From 571662c4598101fd969158b1d337ff5046974a1d Mon Sep 17 00:00:00 2001 From: Gensollen Date: Thu, 30 May 2024 15:54:16 +0200 Subject: [PATCH] [DOC] Update the Python version used for creating the conda environment in README (#600) * update python version used for creating conda env in README * investigate * fix --- .github/workflows/test_cli.yml | 2 +- .github/workflows/test_generate.yml | 2 +- .github/workflows/test_interpret.yml | 2 +- .github/workflows/test_predict.yml | 2 +- .github/workflows/test_prepare_data.yml | 2 +- .github/workflows/test_quality_checks.yml | 2 +- .github/workflows/test_random_search.yml | 2 +- .github/workflows/test_resume.yml | 2 +- .github/workflows/test_train.yml | 2 +- .github/workflows/test_transfer_learning.yml | 2 +- .github/workflows/test_tsvtools.yml | 2 +- README.md | 19 +++++++++---------- 12 files changed, 20 insertions(+), 21 deletions(-) diff --git a/.github/workflows/test_cli.yml b/.github/workflows/test_cli.yml index 802511c9d..4efd2b024 100644 --- a/.github/workflows/test_cli.yml +++ b/.github/workflows/test_cli.yml @@ -36,8 +36,8 @@ jobs: python-version: ${{ env.PYTHON_VERSION }} - name: Run CLI tests run: | - make env.conda source /builds/miniconda3/etc/profile.d/conda.sh + make env.conda conda activate "${{ github.workspace }}"/env make install cd tests diff --git a/.github/workflows/test_generate.yml b/.github/workflows/test_generate.yml index e0149760f..8fc54c025 100644 --- a/.github/workflows/test_generate.yml +++ b/.github/workflows/test_generate.yml @@ -36,8 +36,8 @@ jobs: python-version: ${{ env.PYTHON_VERSION }} - name: Run tests for generate task run: | - make env.conda source /builds/miniconda3/etc/profile.d/conda.sh + make env.conda conda activate "${{ github.workspace }}"/env make install cd tests diff --git a/.github/workflows/test_interpret.yml b/.github/workflows/test_interpret.yml index 7cfd9d56b..13db354a9 100644 --- a/.github/workflows/test_interpret.yml +++ b/.github/workflows/test_interpret.yml @@ -36,8 +36,8 @@ jobs: python-version: ${{ env.PYTHON_VERSION }} - name: Run tests for Interpret task on GPU run: | - make env.conda source "${HOME}/miniconda3/etc/profile.d/conda.sh" + make env.conda conda activate "${{ github.workspace }}"/env make install cd tests diff --git a/.github/workflows/test_predict.yml b/.github/workflows/test_predict.yml index f12740dac..e6d790b2a 100644 --- a/.github/workflows/test_predict.yml +++ b/.github/workflows/test_predict.yml @@ -36,8 +36,8 @@ jobs: python-version: ${{ env.PYTHON_VERSION }} - name: Run tests for predict task run: | - make env.conda source /builds/miniconda3/etc/profile.d/conda.sh + make env.conda conda activate "${{ github.workspace }}"/env make install cd tests diff --git a/.github/workflows/test_prepare_data.yml b/.github/workflows/test_prepare_data.yml index 8209b9fa2..753634f76 100644 --- a/.github/workflows/test_prepare_data.yml +++ b/.github/workflows/test_prepare_data.yml @@ -36,8 +36,8 @@ jobs: python-version: ${{ env.PYTHON_VERSION }} - name: Run tests for prepare data task run: | - make env.conda source /builds/miniconda3/etc/profile.d/conda.sh + make env.conda conda activate "${{ github.workspace }}"/env make install cd tests diff --git a/.github/workflows/test_quality_checks.yml b/.github/workflows/test_quality_checks.yml index 701460266..25d1bc752 100644 --- a/.github/workflows/test_quality_checks.yml +++ b/.github/workflows/test_quality_checks.yml @@ -36,8 +36,8 @@ jobs: python-version: ${{ env.PYTHON_VERSION }} - name: Run tests for Quality Check run: | - make env.conda source /builds/miniconda3/etc/profile.d/conda.sh + make env.conda conda activate "${{ github.workspace }}"/env make install cd tests diff --git a/.github/workflows/test_random_search.yml b/.github/workflows/test_random_search.yml index 314afc353..78ddc2df0 100644 --- a/.github/workflows/test_random_search.yml +++ b/.github/workflows/test_random_search.yml @@ -36,8 +36,8 @@ jobs: python-version: ${{ env.PYTHON_VERSION }} - name: Run Random Search tests on GPU run: | - make env.conda source "${HOME}/miniconda3/etc/profile.d/conda.sh" + make env.conda conda activate "${{ github.workspace }}"/env make install cd tests diff --git a/.github/workflows/test_resume.yml b/.github/workflows/test_resume.yml index 78a229913..6d145339b 100644 --- a/.github/workflows/test_resume.yml +++ b/.github/workflows/test_resume.yml @@ -36,8 +36,8 @@ jobs: python-version: ${{ env.PYTHON_VERSION }} - name: Run resume tests on GPU run: | - make env.conda source "${HOME}/miniconda3/etc/profile.d/conda.sh" + make env.conda conda activate "${{ github.workspace }}"/env make install cd tests diff --git a/.github/workflows/test_train.yml b/.github/workflows/test_train.yml index 599725225..b3852bb09 100644 --- a/.github/workflows/test_train.yml +++ b/.github/workflows/test_train.yml @@ -36,8 +36,8 @@ jobs: python-version: ${{ env.PYTHON_VERSION }} - name: Run tests for Train on GPU run: | - make env.conda source "${HOME}/miniconda3/etc/profile.d/conda.sh" + make env.conda conda activate "${{ github.workspace }}"/env make install cd tests diff --git a/.github/workflows/test_transfer_learning.yml b/.github/workflows/test_transfer_learning.yml index 4664a97a3..9a3a583a3 100644 --- a/.github/workflows/test_transfer_learning.yml +++ b/.github/workflows/test_transfer_learning.yml @@ -36,8 +36,8 @@ jobs: python-version: ${{ env.PYTHON_VERSION }} - name: Run tests for Transfer Learning on GPU run: | - make env.conda source "${HOME}/miniconda3/etc/profile.d/conda.sh" + make env.conda conda activate "${{ github.workspace }}"/env make install cd tests diff --git a/.github/workflows/test_tsvtools.yml b/.github/workflows/test_tsvtools.yml index 9f3bfeb02..9e388b8e7 100644 --- a/.github/workflows/test_tsvtools.yml +++ b/.github/workflows/test_tsvtools.yml @@ -36,8 +36,8 @@ jobs: python-version: ${{ env.PYTHON_VERSION }} - name: Run tests for TSV tools run: | - make env.conda source /builds/miniconda3/etc/profile.d/conda.sh + make env.conda conda activate "${{ github.workspace }}"/env make install cd tests diff --git a/README.md b/README.md index 05b5f3a09..dae486a72 100755 --- a/README.md +++ b/README.md @@ -33,34 +33,33 @@ ## About the project This repository hosts ClinicaDL, the deep learning extension of [Clinica](https://github.com/aramis-lab/clinica), -a python library to process neuroimaging data in [BIDS](https://bids.neuroimaging.io/index.html) format. +a Python library to process neuroimaging data in [BIDS](https://bids.neuroimaging.io/index.html) format. > **Disclaimer:** this software is **under development**. Some features can change between different releases and/or commits. -To access the full documentation of the project, follow the link -[https://clinicadl.readthedocs.io/](https://clinicadl.readthedocs.io/). +To access the full documentation of the project, follow the link [https://clinicadl.readthedocs.io/](https://clinicadl.readthedocs.io/). If you find a problem when using it or if you want to provide us feedback, please [open an issue](https://github.com/aramis-lab/ad-dl/issues) or write on the [forum](https://groups.google.com/forum/#!forum/clinica-user). ## Getting started + ClinicaDL currently supports macOS and Linux. We recommend to use `conda` or `virtualenv` for the installation of ClinicaDL -as it guarantees the correct management of libraries depending on common -packages: +as it guarantees the correct management of libraries depending on common packages: ```{.sourceCode .bash} -conda create --name ClinicaDL python=3.8 +conda create --name ClinicaDL python=3.10 conda activate ClinicaDL pip install clinicadl ``` -## Tutorial -Visit our [hands-on tutorial web -site](https://aramislab.paris.inria.fr/clinicadl/tuto) to start -using **ClinicaDL** directly in a Google Colab instance! +## Tutorial + +Visit our [hands-on tutorial web site](https://aramislab.paris.inria.fr/clinicadl/tuto) +to start using **ClinicaDL** directly in a Google Colab instance! ## Related Repositories