Migrate to python/3.10 and bokeh/3.8

* use TabPanel instead of Panel * use scatter(marker=...) instead of specific marker function * replace gridplot with grid
2026-02-06 18:25:23 +01:00
parent 36cb92f6d5
commit e6e97be58a
13 changed files with 120 additions and 100 deletions
--- a/.gitea/workflows/deploy.yaml
+++ b/.gitea/workflows/deploy.yaml
@@ -21,7 +21,7 @@ jobs:
        uses: actions/checkout@v4
      - run: $CONDA/bin/conda build --no-anaconda-upload --output-folder $BUILD_DIR ./conda-recipe
      - run: $CONDA/bin/conda remove --name test --all --keep-env -y
-      - run: $CONDA/bin/conda install --name test --channel $BUILD_DIR python=3.8 pyzebra -y
+      - run: $CONDA/bin/conda install --name test --channel $BUILD_DIR python=3.10 pyzebra -y
      - run: sudo systemctl restart pyzebra-test.service

  prod-env:
@@ -34,7 +34,7 @@ jobs:
        uses: actions/checkout@v4
      - run: $CONDA/bin/conda build --token ${{ secrets.ANACONDA_TOKEN }} --output-folder $BUILD_DIR ./conda-recipe
      - run: $CONDA/bin/conda remove --name prod --all --keep-env -y
-      - run: $CONDA/bin/conda install --name prod --channel $BUILD_DIR python=3.8 pyzebra -y
+      - run: $CONDA/bin/conda install --name prod --channel $BUILD_DIR python=3.10 pyzebra -y
      - run: sudo systemctl restart pyzebra-prod.service

  cleanup:
@@ -42,4 +42,4 @@ jobs:
    needs: [test-env, prod-env]
    if: always()
    steps:
-      - run: $CONDA/bin/conda build purge-all
+      - run: $CONDA/bin/conda build purge-all
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -5,12 +5,12 @@ build-backend = "hatchling.build"
 [project]
 name = "pyzebra"
 dynamic = ["version"]  # version will be read from __init__.py
-requires-python = ">=3.8"
+requires-python = ">=3.10"
 dependencies = [
    "numpy",
    "scipy",
    "h5py",
-    "bokeh ~=2.4",
+    "bokeh ~=3.8",
    "numba",
    "lmfit >=1.0.2",
 ]
--- a/pyzebra/app/main.py
+++ b/pyzebra/app/main.py
@@ -3,8 +3,8 @@ import logging
 from io import StringIO

 from bokeh.io import curdoc
-from bokeh.layouts import column, row
-from bokeh.models import Button, Panel, Tabs, TextAreaInput, TextInput
+from bokeh.layouts import column
+from bokeh.models import Button, TabPanel, Tabs, TextAreaInput, TextInput

 import pyzebra
 from pyzebra.app import (
@@ -55,14 +55,14 @@ logger.setLevel(logging.INFO)
 logger.addHandler(handler)
 doc.logger = logger

-log_textareainput = TextAreaInput(title="Logging output:")
+log_textareainput = TextAreaInput(title="Logging output:", sizing_mode="stretch_both")


 def proposal_textinput_callback(_attr, _old, _new):
    apply_button.disabled = False


-proposal_textinput = TextInput(title="Proposal number:", name="")
+proposal_textinput = TextInput(title="Proposal number:", name="", sizing_mode="stretch_width")
 proposal_textinput.on_change("value_input", proposal_textinput_callback)
 doc.proposal_textinput = proposal_textinput

@@ -82,7 +82,7 @@ def apply_button_callback():
    proposal_textinput.name = proposal_path


-apply_button = Button(label="Apply", button_type="primary")
+apply_button = Button(label="Apply", button_type="primary", width=300)
 apply_button.on_click(apply_button_callback)

 # Final layout
@@ -90,7 +90,7 @@ doc.add_root(
    column(
        Tabs(
            tabs=[
-                Panel(child=column(proposal_textinput, apply_button), title="user config"),
+                TabPanel(child=column(proposal_textinput, apply_button), title="user config"),
                panel_hdf_viewer.create(),
                panel_hdf_anatric.create(),
                panel_ccl_prepare.create(),
@@ -102,7 +102,8 @@ doc.add_root(
                panel_spind.create(),
            ]
        ),
-        row(log_textareainput, sizing_mode="scale_both"),
+        log_textareainput,
+        sizing_mode="stretch_height",
    )
 )

--- a/pyzebra/app/panel_ccl_compare.py
+++ b/pyzebra/app/panel_ccl_compare.py
@@ -15,13 +15,13 @@ from bokeh.models import (
    Div,
    FileInput,
    MultiSelect,
-    Panel,
    RadioGroup,
    Select,
    Spacer,
    Span,
    Spinner,
    TableColumn,
+    TabPanel,
    TextAreaInput,
    Whisker,
 )
@@ -250,7 +250,8 @@ def create():
    )

    scatter1_source = ColumnDataSource(dict(x=[0], y=[0], y_upper=[0], y_lower=[0]))
-    plot.circle(
+    plot.scatter(
+        marker="circle",
        source=scatter1_source,
        line_color="steelblue",
        fill_color="steelblue",
@@ -259,7 +260,8 @@ def create():
    plot.add_layout(Whisker(source=scatter1_source, base="x", upper="y_upper", lower="y_lower"))

    scatter2_source = ColumnDataSource(dict(x=[0], y=[0], y_upper=[0], y_lower=[0]))
-    plot.circle(
+    plot.scatter(
+        marker="circle",
        source=scatter2_source,
        line_color="firebrick",
        fill_color="firebrick",
@@ -535,4 +537,4 @@ def create():
        row(fitpeak_controls, app_fitctrl.result_textarea),
    )

-    return Panel(child=tab_layout, title="ccl compare")
+    return TabPanel(child=tab_layout, title="ccl compare")
--- a/pyzebra/app/panel_ccl_integrate.py
+++ b/pyzebra/app/panel_ccl_integrate.py
@@ -11,11 +11,11 @@ from bokeh.models import (
    ColumnDataSource,
    DataTable,
    Div,
-    Panel,
    Select,
    Spacer,
    Span,
    TableColumn,
+    TabPanel,
    TextAreaInput,
    Whisker,
 )
@@ -121,8 +121,12 @@ def create():
    )

    scatter_source = ColumnDataSource(dict(x=[0], y=[0], y_upper=[0], y_lower=[0]))
-    plot.circle(
-        source=scatter_source, line_color="steelblue", fill_color="steelblue", legend_label="data"
+    plot.scatter(
+        marker="circle",
+        source=scatter_source,
+        line_color="steelblue",
+        fill_color="steelblue",
+        legend_label="data",
    )
    plot.add_layout(Whisker(source=scatter_source, base="x", upper="y_upper", lower="y_lower"))

@@ -364,4 +368,4 @@ def create():
        row(fitpeak_controls, app_fitctrl.result_textarea),
    )

-    return Panel(child=tab_layout, title="ccl integrate")
+    return TabPanel(child=tab_layout, title="ccl integrate")
--- a/pyzebra/app/panel_ccl_prepare.py
+++ b/pyzebra/app/panel_ccl_prepare.py
@@ -20,11 +20,11 @@ from bokeh.models import (
    MultiSelect,
    NormalHead,
    NumericInput,
-    Panel,
    RadioGroup,
    Select,
    Spacer,
    Spinner,
+    TabPanel,
    TextAreaInput,
    TextInput,
 )
@@ -89,7 +89,7 @@ def create():
            ang_lims = pyzebra.read_geom_file(fileobj)
        _update_ang_lims(ang_lims)

-    open_geom_div = Div(text="Open GEOM:")
+    open_geom_div = Div(text="Open GEOM:", margin=(12, 5, 5, 5))
    open_geom = FileInput(accept=".geom", width=200)
    open_geom.on_change("value", open_geom_callback)

@@ -99,7 +99,7 @@ def create():
            params = pyzebra.read_cfl_file(fileobj)
            _update_params(params)

-    open_cfl_div = Div(text="Open CFL:")
+    open_cfl_div = Div(text="Open CFL:", margin=(12, 5, 5, 5))
    open_cfl = FileInput(accept=".cfl", width=200)
    open_cfl.on_change("value", open_cfl_callback)

@@ -109,7 +109,7 @@ def create():
            cif_data = pyzebra.read_cif_file(fileobj)
            _update_params(cif_data)

-    open_cif_div = Div(text="Open CIF:")
+    open_cif_div = Div(text="Open CIF:", margin=(12, 5, 5, 5))
    open_cif = FileInput(accept=".cif", width=200)
    open_cif.on_change("value", open_cif_callback)

@@ -145,7 +145,7 @@ def create():
    ub_matrix_calc = Button(label="UB matrix:", button_type="primary", width=100)
    ub_matrix_calc.on_click(ub_matrix_calc_callback)

-    ub_matrix = TextInput(title="\u200B", width=600)
+    ub_matrix = TextInput(title="\u200b", width=600)

    ranges_div = Div(text="Ranges:", margin=(5, 5, 0, 5))
    ranges_hkl = TextInput(title="HKL", value="-25 25 -25 25 -25 25", width=250)
@@ -153,7 +153,7 @@ def create():

    magstruct_div = Div(text="Magnetic structure:", margin=(5, 5, 0, 5))
    magstruct_lattice = TextInput(title="lattice", width=100)
-    magstruct_kvec = TextAreaInput(title="k vector", width=150)
+    magstruct_kvec = TextAreaInput(title="k vector", rows=3, width=150)

    def sorting0_callback(_attr, _old, new):
        sorting_0_dt.value = ANG_CHUNK_DEFAULTS[new]
@@ -321,7 +321,7 @@ def create():
    plot_list.on_click(plot_list_callback)

    # Plot
-    upload_data_div = Div(text="Open hkl/mhkl data:")
+    upload_data_div = Div(text="Open hkl/mhkl data:", margin=(12, 5, 5, 5))
    upload_data = FileInput(accept=".hkl,.mhkl", multiple=True, width=200)

    min_grid_x = -10
@@ -667,7 +667,7 @@ def create():
    )

    k_vectors = TextAreaInput(
-        title="k vectors:", value="0.0 0.0 0.0\n0.5 0.0 0.0\n0.5 0.5 0.0", width=150
+        title="k vectors:", value="0.0 0.0 0.0\n0.5 0.0 0.0\n0.5 0.5 0.0", rows=3, width=150
    )
    tol_k_ni = NumericInput(title="k tolerance:", value=0.01, mode="float", width=100)

@@ -721,4 +721,4 @@ def create():

    tab_layout = row(column1_layout, column2_layout)

-    return Panel(child=tab_layout, title="ccl prepare")
+    return TabPanel(child=tab_layout, title="ccl prepare")
--- a/pyzebra/app/panel_hdf_anatric.py
+++ b/pyzebra/app/panel_hdf_anatric.py
@@ -10,9 +10,9 @@ from bokeh.models import (
    Button,
    Div,
    FileInput,
-    Panel,
    Select,
    Spacer,
+    TabPanel,
    Tabs,
    TextAreaInput,
    TextInput,
@@ -82,7 +82,7 @@ def create():
        with io.BytesIO(base64.b64decode(new)) as file:
            _load_config_file(file)

-    upload_div = Div(text="Open .xml config:")
+    upload_div = Div(text="Open .xml config:", margin=(12, 5, 5, 5))
    upload_button = FileInput(accept=".xml", width=200)
    upload_button.on_change("value", upload_button_callback)

@@ -91,7 +91,9 @@ def create():
    def logfile_textinput_callback(_attr, _old, new):
        config.logfile = new

-    logfile_textinput = TextInput(title="Logfile:", value="logfile.log")
+    logfile_textinput = TextInput(
+        title="Logfile:", value="logfile.log", sizing_mode="stretch_width"
+    )
    logfile_textinput.on_change("value", logfile_textinput_callback)

    def logfile_verbosity_callback(_attr, _old, new):
@@ -104,7 +106,7 @@ def create():
    def filelist_type_callback(_attr, _old, new):
        config.filelist_type = new

-    filelist_type = Select(title="File List:", options=["TRICS", "SINQ"], width=100)
+    filelist_type = Select(title="File List:", options=["TRICS", "SINQ"], value="TRICS", width=100)
    filelist_type.on_change("value", filelist_type_callback)

    def filelist_format_textinput_callback(_attr, _old, new):
@@ -116,7 +118,7 @@ def create():
    def filelist_datapath_textinput_callback(_attr, _old, new):
        config.filelist_datapath = new

-    filelist_datapath_textinput = TextInput(title="datapath:")
+    filelist_datapath_textinput = TextInput(title="datapath:", sizing_mode="stretch_width")
    filelist_datapath_textinput.on_change("value", filelist_datapath_textinput_callback)

    def filelist_ranges_textareainput_callback(_attr, _old, new):
@@ -125,7 +127,9 @@ def create():
            ranges.append(re.findall(r"\b\d+\b", line))
        config.filelist_ranges = ranges

-    filelist_ranges_textareainput = TextAreaInput(title="ranges:", rows=1)
+    filelist_ranges_textareainput = TextAreaInput(
+        title="ranges:", rows=1, sizing_mode="stretch_width"
+    )
    filelist_ranges_textareainput.on_change("value", filelist_ranges_textareainput_callback)

    # ---- crystal
@@ -144,7 +148,7 @@ def create():
    def ub_textareainput_callback(_attr, _old, new):
        config.crystal_UB = new

-    ub_textareainput = TextAreaInput(title="UB matrix:", height=100)
+    ub_textareainput = TextAreaInput(title="UB matrix:", height=100, sizing_mode="stretch_width")
    ub_textareainput.on_change("value", ub_textareainput_callback)

    def zeroOM_textinput_callback(_attr, _old, new):
@@ -170,7 +174,10 @@ def create():
        config.dataFactory_implementation = new

    dataFactory_implementation_select = Select(
-        title="DataFactory implement.:", options=DATA_FACTORY_IMPLEMENTATION, width=145
+        title="DataFactory implement.:",
+        options=DATA_FACTORY_IMPLEMENTATION,
+        value=DATA_FACTORY_IMPLEMENTATION[0],
+        width=145,
    )
    dataFactory_implementation_select.on_change("value", dataFactory_implementation_select_callback)

@@ -201,7 +208,10 @@ def create():
        config.reflectionPrinter_format = new

    reflectionPrinter_format_select = Select(
-        title="ReflectionPrinter format:", options=REFLECTION_PRINTER_FORMATS, width=145
+        title="ReflectionPrinter format:",
+        options=REFLECTION_PRINTER_FORMATS,
+        value=REFLECTION_PRINTER_FORMATS[0],
+        width=145,
    )
    reflectionPrinter_format_select.on_change("value", reflectionPrinter_format_select_callback)

@@ -325,14 +335,14 @@ def create():

    algorithm_params = Tabs(
        tabs=[
-            Panel(
+            TabPanel(
                child=column(
                    row(threshold_textinput, shell_textinput, steepness_textinput),
                    row(duplicateDistance_textinput, maxequal_textinput, aps_window_textinput),
                ),
                title="Peak Search",
            ),
-            Panel(
+            TabPanel(
                child=column(
                    row(adm_window_textinput, border_textinput, minWindow_textinput),
                    row(reflectionFile_textinput, targetMonitor_textinput, smoothSize_textinput),
@@ -360,7 +370,7 @@ def create():
            with open(os.path.join(temp_dir, config.reflectionPrinter_file)) as f_res:
                output_res.value = f_res.read()

-    process_button = Button(label="Process", button_type="primary")
+    process_button = Button(label="Process", button_type="primary", width=300)
    process_button.on_click(process_button_callback)

    output_log = TextAreaInput(title="Logfile output:", height=320, width=465, disabled=True)
@@ -368,8 +378,8 @@ def create():
    output_config = TextAreaInput(title="Current config:", height=320, width=465, disabled=True)

    general_params_layout = column(
-        row(column(Spacer(height=2), upload_div), upload_button),
-        row(logfile_textinput, logfile_verbosity),
+        row(upload_div, upload_button),
+        row(logfile_textinput, logfile_verbosity, sizing_mode="stretch_width"),
        row(filelist_type, filelist_format_textinput),
        filelist_datapath_textinput,
        filelist_ranges_textareainput,
@@ -387,7 +397,7 @@ def create():

    tab_layout = row(
        general_params_layout,
-        column(output_config, algorithm_params, row(process_button)),
+        column(output_config, algorithm_params, process_button),
        column(output_log, output_res),
    )

@@ -396,4 +406,4 @@ def create():

    doc.add_periodic_callback(update_config, 1000)

-    return Panel(child=tab_layout, title="hdf anatric")
+    return TabPanel(child=tab_layout, title="hdf anatric")
--- a/pyzebra/app/panel_hdf_param_study.py
+++ b/pyzebra/app/panel_hdf_param_study.py
@@ -4,8 +4,9 @@ import os

 import numpy as np
 from bokeh.io import curdoc
-from bokeh.layouts import column, gridplot, row
+from bokeh.layouts import column, grid, row
 from bokeh.models import (
+    BoxZoomTool,
    Button,
    CellEditor,
    CheckboxGroup,
@@ -17,12 +18,15 @@ from bokeh.models import (
    MultiSelect,
    NumberEditor,
    NumberFormatter,
-    Panel,
+    PanTool,
    Range1d,
+    ResetTool,
    Select,
    Spinner,
    TableColumn,
+    TabPanel,
    Tabs,
+    WheelZoomTool,
 )
 from bokeh.plotting import figure

@@ -293,6 +297,7 @@ def create():
    frame_range = Range1d(0, 1, bounds=(0, 1))
    scanning_motor_range = Range1d(0, 1, bounds=(0, 1))
    color_mapper_proj = LinearColorMapper()
+    shared_tools = [PanTool(), BoxZoomTool(), WheelZoomTool(maintain_focus=False), ResetTool()]

    det_x_range = Range1d(0, IMAGE_W, bounds=(0, IMAGE_W))
    proj_x_plot = figure(
@@ -304,12 +309,11 @@ def create():
        extra_y_ranges={"scanning_motor": scanning_motor_range},
        height=540,
        width=IMAGE_PLOT_W - 3,
-        tools="pan,box_zoom,wheel_zoom,reset",
-        active_scroll="wheel_zoom",
+        tools=shared_tools,
+        toolbar_location=None,
    )

    proj_x_plot.yaxis.major_label_orientation = "vertical"
-    proj_x_plot.toolbar.tools[2].maintain_focus = False

    proj_x_image_source = ColumnDataSource(
        dict(image=[np.zeros((1, 1), dtype="float32")], x=[0], y=[0], dw=[IMAGE_W], dh=[1])
@@ -328,13 +332,13 @@ def create():
        extra_y_ranges={"scanning_motor": scanning_motor_range},
        height=540,
        width=IMAGE_PLOT_H + 22,
-        tools="pan,box_zoom,wheel_zoom,reset",
-        active_scroll="wheel_zoom",
+        tools=shared_tools,
+        active_scroll=shared_tools[2],
    )

    proj_y_plot.yaxis.y_range_name = "scanning_motor"
    proj_y_plot.yaxis.major_label_orientation = "vertical"
-    proj_y_plot.toolbar.tools[2].maintain_focus = False
+    proj_y_plot.toolbar.logo = None

    proj_y_image_source = ColumnDataSource(
        dict(image=[np.zeros((1, 1), dtype="float32")], x=[0], y=[0], dw=[IMAGE_H], dh=[1])
@@ -418,7 +422,7 @@ def create():
    )

    param_scatter_source = ColumnDataSource(dict(x=[], y=[]))
-    param_plot.circle(source=param_scatter_source)
+    param_plot.scatter(marker="circle", source=param_scatter_source)

    param_plot.toolbar.logo = None

@@ -487,18 +491,13 @@ def create():
        proc_all_button,
    )

-    layout_proj = column(
-        gridplot(
-            [[proj_x_plot, proj_y_plot]], toolbar_options={"logo": None}, toolbar_location="right"
-        ),
-        layout_controls,
-    )
+    layout_proj = column(grid([[proj_x_plot, proj_y_plot]]), layout_controls)

    # Plot tabs
    plots = Tabs(
        tabs=[
-            Panel(child=layout_proj, title="single scan"),
-            Panel(child=column(param_plot, row(fit_param_select)), title="parameter plot"),
+            TabPanel(child=layout_proj, title="single scan"),
+            TabPanel(child=column(param_plot, row(fit_param_select)), title="parameter plot"),
        ]
    )

@@ -515,4 +514,4 @@ def create():

    tab_layout = column(row(import_layout, scan_layout, plots))

-    return Panel(child=tab_layout, title="hdf param study")
+    return TabPanel(child=tab_layout, title="hdf param study")
--- a/pyzebra/app/panel_hdf_viewer.py
+++ b/pyzebra/app/panel_hdf_viewer.py
@@ -5,9 +5,10 @@ import os
 import numpy as np
 from bokeh.events import MouseEnter
 from bokeh.io import curdoc
-from bokeh.layouts import column, gridplot, row
+from bokeh.layouts import column, grid, row
 from bokeh.models import (
    BoxEditTool,
+    BoxZoomTool,
    Button,
    CellEditor,
    CheckboxGroup,
@@ -21,15 +22,18 @@ from bokeh.models import (
    LogColorMapper,
    MultiSelect,
    NumberFormatter,
-    Panel,
+    PanTool,
    RadioGroup,
    Range1d,
+    ResetTool,
    Select,
    Slider,
    Spacer,
    Spinner,
    TableColumn,
+    TabPanel,
    Tabs,
+    WheelZoomTool,
 )
 from bokeh.plotting import figure

@@ -579,6 +583,7 @@ def create():
    scanning_motor_range = Range1d(0, 1, bounds=(0, 1))
    lin_color_mapper_proj = LinearColorMapper(low=0, high=1)
    log_color_mapper_proj = LogColorMapper(low=0, high=1)
+    shared_tools = [PanTool(), BoxZoomTool(), WheelZoomTool(maintain_focus=False), ResetTool()]

    det_x_range = Range1d(0, IMAGE_W, bounds=(0, IMAGE_W))
    gamma_range = Range1d(0, 1, bounds=(0, 1))
@@ -592,12 +597,11 @@ def create():
        extra_y_ranges={"scanning_motor": scanning_motor_range},
        height=540,
        width=IMAGE_PLOT_W - 3,
-        tools="pan,box_zoom,wheel_zoom,reset",
-        active_scroll="wheel_zoom",
+        tools=shared_tools,
+        toolbar_location=None,
    )

    proj_x_plot.yaxis.major_label_orientation = "vertical"
-    proj_x_plot.toolbar.tools[2].maintain_focus = False

    proj_x_plot.add_layout(LinearAxis(x_range_name="gamma", axis_label="Gamma, deg"), place="above")

@@ -620,13 +624,13 @@ def create():
        extra_y_ranges={"scanning_motor": scanning_motor_range},
        height=540,
        width=IMAGE_PLOT_H + 22,
-        tools="pan,box_zoom,wheel_zoom,reset",
-        active_scroll="wheel_zoom",
+        tools=shared_tools,
+        active_scroll=shared_tools[2],
    )

    proj_y_plot.yaxis.y_range_name = "scanning_motor"
    proj_y_plot.yaxis.major_label_orientation = "vertical"
-    proj_y_plot.toolbar.tools[2].maintain_focus = False
+    proj_y_plot.toolbar.logo = None

    proj_y_plot.add_layout(LinearAxis(x_range_name="nu", axis_label="Nu, deg"), place="above")

@@ -890,8 +894,8 @@ def create():
    # Final layout
    peak_tables = Tabs(
        tabs=[
-            Panel(child=events_table, title="Actual peak center"),
-            Panel(child=detcenter_table, title="Peak in the detector center"),
+            TabPanel(child=events_table, title="Actual peak center"),
+            TabPanel(child=detcenter_table, title="Peak in the detector center"),
        ]
    )

@@ -905,7 +909,7 @@ def create():
        row(file_open_button, file_append_button),
    )

-    layout_image = column(gridplot([[proj_v, None], [plot, proj_h]], merge_tools=False))
+    layout_image = column(grid([[proj_v, None], [plot, proj_h]]))
    colormap_layout = column(
        row(colormap_select, column(Spacer(height=15), colormap_scale_rg)),
        main_auto_checkbox,
@@ -919,11 +923,7 @@ def create():
        row(column(add_event_button, remove_event_button), peak_tables),
    )

-    layout_proj = column(
-        gridplot(
-            [[proj_x_plot, proj_y_plot]], toolbar_options={"logo": None}, toolbar_location="right"
-        )
-    )
+    layout_proj = grid([[proj_x_plot, proj_y_plot]])

    scan_layout = column(
        scan_table,
@@ -937,7 +937,7 @@ def create():
        column(roi_avg_plot, layout_image),
    )

-    return Panel(child=tab_layout, title="hdf viewer")
+    return TabPanel(child=tab_layout, title="hdf viewer")


 def calculate_hkl(scan, index):
--- a/pyzebra/app/panel_param_study.py
+++ b/pyzebra/app/panel_param_study.py
@@ -15,12 +15,12 @@ from bokeh.models import (
    HoverTool,
    LinearColorMapper,
    NumberEditor,
-    Panel,
    Range1d,
    Select,
    Spacer,
    Span,
    TableColumn,
+    TabPanel,
    Tabs,
    TextAreaInput,
    Whisker,
@@ -218,8 +218,12 @@ def create():
    )

    scatter_source = ColumnDataSource(dict(x=[0], y=[0], y_upper=[0], y_lower=[0]))
-    plot.circle(
-        source=scatter_source, line_color="steelblue", fill_color="steelblue", legend_label="data"
+    plot.scatter(
+        marker="circle",
+        source=scatter_source,
+        line_color="steelblue",
+        fill_color="steelblue",
+        legend_label="data",
    )
    plot.add_layout(Whisker(source=scatter_source, base="x", upper="y_upper", lower="y_lower"))

@@ -274,7 +278,7 @@ def create():
    ov_param_plot.image(source=ov_param_image_source, color_mapper=color_mapper)

    ov_param_scatter_source = ColumnDataSource(dict(x=[], y=[]))
-    ov_param_plot.dot(source=ov_param_scatter_source, size=15, color="black")
+    ov_param_plot.scatter(marker="dot", source=ov_param_scatter_source, size=15, color="black")

    ov_param_plot.toolbar.logo = None

@@ -288,7 +292,7 @@ def create():
    )

    param_scatter_source = ColumnDataSource(dict(x=[], y=[], y_upper=[], y_lower=[]))
-    param_plot.circle(source=param_scatter_source)
+    param_plot.scatter(marker="circle", source=param_scatter_source)
    param_plot.add_layout(
        Whisker(source=param_scatter_source, base="x", upper="y_upper", lower="y_lower")
    )
@@ -304,10 +308,10 @@ def create():
    # Plot tabs
    plots = Tabs(
        tabs=[
-            Panel(child=plot, title="single scan"),
-            Panel(child=ov_plot, title="overview"),
-            Panel(child=ov_param_plot, title="overview map"),
-            Panel(child=column(param_plot, row(fit_param_select)), title="parameter plot"),
+            TabPanel(child=plot, title="single scan"),
+            TabPanel(child=ov_plot, title="overview"),
+            TabPanel(child=ov_param_plot, title="overview map"),
+            TabPanel(child=column(param_plot, row(fit_param_select)), title="parameter plot"),
        ]
    )

@@ -515,4 +519,4 @@ def create():
        row(fitpeak_controls, app_fitctrl.result_textarea),
    )

-    return Panel(child=tab_layout, title="param study")
+    return TabPanel(child=tab_layout, title="param study")
--- a/pyzebra/app/panel_plot_data.py
+++ b/pyzebra/app/panel_plot_data.py
@@ -16,11 +16,11 @@ from bokeh.models import (
    LinearColorMapper,
    LogColorMapper,
    NumericInput,
-    Panel,
    RadioGroup,
    Select,
    Spacer,
    Spinner,
+    TabPanel,
    TextInput,
 )
 from bokeh.plotting import figure
@@ -35,10 +35,10 @@ def create():
    doc = curdoc()
    log = doc.logger
    _update_slice = None
-    measured_data_div = Div(text="Measured <b>HDF</b> data:")
+    measured_data_div = Div(text="Measured <b>HDF</b> data:", margin=(12, 5, 5, 5))
    measured_data = FileInput(accept=".hdf", multiple=True, width=200)

-    upload_hkl_div = Div(text="Open hkl/mhkl data:")
+    upload_hkl_div = Div(text="Open hkl/mhkl data:", margin=(12, 5, 5, 5))
    upload_hkl_fi = FileInput(accept=".hkl,.mhkl", multiple=True, width=200)

    def _prepare_plotting():
@@ -439,4 +439,4 @@ def create():

    tab_layout = row(column1_layout, Spacer(width=50), column2_layout)

-    return Panel(child=tab_layout, title="plot data")
+    return TabPanel(child=tab_layout, title="plot data")
--- a/pyzebra/app/panel_spind.py
+++ b/pyzebra/app/panel_spind.py
@@ -9,9 +9,9 @@ from bokeh.models import (
    Button,
    ColumnDataSource,
    DataTable,
-    Panel,
    Spinner,
    TableColumn,
+    TabPanel,
    TextAreaInput,
    TextInput,
 )
@@ -156,7 +156,7 @@ def create():

            results_table_source.data.update(spind_res)

-    process_button = Button(label="Process", button_type="primary")
+    process_button = Button(label="Process", button_type="primary", width=300)
    process_button.on_click(process_button_callback)

    if doc.spind_path is None:
@@ -220,4 +220,4 @@ def create():

    doc.add_periodic_callback(update_npeaks_spinner, 1000)

-    return Panel(child=tab_layout, title="spind")
+    return TabPanel(child=tab_layout, title="spind")
--- a/pyzebra/app/plot_hkl.py
+++ b/pyzebra/app/plot_hkl.py
@@ -35,10 +35,10 @@ class PlotHKL:
        log = doc.logger

        _update_slice = None
-        measured_data_div = Div(text="Measured <b>CCL</b> data:")
+        measured_data_div = Div(text="Measured <b>CCL</b> data:", margin=(12, 5, 5, 5))
        measured_data = FileInput(accept=".ccl", multiple=True, width=200)

-        upload_hkl_div = Div(text="Open hkl/mhkl data:")
+        upload_hkl_div = Div(text="Open hkl/mhkl data:", margin=(12, 5, 5, 5))
        upload_hkl_fi = FileInput(accept=".hkl,.mhkl", multiple=True, width=200)

        min_grid_x = -10
@@ -515,7 +515,7 @@ class PlotHKL:
        )

        k_vectors = TextAreaInput(
-            title="k vectors:", value="0.0 0.0 0.0\n0.5 0.0 0.0\n0.5 0.5 0.0", width=150
+            title="k vectors:", value="0.0 0.0 0.0\n0.5 0.0 0.0\n0.5 0.5 0.0", rows=3, width=150
        )
        res_mult_ni = NumericInput(title="Resolution mult:", value=10, mode="int", width=100)
        tol_k_ni = NumericInput(title="k tolerance:", value=0.01, mode="float", width=100)