge dependencies: - - apptainer + - python=3.11 - git - git-annex - - pip - p7zip - - python=3.11 + - pip + # Core packages from conda-forge when available + - numpy + - pandas + - pyyaml>=6.0 + - jinja2 + - nibabel + - tqdm + - regex + # Testing packages + - pytest + - coverage + # Pip packages (mainly BABS and DataLad ecosystem) - pip: + - babs>=0.1.0 + - datalad>=0.17.2 + - datalad-container>=1.1.6 + - datalad-osf + - filelock>=3.8.0 - backoff - - coverage - - datalad >= 0.17.2 - - datalad_container >= 1.1.6 - - filelock >= 3.8.0 - - jinja2 - - nibabel - niworkflows - - numpy - - pandas - - pyyaml >= 6.0 - - qstat >= 0.0.5 - - regex - - tqdm - - pytest - - pytest-cov==5.0.0 - - pytest-env==1.1.3 + - qstat>=0.0.5 + - pytest-cov>=5.0.0 + - pytest-env>=1.1.0 - pytest-timeout>=2.2.0 - pytest-xdist - - datalad-osf