DX: freeze slowest TR notebooks (#21)

* DOC: add more icons to navigation bar
* DX: add `pixi.lock` to `.gitignore`
* DX: detect doctests again in VS Code
* DX: export figures to ssubfolders
* DX: merge per-notebook Ruff rules
* DX: recommend VS Code extension for SVG
* FIX: install `mpl-interactions`
* FIX: wrap optional `pip` dependencies in quotation marks
  This is required for zsh

* MAINT: autoupdate Zotero bibliography file
* MAINT: remove `matplotlib` from notebook dependencies
* MAINT: use `plt.cm` instead of `cm`

.cspell.json

@@ -109,6 +109,7 @@
   "ignoreWords": [
     "Kutschke",
     "Marangotto",
+    "PINF",
     "PYTHONHASHSEED",
     "Richman",
     "absl",
@@ -205,6 +206,7 @@
     "maxsize",
     "meshgrid",
     "migrad",
+    "mkpath",
     "mmikhasenko",
     "mname",
     "msigma",

.gitignore

@@ -35,9 +35,10 @@ oryx-build-commands.txt
 prof/
 
 # Virtual environments
-*venv/
 .pixi/
 .tox/
+*venv/
+pixi.lock
 pyvenv*/
 
 # Settings

.pre-commit/pin_nb_requirements.py

@@ -168,7 +168,8 @@ def _format_pip_requirements(
     git_requirements = {r for r in requirements if r.startswith("git+")}
     pip_requirements = set(requirements) - git_requirements
     pip_requirements = {r.lower().replace("_", "-") for r in pip_requirements}
-    sorted_requirements = sorted(pip_requirements) + sorted(git_requirements)
+    pip_requirements = [__wrap_quotation_marks(r) for r in pip_requirements]
+    sorted_requirements = sorted(pip_requirements, key=__key) + sorted(git_requirements)
     expected = f"{__EXPECTED_PIP_INSTALL_LINE} {' '.join(sorted_requirements)}"
     if install_statement != expected:
         notebook["cells"][cell_id]["source"] = expected
@@ -177,6 +178,16 @@ def _format_pip_requirements(
         raise PrecommitError(msg)
 
 
+def __wrap_quotation_marks(requirement: str) -> str:
+    if "[" in requirement and not requirement.startswith("'"):
+        return f"'{requirement}'"
+    return requirement
+
+
+def __key(requirement: str) -> str:
+    return requirement.replace("'", "", 1).lower()
+
+
 def _update_metadata(filename: str, metadata: dict, notebook: NotebookNode) -> None:
     updated_metadata = False
     jupyter_metadata = metadata.get("jupyter")

.vscode/extensions.json

@@ -16,6 +16,7 @@
     "ms-vscode.live-server",
     "ms-vsliveshare.vsliveshare",
     "redhat.vscode-yaml",
+    "simonsiefke.svg-preview",
     "soulcode.vscode-unwanted-extensions",
     "stkb.rewrap",
     "streetsidesoftware.code-spell-checker",

.vscode/settings.json

@@ -51,7 +51,8 @@
   "notebook.gotoSymbols.showAllSymbols": true,
   "python.analysis.autoImportCompletions": false,
   "python.terminal.activateEnvironment": false,
-  "python.testing.pytestEnabled": false,
+  "python.testing.pytestEnabled": true,
+  "python.testing.unittestEnabled": false,
   "redhat.telemetry.enabled": false,
   "rewrap.wrappingColumn": 88,
   "ruff.enable": true,

docs/001.ipynb

@@ -46,7 +46,7 @@
    },
    "outputs": [],
    "source": [
-    "%pip install -q black==21.5b2 jax==0.4.28 jaxlib==0.4.28 matplotlib==3.4.2 numpy==1.26.4 sympy==1.8"
+    "%pip install -q black==21.5b2 jax==0.4.28 jaxlib==0.4.28 numpy~=1.26.4 sympy==1.8"
    ]
   },
   {

docs/002.ipynb

@@ -52,7 +52,7 @@
    },
    "outputs": [],
    "source": [
-    "%pip install -q ampform==0.9.1 numpy==1.19.5 pandas==1.2.4 qrules==0.8.2 sympy==1.8 tensorwaves[jax]==0.2.9 git+https://github.com/zfit/phasespace@7131fbd"
+    "%pip install -q ampform==0.9.1 numpy==1.19.5 pandas==1.2.4 qrules==0.8.2 sympy==1.8 'tensorwaves[jax]==0.2.9' git+https://github.com/zfit/phasespace@7131fbd"
    ]
   },
   {
@@ -77,6 +77,7 @@
     "import timeit\n",
     "import warnings\n",
     "from collections.abc import Generator, Sequence\n",
+    "from pathlib import Path\n",
     "from typing import Callable\n",
     "\n",
     "import ampform\n",
@@ -156,7 +157,9 @@
    },
    "outputs": [],
    "source": [
-    "graphviz.Source(dot).render(\"002-f0(980)-graph\", format=\"svg\");"
+    "output_file = Path(\"002/f0(980)-graph\")\n",
+    "output_file.parent.mkdir(exist_ok=True)\n",
+    "graphviz.Source(dot).render(output_file, format=\"svg\");"
    ]
   },
   {
@@ -373,7 +376,9 @@
    },
    "outputs": [],
    "source": [
-    "graphviz.Source(dot).render(\"002-collapsed-expression-tree\", format=\"svg\");"
+    "output_file = Path(\"002/collapsed-expression-tree\")\n",
+    "output_file.parent.mkdir(exist_ok=True)\n",
+    "graphviz.Source(dot).render(output_file, format=\"svg\");"
    ]
   },
   {
@@ -438,7 +443,9 @@
    },
    "outputs": [],
    "source": [
-    "graphviz.Source(dot).render(\"002-simple-expression-tree\", format=\"svg\");"
+    "output_file = Path(\"002/simple-expression-tree\")\n",
+    "output_file.parent.mkdir(exist_ok=True)\n",
+    "graphviz.Source(dot).render(output_file, format=\"svg\");"
    ]
   },
   {
@@ -850,7 +857,9 @@
    },
    "outputs": [],
    "source": [
-    "fig.savefig(\"002-histogram-m12.svg\");"
+    "output_file = Path(\"002/histogram-m12.svg\")\n",
+    "output_file.parent.mkdir(exist_ok=True)\n",
+    "fig.savefig(output_file);"
    ]
   },
   {
@@ -1381,7 +1390,9 @@
    },
    "outputs": [],
    "source": [
-    "fig.savefig(\"002-runtime-vs-operations.svg\");"
+    "output_file = Path(\"002/runtime-vs-operations.svg\")\n",
+    "output_file.parent.mkdir(exist_ok=True)\n",
+    "fig.savefig(output_file);"
    ]
   },
   {
@@ -1856,7 +1867,9 @@
    },
    "outputs": [],
    "source": [
-    "graphviz.Source(dot).render(\"002-f0-graph\", format=\"svg\");"
+    "output_file = Path(\"002/f0-graph\")\n",
+    "output_file.parent.mkdir(exist_ok=True)\n",
+    "graphviz.Source(dot).render(output_file, format=\"svg\");"
    ]
   },
   {