mne-tools · sappelhoff · Dec 7, 2023 · Dec 7, 2023 · Dec 7, 2023 · Dec 7, 2023
diff --git 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
@@ -9,9 +9,6 @@ on:
     branches: ['**']
   pull_request:
     branches: ['**']
-  create:
-    branches: [main]
-    tags: ['**']
   schedule:
     - cron: "0 4 * * *"
 
@@ -32,7 +29,7 @@ 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 +57,7 @@ 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 +174,13 @@ 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
@@ -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
@@ -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
@@ -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
@@ -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": {
@@ -193,16 +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": [
-            "../test_requirements.txt",
-            "./requirements.txt",
-        ],
-    },
 }
diff --git a/doc/requirements.txt b/doc/requirements.txt
diff --git 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.
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,3 +1,115 @@
+[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 = "[email protected]" },
+]
+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 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 = [
+    "mne_bids[full]",
+    "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 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 +120,65 @@ 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",
+    ]
+