Update installation instructions and Python version requirements in README and notebooks

Author: k-krakowski

README.md

@@ -30,11 +30,10 @@ It provides a convenient graphical interface for running searches and visualizin
 # 🛠️ Installation
 
 ### Basic installation
-
-You can install pLAST directly via:
+pLAST requires Python version 3.9 to 3.12. You can install pLAST directly using:
 
 ```bash
-pip install https://github.com/labstructbioinf/pLAST
+pip install plast
 ```
 
 ---

notebooks/installation.ipynb

@@ -46,6 +46,8 @@
     "`conda env create -n plast -f core-env.yml`\n",
     "\n",
     "Alternatively, install the following dependencies manually:\n",
+    "- `python >=3.9, <=3.12`\n",
+    "- `pip >= 25.3`\n",
     "- `hmmer >= 3.4`\n",
     "- `mmseqs2 >= 17.b804f`\n",
     "- `prodigal >= 2.6.3`\n",
@@ -72,6 +74,26 @@
     "## pip"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "vscode": {
+     "languageId": "shellscript"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "pip install plast"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "or"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,

pyproject.toml

@@ -18,7 +18,7 @@ classifiers = [
     "Operating System :: OS Independent",
 ]
 keywords = ["plasmid", "network", "language", "word2vec", "pLAST", "model"]
-requires-python = ">=3.9, <3.14"
+requires-python = ">=3.9, <=3.12"
 dependencies = [
     "gensim==4.3.3",
     "numba>=0.61.2",