diff --git a/Makefile b/Makefile new file mode 100644 index 00000000..8cb28ad3 --- /dev/null +++ b/Makefile @@ -0,0 +1,7 @@ +.PHONY: test + +test: + pytest test/test_core.py + pytest test/test_main.py + pytest test/test_fit.py + pytest test/test_cli.py diff --git a/peakipy/cli/check_panel.py b/peakipy/cli/check_panel.py index b60de1d7..44bc00d4 100644 --- a/peakipy/cli/check_panel.py +++ b/peakipy/cli/check_panel.py @@ -56,9 +56,15 @@ def get_cluster(cluster): return df_pane +@dataclass +class PlotContainer: + main_figure: pn.pane.Plotly + residual_figure: pn.pane.Plotly + + def create_plotly_pane(cluster, plane): data = data_singleton() - fig = check( + fig, residual_fig = check( fits=data.fits_path, data_path=data.data_path, clusters=[cluster], @@ -69,7 +75,8 @@ def create_plotly_pane(cluster, plane): fig["layout"].update(height=800, width=800) fig = fig.to_dict() - return pn.pane.Plotly(fig) + residual_fig = residual_fig.to_dict() + return pn.Column(pn.pane.Plotly(fig), pn.pane.Plotly(residual_fig)) app = typer.Typer() @@ -96,7 +103,7 @@ def create_check_panel( select_plane = pn.widgets.Select( name="Plane", options={f"{plane}": plane for plane in data.df.plane.unique()} ) - interactive_cluster_pane = pn.bind(get_cluster, select_cluster) + result_table_pane = pn.bind(get_cluster, select_cluster) interactive_plotly_pane = pn.bind( create_plotly_pane, cluster=select_cluster, plane=select_plane ) @@ -104,14 +111,15 @@ def create_check_panel( "Select a cluster and plane to look at from the dropdown menus" ) check_pane = pn.Card( - info_pane, - pn.Row(select_cluster, select_plane), + # info_pane, + # pn.Row(select_cluster, select_plane), pn.Row( pn.Column( - pn.Card(interactive_plotly_pane, title="Fitted cluster"), - pn.Card( - interactive_cluster_pane, title="Fitted parameters for cluster" + pn.Row( + pn.Card(interactive_plotly_pane, title="Fitted cluster"), + pn.Column(info_pane, select_cluster, select_plane), ), + pn.Card(result_table_pane, title="Fitted parameters for cluster"), ) ), title="Peakipy check", diff --git a/peakipy/cli/edit.py b/peakipy/cli/edit.py index 0d85bd96..47fbe766 100644 --- a/peakipy/cli/edit.py +++ b/peakipy/cli/edit.py @@ -17,21 +17,14 @@ import panel as pn -from bokeh.io import curdoc from bokeh.events import ButtonClick, DoubleTap -from bokeh.layouts import row, column, grid -from bokeh.models import ColumnDataSource, Tabs, TabPanel, InlineStyleSheet +from bokeh.layouts import row, column +from bokeh.models import ColumnDataSource from bokeh.models.tools import HoverTool from bokeh.models.widgets import ( Slider, Select, Button, - DataTable, - TableColumn, - NumberFormatter, - NumberEditor, - IntEditor, - SelectEditor, TextInput, RadioButtonGroup, CheckboxGroup, @@ -136,9 +129,15 @@ def tabulator_columns(self): ] return columns + @property + def tabulator_non_editable_columns(self): + editors = {"X_RADIUS_PPM": None, "Y_RADIUS_PPM": None} + return editors + def make_tabulator_widget(self): self.tablulator_widget = pn.widgets.Tabulator( self.peakipy_data.df[self.tabulator_columns], + editors=self.tabulator_non_editable_columns, ) return self.tablulator_widget @@ -321,10 +320,7 @@ def setup_plot(self): self.contour_start = TextInput( value="%.2e" % self.thres, title="Contour level:", width=100 ) - # contour_factor = Slider(title="contour factor", value=1.20, start=1., end=2.,step=0.05) self.contour_start.on_change("value", self.update_contour) - # for w in [contour_num,contour_start,contour_factor]: - # w.on_change("value",update_contour) #  plot mask outlines el = self.p.ellipse( @@ -540,13 +536,6 @@ def fit_selected(self, event): selectionIndex = self.source.selected.indices current = self.peakipy_data.df.iloc[selectionIndex] - # self.peakipy_data.df.loc[selectionIndex, "X_RADIUS_PPM"] = ( - # self.slider_X_RADIUS.value - # ) - # self.peakipy_data.df.loc[selectionIndex, "Y_RADIUS_PPM"] = ( - # self.slider_Y_RADIUS.value - # ) - self.peakipy_data.df.loc[selectionIndex, "X_DIAMETER_PPM"] = ( current["X_RADIUS_PPM"] * 2.0 ) diff --git a/peakipy/cli/edit_panel.py b/peakipy/cli/edit_panel.py index de63f8a4..04b853d0 100644 --- a/peakipy/cli/edit_panel.py +++ b/peakipy/cli/edit_panel.py @@ -102,8 +102,8 @@ def fit_peaks_button_click(event): button.on_click(fit_peaks_button_click) def update_source_selected_indices(event): - print(event) - print(bs.tablulator_widget.selection) + # print(event) + # print(bs.tablulator_widget.selection) bs.source.selected.indices = bs.tablulator_widget.selection bs.tablulator_widget.on_click(update_source_selected_indices) diff --git a/peakipy/cli/main.py b/peakipy/cli/main.py index 2ecb064c..849ab610 100644 --- a/peakipy/cli/main.py +++ b/peakipy/cli/main.py @@ -215,10 +215,6 @@ def read( """ - # verbose_mode = args.get("--verb") - # if verbose_mode: - # print("Using arguments:", args) - clust_args = { "struc_el": struc_el, "struc_size": struc_size, @@ -241,7 +237,6 @@ def read( posF1=y_ppm_column_name, posF2=x_ppm_column_name, ) - # peaks.adaptive_clusters(block_size=151,offset=0) case peaklist_format.a3: peaks = Peaklist( @@ -292,9 +287,6 @@ def read( if fuda: peaks.to_fuda() - # if verbose_mode: - # print(data.head()) - match outfmt.value: case "csv": outname = outname.with_suffix(".csv") @@ -1053,12 +1045,10 @@ def create_matplotlib_figure( # axes will appear inverted ax.view_init(30, 120) - # names = ",".join(plane.assignment) title = f"Plane={plot_data.plane_id},Cluster={plot_data.plane_lineshape_parameters.clustid.iloc[0]}" plt.title(title) print(f"[green]Plotting: {title}[/green]") out_str = "Volumes (Heights)\n===========\n" - # chi2s = [] for _, row in plot_data.plane_lineshape_parameters.iterrows(): out_str += f"{row.assignment} = {row.amp:.3e} ({row.height:.3e})\n" if label: @@ -1199,10 +1189,23 @@ def create_plotly_surfaces(plot_data: PlottingDataForPlane): def create_residual_contours(plot_data: PlottingDataForPlane): - data = [] - contours = go.Contour(x=plot_data.x_plot, y=plot_data.y_plot, z=plot_data.residual) - data.append(contours) - return data + contours = go.Contour( + x=plot_data.x_plot[0], y=plot_data.y_plot.T[0], z=plot_data.residual + ) + return contours + + +def create_residual_figure(plot_data: PlottingDataForPlane): + data = create_residual_contours(plot_data) + fig = go.Figure(data=data) + fig.update_layout( + title="Fit residuals", + xaxis_title=f"{plot_data.pseudo3D.f2_label} ppm", + yaxis_title=f"{plot_data.pseudo3D.f1_label} ppm", + xaxis=dict(range=[plot_data.x_plot.max(), plot_data.x_plot.min()]), + yaxis=dict(range=[plot_data.y_plot.max(), plot_data.y_plot.min()]), + ) + return fig def create_plotly_figure(plot_data: PlottingDataForPlane): @@ -1210,9 +1213,6 @@ def create_plotly_figure(plot_data: PlottingDataForPlane): surfaces = create_plotly_surfaces(plot_data) # residuals = create_residual_contours(plot_data) fig = go.Figure(data=lines + surfaces) - # layout = go.Layout(showlegend=True) - # fig.update_layout(layout) - # fig.update_traces(showlegend=True) fig = update_axis_ranges(fig, plot_data) return fig @@ -1222,6 +1222,8 @@ def update_axis_ranges(fig, plot_data: PlottingDataForPlane): scene=dict( xaxis=dict(range=[plot_data.x_plot.max(), plot_data.x_plot.min()]), yaxis=dict(range=[plot_data.y_plot.max(), plot_data.y_plot.min()]), + xaxis_title=f"{plot_data.pseudo3D.f2_label} ppm", + yaxis_title=f"{plot_data.pseudo3D.f1_label} ppm", annotations=make_annotations(plot_data), ) ) @@ -1474,41 +1476,19 @@ def check( # fig = create_plotly_figure(plot_data) if plotly: fig = create_plotly_figure(plot_data) - return fig + residual_fig = create_residual_figure(plot_data) + return fig, residual_fig else: plt = matplotlib.pyplot create_matplotlib_figure( plot_data, pdf, individual, label, ccpn_flag, show ) - # surf = pn.pane.plotly.Plotly(fig) - # app = pn.Column(surf) - # app.show(threaded=True) if first: break run_log() -@app.command(help="Interactive Bokeh dashboard for configuring fitting parameters") -def edit( - peaklist_path: Path, - data_path: Path, - test: bool = False, -): - from bokeh.util.browser import view - from bokeh.server.server import Server - from .edit import BokehScript - - run_log() - bs = BokehScript(peaklist_path=peaklist_path, data_path=data_path) - if not test: - server = Server({"/edit": bs.init}) - server.start() - print("[green]Opening peakipy: Edit fits on http://localhost:5006/edit[/green]") - server.io_loop.add_callback(server.show, "/edit") - server.io_loop.start() - - def make_yaml_file(name, yaml_file=yaml_file): if os.path.exists(name): print(f"Copying {name} to {name}.bak") diff --git a/peakipy/core.py b/peakipy/core.py index 4d4dad95..f5b2084f 100644 --- a/peakipy/core.py +++ b/peakipy/core.py @@ -23,7 +23,7 @@ import json from datetime import datetime from pathlib import Path -from typing import List, Optional +from typing import List from enum import Enum from dataclasses import dataclass, field @@ -1515,28 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] [package.dependencies] @@ -1832,13 +1832,13 @@ extra = ["pygments (>=2.12)"] [[package]] name = "pyparsing" -version = "3.1.1" +version = "3.1.2" description = "pyparsing module - Classes and methods to define and execute parsing grammars" optional = false python-versions = ">=3.6.8" files = [ - {file = "pyparsing-3.1.1-py3-none-any.whl", hash = "sha256:32c7c0b711493c72ff18a981d24f28aaf9c1fb7ed5e9667c9e84e3db623bdbfb"}, - {file = "pyparsing-3.1.1.tar.gz", hash = "sha256:ede28a1a32462f5a9705e07aea48001a08f7cf81a021585011deba701581a0db"}, + {file = "pyparsing-3.1.2-py3-none-any.whl", hash = "sha256:f9db75911801ed778fe61bb643079ff86601aca99fcae6345aa67292038fb742"}, + {file = "pyparsing-3.1.2.tar.gz", hash = "sha256:a1bac0ce561155ecc3ed78ca94d3c9378656ad4c94c1270de543f621420f94ad"}, ] [package.extras] @@ -1868,13 +1868,13 @@ testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "no [[package]] name = "python-dateutil" -version = "2.8.2" +version = "2.9.0.post0" description = "Extensions to the standard Python datetime module" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7" files = [ - {file = "python-dateutil-2.8.2.tar.gz", hash = "sha256:0123cacc1627ae19ddf3c27a5de5bd67ee4586fbdd6440d9748f8abb483d3e86"}, - {file = "python_dateutil-2.8.2-py2.py3-none-any.whl", hash = "sha256:961d03dc3453ebbc59dbdea9e4e11c5651520a876d0f4db161e8674aae935da9"}, + {file = "python-dateutil-2.9.0.post0.tar.gz", hash = "sha256:37dd54208da7e1cd875388217d5e00ebd4179249f90fb72437e91a35459a0ad3"}, + {file = "python_dateutil-2.9.0.post0-py2.py3-none-any.whl", hash = "sha256:a8b2bc7bffae282281c8140a97d3aa9c14da0b136dfe83f850eea9a5f7470427"}, ] [package.dependencies] @@ -2153,18 +2153,18 @@ test = ["asv", "gmpy2", "hypothesis", "mpmath", "pooch", "pytest", "pytest-cov", [[package]] name = "setuptools" -version = "69.1.1" +version = "69.2.0" description = "Easily download, build, install, upgrade, and uninstall Python packages" optional = false python-versions = ">=3.8" files = [ - {file = "setuptools-69.1.1-py3-none-any.whl", hash = "sha256:02fa291a0471b3a18b2b2481ed902af520c69e8ae0919c13da936542754b4c56"}, - {file = "setuptools-69.1.1.tar.gz", hash = "sha256:5c0806c7d9af348e6dd3777b4f4dbb42c7ad85b190104837488eab9a7c945cf8"}, + {file = "setuptools-69.2.0-py3-none-any.whl", hash = "sha256:c21c49fb1042386df081cb5d86759792ab89efca84cf114889191cd09aacc80c"}, + {file = "setuptools-69.2.0.tar.gz", hash = "sha256:0ff4183f8f42cd8fa3acea16c45205521a4ef28f73c6391d8a25e92893134f2e"}, ] [package.extras] docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier"] -testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "packaging (>=23.2)", "pip (>=19.1)", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-ruff (>=0.2.1)", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"] +testing = ["build[virtualenv]", "filelock (>=3.4.0)", "importlib-metadata", "ini2toml[lite] (>=0.9)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "mypy (==1.9)", "packaging (>=23.2)", "pip (>=19.1)", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-ruff (>=0.2.1)", "pytest-timeout", "pytest-xdist (>=3)", "tomli", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"] testing-integration = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "packaging (>=23.2)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"] [[package]] @@ -2330,18 +2330,18 @@ telegram = ["requests"] [[package]] name = "traitlets" -version = "5.14.1" +version = "5.14.2" description = "Traitlets Python configuration system" optional = false python-versions = ">=3.8" files = [ - {file = "traitlets-5.14.1-py3-none-any.whl", hash = "sha256:2e5a030e6eff91737c643231bfcf04a65b0132078dad75e4936700b213652e74"}, - {file = "traitlets-5.14.1.tar.gz", hash = "sha256:8585105b371a04b8316a43d5ce29c098575c2e477850b62b848b964f1444527e"}, + {file = "traitlets-5.14.2-py3-none-any.whl", hash = "sha256:fcdf85684a772ddeba87db2f398ce00b40ff550d1528c03c14dbf6a02003cd80"}, + {file = "traitlets-5.14.2.tar.gz", hash = "sha256:8cdd83c040dab7d1dee822678e5f5d100b514f7b72b01615b26fc5718916fdf9"}, ] [package.extras] docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"] -test = ["argcomplete (>=3.0.3)", "mypy (>=1.7.0)", "pre-commit", "pytest (>=7.0,<7.5)", "pytest-mock", "pytest-mypy-testing"] +test = ["argcomplete (>=3.0.3)", "mypy (>=1.7.0)", "pre-commit", "pytest (>=7.0,<8.1)", "pytest-mock", "pytest-mypy-testing"] [[package]] name = "typer" diff --git a/test/test_cli.py b/test/test_cli.py index 4b4b2062..95aec4b4 100644 --- a/test/test_cli.py +++ b/test/test_cli.py @@ -154,22 +154,3 @@ def test_check_main_with_pv_pv(protein_L): individual=True, ) peakipy.cli.main.check(**args) - - -# def test_edit_with_default(protein_L): -# args = dict( -# peaklist_path=protein_L / Path("peaks.csv"), -# data_path=protein_L / Path("test1.ft2"), -# test=True, -# ) -# peakipy.cli.main.edit(**args) - - -# if __name__ == "__main__": - -# unittest.TestLoader.sortTestMethodsUsing = None -# unittest.main(verbosity=2) -# to_clean = ["test.csv", "peakipy.config", "run_log.txt", "fits.csv"] -# for i in to_clean: -# print(f"Deleting: {i}") -# shutil.rmtree(i)