Merge remote-tracking branch 'upstream/main' into py3.12

cpp-lln-lab · Aug 1, 2024 · 29f0540 · 29f0540
2 parents dc1ac9a + 7435e94
commit 29f0540
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Showing 30 changed files with 278 additions and 191 deletions.
diff --git a/.all-contributorsrc b/.all-contributorsrc
@@ -27,12 +27,24 @@
         "test",
         "maintenance"
       ]
+    },
+    {
+      "login": "yyang1234",
+      "name": "Ying Yang",
+      "avatar_url": "https://avatars.githubusercontent.com/u/59220868?v=4",
+      "profile": "https://github.com/yyang1234",
+      "contributions": [
+        "bug",
+        "userTesting"
+      ]
     }
   ],
   "contributorsPerLine": 7,
   "projectName": "bidsMReye",
   "projectOwner": "cpp-lln-lab",
   "repoType": "github",
   "repoHost": "https://github.com",
-  "skipCi": true
+  "skipCi": true,
+  "commitType": "docs",
+  "commitConvention": "angular"
 }
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -121,12 +121,13 @@ jobs:
                         user_name=cpplab
                         repo_name=$(echo "${CIRCLE_PROJECT_REPONAME}" | tr '[:upper:]' '[:lower:]')
                         if [[ -n "${DOCKER_TOKEN}" ]]; then
-                            echo "${DOCKER_TOKEN}" | docker login -u "${DOCKER_USER}" --password-stdin
+                            echo "${DOCKER_TOKEN}" | docker login -u remigau --password-stdin
                             : "Pushing to DockerHub ${user_name}/${repo_name}:unstable"
                             docker tag "${user_name}/${repo_name}" "${user_name}/${repo_name}:unstable"
                             docker push "${user_name}/${repo_name}:unstable"
                             if [[ -n "${CIRCLE_TAG}" ]]; then
                                 : "Pushing to DockerHub ${user_name}/${repo_name}:${CIRCLE_TAG}"
+                                docker tag "${user_name}/${repo_name}" "${user_name}/${repo_name}:latest"
                                 docker push "${user_name}/${repo_name}:latest"
                                 docker tag "${user_name}/${repo_name}" "${user_name}/${repo_name}:${CIRCLE_TAG}"
                                 docker push "${user_name}/${repo_name}:${CIRCLE_TAG}"
@@ -141,21 +142,16 @@ workflows:
     build-test-deploy:
         jobs:
         -   build
-
         -   get_data
         -   test:
                 requires:
                 -   build
                 -   get_data
-
         -   deploy:
                 context:
                 -   DOCKER_HUB
                 requires:
                 -   test
-                filters:
-                    tags:
-                        only: /.*/
 
 
 

diff --git a/.github/workflows/new_issue.yml b/.github/workflows/new_issue.yml
@@ -22,7 +22,7 @@ jobs:
             with:
                 path: ./suggest.md
         -   name: Suggest FAQ
-            uses: peter-evans/create-or-update-comment@c6c9a1a66007646a28c153e2a8580a5bad27bcfa
+            uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043
             with:
                 issue-number: ${{ github.event.issue.number }}
                 body: ${{ steps.suggest.outputs.content }}
diff --git a/.github/workflows/package.yml b/.github/workflows/package.yml
@@ -32,7 +32,7 @@ jobs:
                 fetch-depth: 0
 
         -   name: Set up Python ${{ matrix.python-version }}
-            uses: actions/setup-python@v4
+            uses: actions/setup-python@v5
             with:
                 python-version: ${{ matrix.python-version }}
 

diff --git a/.github/workflows/system_tests.yml b/.github/workflows/system_tests.yml
@@ -27,7 +27,7 @@ jobs:
             uses: actions/checkout@v4
 
         -   name: Set up Python ${{ matrix.python-version }}
-            uses: actions/setup-python@v4
+            uses: actions/setup-python@v5
             with:
                 python-version: ${{ matrix.python-version }}
                 allow-prereleases: true

diff --git a/.github/workflows/test_and_coverage.yml b/.github/workflows/test_and_coverage.yml
@@ -18,7 +18,7 @@ jobs:
         strategy:
             matrix:
                 os: [ubuntu-latest, macOS-latest] # windows-latest: do not work. antspyx is not available for windows
-                python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+                python-version: ['3.9', '3.10', '3.11', '3.12']
                 exclude:
                 -   os: macOS-latest # anstpyx install is messed up with macOS and python 3.9
                     python-version: '3.9'
@@ -30,7 +30,7 @@ jobs:
             uses: actions/checkout@v4
 
         -   name: Set up Python ${{ matrix.python-version }}
-            uses: actions/setup-python@v4
+            uses: actions/setup-python@v5
             with:
                 python-version: ${{ matrix.python-version }}
                 allow-prereleases: true
@@ -44,7 +44,7 @@ jobs:
             run: pytest --cov bidsmreye --cov-report=xml
 
         -   name: Upload coverage to Codecov
-            uses: codecov/codecov-action@v3
+            uses: codecov/codecov-action@v4
             with:
                 file: ./coverage.xml
                 flags: tests

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -3,7 +3,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.6.0
     hooks:
     -   id: end-of-file-fixer
     -   id: check-added-large-files
@@ -20,8 +20,14 @@ repos:
     -   id: yamlfmt
         args: [--mapping, '4', --sequence, '4', --offset, '0']
 
+-   repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
+    rev: v2.14.0
+    hooks:
+    -   id: pretty-format-toml
+        args: [--autofix, --indent, '4']
+
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.13.0
+    rev: v3.17.0
     hooks:
     -   id: pyupgrade
         args: [--py38-plus]
@@ -31,42 +37,58 @@ repos:
     hooks:
     -   id: flynt
 
--   repo: https://github.com/asottile/reorder-python-imports
-    rev: v3.11.0
+-   repo: https://github.com/seddonym/import-linter
+    rev: v2.0
+    hooks:
+    -   id: import-linter
+
+-   repo: https://github.com/pycqa/isort
+    rev: 5.13.2
     hooks:
-    -   id: reorder-python-imports
-        args: [--py37-plus, --add-import, from __future__ import annotations]
+    -   id: isort
+        args: [--profile, black]
 
--   repo: https://github.com/psf/black
-    rev: 23.9.1
+-   repo: https://github.com/adamchainz/blacken-docs
+    rev: 1.18.0
+    hooks:
+    -   id: blacken-docs
+        additional_dependencies:
+        -   black==24.2.0
+
+-   repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 24.4.2
     hooks:
     -   id: black
         args: [--config=pyproject.toml, --verbose]
 
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.5.1
+    rev: v1.11.0
     hooks:
     -   id: mypy
         additional_dependencies: [types-all, pydantic]
         files: bidsmreye
         args: [--config-file, pyproject.toml]
 
 -   repo: https://github.com/codespell-project/codespell
-    rev: v2.2.5
+    rev: v2.3.0
     hooks:
     -   id: codespell
         args: [--toml=pyproject.toml]
         additional_dependencies: [tomli]
 
 -   repo: https://github.com/jendrikseipp/vulture
-    rev: v2.9.1
+    rev: v2.11
     hooks:
     -   id: vulture
 
 -   repo: https://github.com/pycqa/flake8
-    rev: 6.1.0
+    rev: 7.1.0
     hooks:
     -   id: flake8
         exclude: tests_.*.py|version.*.py|setup.py     # ignore tests and versioneer related code
         args: [--verbose]
         additional_dependencies: [flake8-docstrings]
+
+
+ci:
+    autoupdate_commit_msg: 'chore: update pre-commit hooks'
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -6,6 +6,11 @@
 # Required
 version: 2
 
+build:
+    os: ubuntu-22.04
+    tools:
+        python: '3.11'
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
     configuration: docs/source/conf.py
@@ -14,7 +19,6 @@ sphinx:
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-    version: '3.8'
     install:
     -   method: pip
         path: .

diff --git a/CITATION.cff b/CITATION.cff
@@ -20,20 +20,25 @@ identifiers:
     value: "10.5281/zenodo.7493322"
 
 contact:
-  - affiliation: "Université catholique de Louvain"
-    email: remi.gau@uclouvain.be
+  - affiliation: "McGill university"
+    email: remi.gau2@mcgill.ca
     family-names: Gau
     given-names: Rémi
 
 authors:
   - family-names: "Gau"
     given-names: "Rémi"
     orcid: "https://orcid.org/0000-0002-1535-9767"
-    affiliation: "Université catholique de Louvain"
+    affiliation: "McGill university"
 
   - family-names: "Cabee"
     given-names: "Pauline"
 
+  - family-names: "Yang"
+    given-names: "Ying"
+    orcid: "https://orcid.org/0000-0002-4157-2975"
+    affiliation: "Université catholique de Louvain"
+
 license: GPL-3.0
 
 keywords:

diff --git a/Makefile b/Makefile
@@ -69,8 +69,8 @@ dist: clean ## builds source and wheel package
 clean-models: ## remove pretrained models
 	rm -fr models/
 
-models: ## gets all pretrained models from OSF
-	bidsmreye_model --model_name all
+models:
+	bidsmreye_model --model_name 1to6
 models/dataset1_guided_fixations.h5:
 	bidsmreye_model
 models/dataset2_pursuit.h5:

diff --git a/README.md b/README.md
@@ -212,10 +212,13 @@ Thanks goes to these wonderful people
 <!-- prettier-ignore-start -->
 <!-- markdownlint-disable -->
 <table>
-  <tr>
-    <td align="center"><a href="https://weexee.github.io/Portfolio/"><img src="https://avatars.githubusercontent.com/u/91776803?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Pauline Cabee</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/bidsMReye/commits?author=WeeXee" title="Code">💻</a> <a href="#ideas-WeeXee" title="Ideas, Planning, & Feedback">🤔</a> <a href="#infra-WeeXee" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a></td>
-    <td align="center"><a href="https://remi-gau.github.io/"><img src="https://avatars.githubusercontent.com/u/6961185?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Remi Gau</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/bidsMReye/commits?author=Remi-Gau" title="Code">💻</a> <a href="#ideas-Remi-Gau" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/cpp-lln-lab/bidsMReye/commits?author=Remi-Gau" title="Tests">⚠️</a> <a href="#maintenance-Remi-Gau" title="Maintenance">🚧</a></td>
-  </tr>
+  <tbody>
+    <tr>
+      <td align="center" valign="top" width="14.28%"><a href="https://weexee.github.io/Portfolio/"><img src="https://avatars.githubusercontent.com/u/91776803?v=4?s=100" width="100px;" alt="Pauline Cabee"/><br /><sub><b>Pauline Cabee</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/bidsMReye/commits?author=WeeXee" title="Code">💻</a> <a href="#ideas-WeeXee" title="Ideas, Planning, & Feedback">🤔</a> <a href="#infra-WeeXee" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://remi-gau.github.io/"><img src="https://avatars.githubusercontent.com/u/6961185?v=4?s=100" width="100px;" alt="Remi Gau"/><br /><sub><b>Remi Gau</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/bidsMReye/commits?author=Remi-Gau" title="Code">💻</a> <a href="#ideas-Remi-Gau" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/cpp-lln-lab/bidsMReye/commits?author=Remi-Gau" title="Tests">⚠️</a> <a href="#maintenance-Remi-Gau" title="Maintenance">🚧</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/yyang1234"><img src="https://avatars.githubusercontent.com/u/59220868?v=4?s=100" width="100px;" alt="Ying Yang"/><br /><sub><b>Ying Yang</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/bidsMReye/issues?q=author%3Ayyang1234" title="Bug reports">🐛</a> <a href="#userTesting-yyang1234" title="User Testing">📓</a></td>
+    </tr>
+  </tbody>
 </table>
 
 <!-- markdownlint-restore -->

diff --git a/bidsmreye/__init__.py b/bidsmreye/__init__.py
@@ -1,2 +1,3 @@
 """Bidsmreye package."""
+
 from __future__ import annotations
diff --git a/bidsmreye/bids_utils.py b/bidsmreye/bids_utils.py
@@ -8,15 +8,16 @@
 from bids import BIDSLayout  # type: ignore
 
 from bidsmreye._version import __version__
-from bidsmreye.configuration import Config
-from bidsmreye.configuration import config_to_dict
-from bidsmreye.configuration import get_bids_filter_config
-from bidsmreye.configuration import get_bidsname_config
-from bidsmreye.configuration import get_pybids_config
+from bidsmreye.configuration import (
+    Config,
+    config_to_dict,
+    get_bids_filter_config,
+    get_bidsname_config,
+    get_pybids_config,
+)
 from bidsmreye.logging import bidsmreye_log
 from bidsmreye.methods import methods
-from bidsmreye.utils import copy_license
-from bidsmreye.utils import create_dir_if_absent
+from bidsmreye.utils import copy_license, create_dir_if_absent
 
 log = bidsmreye_log("bidsmreye")
 

diff --git a/bidsmreye/bidsmreye.py b/bidsmreye/bidsmreye.py
@@ -6,18 +6,19 @@
 import json
 import sys
 from pathlib import Path
-from typing import Any
-from typing import IO
+from typing import IO, Any
 
 import rich
 
 from bidsmreye._version import __version__
 from bidsmreye.configuration import Config
-from bidsmreye.defaults import allowed_actions
-from bidsmreye.defaults import available_models
-from bidsmreye.defaults import default_log_level
-from bidsmreye.defaults import default_model
-from bidsmreye.defaults import log_levels
+from bidsmreye.defaults import (
+    allowed_actions,
+    available_models,
+    default_log_level,
+    default_model,
+    log_levels,
+)
 from bidsmreye.download import download
 from bidsmreye.generalize import generalize
 from bidsmreye.logging import bidsmreye_log

diff --git a/bidsmreye/configuration.py b/bidsmreye/configuration.py
@@ -6,10 +6,7 @@
 from pathlib import Path
 from typing import Any
 
-from attrs import asdict
-from attrs import converters
-from attrs import define
-from attrs import field
+from attrs import asdict, converters, define, field
 from bids import BIDSLayout  # type: ignore
 
 from bidsmreye.logging import bidsmreye_log

diff --git a/bidsmreye/defaults.py b/bidsmreye/defaults.py
@@ -1,4 +1,5 @@
 """Store defaults."""
+
 from __future__ import annotations
 
 

diff --git a/bidsmreye/download.py b/bidsmreye/download.py
@@ -1,19 +1,19 @@
 """Download the models from OSF."""
+
 from __future__ import annotations
 
 import argparse
 import sys
 import warnings
+from importlib import resources
 from pathlib import Path
-from typing import Any
-from typing import IO
+from typing import IO, Any
 
-import pkg_resources
 import pooch
 import rich
 
-from bidsmreye.defaults import available_models
-from bidsmreye.defaults import default_model
+import bidsmreye
+from bidsmreye.defaults import available_models, default_model
 from bidsmreye.logging import bidsmreye_log
 
 log = bidsmreye_log(name="bidsmreye")
@@ -99,8 +99,9 @@ def download(
         base_url="https://osf.io/download/",
         registry=None,
     )
-    registry_file = pkg_resources.resource_stream("bidsmreye", "models/registry.txt")
-    POOCH.load_registry(registry_file)
+    source = resources.files(bidsmreye).joinpath("models/registry.txt")
+    with resources.as_file(source) as registry_file:
+        POOCH.load_registry(registry_file)
 
     output_file = output_dir.joinpath(f"dataset_{model_name}")