diff --git a/.github/workflows/conda-installation.yml b/.github/workflows/conda-installation.yml index c7d1079..3758032 100644 --- a/.github/workflows/conda-installation.yml +++ b/.github/workflows/conda-installation.yml @@ -22,10 +22,7 @@ jobs: - name: Install dependencies shell: bash -el {0} run: | - conda config --set pip_interop_enabled True - python -m pip install . - conda update --all - conda install -c conda-forge heudiconv bids-validator dcm2niix git-annex=*=alldep* datalad + conda install -c conda-forge -c https://conda.anaconda.org/simpleitk SimpleITK brotli bids-validator certifi charset-normalizer dicom-anonymizer idna importlib-metadata 'numpy<2.0' pandas py7zr pybcj pycryptodomex pyppmd pytz pydicom python-dotenv python-dateutil requests six texttable tqdm typing_extensions urllib3 zipp pydicom dicom2nifti Pillow heudiconv git-annex=*=alldep* datalad # Create virtual env under each python version # (optional and a bit redundant because we are already on a specific python) diff --git a/README.md b/README.md index eaeb567..4ab5010 100644 --- a/README.md +++ b/README.md @@ -23,12 +23,9 @@ Optionally, rename the `.env.example` to `.env` and set the variables (`shanoir_ In an active conda virtual environment type ```bash #use pip packages as dependencies -conda config --set pip_interop_enabled True -pip install . -#replace pip packages with conda packages when equivalent -conda update --all # install missing conda packages (far simpler than using pip) -conda install -c conda-forge heudiconv git-annex=*=alldep* datalad +conda install -c conda-forge -c https://conda.anaconda.org/simpleitk SimpleITK brotli bids-validator certifi charset-normalizer dicom-anonymizer idna importlib-metadata 'numpy<2.0' pandas py7zr pybcj pycryptodomex pyppmd pytz pydicom python-dotenv python-dateutil requests six texttable tqdm typing_extensions urllib3 zipp pydicom dicom2nifti Pillow heudiconv git-annex=*=alldep* datalad + ``` ## Usage