icplot 0.1.3__tar.gz → 0.1.5__tar.gz

{icplot-0.1.3/src/icplot.egg-info → icplot-0.1.5}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: icplot
-Version: 0.1.3
+Version: 0.1.5
 Summary: Utilities for generating plots and graphics for technical reports.
 Author-email: "James Grogan, Irish Centre for High End Computing" <james.grogan@ichec.ie>
 Project-URL: Repository, https://git.ichec.ie/performance/toolshed/icplot
@@ -11,12 +11,12 @@ Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
 Classifier: Operating System :: OS Independent
 Classifier: Topic :: System :: Distributed Computing
-Requires-Python: >=3.8
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: wand
 Requires-Dist: matplotlib
-Requires-Dist: iccore==0.1.8
+Requires-Dist: iccore==0.1.9
 Provides-Extra: test
 Requires-Dist: pytest; extra == "test"
 Requires-Dist: pytest-cov; extra == "test"
@@ -28,6 +28,7 @@ Requires-Dist: pylint; extra == "test"
 Provides-Extra: cairo
 Requires-Dist: pycairo; extra == "cairo"
 Requires-Dist: CairoSVG; extra == "cairo"
+Dynamic: license-file
 
 # icplot
 
@@ -38,8 +39,9 @@ This is a library used at [The Irish Centre for High End Computing (ICHEC)](http
 The project has support for:
 
 * Coverting image formats between pdf, svg and png
-* Building pdf output from tex files, including tikz.
+* Building pdf and png output from tex files, including tikz.
 * Generating plots based on a serializable data model to support reproducible research
+* Generating mermaid plots
 
 To covert between image formats you can do:
 
@@ -53,6 +55,12 @@ To render a Tex tikz image as pdf and png you can do:
 icplot convert --source my_tikz.tex
 ```
 
+To render a Mermaid plot as png you can do:
+
+``` shell
+icplot convert --source my_mermaid.mmd
+```
+
 To generate a plot or collection of plots from a yaml description you can do:
 
 ``` shell

{icplot-0.1.3 → icplot-0.1.5}/README.md

@@ -7,8 +7,9 @@ This is a library used at [The Irish Centre for High End Computing (ICHEC)](http
 The project has support for:
 
 * Coverting image formats between pdf, svg and png
-* Building pdf output from tex files, including tikz.
+* Building pdf and png output from tex files, including tikz.
 * Generating plots based on a serializable data model to support reproducible research
+* Generating mermaid plots
 
 To covert between image formats you can do:
 
@@ -22,6 +23,12 @@ To render a Tex tikz image as pdf and png you can do:
 icplot convert --source my_tikz.tex
 ```
 
+To render a Mermaid plot as png you can do:
+
+``` shell
+icplot convert --source my_mermaid.mmd
+```
+
 To generate a plot or collection of plots from a yaml description you can do:
 
 ``` shell

{icplot-0.1.3 → icplot-0.1.5}/pyproject.toml

@@ -1,12 +1,12 @@
 [project]
 name = "icplot"
-version = "0.1.3"
+version = "0.1.5"
 authors = [
   { name="James Grogan, Irish Centre for High End Computing", email="james.grogan@ichec.ie" },
 ]
 description = "Utilities for generating plots and graphics for technical reports."
 readme = "README.md"
-requires-python = ">=3.8"
+requires-python = ">=3.10"
 classifiers = [
     "Development Status :: 3 - Alpha",
     "Programming Language :: Python :: 3",
@@ -18,7 +18,7 @@ keywords = ["Publishing", "Technical Reports", "Graphics"]
 
 dependencies = ["wand",
 	       "matplotlib",
-	       "iccore==0.1.8"]
+	       "iccore==0.1.9"]
 
 [project.urls]
 Repository = "https://git.ichec.ie/performance/toolshed/icplot"

{icplot-0.1.3 → icplot-0.1.5}/src/icplot/convert.py

@@ -1,8 +1,12 @@
+"""
+Module supporting conversion between various formats
+"""
+
 import logging
 import os
 from pathlib import Path
 
-from icplot import tex
+from icplot import tex, mermaid
 from icplot.tex import TexBuildSettings
 from icplot.image_utils import pdf_to_png, svg_to_pdf, svg_to_png
 
@@ -10,7 +14,9 @@ from icplot.image_utils import pdf_to_png, svg_to_pdf, svg_to_png
 logger = logging.getLogger(__name__)
 
 
-def convert(source: Path, target: Path, build_dir: Path):
+def convert(
+    source: Path, target: Path, build_dir: Path, extra_config: Path | None = None
+):
     """
     Convert the file at source outputing at target and using
     the source and target file extensions as format hints.
@@ -36,5 +42,10 @@ def convert(source: Path, target: Path, build_dir: Path):
             target = Path(os.getcwd())
         settings = TexBuildSettings(source, build_dir, target)
         tex.build(settings)
+    elif source.suffix == ".mmd":
+        if not target:
+            target = Path(os.getcwd())
+        settings = TexBuildSettings(source, build_dir, target)
+        mermaid.convert(source, target, extra_config)
 
     logger.info("Finished conversion")

{icplot-0.1.3 → icplot-0.1.5}/src/icplot/graph/axis.py

@@ -30,6 +30,10 @@ class PlotAxis(BaseModel, frozen=True):
     label: str = ""
     ticks: Range | None = None
     scale: str = "linear"
+    text_fontsize: int = 10
+    tick_fontsize: int = 10
+    max_ticks: int = 0
+    limits: dict = {}
 
     @property
     def resolved_ticks(self) -> list:

{icplot-0.1.3 → icplot-0.1.5}/src/icplot/graph/matplotlib.py

@@ -8,10 +8,12 @@ import matplotlib as mpl  # NOQA
 default_backend = mpl.get_backend()
 mpl.use("Agg")
 import matplotlib.pyplot as plt  # NOQA
+from matplotlib.ticker import FuncFormatter  # NOQA
 
 from icplot.color import ColorMap, Color  # NOQA
 from .series import PlotSeries, LinePlotSeries, ScatterPlotSeries, ImageSeries  # NOQA
 from .plot import Plot, GridPlot, get_series_colors  # NOQA
+from .axis import PlotAxis  # NOQA
 
 
 class MatplotlibColorMap(ColorMap):
@@ -23,26 +25,74 @@ class MatplotlibColorMap(ColorMap):
         super().__init__(label, mpl.colormaps[label])
 
 
-def _set_decorations(axs, plot: Plot):
-    ax = axs[0]
+def str_exact_values_formatter(x, pos):
+    """
+    When using log scale, axis ticks come out as scientific notation by default,
+    then when using plain formatter values less than 1 come out as 0. A way around
+    this is this custom formatter.
+    """
+    if x.is_integer():
+        return str(int(x))
+    else:
+        return str(x)
+
+
+def _set_legend_decorations(axs, plot):
     if plot.legend.lower() != "none":
-        lines = []
-        for axis in axs:
-            for line in axis.lines:
-                lines.append(line)
-        ax.legend(handles=lines, loc=plot.legend)
-    if plot.x_axis.label:
-        ax.set_xlabel(plot.x_axis.label)
-    for idx, y_axis in enumerate(plot.y_axes):
+        if len(axs) == 1:
+            axs[0].legend(loc=plot.legend, frameon=False, fontsize=plot.legend_fontsize)
+        else:
+            axs[0].legend(
+                loc="upper left", frameon=False, fontsize=plot.legend_fontsize
+            )
+            axs[1].legend(
+                loc="upper right", frameon=False, fontsize=plot.legend_fontsize
+            )
+
+
+def _set_x_axis_decorations(x_axis: PlotAxis, ax):
+    ax.set_yscale(x_axis.scale)
+    ax.tick_params(axis="x", labelsize=x_axis.tick_fontsize)
+    if x_axis.label:
+        ax.set_xlabel(x_axis.label, fontsize=x_axis.text_fontsize)
+    if x_axis.ticks:
+        ax.set_xticks(x_axis.resolved_ticks)
+    if x_axis.max_ticks:
+        ax.xaxis.set_major_locator(plt.MaxNLocator(x_axis.max_ticks))
+    for key, item in x_axis.limits.items():
+        if key == "left" or key == "xmin":
+            ax.set_xlim(xmin=item)
+        elif key == "right" or key == "xmax":
+            ax.set_xlim(xmax=item)
+
+
+def _set_y_axes_decorations(y_axes: list[PlotAxis], axs):
+    for idx, y_axis in enumerate(y_axes):
         axs[idx].set_yscale(y_axis.scale)
+        axs[idx].tick_params(axis="y", labelsize=y_axis.tick_fontsize)
+        if y_axis.scale == "log":
+            formatter = FuncFormatter(str_exact_values_formatter)
+            axs[idx].yaxis.set_major_formatter(formatter)
         if y_axis.label:
-            axs[idx].set_ylabel(y_axis.label)
+            axs[idx].set_ylabel(y_axis.label, fontsize=y_axis.text_fontsize)
         if y_axis.ticks:
             axs[idx].set_yticks(y_axis.resolved_ticks)
-    if plot.x_axis.ticks:
-        ax.set_xticks(plot.x_axis.resolved_ticks)
+        if y_axis.max_ticks:
+            axs[idx].yaxis.set_major_locator(plt.MaxNLocator(y_axis.max_ticks))
+        for key, item in y_axis.limits.items():
+            if key == "bottom" or key == "ymin":
+                axs[idx].set_ylim(ymin=item)
+            elif key == "top" or key == "ymax":
+                axs[idx].set_ylim(ymax=item)
+
+
+def _set_decorations(axs, plot: Plot):
+    _set_legend_decorations(axs, plot)
+    _set_x_axis_decorations(plot.x_axis, axs[0])
+    _set_y_axes_decorations(plot.y_axes, axs)
     if plot.title:
-        ax.set_title(plot.title)
+        axs[0].set_title(plot.title, fontsize=plot.title_fontsize)
+    axs[0].set_aspect(plot.aspect)
 
 
 def _plot_line(axs, series: LinePlotSeries, color: Color | None):
@@ -55,10 +105,12 @@ def _plot_line(axs, series: LinePlotSeries, color: Color | None):
         render_color: list | None = color.as_list()
     else:
         render_color = None
-
-    ax.plot(
+    ax.errorbar(
         series.x,
         series.y,
+        xerr=series.x_err,
+        yerr=series.y_err,
+        capsize=series.err_capsize,
         label=series.label,
         color=render_color,
         marker=series.marker,

{icplot-0.1.3 → icplot-0.1.5}/src/icplot/graph/plot.py

@@ -18,13 +18,15 @@ class Plot(BaseModel, frozen=True):
     """
 
     title: str = ""
-    legend_label: str = ""
     name: str = ""
     x_axis: PlotAxis = PlotAxis()
     y_axes: list[PlotAxis] = [PlotAxis()]
     plot_type: str = ""
     series: list[PlotSeries] = []
     legend: str = "none"
+    aspect: str = "auto"
+    legend_fontsize: int = 10
+    title_fontsize: int = 10
 
 
 class GridPlot(Plot, frozen=True):
@@ -65,7 +67,7 @@ class GridPlot(Plot, frozen=True):
         return rows, cols, subplots
 
 
-def get_series_colors(cmap: ColorMap, plot: Plot) -> list[Color | None]:
+def get_series_colors(cmap: ColorMap, plot: Plot) -> list[Color]:
 
     count = 0
     num_colorable = len([s for s in plot.series if not s.highlight])
@@ -75,6 +77,6 @@ def get_series_colors(cmap: ColorMap, plot: Plot) -> list[Color | None]:
             color = cmap.get_color(count, num_colorable)
             count = count + 1
         else:
-            color = None
+            color = s.color
         colors.append(color)
     return colors

{icplot-0.1.3 → icplot-0.1.5}/src/icplot/graph/series.py

@@ -41,6 +41,9 @@ class LinePlotSeries(PlotSeries, frozen=True):
 
     x: list
     y: list
+    x_err: float | list[float] | list[list[float]] | None = None
+    y_err: float | list[float] | list[list[float]] | None = None
+    err_capsize: float = 2.0
     marker: str = "o"
     series_type: str = "line"
     drawstyle: str = "default"

{icplot-0.1.3 → icplot-0.1.5}/src/icplot/main_cli.py

@@ -20,7 +20,12 @@ def convert_cli(args):
     else:
         target = None
 
-    icplot.convert(args.source.resolve(), target, args.buid_dir.resolve())
+    if args.extra_config:
+        extra_config = Path(args.extra_config).resolve()
+    else:
+        extra_config = None
+
+    icplot.convert(args.source.resolve(), target, args.buid_dir.resolve(), extra_config)
 
 
 def plot_cli(args):
@@ -57,6 +62,12 @@ def main_cli():
         default=Path(os.getcwd()) / "_build/tikz",
         help="Path for build output",
     )
+    convert_parser.add_argument(
+        "--extra_config",
+        type=str,
+        default="",
+        help="Extra config for third party tooling, e.g. puppeteer for mermaid",
+    )
     convert_parser.set_defaults(func=convert_cli)
 
     plot_parser = subparsers.add_parser("plot")

icplot-0.1.5/src/icplot/mermaid.py

@@ -0,0 +1,39 @@
+"""
+Interface for generating mermaid plots.
+
+Mermaid must already be set up on the system, eg. via the npm ecosystem.
+"""
+
+import subprocess
+import shutil
+import os
+from pathlib import Path
+import logging
+
+
+logger = logging.getLogger(__name__)
+
+
+def has_mermaid() -> bool:
+    """
+    True if the mermaid cli is found in the environment
+    """
+
+    return bool(shutil.which("mmdc"))
+
+
+def convert(input_path: Path, work_dir: Path, browser_config: Path | None = None):
+
+    if not has_mermaid():
+        raise RuntimeError("Mermaid CLI 'mmdc' not found in path.")
+
+    os.makedirs(work_dir, exist_ok=True)
+
+    output_path = work_dir / f"{input_path.stem}.png"
+
+    logger.info("Converting: %s to %s", input_path, output_path)
+
+    cmd = f"mmdc -i {input_path} -o {output_path}"
+    if browser_config:
+        cmd += f" -p {browser_config}"
+    subprocess.run(cmd, shell=True, check=True)

{icplot-0.1.3 → icplot-0.1.5/src/icplot.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: icplot
-Version: 0.1.3
+Version: 0.1.5
 Summary: Utilities for generating plots and graphics for technical reports.
 Author-email: "James Grogan, Irish Centre for High End Computing" <james.grogan@ichec.ie>
 Project-URL: Repository, https://git.ichec.ie/performance/toolshed/icplot
@@ -11,12 +11,12 @@ Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
 Classifier: Operating System :: OS Independent
 Classifier: Topic :: System :: Distributed Computing
-Requires-Python: >=3.8
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: wand
 Requires-Dist: matplotlib
-Requires-Dist: iccore==0.1.8
+Requires-Dist: iccore==0.1.9
 Provides-Extra: test
 Requires-Dist: pytest; extra == "test"
 Requires-Dist: pytest-cov; extra == "test"
@@ -28,6 +28,7 @@ Requires-Dist: pylint; extra == "test"
 Provides-Extra: cairo
 Requires-Dist: pycairo; extra == "cairo"
 Requires-Dist: CairoSVG; extra == "cairo"
+Dynamic: license-file
 
 # icplot
 
@@ -38,8 +39,9 @@ This is a library used at [The Irish Centre for High End Computing (ICHEC)](http
 The project has support for:
 
 * Coverting image formats between pdf, svg and png
-* Building pdf output from tex files, including tikz.
+* Building pdf and png output from tex files, including tikz.
 * Generating plots based on a serializable data model to support reproducible research
+* Generating mermaid plots
 
 To covert between image formats you can do:
 
@@ -53,6 +55,12 @@ To render a Tex tikz image as pdf and png you can do:
 icplot convert --source my_tikz.tex
 ```
 
+To render a Mermaid plot as png you can do:
+
+``` shell
+icplot convert --source my_mermaid.mmd
+```
+
 To generate a plot or collection of plots from a yaml description you can do:
 
 ``` shell

{icplot-0.1.3 → icplot-0.1.5}/src/icplot.egg-info/SOURCES.txt

@@ -9,6 +9,7 @@ src/icplot/convert.py
 src/icplot/geometry.py
 src/icplot/image_utils.py
 src/icplot/main_cli.py
+src/icplot/mermaid.py
 src/icplot/py.typed
 src/icplot/tex.py
 src/icplot.egg-info/PKG-INFO
@@ -33,4 +34,5 @@ test/test_cairo_interface.py
 test/test_gantt_chart.py
 test/test_image_utils.py
 test/test_line_plots.py
-test/test_tex_interface.py
+test/test_mermaid.py
+test/test_tex.py

{icplot-0.1.3 → icplot-0.1.5}/src/icplot.egg-info/requires.txt

@@ -1,6 +1,6 @@
 wand
 matplotlib
-iccore==0.1.8
+iccore==0.1.9
 
 [cairo]
 pycairo

icplot-0.1.5/test/test_line_plots.py

@@ -0,0 +1,63 @@
+from pathlib import Path
+
+from icplot.graph import Plot, LinePlotSeries, PlotAxis, Range
+from icplot.graph import matplotlib
+
+
+def test_line_plot():
+
+    data = [([0, 5, 10], [1, 2, 3]), ([0, 5, 10], [3, 6, 9]), ([0, 5, 10], [4, 8, 12])]
+
+    series = []
+    for idx, [x, y] in enumerate(data):
+        series_config = {"label": f"Series {idx}", "x": x, "y": y}
+        series.append(LinePlotSeries(**series_config))
+
+    x_axis_config = {
+        "label": "x_axis",
+        "ticks": Range(lower=0, upper=11, step=2),
+        "scale": "linear",
+        "text_fontsize": 10,
+        "tick_fontsize": 10,
+        "max_ticks": 0,
+        "limits": {"bottom": 0},
+    }
+    x_axis = PlotAxis(**x_axis_config)
+    y_axis_config = {
+        "label": "y_axis",
+        "ticks": Range(lower=0, upper=16, step=5),
+        "scale": "linear",
+        "text_fontsize": 10,
+        "tick_fontsize": 10,
+        "max_ticks": 0,
+        "limits": {"upper": 15},
+    }
+    y_axis = PlotAxis(**y_axis_config)
+    plot_config = {
+        "title": "Title",
+        "name": "test",
+        "x_axis": x_axis,
+        "y_axes": [y_axis],
+        "plot_type": "",
+        "series": series,
+        "legend": "upper left",
+        "aspect": "auto",
+        "legend_fontsize": 10,
+        "title_fontsize": 10,
+    }
+
+    plot = Plot(**plot_config)
+
+    output_path = Path() / "output.svg"
+    matplotlib.render(plot, output_path)
+
+    assert output_path.exists()
+    output_path.unlink()
+
+
+def test_error_line_plot():
+    pass
+
+
+def test_twin_line_plot():
+    pass

icplot-0.1.5/test/test_mermaid.py

@@ -0,0 +1,24 @@
+import shutil
+from pathlib import Path
+
+from iccore.test_utils import get_test_data_dir, get_test_output_dir
+
+from icplot import mermaid
+
+
+def test_mermaid():
+
+    if not mermaid.has_mermaid():
+        return
+
+    # Pass in the browser config so we can also run headless
+    # on the CI
+    browser_config = Path(__file__).parent.parent / "infra/puppeteer-config.json"
+
+    output_dir = get_test_output_dir()
+    source = get_test_data_dir() / "test.mmd"
+
+    mermaid.convert(source, output_dir, browser_config)
+    assert Path(output_dir / "test.png").exists()
+
+    shutil.rmtree(output_dir)

icplot-0.1.3/test/test_tex_interface.py → icplot-0.1.5/test/test_tex.py

@@ -7,7 +7,7 @@ from icplot import tex
 from icplot.tex import TexBuildSettings
 
 
-def test_tex_interface():
+def test_tex():
 
     data_dir = get_test_data_dir()
     build_dir = get_test_output_dir()

icplot-0.1.3/test/test_line_plots.py

@@ -1,29 +0,0 @@
-from pathlib import Path
-
-from icplot.graph import Plot, LinePlotSeries
-from icplot.graph import matplotlib
-
-
-def test_line_plot():
-
-    data = [([0, 5, 10], [1, 2, 3]), ([0, 5, 10], [3, 6, 9]), ([0, 5, 10], [4, 8, 12])]
-
-    series = []
-    for idx, [x, y] in enumerate(data):
-        series_config = {"label": f"Series {idx}", "x": x, "y": y}
-        series.append(LinePlotSeries(**series_config))
-
-    plot_config = {
-        "title": "test",
-        "legend_label": "test_legend",
-        "series": series,
-        "x_axis": {"label": "test_x", "ticks": {"lower": 0, "upper": 10, "step": 5}},
-    }
-
-    plot = Plot(**plot_config)
-
-    output_path = Path() / "output.svg"
-    matplotlib.render(plot, output_path)
-
-    assert output_path.exists()
-    output_path.unlink()