[DO NOT MERGE] Integration: backlog

.github/workflows/master.yml

@@ -19,7 +19,7 @@ jobs:
       matrix:
         os: [windows-latest, ubuntu-22.04, macos-latest]
         # https://devguide.python.org/versions/
-        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
         exclude:
           - os: windows-latest
             python-version: "3.11"

.github/workflows/sphinx.yml

@@ -16,7 +16,6 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install .[dev,docs]
-        pip install git+https://github.com/petercorke/sphinx-autorun.git
         pip install sympy
         sudo apt-get install graphviz
     - name: Build docs

benchmarks/benchmark_smtb.py

@@ -0,0 +1,292 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Micro-benchmarks for spatialmath: base functions and classes for SO(3),
+SE(3), quaternions and twists, plus a NumPy baseline.  Run from a checkout::
+
+    python benchmarks/benchmark_smtb.py
+
+The output starts with a summary of the machine and package versions, so a
+pasted table is self-describing.
+
+Created on Fri Apr 10 14:22:36 2020
+
+@author: Peter Corke
+"""
+
+import os
+import platform
+import subprocess
+import timeit as _timeit
+
+import numpy as np
+from ansitable import ANSITable, Column
+
+import spatialmath
+
+N = 10_000
+REPEATS = 5
+
+table = None
+
+
+def cpu_info() -> str:
+    """Best-effort, portable one-line CPU description
+
+    :return: CPU name and core count, plus clock speed if available
+    :rtype: str
+
+    No new hard dependency: psutil is used for clock speed only if already
+    installed.  Some platforms (e.g. Apple Silicon) don't expose a single
+    meaningful clock speed, so a missing or nonsensical reading is omitted.
+    """
+    system = platform.system()
+    name = None
+
+    if system == "Darwin":
+        try:
+            name = subprocess.check_output(
+                ["sysctl", "-n", "machdep.cpu.brand_string"], text=True
+            ).strip()
+        except Exception:
+            pass
+    elif system == "Linux":
+        try:
+            with open("/proc/cpuinfo") as f:
+                for line in f:
+                    if line.lower().startswith("model name"):
+                        name = line.split(":", 1)[1].strip()
+                        break
+        except Exception:
+            pass
+    elif system == "Windows":
+        name = platform.processor() or None
+
+    if not name:
+        name = platform.processor() or platform.machine() or "unknown CPU"
+
+    info = f"{name} ({os.cpu_count() or '?'} cores)"
+
+    try:
+        import psutil
+
+        freq = psutil.cpu_freq()
+        # real clock speeds are hundreds to thousands of MHz; some platforms
+        # report bogus single-digit values instead of raising
+        if freq and freq.max and freq.max > 100:
+            info += f", {freq.max:.0f} MHz"
+    except Exception:
+        pass
+
+    return info
+
+
+def print_machine_summary() -> None:
+    print(f"CPU:          {cpu_info()}")
+    print(f"OS:           {platform.platform()}")
+    print(f"Python:       {platform.python_version()}")
+    print(f"numpy:        {np.__version__}")
+    print(f"spatialmath:  {spatialmath.__version__}")
+    print(f"Timing:       min of {REPEATS} repeats x {N} calls")
+
+
+def new_table():
+    return ANSITable(
+        Column("Operation", headalign="^"),
+        Column("Time (μs)", headalign="^", fmt="{:.2f}"),
+        border="thick",
+    )
+
+
+def timeit(stmt, label, setup):
+    # min-of-repeats suppresses system jitter (GC pauses, OS scheduling)
+    # much better than a single long run of the same total work
+    t = min(_timeit.repeat(stmt=stmt, setup=setup, number=N, repeat=REPEATS))
+    table.row(label, t / N * 1e6)
+
+
+def section(title):
+    # print the previous table (if any), then start a fresh one under a
+    # plain header naming the category of test that follows
+    global table
+    if table is not None:
+        table.print()
+    print(f"\n{title}\n")
+    table = new_table()
+
+
+print_machine_summary()
+
+# ------------------------------------------------------------------------- #
+transforms_setup = '''
+from spatialmath import SE3
+from spatialmath import base
+
+import numpy as np
+from collections import namedtuple
+Rt = namedtuple('Rt', 'R t')
+X1 = SE3.Rand()
+X2 = SE3.Rand()
+T1 = X1.A
+T2 = X2.A
+R1 = base.t2r(T1)
+R2 = base.t2r(T2)
+t1 = base.transl(T1)
+t2 = base.transl(T2)
+Rt1 = Rt(R1, t1)
+Rt2 = Rt(R2, t2)
+v = np.r_[1,2,3]
+v2 = np.r_[1,2,3, 1]
+'''
+
+section("SO(3) / SE(3) base functions")
+
+timeit('base.getvector(0.2)', "base.getvector(x)", transforms_setup)
+timeit('base.rotx(0.2, unit="rad")', "base.rotx(x)", transforms_setup)
+timeit('base.trotx(0.2, unit="rad")', "base.trotx(x)", transforms_setup)
+timeit('base.t2r(T1)', "base.t2r(T1)", transforms_setup)
+timeit('base.r2t(R1)', "base.r2t(R1)", transforms_setup)
+timeit('T1 @ T2', "T1 @ T2 (4x4)", transforms_setup)
+timeit(
+    'T1[:3,:3] @ T2[:3,:3] + T1[:3,:3] @ T2[:3,3]',
+    "T1 @ T2 decomposed (slice)",
+    transforms_setup,
+)
+timeit(
+    '(Rt1.R @ Rt2.R, Rt1.R @ Rt2.t)',
+    "T1 @ T2 decomposed (namedtuple)",
+    transforms_setup,
+)
+timeit('base.trinv(T1)', "base.trinv(T1)", transforms_setup)
+timeit(
+    '(Rt1.R.T, -Rt1.R.T @ Rt1.t)', "T1 inverse decomposed (R,t)", transforms_setup
+)
+timeit('np.linalg.inv(T1)', "np.linalg.inv(T1)", transforms_setup)
+timeit('T1 @ v2', "T1 @ v2 (4,4)*(4,)", transforms_setup)
+
+# ------------------------------------------------------------------------- #
+section("SE3 class")
+
+timeit('SE3()', "SE3()", transforms_setup)
+timeit('SE3.Rx(0.2)', "SE3.Rx(x)", transforms_setup)
+timeit('SE3(T1)', "SE3(T1)", transforms_setup)
+timeit('SE3(T1, check=False)', "SE3(T1, check=False)", transforms_setup)
+timeit('SE3([T1], check=False)', "SE3([T1], check=False)", transforms_setup)
+timeit('T1[:3,:3]', "T1[:3,:3] (raw slice)", transforms_setup)
+timeit('X1.A', "X1.A (property)", transforms_setup)
+timeit('X1 * X2', "X1 * X2", transforms_setup)
+timeit('X1 @ X2', "X1 @ X2 (normalized)", transforms_setup)
+timeit('X1.inv()', "X1.inv()", transforms_setup)
+timeit('X1 * v', "X1 * v", transforms_setup)
+timeit('a = X1.log()', "X1.log()", transforms_setup)
+timeit('SE3.RPY([0.1, 0.2, 0.3])', "SE3.RPY(rpy)", transforms_setup)
+timeit('X1.rpy()', "X1.rpy()", transforms_setup)
+timeit('SE3.Eul([0.1, 0.2, 0.3])', "SE3.Eul(eul)", transforms_setup)
+timeit('X1.eul()', "X1.eul()", transforms_setup)
+timeit('X1.UnitQuaternion()', "X1.UnitQuaternion()", transforms_setup)
+
+# ------------------------------------------------------------------------- #
+quat_setup = '''
+from spatialmath import base
+from spatialmath import UnitQuaternion, SO3
+import numpy as np
+q1 = base.qrand()
+q2 = base.qrand()
+v = np.r_[1,2,3]
+R1 = SO3.Rand().R
+Q1 = UnitQuaternion.Rx(0.2)
+Q2 = UnitQuaternion.Ry(0.3)
+'''
+
+section("Quaternion base functions")
+
+timeit('a = base.qqmul(q1,q2)', "base.qqmul(q1, q2)", quat_setup)
+timeit('a = base.qvmul(q1,v)', "base.qvmul(q1, v)", quat_setup)
+
+# ------------------------------------------------------------------------- #
+section("UnitQuaternion class")
+
+timeit('a = UnitQuaternion()', "UnitQuaternion()", quat_setup)
+timeit('a = UnitQuaternion.Rx(0.2)', "UnitQuaternion.Rx(x)", quat_setup)
+timeit('a = UnitQuaternion(R1)', "UnitQuaternion(R1)", quat_setup)
+timeit('a = Q1.R', "Q1.R (property)", quat_setup)
+timeit('a = Q1 * Q2', "Q1 * Q2", quat_setup)
+timeit('a = Q1 * v', "Q1 * v", quat_setup)
+timeit('a = Q1.SE3()', "Q1.SE3()", quat_setup)
+
+# ------------------------------------------------------------------------- #
+twist_setup = '''
+from spatialmath import SE3, Twist3
+from spatialmath import base
+import numpy as np
+from math import cos
+S1 = Twist3(SE3.Rand())
+S2 = Twist3(SE3.Rand())
+X1 = SE3.Rand()
+T1 = X1.A
+A1 = X1.Ad()
+se3 = S1.skewa()
+s = np.r_[1,2,3,4,5,6]
+v = np.r_[1,2,3]
+'''
+
+section("Twist / exponential-map base functions")
+
+timeit('a = base.skew(v)', "base.skew(v)", twist_setup)
+timeit('a = base.skewa(s)', "base.skewa(s)", twist_setup)
+timeit('a = base.vexa(se3)', "base.vexa(se3)", twist_setup)
+timeit('a = base.trlog(T1)', "base.trlog(T1)", twist_setup)
+timeit('a = base.trlog(T1, twist=True)', "base.trlog(T1, twist=True)", twist_setup)
+timeit('a = base.trexp(se3)', "base.trexp(se3)", twist_setup)
+timeit('a = base.rodrigues(v)', "base.rodrigues(v)", twist_setup)
+timeit('a = A1 @ s', "A1 @ s (6,6)*(6,)", twist_setup)
+timeit('a = cos(0.3)', "math.cos(x)", twist_setup)
+timeit('a = np.cos(0.3)', "np.cos(x)", twist_setup)
+
+# ------------------------------------------------------------------------- #
+section("Twist3 class")
+
+# NB: Twist3 * Twist3 and Twist3.Ad() both round-trip through the SE3
+# exponential/logarithm maps (trexp/trlog above), which is why they cost
+# several times more than a single trexp or trlog call - see
+# claude-notes/twist3-timing-investigation.md for the profiling detail.
+
+timeit('a = Twist3()', "Twist3()", twist_setup)
+timeit('a = Twist3(X1)', "Twist3(X1) (via log)", twist_setup)
+timeit('a = S1.inv()', "S1.inv()", twist_setup)
+timeit('a = S1 * S2', "S1 * S2 (product of exponentials)", twist_setup)
+timeit('a = S1.Ad()', "S1.Ad() (via SE3 + tr2adjoint)", twist_setup)
+timeit('a = S1.exp(1)', "S1.exp() -> SE3", twist_setup)
+
+# ------------------------------------------------------------------------- #
+misc_setup = """
+from spatialmath import base
+import numpy as np
+s = np.r_[1.0,2,3,4,5,6]
+s3 = np.r_[1.0,2,3]
+a = np.r_[1.0, 2.0, 3.0]
+b = np.r_[-5.0, 4.0, 3.0]
+
+A = np.random.randn(6,6)
+As = (A + A.T) / 2
+bb = np.random.randn(6)
+"""
+
+section("NumPy linear-algebra baseline")
+
+timeit("c = np.linalg.inv(As)", "np.linalg.inv(As)", misc_setup)
+timeit("c = np.linalg.pinv(As)", "np.linalg.pinv(As)", misc_setup)
+timeit("c = np.linalg.solve(As, bb)", "np.linalg.solve(As, b)", misc_setup)
+timeit("c = np.cross(a,b)", "np.cross(a, b)", misc_setup)
+timeit("c = base.cross(a,b)", "base.cross(a, b)", misc_setup)
+timeit("a = np.inner(s,s).sum()", "np.inner(s, s).sum()", misc_setup)
+timeit("a = np.linalg.norm(s) ** 2", "np.linalg.norm(s) ** 2", misc_setup)
+timeit("a = base.normsq(s)", "base.normsq(s)", misc_setup)
+timeit("a = (s ** 2).sum()", "(s ** 2).sum()", misc_setup)
+timeit("a = np.sum(s ** 2)", "np.sum(s ** 2)", misc_setup)
+timeit("a = np.linalg.norm(s)", "np.linalg.norm(s) [R6]", misc_setup)
+timeit("a = base.norm(s)", "base.norm(s) [R6]", misc_setup)
+timeit("a = np.linalg.norm(s3)", "np.linalg.norm(s3) [R3]", misc_setup)
+timeit("a = base.norm(s3)", "base.norm(s3) [R3]", misc_setup)
+
+table.print()

docs/source/conf.py

@@ -15,6 +15,7 @@
 # sys.path.insert(0, os.path.abspath('.'))
 # sys.path.insert(0, os.path.abspath('..'))
 
+from sphinx_codeautolink import clean_ipython, clean_pycon
 
 # -- Project information -----------------------------------------------------
 
@@ -47,9 +48,17 @@
     "sphinx.ext.inheritance_diagram",
     "matplotlib.sphinxext.plot_directive",
     "sphinx_autodoc_typehints",
-    "sphinx_autorun",
+    "sphinx_pyrunblock",
     "sphinx.ext.intersphinx",
     "sphinx_favicon",
+    "sphinx_copybutton",
+    "sphinx_codeautolink",
+]
+
+suppress_warnings = [
+    "codeautolink.match_block",
+    "codeautolink.match_name",
+    "config.cache",  # codeautolink_custom_blocks holds function refs, not picklable
 ]
 #'sphinx.ext.autosummary',
 # typehints_use_signature_return = True
@@ -184,6 +193,24 @@
 np.set_printoptions(precision=4, suppress=True)
 """
 
+# -------- sphinx-codeautolink options --------------------------------------------#
+
+codeautolink_custom_blocks = {
+    "pycon": clean_pycon,
+    "ipython": clean_ipython,
+    "ipython3": clean_ipython,
+}
+# Ensure pycon (Python console) blocks are included in the autolink search.
+codeautolink_search_css_classes = ["highlight-python", "highlight-pycon"]
+
+# -------- sphinx-copybutton options ----------------------------------------------#
+# Strip interactive prompts (Python and shell) when users copy code snippets.
+
+copybutton_prompt_text = r">>> |\.\.\. |\$ "
+copybutton_prompt_is_regexp = True
+copybutton_only_copy_prompt_lines = False
+copybutton_remove_prompts = True
+
 intersphinx_mapping = {
     "numpy": ("http://docs.scipy.org/doc/numpy/", None),
     "scipy": ("http://docs.scipy.org/doc/scipy/reference/", None),

docs/source/intro.rst

@@ -629,7 +629,7 @@ Graphics
 If ``matplotlib`` is installed then we can add 2D coordinate frames to a figure in a variety of styles:
 
 .. code-block:: python
-   :linenos:
+    :linenos:
 
     >>> trplot2( transl2(1,2), frame='A', rviz=True, width=1)
     >>> trplot2( transl2(3,1), color='red', arrow=True, width=3, frame='B')
@@ -646,7 +646,7 @@ If a figure does not yet exist one is added.  If a figure exists but there is no
 Similarly, we can plot 3D coordinate frames in a variety of styles:
 
 .. code-block:: python
-   :linenos:
+    :linenos:
 
     >>> trplot( transl(1,2,3), frame='A', rviz=True, width=1, dims=[0, 10, 0, 10, 0, 10])
     >>> trplot( transl(3,1, 2), color='red', width=3, frame='B')