Minor fixes

CHANGELOG.md

@@ -1,3 +1,8 @@
+## a14
+
+- Internal SVG drawing routines, removing drawSvg_svgy and lxml dependencies.
+- Xgrow release dependency.
+
 ## a13
 
 - Python 3.11 compatibility.
@@ -8,11 +13,15 @@
 
 ## Previous
 
-
-
 - MultiFixedConcentration allows a `min_volume` setting, which will raise an error of the minimum
   volume to be transferred for any component is too low.
 - Volume and concentration settings can now be changed, not just initialized, as strings.
 - Reference data for mixes is now its own class, `Reference`, and rounds to 1e-6 nM.
 - Mixes now use Decimal instead of floats throughout for units, solving floating point errors.
 - Formatting for mix table entries now takes place in `MixLine`.
+
+
+# v1.1.0
+
+Fixes broken workaround for ruamel.yaml bug now fixed upstream, adds double-tile sensitivity, includes
+seed file to make xor example work.

README.md

@@ -1,11 +1,8 @@
 # NOTE
 
-**This is a development branch that breaks many features. To install the
-the prerelease, use the [1.1 release](https://github.com/DNA-and-Natural-Algorithms-Group/alhambra/releases/tag/v1.1.0), or the [main branch](https://github.com/DNA-and-Natural-Algorithms-Group/alhambra/tree/main), or just use
-
-```
-pip install -U alhambra
-```
+**This is a development branch that breaks many features.** To install
+the the previous release, use the [1.1 release], the [main branch], or
+`pip install -U alhambra`.
 
 # Introduction
 
@@ -20,40 +17,41 @@ peppercompiler with spuriousSSM to create core sequences. For SSTs, it
 will use DSD. It uses an extensible system for tileset design, and can
 flexibly take inputs of YAML or similar formats.
 
-
 # Installation
 
 Alhambra is designed to be installed as a Python package.
 
-```
-pip install -U 'alhambra @ git+https://github.com/DNA-and-Natural-Algorithms-Group/alhambra@v2'
-```
+To install the prerelease version, use
+
+    pip install -U --pre alhambra
+
+To install the latest git version (which may be broken), use
+
+    pip install -U 'alhambra @ git+https://github.com/DNA-and-Natural-Algorithms-Group/alhambra@v2'
 
 Alhambra 2 is designed to work with Python 3.9 or later.
 
-To install development versions, you can check out this github repository, and
-use `pip -e` or some other method for installing Python packages.  Multiple
-versions can be handled through `virtualenv`.
+To install development versions, you can check out this github
+repository, and use `pip -e` or some other method for installing Python
+packages. Multiple versions can be handled through `virtualenv`.
 
-All Alhambra requirements should be handled through setuptools dependencies, but
-note that xgrow and peppercompiler both rely on C code being compiled, which may
-fail.
+All Alhambra requirements should be handled through setuptools
+dependencies, but note that xgrow and peppercompiler both rely on C code
+being compiled, which may fail.
 
 # Usage
 
-[Documentation is available online on readthedocs.io](https://alhambra.readthedocs.io/en/latest/).  In particular, see
-[the tutorial](https://alhambra.readthedocs.io/en/latest/tutorial.html).  It is also available in the docs/ folder.
+[Documentation is available online on readthedocs.io]. In particular,
+see [the tutorial]. It is also available in the docs/ folder.
 
 Most user-facing functions are on the TileSet class.
 
 # Questions
 
-Please send any questions to Constantine Evans, at cevans@evanslabs.org or cge@dna.caltech.edu.
-
-# Versions
-
--   v2.0.0.a1
+Please send any questions to Constantine Evans, at cevans@evanslabs.org
+or cge@dna.caltech.edu.
 
--   v1.1.0: fixes broken workaround for ruamel.yaml bug now fixed
-    upstream, adds double-tile sensitivity, includes seed file to make
-    xor example work.
+  [1.1 release]: https://github.com/DNA-and-Natural-Algorithms-Group/alhambra/releases/tag/v1.1.0
+  [main branch]: https://github.com/DNA-and-Natural-Algorithms-Group/alhambra/tree/main
+  [Documentation is available online on readthedocs.io]: https://alhambra.readthedocs.io/en/latest/
+  [the tutorial]: https://alhambra.readthedocs.io/en/latest/tutorial.html

setup.cfg

@@ -27,8 +27,6 @@ packages = find_namespace:
 install_requires =
     numpy
     stickydesign >= 0.8.3
-    drawSvg_svgy @ git+https://github.com/cgevans/drawSvg_svgy@master
-    lxml
     shutilwhich
     peppercompiler >= 0.1.2
     ruamel.yaml >= 0.15.100

src/alhambra/drawing.py

@@ -0,0 +1,164 @@
+from __future__ import annotations
+import base64
+import re
+from typing import Any, Optional, Union
+from typing_extensions import TypeAlias
+import xml.etree.ElementTree as ET
+import attrs
+from attrs import Factory
+from abc import ABC, abstractmethod
+
+Number: TypeAlias = Union[int, float]
+
+
+class DrawingElement(ABC):
+    @abstractmethod
+    def to_xml(self) -> ET.Element:
+        ...
+
+
+class XMLElement(DrawingElement, ET.Element):
+    def to_xml(self) -> ET.Element:
+        return self
+
+
+@attrs.define()
+class Group(DrawingElement):
+    elements: list[DrawingElement] = Factory(list)
+    id: Optional[str] = None
+
+    def to_xml(self) -> ET.Element:
+        e = ET.Element("g")
+        if self.id is not None:
+            e.attrib["id"] = self.id
+        for elem in self.elements:
+            e.append(elem.to_xml())
+        return e
+
+    def append(self, v: DrawingElement) -> None:
+        self.elements.append(v)
+
+
+class Rectangle(DrawingElement):
+    _el: ET.Element
+
+    def to_xml(self):
+        return self._el
+
+    def __init__(
+        self,
+        x: Number = 0,
+        y: Number = 0,
+        width: Number = 1,
+        height: Number = 1,
+        /,
+        **kwargs,
+    ):
+        e = ET.Element("rect")
+        e.attrib["x"] = str(x)
+        e.attrib["y"] = str(y)
+        e.attrib["width"] = str(width)
+        e.attrib["height"] = str(height)
+        for k, v in kwargs.items():
+            e.attrib[k] = str(v)
+        self._el = e
+
+
+class Text(DrawingElement):
+    _el: ET.Element
+
+    def to_xml(self):
+        return self._el
+
+    def __init__(
+        self, text: str, size: Number = 10, x: Number = 0, y: Number = 0, /, **kwargs
+    ):
+        e = ET.Element("text")
+        e.attrib["x"] = str(x)
+        e.attrib["y"] = str(y)
+        e.attrib["font-size"] = str(size)
+        e.text = text
+        for k, v in kwargs.items():
+            e.attrib[k.replace("_", "-")] = str(v)
+        self._el = e
+
+
+class Use(DrawingElement):
+    _el: ET.Element
+
+    def to_xml(self):
+        return self._el
+
+    def __init__(
+        self, id_or_link: str | Any, x: Number = 0, y: Number = 0, /, **kwargs
+    ):
+        e = ET.Element("use")
+        e.attrib["x"] = str(x)
+        e.attrib["y"] = str(y)
+        if not isinstance(id_or_link, str):
+            assert hasattr(id_or_link, "id")
+            id = str(id_or_link.id)
+        else:
+            id = id_or_link
+        e.attrib["xlink:href"] = "#" + id
+        for k, v in kwargs.items():
+            e.attrib[k] = str(v)
+        self._el = e
+
+
+@attrs.define()
+class Drawing(DrawingElement):
+    width: int
+    height: int
+    defs: list[DrawingElement] = Factory(list)
+    elements: list[DrawingElement] = Factory(list)
+    viewBox: Optional[tuple[Number, Number, Number, Number]] = None
+
+    def to_xml(self) -> ET.Element:
+        e = ET.Element("svg")
+
+        e.attrib["xmlns"] = "http://www.w3.org/2000/svg"
+        e.attrib["xmlns:xlink"] = "http://www.w3.org/1999/xlink"
+        e.attrib["width"] = str(self.width)
+        e.attrib["height"] = str(self.height)
+
+        if self.viewBox is not None:
+            e.attrib["viewBox"] = " ".join(str(i) for i in self.viewBox)
+
+        if self.defs:
+            s = ET.SubElement(e, "defs")
+            for se in self.defs:
+                s.append(se.to_xml())
+        for se in self.elements:
+            e.append(se.to_xml())
+        return e
+
+    def save_svg(self, filename: str):
+        e = self.to_xml()
+
+        d = ET.ElementTree(e)
+
+        d.write(filename)
+
+    saveSvg = save_svg  # for backwards compatibility
+
+    def to_et(self) -> ET.ElementTree:
+        return ET.ElementTree(self.to_xml())
+
+    def to_string(self) -> str:
+        e = self.to_xml()
+        return ET.tostring(e, encoding="unicode", xml_declaration=True)
+
+    def to_bytes(self) -> bytes:
+        e = self.to_xml()
+        return ET.tostring(e, encoding="utf-8", xml_declaration=True)
+
+    def _repr_svg_(self):
+        return self.to_string()
+
+    # From https://github.com/cduck/drawSvg
+    def _repr_html_(self):
+        prefix = b"data:image/svg+xml;base64,"
+        data = base64.b64encode(self.to_bytes())
+        src = (prefix + data).decode(encoding="ascii")
+        return '<img src="{}">'.format(src)

src/alhambra/fastlatticedefect.py

@@ -3,7 +3,7 @@
 
 import numpy as np
 
-from .sensitivitynew import _fakesingles
+from .sensitivitynew import _fakesingles  # type: ignore
 from .tiles import TileList
 from .util import GlueMergeSpec, comp
 

src/alhambra/fastreduceD.py

@@ -1,3 +1,5 @@
+# type: ignore
+
 from __future__ import annotations
 
 from copy import copy

src/alhambra/flatish.py

@@ -393,7 +393,7 @@ def __init__(
     def to_dict(self, glues_as_refs: bool = False) -> dict:
         d: dict[str, Any] = {}
         d["adapter_tiles"] = [
-            [str(g), t.to_dict()] for g, t in self.adapter_tiles  # FIXME
+            [str(g.name), t.to_dict()] for g, t in self.adapter_tiles  # FIXME
         ]
         d["type"] = self.__class__.__name__
         return d

src/alhambra/latticedefect.py

@@ -1,7 +1,7 @@
 import itertools
 import re
 
-from .sensitivitynew import _fakesingles
+from .sensitivitynew import _fakesingles  # type: ignore
 from .tiles import TileList
 from .util import GlueMergeSpec, comp
 

src/alhambra/sensitivitynew.py

@@ -1,3 +1,4 @@
+# type: ignore
 # New sensitivity code.
 # from .tilestructures import tile_daoe_single
 from collections import Counter