Move project config to pyproject.toml, remove BINDER support (#1202)

* move project config to pyproject.toml * remove BINDER support * do not repeat deps in opt deps * organize opt dep subgroups more DRY * need defusedxml for some BrainVision ops * Reformat pyproject.toml with Even better TOML extension https://marketplace.visualstudio.com/items?itemName=tamasfe.even-better-toml * defusedxml only for doc, not proj * ignore .ruff_cache --------- Co-authored-by: Richard Höchenberger <[email protected]>
mne-tools · Dec 7, 2023 · a34274d · a34274d
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Showing 14 changed files with 189 additions and 192 deletions.
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/.gitignore b/.gitignore
@@ -6,6 +6,7 @@ build
 coverage
 *.xml
 .venv
+.ruff_cache
 
 # Sphinx documentation
 doc/_build/

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/install.rst b/doc/install.rst
@@ -27,7 +27,6 @@ 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/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.