MAINT: Future compatibility with MNE 1.6 (#120)

* compatibility for meas_info * compatibility for fiff.py and ch_data.py * compatibility for test_meas_info * fix missed for _picks_to_idx * fix missed * fix style * trigger cis * fix cis MNE-main which should install the dependencies required by main instead of stable * trigger cis * install pre-release binaries for numpy and scipy when running MNE-main tests * try again to install pre-release binaries * try again * trigger cis * Update azure-pipelines.yml * increase timeout, upgrade instead of force-reinstall, and add matplotlib * fix numpy 1.25 deprecation * sort alphabetically * rm duplicate junitxml and use the set coverage config
vferat · Sep 14, 2023 · a8416cc · a8416cc
1 parent d39ad93
commit a8416cc
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diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -48,67 +48,67 @@ stages:
         linux 3.8:
           VM_IMAGE: 'ubuntu-latest'
           PYTHON_VERSION: '3.8'
-          MNE_DEV: false
+          PRE: false
           CACHE_MNE_PATH: $(CACHE_PATH_MNE_LINUX)
         linux 3.9:
           VM_IMAGE: 'ubuntu-latest'
           PYTHON_VERSION: '3.9'
-          MNE_DEV: false
+          PRE: false
           CACHE_MNE_PATH: $(CACHE_PATH_MNE_LINUX)
         linux 3.10:
           VM_IMAGE: 'ubuntu-latest'
           PYTHON_VERSION: '3.10'
-          MNE_DEV: false
+          PRE: false
           CACHE_MNE_PATH: $(CACHE_PATH_MNE_LINUX)
         linux 3.11:
           VM_IMAGE: 'ubuntu-latest'
           PYTHON_VERSION: '3.11'
-          MNE_DEV: false
+          PRE: false
           CACHE_MNE_PATH: $(CACHE_PATH_MNE_LINUX)
         linux 3.10 MNE-dev:
           VM_IMAGE: 'ubuntu-latest'
           PYTHON_VERSION: '3.10'
-          MNE_DEV: true
+          PRE: true
           CACHE_MNE_PATH: $(CACHE_PATH_MNE_LINUX)
         macOS 3.8:
           VM_IMAGE: 'macOS-latest'
           PYTHON_VERSION: '3.8'
-          MNE_DEV: false
+          PRE: false
           CACHE_MNE_PATH: $(CACHE_PATH_MNE_MACOS)
         macOS 3.9:
           VM_IMAGE: 'macOS-latest'
           PYTHON_VERSION: '3.9'
-          MNE_DEV: false
+          PRE: false
           CACHE_MNE_PATH: $(CACHE_PATH_MNE_MACOS)
         macOS 3.10:
           VM_IMAGE: 'macOS-latest'
           PYTHON_VERSION: '3.10'
-          MNE_DEV: false
+          PRE: false
           CACHE_MNE_PATH: $(CACHE_PATH_MNE_MACOS)
         macOS 3.11:
           VM_IMAGE: 'macOS-latest'
           PYTHON_VERSION: '3.11'
-          MNE_DEV: false
+          PRE: false
           CACHE_MNE_PATH: $(CACHE_PATH_MNE_MACOS)
         windows 3.8:
           VM_IMAGE: 'windows-latest'
           PYTHON_VERSION: '3.8'
-          MNE_DEV: false
+          PRE: false
           CACHE_MNE_PATH: $(CACHE_PATH_MNE_WINDOWS)
         windows 3.9:
           VM_IMAGE: 'windows-latest'
           PYTHON_VERSION: '3.9'
-          MNE_DEV: false
+          PRE: false
           CACHE_MNE_PATH: $(CACHE_PATH_MNE_WINDOWS)
         windows 3.10:
           VM_IMAGE: 'windows-latest'
           PYTHON_VERSION: '3.10'
-          MNE_DEV: false
+          PRE: false
           CACHE_MNE_PATH: $(CACHE_PATH_MNE_WINDOWS)
         windows 3.11:
           VM_IMAGE: 'windows-latest'
           PYTHON_VERSION: '3.11'
-          MNE_DEV: false
+          PRE: false
           CACHE_MNE_PATH: $(CACHE_PATH_MNE_WINDOWS)
     pool:
       vmImage: $(VM_IMAGE)
@@ -121,13 +121,13 @@ stages:
       displayName: 'Setup Python $(PYTHON_VERSION)'
     - script: |
         python -m pip install --progress-bar off --upgrade pip setuptools wheel
-        python -m pip install --progress-bar off .[test]
-      displayName: 'Install dependencies and MNE (stable)'
+        python -m pip install --progress-bar off --upgrade .[test]
+      displayName: 'Install package'
     - script: |
-        python -m pip uninstall -y mne
-        python -m pip install --progress-bar off --no-deps git+https://github.com/mne-tools/mne-python
-      condition: eq(variables.MNE_DEV, 'true')
-      displayName: 'Install MNE (main)'
+        python -m pip install --progress-bar off --force-reinstall git+https://github.com/mne-tools/mne-python
+        python -m pip install --progress-bar off --upgrade --pre --only-binary :all: -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple --timeout=180 numpy scipy scikit-learn matplotlib
+      condition: eq(variables.PRE, 'true')
+      displayName: 'Install pre-release dependencies'
     - script: mne sys_info -pd
       displayName: 'Display MNE config'
     - script: |
@@ -142,7 +142,7 @@ stages:
     - script: python -c "import mne; mne.datasets.testing.data_path(verbose=True)"
       displayName: 'Get MNE testing datataset'
       condition: ne(variables.CACHE_MNE_RESTORED, 'true')
-    - script: pytest pycrostates --junitxml=junit/test-results.xml --cov=pycrostates --cov-report=xml
+    - script: pytest pycrostates --cov=pycrostates --cov-report=xml --cov-config=pyproject.toml
       displayName: 'Run unit tests'
     - task: PublishCodeCoverageResults@1
       inputs:

diff --git a/pycrostates/cluster/_base.py b/pycrostates/cluster/_base.py
@@ -9,10 +9,15 @@
 from mne import BaseEpochs, pick_info
 from mne.annotations import _annotations_starts_stops
 from mne.io import BaseRaw
-from mne.io.pick import _picks_to_idx
+from mne.utils import check_version
 from numpy.typing import NDArray
 from scipy.signal import convolve2d
 
+if check_version("mne", "1.6"):
+    from mne._fiff.pick import _picks_to_idx
+else:
+    from mne.io.pick import _picks_to_idx
+
 from .._typing import CHData, Cluster, Picks
 from ..segmentation import EpochsSegmentation, RawSegmentation
 from ..utils import _corr_vectors

diff --git a/pycrostates/cluster/tests/test_aahc.py b/pycrostates/cluster/tests/test_aahc.py
@@ -13,9 +13,14 @@
 from mne.channels import DigMontage
 from mne.datasets import testing
 from mne.io import RawArray, read_raw_fif
-from mne.io.pick import _picks_to_idx
+from mne.utils import check_version
 from numpy.testing import assert_allclose
 
+if check_version("mne", "1.6"):
+    from mne._fiff.pick import _picks_to_idx
+else:
+    from mne.io.pick import _picks_to_idx
+
 from pycrostates import __version__
 from pycrostates.cluster import AAHCluster
 from pycrostates.io import ChData, ChInfo, read_cluster

diff --git a/pycrostates/cluster/tests/test_kmeans.py b/pycrostates/cluster/tests/test_kmeans.py
@@ -13,9 +13,14 @@
 from mne.channels import DigMontage
 from mne.datasets import testing
 from mne.io import RawArray, read_raw_fif
-from mne.io.pick import _picks_to_idx
+from mne.utils import check_version
 from numpy.testing import assert_allclose
 
+if check_version("mne", "1.6"):
+    from mne._fiff.pick import _picks_to_idx
+else:
+    from mne.io.pick import _picks_to_idx
+
 from pycrostates import __version__
 from pycrostates.cluster import ModKMeans
 from pycrostates.io import ChData, ChInfo, read_cluster

diff --git a/pycrostates/io/ch_data.py b/pycrostates/io/ch_data.py
@@ -3,10 +3,15 @@
 from typing import Any, Union
 
 import numpy as np
-from mne.io import Info
-from mne.io.pick import _picks_to_idx, pick_info
+from mne import Info, pick_info
+from mne.utils import check_version
 from numpy.typing import NDArray
 
+if check_version("mne", "1.6"):
+    from mne._fiff.pick import _picks_to_idx
+else:
+    from mne.io.pick import _picks_to_idx
+
 from .._typing import CHData, CHInfo
 from ..utils._checks import _check_type
 from ..utils._docs import fill_doc

diff --git a/pycrostates/io/fiff.py b/pycrostates/io/fiff.py
@@ -8,30 +8,53 @@
 from typing import List, Union
 
 import numpy as np
-from mne.io import Info
-from mne.io._digitization import _format_dig_points, _read_dig_fif
+from mne import Info, Transform
 from mne.io.constants import FIFF
-from mne.io.ctf_comp import _read_ctf_comp, write_ctf_comp
-from mne.io.meas_info import _read_bad_channels, _write_ch_infos
-from mne.io.open import fiff_open
-from mne.io.proj import _read_proj, _write_proj
-from mne.io.tag import read_tag
-from mne.io.tree import dir_tree_find
-from mne.io.write import (
-    end_block,
-    start_and_end_file,
-    start_block,
-    write_coord_trans,
-    write_dig_points,
-    write_double_matrix,
-    write_id,
-    write_int,
-    write_name_list,
-    write_string,
-)
-from mne.transforms import Transform, invert_transform
+from mne.transforms import invert_transform
+from mne.utils import check_version
 from numpy.typing import NDArray
 
+if check_version("mne", "1.6"):
+    from mne._fiff._digitization import _format_dig_points, _read_dig_fif
+    from mne._fiff.ctf_comp import _read_ctf_comp, write_ctf_comp
+    from mne._fiff.meas_info import _read_bad_channels, _write_ch_infos
+    from mne._fiff.open import fiff_open
+    from mne._fiff.proj import _read_proj, _write_proj
+    from mne._fiff.tag import read_tag
+    from mne._fiff.tree import dir_tree_find
+    from mne._fiff.write import (
+        end_block,
+        start_and_end_file,
+        start_block,
+        write_coord_trans,
+        write_dig_points,
+        write_double_matrix,
+        write_id,
+        write_int,
+        write_name_list,
+        write_string,
+    )
+else:
+    from mne.io._digitization import _format_dig_points, _read_dig_fif
+    from mne.io.ctf_comp import _read_ctf_comp, write_ctf_comp
+    from mne.io.meas_info import _read_bad_channels, _write_ch_infos
+    from mne.io.open import fiff_open
+    from mne.io.proj import _read_proj, _write_proj
+    from mne.io.tag import read_tag
+    from mne.io.tree import dir_tree_find
+    from mne.io.write import (
+        end_block,
+        start_and_end_file,
+        start_block,
+        write_coord_trans,
+        write_dig_points,
+        write_double_matrix,
+        write_id,
+        write_int,
+        write_name_list,
+        write_string,
+    )
+
 from .. import __version__
 from .._typing import CHInfo
 from ..cluster import AAHCluster, ModKMeans
@@ -521,13 +544,13 @@ def _read_meas_info(fid, tree):
         pos = meas_info["directory"][k].pos
         if kind == FIFF.FIFF_NCHAN:
             tag = read_tag(fid, pos)
-            nchan = int(tag.data)
+            nchan = int(tag.data.item())
         elif kind == FIFF.FIFF_CH_INFO:
             tag = read_tag(fid, pos)
             chs.append(tag.data)
         elif kind == FIFF.FIFF_MNE_CUSTOM_REF:
             tag = read_tag(fid, pos)
-            custom_ref_applied = int(tag.data)
+            custom_ref_applied = int(tag.data.item())
         elif kind == FIFF.FIFF_COORD_TRANS:
             tag = read_tag(fid, pos)
             cand = tag.data

diff --git a/pycrostates/io/meas_info.py b/pycrostates/io/meas_info.py
@@ -5,20 +5,29 @@
 from typing import List, Optional, Tuple, Union
 
 import numpy as np
-from mne.io import Info
+from mne import Info, Projection, Transform
 from mne.io.constants import FIFF
-from mne.io.meas_info import (
-    _check_bads,
-    _check_ch_keys,
-    _check_dev_head_t,
-    _unique_channel_names,
-)
-from mne.io.pick import get_channel_type_constants
-from mne.io.proj import Projection
-from mne.io.tag import _ch_coord_dict
-from mne.transforms import Transform
 from mne.utils import check_version
 
+if check_version("mne", "1.6"):
+    from mne._fiff.meas_info import (
+        _check_bads,
+        _check_ch_keys,
+        _check_dev_head_t,
+        _unique_channel_names,
+    )
+    from mne._fiff.pick import get_channel_type_constants
+    from mne._fiff.tag import _ch_coord_dict
+else:
+    from mne.io.meas_info import (
+        _check_bads,
+        _check_ch_keys,
+        _check_dev_head_t,
+        _unique_channel_names,
+    )
+    from mne.io.pick import get_channel_type_constants
+    from mne.io.tag import _ch_coord_dict
+
 from .._typing import CHInfo
 from ..utils._checks import _check_type, _IntLike
 from ..utils._logs import logger

diff --git a/pycrostates/io/tests/test_meas_info.py b/pycrostates/io/tests/test_meas_info.py
@@ -4,12 +4,11 @@
 
 import numpy as np
 import pytest
-from mne import create_info
+from mne import Transform, create_info
 from mne.channels import DigMontage
 from mne.datasets import testing
 from mne.io import read_raw_fif
 from mne.io.constants import FIFF
-from mne.transforms import Transform
 from mne.utils import check_version
 from numpy.testing import assert_allclose
 

diff --git a/pycrostates/preprocessing/extract_gfp_peaks.py b/pycrostates/preprocessing/extract_gfp_peaks.py
@@ -4,10 +4,15 @@
 import numpy as np
 from mne import BaseEpochs, pick_info
 from mne.io import BaseRaw
-from mne.io.pick import _picks_to_idx
+from mne.utils import check_version
 from numpy.typing import NDArray
 from scipy.signal import find_peaks
 
+if check_version("mne", "1.6"):
+    from mne._fiff.pick import _picks_to_idx
+else:
+    from mne.io.pick import _picks_to_idx
+
 from .._typing import CHData, Picks
 from ..utils._checks import (
     _check_picks_uniqueness,

diff --git a/pycrostates/preprocessing/resample.py b/pycrostates/preprocessing/resample.py
@@ -5,7 +5,12 @@
 import numpy as np
 from mne import BaseEpochs, pick_info
 from mne.io import BaseRaw
-from mne.io.pick import _picks_to_idx
+from mne.utils import check_version
+
+if check_version("mne", "1.6"):
+    from mne._fiff.pick import _picks_to_idx
+else:
+    from mne.io.pick import _picks_to_idx
 
 from .._typing import CHData, Picks, RANDomState
 from ..utils._checks import (

diff --git a/pycrostates/preprocessing/spatial_filter.py b/pycrostates/preprocessing/spatial_filter.py
@@ -6,12 +6,17 @@
 from mne.channels import find_ch_adjacency
 from mne.channels.interpolation import _make_interpolation_matrix
 from mne.io import BaseRaw
-from mne.io.pick import _picks_by_type
 from mne.parallel import parallel_func
+from mne.utils import check_version
 from mne.utils.check import _check_preload
 from numpy.typing import NDArray
 from scipy.sparse import csr_matrix
 
+if check_version("mne", "1.6"):
+    from mne._fiff.pick import _picks_by_type
+else:
+    from mne.io.pick import _picks_by_type
+
 from .._typing import CHData
 from ..utils._checks import _check_n_jobs, _check_type, _check_value
 from ..utils._docs import fill_doc

diff --git a/pycrostates/preprocessing/tests/test_extract_gfp_peaks.py b/pycrostates/preprocessing/tests/test_extract_gfp_peaks.py
@@ -2,7 +2,12 @@
 import pytest
 from mne import pick_info
 from mne.datasets import testing
-from mne.io.pick import _picks_to_idx
+from mne.utils import check_version
+
+if check_version("mne", "1.6"):
+    from mne._fiff.pick import _picks_to_idx
+else:
+    from mne.io.pick import _picks_to_idx
 
 from pycrostates.io import ChData
 from pycrostates.preprocessing import extract_gfp_peaks