icplot 0.2.4__tar.gz → 0.3.0__tar.gz

{icplot-0.2.4/src/icplot.egg-info → icplot-0.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: icplot
-Version: 0.2.4
+Version: 0.3.0
 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
@@ -21,11 +21,13 @@ Requires-Dist: moviepy
 Requires-Dist: scipy
 Requires-Dist: iccore==0.2.3
 Requires-Dist: graphviz
+Requires-Dist: Jinja2
 Provides-Extra: test
 Requires-Dist: pytest; extra == "test"
 Requires-Dist: pytest-cov; extra == "test"
 Requires-Dist: pytest-sugar; extra == "test"
 Requires-Dist: black; extra == "test"
+Requires-Dist: isort; extra == "test"
 Requires-Dist: mypy; extra == "test"
 Requires-Dist: flake8; extra == "test"
 Requires-Dist: pylint; extra == "test"
@@ -36,16 +38,18 @@ Dynamic: license-file
 
 # icplot
 
-This is a library used at [The Irish Centre for High End Computing (ICHEC)](https://www.ichec.ie) for generating plots and graphics for technical documents.
+This is a library used at [The Irish Centre for High End Computing (ICHEC)](https://www.ichec.ie) for generating plots, diagrams and other graphics for technical documents.
 
 # Features #
 
-The project has support for:
+The project has three primary modules:
 
-* Coverting image formats between pdf, svg and png
-* 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
+`converter`: Converts between image formats, such as pdf, svg and png
+`renderer`: Render text based inputs as svg, pdf or png images or videos
+`theme`: Generate and apply themes from a design system
+
+
+## Converter ##
 
 To covert between image formats you can do:
 
@@ -53,24 +57,68 @@ To covert between image formats you can do:
 icplot convert --source my_image.svg --target my_image.png
 ```
 
-To render a Tex tikz image as pdf and png you can do:
+Supported conversions are:
 
-``` shell
-icplot convert --source my_tikz.tex
-```
+* svg -> png
+* svg -> pdf
+* pdf -> png
 
-To render a Mermaid plot as png you can do:
-
-``` shell
-icplot convert --source my_mermaid.mmd
-```
+## Renderer ##
 
-To generate a plot or collection of plots from a yaml description you can do:
+Render a range of text based formats to images or videos. For example,
 
 ``` shell
-icplot plot --config my_plot.yml
+icplot render --file uml_diagram.puml
 ```
 
+renders the PlantUML file to png and svg. 
+
+Supported render inputs and targets are:
+
+* PlantUml
+  * SVG
+  * PNG
+* Latex/Tikz
+  * PDF
+  * SVG
+  * PNG
+* Mermaid
+  * SVG
+  * PNG
+* Custom JSON 
+  * Graph
+    * Backends:
+      * Matplotlib
+      * VTK
+    * Output formats:
+      * SVG
+      * PNG
+      * MP4
+  * Tree
+    * Backends:
+      * Graphviz
+    * Output formats:
+      * SVG
+      * PNG
+  * Gantt
+    * Backends:
+      * Cairo
+      * PgfGantt
+    * Output formats:
+      * SVG
+      * PNG
+  * Scene
+    * Backends:
+      * Cairo
+      * VTK
+    * Output formats:
+      * SVG
+      * VTK
+      
+## Themes ##
+
+The library supports themeing with an Angular Material 3 motivated design system. Plots can be themed by adapting a version of `theme.json` included in this module's source.  Currently Tikz and PlantUML support themeing.
+  
 # Installation #
 
 The package is available on PyPI. For a minimal installation you can do:

icplot-0.3.0/README.md

@@ -0,0 +1,103 @@
+# icplot
+
+This is a library used at [The Irish Centre for High End Computing (ICHEC)](https://www.ichec.ie) for generating plots, diagrams and other graphics for technical documents.
+
+# Features #
+
+The project has three primary modules:
+
+`converter`: Converts between image formats, such as pdf, svg and png
+`renderer`: Render text based inputs as svg, pdf or png images or videos
+`theme`: Generate and apply themes from a design system
+
+
+## Converter ##
+
+To covert between image formats you can do:
+
+``` shell
+icplot convert --source my_image.svg --target my_image.png
+```
+
+Supported conversions are:
+
+* svg -> png
+* svg -> pdf
+* pdf -> png
+
+## Renderer ##
+
+Render a range of text based formats to images or videos. For example,
+
+``` shell
+icplot render --file uml_diagram.puml
+```
+
+renders the PlantUML file to png and svg. 
+
+Supported render inputs and targets are:
+
+* PlantUml
+  * SVG
+  * PNG
+* Latex/Tikz
+  * PDF
+  * SVG
+  * PNG
+* Mermaid
+  * SVG
+  * PNG
+* Custom JSON 
+  * Graph
+    * Backends:
+      * Matplotlib
+      * VTK
+    * Output formats:
+      * SVG
+      * PNG
+      * MP4
+  * Tree
+    * Backends:
+      * Graphviz
+    * Output formats:
+      * SVG
+      * PNG
+  * Gantt
+    * Backends:
+      * Cairo
+      * PgfGantt
+    * Output formats:
+      * SVG
+      * PNG
+  * Scene
+    * Backends:
+      * Cairo
+      * VTK
+    * Output formats:
+      * SVG
+      * VTK
+      
+## Themes ##
+
+The library supports themeing with an Angular Material 3 motivated design system. Plots can be themed by adapting a version of `theme.json` included in this module's source.  Currently Tikz and PlantUML support themeing.
+  
+# Installation #
+
+The package is available on PyPI. For a minimal installation you can do:
+
+``` shell
+pip install icplot
+```
+
+For full functionality, particularly conversion of image formats, `imagemagick` and `cairo` are required. On Mac you can install them with:
+
+``` shell
+brew install imagemagick cairo
+```
+
+# Copyright #
+
+Copyright 2024 Irish Centre for High End Computing
+
+The software in this repository can be used under the conditions of the GPLv3+ license, which is available for reading in the accompanying LICENSE file.
+

{icplot-0.2.4 → icplot-0.3.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "icplot"
-version = "0.2.4"
+version = "0.3.0"
 authors = [
   { name="James Grogan, Irish Centre for High End Computing", email="james.grogan@ichec.ie" },
 ]
@@ -22,7 +22,8 @@ dependencies = ["wand",
                "moviepy",
                "scipy",
 	       "iccore==0.2.3",
-               "graphviz"]
+               "graphviz",
+               "Jinja2"]
 
 [project.urls]
 Repository = "https://git.ichec.ie/performance/toolshed/icplot"
@@ -34,6 +35,7 @@ test = [
     "pytest-cov",
     "pytest-sugar",
     "black",
+    "isort",
     "mypy",
     "flake8",
     "pylint"
@@ -52,7 +54,7 @@ build-backend = "setuptools.build_meta"
 icplot = "icplot.main_cli:main_cli"
 
 [tool.setuptools.package-data]
-"icplot" = ["py.typed", "controlDict"]
+"icplot" = ["py.typed", "controlDict", "theme/theme.json", "theme/templates/*.j2"]
 
 [tool.setuptools.packages.find]
 where = ["src"]
@@ -122,16 +124,21 @@ commands = [["pytest", "test"]]
 [tool.tox.env.format_apply]
 description = "Run Format Apply"
 skip_install = true
-deps = ["black"]
-commands = [["black", "src"], ["black", "test"]]
+deps = ["black", "isort"]
+commands = [["black", "src"], ["black", "test"], ["isort", "src"], ["isort", "test"]]
 
 [tool.tox.env.format_check]
 description = "Run Format Check"
 skip_install = true
-deps = ["black"]
+deps = ["black", "isort"]
 commands = [
          ["black", "--check", "--diff", "src"],
-         ["black", "--check", "--diff", "test"]]
+         ["black", "--check", "--diff", "test"],
+         ["isort", "--check", "--diff", "src"],
+         ["isort", "--check", "--diff", "test"]]
+
+[tool.isort]
+profile = "black"
 
 [tool.tox.env.lint]
 description = "Run Linter"

icplot-0.3.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

{icplot-0.2.4/src/icplot/gantt → icplot-0.3.0/src/icplot/charts}/gantt.py

@@ -4,11 +4,10 @@ This module represents a gantt chard
 
 from datetime import datetime
 
-from pydantic import BaseModel
-
 from iccore.project import Milestone
+from pydantic import BaseModel
 
-from icplot.color import Color
+from icplot.theme.color import Color
 
 
 class GanttChart(BaseModel, frozen=True):

{icplot-0.2.4/src/icplot → icplot-0.3.0/src/icplot/charts}/tree.py

@@ -1,13 +1,12 @@
+import logging
 import os
 import shutil
-import logging
 from dataclasses import dataclass
-from typing import Callable
 from pathlib import Path
+from typing import Callable
 
 import graphviz
 
-
 logger = logging.getLogger(__name__)
 
 

icplot-0.3.0/src/icplot/converter/__init__.py

@@ -0,0 +1,3 @@
+from .image import pdf_to_png, svg_to_pdf, svg_to_png
+
+__all__ = ["pdf_to_png", "svg_to_pdf", "svg_to_png"]

icplot-0.3.0/src/icplot/converter/cli.py

@@ -0,0 +1,27 @@
+from pathlib import Path
+
+from .convert import convert
+
+
+def convert_cli(args):
+
+    source = args.source.resolve()
+    target = Path(args.target).resolve() if args.target else None
+    convert(source, target)
+
+
+def register_parser(subparsers):
+
+    convert_parser = subparsers.add_parser("convert")
+    convert_parser.add_argument(
+        "source",
+        type=Path,
+        help="Path to file to be converted from",
+    )
+    convert_parser.add_argument(
+        "--target",
+        type=str,
+        default="",
+        help="Path to file to be converted to",
+    )
+    convert_parser.set_defaults(func=convert_cli)

icplot-0.3.0/src/icplot/converter/convert.py

@@ -0,0 +1,32 @@
+"""
+Module supporting conversion between image formats
+"""
+
+import logging
+from pathlib import Path
+
+from .image import pdf_to_png, svg_to_pdf, svg_to_png
+
+logger = logging.getLogger(__name__)
+
+
+def convert(source: Path, target: Path | None = None):
+    """
+    Convert between image formats using the source and target
+    file extensions as format hints.
+    """
+
+    logger.info("Converting %s", source)
+
+    if source.suffix == ".pdf":
+        pdf_to_png(source, target)
+    elif source.suffix == ".svg":
+        if target:
+            if target.suffix == ".png":
+                svg_to_png(source, target)
+            elif target.suffix == ".pdf":
+                svg_to_pdf(source, target)
+        else:
+            svg_to_png(source)
+
+    logger.info("Finished conversion")

icplot-0.2.4/src/icplot/image_utils.py → icplot-0.3.0/src/icplot/converter/image.py

@@ -7,27 +7,23 @@ import logging
 import os
 from pathlib import Path
 
+logger = logging.getLogger(__name__)
+
 _HAS_WAND = True
 try:
-    from wand.image import Image
     from wand.color import Color
+    from wand.image import Image
 except ImportError as e:
-    logging.getLogger(__name__).warning(
-        "Disabling Wand stupport. Failed to load with: %s", e
-    )
+    logger.debug("wand not available: %s", e)
     _HAS_WAND = False
 
 _HAS_CAIRO_SVG = True
 try:
     import cairosvg
 except ImportError as e:
-    logging.getLogger(__name__).warning(
-        "Disabling CairoSVG stupport. Failed to load with: %s", e
-    )
+    logger.debug("cairosvg not available: %s", e)
     _HAS_CAIRO_SVG = False
 
-logger = logging.getLogger(__name__)
-
 
 def has_wand() -> bool:
     return _HAS_WAND

{icplot-0.2.4 → icplot-0.3.0}/src/icplot/geometry/base.py

@@ -1,8 +1,11 @@
 from __future__ import annotations
+
 from dataclasses import dataclass
 
 import numpy as np
 
+from .operations import get_point_distance
+
 
 @dataclass(frozen=True)
 class Vector:
@@ -47,6 +50,9 @@ class Point:
     def subtract(self, v: Vector) -> Vector:
         return Vector(self.x - v.x, self.y - v.y, self.z - v.z)
 
+    def get_distance(self, p: Point) -> float:
+        return get_point_distance(p.as_array(), self.as_array())
+
 
 @dataclass(frozen=True)
 class Bounds:

{icplot-0.2.4/src/icplot → icplot-0.3.0/src/icplot/geometry}/mesh/edge.py

@@ -1,6 +1,6 @@
 from dataclasses import dataclass
 
-from icplot.geometry import Point, segment_contains_point, get_segment_distance
+from icplot.geometry import Point, get_segment_distance, segment_contains_point
 
 from .vertex import Vertex
 

{icplot-0.2.4/src/icplot → icplot-0.3.0/src/icplot/geometry}/mesh/mesh.py

@@ -4,13 +4,14 @@ over performance. Consider something else for high performance meshing.
 """
 
 from __future__ import annotations
+
 from dataclasses import dataclass
 
-from icplot.geometry import Point, Vector, Transform, Bounds
+from icplot.geometry import Bounds, Point, Shape, Transform, Vector
 
-from .vertex import Vertex, find_closest_vertex
 from .cell import Cell, flip_normals
 from .edge import Edge, contains_point, get_distance
+from .vertex import Vertex, find_closest_vertex
 
 
 @dataclass(frozen=True)
@@ -49,7 +50,7 @@ class Mesh:
             ymin = min(ymin, v.y)
             ymax = max(ymax, v.y)
             zmin = min(zmin, v.z)
-            zmax = min(zmax, v.z)
+            zmax = max(zmax, v.z)
         return Bounds(xmin=xmin, xmax=xmax, ymin=ymin, ymax=ymax, zmin=zmin, zmax=zmax)
 
     def flip_normals(self) -> Mesh:
@@ -67,8 +68,28 @@ class Mesh:
             vertices=tuple(v.translate(delta) for v in self.vertices), cells=self.cells
         )
 
-    def move_by(self, x: float, y: float, z: float) -> Mesh:
+    def scale_by(self, factor: float) -> Mesh:
+        return Mesh(
+            vertices=tuple(v.scale(factor) for v in self.vertices), cells=self.cells
+        )
+
+    def rotate_to(self, vec: Vector) -> Mesh:
+        return Mesh(
+            vertices=tuple(v.rotate_to(vec) for v in self.vertices), cells=self.cells
+        )
+
+    def move_by(
+        self, x: float, y: float, z: float, selection: list[int] | None = None
+    ) -> Mesh:
         delta = Vector(x, y, z)
+        if selection:
+            return Mesh(
+                vertices=tuple(
+                    v.translate(delta) if v.id in selection else v.copy()
+                    for v in self.vertices
+                ),
+                cells=self.cells,
+            )
         return Mesh(
             vertices=tuple(v.translate(delta) for v in self.vertices), cells=self.cells
         )
@@ -105,3 +126,8 @@ class Mesh:
             vertices=tuple(Vertex(v.x, v.y, v.z, v.id) for v in self.vertices),
             cells=tuple(Cell(c.vertices, c.type) for c in self.cells),
         )
+
+    def select_region(self, region: Shape) -> list[int]:
+        return [
+            v.id for v in self.vertices if region.contains_point(Point(v.x, v.y, v.z))
+        ]

{icplot-0.2.4/src/icplot → icplot-0.3.0/src/icplot/geometry}/mesh/openfoam/blockmesh.py

@@ -2,14 +2,13 @@
 Meshing utilities for use in openfoam
 """
 
+import os
 import shutil
 import subprocess
-import os
 from pathlib import Path
 from typing import cast
 
-
-from icplot.mesh import Edge, HexCell, Mesh, Patch
+from icplot.geometry.mesh import Edge, HexCell, Mesh, Patch
 
 from .foamfile import FoamFile, write_header
 

{icplot-0.2.4/src/icplot → icplot-0.3.0/src/icplot/geometry}/mesh/openfoam/polymesh.py

@@ -1,11 +1,11 @@
 from dataclasses import dataclass
-from pathlib import Path
 from functools import cmp_to_key
+from pathlib import Path
 
 from icplot.geometry import Point
-from icplot.mesh import Vertex, Mesh, get_hex_faces
+from icplot.geometry.mesh import Mesh, Vertex, get_hex_faces
 
-from .foamfile import read_foamfile, FoamFile, write_header
+from .foamfile import FoamFile, read_foamfile, write_header
 
 
 @dataclass(frozen=True)
@@ -65,10 +65,8 @@ class PolymeshPatch:
 
 def read_polymesh(path: Path) -> Polymesh:
 
-    points_file = read_foamfile(path / "points")
+    _ = read_foamfile(path / "points")
     # faces_file = read_foamfile(path / "faces")
-    print(points_file)
-    # print(faces_file)
     return Polymesh((), (), ())
 
 

{icplot-0.2.4/src/icplot → icplot-0.3.0/src/icplot/geometry}/mesh/shapes.py

@@ -1,21 +1,21 @@
 import numpy as np
 
 from icplot.geometry import (
-    Point,
-    Quad,
     Annulus,
-    Transform,
     Circle,
     Cuboid,
-    Vector,
     Cylinder,
+    Point,
+    Quad,
+    Shape,
+    Transform,
+    Vector,
 )
 
+from .cell import Cell, HexCell
 from .mesh import Mesh
+from .operations import close_mesh, map_radial, merge_meshes, mesh_extrude
 from .vertex import Vertex, find_closest
-from .cell import Cell, HexCell
-
-from .operations import map_radial, close_mesh, merge_meshes, mesh_extrude
 
 
 def mesh_rectangle(rect: Quad, num_width: int = 10, num_height: int = 10) -> Mesh:
@@ -187,6 +187,73 @@ def mesh_cylinder_basic(
     )
 
 
+"""
+def _mesh_cylinder_block(radius,
+                         top_loc,
+                         bottom_loc,
+                         boundary_fraction,
+                         num_radial,
+                         num_circumferential,
+                         cell_height,
+                         top_hole: Hole | None = None,
+                         bottom_hole: Hole | None = None) -> Mesh:
+    length = height - hole_loc.z
+    num_cells_in_block = int(num_height*length/height) + 1
+    block = mesh_cylinder_basic(Cylinder(diameter=radius*2, length=length),
+                                boundary_fraction,
+                                num_radial,
+                                num_circumferential,
+                                num_cells_in_block)
+    block = block.move_by(0.0, 0.0, hole_loc.z)
+    selection = block.select_region(holes[0])
+    block = block.move_by(0.0, 0.0, (length/num_cells_in_block)/8.0, selection)
+"""
+
+
+def _mesh_compound_cylinder_with_holes(
+    inlet_radius,
+    inlet_height,
+    radius,
+    height,
+    boundary_fraction,
+    num_circumferential,
+    num_radial,
+    num_height,
+    holes: list[Shape],
+) -> Mesh:
+
+    # Mesh the core cylinder in blocks at the hole locations
+    hole_loc = holes[0].transform.location
+
+    length = height - hole_loc.z
+    num_cells_in_block = int(num_height * length / height) + 1
+    block = mesh_cylinder_basic(
+        Cylinder(diameter=radius * 2, length=length),
+        boundary_fraction,
+        num_radial,
+        num_circumferential,
+        num_cells_in_block,
+    )
+    block = block.move_by(0.0, 0.0, hole_loc.z)
+    selection = block.select_region(holes[0])
+    block = block.move_by(0.0, 0.0, (length / num_cells_in_block) / 8.0, selection)
+
+    length = hole_loc.z
+    num_cells_in_block = int(num_height * length / height) + 1
+    block = mesh_cylinder_basic(
+        Cylinder(diameter=radius * 2, length=length),
+        boundary_fraction,
+        num_radial,
+        num_circumferential,
+        num_cells_in_block,
+    )
+    block = block.move_by(0.0, 0.0, 0.0)
+    selection = block.select_region(holes[0])
+    block = block.move_by(0.0, 0.0, -(length / num_cells_in_block) / 8.0, selection)
+
+    return merge_meshes(block, block)
+
+
 def mesh_compound_cylinder(
     inlet_radius,
     inlet_height,
@@ -196,8 +263,21 @@ def mesh_compound_cylinder(
     num_circumferential,
     num_radial,
     num_height,
+    holes: list[Shape] | None = None,
 ) -> Mesh:
 
+    if holes:
+        return _mesh_compound_cylinder_with_holes(
+            inlet_radius,
+            inlet_height,
+            radius,
+            height,
+            boundary_fraction,
+            num_circumferential,
+            num_radial,
+            num_height,
+            holes,
+        )
     inner = mesh_cylinder_basic(
         Cylinder(diameter=inlet_radius * 2, length=2 * inlet_height + height),
         boundary_fraction,