Merge pull request #445 from smoia/int/pre-commit

smoia · web-flow · commit 977089484ce5 · 2023-04-27T00:55:49.000+02:00
Fix pre-commit configuration
diff --git a/.autorc b/.autorc
@@ -89,4 +89,4 @@
       "color": "#FFFFFF"
     }
   ]
-}
+}
diff --git a/.github/ISSUE_TEMPLATE/ISSUE_TEMPLATE_BUGS.md b/.github/ISSUE_TEMPLATE/ISSUE_TEMPLATE_BUGS.md
@@ -26,7 +26,7 @@ assignees:
 
 ## Specifications
 <!--- Point out the version of phys2bids you are running and your OS version -->
-    - Python version: 
+    - Python version:
     - phys2bids version:
     - Platform:
 
diff --git a/.github/ISSUE_TEMPLATE/ISSUE_TEMPLATE_DISCUSSION.md b/.github/ISSUE_TEMPLATE/ISSUE_TEMPLATE_DISCUSSION.md
@@ -1,6 +1,6 @@
 ---
 name: Discussion
-about: Use this template to start a discussion issue, i.e. an issue that 
+about: Use this template to start a discussion issue, i.e. an issue that
 title: ''
 labels: Discussion
 assignees: ''
@@ -22,6 +22,6 @@ I'm opening this discussion because/I think that/I noticed that...
 <!--- Repeat the concept in a very few, short (max 3) questions -->
 <!--- Remember that the aim is not to give a "tldr", but to help address salient points. -->
 
-    - 
-    - 
-    - 
+    -
+    -
+    -
diff --git a/.github/ISSUE_TEMPLATE/ISSUE_TEMPLATE_GENERAL.md b/.github/ISSUE_TEMPLATE/ISSUE_TEMPLATE_GENERAL.md
@@ -18,6 +18,6 @@ assignees: ''
 ## Next Steps
 <!--- Provide possible steps to take in order to address the issue -->
 
-    * 
-    * 
-    * 
+    *
+    *
+    *
diff --git a/.github/ISSUE_TEMPLATE/ISSUE_TEMPLATE_MEETING.md b/.github/ISSUE_TEMPLATE/ISSUE_TEMPLATE_MEETING.md
@@ -8,6 +8,6 @@ assignees: smoia
 
 The call will take place over **Skype** [here](https://join.skype.com/Rm4B7R30TG6g).
 
-Find the agenda [here]() and don't be scared to add/suggest/press for topics! 
+Find the agenda [here]() and don't be scared to add/suggest/press for topics!
 
 Old minutes are [here](https://drive.google.com/open?id=1zfc-hgRcU1k2XdqKD8v6TGwQX_jeCUea)
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -20,4 +20,4 @@ python:
       path: .
       extra_requirements:
         - doc
-  system_packages: true
+  system_packages: true
diff --git a/.zenodo.json b/.zenodo.json
@@ -1,82 +1,82 @@
 {
-    "license": "Apache-2.0", 
+    "license": "Apache-2.0",
     "title": "physiopy/phys2bids: BIDS formatting of physiological recordings",
     "upload_type": "software",
     "creators": [
         {
-            "affiliation": "BCBL - Basque Center on Cognition, Brain and Language", 
+            "affiliation": "BCBL - Basque Center on Cognition, Brain and Language",
             "name": "Daniel Alcal\u00e1"
-        }, 
+        },
         {
-            "affiliation": "Northwestern University", 
+            "affiliation": "Northwestern University",
             "name": "Apoorva Ayyagari"
-        }, 
+        },
         {
             "orcid": "0000-0002-7796-8795",
-            "affiliation": "Florida International University", 
+            "affiliation": "Florida International University",
             "name": "Katie Bottenhorn"
-        }, 
+        },
         {
-            "affiliation": "Northwestern University", 
+            "affiliation": "Northwestern University",
             "name": "Molly Bright"
-        }, 
+        },
         {
             "orcid": "0000-0002-9068-5810",
-            "affiliation": "BCBL - Basque Center on Cognition, Brain and Language", 
+            "affiliation": "BCBL - Basque Center on Cognition, Brain and Language",
             "name": "C\u00e9sar Caballero-Gaudes"
-        }, 
+        },
         {
-            "affiliation": "BCBL - Basque Center on Cognition, Brain and Language", 
+            "affiliation": "BCBL - Basque Center on Cognition, Brain and Language",
             "name": "In\u00e9s Chavarr\u00eda"
-        }, 
+        },
         {
-            "affiliation": "BCBL - Basque Center on Cognition, Brain and Language", 
+            "affiliation": "BCBL - Basque Center on Cognition, Brain and Language",
             "name": "Vicente Ferrer"
-        }, 
+        },
         {
             "name": "Soichi Hayashi"
-        }, 
+        },
         {
             "name": "Vittorio Iacovella"
-        }, 
+        },
         {
             "name": "Fran\u00e7ois Lespinasse"
-        }, 
+        },
         {
             "orcid": "0000-0003-1057-1336",
-            "affiliation": "McGill University", 
+            "affiliation": "McGill University",
             "name": "Ross Markello"
-        }, 
+        },
         {
-            "orcid": "0000-0002-2553-3327", 
-            "affiliation": "BCBL - Basque Center on Cognition, Brain and Language", 
+            "orcid": "0000-0002-2553-3327",
+            "affiliation": "BCBL - Basque Center on Cognition, Brain and Language",
             "name": "Stefano Moia"
-        }, 
+        },
         {
             "name": "Robert Oostenveld"
-        }, 
+        },
         {
             "orcid": "0000-0001-9813-3167",
-            "affiliation": "Florida International University", 
+            "affiliation": "Florida International University",
             "name": "Taylor Salo"
-        }, 
+        },
         {
-            "affiliation": "Northwestern University", 
+            "affiliation": "Northwestern University",
             "name": "Rachael Stickland"
-        }, 
+        },
         {
             "orcid": "0000-0001-6849-9088",
-            "affiliation": "BCBL - Basque Center on Cognition, Brain and Language", 
+            "affiliation": "BCBL - Basque Center on Cognition, Brain and Language",
             "name": "Eneko Uru\u00f1uela"
-        },  
+        },
         {
-            "affiliation": "Maastricht University", 
+            "affiliation": "Maastricht University",
             "name": "Merel van der Thiel"
-        }, 
+        },
         {
-            "affiliation": "Northwestern University", 
+            "affiliation": "Northwestern University",
             "name": "Kristina Zvolanek"
         }
-    ], 
+    ],
     "access_right": "open"
 }
diff --git a/Makefile b/Makefile
@@ -18,4 +18,4 @@ unittest:
 
 integration:
 	@pip install -e ".[test]"
-	@py.test --log-cli-level=INFO --cov-append --cov-report term-missing --cov=phys2bids -k test_integration phys2bids/tests/test_integration.py
+	@py.test --log-cli-level=INFO --cov-append --cov-report term-missing --cov=phys2bids -k test_integration phys2bids/tests/test_integration.py
diff --git a/README.md b/README.md
@@ -54,7 +54,7 @@ While all version until `2.6.2` were tested on Linux and Windows, starting from
 
 Hence, while **we cannot ensure that phys2bids will run on Windows**, however we don't see any reason it shouldn't. Besides, it will run on Linux Subsistems.
 
-We apologise for the discomfort. 
+We apologise for the discomfort.
 
 
 <!-- ## Hacktoberfest
@@ -65,7 +65,7 @@ Feel free to ask help to the contributors over gitter, happy coding and (hopeful
 
 ## The BrainWeb
 BrainWeb participants, welcome!
-We have a milestone [here](https://github.com/physiopy/phys2bids/milestone/5) as a collection of issues you could work on with our help. 
+We have a milestone [here](https://github.com/physiopy/phys2bids/milestone/5) as a collection of issues you could work on with our help.
 Check the issues with a `BrainWeb` label. Of course, they are only suggestions, so feel free to tackle any issue you want, even open new ones!
 You can also contact us on Gitter, in the BrainHack Mattermost (<a href="https://mattermost.brainhack.org/brainhack/channels/physiopy">#physiopy</a>), and don't hesitate to contact [Stefano](https://github.com/smoia) in other ways to jump in the development!
 -->
diff --git a/docs/_static/favicon.txt b/docs/_static/favicon.txt
@@ -14,4 +14,4 @@
 <link rel="manifest" href="/manifest.json">
 <meta name="msapplication-TileColor" content="#ffffff">
 <meta name="msapplication-TileImage" content="/ms-icon-144x144.png">
-<meta name="theme-color" content="#ffffff">
+<meta name="theme-color" content="#ffffff">
diff --git a/docs/_static/favicon/browserconfig.xml b/docs/_static/favicon/browserconfig.xml
@@ -1,2 +1,2 @@
 <?xml version="1.0" encoding="utf-8"?>
-<browserconfig><msapplication><tile><square70x70logo src="/ms-icon-70x70.png"/><square150x150logo src="/ms-icon-150x150.png"/><square310x310logo src="/ms-icon-310x310.png"/><TileColor>#ffffff</TileColor></tile></msapplication></browserconfig>
+<browserconfig><msapplication><tile><square70x70logo src="/ms-icon-70x70.png"/><square150x150logo src="/ms-icon-150x150.png"/><square310x310logo src="/ms-icon-310x310.png"/><TileColor>#ffffff</TileColor></tile></msapplication></browserconfig>
diff --git a/docs/_static/favicon/manifest.json b/docs/_static/favicon/manifest.json
@@ -38,4 +38,4 @@
    "density": "4.0"
   }
  ]
-}
+}
diff --git a/docs/api.rst b/docs/api.rst
@@ -73,4 +73,3 @@ API
    load_acq
    load_mat
    load_gep
-
diff --git a/docs/contributing.rst b/docs/contributing.rst
@@ -26,18 +26,18 @@ Follow these steps to get started:
 Linux, Mac, and Windows developer installation
 ----------------------------------------------
 
-Be sure to have ``git`` and ``pip`` installed. Fork the phys2bids repository in GitHub, then open a terminal and run the following code to clone the forked repository and set it as your `origin`::
+Be sure to have ``git`` and ``pip`` installed. Fork the phys2bids repository in GitHub, then open a terminal and run the following code to clone the forked repository and set it as your ``origin``::
 
     git clone https://github.com/{username}/phys2bids.git
     # or in case you prefer to use ssh:
     git clone git@github.com:{username}/phys2bids.git
 
-We also recommend to set up the physiopy/phys2bids repository as `upstream`.
-In this way you can always keep your main branch up to date with the command `git pull upstream master`::
+We also recommend to set up the physiopy/phys2bids repository as ``upstream``.
+In this way you can always keep your main branch up to date with the command ``git pull upstream master``::
 
     cd phys2bids
     git remote add upstream https://github.com/physiopy/phys2bids.git
-    git pull upstream master 
+    git pull upstream master
 
 
 Basic installation
diff --git a/docs/contributorfile.rst b/docs/contributorfile.rst
@@ -198,7 +198,7 @@ Pull Requests
 -------------
 To improve understanding pull requests "at a glance" and use the power of ``auto``, we use the labels listed above. Multiple labels can be assigned to a PR - in fact, all those that you think are relevant.
 We strongly advise to keep the changes you're introducing with your PR limited to your original goal. Adding to the scope of your PR little style corrections or code refactoring here and there in the code that you're already modifying is a great help, but when they become too much (and they are not relevant to your PR) they risk complicating the nature of the PR and the reviewing process. It is much better to open another PR with the objective of doing such corrections!
-Moreover, if you're tempted to assign more than one label that would trigger a release (e.g. `bug` and `minormod`, or `bug` and `majormod`, etc. etc.), you might want to split your PR instead.
+Moreover, if you're tempted to assign more than one label that would trigger a release (e.g. ``bug`` and ``minormod``, or ``bug`` and ``majormod``, etc. etc.), you might want to split your PR instead.
 When opening a pull request, assign it at least one label.
 
 We encourage you to open a PR as soon as possible - even before you finish working on them. This is useful especially to you - so that you can receive comments and suggestions early on, rather than having to process a lot of comments in the final review step!
@@ -207,8 +207,8 @@ However, if it’s an incomplete PR, please open a **Draft PR**. That helps us p
 Reviewing PRs is a time consuming task and it can be stressful for both the reviewer and the author. Avoiding wasting time and the need of little fixes - such as fixing grammar mistakes and typos, styling code, or adopting conventions - is a good start for a successful (and quick) review. Before graduating a Draft PR to a PR ready for review, please check that:
 
 - You did all you wanted to include in your PR. If at a later stage you realise something is missing and it's not a minor thing, you will need to open a new PR.
-- If your contribution contains code or tests, you ran and passed all of the tests locally with `pytest`.
-- If you're writing documentation, you built it locally with `sphinx` and the format is what you intended.
+- If your contribution contains code or tests, you ran and passed all of the tests locally with ``pytest``.
+- If you're writing documentation, you built it locally with ``sphinx`` and the format is what you intended.
 - Your code is harmonious with the rest of the code - no repetitions of any sort!
 - Your code respects the `adopted Style <#styling>`_, especially:
     - Your code is lintered adequately and respects the `PEP8 <https://www.python.org/dev/peps/pep-0008/>`_ convention.
@@ -222,7 +222,7 @@ To be merged, PRs have to:
 
 1. Pass all the CircleCI tests, and possibly all the codecov checks.
 2. Have the necessary amount of approving reviews, even if you’re a long time contributor. You can ask one (or more) contributor to do that review, if you think they align more with the content of your PR. You need **one** review for documentation, tests, and small changes, and **two** reviews for bugs, refactoring and enhancements.
-3. Have at least a release-related label (or a `Skip release` label).
+3. Have at least a release-related label (or a ``Skip release`` label).
 4. Have a short title that clearly explains in one sentence the aim of the PR.
 5. Contain at least a unit test for your contribution, if the PR contains code (it would be better if it contains an integration or function test and all the breaking tests necessary). If you’re not confident about writing tests, it is possible to refer to an issue that asks for the test to be written, or another (Draft) PR that contains the tests required.
 
@@ -245,7 +245,7 @@ There are many best practices to review code online, for instance `this one <htt
 - If the PR graduated from Draft to full PR, check that it follows the sections `Pull requests <#pr>`_ and `Style Guide <#styling>`_ of these guidelines. If not, invite the author to do so before starting a review.
 - **Don't limit your review to the parts that are changed**. Look at the entire file, see if the changes fit well in it, and see if the changes are properly addressed everywhere in the code - in the documentation, in the tests, and in other functions. Sometimes the differences reported don't show the full impact of the PR in the repository!
 - If your want to make Pull Requests an educational process, invite the author of the PR to make changes before actually doing them yourself. Request changes via comments or in the message board or by checking out the PR locally, making changes and then submitting a PR to the author's branch.
-- If you decide to use the suggestion tool in reviews, or to start a PR to the branch under review, please alert the Project Manager. Bots might automatically assign you contribution types that will have to be removed (remember, your contribution in this case is "Reviewer"). Instead of starting a PR to the branch under review, think about opening a new PR with those modifications (unless they are needed to pass tests), and alert the Main Reviewer. In any case **don't commit directly to the branch under review**! 
+- If you decide to use the suggestion tool in reviews, or to start a PR to the branch under review, please alert the Project Manager. Bots might automatically assign you contribution types that will have to be removed (remember, your contribution in this case is "Reviewer"). Instead of starting a PR to the branch under review, think about opening a new PR with those modifications (unless they are needed to pass tests), and alert the Main Reviewer. In any case **don't commit directly to the branch under review**!
 - If you're reviewing documentation, build it locally with ``sphinx``.
 - If you're asking for changes, **don't approve the PR**. Approve it only after everything was sufficiently addressed. Someone else might merge the PR in taking your word for granted.
 - If you are the main reviewer, and the last reviewer required to approve the PR, merge the PR!
@@ -261,7 +261,7 @@ Before approving and/or merging PRs, be sure that:
 
 Main reviewer
 ~~~~~~~~~~~~~
-At ``physiopy`` we use the "Assignees" section of a PR to mark the **main reviewer** for that PR. The main reviewer is the primary person responsible **for the quality of the repository and its next version release**, as well as **for the behaviour of the other reviewers**. 
+At ``physiopy`` we use the "Assignees" section of a PR to mark the **main reviewer** for that PR. The main reviewer is the primary person responsible **for the quality of the repository and its next version release**, as well as **for the behaviour of the other reviewers**.
 The main reviewer:
 
 - Takes care of the reviewing process of the PR, in particular:
diff --git a/docs/heuristic.rst b/docs/heuristic.rst
@@ -31,7 +31,7 @@ It's important **not to modify this part of the file**. Instead, you can copy an
 This file looks like a python function, initialised by a mandatory parameter, ``physinfo``.
 | ``physinfo`` is the information used to label your file. **At the moment, it corresponds to the name of the input file itself**. This is what you need to build your heuristic.
 
-The function initialises ``info``, a `python dictionary <https://www.w3schools.com/python/python_dictionaries.asp>`_ that contains the BIDS keys, such as `sub` and `ses`, as well as all the possible keys you can add to your heuristics. This is what you will work with in creating your heuristic.
+The function initialises ``info``, a ``python dictionary <https://www.w3schools.com/python/python_dictionaries.asp>``_ that contains the BIDS keys, such as ``sub`` and ``ses``, as well as all the possible keys you can add to your heuristics. This is what you will work with in creating your heuristic.
 
 The scripts also imports ``fnmatch``, a nice python module that lets you use bash-like wildcards.
 
diff --git a/docs/installation.rst b/docs/installation.rst
@@ -44,7 +44,7 @@ Install ``phys2bids`` alone
 To install ``phys2bids`` along with the basic required modules just run::
 
     pip3 install phys2bids
-    
+
 You can now proceed to check your installation and start using ``phys2bids``!
 
 Install ``phys2bids`` with extra modules
@@ -67,7 +67,7 @@ You can now proceed to check your installation and start using ``phys2bids``!
 
 .. note::
     If you "missed" or skipped this trick when you installed ``phys2bids`` the first time, don't worry!
-    You can do it any time - this will update ``phys2bids`` and install all extra modules you want. 
+    You can do it any time - this will update ``phys2bids`` and install all extra modules you want.
 
 
 Install without ``pip``
@@ -82,7 +82,7 @@ Open a terminal in the ``phys2bids`` folder and execute the command::
 
     python3 setup.py install
 
-This should have installed ``phys2bids`` along with the basic required modules. If you need any of the extra modules listed at the beginning of the page you might need to install them manually. Otherwise, you can proceed to check your installation and start using ``phys2bids``. 
+This should have installed ``phys2bids`` along with the basic required modules. If you need any of the extra modules listed at the beginning of the page you might need to install them manually. Otherwise, you can proceed to check your installation and start using ``phys2bids``.
 
 .. note::
     If python 3 is already your default, you might use ``python`` rather than ``python3``
diff --git a/docs/license.rst b/docs/license.rst
@@ -16,4 +16,4 @@ Unless required by applicable law or agreed to in writing, software
 distributed under the License is distributed on an "AS IS" BASIS,
 WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 See the License for the specific language governing permissions and
-limitations under the License.
+limitations under the License.
diff --git a/phys2bids/heuristics/participant.yml b/phys2bids/heuristics/participant.yml
@@ -2,4 +2,4 @@ participant:
     participant_id: # Required
     age: n/a
     sex: n/a
-    handedness: n/a
+    handedness: n/a
diff --git a/phys2bids/phys2bids.py b/phys2bids/phys2bids.py
diff --git a/phys2bids/tests/test_integration.py b/phys2bids/tests/test_integration.py
diff --git a/phys2bids/tests/test_io.py b/phys2bids/tests/test_io.py
diff --git a/setup.cfg b/setup.cfg

Original file line number	Diff line number	Diff line change
`@@ -89,4 +89,4 @@`
`89`	`89`	`"color": "#FFFFFF"`
`90`	`90`	`}`
`91`	`91`	`]`
`92`		`-}`
	`92`	`+}`