Merge pull request #74 from kmnhan/manager-jupyter

Add lazy-loader support and improve imagetool functionality
kmnhan · Dec 14, 2024 · e7c8ea8 · e7c8ea8
2 parents 5a68584 + 8048b36
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -8,6 +8,9 @@ on:
   schedule:
     # Every friday at 22:00 UTC (Every saturday at 07:00 KST/JST)
     - cron: "0 22 * * FRI"
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 env:
   FORCE_COLOR: 1
 
@@ -22,7 +25,6 @@ jobs:
       matrix:
         python-version: ["3.11", "3.12"]
         qt-api: ["pyqt6", "pyside6"]
-
     steps:
       - uses: actions/checkout@v4
         with:

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -4,6 +4,9 @@ on:
   workflow_dispatch:
 env:
   FORCE_COLOR: 1
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 jobs:
   release:

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -37,7 +37,7 @@ repos:
     hooks:
       # Run the linter.
       - id: ruff
-        args: [ --fix ]
+        args: [ --fix, --show-fixes ]
       # Run the formatter.
       - id: ruff-format
 

diff --git a/README.md b/README.md
@@ -1,25 +1,14 @@
-<h1 align="center">
-ERLabPy
-</h1>
-<p align="center">
-    <a href="https://pypi.org/project/erlab/" alt="Supported Python Versions">
-        <img src="https://img.shields.io/pypi/pyversions/erlab?logo=python&logoColor=white" /></a>
-    <a href="https://pypi.org/project/erlab/" alt="PyPi">
-        <img src="https://img.shields.io/pypi/v/erlab?logo=pypi&logoColor=white" /></a>
-    <a href="https://anaconda.org/conda-forge/erlab" alt="Conda Version">
-        <img src="https://img.shields.io/conda/vn/conda-forge/erlab?logo=condaforge&logoColor=white" /></a>
-</p><p align="center">
-    <a href="https://github.com/kmnhan/erlabpy/actions/workflows/ci.yml" alt="Workflow Status">
-        <img src="https://img.shields.io/github/actions/workflow/status/kmnhan/erlabpy/ci.yml?logo=github&label=tests" /></a>
-    <a href="https://erlabpy.readthedocs.io/" alt="Documentation Status">
-        <img src="https://img.shields.io/readthedocs/erlabpy?logo=readthedocs&logoColor=white" /></a>
-    <a href="https://results.pre-commit.ci/latest/github/kmnhan/erlabpy/main" alt="pre-commit.ci status">
-        <img src="https://results.pre-commit.ci/badge/github/kmnhan/erlabpy/main.svg" /></a>
-    <a href="https://codecov.io/gh/kmnhan/erlabpy" alt="Codecov Coverage">
-        <img src="https://img.shields.io/codecov/c/github/kmnhan/erlabpy?logo=codecov&logoColor=white" /></a>
-    <a href="https://github.com/astral-sh/ruff" alt="Ruff">
-        <img src="https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json" /></a>
-</p>
+# ERLabPy
+
+[![Supported Python Versions](https://img.shields.io/pypi/pyversions/erlab?logo=python&logoColor=white)](https://pypi.org/project/erlab/)
+[![PyPi](https://img.shields.io/pypi/v/erlab?logo=pypi&logoColor=white)](https://pypi.org/project/erlab/)
+[![Conda Version](https://img.shields.io/conda/vn/conda-forge/erlab?logo=condaforge&logoColor=white)](https://anaconda.org/conda-forge/erlab)
+[![Workflow Status](https://img.shields.io/github/actions/workflow/status/kmnhan/erlabpy/ci.yml?logo=github&label=tests)](https://github.com/kmnhan/erlabpy/actions/workflows/ci.yml)
+[![Documentation Status](https://img.shields.io/readthedocs/erlabpy?logo=readthedocs&logoColor=white)](https://erlabpy.readthedocs.io/)
+[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/kmnhan/erlabpy/main.svg)](https://results.pre-commit.ci/latest/github/kmnhan/erlabpy/main)
+[![Codecov Coverage](https://img.shields.io/codecov/c/github/kmnhan/erlabpy?logo=codecov&logoColor=white)](https://codecov.io/gh/kmnhan/erlabpy)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
+[![SPEC 1 — Lazy Loading of Submodules and Functions](https://img.shields.io/badge/SPEC-1-green?labelColor=%23004811&color=%235CA038)](https://scientific-python.org/specs/spec-0001/)
 
 A library that provides a set of tools and utilities to handle, manipulate, and
 visualize data from condensed matter physics experiments, with a focus on angle-resolved
@@ -71,7 +60,6 @@ with dark mode enabled will show the dark mode screenshots.
   <img alt="Imagetool in action." src="https://github.com/kmnhan/erlabpy/blob/main/docs/source/images/ktool_1_light.png?raw=true">
 </picture>
 
-
 ## Getting Started
 
 To get started, see [installation instructions](https://erlabpy.readthedocs.io/en/stable/getting-started.html).

diff --git a/docs/source/erlab.plotting.rst b/docs/source/erlab.plotting.rst
@@ -2,15 +2,3 @@
 ================================
 
 .. automodule:: erlab.plotting
-
-
-
-
-
-
-
-   .. rubric:: Functions
-
-   .. autosummary::
-
-      load_igor_ct
diff --git a/docs/source/getting-started.rst b/docs/source/getting-started.rst
@@ -75,17 +75,17 @@ Once installed, you can import ERLabPy in your Python scripts or interactive ses
 
 The following import conventions are recommended for ERLabPy modules: ::
 
+  import erlab
   import erlab.analysis as era
   import erlab.interactive as eri
-  import erlab.io
-  import erlab.plotting.erplot as eplt
+  import erlab.plotting as eplt
 
 Along with frequently used modules, your import statements may look like this: ::
 
+  import erlab
   import erlab.analysis as era
   import erlab.interactive as eri
-  import erlab.io
-  import erlab.plotting.erplot as eplt
+  import erlab.plotting as eplt
   import matplotlib.pyplot as plt
   import numpy as np
   import xarray as xr

diff --git a/docs/source/pyplots/norms.py b/docs/source/pyplots/norms.py
@@ -3,7 +3,7 @@
 import numpy as np
 from pyqtgraph.colormap import modulatedBarData
 
-import erlab.plotting.erplot as eplt
+import erlab.plotting as eplt
 
 plt.style.use("khan")
 

diff --git a/docs/source/user-guide/curve-fitting.ipynb b/docs/source/user-guide/curve-fitting.ipynb
@@ -46,11 +46,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import erlab.plotting.erplot as eplt\n",
+    "import erlab.analysis as era\n",
+    "import erlab.plotting as eplt\n",
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
-    "import xarray as xr\n",
-    "from erlab.io.exampledata import generate_data"
+    "import xarray as xr"
    ]
   },
   {
@@ -351,9 +351,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from erlab.analysis.fit.models import MultiPeakModel\n",
-    "\n",
-    "model = MultiPeakModel(npeaks=1, peak_shapes=[\"gaussian\"], fd=False, convolve=False)\n",
+    "model = era.fit.models.MultiPeakModel(\n",
+    "    npeaks=1, peak_shapes=[\"gaussian\"], fd=False, background=\"linear\", convolve=False\n",
+    ")\n",
     "params = model.make_params(p0_center=5.0, p0_width=0.2, p0_height=3.0)\n",
     "params"
    ]
@@ -402,7 +402,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "data = generate_data(bandshift=-0.2, count=5e8, seed=1).T\n",
+    "from erlab.io.exampledata import generate_data\n",
+    "\n",
+    "data = generate_data(seed=1).T\n",
     "cut = data.qsel(ky=0.3)\n",
     "cut.qplot(colorbar=True)"
    ]
@@ -430,19 +432,15 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from erlab.analysis.fit.models import MultiPeakModel\n",
-    "\n",
-    "model = MultiPeakModel(npeaks=4, peak_shapes=[\"lorentzian\"], fd=False, convolve=True)\n",
+    "model = era.fit.models.MultiPeakModel(\n",
+    "    npeaks=2, peak_shapes=[\"lorentzian\"], fd=False, background=\"linear\", convolve=True\n",
+    ")\n",
     "\n",
     "params = model.make_params(\n",
-    "    p0_center=-0.6,\n",
-    "    p1_center=-0.45,\n",
-    "    p2_center=0.45,\n",
-    "    p3_center=0.6,\n",
-    "    p0_width=0.02,\n",
-    "    p1_width=0.02,\n",
-    "    p2_width=0.02,\n",
-    "    p3_width=0.02,\n",
+    "    p0_center=-0.5,\n",
+    "    p1_center=0.5,\n",
+    "    p0_width=0.03,\n",
+    "    p1_width=0.03,\n",
     "    lin_bkg={\"value\": 0.0, \"vary\": False},\n",
     "    const_bkg=0.0,\n",
     "    resolution=0.03,\n",
@@ -557,10 +555,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from erlab.analysis.fit.models import FermiEdgeModel\n",
     "from erlab.io.exampledata import generate_gold_edge\n",
     "\n",
-    "gold = generate_gold_edge(temp=100, Eres=0.02, count=5e5, seed=1)\n",
+    "gold = generate_gold_edge(temp=100, Eres=0.02, seed=1)\n",
     "gold.qplot(cmap=\"Greys\")"
    ]
   },
@@ -580,7 +577,10 @@
    "source": [
     "gold_selected = gold.sel(eV=slice(-0.2, 0.2))\n",
     "result_ds = gold_selected.modelfit(\n",
-    "    \"eV\", FermiEdgeModel(), params={\"temp\": {\"value\": 100.0, \"vary\": False}}, guess=True\n",
+    "    \"eV\",\n",
+    "    era.fit.models.FermiEdgeModel(),\n",
+    "    params={\"temp\": {\"value\": 100.0, \"vary\": False}},\n",
+    "    guess=True,\n",
     ")\n",
     "result_ds"
    ]
@@ -649,12 +649,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from erlab.analysis.fit.models import FermiEdge2dModel\n",
-    "\n",
     "gold_norm = gold_selected / gold_selected.mean(\"eV\")\n",
     "result_ds = gold_norm.T.modelfit(\n",
     "    coords=[\"eV\", \"alpha\"],\n",
-    "    model=FermiEdge2dModel(),\n",
+    "    model=era.fit.models.FermiEdge2dModel(),\n",
     "    params={\"temp\": {\"value\": 100.0, \"vary\": False}},\n",
     "    guess=True,\n",
     ")\n",
@@ -1001,6 +999,7 @@
    "outputs": [],
    "source": [
     "from erlab.io.exampledata import generate_gold_edge\n",
+    "import erlab.plotting as eplt\n",
     "\n",
     "plt.rcParams[\"figure.constrained_layout.use\"] = True"
    ]
@@ -1011,10 +1010,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import erlab.analysis as era\n",
-    "import erlab.plotting.erplot as eplt\n",
-    "\n",
     "gold = generate_gold_edge(temp=100, seed=1)\n",
+    "\n",
     "result = era.gold.poly(\n",
     "    gold,\n",
     "    angle_range=(-15, 15),\n",
@@ -1093,27 +1090,20 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from erlab.analysis.fit.minuit import Minuit\n",
-    "from erlab.analysis.fit.models import MultiPeakModel\n",
-    "\n",
-    "model = MultiPeakModel(npeaks=4, peak_shapes=[\"lorentzian\"], fd=False, convolve=True)\n",
+    "model = era.fit.models.MultiPeakModel(\n",
+    "    npeaks=2, peak_shapes=[\"lorentzian\"], fd=False, convolve=True\n",
+    ")\n",
     "\n",
-    "m = Minuit.from_lmfit(\n",
+    "m = era.fit.minuit.Minuit.from_lmfit(\n",
     "    model,\n",
     "    mdc,\n",
     "    mdc.kx,\n",
-    "    p0_center=-0.6,\n",
-    "    p1_center=-0.45,\n",
-    "    p2_center=0.45,\n",
-    "    p3_center=0.6,\n",
-    "    p0_width=0.02,\n",
-    "    p1_width=0.02,\n",
-    "    p2_width=0.02,\n",
-    "    p3_width=0.02,\n",
-    "    p0_height=1500,\n",
-    "    p1_height=50,\n",
-    "    p2_height=50,\n",
-    "    p3_height=1500,\n",
+    "    p0_center=-0.5,\n",
+    "    p1_center=0.5,\n",
+    "    p0_width=0.03,\n",
+    "    p1_width=0.03,\n",
+    "    p0_height=1000,\n",
+    "    p1_height=1000,\n",
     "    lin_bkg={\"value\": 0.0, \"vary\": False},\n",
     "    const_bkg=0.0,\n",
     "    resolution=0.03,\n",
@@ -1162,11 +1152,18 @@
    "source": [
     "m.interactive()"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "erlab",
    "language": "python",
    "name": "python3"
   },
@@ -1180,7 +1177,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.6"
+   "version": "3.12.7"
   }
  },
  "nbformat": 4,

diff --git a/docs/source/user-guide/indexing.ipynb b/docs/source/user-guide/indexing.ipynb
@@ -57,7 +57,8 @@
    "id": "fd4ee1a3",
    "metadata": {},
    "source": [
-    "First, let us generate some example data: a simple tight binding simulation of graphene."
+    "First, let us generate some example data: a simple tight binding simulation of\n",
+    "graphene-like bands with an exaggerated lattice constant."
    ]
   },
   {
@@ -426,7 +427,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import erlab.plotting.erplot as eplt\n",
+    "import erlab.plotting as eplt\n",
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
     "\n",
@@ -529,7 +530,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "erlab",
    "language": "python",
    "name": "python3"
   },
@@ -543,7 +544,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.6"
+   "version": "3.12.7"
   }
  },
  "nbformat": 4,

diff --git a/docs/source/user-guide/io.ipynb b/docs/source/user-guide/io.ipynb
@@ -354,7 +354,7 @@
    },
    "outputs": [],
    "source": [
-    "import erlab.io\n",
+    "import erlab\n",
     "\n",
     "erlab.io.loaders"
    ]
@@ -925,7 +925,7 @@
     "\n",
     "import numpy as np\n",
     "\n",
-    "import erlab.io\n",
+    "import erlab\n",
     "from erlab.io.exampledata import generate_data_angles\n",
     "\n",
     "\n",
@@ -1494,7 +1494,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "erlab",
    "language": "python",
    "name": "python3"
   },