Merge pull request #43 from yarikoptic/enh-codespell

codespell: config, workflow + typos fixed

.codespellrc

@@ -0,0 +1,4 @@
+[codespell]
+skip = .git,*.pdf,*.svg
+#
+# ignore-words-list =

.github/workflows/codespell.yml

@@ -0,0 +1,22 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

.gitignore

@@ -2,3 +2,4 @@
 _build
 build
 .vscode
+.DS_Store

LICENSE

@@ -34,7 +34,7 @@ CONDITIONS.
     Collection will not be considered an Adaptation for the purpose of
     this License. For the avoidance of doubt, where the Work is a musical
     work, performance or phonogram, the synchronization of the Work in
-    timed-relation with a moving image ("synching") will be considered an
+    timed-relation with a moving image ("syncing") will be considered an
     Adaptation for the purpose of this License.
  b. "Collection" means a collection of literary or artistic works, such as
     encyclopedias and anthologies, or performances, phonograms or
@@ -224,7 +224,7 @@ subject to and limited by the following restrictions:
 UNLESS OTHERWISE MUTUALLY AGREED TO BY THE PARTIES IN WRITING, LICENSOR
 OFFERS THE WORK AS-IS AND MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY
 KIND CONCERNING THE WORK, EXPRESS, IMPLIED, STATUTORY OR OTHERWISE,
-INCLUDING, WITHOUT LIMITATION, WARRANTIES OF TITLE, MERCHANTIBILITY,
+INCLUDING, WITHOUT LIMITATION, WARRANTIES OF TITLE, MERCHANTABILITY,
 FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF
 LATENT OR OTHER DEFECTS, ACCURACY, OR THE PRESENCE OF ABSENCE OF ERRORS,
 WHETHER OR NOT DISCOVERABLE. SOME JURISDICTIONS DO NOT ALLOW THE EXCLUSION

source/BAREMETAL_TO_BINDERHUB.rst

@@ -2,10 +2,10 @@ Bare-metal to BinderHub
 =======================
 
 Installation of the BinderHub  from bare-metal is fully automatic and reproducible through `terraform <https://www.terraform.io/>`_ configuration
-runned using `this Docker container <https://github.com/neurolibre/neurolibre-binderhub/blob/master/Dockerfile>`_.
+ran using `this Docker container <https://github.com/neurolibre/neurolibre-binderhub/blob/master/Dockerfile>`_.
 
-The following is intended for neurolibre backend developpers, but can be read by anyone interrested in our process.
-It assumes that you have basic knowledge on using the command line on a remote server (bash, ssh authentification..).
+The following is intended for neurolibre backend developers, but can be read by anyone interested in our process.
+It assumes that you have basic knowledge on using the command line on a remote server (bash, ssh authentication..).
 
 The sections :ref:`Pre-setup` and :ref:`Docker-specific preparations` should be done just the first time.
 Once it is done, you can directly go to the section :ref:`Spawn a BinderHub instance using Docker`.
@@ -15,11 +15,11 @@ Pre-setup
 
 You first need to prepare the necessary files that will be used later to install and ssh to the newly spawned BinderHub  instance.
 
-We are using `git-crypt <https://github.com/AGWA/git-crypt>`_ to encrypt our password files for the whole process, these can be uncrypted with the appropriate :code:`gitcrypt-key`.
+We are using `git-crypt <https://github.com/AGWA/git-crypt>`_ to encrypt our password files for the whole process, these can be unencrypted with the appropriate :code:`gitcrypt-key`.
 For the ssh authentication on the BinderHub  server, you have two choices : i) use neurolibre’s key (recommended) or ii) use your own ssh key.
 
 .. note:: You can request the :code:`gitcrypt-key`, :code:`neurolibre’s ssh key`, :code:`cloudflare` and :code:`arbutus API keys` to any infrastructure admin if authorized.
-.. warning:: You should never share the aformentioned file to anyone.
+.. warning:: You should never share the aforementioned file to anyone.
 
 1. Create a folder on your local machine, which is later to be mounted to the Docker container for securely using your keys during spawning a BinderHub instance.
    Here, we will call it :code:`my-keys` for convenience:

source/BAREMETAL_TO_DOCKER_REGISTRY.rst

@@ -11,7 +11,7 @@ The binderhub was stuck at the building phase, trying in vain to pull images fro
 Among many `ideas <https://github.com/jupyterhub/binderhub/issues/864>`_, one of them that came up pretty quickly was to simply create our own local docker registry on arbutus. 
 This would allow for low latency when pulling the images from the registry (connected to the local network where the binderhub resides).
 
-The following documentation explains how we built our own docker registry on Arbutus, it is intended for developpers who want to spawn a new ``Binderhub`` on another ``openstack`` host.
+The following documentation explains how we built our own docker registry on Arbutus, it is intended for developers who want to spawn a new ``Binderhub`` on another ``openstack`` host.
 It contains also instructions on how to create volumes on ``openstack`` (for the ``Repo2Data`` databases) and attach them to the docker registry.
 
 .. note:: It is still not the case, but in the future we expect the docker registry spawning to be part of the terrafrom configurations.
@@ -20,7 +20,7 @@ Instance spawning
 -----------------
 
 The first thing to do is to create a new instance on Arbutus using ``openstack``. 
-It provides a graphical interface to interract with our openstack project from computecanada.
+It provides a graphical interface to interact with our openstack project from computecanada.
 
 You will first need to `log-in into the openstack dashboard <https://arbutus.cloud.computecanada.ca/>`_.
 
@@ -51,7 +51,7 @@ When it is done, click on the right of the instance under ``Compute/Instances``
 .. image:: img/instance_menu.png
   :width: 150px
 
-.. warning:: You have a limited amount of floating IPs, so be carefull before using one.
+.. warning:: You have a limited amount of floating IPs, so be careful before using one.
 
 Firewall
 --------

source/BINDERHUB_TEST_MODE.rst

@@ -109,7 +109,7 @@ is to be done in a remote node via :code:`ssh` access.
      helm repo add jupyterhub https://jupyterhub.github.io/helm-chart/
      helm repo update
 
-   The process is successfull if you see the :code:`Hub is up` message.
+   The process is successful if you see the :code:`Hub is up` message.
 
 10. Install BinderHub and its development requirements:
 

source/FAQ.rst

@@ -47,7 +47,7 @@ For more information please check `the data related section <SUBMISSION_STRUCTUR
 Which version of ``jupyter-book`` and ``repo2data`` should I use ?
 ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
 We always recommend latest versions for better compatibility.
-For ``jupyter-book`` you are free to use any version you like, since we rely only on the compiled artifcats.
+For ``jupyter-book`` you are free to use any version you like, since we rely only on the compiled artifacts.
 For ``repo2data``, we highly advise to match latest version because this is what is used on the backend.
 
 How can I cache my experiments ?

source/INFRASTRUCTURE.rst

@@ -2,13 +2,13 @@ Infrastructure overview
 =======================
 
 At the bottom of our infrastructure, we rely on `openstack <https://www.openstack.org/>`_ which spawns our multiple VMs (what we will reffer later as instance) and virtual volumes.
-After successfull spawning of the instance, it is assigned a floating IP used to connect to it from the outside world.
-The `cloudflare DNS <https://www.cloudflare.com/>`_ then properly configure the choosen domain name under :code:`*.conp.cloud` automatically pointing to the assigned floating IP.
+After successful spawning of the instance, it is assigned a floating IP used to connect to it from the outside world.
+The `cloudflare DNS <https://www.cloudflare.com/>`_ then properly configure the chosen domain name under :code:`*.conp.cloud` automatically pointing to the assigned floating IP.
 When the network has been properly setup, the installation can continue with `kubernetes <https://kubernetes.io/>`_ and finishes with `BinderHub  <https://BinderHub .readthedocs.io/en/latest/index.html>`_.
 
 We want to share our experience with the community, hence all our installation scripts are open-source available under
 `neurolibre/kubeadm-boostrap <https://github.com/neurolibre/kubeadm-bootstrap>`_ and `neurolibre/terraform-binderhub <https://github.com/neurolibre/terraform-binderhub>`_.
 
-.. warning:: NeuroLibre is still at an alpha stage of development, the github repositories will change frequently so be carefull if you use them.
+.. warning:: NeuroLibre is still at an alpha stage of development, the github repositories will change frequently so be careful if you use them.
 
 You can find more details on the installation at :doc:`BAREMETAL_TO_BINDERHUB`.

source/REVIEWER.md

@@ -18,7 +18,7 @@ Note that you are not expected to review code libraries shipped with the noteboo
  * are there automated tests implemented?
 
 ## Scientific review
-Your are not expected to review the scientific soundness of the work. This step is typically handled by traditional peer-review in scientific journals. However, if a work appears to be of obvious unsufficient quality, we encourage you to contact the editors privately and suggest that the submission be withdrawn.
+Your are not expected to review the scientific soundness of the work. This step is typically handled by traditional peer-review in scientific journals. However, if a work appears to be of obvious insufficient quality, we encourage you to contact the editors privately and suggest that the submission be withdrawn.
 
 ## How to interact with authors
 We encourage you to open as many issues as necessary to reach a high quality for the submission. For this purpose, you will use the github issue tracking system on the repository associated with the submission.  Please assign the issues to the lead author of the submission, who will submit a pull request in order to address your comments. Review the pull request and merge it if you think it is appropriate. You can also submit a pull request yourself and ask the author to approve the changes. Please remain courteous and constructive in your feedback, and follow our [code of conduct](COC.md).

source/SUBMISSION_STRUCTURE.rst

@@ -18,7 +18,7 @@ We expect to find all the submission material in a **public** GitHub repository
 | ├── `paper.md <#static-summary>`_
 | └── `paper.bib <#static-summary>`_
 
-Our meta anlaysis on myelin submission which is publically available `in this github repository <https://github.com/Notebook-Factory/myelin-meta-analysis>`_ should help you understand the layout.
+Our meta anlaysis on myelin submission which is publicly available `in this github repository <https://github.com/Notebook-Factory/myelin-meta-analysis>`_ should help you understand the layout.
 
 .. warning:: If RoboNeuro does not see this file layout, it will fail to build the jupyter book build (but may be able to build the computing environment).
             Make sure that your file layout never change during runtime (especially if using a Dockerfile).
@@ -74,7 +74,7 @@ or a ``Dockerfile``.
 1.1.2 Environment configuration for NeuroLibre
 ..............................................
 
-You should try to make your environment clean and concize, that is why the prefered configuration file for NeuroLibre are the
+You should try to make your environment clean and concize, that is why the preferred configuration file for NeuroLibre are the
 ``requirements.txt``.
 
 It should be small (to keep environment building and loading as short as possible), and versionnized (so your
@@ -115,7 +115,7 @@ On the other hand, this one is concise, reproducible and will take much less tim
 
 .. topic:: Best practices when using Dockerfiles
 
-  While Neurolibre can build a Dockerfile environment, we don't recommend it as this can be a source of lot of erros during build.
+  While Neurolibre can build a Dockerfile environment, we don't recommend it as this can be a source of lot of errors during build.
   If you don't have choice, please make sure to follow these specific instructions:
 
   1. We recommend that you use our base image to help you build your Dockerfile for Neurolibre:

source/SUBMIT.rst

@@ -33,7 +33,7 @@ After your submission, the managing editor will initiate a pre-review issue in t
 content moderation is successful. During the pre-review, a **technical screener** will be assigned to your submission and the "review" will be started, which
 is a GitHub issue on the reviews repository.
 
-.. admonition:: Techical screening vs peer review
+.. admonition:: Technical screening vs peer review
    :class: warning
 
    Technical screening is conducted to verify the functionality of your NRP. 

source/TEST_SUBMISSION.rst

@@ -113,7 +113,7 @@ Debugging for long NeuroLibre submission
 As for ``mybinder``, we also provide a binder submission page so you can play with your notebooks on our servers.
 Our binder submission page is available here: https://test.conp.cloud.
 
-When this process is really usefull for debugging your submission live, it can be verry long to get it.
+When this process is really useful for debugging your submission live, it can be very long to get it.
 Indeed, a jupyter book build will always occur under the hood, and as part of the build process it will try to execute everything within your submission.
 This can make the build process very long (especially if you have a lot of long-running notebooks), and so you will end up waiting forever to get the binder instance.