Merge branch 'refs/heads/main' into nodes

marsipu · May 13, 2024 · 3c64cc1 · 3c64cc1
2 parents 538b77f + 5f214fd
commit 3c64cc1
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diff --git a/.github/workflows/pypi_release.yml b/.github/workflows/pypi_release.yml
@@ -10,8 +10,8 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
       - name: Install dependencies
         run: |
           python3 -m pip install --upgrade pip
@@ -21,6 +21,6 @@ jobs:
           TWINE_USERNAME: __token__
           TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
         run: |
-          python3 -m build
+          python -m build
           twine check dist/*
           twine upload dist/*
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,7 +1,7 @@
 repos:
   # Pre-commit hooks
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
     - id: check-json
     - id: check-toml
@@ -12,13 +12,13 @@ repos:
 
   # Black
   - repo: https://github.com/psf/black
-    rev: 23.11.0
+    rev: 24.4.2
     hooks:
       - id: black
 
   # Ruff
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.6
+    rev: v0.4.4
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
diff --git a/LICENSE.txt → LICENSE b/LICENSE.txt → LICENSE
diff --git a/MANIFEST.in b/MANIFEST.in
diff --git a/README.md b/README.md
@@ -7,11 +7,8 @@
 ## Installation
 
 1. Install MNE-python as instructed on
-   the [website](https://www.martinos.org/mne/stable/install_mne_python.html),
-   I would recommend to install in a separate conda environment with:
-   `conda env create -n mne_p -f environment.yml`
-2. `conda activate mne_p`
-3. `pip install https://github.com/marsipu/mne-pipeline-hd/zipball/main`
+   the [website](https://www.martinos.org/mne/stable/install_mne_python.html)
+2. Then run `pip install https://github.com/marsipu/mne-pipeline-hd/zipball/main` in the conda-enviroment you created in step 1 for MNE-Python.
 
 ## Update
 
@@ -21,7 +18,7 @@ or `pip install --upgrade mne-pipeline-hd` for the latest release.
 
 ## Start
 
-Run `mne_pipeline_hd` in your mne_pipeline-environment (`conda activate mne_p`)
+Run `mne_pipeline_hd` in your conda-environment where you installed mne-python and mne-pipeline-hd.
 
 **or**
 
@@ -64,7 +61,7 @@ installed.
 9. Push changes to your forked repository on GitHub: `git push`
 10. Make "New pull request" from your new feature branch
 
-You can always [write me](mailto:[email protected]), if you have questions
+You can always [write me an e-mail](mailto:[email protected]), if you have questions
 about the contribution-process
 or about the program-structure.
 

diff --git a/mne_pipeline_hd/__init__.py b/mne_pipeline_hd/__init__.py
@@ -5,8 +5,6 @@
 Github: https://github.com/marsipu/mne-pipeline-hd
 """
 
-from mne_pipeline_hd._version import __version__  # noqa: F401
-
 # Keep reference to Qt-objects without parent for tests
 # and to avoid garbage collection
 _object_refs = {

diff --git a/mne_pipeline_hd/_version.py b/mne_pipeline_hd/_version.py
diff --git a/mne_pipeline_hd/functions/operations.py b/mne_pipeline_hd/functions/operations.py
@@ -447,9 +447,7 @@ def find_6ch_binary_events(meeg, min_duration, shortest_event, adjust_timeline_b
                 and q not in events[:, 0] + 1
                 and q not in events[:, 0] - 1
             ):
-                events = np.append(
-                    events, [[q, 0, int(2**a + 2**b + 2**c)]], axis=0
-                )
+                events = np.append(events, [[q, 0, int(2**a + 2**b + 2**c)]], axis=0)
 
     for a, b in combinations(range(6), 2):
         equals = np.intersect1d(evs_tol[a], evs_tol[b])

diff --git a/mne_pipeline_hd/gui/function_widgets.py b/mne_pipeline_hd/gui/function_widgets.py
@@ -915,9 +915,9 @@ def populate_guitype_cmbx(self):
 
     def target_cmbx_changed(self, idx):
         if self.current_function:
-            self.add_pd_funcs.loc[
-                self.current_function, "target"
-            ] = self.target_cmbx.itemText(idx)
+            self.add_pd_funcs.loc[self.current_function, "target"] = (
+                self.target_cmbx.itemText(idx)
+            )
             self.target_chkl.setPixmap(self.yes_icon.pixmap(QSize(16, 16)))
             self.check_func_setup()
 
@@ -926,9 +926,9 @@ def tab_cmbx_changed(self, idx):
         self.populate_tab_cmbx()
         self.tab_cmbx.setCurrentIndex(idx)
         if self.current_function:
-            self.add_pd_funcs.loc[
-                self.current_function, "tab"
-            ] = self.tab_cmbx.itemText(idx)
+            self.add_pd_funcs.loc[self.current_function, "tab"] = (
+                self.tab_cmbx.itemText(idx)
+            )
             self.tab_chkl.setPixmap(self.yes_icon.pixmap(QSize(16, 16)))
             self.check_func_setup()
 
@@ -1040,7 +1040,7 @@ def get_functions(self):
         cf_path_string = compat.getopenfilename(
             self,
             "Choose the Python-File containing your function to import",
-            filter="Python-File (*.py)",
+            filters="Python-File (*.py)",
         )[0]
         if cf_path_string:
             self.file_path = Path(cf_path_string)
@@ -1057,7 +1057,7 @@ def edit_functions(self):
         cf_path_string = compat.getopenfilename(
             self,
             "Choose the Python-File containing the functions to edit",
-            filter="Python-File (*.py)",
+            filters="Python-File (*.py)",
             directory=self.ct.custom_pkg_path,
         )[0]
         if cf_path_string:
@@ -1339,9 +1339,9 @@ def load_selected_functions(self):
                                     param_key, "functions"
                                 ] += func_key
                             else:
-                                self.cf.add_pd_params.loc[
-                                    param_key, "functions"
-                                ] = func_key
+                                self.cf.add_pd_params.loc[param_key, "functions"] = (
+                                    func_key
+                                )
                         else:
                             self.cf.add_pd_params.loc[param_key, "functions"] = func_key
                     else:

diff --git a/mne_pipeline_hd/gui/loading_widgets.py b/mne_pipeline_hd/gui/loading_widgets.py
@@ -1835,13 +1835,13 @@ def get_file_tables(self, kind):
                         for parameter in result_dict:
                             if isinstance(result_dict[parameter], tuple):
                                 if result_dict[parameter][2]:
-                                    obj_pd.loc[
-                                        obj_name, path_type
-                                    ] = "critical_conflict"
+                                    obj_pd.loc[obj_name, path_type] = (
+                                        "critical_conflict"
+                                    )
                                 else:
-                                    obj_pd.loc[
-                                        obj_name, path_type
-                                    ] = "possible_conflict"
+                                    obj_pd.loc[obj_name, path_type] = (
+                                        "possible_conflict"
+                                    )
 
     def open_prog_dlg(self):
         # Create Progress-Dialog

diff --git a/mne_pipeline_hd/gui/parameter_widgets.py b/mne_pipeline_hd/gui/parameter_widgets.py
@@ -1255,8 +1255,6 @@ def __init__(
         # Title text
         self.add_text(0, 0.9, "", color="w", font_size=14, name="title")
 
-        self.show_view(roll=0, elevation=60, azimuth=70)
-
         self._set_annotations(parcellation)
         self._init_picking()
 
@@ -1274,9 +1272,7 @@ def _set_annotations(self, parcellation):
         labels = fsmri.get_labels(parcellation=parcellation)
         if parcellation == "Other":
             for label in labels:
-                self.add_label(
-                    label, borders=True, color="k", alpha=0.75, reset_camera=False
-                )
+                self.add_label(label, borders=True, color="k", alpha=0.75)
         else:
             self.add_annotation(
                 parcellation, borders=True, color="k", alpha=0.75, remove_existing=True
@@ -1362,7 +1358,7 @@ def _add_label_name(self, label_name, hemi, label=None):
                     label = lb
                     break
         if label is not None:
-            self.add_label(label, borders=False, reset_camera=False)
+            self.add_label(label, borders=False)
             self._shown_labels.append(label_name)
 
     def _remove_label_name(self, label_name, hemi):
@@ -1504,7 +1500,6 @@ def _subject_changed(self):
         self._selected_parc_labels += [
             lb for lb in old_selected_parc if lb in all_labels_exept_other
         ]
-        self.parc_label_list.content_changed()
 
         # Update pickers if open
         if self._parc_picker is not None and not self._parc_picker.isclosed():
@@ -1528,6 +1523,8 @@ def _parc_changed(self):
                 lb.name for lb in self._fsmri.labels[self._parcellation]
             ]
 
+        self.parc_label_list.content_changed()
+
         if self._parc_picker is not None and not self._parc_picker.isclosed():
             self._parc_picker._set_annotations(self._parcellation)
             for label_name in [

diff --git a/mne_pipeline_hd/tests/test_parameter_widgets.py b/mne_pipeline_hd/tests/test_parameter_widgets.py
@@ -198,7 +198,7 @@ def test_label_gui(qtbot, controller):
     assert "postcentral-lh" in dlg._parc_picker._shown_labels
     # Add label by clicking on plot
     qtbot.mouseClick(parc_plot, Qt.LeftButton, pos=parc_plot.rect().center(), delay=100)
-    assert "superiorfrontal-rh" in dlg._selected_parc_labels
+    assert "supramarginal-rh" in dlg._selected_parc_labels
     # Remove label by clicking on plot
     qtbot.mouseClick(parc_plot, Qt.LeftButton, pos=parc_plot.rect().center(), delay=100)
     assert "superiorfrontal-rh" not in dlg._selected_parc_labels
@@ -220,20 +220,20 @@ def test_label_gui(qtbot, controller):
     assert "lh.BA1-lh" in dlg._extra_picker._shown_labels
 
     # Change parcellation
-    dlg.parcellation_cmbx.setCurrentText("aparc.a2009s")
+    dlg.parcellation_cmbx.setCurrentText("aparc_sub")
     dlg._parc_changed()  # Only triggered by mouse click with .activated
     # Add label by clicking on plot
     qtbot.mouseClick(parc_plot, Qt.LeftButton, pos=parc_plot.rect().center(), delay=100)
-    assert "G_front_sup-rh" in dlg._selected_parc_labels
+    assert "supramarginal_9-rh" in dlg._selected_parc_labels
     # Add label by selecting from list
     toggle_checked_list_model(dlg.parc_label_list.model, value=1, row=0)
-    assert "G_Ins_lg_and_S_cent_ins-lh" in dlg._selected_parc_labels
+    assert "bankssts_1-lh" in dlg._selected_parc_labels
 
     final_selection = [
         "insula-lh",
         "postcentral-lh",
-        "G_front_sup-rh",
-        "G_Ins_lg_and_S_cent_ins-lh",
+        "supramarginal_9-rh",
+        "bankssts_1-lh",
         "lh.BA1-lh",
     ]
     # Check display widget

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [build-system]
-requires = ["setuptools", "wheel"]
-build-backend = "setuptools.build_meta"
+requires = ["hatchling", "hatch-vcs"]
+build-backend = "hatchling.build"
 
 [project]
 name = "mne-pipeline-hd"
@@ -10,26 +10,44 @@ authors = [
 description = "A Pipeline-GUI for MNE-Python from MEG-Lab Heidelberg"
 readme = "README.md"
 requires-python = ">=3.9"
-license = { "text" = "BSD-3-Clause" }
+license = { file = "LICENSE" }
 keywords = ["mne-python", "meg", "eeg", "pipeline", "gui", "heidelberg"]
 classifiers = [
-    "Programming Language :: Python :: 3",
+    "Programming Language :: Python",
     "License :: OSI Approved :: BSD License",
     "Operating System :: OS Independent",
     "Intended Audience :: Science/Research",
     "Topic :: Scientific/Engineering",
 ]
-dynamic = ["version", "dependencies"]
-
+dependencies = [
+    # MNE
+    "mne",
+    "mne-qt-browser",
+    "mne-connectivity",
+    # MNE related
+    "vtk", # needed for CIs
+    "nibabel", # needed for CIs
+    "pyvistaqt", # needed for CIs
+    "autoreject",
+    "h5io",
+    "h5netcdf",
+    # PyQt
+    "qtpy",
+    "pyqtdarktheme",
+    "pyobjc-framework-Cocoa; sys_platform == 'Darwin'",
+    # Other
+    "psutil",
+]
+dynamic = [ "version" ]
 [project.optional-dependencies]
 tests = [
-    "black",
-    "pre-commit",
-    "pydata-sphinx-theme",
     "pytest",
     "pytest-qt",
+    "pre-commit",
+    "black",
     "ruff",
-    "sphinx"
+    "sphinx",
+    "pydata-sphinx-theme",
 ]
 
 [project.urls]
@@ -39,9 +57,15 @@ Repository = "https://github.com/marsipu/mne-pipeline-hd.git"
 [project.scripts]
 mne_pipeline_hd = "mne_pipeline_hd.__main__:main"
 
-[tool.setuptools.dynamic]
-version = { attr = "mne_pipeline_hd.__version__" }
-dependencies = { file = "requirements.txt" }
+[tool.hatch.build]
+exclude = [
+    "/.*",
+    "/*.yml",
+]
+
+[tool.hatch.version]
+source = "vcs"
+raw-options = { version_scheme = "release-branch-semver" }
 
 [tool.black]
 line-lenght = 88

diff --git a/requirements.txt b/requirements.txt