From 24b1a46234f5d81efd4a8de8d6c279cb32115502 Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Thu, 7 Dec 2023 12:47:54 +0100
Subject: [PATCH 1/8] move project config to pyproject.toml

---
 .circleci/config.yml             |  18 ++-
 .github/workflows/unit_tests.yml |   9 +-
 CONTRIBUTING.md                  |  14 +--
 MANIFEST.in                      |   2 +-
 Makefile                         |   2 +-
 doc/conf.py                      |   5 +-
 doc/requirements.txt             |  12 --
 pyproject.toml                   | 186 ++++++++++++++++++++++++++++++-
 setup.cfg                        |  74 ------------
 setup.py                         |  27 -----
 test_requirements.txt            |  18 ---
 11 files changed, 200 insertions(+), 167 deletions(-)
 delete mode 100644 doc/requirements.txt
 delete mode 100644 setup.py
 delete mode 100644 test_requirements.txt

diff --git a/.circleci/config.yml b/.circleci/config.yml
index a67878688..7b249d293 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -24,12 +24,12 @@ jobs:
         # restore cache from last build. Unless __init__.py has changed since then
         - restore_cache:
             keys:
-              - data-cache-5-{{ checksum "./mne_bids/__init__.py" }}
+              - data-cache-0-{{ checksum "./mne_bids/__init__.py" }}
 
         # Also restore pip cache to speed up installations
         - restore_cache:
             keys:
-              - pip-cache-1-{{ checksum "./test_requirements.txt" }}-{{ checksum "./doc/requirements.txt" }}
+              - pip-cache-0-{{ checksum "./pyproject.toml" }}
 
         - run:
             name: Setup Python3 environment
@@ -41,10 +41,8 @@ jobs:
             name: Install Python packages
             command: |
               python -m pip install --upgrade --progress-bar off pip
-              python -m pip install --upgrade --progress-bar off -r test_requirements.txt
-              python -m pip install --upgrade --progress-bar off -r doc/requirements.txt
               python -m pip install --upgrade https://github.com/mne-tools/mne-python/archive/refs/heads/main.zip
-              python -m pip install -e .
+              python -m pip install -e .[test,doc]
 
         - run:
             name: Build the documentation
@@ -62,13 +60,13 @@ jobs:
 
         # Store the data cache
         - save_cache:
-            key: data-cache-5-{{ checksum "./mne_bids/__init__.py" }}
+            key: data-cache-0-{{ checksum "./mne_bids/__init__.py" }}
             paths:
               - ~/mne_data
 
         # Store pip cache
         - save_cache:
-            key: pip-cache-1-{{ checksum "./test_requirements.txt" }}-{{ checksum "./doc/requirements.txt" }}
+            key: pip-cache-0-{{ checksum "./pyproject.toml" }}
             paths:
               - ~/.cache/pip
 
@@ -112,7 +110,7 @@ jobs:
 
       - restore_cache:
           keys:
-            - pip-cache-1-{{ checksum "./test_requirements.txt" }}-{{ checksum "./doc/requirements.txt" }}
+            - pip-cache-0-{{ checksum "./pyproject.toml" }}
 
       - run:
           name: Setup Python3 environment
@@ -124,10 +122,8 @@ jobs:
           name: Install Python packages
           command: |
             python -m pip install --upgrade --progress-bar off pip
-            python -m pip install --upgrade --progress-bar off -r test_requirements.txt
-            python -m pip install --upgrade --progress-bar off -r doc/requirements.txt
             python -m pip install --upgrade https://github.com/mne-tools/mne-python/archive/refs/heads/main.zip
-            python -m pip install -e .
+            python -m pip install -e .[test,doc]
 
       - run:
           name: Check links
diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml
index ba13791c9..39a4176e7 100644
--- a/.github/workflows/unit_tests.yml
+++ b/.github/workflows/unit_tests.yml
@@ -32,7 +32,7 @@ jobs:
     - uses: actions/cache@v3
       with:
         path: ${{ env.pythonLocation }}
-        key: style-0-${{ env.pythonLocation }}-${{ hashFiles('setup.cfg') }}-${{ hashFiles('test_requirements.txt') }}
+        key: style-0-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
@@ -60,7 +60,7 @@ jobs:
     - uses: actions/cache@v3
       with:
         path: ${{ env.pythonLocation }}
-        key: build-2-${{ env.pythonLocation }}-${{ hashFiles('setup.cfg') }}-${{ hashFiles('test_requirements.txt') }}
+        key: build-0-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
 
     - name: Install dependencies
       run: |
@@ -177,12 +177,13 @@ jobs:
       uses: actions/cache@v3
       with:
         path: ${{ env.pythonLocation }}
-        key: test-1-${{ env.pythonLocation }}-${{ env.os }}-${{ hashFiles('setup.cfg') }}-${{ hashFiles('test_requirements.txt') }}
+        key: test-0-${{ env.pythonLocation }}-${{ env.os }}-${{ hashFiles('pyproject.toml') }}
 
     - name: Install Python dependencies using pip
+      # This would be nicer once this feature is implemented: https://github.com/pypa/pip/issues/11440
       run: |
         python -m pip install --upgrade pip
-        python -m pip install --upgrade -r test_requirements.txt
+        python -m pip install -e .[test]
 
     - name: Install MNE (stable)
       if: matrix.mne-version == 'mne-stable'
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 875fea757..2099cca54 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -53,24 +53,13 @@ Then, `git clone` your fork and install it in "editable" mode.
 ```Shell
 git clone https://github.com/<your-GitHub-username>/mne-bids
 cd ./mne-bids
-pip install -e .[full]
+pip install -e .[dev]
 git config --local blame.ignoreRevsFile .git-blame-ignore-revs
 ```
 
 The last command is needed for `git diff` to work properly.
 You should now have both the `mne` and `mne-bids` development versions available in your Python environment.
 
-### Install additional Python packages required for development
-
-Navigate to the root of the `mne-bids` repository and call:
-
-```Shell
-pip install -r test_requirements.txt
-pip install -r doc/requirements.txt
-```
-
-This will install several packages for running tests and building the documentation for `mne-bids`.
-
 ### Install the BIDS validator
 
 For a complete development setup of `mne-bids`, it is necessary to install the
@@ -137,7 +126,6 @@ We suggest installing our git pre-commit hooks to automatically run style
 checks before a commit is created:
 
 ```Shell
-pip install pre-commit
 pre-commit install
 ```
 
diff --git a/MANIFEST.in b/MANIFEST.in
index 188f5408d..8c5aba9e4 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -29,5 +29,5 @@ exclude Makefile
 exclude CONTRIBUTING.md
 exclude *.yml
 exclude .mailmap
-exclude test_requirements.txt
 exclude .gitignore
+exclude .pre-commit-config.yaml
diff --git a/Makefile b/Makefile
index c3deb90f9..ebf9ab0e1 100755
--- a/Makefile
+++ b/Makefile
@@ -32,7 +32,7 @@ test:
 	--doctest-modules \
 	--cov=mne_bids mne_bids/tests/ mne_bids/commands/tests/ \
 	--cov-report=xml \
-	--cov-config=setup.cfg \
+	--cov-config=pyproject.toml \
 	--verbose \
 	--ignore mne-python \
 	--ignore examples
diff --git a/doc/conf.py b/doc/conf.py
index e1b003df8..c2ae7b0d6 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -200,9 +200,6 @@
         "branch": "gh-pages",  # noqa: E501 Can be any branch, tag, or commit hash. Use a branch that hosts your docs.
         "binderhub_url": "https://mybinder.org",  # noqa: E501 Any URL of a binderhub deployment. Must be full URL (e.g. https://mybinder.org).
         "filepath_prefix": filepath_prefix,  # noqa: E501 A prefix to prepend to any filepaths in Binder links.
-        "dependencies": [
-            "../test_requirements.txt",
-            "./requirements.txt",
-        ],
+        "dependencies": ["mne_bids[test,doc]"],
     },
 }
diff --git a/doc/requirements.txt b/doc/requirements.txt
deleted file mode 100644
index ec8f884a2..000000000
--- a/doc/requirements.txt
+++ /dev/null
@@ -1,12 +0,0 @@
-nilearn
-sphinx
-sphinx_gallery
-sphinx-copybutton
-pydata-sphinx-theme
-numpydoc
-matplotlib
-pillow
-pandas
-https://github.com/mne-tools/mne-nirs/archive/refs/heads/main.zip
-seaborn
-openneuro-py
diff --git a/pyproject.toml b/pyproject.toml
index a2ea6d3be..e314c821a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,3 +1,125 @@
+[build-system]
+requires = ["setuptools",  "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "mne-bids"
+description = "MNE-BIDS: Organizing MEG, EEG, and iEEG data according to the BIDS specification and facilitating their analysis with MNE-Python"
+dynamic = ["version"]
+authors = [
+    { name = "MNE-BIDS Developers" },
+]
+maintainers = [
+    { name = "Stefan Appelhoff", email = "stefan.appelhoff@mailbox.org" },
+]
+license = { text = "BSD-3-Clause" }
+readme = { file = "README.md", content-type = "text/markdown" }
+requires-python = ">=3.9"
+keywords = [
+    "meg",
+    "eeg",
+    "ieeg",
+    "bids",
+    "brain imaging data structure",
+    "neuroscience",
+    "neuroimaging",
+]
+classifiers = [
+    "Topic :: Scientific/Engineering",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Developers",
+    "License :: OSI Approved",
+    "Topic :: Software Development",
+    "Topic :: Scientific/Engineering",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: POSIX :: Linux",
+    "Operating System :: MacOS",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+]
+scripts = { mne_bids = "mne_bids.commands.run:main" }
+dependencies = [
+    "mne>=1.5",
+    "numpy>=1.21.2",
+    "scipy>=1.7.1",
+]
+[project.optional-dependencies]
+# Variants with dependencies that will get installed on top of those listed unter
+# project.dependencies
+
+# Dependencies for running the test infrastructure
+test = [
+    "mne>=1.5",
+    "numpy>=1.21.2",
+    "scipy>=1.7.1",
+    "nibabel>=3.2.1",
+    "pybv>=0.7.5",
+    "eeglabio>=0.0.2",
+    "pymatreader>=0.0.30",
+    "matplotlib>=3.5.0",
+    "pandas>=1.3.2",
+    "EDFlib-Python>=1.0.6",  # drop once mne <1.7 is no longer supported
+    "edfio >= 0.2.1",
+    "pytest",
+    "pytest-cov",
+    "pytest-sugar",
+    "check-manifest",
+    "pydocstyle",
+    "flake8",
+    "black",
+]
+
+# Dependencies for building the documentation
+doc = [
+    "nilearn",
+    "sphinx",
+    "sphinx_gallery",
+    "sphinx-copybutton",
+    "pydata-sphinx-theme",
+    "numpydoc",
+    "matplotlib",
+    "pillow",
+    "pandas",
+    "mne-nirs @ https://github.com/mne-tools/mne-nirs/archive/refs/heads/main.zip",
+    "seaborn",
+    "openneuro-py",
+]
+
+# Dependencies for using all mne_bids features
+full = [
+    "nibabel >= 3.2.1",
+    "pybv >= 0.7.5",
+    "eeglabio >= 0.0.2",
+    "pymatreader >= 0.0.30",
+    "matplotlib >= 3.5.0",
+    "pandas >= 1.3.2",
+    "EDFlib-Python >= 1.0.6",  # drop once mne <1.7 is no longer supported
+    "edfio >= 0.2.1",
+]
+
+# Dependencies for developer installations
+dev = ["mne_bids[test,doc,full]", "pre-commit"]
+
+[project.urls]
+"Homepage" = "https://mne.tools/mne-bids"
+"Download" = "https://pypi.org/project/mne-bids/#files"
+"Bug Tracker" = "https://github.com/mne-tools/mne-bids/issues/"
+"Documentation" = "https://mne.tools/mne-bids"
+"Forum" = "https://mne.discourse.group/"
+"Source Code" = "https://github.com/mne-tools/mne-bids"
+
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["mne_bids"]
+exclude = ["tests"]
+namespaces = false
+
+[tool.setuptools.dynamic]
+version = {attr = "mne_bids.__version__"}
+
 [tool.ruff]
 select = ["E", "F", "W", "D"]
 exclude = ["__init__.py"]
@@ -8,5 +130,65 @@ convention = "numpy"
 [tool.black]
 exclude = "(dist/)|(build/)|(.*\\.ipynb)"
 
-[tool.check-manifest]
-ignore = [".pre-commit-config.yaml"]
+[tool.coverage.run]
+omit = [
+  "*tests*",
+  ]
+
+[tool.coverage.report]
+# Regexes for lines to exclude from consideration
+exclude_lines = [
+  "pragma: no cover",
+  "if 0:",
+  "if __name__ == .__main__.:",
+  ]
+
+[tool.isort]
+skip_glob = "*/*"
+
+[tool.pydocstyle]
+convention = "pep257"
+match_dir = "^(?!\\.|doc|examples).*$"
+add-ignore = ["D100", "D104", "D107", "D413"]
+add-select = ["D214", "D215", "D404", "D405", "D406", "D407", "D408", "D409", "D410", "D411"]
+ignore-decorators = "property"
+
+[tool.flake8]
+max-line-length = 88
+exclude = "__init__.py"
+ignore = ["I101", "I100", "I201"]
+extend-ignore = ["W503", "E203"]
+per-file-ignores = [
+    "mne_bids/commands/tests/test_*.py:E402",
+    "mne_bids/tests/test_*.py:E402",
+    ]
+
+[tool.pytest]
+addopts = """--durations=20 -ra --junit-xml=junit-results.xml --tb=short
+    --ignore=doc --ignore=examples --ignore=mne_bids/tests/data"""
+filterwarnings = [
+    "error",
+    "ignore:Estimation of line frequency only supports.*:RuntimeWarning",
+    "ignore:There are channels without locations (n/a)*:RuntimeWarning",
+    "ignore:Did not find any electrodes.tsv.*:RuntimeWarning",
+    "ignore:Did not find any coordsystem.json.*:RuntimeWarning",
+    "ignore:Did not find any events.tsv.*:RuntimeWarning",
+    "ignore:No events found or provided.*:RuntimeWarning",
+    "ignore:Participants file not found for.*:RuntimeWarning",
+    "ignore:Converting to FIF for anonymization:RuntimeWarning",
+    "ignore:Converting to BV for anonymization:RuntimeWarning",
+    "ignore:Converting data files to BrainVision format:RuntimeWarning",
+    "ignore:Writing of electrodes.tsv is not supported for datatype.*:RuntimeWarning",
+    "ignore:numpy.ufunc size changed.*:RuntimeWarning",
+    "ignore:tostring\\(\\) is deprecated.*:DeprecationWarning",
+    "ignore:MEG ref channel RMSP did not.*:RuntimeWarning",
+    "ignore:`product` is deprecated as of NumPy.*:DeprecationWarning",
+    # Python 3.10+ and NumPy 1.22 (and maybe also newer NumPy versions?)
+    "ignore:.*distutils\\.sysconfig module is deprecated.*:DeprecationWarning",
+    # numba with NumPy dev
+    "ignore:`np.MachAr` is deprecated.*:DeprecationWarning",
+    # old MNE _fake_click
+    "ignore:The .*_event function was deprecated in Matplotlib.*:",
+    "ignore:datetime\\.datetime\\.utcfromtimestamp.* is deprecated and scheduled for removal in a future version.*:DeprecationWarning",
+    ]
+
diff --git a/setup.cfg b/setup.cfg
index 8971178c2..f4781fc8a 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,60 +1,3 @@
-[metadata]
-name = mne-bids
-url = https://github.com/mne-tools/mne-bids
-author = mne-bids developers
-maintainer = Stefan Appelhoff
-maintainer_email = stefan.appelhoff@mailbox.org
-description = MNE-BIDS: Organizing MEG, EEG, and iEEG data according to the BIDS specification and facilitating their analysis with MNE-Python
-keywords = meg, eeg, ieeg, bids, brain imaging data structure, neuroscience, neuroimaging
-long_description = file: README.md
-long_description_content_type = text/markdown; charset=UTF-8
-license = BSD-3-Clause
-license_files = LICENSE
-platforms = any
-classifiers =
-  Topic :: Scientific/Engineering
-  Intended Audience :: Science/Research
-  Intended Audience :: Developers
-  License :: OSI Approved
-  Topic :: Software Development
-  Topic :: Scientific/Engineering
-  Operating System :: Microsoft :: Windows
-  Operating System :: POSIX :: Linux
-  Operating System :: MacOS
-  Programming Language :: Python
-  Programming Language :: Python :: 3.9
-  Programming Language :: Python :: 3.10
-  Programming Language :: Python :: 3.11
-  Programming Language :: Python :: 3.12
-project_urls =
-  Documentation = https://mne.tools/mne-bids
-  Bug Reports = https://github.com/mne-tools/mne-bids/issues
-  Source = https://github.com/mne-tools/mne-bids
-
-[options]
-python_requires = ~= 3.9
-install_requires =
-  mne >= 1.5
-  numpy >= 1.21.2
-  scipy >= 1.7.1
-packages = find:
-include_package_data = True
-
-[options.extras_require]
-full =
-  nibabel >= 3.2.1
-  pybv >= 0.7.5
-  eeglabio >= 0.0.2
-  pymatreader >= 0.0.30
-  matplotlib >= 3.5.0
-  pandas >= 1.3.2
-  EDFlib-Python >= 1.0.6  # drop once mne <1.7 is no longer supported
-  edfio >= 0.2.1
-
-[options.entry_points]
-console_scripts =
-    mne_bids = mne_bids.commands.run:main
-
 [flake8]
 max-line-length = 88
 exclude = __init__.py
@@ -99,20 +42,3 @@ match_dir = ^(?!\.|doc|examples).*$
 add-ignore = D100,D104,D107,D413
 add-select = D214,D215,D404,D405,D406,D407,D408,D409,D410,D411
 ignore-decorators = property
-
-[coverage:run]
-omit =
-    # Do not include test script in coverage report
-    *tests*
-
-[coverage:report]
-# Regexes for lines to exclude from consideration
-exclude_lines =
-    # Have to re-enable the standard pragma
-    pragma: no cover
-
-    # Don't complain if non-runnable code isn't run:
-    if __name__ == .__main__.:
-
-[isort]
-skip_glob = */*
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 9d8038fff..000000000
--- a/setup.py
+++ /dev/null
@@ -1,27 +0,0 @@
-"""Setup MNE-BIDS."""
-import os
-import sys
-
-from setuptools import setup
-
-# Give setuptools a hint to complain if it's too old a version
-SETUP_REQUIRES = ["setuptools >= 46.4.0"]
-# This enables setuptools to install wheel on-the-fly
-SETUP_REQUIRES += ["wheel"] if "bdist_wheel" in sys.argv else []
-
-version = None
-with open(os.path.join("mne_bids", "__init__.py"), "r") as fid:
-    for line in fid:
-        line = line.strip()
-        if line.startswith("__version__ = "):
-            version = line.split(" = ")[1].split("#")[0].strip('"')
-            break
-if version is None:
-    raise RuntimeError("Could not determine version")
-
-
-if __name__ == "__main__":
-    setup(
-        version=version,
-        setup_requires=SETUP_REQUIRES,
-    )
diff --git a/test_requirements.txt b/test_requirements.txt
deleted file mode 100644
index 759c2abf5..000000000
--- a/test_requirements.txt
+++ /dev/null
@@ -1,18 +0,0 @@
-mne>=1.5
-numpy>=1.21.2
-scipy>=1.7.1
-nibabel>=3.2.1
-pybv>=0.7.5
-eeglabio>=0.0.2
-pymatreader>=0.0.30
-matplotlib>=3.5.0
-pandas>=1.3.2
-EDFlib-Python>=1.0.6  # drop once mne <1.7 is no longer supported
-edfio >= 0.2.1
-pytest
-pytest-cov
-pytest-sugar
-check-manifest
-pydocstyle
-flake8
-black

From 7953f2dfad1f5488482d637de0a5d9c62f3aa546 Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Thu, 7 Dec 2023 13:02:33 +0100
Subject: [PATCH 2/8] remove BINDER support

---
 .github/workflows/unit_tests.yml |  3 ---
 doc/conf.py                      | 20 --------------------
 examples/README.rst              |  2 --
 3 files changed, 25 deletions(-)

diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml
index 39a4176e7..ea27b17b1 100644
--- a/.github/workflows/unit_tests.yml
+++ b/.github/workflows/unit_tests.yml
@@ -9,9 +9,6 @@ on:
     branches: ['**']
   pull_request:
     branches: ['**']
-  create:
-    branches: [main]
-    tags: ['**']
   schedule:
     - cron: "0 4 * * *"
 
diff --git a/doc/conf.py b/doc/conf.py
index c2ae7b0d6..3bf2f4e76 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -172,17 +172,6 @@
 }
 intersphinx_timeout = 5
 
-# Resolve binder filepath_prefix. From the docs:
-# "A prefix to append to the filepath in the Binder links. You should use this
-# if you will store your built documentation in a sub-folder of a repository,
-# instead of in the root."
-# we will store dev docs in a `dev` subdirectory and all other docs in a
-# directory "v" + version_str. E.g., "v0.3"
-if "dev" in version:
-    filepath_prefix = "dev"
-else:
-    filepath_prefix = "v{}".format(version)
-
 sphinx_gallery_conf = {
     "doc_module": "mne_bids",
     "reference_url": {
@@ -193,13 +182,4 @@
     "within_subsection_order": ExampleTitleSortKey,
     "gallery_dirs": "auto_examples",
     "filename_pattern": "^((?!sgskip).)*$",
-    "binder": {
-        # Required keys
-        "org": "mne-tools",
-        "repo": "mne-bids",
-        "branch": "gh-pages",  # noqa: E501 Can be any branch, tag, or commit hash. Use a branch that hosts your docs.
-        "binderhub_url": "https://mybinder.org",  # noqa: E501 Any URL of a binderhub deployment. Must be full URL (e.g. https://mybinder.org).
-        "filepath_prefix": filepath_prefix,  # noqa: E501 A prefix to prepend to any filepaths in Binder links.
-        "dependencies": ["mne_bids[test,doc]"],
-    },
 }
diff --git a/examples/README.rst b/examples/README.rst
index 79c74ee84..8456cf64e 100644
--- a/examples/README.rst
+++ b/examples/README.rst
@@ -2,7 +2,5 @@ Examples
 --------
 
 The following examples demonstrate some common use-cases of MNE-BIDS.
-Each example has a badge called "Binder" at the end. By clicking on that badge,
-you can interactively run the examples in your browser.
 
 The examples are loosely ordered from basic to more advanced use cases.

From 9b9a28285eb171afb4a03698cb39169c33b97521 Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Thu, 7 Dec 2023 13:04:37 +0100
Subject: [PATCH 3/8] do not repeat deps in opt deps

---
 pyproject.toml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index e314c821a..19e619184 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -52,9 +52,6 @@ dependencies = [
 
 # Dependencies for running the test infrastructure
 test = [
-    "mne>=1.5",
-    "numpy>=1.21.2",
-    "scipy>=1.7.1",
     "nibabel>=3.2.1",
     "pybv>=0.7.5",
     "eeglabio>=0.0.2",

From ff1435d3de0447c8b435165533434303c052347e Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Thu, 7 Dec 2023 13:07:43 +0100
Subject: [PATCH 4/8] organize opt dep subgroups more DRY

---
 pyproject.toml | 33 +++++++++++++--------------------
 1 file changed, 13 insertions(+), 20 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 19e619184..64e2b66e0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -50,16 +50,21 @@ dependencies = [
 # Variants with dependencies that will get installed on top of those listed unter
 # project.dependencies
 
+# Dependencies for using all mne_bids features
+full = [
+    "nibabel >= 3.2.1",
+    "pybv >= 0.7.5",
+    "eeglabio >= 0.0.2",
+    "pymatreader >= 0.0.30",
+    "matplotlib >= 3.5.0",
+    "pandas >= 1.3.2",
+    "EDFlib-Python >= 1.0.6",  # drop once mne <1.7 is no longer supported
+    "edfio >= 0.2.1",
+]
+
 # Dependencies for running the test infrastructure
 test = [
-    "nibabel>=3.2.1",
-    "pybv>=0.7.5",
-    "eeglabio>=0.0.2",
-    "pymatreader>=0.0.30",
-    "matplotlib>=3.5.0",
-    "pandas>=1.3.2",
-    "EDFlib-Python>=1.0.6",  # drop once mne <1.7 is no longer supported
-    "edfio >= 0.2.1",
+    "mne_bids[full]",
     "pytest",
     "pytest-cov",
     "pytest-sugar",
@@ -85,18 +90,6 @@ doc = [
     "openneuro-py",
 ]
 
-# Dependencies for using all mne_bids features
-full = [
-    "nibabel >= 3.2.1",
-    "pybv >= 0.7.5",
-    "eeglabio >= 0.0.2",
-    "pymatreader >= 0.0.30",
-    "matplotlib >= 3.5.0",
-    "pandas >= 1.3.2",
-    "EDFlib-Python >= 1.0.6",  # drop once mne <1.7 is no longer supported
-    "edfio >= 0.2.1",
-]
-
 # Dependencies for developer installations
 dev = ["mne_bids[test,doc,full]", "pre-commit"]
 

From 29d1bd660cef12e7f429e94bf39e1a902057ca2e Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Thu, 7 Dec 2023 13:21:53 +0100
Subject: [PATCH 5/8] need defusedxml for some BrainVision ops

---
 doc/install.rst   | 2 +-
 doc/whats_new.rst | 1 +
 pyproject.toml    | 1 +
 3 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/doc/install.rst b/doc/install.rst
index a433819d8..726096d4a 100644
--- a/doc/install.rst
+++ b/doc/install.rst
@@ -20,6 +20,7 @@ Optional:
 
 * ``nibabel`` (>=3.2.1, for processing MRI data)
 * ``pybv`` (>=0.7.5, for writing BrainVision data)
+* ``defusedxml`` (for some BrainVision data operations)
 * ``eeglabio`` (>=0.0.2, for writing EEGLAB data)
 * ``pymatreader`` (>=0.0.30, for other operations with EEGLAB data)
 * ``matplotlib`` (>=3.5.0, for using the interactive data inspector)
@@ -27,7 +28,6 @@ Optional:
 * ``EDFlib-Python`` (>=1.0.6, for writing EDF data with ``mne`` versions <1.7)
 * ``edfio`` (>=0.2.1, for writing EDF data)
 
-
 We recommend installing ``mne-bids`` into an isolated Python environment,
 for example created via ``conda``
 (may be obtained through `miniconda <https://docs.conda.io/en/latest/miniconda.html>`_).
diff --git a/doc/whats_new.rst b/doc/whats_new.rst
index 04534c223..48c140032 100644
--- a/doc/whats_new.rst
+++ b/doc/whats_new.rst
@@ -45,6 +45,7 @@ Detailed list of changes
 - MNE-BIDS now requires MNE-Python 1.5.0 or higher.
 - ``edfio`` replaces ``EDFlib-Python`` for export to EDF with MNE-Python >= 1.7.0.
 - Version requirements for optional dependency packages have been bumped up, see installation instructions.
+- ``defusedxml`` is now required for some BrainVision data operations.
 
 🪲 Bug fixes
 ^^^^^^^^^^^^
diff --git a/pyproject.toml b/pyproject.toml
index 64e2b66e0..16c7a67a8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -60,6 +60,7 @@ full = [
     "pandas >= 1.3.2",
     "EDFlib-Python >= 1.0.6",  # drop once mne <1.7 is no longer supported
     "edfio >= 0.2.1",
+    "defusedxml",
 ]
 
 # Dependencies for running the test infrastructure

From e255b10aa0fd9208e565a48665be0c058e17933a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Richard=20H=C3=B6chenberger?=
 <richard.hoechenberger@gmail.com>
Date: Thu, 7 Dec 2023 13:28:41 +0100
Subject: [PATCH 6/8] Reformat pyproject.toml with Even better TOML extension

https://marketplace.visualstudio.com/items?itemName=tamasfe.even-better-toml
---
 pyproject.toml | 44 +++++++++++++++++++++-----------------------
 1 file changed, 21 insertions(+), 23 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 16c7a67a8..f883d62d7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,14 +1,12 @@
 [build-system]
-requires = ["setuptools",  "wheel"]
+requires = ["setuptools", "wheel"]
 build-backend = "setuptools.build_meta"
 
 [project]
 name = "mne-bids"
 description = "MNE-BIDS: Organizing MEG, EEG, and iEEG data according to the BIDS specification and facilitating their analysis with MNE-Python"
 dynamic = ["version"]
-authors = [
-    { name = "MNE-BIDS Developers" },
-]
+authors = [{ name = "MNE-BIDS Developers" }]
 maintainers = [
     { name = "Stefan Appelhoff", email = "stefan.appelhoff@mailbox.org" },
 ]
@@ -41,11 +39,7 @@ classifiers = [
     "Programming Language :: Python :: 3.12",
 ]
 scripts = { mne_bids = "mne_bids.commands.run:main" }
-dependencies = [
-    "mne>=1.5",
-    "numpy>=1.21.2",
-    "scipy>=1.7.1",
-]
+dependencies = ["mne>=1.5", "numpy>=1.21.2", "scipy>=1.7.1"]
 [project.optional-dependencies]
 # Variants with dependencies that will get installed on top of those listed unter
 # project.dependencies
@@ -58,7 +52,7 @@ full = [
     "pymatreader >= 0.0.30",
     "matplotlib >= 3.5.0",
     "pandas >= 1.3.2",
-    "EDFlib-Python >= 1.0.6",  # drop once mne <1.7 is no longer supported
+    "EDFlib-Python >= 1.0.6", # drop once mne <1.7 is no longer supported
     "edfio >= 0.2.1",
     "defusedxml",
 ]
@@ -109,7 +103,7 @@ exclude = ["tests"]
 namespaces = false
 
 [tool.setuptools.dynamic]
-version = {attr = "mne_bids.__version__"}
+version = { attr = "mne_bids.__version__" }
 
 [tool.ruff]
 select = ["E", "F", "W", "D"]
@@ -122,17 +116,11 @@ convention = "numpy"
 exclude = "(dist/)|(build/)|(.*\\.ipynb)"
 
 [tool.coverage.run]
-omit = [
-  "*tests*",
-  ]
+omit = ["*tests*"]
 
 [tool.coverage.report]
 # Regexes for lines to exclude from consideration
-exclude_lines = [
-  "pragma: no cover",
-  "if 0:",
-  "if __name__ == .__main__.:",
-  ]
+exclude_lines = ["pragma: no cover", "if 0:", "if __name__ == .__main__.:"]
 
 [tool.isort]
 skip_glob = "*/*"
@@ -141,7 +129,18 @@ skip_glob = "*/*"
 convention = "pep257"
 match_dir = "^(?!\\.|doc|examples).*$"
 add-ignore = ["D100", "D104", "D107", "D413"]
-add-select = ["D214", "D215", "D404", "D405", "D406", "D407", "D408", "D409", "D410", "D411"]
+add-select = [
+    "D214",
+    "D215",
+    "D404",
+    "D405",
+    "D406",
+    "D407",
+    "D408",
+    "D409",
+    "D410",
+    "D411",
+]
 ignore-decorators = "property"
 
 [tool.flake8]
@@ -152,7 +151,7 @@ extend-ignore = ["W503", "E203"]
 per-file-ignores = [
     "mne_bids/commands/tests/test_*.py:E402",
     "mne_bids/tests/test_*.py:E402",
-    ]
+]
 
 [tool.pytest]
 addopts = """--durations=20 -ra --junit-xml=junit-results.xml --tb=short
@@ -181,5 +180,4 @@ filterwarnings = [
     # old MNE _fake_click
     "ignore:The .*_event function was deprecated in Matplotlib.*:",
     "ignore:datetime\\.datetime\\.utcfromtimestamp.* is deprecated and scheduled for removal in a future version.*:DeprecationWarning",
-    ]
-
+]

From 1eaa36ffe42448320156a8f66aee5de593d0ef76 Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Thu, 7 Dec 2023 15:51:33 +0100
Subject: [PATCH 7/8] defusedxml only for doc, not proj

---
 doc/install.rst   | 1 -
 doc/whats_new.rst | 1 -
 pyproject.toml    | 2 +-
 3 files changed, 1 insertion(+), 3 deletions(-)

diff --git a/doc/install.rst b/doc/install.rst
index 726096d4a..90d2e22b1 100644
--- a/doc/install.rst
+++ b/doc/install.rst
@@ -20,7 +20,6 @@ Optional:
 
 * ``nibabel`` (>=3.2.1, for processing MRI data)
 * ``pybv`` (>=0.7.5, for writing BrainVision data)
-* ``defusedxml`` (for some BrainVision data operations)
 * ``eeglabio`` (>=0.0.2, for writing EEGLAB data)
 * ``pymatreader`` (>=0.0.30, for other operations with EEGLAB data)
 * ``matplotlib`` (>=3.5.0, for using the interactive data inspector)
diff --git a/doc/whats_new.rst b/doc/whats_new.rst
index 48c140032..04534c223 100644
--- a/doc/whats_new.rst
+++ b/doc/whats_new.rst
@@ -45,7 +45,6 @@ Detailed list of changes
 - MNE-BIDS now requires MNE-Python 1.5.0 or higher.
 - ``edfio`` replaces ``EDFlib-Python`` for export to EDF with MNE-Python >= 1.7.0.
 - Version requirements for optional dependency packages have been bumped up, see installation instructions.
-- ``defusedxml`` is now required for some BrainVision data operations.
 
 🪲 Bug fixes
 ^^^^^^^^^^^^
diff --git a/pyproject.toml b/pyproject.toml
index f883d62d7..60f33f355 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -54,7 +54,6 @@ full = [
     "pandas >= 1.3.2",
     "EDFlib-Python >= 1.0.6", # drop once mne <1.7 is no longer supported
     "edfio >= 0.2.1",
-    "defusedxml",
 ]
 
 # Dependencies for running the test infrastructure
@@ -83,6 +82,7 @@ doc = [
     "mne-nirs @ https://github.com/mne-tools/mne-nirs/archive/refs/heads/main.zip",
     "seaborn",
     "openneuro-py",
+    "defusedxml",  # for reading BrainVision montages: `examples/convert_eeg_to_bids.py`
 ]
 
 # Dependencies for developer installations

From 83ef6faea4186dad0a8f010395f2476c710dc668 Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Thu, 7 Dec 2023 16:05:33 +0100
Subject: [PATCH 8/8] ignore .ruff_cache

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index 395fbd700..b8d24ce2e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,6 +6,7 @@ build
 coverage
 *.xml
 .venv
+.ruff_cache
 
 # Sphinx documentation
 doc/_build/