enable display of large curves via marimo

.github/workflows/test.yml

@@ -20,7 +20,7 @@ jobs:
       - name: install python
         uses: actions/setup-python@v4
         with:
-          python-version: "3.11"
+          python-version: "3.13"
 
       - name: install package and dependencies
         run: pip install -e . && pip install -r test_requirements.txt

CHANGELOG.rst

@@ -6,6 +6,17 @@ All notable changes to this project will be documented in this file.
 
 The format is based on `Keep a Changelog <https://keepachangelog.com>`_.
 
+2.3.0
+-----
+Added
++++++
+- Start testing on Python 3.13, and up minimum version to 3.9.
+- Added ``marimo_utils.display_fig_marimo`` to enable easy display of large curves via `marimo`
+
+Removed
++++++++
+- Removed obsolete ``parse_excel`` module.
+
 2.2.0
 -----
 

docs/installation.rst

@@ -1,7 +1,7 @@
 Installation
 --------------
 
-`neutcurve` requires Python 3.8 or newer.
+`neutcurve` requires Python 3.9 or newer.
 
 The easiest way to install `neutcurve` is from `PyPI <https://pypi.org/>`_ using `pip <https://pip.pypa.io>`_ with::
 

neutcurve/__init__.py

@@ -16,7 +16,7 @@
 
 __author__ = "Jesse Bloom"
 __email__ = "jbloom@fredhutch.org"
-__version__ = "2.2.0"
+__version__ = "2.3.0"
 __url__ = "https://github.com/jbloomlab/neutcurve"
 
 from neutcurve.curvefits import CurveFits  # noqa: F401

neutcurve/marimo_utils.py

@@ -0,0 +1,114 @@
+"""
+============
+marimo_utils
+============
+
+Utilities for working with `marimo <https://marimo.io/>`_ notebooks.
+"""
+
+import base64
+import io
+
+import matplotlib
+import matplotlib.figure
+
+
+def display_fig_marimo(fig, display_method):
+    """Display large matplotlib figure via marimo.
+
+    This function is designed when you have a very large matplotlib figure (eg, as
+    produced by the plotting functions of :class:`neutcurve.curvefits.CurveFits`)
+    and you want to display it in marimo notebook.
+
+    Running this function requires you to have separately installed
+    `marimo <https://marimo.io/>`_ and (if you are using `display_method="png8")
+    `pillow <https://python-pillow.github.io/>`_
+
+    Args:
+        `fig` (matplotlib..figure.Figure)
+            The figure we want to display.
+        `display_method` {"inline", "svg", "pdf", "png8"}
+            Display the figure just inline, as a SVG, as a PDF, or as a PNG8.
+            In general, displaying as a PNG8 will be the smallest size although
+            also the lowest resolution.
+
+    Returns:
+        output_obj
+            The returned object can be display in marimo, via
+            ``marimo.output.append(output_obj)``
+
+    """
+    if not isinstance(fig, matplotlib.figure.Figure):
+        raise ValueError(
+            f"Expected `fig` to be matplotlib.figure.Figure, instead {type(fig)=}"
+        )
+
+    if display_method == "inline":
+        return fig
+
+    import marimo as mo
+
+    if display_method == "svg":
+        buf = io.BytesIO()
+        with matplotlib.rc_context(
+            {
+                "svg.fonttype": "none",  # keep text as text, not paths
+                "svg.image_inline": True,  # embed small images if present
+                "svg.hashsalt": "fixed-1",  # deterministic ids in the SVG
+                "path.simplify": True,
+                "path.simplify_threshold": 0.2,
+            }
+        ):
+            fig.savefig(buf, format="svg", metadata={})
+        svg_text = buf.getvalue().decode("utf-8")
+        return mo.Html(
+            f"""
+<style>
+#svgwrap svg {{
+  width: 100% !important;
+  height: auto !important;
+  max-width: 100%;
+  display: block;
+}}
+</style>
+<div id="svgwrap" style="width:100%;height:80vh;overflow:auto">
+  {svg_text}
+</div>
+"""
+        )
+
+    elif display_method == "pdf":
+        buf = io.BytesIO()
+        with matplotlib.rc_context(
+            {
+                "pdf.fonttype": 42,
+                "pdf.compression": 7,
+                "path.simplify": True,
+                "path.simplify_threshold": 0.2,
+            }
+        ):
+            fig.savefig(buf, format="pdf", metadata={})
+        buf.seek(0)
+        return mo.pdf(src=buf, width="100%", height="80vh")
+
+    elif display_method == "png8":
+        import PIL
+
+        buf = io.BytesIO()
+        fig.savefig(buf, format="png", dpi=80, metadata={})
+        im = PIL.Image.open(io.BytesIO(buf.getvalue())).quantize(
+            colors=48, dither=PIL.Image.NONE
+        )
+        out = io.BytesIO()
+        im.save(out, format="PNG", optimize=True, pnginfo=PIL.PngImagePlugin.PngInfo())
+        data = base64.b64encode(out.getvalue()).decode("ascii")
+        return mo.Html(f'<img src="data:image/png;base64,{data}" alt="figure">')
+
+    else:
+        raise ValueError(f"Invalid {display_method=}")
+
+
+if __name__ == "__main__":
+    import doctest
+
+    doctest.testmod()

setup.py

@@ -11,9 +11,9 @@
 except ImportError:
     raise ImportError("You must install `setuptools`")
 
-if not (sys.version_info[0] == 3 and sys.version_info[1] >= 8):
+if not (sys.version_info[0] == 3 and sys.version_info[1] >= 9):
     raise RuntimeError(
-        "neutcurve requires Python 3.8 or higher.\n"
+        "neutcurve requires Python 3.9 or higher.\n"
         f"You are using Python {sys.version_info[0]}.{sys.version_info[1]}"
     )