Merge pull request #432 from hakonanes/main-into-develop-post-0.11-re…

…lease Main into develop post 0.11 release
pyxem · Feb 27, 2023 · e3e10a4 · e3e10a4
2 parents 4eb6151 + c7af446
commit e3e10a4
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -36,7 +36,7 @@ jobs:
 
       - name: Check code style of Jupyter notebooks
         run: |
-          black doc/**/*.ipynb --check
+          black --diff --line-length 77 doc/tutorials/*.ipynb
 
   # Make sure all necessary files will be included in a release
   manifest:

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,17 +1,15 @@
 repos:
   - repo: https://github.com/psf/black
-    rev: 22.3.0
+    rev: 23.1.0
     hooks:
+      - id: black
       - id: black-jupyter
+        files: \.ipynb
+        args: [--line-length=77]
   - repo: https://github.com/pycqa/isort
-    rev: 5.10.1
+    rev: 5.12.0
     hooks:
       - id: isort
         name: isort (python)
         args:
-          [
-            "--profile",
-            "black",
-            "--filter-files",
-            "--force-sort-within-sections",
-          ]
+          [--profile=black, --filter-files, --force-sort-within-sections]
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -2,13 +2,12 @@
 Changelog
 =========
 
-All notable changes to the ``orix`` project are documented in this file.
+All user facing changes to this project are documented in this file. The format is based
+on `Keep a Changelog <https://keepachangelog.com/en/1.0.0/>`__, and this project tries
+its best to adhere to `Semantic Versioning <https://semver.org/spec/v2.0.0.html>`__.
 
-The format is based on `Keep a Changelog <https://keepachangelog.com/en/1.0.0/>`__, and
-this project adheres to `Semantic Versioning <https://semver.org/spec/v2.0.0.html>`__.
-
-Unreleased
-==========
+2023-02-09 - version 0.11.0
+===========================
 
 Added
 -----
@@ -46,9 +45,6 @@ Changed
 - Bumped minimal version of ``diffpy.structure >= 3.0.2``.
 - Only ASTAR .ang files return crystal maps with ``"nm"`` as scan unit.
 
-Deprecated
-----------
-
 Removed
 -------
 - Parameter ``z`` when creating a ``CrystalMap`` and the ``z`` and ``dz`` attributes of
@@ -64,9 +60,6 @@ Fixed
 -----
 - Reading of EDAX TSL .ang files with ten columns should now work.
 
-Security
---------
-
 2022-10-25 - version 0.10.2
 ===========================
 

diff --git a/doc/tutorials/clustering_across_fundamental_region_boundaries.ipynb b/doc/tutorials/clustering_across_fundamental_region_boundaries.ipynb
@@ -76,11 +76,15 @@
     "\n",
     "# Cluster 2\n",
     "centre2 = Rotation.from_axes_angles((1, 0, 0), np.pi / 4)\n",
-    "cluster2 = Rotation.random_vonmises(n_orientations, alpha=alpha, reference=centre2)\n",
+    "cluster2 = Rotation.random_vonmises(\n",
+    "    n_orientations, alpha=alpha, reference=centre2\n",
+    ")\n",
     "\n",
     "# Cluster 3\n",
     "centre3 = Rotation.from_axes_angles((1, 1, 0), np.pi / 3)\n",
-    "cluster3 = Rotation.random_vonmises(n_orientations, alpha=alpha, reference=centre3)\n",
+    "cluster3 = Rotation.random_vonmises(\n",
+    "    n_orientations, alpha=alpha, reference=centre3\n",
+    ")\n",
     "\n",
     "# Stack and map into the Oh fundamental zone\n",
     "ori = Orientation.stack([cluster1, cluster2, cluster3]).flatten()\n",
@@ -172,9 +176,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "dbscan = DBSCAN(eps=np.deg2rad(17), min_samples=20, metric=\"precomputed\").fit(\n",
-    "    D2.astype(np.float32)\n",
-    ")\n",
+    "dbscan = DBSCAN(\n",
+    "    eps=np.deg2rad(17), min_samples=20, metric=\"precomputed\"\n",
+    ").fit(D2.astype(np.float32))\n",
     "print(\"Labels:\", np.unique(dbscan.labels_))"
    ]
   },
@@ -202,7 +206,9 @@
    "source": [
     "color_names = [to_rgb(f\"C{i}\") for i in range(6)]  # ['C0', 'C1', ...]\n",
     "\n",
-    "colors_naive = label2rgb(dbscan_naive.labels_, colors=color_names, bg_label=-1)\n",
+    "colors_naive = label2rgb(\n",
+    "    dbscan_naive.labels_, colors=color_names, bg_label=-1\n",
+    ")\n",
     "colors = label2rgb(dbscan.labels_, colors=color_names, bg_label=-1)"
    ]
   },
@@ -256,7 +262,9 @@
     "    plt.draw()\n",
     "\n",
     "\n",
-    "ani = animation.FuncAnimation(fig, animate, np.linspace(75, 360 + 74, 720), interval=25)"
+    "ani = animation.FuncAnimation(\n",
+    "    fig, animate, np.linspace(75, 360 + 74, 720), interval=25\n",
+    ")"
    ]
   }
  ],
@@ -276,7 +284,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13"
+   "version": "3.10.8"
   }
  },
  "nbformat": 4,

diff --git a/doc/tutorials/clustering_misorientations.ipynb b/doc/tutorials/clustering_misorientations.ipynb
@@ -127,25 +127,27 @@
    "outputs": [],
    "source": [
     "ckey = plot.IPFColorKeyTSL(D6)\n",
-    "ckey.plot()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "fig, ax = plt.subplots(ncols=2, figsize=(15, 10))\n",
+    "\n",
     "directions = [(1, 0, 0), (0, 1, 0)]\n",
     "titles = [\"X\", \"Y\"]\n",
-    "for i in range(len(ax)):\n",
+    "\n",
+    "fig, axes = plt.subplots(ncols=2, figsize=(15, 10))\n",
+    "for i, ax in enumerate(axes):\n",
     "    ckey.direction = Vector3d(directions[i])\n",
     "    # Invert because orix assumes lab2crystal when coloring orientations\n",
-    "    ax[i].imshow(ckey.orientation2color(~ori))\n",
-    "    ax[i].set_title(f\"IPF-{titles[i]}\")\n",
-    "    ax[i].axis(\"off\")\n",
-    "fig.tight_layout()"
+    "    ax.imshow(ckey.orientation2color(~ori))\n",
+    "    ax.set_title(f\"IPF-{titles[i]}\")\n",
+    "    ax.axis(\"off\")\n",
+    "\n",
+    "# Add color key\n",
+    "ax_ipfkey = fig.add_axes(\n",
+    "    [0.932, 0.37, 0.1, 0.1],  # (Left, bottom, width, height)\n",
+    "    projection=\"ipf\",\n",
+    "    symmetry=ori.symmetry.laue,\n",
+    ")\n",
+    "ax_ipfkey.plot_ipf_color_key()\n",
+    "ax_ipfkey.set_title(\"\")\n",
+    "fig.subplots_adjust(wspace=0.01)"
    ]
   },
   {
@@ -267,7 +269,9 @@
     "# Compute clusters\n",
     "dbscan = DBSCAN(eps=0.05, min_samples=10, metric=\"precomputed\").fit(D)\n",
     "\n",
-    "unique_labels, all_cluster_sizes = np.unique(dbscan.labels_, return_counts=True)\n",
+    "unique_labels, all_cluster_sizes = np.unique(\n",
+    "    dbscan.labels_, return_counts=True\n",
+    ")\n",
     "print(\"Labels:\", unique_labels)\n",
     "\n",
     "n_clusters = unique_labels.size - 1\n",
@@ -287,7 +291,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "unique_cluster_labels = unique_labels[1:]  # Without the \"no-cluster\" label -1\n",
+    "unique_cluster_labels = unique_labels[\n",
+    "    1:\n",
+    "]  # Without the \"no-cluster\" label -1\n",
     "cluster_sizes = all_cluster_sizes[1:]\n",
     "\n",
     "rc = Rotation.from_axes_angles((0, 0, 1), 15, degrees=True)\n",
@@ -383,7 +389,9 @@
    "source": [
     "mori2 = (~twin_theory).outer(cluster_means)\n",
     "sym_op = D6.outer(D6).unique()\n",
-    "mori2_equiv = D6.outer(~twin_theory).outer(sym_op).outer(cluster_means).outer(D6)\n",
+    "mori2_equiv = (\n",
+    "    D6.outer(~twin_theory).outer(sym_op).outer(cluster_means).outer(D6)\n",
+    ")\n",
     "D2 = mori2_equiv.angle.min(axis=(0, 2, 4))"
    ]
   },
@@ -438,8 +446,12 @@
     "cluster_sizes = all_cluster_sizes[1:]\n",
     "cluster_sizes_scaled = 1000 * cluster_sizes / cluster_sizes.max()\n",
     "\n",
-    "fig, ax = plt.subplots(figsize=(5, 5), subplot_kw=dict(projection=\"ipf\", symmetry=D6))\n",
-    "ax.scatter(cluster_means.axis, c=colors, s=cluster_sizes_scaled, alpha=0.5, ec=\"k\")"
+    "fig, ax = plt.subplots(\n",
+    "    figsize=(5, 5), subplot_kw=dict(projection=\"ipf\", symmetry=D6)\n",
+    ")\n",
+    "ax.scatter(\n",
+    "    cluster_means.axis, c=colors, s=cluster_sizes_scaled, alpha=0.5, ec=\"k\"\n",
+    ")"
    ]
   },
   {
@@ -462,7 +474,9 @@
    },
    "outputs": [],
    "source": [
-    "wireframe_kwargs = dict(color=\"black\", linewidth=0.5, alpha=0.1, rcount=361, ccount=361)\n",
+    "wireframe_kwargs = dict(\n",
+    "    color=\"black\", linewidth=0.5, alpha=0.1, rcount=361, ccount=361\n",
+    ")\n",
     "fig = mori.scatter(\n",
     "    projection=\"axangle\",\n",
     "    wireframe_kwargs=wireframe_kwargs,\n",
@@ -477,7 +491,9 @@
     "handle_kwds = dict(marker=\"o\", color=\"none\", markersize=10)\n",
     "handles = []\n",
     "for i in range(n_clusters):\n",
-    "    line = Line2D([0], [0], label=i + 1, markerfacecolor=colors[i], **handle_kwds)\n",
+    "    line = Line2D(\n",
+    "        [0], [0], label=i + 1, markerfacecolor=colors[i], **handle_kwds\n",
+    "    )\n",
     "    handles.append(line)\n",
     "ax.legend(\n",
     "    handles=handles,\n",

diff --git a/doc/tutorials/clustering_orientations.ipynb b/doc/tutorials/clustering_orientations.ipynb
diff --git a/doc/tutorials/crystal_directions.ipynb b/doc/tutorials/crystal_directions.ipynb
@@ -66,7 +66,8 @@
    "outputs": [],
    "source": [
     "tetragonal = Phase(\n",
-    "    point_group=\"4\", structure=Structure(lattice=Lattice(0.5, 0.5, 1, 90, 90, 90))\n",
+    "    point_group=\"4\",\n",
+    "    structure=Structure(lattice=Lattice(0.5, 0.5, 1, 90, 90, 90)),\n",
     ")\n",
     "print(tetragonal)\n",
     "print(tetragonal.structure.lattice)"
@@ -383,7 +384,8 @@
    "outputs": [],
    "source": [
     "trigonal = Phase(\n",
-    "    point_group=\"321\", structure=Structure(lattice=Lattice(4.9, 4.9, 5.4, 90, 90, 120))\n",
+    "    point_group=\"321\",\n",
+    "    structure=Structure(lattice=Lattice(4.9, 4.9, 5.4, 90, 90, 120)),\n",
     ")\n",
     "trigonal"
    ]
@@ -733,7 +735,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "o2 = Orientation.from_euler([10, 20, 30], symmetry=trigonal.point_group, degrees=True)\n",
+    "o2 = Orientation.from_euler(\n",
+    "    [10, 20, 30], symmetry=trigonal.point_group, degrees=True\n",
+    ")\n",
     "o2"
    ]
   },