Use PyPI release of AtomDB when possible

theochem · Oct 5, 2024 · 754ec58 · 754ec58
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Showing 4 changed files with 30 additions and 12 deletions.
diff --git a/website/examples/getting_started.ipynb b/website/examples/getting_started.ipynb
@@ -37,6 +37,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "## Install the AtomDB package\n",
+    "## prefer to use the release from PyPI\n",
+    "#! pip install qc-AtomDB\n",
+    "## alternatively, install the development version from GitHub\n",
     "# ! python -m pip install git+https://github.com/theochem/AtomDB.git"
    ]
   },
@@ -114,7 +118,7 @@
     }
    ],
    "source": [
-    "%%bash \n",
+    "%%bash\n",
     "c_0_3_json_output=$(python -m atomdb -q slater C 0 3)\n",
     "\n",
     "# Define an array of keys\n",
@@ -159,7 +163,7 @@
    "source": [
     "from atomdb import load\n",
     "\n",
-    "c_slater = load(elem='C', charge=0, mult=3, dataset='slater')"
+    "c_slater = load(elem=\"C\", charge=0, mult=3, dataset=\"slater\")"
    ]
   },
   {
@@ -268,10 +272,10 @@
     "import numpy as np\n",
     "\n",
     "# Define a uniform radial grid and evaluate the density\n",
-    "rad_grid = np.linspace(0., 6., num=100)\n",
+    "rad_grid = np.linspace(0.0, 6.0, num=100)\n",
     "# density and kinetic energy density functions (total)\n",
-    "dens_spline = c_slater.dens_func(spin='t',log=True)\n",
-    "ked_spline = c_slater.ked_func(spin='t')\n",
+    "dens_spline = c_slater.dens_func(spin=\"t\", log=True)\n",
+    "ked_spline = c_slater.ked_func(spin=\"t\")\n",
     "\n",
     "dens = dens_spline(rad_grid)\n",
     "ked = ked_spline(rad_grid)\n",
@@ -311,14 +315,14 @@
     "ax1 = fig.add_subplot(121)\n",
     "ax2 = fig.add_subplot(122)\n",
     "\n",
-    "ax1.plot(rad_grid, dens, '-r', linewidth=2)\n",
+    "ax1.plot(rad_grid, dens, \"-r\", linewidth=2)\n",
     "ax1.set(xlabel=\"Radial distance [Bohr]\", ylabel=\"Density [Bohr$^{-3}$]\")\n",
-    "ax1.set_yscale('log')\n",
+    "ax1.set_yscale(\"log\")\n",
     "ax1.set_ylim(top=1000, bottom=0.00001)\n",
-    "ax1.set_xlim(left=0., right=6)\n",
-    "ax1.set_title(f'Spherically averaged density')\n",
+    "ax1.set_xlim(left=0.0, right=6)\n",
+    "ax1.set_title(f\"Spherically averaged density\")\n",
     "\n",
-    "ax2.plot(rad_grid, ked, '-b', linewidth=2)\n",
+    "ax2.plot(rad_grid, ked, \"-b\", linewidth=2)\n",
     "ax2.set(xlabel=\"Radial distance [Bohr]\", ylabel=\"KED E$_{h}$ Bohr$^{-3}$\")\n",
     "plt.show()"
    ]
@@ -354,7 +358,7 @@
    ],
    "source": [
     "# Dumping Data to a JSON string\n",
-    "c_slater_json= c_slater.to_json()\n",
+    "c_slater_json = c_slater.to_json()\n",
     "\n",
     "# Print the first 90 characters of the JSON string\n",
     "print(c_slater_json[:90])"

diff --git a/website/examples/hello_atomdb.ipynb b/website/examples/hello_atomdb.ipynb
@@ -48,9 +48,15 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "# # Install packages in Google Colab.\n",
+    "# # Don't run this cell if packages/data is already in your environment\n",
     "# ! pip install git+https://github.com/theochem/iodata.git\n",
     "# ! pip install git+https://github.com/theochem/grid.git\n",
-    "# ! pip install git+https://github.com/theochem/AtomDB.git@dev"
+    "## Install the AtomDB package\n",
+    "## prefer to use the release from PyPI\n",
+    "#! pip install qc-AtomDB\n",
+    "## alternatively, install the development version from GitHub\n",
+    "# ! python -m pip install git+https://github.com/theochem/AtomDB.git"
    ]
   },
   {

diff --git a/website/examples/promolecule_intro.ipynb b/website/examples/promolecule_intro.ipynb
@@ -21,6 +21,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "## Install the AtomDB package\n",
+    "## prefer to use the release from PyPI\n",
+    "#! pip install qc-AtomDB\n",
+    "## alternatively, install the development version from GitHub\n",
     "# ! python -m pip install git+https://github.com/theochem/AtomDB.git"
    ]
   },

diff --git a/website/examples/promolecule_nci.ipynb b/website/examples/promolecule_nci.ipynb
@@ -30,6 +30,10 @@
     "# # Don't run this cell if packages/data is already in your environment\n",
     "# ! pip install git+https://github.com/theochem/iodata.git\n",
     "# ! pip install git+https://github.com/theochem/grid.git\n",
+    "## Install the AtomDB package\n",
+    "## prefer to use the release from PyPI\n",
+    "#! pip install qc-AtomDB\n",
+    "## alternatively, install the development version from GitHub\n",
     "# ! python -m pip install git+https://github.com/theochem/AtomDB.git\n",
     "\n",
     "# # Download the example files\n",