Update workflows

.github/workflows/build.yml

@@ -15,20 +15,19 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu, macos, windows]
-        python-version: [3.8, 3.9, "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
     name: ${{ matrix.os }} - py${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}-latest
     defaults:
       run:
         shell: bash
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Setup Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-          #architecture: 'x64'
       - name: Install dependencies
         run: |
           python -m pip install --progress-bar off --upgrade pip setuptools wheel

.github/workflows/code-style.yml

@@ -14,25 +14,18 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
-      - name: Setup Python 3.9
-        uses: actions/setup-python@v4
+        uses: actions/checkout@v4
+      - name: Setup Python 3.10
+        uses: actions/setup-python@v5
         with:
-          python-version: '3.9'
+          python-version: '3.10'
           architecture: 'x64'
       - name: Install dependencies
         run: |
           python -m pip install --progress-bar off --upgrade pip setuptools wheel
           python -m pip install --progress-bar off .[style]
       - name: Run Ruff
         run: ruff check .
-      - name: Run isort
-        uses: isort/isort-action@master
-      - name: Run black
-        uses: psf/black@stable
-        with:
-          options: "--check --verbose"
-          version: "23.10.1"
       - name: Run codespell
         uses: codespell-project/actions-codespell@master
         with:

.github/workflows/doc.yml

@@ -20,10 +20,10 @@ jobs:
         uses: actions/checkout@v4
         with:
           path: ./main
-      - name: Setup Python 3.9
-        uses: actions/setup-python@v4
+      - name: Setup Python 3.10
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: '3.10'
           architecture: 'x64'
       - name: Install package
         run: |
@@ -56,7 +56,7 @@ jobs:
           name: doc-dev
           path: ./doc-dev
       - name: Deploy dev documentation
-        uses: peaceiris/actions-gh-pages@v3
+        uses: peaceiris/actions-gh-pages@v4
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: ./doc-dev

.github/workflows/publish.yml

@@ -10,11 +10,11 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
-      - name: Setup Python 3.9
-        uses: actions/setup-python@v4
+        uses: actions/checkout@v4
+      - name: Setup Python 3.10
+        uses: actions/setup-python@v5
         with:
-          python-version: '3.9'
+          python-version: '3.10'
           architecture: 'x64'
       - name: Install dependencies
         run: |

fsqc/checkCCSize.py

@@ -70,7 +70,7 @@ def checkCCSize(subjects_dir, subject):
     relative_cc = sum_cc / intracranial_volume
 
     logging.info(
-        "Relative size of the corpus callosum is " + "{:.4}".format(relative_cc)
+        "Relative size of the corpus callosum is " + f"{relative_cc:.4}"
     )
 
     # Return

fsqc/checkContrast.py

@@ -49,20 +49,23 @@ def checkContrast(subjects_dir, subject):
     # Check if files exist
     path_pct_lh = os.path.join(subjects_dir, subject, "surf", "lh.w-g.pct.mgh")
     if not os.path.exists(path_pct_lh):
-        warnings.warn("WARNING: could not find " + path_pct_lh + ", returning NaNs")
+        warnings.warn("WARNING: could not find " + path_pct_lh + ", returning NaNs",
+            stacklevel = 2)
         return numpy.nan
 
     path_pct_rh = os.path.join(subjects_dir, subject, "surf", "rh.w-g.pct.mgh")
     if not os.path.exists(path_pct_rh):
-        warnings.warn("WARNING: could not find " + path_pct_rh + ", returning NaNs")
+        warnings.warn("WARNING: could not find " + path_pct_rh + ", returning NaNs",
+            stacklevel = 2)
         return numpy.nan
 
     path_label_cortex_lh = os.path.join(
         subjects_dir, subject, "label", "lh.cortex.label"
     )
     if not os.path.exists(path_label_cortex_lh):
         warnings.warn(
-            "WARNING: could not find " + path_label_cortex_lh + ", returning NaNs"
+            "WARNING: could not find " + path_label_cortex_lh + ", returning NaNs",
+            stacklevel = 2
         )
         return numpy.nan
 
@@ -71,7 +74,8 @@ def checkContrast(subjects_dir, subject):
     )
     if not os.path.exists(path_label_cortex_rh):
         warnings.warn(
-            "WARNING: could not find " + path_label_cortex_rh + ", returning NaNs"
+            "WARNING: could not find " + path_label_cortex_rh + ", returning NaNs",
+            stacklevel = 2
         )
         return numpy.nan
 
@@ -91,14 +95,14 @@ def checkContrast(subjects_dir, subject):
     con_lh_std = numpy.std(con_lh)
     con_lh_snr = con_lh_mean / con_lh_std
     logging.info(
-        "WM/GM contrast SNR for the left hemisphere: " + "{:.4}".format(con_lh_snr)
+        "WM/GM contrast SNR for the left hemisphere: " + f"{con_lh_snr:.4}"
     )
 
     con_rh_mean = numpy.mean(con_rh)
     con_rh_std = numpy.std(con_rh)
     con_rh_snr = con_rh_mean / con_rh_std
     logging.info(
-        "WM/GM contrast SNR for the right hemisphere: " + "{:.4}".format(con_rh_snr)
+        "WM/GM contrast SNR for the right hemisphere: " + f"{con_rh_snr:.4}"
     )
 
     # Return

fsqc/checkRotation.py

@@ -50,7 +50,8 @@ def checkRotation(subjects_dir, subject):
 
     if importlib.util.find_spec("transforms3d") is None:
         warnings.warn(
-            "WARNING: 'transforms3d' package required for running this script, returning NaNs."
+            "WARNING: 'transforms3d' package required for running this script, returning NaNs.",
+            stacklevel = 2
         )
         return np.nan, np.nan, np.nan
     else:
@@ -64,12 +65,13 @@ def checkRotation(subjects_dir, subject):
         warnings.warn(
             "WARNING: could not open "
             + os.path.join(subjects_dir, subject, "mri", "transforms", "talairach.lta")
-            + ", returning NaNs."
+            + ", returning NaNs.",
+            stacklevel = 2
         )
         return np.nan, np.nan, np.nan
 
     with open(
-        os.path.join(subjects_dir, subject, "mri", "transforms", "talairach.lta"), "r"
+        os.path.join(subjects_dir, subject, "mri", "transforms", "talairach.lta")
     ) as datafile:
         lines = datafile.readlines()
 
@@ -102,11 +104,11 @@ def checkRotation(subjects_dir, subject):
 
     logging.info(
         "Found Talairach rotation angles: x = "
-        + "{:.3}".format(rot_x)
+        + f"{rot_x:.3}"
         + ", y = "
-        + "{:.3}".format(rot_y)
+        + f"{rot_y:.3}"
         + ", z = "
-        + "{:.3}".format(rot_z)
+        + f"{rot_z:.3}"
         + " radians.",
     )
 

fsqc/checkSNR.py

@@ -77,7 +77,8 @@ def checkSNR(
         norm_data = norm.get_fdata()
     else:
         warnings.warn(
-            "WARNING: could not open " + path_reference_image + ", returning NaNs."
+            "WARNING: could not open " + path_reference_image + ", returning NaNs.",
+            stacklevel = 2
         )
         return np.nan, np.nan
 
@@ -86,7 +87,8 @@ def checkSNR(
         aseg = nib.load(path_aseg)
         data_aseg = aseg.get_fdata()
     else:
-        warnings.warn("WARNING: could not open " + path_aseg + ", returning NaNs.")
+        warnings.warn("WARNING: could not open " + path_aseg + ", returning NaNs.",
+            stacklevel = 2)
         return np.nan, np.nan
 
     path_aparc_aseg = os.path.join(subjects_dir, subject, "mri", aparc_image)
@@ -95,7 +97,8 @@ def checkSNR(
         data_aparc_aseg = inseg.get_fdata()
     else:
         warnings.warn(
-            "WARNING: could not open " + path_aparc_aseg + ", returning NaNs."
+            "WARNING: could not open " + path_aparc_aseg + ", returning NaNs.",
+            stacklevel = 2
         )
         return np.nan, np.nan
 
@@ -122,7 +125,7 @@ def checkSNR(
     signal_wm_mean = np.mean(signal_wm)
     signal_wm_std = np.std(signal_wm)
     wm_snr = signal_wm_mean / signal_wm_std
-    logging.info("White matter signal to noise ratio: " + "{:.4}".format(wm_snr))
+    logging.info("White matter signal to noise ratio: " + f"{wm_snr:.4}")
 
     # Process gray matter image
 
@@ -143,7 +146,7 @@ def checkSNR(
     signal_gm_mean = np.mean(signal_gm)
     signal_gm_std = np.std(signal_gm)
     gm_snr = signal_gm_mean / signal_gm_std
-    logging.info("Gray matter signal to noise ratio: " + "{:.4}".format(gm_snr))
+    logging.info("Gray matter signal to noise ratio: " + f"{gm_snr:.4}")
 
     # Return
     return wm_snr, gm_snr

fsqc/checkTopology.py

@@ -61,10 +61,11 @@ def checkTopology(subjects_dir, subject):
     path_log_file = os.path.join(subjects_dir, subject, "scripts", "recon-all.log")
 
     if os.path.exists(path_log_file):
-        with open(path_log_file, "r") as logfile:
+        with open(path_log_file) as logfile:
             lines_log_file = logfile.read().splitlines()
     else:
-        warnings.warn("WARNING: could not find " + path_log_file + ", returning NaNs.")
+        warnings.warn("WARNING: could not find " + path_log_file + ", returning NaNs.",
+            stacklevel = 2)
         return np.nan, np.nan, np.nan, np.nan, np.nan, np.nan
 
     # Initialize

fsqc/createScreenshots.py

@@ -12,16 +12,16 @@ def createScreenshots(
     OUTFILE,
     INTERACTIVE=True,
     LAYOUT=None,
-    BASE=["default"],
-    OVERLAY=["default"],
+    BASE="default",
+    OVERLAY="default",
     LABELS=None,
-    SURF=["default"],
-    SURFCOLOR=["default"],
-    VIEWS=["default"],
+    SURF="default",
+    SURFCOLOR="default",
+    VIEWS="default",
     XLIM=None,
     YLIM=None,
     BINARIZE=False,
-    ORIENTATION=["radiological"],
+    ORIENTATION=None,
 ):
     """
     Function to create screenshots.
@@ -39,31 +39,34 @@ def createScreenshots(
     LAYOUT : str, optional
         The layout, default is None.
     BASE : list, optional
-        The base, default is ["default"].
+        The base, default is "default".
+        Load norm.mgz as default.
     OVERLAY : list, optional
-        The overlay, default is ["default"].
+        The overlay, default is "default".
+        Load aseg.mgz as default.
     LABELS : None or str, optional
         The labels, default is None.
     SURF : list, optional
-        The surface, default is ["default"].
+        The surface, default is "default".
     SURFCOLOR : list, optional
-        The surface color, default is ["default"].
+        The surface color, default is "default".
     VIEWS : list, optional
-        The views, default is ["default"].
+        The views, default is "default".
     XLIM : None or list, optional
         The x limits, default is None.
     YLIM : None or list, optional
         The y limits, default is None.
     BINARIZE : bool, optional
         Flag for binarization, default is False.
     ORIENTATION : list, optional
-        The orientation, default is ["radiological"].
+        The orientation, default is None.
+        Will use ["radiological"] per default.
 
     Notes
     -----
-    BASE, VIEWS must be lists, can be ["default"].
+    BASE, VIEWS must be lists, can be "default".
 
-    OVERLAY, SURF, SURFCOLOR can be lists or None, can be ["default"].
+    OVERLAY, SURF, SURFCOLOR can be lists, None, or "default".
 
     XLIM, YLIM can be lists of list two-element numeric lists or None; if given,
     length must match length of VIEWS. x and y refer to final image dimensions,
@@ -92,6 +95,9 @@ def computeLayout(n):
     import nibabel as nb
     import numpy as np
 
+    if ORIENTATION is None:
+        ORIENTATION = ["radiological"]
+
     if not INTERACTIVE:
         matplotlib.use("Agg")
 
@@ -115,22 +121,22 @@ def computeLayout(n):
     # -----------------------------------------------------------------------------
     # import image data
 
-    if BASE == ["default"]:
+    if BASE == "default":
         norm = nb.load(os.path.join(SUBJECTS_DIR, SUBJECT, "mri", "norm.mgz"))
     else:
         norm = nb.load(BASE[0])
 
     if OVERLAY is None:
         aseg = None
-    elif OVERLAY == ["default"]:
+    elif OVERLAY == "default":
         aseg = nb.load(os.path.join(SUBJECTS_DIR, SUBJECT, "mri", "aseg.mgz"))
     else:
         aseg = nb.load(OVERLAY[0])
 
     # -----------------------------------------------------------------------------
     # import surface data
 
-    if SURF == ["default"]:
+    if SURF == "default":
         surflist = [
             os.path.join(SUBJECTS_DIR, SUBJECT, "surf", "lh.white"),
             os.path.join(SUBJECTS_DIR, SUBJECT, "surf", "rh.white"),
@@ -146,9 +152,9 @@ def computeLayout(n):
         for i in range(len(surflist)):
             surf.append(nb.freesurfer.io.read_geometry(surflist[i], read_metadata=True))
 
-    if SURFCOLOR == ["default"] and SURF == ["default"]:
+    if SURFCOLOR == "default" and SURF == "default":
         surfcolor = ["yellow", "yellow", "red", "red"]
-    elif SURFCOLOR == ["default"] and SURF != ["default"]:
+    elif SURFCOLOR == "default" and SURF != "default":
         surfcolor = ["yellow"] * len(surf)
     else:
         surfcolor = SURFCOLOR
@@ -211,7 +217,7 @@ def computeLayout(n):
     # -----------------------------------------------------------------------------
     # determine VIEWS
 
-    if VIEWS == ["default"]:
+    if VIEWS == "default":
         CutsRRAS = [("x", -10), ("x", 10), ("y", 0), ("z", 0)]
     else:
         CutsRRAS = VIEWS
@@ -678,7 +684,8 @@ def computeLayout(n):
                         sortIdx = np.delete(sortIdx, findIdx[0, 0])
                     elif findIdx.shape[0] > 1:
                         warnings.warn(
-                            "WARNING: a problem occurred with the surface overlays"
+                            "WARNING: a problem occurred with the surface overlays",
+                            stacklevel = 2
                         )
                 # now final plot
                 axs[axsx, axsy].plot(