From 84925b6a12b6d58c6464b6086a2ecadb32d815b7 Mon Sep 17 00:00:00 2001 From: B-Sevchik <78758419+B-Sevchik@users.noreply.github.com> Date: Wed, 15 Jan 2025 13:01:07 -0500 Subject: [PATCH 1/7] update installation instructions to use miniforge --- docs/installation.rst | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/docs/installation.rst b/docs/installation.rst index b6ebda3bb..0bd7ae838 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -8,8 +8,7 @@ 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: @@ -19,6 +18,13 @@ initialize a new conda environment (for example, named ``cubids``) as follows: $ conda create -n cubids python=3.12 pip $ conda activate cubids +Or as follows: + +.. code-block:: console + + $ 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. From 9430e6c082671d12c42e573006e2f1f0faaa6d68 Mon Sep 17 00:00:00 2001 From: B-Sevchik <78758419+B-Sevchik@users.noreply.github.com> Date: Thu, 16 Jan 2025 11:01:42 -0500 Subject: [PATCH 2/7] edit miniforge installation instructions to specify which sections are for developers --- docs/installation.rst | 20 +++++++++++--------- 1 file changed, 11 insertions(+), 9 deletions(-) diff --git a/docs/installation.rst b/docs/installation.rst index 0bd7ae838..b7d868e4d 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -13,13 +13,6 @@ Installation Once you've installed conda, initialize a new conda environment (for example, named ``cubids``) as follows: -.. code-block:: console - - $ conda create -n cubids python=3.12 pip - $ conda activate cubids - -Or as follows: - .. code-block:: console $ mamba create -n cubids python=3.12 pip @@ -35,7 +28,8 @@ To obtain ``CuBIDS`` locally, we can use ``pip`` to download our software from t $ pip install CuBIDS -Alternatively, + +**For developers:** Alternatively, you can clone the source code for ``CuBIDS`` from our `GitHub repository`_ using the following command: .. code-block:: console @@ -49,13 +43,21 @@ Once you have a copy of the source, you can install it with: $ cd CuBIDS $ pip install -e . +**For developers:** If you want to install so that you can also contribute code, you can install it with: + +.. code-block:: console + + $ cd CuBIDS + $ pip install -e .[all] + + 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 From 721c372713fe61f0bd02dbf9a2c8f1cd317439de Mon Sep 17 00:00:00 2001 From: B-Sevchik <78758419+B-Sevchik@users.noreply.github.com> Date: Thu, 16 Jan 2025 11:19:19 -0500 Subject: [PATCH 3/7] edited CONTRIBUTING.rst instructions to use miniforge instead of venv --- CONTRIBUTING.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst index 65a6e2ec6..85df8fd4f 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 From 1653215013e6769067f2ae213d382429feae9889 Mon Sep 17 00:00:00 2001 From: B-Sevchik <78758419+B-Sevchik@users.noreply.github.com> Date: Thu, 16 Jan 2025 11:25:22 -0500 Subject: [PATCH 4/7] link to contributors guide in installation.rst --- docs/installation.rst | 17 ++++++++--------- 1 file changed, 8 insertions(+), 9 deletions(-) diff --git a/docs/installation.rst b/docs/installation.rst index b7d868e4d..8668099fc 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -28,8 +28,7 @@ To obtain ``CuBIDS`` locally, we can use ``pip`` to download our software from t $ pip install CuBIDS - -**For developers:** Alternatively, + Alternatively, you can clone the source code for ``CuBIDS`` from our `GitHub repository`_ using the following command: .. code-block:: console @@ -43,13 +42,6 @@ Once you have a copy of the source, you can install it with: $ cd CuBIDS $ pip install -e . -**For developers:** If you want to install so that you can also contribute code, you can install it with: - -.. code-block:: console - - $ cd CuBIDS - $ pip install -e .[all] - We will now need to install some dependencies of ``CuBIDS``. To do this, we first must install deno to run `bids-validator`. @@ -63,6 +55,13 @@ The new schema-based ``bids-validator`` doesn't need to be installed and will be implemented automatically when `cubids validate` is called +.. 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 `. From ee8ce735c7951f1e17fb634f9ff234a3634410f6 Mon Sep 17 00:00:00 2001 From: B-Sevchik <78758419+B-Sevchik@users.noreply.github.com> Date: Thu, 16 Jan 2025 11:28:44 -0500 Subject: [PATCH 5/7] fixed weird formatting error in installation.rst --- docs/installation.rst | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/installation.rst b/docs/installation.rst index 8668099fc..d5620a716 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -28,8 +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 From dd956606d6e5e59af6e07d9f9af6455b1d6364e8 Mon Sep 17 00:00:00 2001 From: B-Sevchik <78758419+B-Sevchik@users.noreply.github.com> Date: Fri, 17 Jan 2025 10:06:28 -0500 Subject: [PATCH 6/7] Update docs/installation.rst Co-authored-by: Taylor Salo --- docs/installation.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/installation.rst b/docs/installation.rst index d5620a716..afa23cab2 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -10,8 +10,8 @@ Installation We **strongly recommend** using ``CuBIDS`` with environment management. 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 From 115018698d0af4363a3db4c993ce2c310331ccf1 Mon Sep 17 00:00:00 2001 From: B-Sevchik <78758419+B-Sevchik@users.noreply.github.com> Date: Fri, 17 Jan 2025 10:06:39 -0500 Subject: [PATCH 7/7] Update docs/installation.rst Co-authored-by: Taylor Salo --- docs/installation.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/installation.rst b/docs/installation.rst index afa23cab2..201ab2a4d 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -28,7 +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