Merge branch 'physiopy:master' into enh/report-bokeh

Author: me-pic

.all-contributorsrc

@@ -243,7 +243,8 @@
         "data",
         "doc",
         "userTesting",
-        "review"
+        "review",
+        "infra"
       ]
     },
     {
@@ -310,6 +311,16 @@
       "contributions": [
         "doc"
       ]
+    },
+    {
+      "login": "me-pic",
+      "name": "Marie-Eve Picard",
+      "avatar_url": "https://avatars.githubusercontent.com/u/77584086?v=4",
+      "profile": "https://github.com/me-pic",
+      "contributions": [
+        "review"
+      ]
     }
-  ]
+  ],
+  "commitType": "docs"
 }

.github/config.yml

@@ -0,0 +1,26 @@
+# Configuration for welcome - https://github.com/behaviorbot/welcome
+
+# Configuration for new-issue-welcome - https://github.com/behaviorbot/new-issue-welcome
+
+# Comment to be posted to on first time issues
+newIssueWelcomeComment: >
+  ![Thank You Banner](https://raw.githubusercontent.com/physiopy/physiopy-test-workflows/master/welcome_banner.png)
+
+  🎉 Thank you for opening your first issue in this Physiopy repo! Please check our [contributor guide](https://physiopy.github.io/contributors-guide/) and follow the issue template.
+
+# Configuration for new-pr-welcome - https://github.com/behaviorbot/new-pr-welcome
+
+# Comment to be posted to on PRs from first time contributors in your repository
+newPRWelcomeComment: >
+  ![Thank You Banner](https://raw.githubusercontent.com/physiopy/physiopy-test-workflows/master/welcome_banner.png)
+
+  🎉 Thanks for opening your first pull request in this Physiopy repo! Please check our [contributor guide](https://physiopy.github.io/contributors-guide/) and follow the PR template.
+
+# Configuration for first-pr-merge - https://github.com/behaviorbot/first-pr-merge
+
+# Comment to be posted to on pull requests merged by a first time user
+firstPRMergeComment: >
+  ![Thank You Banner](https://raw.githubusercontent.com/physiopy/physiopy-test-workflows/master/welcome_banner.png)
+
+  🎉 Congrats on merging your first pull request in this repo! We appreciate your contribution to the Physiopy community!
+  :eyes: Please check that your contribution is correctly reported in the README of this repo and on [Physiopy's website](https://physiopy.github.io/community/team/)!

.pre-commit-config.yaml

@@ -2,7 +2,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v5.0.0
     hooks:
     -   id: trailing-whitespace
     -   id: end-of-file-fixer
@@ -11,15 +11,15 @@ repos:
     -   id: check-case-conflict
     -   id: check-merge-conflict
 -   repo: https://github.com/psf/black
-    rev: 23.11.0
+    rev: 25.1.0
     hooks:
     -   id: black
 -   repo: https://github.com/pycqa/isort
-    rev: 5.13.0
+    rev: 6.0.1
     hooks:
     -   id: isort
 -   repo: https://github.com/pycqa/flake8
-    rev: 6.1.0
+    rev: 7.2.0
     hooks:
     -   id: flake8
 -   repo: https://github.com/pycqa/pydocstyle
@@ -33,6 +33,6 @@ repos:
       - id: rst-directive-colons
       - id: rst-inline-touching-normal
 -   repo: https://github.com/codespell-project/codespell
-    rev: v2.2.6
+    rev: v2.4.1
     hooks:
       - id: codespell

README.md

@@ -24,7 +24,7 @@ phys2bids
 [![Supports python version](https://img.shields.io/pypi/pyversions/phys2bids)](https://pypi.org/project/phys2bids/)
 
 <!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
-[![All Contributors](https://img.shields.io/badge/all_contributors-26-orange.svg?style=flat)](#contributors)
+[![All Contributors](https://img.shields.io/badge/all_contributors-27-orange.svg?style=flat)](#contributors)
 <!-- ALL-CONTRIBUTORS-BADGE:END -->
 
 ``phys2bids`` is a python3 library meant to format physiological files in BIDS.
@@ -65,15 +65,14 @@ We apologise for any discomfort.
 Hacktoberfest participants, welcome!
 We have some issues for you [here](https://github.com/physiopy/phys2bids/issues?q=is%3Aissue+is%3Aopen+label%3Ahacktoberfest)!
 However, feel free to tackle any issue you'd like. Depending on the issue and extent of contribution, Hacktoberfest related PRs might not count toward being listed as contributors and authors (unless there is the specific interest). You can ask about it in the issue itself!
-Feel free to ask help to the contributors through issues or contactign directly Stefano, happy coding and (hopefully) enjoy your tee (or tree)!
+Feel free to ask help to the contributors through issues or contactign directly Stefano, happy coding and (hopefully) enjoy your tee (or tree)!-->
 
+## Contributors ✨
 
 **We're always looking for code contributors,** but any suggestion/bug report is welcome! Feel free to open issues!
 
 This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome!
 
-## Contributors ✨
-
 Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/docs/en/emoji-key)):
 <!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
 <!-- prettier-ignore-start -->
@@ -108,7 +107,7 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
       <td align="center" valign="top" width="25%"><a href="https://github.com/bpinsard"><img src="https://avatars.githubusercontent.com/u/1155388?v=4?s=100" width="100px;" alt="Basile"/><br /><sub><b>Basile</b></sub></a><br /><a href="https://github.com/physiopy/phys2bids/commits?author=bpinsard" title="Code">💻</a> <a href="https://github.com/physiopy/phys2bids/commits?author=bpinsard" title="Tests">⚠️</a></td>
       <td align="center" valign="top" width="25%"><a href="https://github.com/drombas"><img src="https://avatars.githubusercontent.com/u/50577357?v=4?s=100" width="100px;" alt="David Romero-Bascones"/><br /><sub><b>David Romero-Bascones</b></sub></a><br /><a href="https://github.com/physiopy/phys2bids/issues?q=author%3Adrombas" title="Bug reports">🐛</a> <a href="https://github.com/physiopy/phys2bids/commits?author=drombas" title="Code">💻</a> <a href="https://github.com/physiopy/phys2bids/commits?author=drombas" title="Documentation">📖</a> <a href="#content-drombas" title="Content">🖋</a></td>
       <td align="center" valign="top" width="25%"><a href="https://github.com/tsalo"><img src="https://avatars3.githubusercontent.com/u/8228902?v=4?s=100" width="100px;" alt="Taylor Salo"/><br /><sub><b>Taylor Salo</b></sub></a><br /><a href="#ideas-tsalo" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/physiopy/phys2bids/commits?author=tsalo" title="Code">💻</a> <a href="https://github.com/physiopy/phys2bids/pulls?q=is%3Apr+reviewed-by%3Atsalo" title="Reviewed Pull Requests">👀</a> <a href="#infra-tsalo" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a></td>
-      <td align="center" valign="top" width="25%"><a href="https://github.com/RayStick"><img src="https://avatars3.githubusercontent.com/u/50215726?v=4?s=100" width="100px;" alt="Rachael Stickland"/><br /><sub><b>Rachael Stickland</b></sub></a><br /><a href="https://github.com/physiopy/phys2bids/issues?q=author%3ARayStick" title="Bug reports">🐛</a> <a href="https://github.com/physiopy/phys2bids/commits?author=RayStick" title="Code">💻</a> <a href="#data-RayStick" title="Data">🔣</a> <a href="https://github.com/physiopy/phys2bids/commits?author=RayStick" title="Documentation">📖</a> <a href="#userTesting-RayStick" title="User Testing">📓</a> <a href="https://github.com/physiopy/phys2bids/pulls?q=is%3Apr+reviewed-by%3ARayStick" title="Reviewed Pull Requests">👀</a></td>
+      <td align="center" valign="top" width="25%"><a href="https://github.com/RayStick"><img src="https://avatars3.githubusercontent.com/u/50215726?v=4?s=100" width="100px;" alt="Rachael Stickland"/><br /><sub><b>Rachael Stickland</b></sub></a><br /><a href="https://github.com/physiopy/phys2bids/issues?q=author%3ARayStick" title="Bug reports">🐛</a> <a href="https://github.com/physiopy/phys2bids/commits?author=RayStick" title="Code">💻</a> <a href="#data-RayStick" title="Data">🔣</a> <a href="https://github.com/physiopy/phys2bids/commits?author=RayStick" title="Documentation">📖</a> <a href="#userTesting-RayStick" title="User Testing">📓</a> <a href="https://github.com/physiopy/phys2bids/pulls?q=is%3Apr+reviewed-by%3ARayStick" title="Reviewed Pull Requests">👀</a> <a href="#infra-RayStick" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a></td>
     </tr>
     <tr>
       <td align="center" valign="top" width="25%"><a href="https://github.com/eurunuela"><img src="https://avatars0.githubusercontent.com/u/13706448?v=4?s=100" width="100px;" alt="Eneko Uruñuela"/><br /><sub><b>Eneko Uruñuela</b></sub></a><br /><a href="https://github.com/physiopy/phys2bids/issues?q=author%3Aeurunuela" title="Bug reports">🐛</a> <a href="https://github.com/physiopy/phys2bids/commits?author=eurunuela" title="Code">💻</a> <a href="#infra-eurunuela" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="https://github.com/physiopy/phys2bids/pulls?q=is%3Apr+reviewed-by%3Aeurunuela" title="Reviewed Pull Requests">👀</a> <a href="https://github.com/physiopy/phys2bids/commits?author=eurunuela" title="Tests">⚠️</a> <a href="#mentoring-eurunuela" title="Mentoring">🧑‍🏫</a></td>
@@ -119,6 +118,7 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
     <tr>
       <td align="center" valign="top" width="25%"><a href="https://github.com/marcelzwiers"><img src="https://avatars.githubusercontent.com/u/15156015?v=4?s=100" width="100px;" alt="Marcel Zwiers"/><br /><sub><b>Marcel Zwiers</b></sub></a><br /><a href="#plugin-marcelzwiers" title="Plugin/utility libraries">🔌</a></td>
       <td align="center" valign="top" width="25%"><a href="https://github.com/victox5"><img src="https://avatars1.githubusercontent.com/u/56017659?v=4?s=100" width="100px;" alt="victox5"/><br /><sub><b>victox5</b></sub></a><br /><a href="https://github.com/physiopy/phys2bids/commits?author=victox5" title="Documentation">📖</a></td>
+      <td align="center" valign="top" width="25%"><a href="https://github.com/me-pic"><img src="https://avatars.githubusercontent.com/u/77584086?v=4?s=100" width="100px;" alt="Marie-Eve Picard"/><br /><sub><b>Marie-Eve Picard</b></sub></a><br /><a href="https://github.com/physiopy/phys2bids/pulls?q=is%3Apr+reviewed-by%3Ame-pic" title="Reviewed Pull Requests">👀</a></td>
     </tr>
   </tbody>
 </table>

docs/conduct.rst

@@ -16,7 +16,7 @@ We as members, contributors, and leaders pledge to make participation in
 our community a harassment-free experience for everyone, regardless of
 age, body size, visible or invisible disability, ethnicity, sex
 characteristics, gender identity and expression, level of experience,
-education, socio-economic status, nationality, personal appearance,
+education, socioeconomic status, nationality, personal appearance,
 race, religion, or sexual identity and orientation.
 
 We pledge to act and interact in ways that contribute to an open,

phys2bids/__init__.py

@@ -1,4 +1,5 @@
 """Main init for phys2bids package."""
+
 from ._version import get_versions
 
 __version__ = get_versions()["version"]

phys2bids/bids.py

@@ -1,4 +1,5 @@
 """BIDS functions for phys2bids package."""
+
 import logging
 import os
 from csv import reader

phys2bids/tests/conftest.py

@@ -1,8 +1,8 @@
 import os
 import ssl
-from urllib.request import urlretrieve
 
 import pytest
+import requests
 
 
 def pytest_addoption(parser):
@@ -50,7 +50,11 @@ def fetch_file(osf_id, path, filename):
     url = "https://osf.io/{}/download".format(osf_id)
     full_path = os.path.join(path, filename)
     if not os.path.isfile(full_path):
-        urlretrieve(url, full_path)
+        req = requests.get(url, allow_redirects=True)
+        req.raise_for_status()
+        with open(full_path, "wb") as f:
+            f.write(req.content)
+            f.close()
     return full_path
 
 

phys2bids/tests/test_utils.py

@@ -1,5 +1,5 @@
 """
-    Runs unit tests on utils.py
+Runs unit tests on utils.py
 """
 
 import json

phys2bids/utils.py

@@ -1,4 +1,5 @@
 """Utilities for phys2bids package."""
+
 import json
 import logging
 import os