From 138313f02da59a2a563f55ec1fc91567f08f570f Mon Sep 17 00:00:00 2001
From: jgostick <jgostick@gmail.com>
Date: Sun, 1 Mar 2026 11:26:36 -0500
Subject: [PATCH 01/11] Update documentation generation workflow

Added '--extra extras' to the 'uv sync' command for documentation generation.
---
 .github/workflows/generate-docs.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/generate-docs.yml b/.github/workflows/generate-docs.yml
index c2ec1bc47b..20bb8d5230 100644
--- a/.github/workflows/generate-docs.yml
+++ b/.github/workflows/generate-docs.yml
@@ -27,7 +27,7 @@ jobs:
 
       - name: Install dependencies
         run: |
-          uv sync --group docs --group interactive
+          uv sync --group docs --group interactive --extra extras
 
       - name: Build the documentation
         run: |

From 64d3f2ae45f659777f89dc35bb98cc4299679935 Mon Sep 17 00:00:00 2001
From: GitHub Action <action@github.com>
Date: Sun, 1 Mar 2026 16:27:22 +0000
Subject: [PATCH 02/11] =?UTF-8?q?maint:=20bump=20version:=203.6.1=20?=
 =?UTF-8?q?=E2=86=92=203.6.1-dev1=20[skip=20bump]?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 pyproject.toml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 68d72eeca4..19ccb1ad89 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "openpnm"
-version = "3.6.1"
+version = "3.6.1-dev1"
 description = "A framework for conducting pore network modeling simulations of multiphase transport in porous materials"
 authors = [{ name = "OpenPNM Team", email = "jgostick@gmail.com" }]
 maintainers = [
@@ -220,7 +220,7 @@ path = "src/openpnm/__version__.py"
 packages = ["src/openpnm"]
 
 [tool.bumpversion]
-current_version = "3.6.1"
+current_version = "3.6.1-dev1"
 parse = """(?x)
     (?P<major>0|[1-9]\\d*)\\.
     (?P<minor>0|[1-9]\\d*)\\.

From 7271519475bc5ba8958d8802e60c873dfb848448 Mon Sep 17 00:00:00 2001
From: jgostick <jgostick@gmail.com>
Date: Thu, 12 Mar 2026 23:06:22 -0400
Subject: [PATCH 03/11] updating example

---
 examples/applications/porosity.ipynb | 34 ++++++++++++++++------------
 1 file changed, 20 insertions(+), 14 deletions(-)

diff --git a/examples/applications/porosity.ipynb b/examples/applications/porosity.ipynb
index 05c99f27b2..a5053bc0ac 100644
--- a/examples/applications/porosity.ipynb
+++ b/examples/applications/porosity.ipynb
@@ -16,7 +16,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -41,7 +41,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -59,7 +59,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 12,
    "metadata": {},
    "outputs": [
     {
@@ -133,7 +133,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 13,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -143,7 +143,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 14,
    "metadata": {},
    "outputs": [
     {
@@ -203,19 +203,19 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 15,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Porosity from image: 63.3%\n"
+      "Porosity from image: 64.9%\n"
      ]
     },
     {
      "data": {
-      "image/png": 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HCQAZBCcAZBCcAFBNNc79qaV0Rf1EDRPa9/miDlrdzm/hdbpSXkf1OAEgg+AEgAyCEwAyCE4AqObBQW1RKQVmoPoXP6H66HECQAbBCQAZBCcAZBCcAJBBcAJABsEJABkEJwDU+jxOoPbmZ5vnSWfR4wSADIITADIITgDIoMYJVAVr29JZ9DgBIIPgBIAMghMAMqhxAlWpXN+X13zTyqfHCQAZBCcAZBCcAJBBcAJABoODakw5Dkwo10EcAC3R4wSADIITADIITgDIoMZZRcqxftke560GSjWxGH3lP6/1OAEgg+AEgAyCEwAyqHFWkEqtYXbE467k+ghQ2fQ4ASCD4ASADIITADKocVIVdU81z85r685SK7/TWpnXuaiKfp96nADQ0cG5cuXKuPjii2PIkCHRr1+/GD16dNx9991Njlm+fHmceeaZxf7hw4fHTTfdFFu2bNmfHwcAlXur9pFHHomLLrooTjnllLjjjjtiwIAB8eyzz8a6desaj1m9enWcc845cfzxx8ddd91V7Js9e3asXbs2Fi5c2N6PAQDKMzg3b94c11xzTVx44YWxYMGC6N695Q7r7bffHoMHD45HH300Bg4cWGw76qij4vrrry+C97zzzmufs69y1Vrr6Ahqnh3Xll2lVn+n1VLzXFTFv6+sW7U/+MEPYsOGDTFz5swiNN9+++3YvXt3s3BdvHhxXHXVVY2hmaTATb3TBx54oP3OHgDKuce5ZMmSIgzXr18fH//4x2PNmjXRv3//uPrqq2Pu3LnRp0+fePrpp2Pnzp0xbty4Jl/bq1evGDNmTKxatWqfP6d+w64YOfb3Le6bNuUDMW3q4JzTBoCYe+/GmDtvU6u50yHBmWqUKRQ/9rGPxeTJk+Nv//Zvi9ux//iP/xibNm2KH/7wh1FfX18cW1dX1+zr07alS5fu8+ekTuz6+pYfxOYtTXu4ANAWKT9ay5YcWcGZRsW+8847MXXq1MZRtJdcckns2LEj7rvvvpgxY0Zs3bq12N67d+9mX596pA379yaVTuuG9Whx38ABZtBAe6qUGpqaZ9vbpjMsqsAaZsqPw+t6tNrj3KPy2D7B2bdv3+LzFVdc0WT7lVdeWQTnY489Vkw/SbZv397s67dt29b4PfYmheYLK4/OOTUA2KtU5mut1JfKg23tjWZ130aMGFF8HjZsWJPthx12WPF548aNjbdoG27Zvl/a1vA9AKASZQXnqaeeWnxOg4Pe76WXXio+Dx06tFgMoWfPnrFixYomx6TbuWl+ZxogBAA1EZyXXXZZ8fnb3/52k+3f+ta3irA8++yzY9CgQXHuuefG/fffH2+99VbjMfPnzy9qpJMmTWqvcweATpdV40yrBV177bXxL//yL8Xo2rPOOqsYVfvjH/84brvttsbbsGme5/jx44v9U6ZMKVYOmjNnTrHwwcSJEzvqsVS8ShmkUQk6oy0rcXAE1cm1WOZL7t17770xcuTI+M53vhMPPvhgHHnkkcUczptvvrnxmLFjxxZzPqdPnx7Tpk2Lgw8+uHH6CgDUVHAedNBB8eUvf7n42Ju0wPuyZcsO5NwAoOyYFAkAGbyRNeynWp2QD7VOjxMAMghOAMggOAEggxontBM1z8qbq6suzf7Q4wSADIITADIITgDIoMZZRvast1i7FjrWvp5jaqC0RI8TADIITgDIIDgBIIMaJ0ArzM2lJXqcAJBBcAJABsEJABnUOLuIOZpQG89bc0Grjx4nAGQQnACQQXACQAbBCQAZDA6CGufNBTqWRRSqjx4nAGQQnACQQXACQAY1zk5iwQMqhZpnx1LzrHx6nACQQXACQAbBCQAZ1DiB7EXK1ezbj5pn5dHjBIAMghMAMghOAMigxgntxBsW0x7UPMufHicAZBCcAJBBcAJABjXOTmL9z+prTzVNqE16nACQQXACQAbBCQAZ1DipCuqNHce6tNCUHicAZBCcAJBBcAJABsEJABkMDgKaMBiovFj0vfzocQJABsEJABkEJwBkEJwAkEFwAkAGwQkAGQQnAGQQnACQQXACQAbBCQAZBCcAZLBWbRm98bI1QtveVrQf1115q9Tr//wRY6q2rfQ4ASCD4ASADIITADKocQJQFbXx89twTu1RB9XjBIAMghMAMghOAKj0Gudr9b3K7v55Z8wP2vNnlFsbdJZKnbcG1axaXo/O3+Nx7M/rjR4nAHRkcK5duzY++clPxhFHHBH9+vWLD33oQzFjxox45513mhy3fPnyOPPMM4tjhg8fHjfddFNs2bIl98cBQOXeqn3xxRfjtNNOi0GDBsWNN94YQ4YMicceeyy+/OUvx1NPPRU//elPi+NWr14d55xzThx//PFx1113xbp162L27NlF6C5cuLCjHgsAlFdwzp8/PzZt2hS//vWv48QTTyy2TZkyJXbv3h3f+973YuPGjTF48OC4/fbbi8+PPvpoDBw4sDjuqKOOiuuvvz4eeeSROO+88zrm0QBAOQXn5s2bi8/Dhg1rsr2uri66d+8evXr1Ko5ZvHhxTJs2rTE0k2uuuabY9sADD1RkcLZHQTlXrQwWMhiovNq/Wq+zSlEOz4daugbO/7/H+lppfURsbf/gPPvss+NrX/taTJ48Ob7yla/EIYccUtQy77nnnqKG2b9//1i2bFns3Lkzxo0b1+RrU6iOGTMmVq1atc+fsz22xtLSwy3uGxnHxZHdRuWcNgDE86U18UKsbTV32iorOCdOnBhf/epXY9asWfGzn/2scfsXvvCF+Ju/+Zvi3/X19Y290D2lbUuXLm3Tz2rtQeyMd3NOGQAa8yMnINttHmeqVU6YMCEuvfTSosf58MMPF0GaRs6mAUNbt753Ur179272tX369Gncvy+9o28rJ3xQ7ikDQKT8aC1bOqzH+aMf/agYDLRmzZpiOkpyySWXFIODpk+fHldccUX07fveSW3fvr3Z12/btq1x/96kB/bhbhdGOdtXDaAj6hTVUosqhxoOlItyeD5U6mtJrlTmOzJaLvWl8mBbwzNrHuc3v/nNOOWUUxpDs8HFF19czONM9cuGW7QNt2zfL20bMWJEzo8EgLKSFZwbNmyIXbt2Ndv+7rvv1R3ToKDRo0dHz549Y8WKFU2O2bFjRzG/Mw0QAoCaCM5Ro0YVvcp0q/b9fvjDHxbTUU4++eRicYRzzz037r///njrrbeazAFNKwdNmjSp/c4eADpZVo3z1ltvLVb++fCHP1wMBEqDgx566KFi23XXXdd4G3bmzJkxfvz4OOuss4qaaFo5aM6cOcX8zTQyl86pjXRV3aIcajZQrjw/aqzHmUbTpnmbp556alHvvPnmm+PZZ58tgjLN5WwwduzYWLJkSTEQKC16MG/evGLu54IFCzriMQBAp8mejpLWqv35z3++z+PSAu9pMQQAqCbeVgwAKv2NrKtBV6xtuye1FNrjuqmVOX6dpSva0++0felxAkAGwQkAGQQnAGRQ46yhmifsj5auVXXPyuL31b70OAEgg+AEgAyCEwAyCE4AyCA4ASCD4ASADIITADIITgDIYAEEIJtFw6llepwAkEFwAkAGwQkAGdQ4gQOm5kkt0eMEgAyCEwAyCE4AyCA4ASCD4ASADIITADIITgDIYB4n0OHzOvd0/ogxWp2KpccJABkEJwBkEJwAkEGNE+h01ralkulxAkAGwQkAGQQnAGRQ4wTKft5nezB3lPaixwkAGQQnAGQQnACQQXACQAbBCQAZBCcAZBCcAJBBcAJABgsgVNEEbwA6nh4nAGQQnACQQXACQAY1zg6ipglQnfQ4ASCD4ASADIITADKocVax/XnjXrVZgL3T4wSADIITADIITgDIoMa5n8qhFrg/NcwD/Z7l8LgBupIeJwBkEJwAkEFwAkAGNc42UtuD6nsOd8Q4AaqfHicAZBCcAJBBcAJABsEJAJU+OKjPwdtj/JRfxsAB3WPa1MFdfTplY38GMjxfWhM7493oGQfFkd1Gtfs51Nqgqbn3bozNW3a7NrVlWWnv5zkVGJxvvb07ZszZGIfX9RCcB+iFWBvbY2v0jr5xZHhCHai58zbF+vpdrs12oC3bj+d553KrFgAyCE4AqPRbtQCdYc8avQURaAs9TgDIIDgBIEO3UqlUijLRq1evePfddxv/3717RN2wHl16TuXktfpe2V+TRtQ2SCNr29uhdTuiltRv2BW7d7s2q7Ut9+c5Vg46+nleC7b/XxsedNBBsWPHjsoJzh49esTu9EwCgC7QvXv32LVrV+UMDurTp09s27atCNDDDjusq08HgBrxyiuvFIGZcmhfyqrHCQDlzuAgAMggOAEgg+AEgAyCEwAqNTi3b98e06dPjxEjRkTfvn3j9NNPj8WLF3f1aZW13/zmN3HjjTfGiSeeGP3794+RI0fGZZddFmvWrGl27G9/+9uYOHFiDBgwIIYMGRJXX311vPrqq11y3pVi5syZ0a1btxg9enSzfcuXL48zzzwz+vXrF8OHD4+bbroptmzZ0iXnWa5WrlwZF198cXG9pXZK7Xj33Xc3OUY7ts3atWvjk5/8ZBxxxBFFW37oQx+KGTNmxDvvvKM9O1lZjaq94oorYsGCBXHzzTfHcccdF9/97neLYPiP//iP4gWK5j7xiU/EsmXLYtKkSXHyySfHyy+/HN/4xjeKF/DHH3+88QV/3bp1ccopp8SgQYMaX+Bnz55dBO2TTz5ZLD5BU6nN/uAP/qAIzqOOOiqeeeaZxn2rV6+OM844I44//viYMmVKcWxqz4985COxcOFCTRkRjzzySFx00UXFdXf55ZcXf7A9++yzxVztv//7v9eOGV588cXi+Z2ev1OnTi3+EHnssceK18j0h8lPf/pT7dmZSmXiiSeeSAFeuvPOOxu3bd26tXTMMceUzjjjjC49t3K2bNmy0vbt25tsW7NmTal3796lT33qU43bPvvZz5b69u1bev755xu3LV68uGjz++67r1PPuVJcfvnlpT/+4z8unXXWWaUTTzyxyb4LLrigVFdXV3rzzTcbt/3zP/9z0Z6LFi0q1brULsOGDSv92Z/9WWnXrl2tHqcd22bmzJnFtfXMM8802X7NNdcU29944w3t2YnKJjhvvfXWUo8ePZq8ECWzZs0qLowXXnihy86tEo0dO7b4aHDYYYeVJk2a1Oy4UaNGlc4555xOPrvy96tf/aq4Hv/rv/6rWXCma7Rnz57FNft+6Q+YAQMGlCZPnlyqdffcc0/xvP3v//7v4v9btmxpFqDase2mT59etOerr77abHv37t2L9tWenadsapyrVq2KUaNGxcCBA5tsP+200xpvjdE26Q+iDRs2xKGHHlr8f/369cWqGOPGjWt2bGrf1Pb8v7R6yOc+97m47rrr4qSTTmrWNE8//XTs3LmzWXum291jxozRnhGxZMmS4rmcrr10uzvdpk3//+xnP1usDqYd85x99tnF58mTJxevhenW7b/927/FPffcU5Re0vgG12XnKZvgrK+vj7q6umbbG7a99NJLXXBWlen73/9+8YKV6koNbZu01r5vvPFGMTCL99x7773x/PPPx1e/+tUWm2Rf7elafW8gS/rj4mMf+1icf/758ZOf/CSuvfbaom0/85nPaMdMaVBfuh7TYMlUM05jE9JAofQH3ty5c7VnJyubtWq3bt0avXv3bra9Yd3AtJ99+93vfhc33HBDMXDl05/+dJO221f7trS/1rz++uvxpS99Ke64444YOnRoi8fsqz1dq1EMPkujPdNAloZRtJdccknxrhP33XdfMRpUO+ZJA9QmTJgQl156aRxyyCHx8MMPx6xZs4oR3WlkvfasweBM009a6vU03NZJ+9m7NKL2wgsvLEbepdHJabH897ed9t23L37xi8WIxfSX/N6u1b21p2v1/9sojZR/vyuvvLIIzjQiNE2p0I5t86Mf/agYvZ2mmaXpKA1/iKQRymkKX2pn12UN3qpNt7gaboG9X8O2NLeT1r355ptxwQUXxKZNm+IXv/hFk/ZquKXYWvumoNDbfO/24rx584qaUbrd+txzzxUfKQzT+8Smf6fb2vtqT9fq/z9fhw0b1qR9Gt71aOPGjdoxwze/+c3iFm1DaDZIU1FSzz6NU3Bd1mBwpkEV6a+pzZs3N9n+xBNPNO6nZemFPc2XS+330EMPxQknnNBk/+GHH17cdlyxYkWzr01zOLXte1JdOP0Fn4Lz6KOPbvxI12Bq2/TvdIsxzY3t2bNns/ZMtyHTwA3tGXHqqac2tun7NdR/0/WoHdsuDfZr6T0i0x90Saona89OVCoTjz/+eLN5nNu2bSsde+yxpdNPP71Lz62c7dy5s3TxxRcX0yMefvjhVo+bOnVqMY/z/dN6lixZUrR5mjpAqRjq/+CDDzb7SFNRRo4cWfw7TU9JJk6cWMzj3Lx5c2PTfetb3yrac+HChTXfnCtXriza4sorr2zSFldccUVxra5fv147ZvjoRz9a6tWrV+l//ud/mmz/+Mc/XkxH0Z6dq2yCM0nzDBvmx6VJ+ePHjy/+n+bU0bLPf/7zxQvURRddVJo/f36zjwYpMA855JBiQYm77767mB87ePDg0kknnVT8gULrWloA4amnnioWmTjllFOKPzy+8IUvlPr06VM677zzNOX/ufbaa4tr87LLLiv90z/9U/H8Tv+/7bbbtON+zitO87FnzJhRtGdaPCK153XXXac9azk400pBt9xyS2n48OHFi9If/uEfln7xi1909WmV/Yt6evK09vF+adWR9MLer1+/0gc+8IFiZaGXX365y869koMzWbp0afHHXQrMoUOHlm644YYmPdBat2PHjtJf//Vfl4488sjSQQcdVNw9mjt3brPjtGPbV1dLYZleH1N7psVL0opC7777rvbsZGW1Vi0AlLuyGRwEAJVAcAJABsEJABkEJwBkEJwAkEFwAkAGwQkAGQQnAGQQnACQQXACQAbBCQAZBCcARNv9L/ALWwDAkptqAAAAAElFTkSuQmCC",
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",
       "text/plain": [
        "<Figure size 640x480 with 1 Axes>"
       ]
@@ -226,7 +226,13 @@
    ],
    "source": [
     "np.random.seed(10)\n",
-    "im = ps.generators.overlapping_spheres(shape=[100, 100, 100], r=10, porosity=0.5, maxiter=0)\n",
+    "im = ps.generators.overlapping_spheres(\n",
+    "    shape=[100, 100, 100],\n",
+    "    r=10,\n",
+    "    porosity=0.5,\n",
+    "    maxiter=0,\n",
+    "    seed=0,\n",
+    ")\n",
     "plt.imshow(im[:, :, 50])\n",
     "im_poro = ps.metrics.porosity(im)\n",
     "print(f\"Porosity from image: {im_poro*100:.1f}%\")"
@@ -234,17 +240,17 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 16,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/html": [
-       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\"><span style=\"color: #7fbfbf; text-decoration-color: #7fbfbf\">[09:28:01] </span><span style=\"color: #808000; text-decoration-color: #808000\">WARNING </span> Disabling paralelization as overlap exceeds than chunk size.                      <span style=\"color: #7f7f7f; text-decoration-color: #7f7f7f\">_snow2.py:214</span>\n",
+       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\"><span style=\"color: #7fbfbf; text-decoration-color: #7fbfbf\">[10:39:29] </span><span style=\"color: #808000; text-decoration-color: #808000\">WARNING </span> Disabling paralelization as overlap exceeds than chunk size.                      <span style=\"color: #7f7f7f; text-decoration-color: #7f7f7f\">_snow2.py:214</span>\n",
        "</pre>\n"
       ],
       "text/plain": [
-       "\u001b[2;36m[09:28:01]\u001b[0m\u001b[2;36m \u001b[0m\u001b[33mWARNING \u001b[0m Disabling paralelization as overlap exceeds than chunk size.                      \u001b[2m_snow2.py\u001b[0m\u001b[2m:\u001b[0m\u001b[2m214\u001b[0m\n"
+       "\u001b[2;36m[10:39:29]\u001b[0m\u001b[2;36m \u001b[0m\u001b[33mWARNING \u001b[0m Disabling paralelization as overlap exceeds than chunk size.                      \u001b[2m_snow2.py\u001b[0m\u001b[2m:\u001b[0m\u001b[2m214\u001b[0m\n"
       ]
      },
      "metadata": {},
@@ -274,14 +280,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 17,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Porosity from pnm: 67.7%\n"
+      "Porosity from pnm: 73.7%\n"
      ]
     }
    ],

From aa88da5de56096b7e6e5b6413e8802a62f03a8fe Mon Sep 17 00:00:00 2001
From: jgostick <jgostick@gmail.com>
Date: Thu, 12 Mar 2026 23:06:29 -0400
Subject: [PATCH 04/11] more fixes

---
 src/openpnm/visualization/_plottools.py | 49 ++++++++++++++++---------
 1 file changed, 32 insertions(+), 17 deletions(-)

diff --git a/src/openpnm/visualization/_plottools.py b/src/openpnm/visualization/_plottools.py
index 5ed9f3da97..852cfccb54 100644
--- a/src/openpnm/visualization/_plottools.py
+++ b/src/openpnm/visualization/_plottools.py
@@ -148,23 +148,27 @@ class of matplotlib, so check their documentation for additional
     throat_pos = np.column_stack((xyz[P1], xyz[P2])).reshape((Ts.size, 2, dim.sum()))
 
     # Deal with optional style related arguments
-    if 'c' in kwargs.keys():
-        color = kwargs.pop('c')
-    color = mcolors.to_rgb(color) + tuple([alpha])
     if isinstance(cmap, str):
         try:
             cmap = plt.colormaps.get_cmap(cmap)
         except AttributeError:
             cmap = plt.cm.get_cmap(cmap)
+    kwargs['cmap'] = cmap
     # Override colors with color_by if given
-    if color_by is not None:
+    if color_by is None:
+        if 'c' in kwargs.keys():
+            color = kwargs.pop('c')
+        color = mcolors.to_rgb(color) + tuple([alpha])
+        kwargs['color'] = color
+        _ = kwargs.pop('cmap', None)
+    else:
         color_by = np.array(color_by)
         if len(color_by) != len(Ts):
             color_by = color_by[Ts]
         if not np.all(np.isfinite(color_by)):
             color_by[~np.isfinite(color_by)] = 0
             logger.warning('nans or infs found in color_by array, setting to 0')
-        color = color_by
+        kwargs['array'] = color_by
     if size_by is not None:
         if len(size_by) != len(Ts):
             size_by = size_by[Ts]
@@ -180,13 +184,22 @@ class of matplotlib, so check their documentation for additional
     vmax = kwargs.pop('vmax', None)
 
     if ThreeD:
-        lc = Line3DCollection(throat_pos, array=color, cmap=cmap, alpha=alpha,
-                              linestyles=linestyle, linewidths=linewidth,
-                              antialiaseds=np.ones_like(network.Ts), **kwargs)
+        lc = Line3DCollection(
+            throat_pos,
+            alpha=alpha,
+            linestyles=linestyle,
+            linewidths=linewidth,
+            antialiaseds=np.ones_like(network.Ts),
+            **kwargs,
+        )
     else:
-        lc = LineCollection(throat_pos, array=color, cmap=cmap, alpha=alpha,
-                            linestyles=linestyle, linewidths=linewidth,
-                            antialiaseds=np.ones_like(network.Ts), **kwargs)
+        lc = LineCollection(
+            throat_pos, alpha=alpha,
+            linestyles=linestyle,
+            linewidths=linewidth,
+            antialiaseds=np.ones_like(network.Ts),
+            **kwargs,
+        )
         if label_by is not None:
             for count, (P1, P2) in enumerate(network.conns[Ts, :]):
                 i, j, k = np.mean(network.coords[[P1, P2], :], axis=0)
@@ -332,16 +345,17 @@ def plot_coordinates(network,
     Xl, Yl, Zl = network['pore.coords'].T
 
     # Parse formatting kwargs
-    if 'c' in kwargs.keys():
-        color = kwargs.pop('c')
-    if 's' in kwargs.keys():
-        markersize = kwargs.pop('s')
     if isinstance(cmap, str):
         try:
             cmap = plt.colormaps.get_cmap(cmap)
         except AttributeError:
             cmap = plt.cm.get_cmap(cmap)
-    if color_by is not None:
+    kwargs['cmap'] = cmap
+    if color_by is None:
+        if 'c' in kwargs.keys():
+            color = kwargs.pop('c')
+        _ = kwargs.pop('cmap')
+    else:
         color_by = np.array(color_by)
         if len(color_by) != len(Ps):
             color_by = color_by[Ps]
@@ -349,6 +363,8 @@ def plot_coordinates(network,
             color_by[~np.isfinite(color_by)] = 0
             logger.warning('nans or infs found in color_by array, setting to 0')
         color = color_by
+    if 's' in kwargs.keys():
+        markersize = kwargs.pop('s')
     if size_by is not None:
         if len(size_by) != len(Ps):
             size_by = size_by[Ps]
@@ -375,7 +391,6 @@ def plot_coordinates(network,
                         s=markersize,
                         marker=marker,
                         alpha=alpha,
-                        cmap=cmap,
                         **kwargs)
         if label_by is not None:
             for count, (i, j, k) in enumerate(network.coords[Ps, :]):

From 9fe4d415cadd290e4e7344213229f1b686925385 Mon Sep 17 00:00:00 2001
From: GitHub Action <action@github.com>
Date: Fri, 13 Mar 2026 03:42:24 +0000
Subject: [PATCH 05/11] =?UTF-8?q?maint:=20bump=20version:=203.6.1-dev1=20?=
 =?UTF-8?q?=E2=86=92=203.6.1-dev2=20[skip=20bump]?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 pyproject.toml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 19ccb1ad89..552a398362 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "openpnm"
-version = "3.6.1-dev1"
+version = "3.6.1-dev2"
 description = "A framework for conducting pore network modeling simulations of multiphase transport in porous materials"
 authors = [{ name = "OpenPNM Team", email = "jgostick@gmail.com" }]
 maintainers = [
@@ -220,7 +220,7 @@ path = "src/openpnm/__version__.py"
 packages = ["src/openpnm"]
 
 [tool.bumpversion]
-current_version = "3.6.1-dev1"
+current_version = "3.6.1-dev2"
 parse = """(?x)
     (?P<major>0|[1-9]\\d*)\\.
     (?P<minor>0|[1-9]\\d*)\\.

From 93b7c79c9e218e4c7a8332e05ea3195c06110694 Mon Sep 17 00:00:00 2001
From: TKlokgieters <72444546+TKlokgieters@users.noreply.github.com>
Date: Wed, 15 Apr 2026 15:59:20 +0200
Subject: [PATCH 06/11] Fix variable name from 'newshape' to 'shape' in reshape

Numpy 2.1 changed variable name to shape. In Numpy 2.4 newshape is definitely removed
---
 src/openpnm/_skgraph/queries/_funcs.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/openpnm/_skgraph/queries/_funcs.py b/src/openpnm/_skgraph/queries/_funcs.py
index a73346e9c2..a17ea1c9bc 100644
--- a/src/openpnm/_skgraph/queries/_funcs.py
+++ b/src/openpnm/_skgraph/queries/_funcs.py
@@ -168,7 +168,7 @@ def find_connected_nodes(network, inds, flatten=True, logic="or"):
             if len(inds):
                 temp = temp.astype(float)
                 temp[inds] = np.nan
-            temp = np.reshape(temp, newshape=[len(edges), 2], order="F")
+            temp = np.reshape(temp, shape=[len(edges), 2], order="F")
             neighbors = temp
         else:
             neighbors = [np.array([], dtype=np.int64) for i in range(len(edges))]

From 17a3b32f01f65e03b07be1847e8dab752bd867b2 Mon Sep 17 00:00:00 2001
From: TKlokgieters <72444546+TKlokgieters@users.noreply.github.com>
Date: Wed, 15 Apr 2026 16:05:48 +0200
Subject: [PATCH 07/11] Update numpy version constraint in pyproject.toml

Required for newshape name change to shape in np.reshape

Possibly later versions also allowed
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 552a398362..4cbe9121e1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -25,7 +25,7 @@ dependencies = [
     "matplotlib-inline>=0.1.7",
     "networkx>=3.5",
     "numba>=0.61",
-    "numpy<2.2",
+    "numpy=2.1",
     "pandas>=2.3.2",
     "pyamg>=5.3.0",
     "pypardiso; platform_system != 'Darwin' and (platform_machine == 'x86_64' or platform_machine == 'AMD64')",

From acc6ddaf8fe7bc34040c1a330b585160229dbd91 Mon Sep 17 00:00:00 2001
From: TKlokgieters <72444546+TKlokgieters@users.noreply.github.com>
Date: Wed, 15 Apr 2026 16:20:02 +0200
Subject: [PATCH 08/11] Update numpy version constraint in pyproject.toml

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 4cbe9121e1..faf78a908b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -25,7 +25,7 @@ dependencies = [
     "matplotlib-inline>=0.1.7",
     "networkx>=3.5",
     "numba>=0.61",
-    "numpy=2.1",
+    "numpy>=2.1,<2.2",
     "pandas>=2.3.2",
     "pyamg>=5.3.0",
     "pypardiso; platform_system != 'Darwin' and (platform_machine == 'x86_64' or platform_machine == 'AMD64')",

From cf4969d4a64c549850ac103d4b4e9a7e78a6f1e3 Mon Sep 17 00:00:00 2001
From: TKlokgieters <72444546+TKlokgieters@users.noreply.github.com>
Date: Wed, 15 Apr 2026 17:26:31 +0200
Subject: [PATCH 09/11] Use positional np.reshape argument for (new)shape

As suggested by @gerlero
---
 src/openpnm/_skgraph/queries/_funcs.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/openpnm/_skgraph/queries/_funcs.py b/src/openpnm/_skgraph/queries/_funcs.py
index a17ea1c9bc..3d11783ecc 100644
--- a/src/openpnm/_skgraph/queries/_funcs.py
+++ b/src/openpnm/_skgraph/queries/_funcs.py
@@ -168,7 +168,7 @@ def find_connected_nodes(network, inds, flatten=True, logic="or"):
             if len(inds):
                 temp = temp.astype(float)
                 temp[inds] = np.nan
-            temp = np.reshape(temp, shape=[len(edges), 2], order="F")
+            temp = np.reshape(temp, [len(edges), 2], order="F")
             neighbors = temp
         else:
             neighbors = [np.array([], dtype=np.int64) for i in range(len(edges))]

From 22a84998bf49ff95c3366f6a30913d1f51d2cc22 Mon Sep 17 00:00:00 2001
From: TKlokgieters <72444546+TKlokgieters@users.noreply.github.com>
Date: Wed, 15 Apr 2026 17:27:40 +0200
Subject: [PATCH 10/11] Restate original numpy versioning

Due to positional reshape argument no version constraint necessary
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index faf78a908b..552a398362 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -25,7 +25,7 @@ dependencies = [
     "matplotlib-inline>=0.1.7",
     "networkx>=3.5",
     "numba>=0.61",
-    "numpy>=2.1,<2.2",
+    "numpy<2.2",
     "pandas>=2.3.2",
     "pyamg>=5.3.0",
     "pypardiso; platform_system != 'Darwin' and (platform_machine == 'x86_64' or platform_machine == 'AMD64')",

From 94762df8596c64890e4936227b94b41bd810f735 Mon Sep 17 00:00:00 2001
From: GitHub Action <action@github.com>
Date: Thu, 16 Apr 2026 13:01:43 +0000
Subject: [PATCH 11/11] =?UTF-8?q?maint:=20bump=20version:=203.6.1-dev2=20?=
 =?UTF-8?q?=E2=86=92=203.6.1-dev3=20[skip=20bump]?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 pyproject.toml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 552a398362..fcfc846cbd 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "openpnm"
-version = "3.6.1-dev2"
+version = "3.6.1-dev3"
 description = "A framework for conducting pore network modeling simulations of multiphase transport in porous materials"
 authors = [{ name = "OpenPNM Team", email = "jgostick@gmail.com" }]
 maintainers = [
@@ -220,7 +220,7 @@ path = "src/openpnm/__version__.py"
 packages = ["src/openpnm"]
 
 [tool.bumpversion]
-current_version = "3.6.1-dev2"
+current_version = "3.6.1-dev3"
 parse = """(?x)
     (?P<major>0|[1-9]\\d*)\\.
     (?P<minor>0|[1-9]\\d*)\\.