From 70bc4f4fac82b2d3022ebe0d541cf56dea818289 Mon Sep 17 00:00:00 2001 From: B-Sevchik <78758419+B-Sevchik@users.noreply.github.com> Date: Thu, 23 Jan 2025 10:15:52 -0500 Subject: [PATCH] Update installation instructions to use miniforge (#375) * update installation instructions to use miniforge * edit miniforge installation instructions to specify which sections are for developers * edited CONTRIBUTING.rst instructions to use miniforge instead of venv * link to contributors guide in installation.rst * fixed weird formatting error in installation.rst * Update docs/installation.rst Co-authored-by: Taylor Salo * Update docs/installation.rst Co-authored-by: Taylor Salo --------- Co-authored-by: Taylor Salo Co-authored-by: Taylor Salo --- CONTRIBUTING.rst | 8 ++++---- docs/installation.rst | 24 +++++++++++++++--------- 2 files changed, 19 insertions(+), 13 deletions(-) diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst index 8597fc6fc..21c6be1c4 100644 --- a/CONTRIBUTING.rst +++ b/CONTRIBUTING.rst @@ -63,11 +63,11 @@ Ready to contribute? Here's how to set up `cubids` for local development. $ git clone git@github.com:your_name_here/cubids.git -3. Install your local copy into a virtualenv. - Assuming you have virtualenvwrapper installed, - this is how you set up your fork for local development:: +3. Install your local copy into a miniforge environment. + This is how you set up your fork for local development:: - $ mkvirtualenv cubids + $ mamba create -n cubids python=3.12 + $ mamba activate cubids $ cd cubids/ $ python setup.py develop diff --git a/docs/installation.rst b/docs/installation.rst index b8c323e7f..53e5d4734 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -8,16 +8,15 @@ Installation .. note:: We **strongly recommend** using ``CuBIDS`` with environment management. - For this, we recommend `miniconda `_ - (`miniforge `_ for M1 Chip Mac Machines). + For this, we recommend `miniforge `_. -Once you've installed conda, -initialize a new conda environment (for example, named ``cubids``) as follows: +Once you've installed mamba, +initialize a new mamba environment (for example, named ``cubids``) as follows: .. code-block:: console - $ conda create -n cubids python=3.12 pip - $ conda activate cubids + $ mamba create -n cubids python=3.12 pip + $ mamba activate cubids You are now ready to install CuBIDS. You can do so in one of two ways. @@ -29,8 +28,7 @@ To obtain ``CuBIDS`` locally, we can use ``pip`` to download our software from t $ pip install CuBIDS -Alternatively, -you can clone the source code for ``CuBIDS`` from our `GitHub repository`_ using the following command: +Alternatively, you can clone the source code for ``CuBIDS`` from our `GitHub repository`_ using the following command: .. code-block:: console @@ -43,13 +41,14 @@ Once you have a copy of the source, you can install it with: $ cd CuBIDS $ pip install -e . + We will now need to install some dependencies of ``CuBIDS``. To do this, we first must install deno to run `bids-validator`. We can accomplish this using the following command: .. code-block:: console - $ conda install deno + $ mamba install deno The new schema-based ``bids-validator`` doesn't need to be installed and will be implemented automatically when `cubids validate` is called @@ -75,6 +74,13 @@ and will be implemented automatically when `cubids validate` is called For more information, you can read: https://bids-validator.readthedocs.io/en/latest/user_guide/command-line.html +.. tip:: + If you want to modify the CuBIDS codebase + (e.g., if you are looking to contribute to CuBIDS), + please follow the installation instructions in + `our contributing guidelines `_. + + We also recommend using ``CuBIDS`` with the optional ``DataLad`` version control capabilities. We use ``DataLad`` throughout our walkthrough of the CuBIDS Workflow on :doc:`the Example Walkthrough page `.