From aefadd8523b91f20c21dd461b3c637ca4044677c Mon Sep 17 00:00:00 2001 From: Alexandre Pron Date: Mon, 22 Jul 2024 11:47:40 +0200 Subject: [PATCH 1/3] [ENH] added explicit conda command installation --- .github/workflows/conda-installation.yml | 5 +---- README.md | 7 ++----- 2 files changed, 3 insertions(+), 9 deletions(-) diff --git a/.github/workflows/conda-installation.yml b/.github/workflows/conda-installation.yml index c7d1079..f15c755 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 certifi charset-normalizer dicom-anonymizer idna importlib-metadata numpy 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..29540de 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 certifi charset-normalizer dicom-anonymizer idna importlib-metadata numpy 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 From 8ab6edfca6a854f86cb0cda599bd5b2895c79cca Mon Sep 17 00:00:00 2001 From: Alexandre Pron Date: Mon, 22 Jul 2024 14:00:56 +0200 Subject: [PATCH 2/3] [BF]: constrained numpy to version <2.0 (heudiconv incompatible with numpy 2.0.x) --- .github/workflows/conda-installation.yml | 2 +- README.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/conda-installation.yml b/.github/workflows/conda-installation.yml index f15c755..fe17e8b 100644 --- a/.github/workflows/conda-installation.yml +++ b/.github/workflows/conda-installation.yml @@ -22,7 +22,7 @@ jobs: - name: Install dependencies shell: bash -el {0} run: | - conda install -c conda-forge -c https://conda.anaconda.org/simpleitk SimpleITK brotli certifi charset-normalizer dicom-anonymizer idna importlib-metadata numpy 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 + conda install -c conda-forge -c https://conda.anaconda.org/simpleitk SimpleITK brotli 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 29540de..69818ee 100644 --- a/README.md +++ b/README.md @@ -24,7 +24,7 @@ In an active conda virtual environment type ```bash #use pip packages as dependencies # install missing conda packages (far simpler than using pip) -conda install -c conda-forge -c https://conda.anaconda.org/simpleitk SimpleITK brotli certifi charset-normalizer dicom-anonymizer idna importlib-metadata numpy 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 +conda install -c conda-forge -c https://conda.anaconda.org/simpleitk SimpleITK brotli 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 From 92cba08c8c8fb29465ef9bc115880ead0b0771c8 Mon Sep 17 00:00:00 2001 From: Alexandre Pron Date: Mon, 22 Jul 2024 14:04:55 +0200 Subject: [PATCH 3/3] [BF]: added bids-validator package --- .github/workflows/conda-installation.yml | 2 +- README.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/conda-installation.yml b/.github/workflows/conda-installation.yml index fe17e8b..3758032 100644 --- a/.github/workflows/conda-installation.yml +++ b/.github/workflows/conda-installation.yml @@ -22,7 +22,7 @@ jobs: - name: Install dependencies shell: bash -el {0} run: | - conda install -c conda-forge -c https://conda.anaconda.org/simpleitk SimpleITK brotli 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 + 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 69818ee..4ab5010 100644 --- a/README.md +++ b/README.md @@ -24,7 +24,7 @@ In an active conda virtual environment type ```bash #use pip packages as dependencies # install missing conda packages (far simpler than using pip) -conda install -c conda-forge -c https://conda.anaconda.org/simpleitk SimpleITK brotli 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 +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