From bca0de4f3524bd9a571a17e9754cbb7a37de796c Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Wed, 17 May 2023 14:49:16 +0200 Subject: [PATCH 1/7] update: move codespell config from tox.ini to pyproject.toml --- pyproject.toml | 10 +++++++++- tox.ini | 10 +--------- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index f05b5b7c5..3691e34ce 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -95,6 +95,14 @@ extend-exclude = """ ) """ +[tool.codespell] +skip = "*/auto_examples/*,*.html,.git/,*.pyc,*/_build/*,*/h5io/*" +count = "" +quiet-level = 3 +ignore-words = "ignore_words.txt" +interactive = 0 +builtin = "clear,rare,informal,names,usage,code" + [tool.pytest.ini_options] minversion = "7.0" addopts = "--ignore=junifer/external/h5io -vv" @@ -140,4 +148,4 @@ showcontent = true # Add custom towncrier fragment for API changes [tool.towncrier.fragment.change] name = "API Changes" -showcontent = true \ No newline at end of file +showcontent = true diff --git a/tox.ini b/tox.ini index 0b6688fa0..3fcfadda7 100644 --- a/tox.ini +++ b/tox.ini @@ -150,12 +150,4 @@ exclude_lines = if TYPE_CHECKING: # Don't complain if non-runnable code isn't run: if __name__ == .__main__.: -precision = 2 - -[codespell] -skip = docs/auto_*,*.html,.git/,*.pyc,docs/_build,junifer/external/h5io/ -count = -quiet-level = 3 -ignore-words = ignore_words.txt -interactive = 0 -builtin = clear,rare,informal,names,usage +precision = 2 \ No newline at end of file -- 2.52.0 From fc92e63810ceba92fcdef20d59dcfa6248813d44 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Wed, 17 May 2023 14:49:51 +0200 Subject: [PATCH 2/7] update: use --toml config for codespell command in tox.ini --- tox.ini | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/tox.ini b/tox.ini index 3fcfadda7..a5af5db60 100644 --- a/tox.ini +++ b/tox.ini @@ -63,8 +63,9 @@ commands = skip_install = true deps = codespell + tomli commands = - codespell --config tox.ini examples/ junifer/ scratch/ tools/ + codespell --toml {toxinidir}/pyproject.toml {toxinidir}/docs/ {toxinidir}/examples/ {toxinidir}/junifer/ {toxinidir}/tools/ ################ # Tool configs # -- 2.52.0 From f5c1eb6af393eb1cbd12ff515464de8159612a3f Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Wed, 17 May 2023 14:50:18 +0200 Subject: [PATCH 3/7] chore: update ignore_words.txt --- docs/contribution.rst | 2 +- docs/extending/datagrabber.rst | 6 +++--- docs/extending/marker.rst | 4 ++-- docs/help.rst | 2 +- docs/index.rst | 2 +- docs/installation.rst | 2 +- docs/maintaining.rst | 2 +- docs/understanding/pipeline.rst | 2 +- docs/understanding/preprocess.rst | 2 +- docs/using/queueing.rst | 10 +++++----- docs/whats_new.rst | 4 ++-- ignore_words.txt | 5 ++++- 12 files changed, 23 insertions(+), 20 deletions(-) diff --git a/docs/contribution.rst b/docs/contribution.rst index f62430e59..29239f690 100644 --- a/docs/contribution.rst +++ b/docs/contribution.rst @@ -13,7 +13,7 @@ Setting up the local development environment `_. #. Clone your fork locally as described in the same guide but also add the flag to sync the submodules as well by appending the following to the - clone commmand: + clone command: .. code-block:: bash diff --git a/docs/extending/datagrabber.rst b/docs/extending/datagrabber.rst index b5debbf35..22c388a80 100644 --- a/docs/extending/datagrabber.rst +++ b/docs/extending/datagrabber.rst @@ -36,7 +36,7 @@ c. the experiment included resting-stage fMRI and a task named *stroop* then the *element* should be composed of 3 items: * ``subject``: The subject IDs, e.g. `sub001`, `sub002`, ... `sub020` -* ``session``: The sesion number, e.g. `ses1`, `ses2` +* ``session``: The session number, e.g. `ses1`, `ses2` * ``task``: The task performed, e.g. `rest`, `stroop` If any of these items were not part of the element, then we will have more than @@ -98,7 +98,7 @@ Option A: Extending from PatternDataGrabber ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ The :class:`.PatternDataGrabber` class is an abstract class that has the -functionality of understanding patterns embeded in it. +functionality of understanding patterns embedded in it. Before creating the datagrabber, we need to define 3 variables: @@ -385,7 +385,7 @@ Step 4: Optional: Adding *BOLD confounds* For some analyses, it is useful to have the confounds associated with the BOLD data. This corresponds to the ``BOLD_confounds`` item in the :ref:`Data Object ` (see :ref:`data_types`). However, the -``BOLD_confounds`` element does not only consists of a ``path``, but it requries +``BOLD_confounds`` element does not only consists of a ``path``, but it requires more information about the format of the confounds file. Thus, the ``BOLD_confounds`` element is a dictionary with the following keys: diff --git a/docs/extending/marker.rst b/docs/extending/marker.rst index e50392554..1e1db29fb 100644 --- a/docs/extending/marker.rst +++ b/docs/extending/marker.rst @@ -76,7 +76,7 @@ The parameters of the marker are defined in the ``__init__`` method. The are allowed as parameters. This is because the parameters are stored in JSON format, and JSON only supports these types. -In this example, only paramater required for the computation is the name of the +In this example, only parameter required for the computation is the name of the parcellation to use. Thus, we can define the ``__init__`` method as follows: .. code-block:: python @@ -109,7 +109,7 @@ arguments: * ``input``: a dictionary with the data to be used to compute the marker. This will be the corresponding element in the :ref:`Data Object` - alredy indexed. Thus, the dictionary has at least two keys: ``data`` and + already indexed. Thus, the dictionary has at least two keys: ``data`` and ``path``. The first one contains the data, while the second one contains the path to the data. The dictionary can also contain other keys, depending on the data type. diff --git a/docs/help.rst b/docs/help.rst index f414c55a2..39c65de0d 100644 --- a/docs/help.rst +++ b/docs/help.rst @@ -21,7 +21,7 @@ While the song might have been written with another meaning in mind, it is a goo way to describe the situation of many researchers who are presented with a new toolbox. Indeed, the situation of many researchers is that the projects they are working on are becoming more and more complex in terms of methods and data. Thus, -we *open up the doors* to new possibilites: +we *open up the doors* to new possibilities: | When I was younger, so much younger than today | I never needed anybody's help in any way diff --git a/docs/index.rst b/docs/index.rst index f74b5443e..23a734cb4 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -11,7 +11,7 @@ junifer (JUelich NeuroImaging FEature extractoR) is a data handling and feature extraction library targeted towards neuroimaging data specifically functional MRI data. -It is curently being developed and maintained at the Applied Machine Learning +It is currently being developed and maintained at the Applied Machine Learning (`AML`_) group at Forschungszentrum Juelich, Germany. Although the library is designed for people working at Institute of Neuroscience and Medicine - Brain and Behaviour (`INM-7`_), it is designed to be as modular as possible thus diff --git a/docs/installation.rst b/docs/installation.rst index e6611abbb..f89363c2c 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -113,7 +113,7 @@ the AFNI Docker container in your local system. Take the last line and copy it to your ``.bashrc`` or ``.zshrc`` file. -Or, alternatively, you can exceute this command which will update the +Or, alternatively, you can execute this command which will update the ``~/.bashrc`` for you: .. code-block:: bash diff --git a/docs/maintaining.rst b/docs/maintaining.rst index 2c883005c..c9ba6f5e8 100644 --- a/docs/maintaining.rst +++ b/docs/maintaining.rst @@ -50,7 +50,7 @@ before proceeding. to generate the proper changelog that should be reflected in ``docs/whats_new.rst``. -#. Commit the chages, make a PR and merge via a merge commit. +#. Commit the changes, make a PR and merge via a merge commit. #. Make sure you are in sync with the main branch. diff --git a/docs/understanding/pipeline.rst b/docs/understanding/pipeline.rst index 15e809b51..59f90c7f2 100644 --- a/docs/understanding/pipeline.rst +++ b/docs/understanding/pipeline.rst @@ -16,7 +16,7 @@ steps: 4. :ref:`Marker Computation `: Compute the marker. 5. :ref:`Storage `: Store the marker values. -The element that is passed accross the pipeline is called the +The element that is passed across the pipeline is called the :ref:`Data Object`. The following is a graphical representation of the pipeline: diff --git a/docs/understanding/preprocess.rst b/docs/understanding/preprocess.rst index 96c1bfd51..0a5194f79 100644 --- a/docs/understanding/preprocess.rst +++ b/docs/understanding/preprocess.rst @@ -94,7 +94,7 @@ The default value is to use all the *noise components* with the ``full`` *confou Other Parameters ~~~~~~~~~~~~~~~~ -Additionaly, the :class:`.fMRIPrepConfoundRemover` supports the following +Additionally, the :class:`.fMRIPrepConfoundRemover` supports the following parameters: .. list-table:: diff --git a/docs/using/queueing.rst b/docs/using/queueing.rst index 615d5b61b..8861cd51b 100644 --- a/docs/using/queueing.rst +++ b/docs/using/queueing.rst @@ -11,7 +11,7 @@ computational clusters. This is done by adding the ``queue`` section in the While junifer is meant to support `HTCondor`_, `SLURM`_ and local queueing using `GNU Parallel`_, only HTCondor is currently supported. This will be -implemented in future relases of junifer. If you are in immediate need of any of +implemented in future releases of junifer. If you are in immediate need of any of these schedulers, please create an issue on the `junifer github`_ repository. The ``queue`` section of the :ref:`codeless` must start by defining the @@ -45,17 +45,17 @@ When using HTCondor, junifer will use a DAG to queue one job per element (``junifer collect``) to collect the results once all of the individual element jobs are finished. -The following parameters are avilable for HTCondor: +The following parameters are available for HTCondor: -* ``env``: Definition of the Python enviroment. It must provide two variables: +* ``env``: Definition of the Python environment. It must provide two variables: * ``kind``: This is the kind of virtual environment to use: * ``conda`` * ``virtualenv`` (not yet supported) - * ``local`` (no virtual enviroment) + * ``local`` (no virtual environment) - * ``name``: This is the name of the enviroment to use in case a virtual + * ``name``: This is the name of the environment to use in case a virtual environment is used. * ``mem``: Memory to be used by the job. It must be provided as a string with diff --git a/docs/whats_new.rst b/docs/whats_new.rst index e4afcfec1..7caa0e4a0 100644 --- a/docs/whats_new.rst +++ b/docs/whats_new.rst @@ -18,7 +18,7 @@ Bugfixes and not to the location of the YAML file by `Fede Raimondo`_. (:gh:`127`) - Fix ``junifer run`` to respect preprocess step specified in the pipeline by `Synchon Mandal`_ (:gh:`159`) -- Fix a bug in which only ``REST1`` and ``REST2`` tasks could be accesed in +- Fix a bug in which only ``REST1`` and ``REST2`` tasks could be accessed in :class:`.DataladHCP1200` and :class:`.HCP1200` datagrabbers by `Fede Raimondo`_ (:gh:`183`) - Fix a bug in which fitting a marker (e.g. ``SphereAggregation``) on a @@ -41,7 +41,7 @@ Bugfixes `Fede Raimondo`_ (:gh:`194`) - Fix a bug in which :func:`.count` will not be correctly applied across an axis by `Fede Raimondo`_ (:gh:`195`) -- Fix an issue with datalad cache and locks in which the overriden settings in +- Fix an issue with datalad cache and locks in which the overridden settings in Junifer were not propagated to subprocesses, resulting in using the default settings by `Fede Raimondo`_ (:gh:`199`) - Fix a bug in which :func:`.get_mask` fails for FunctionalConnectivityBase diff --git a/ignore_words.txt b/ignore_words.txt index 8b25206ff..e1efe7acb 100644 --- a/ignore_words.txt +++ b/ignore_words.txt @@ -1 +1,4 @@ -master \ No newline at end of file +master +nin +Sepulcre +Chang -- 2.52.0 From 091ce34d7650c299419c6c8c7c42ae5cd6aa5006 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Wed, 17 May 2023 14:52:47 +0200 Subject: [PATCH 4/7] chore: codespell README --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 43cfb4ea5..a2c412c1d 100644 --- a/README.md +++ b/README.md @@ -14,7 +14,7 @@ junifer is a data handling and feature extraction library targeted towards neuroimaging data specifically functional MRI data. -It is curently being developed and maintained at the [Applied Machine Learning](https://www.fz-juelich.de/en/inm/inm-7/research-groups/applied-machine-learning-aml) group at [Forschungszentrum Juelich](https://www.fz-juelich.de/en), Germany. Although the library is designed for people working at [Institute of Neuroscience and Medicine - Brain and Behaviour (INM-7)](https://www.fz-juelich.de/en/inm/inm-7), it is designed to be as modular as possible thus enabling others to extend it easily. +It is currently being developed and maintained at the [Applied Machine Learning](https://www.fz-juelich.de/en/inm/inm-7/research-groups/applied-machine-learning-aml) group at [Forschungszentrum Juelich](https://www.fz-juelich.de/en), Germany. Although the library is designed for people working at [Institute of Neuroscience and Medicine - Brain and Behaviour (INM-7)](https://www.fz-juelich.de/en/inm/inm-7), it is designed to be as modular as possible thus enabling others to extend it easily. The documentation is available at [https://juaml.github.io/junifer](https://juaml.github.io/junifer/main/index.html). -- 2.52.0 From f05ca7ce0330c4b4a845423884eeca455039a5f9 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Wed, 17 May 2023 14:53:06 +0200 Subject: [PATCH 5/7] chore: add README.md for codespell in tox.ini --- tox.ini | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tox.ini b/tox.ini index a5af5db60..2b5f505d8 100644 --- a/tox.ini +++ b/tox.ini @@ -65,7 +65,7 @@ deps = codespell tomli commands = - codespell --toml {toxinidir}/pyproject.toml {toxinidir}/docs/ {toxinidir}/examples/ {toxinidir}/junifer/ {toxinidir}/tools/ + codespell --toml {toxinidir}/pyproject.toml {toxinidir}/docs/ {toxinidir}/examples/ {toxinidir}/junifer/ {toxinidir}/tools/ {toxinidir}/README.md ################ # Tool configs # -- 2.52.0 From 6e419f9b8767895cfa1b41a109edcecdc14a0083 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Wed, 17 May 2023 14:57:10 +0200 Subject: [PATCH 6/7] chore: add changelog 230.misc --- docs/changes/newsfragments/230.misc | 1 + 1 file changed, 1 insertion(+) create mode 100644 docs/changes/newsfragments/230.misc diff --git a/docs/changes/newsfragments/230.misc b/docs/changes/newsfragments/230.misc new file mode 100644 index 000000000..d29c02341 --- /dev/null +++ b/docs/changes/newsfragments/230.misc @@ -0,0 +1 @@ +Improve ``codespell`` support by fixing typos in documentation by `Synchon Mandal`_ \ No newline at end of file -- 2.52.0 From a894b3be36c5d93048a7b7642889a5416942e2f4 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 5 Jun 2023 13:45:21 +0200 Subject: [PATCH 7/7] fix: lowercase ignore words for codespell --- ignore_words.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/ignore_words.txt b/ignore_words.txt index e1efe7acb..1ac8c4893 100644 --- a/ignore_words.txt +++ b/ignore_words.txt @@ -1,4 +1,4 @@ master nin -Sepulcre -Chang +chang +sepulcre -- 2.52.0