Merge pull request #4 from quadbio/update_package

Update package

analysis/ML-2024-04-24_sample_notebook.ipynb → analysis/[INITIALS]-[DATE]_sample_notebook.ipynb

@@ -50,14 +50,23 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 2,
    "metadata": {
     "ExecuteTime": {
      "end_time": "2021-05-31T09:25:02.307098Z",
      "start_time": "2021-05-31T09:25:02.291254Z"
     }
    },
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "The autoreload extension is already loaded. To reload it, use:\n",
+      "  %reload_ext autoreload\n"
+     ]
+    }
+   ],
    "source": [
     "%load_ext autoreload\n",
     "%autoreload 2"
@@ -72,7 +81,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 3,
    "metadata": {
     "ExecuteTime": {
      "end_time": "2021-05-31T09:25:05.984402Z",
@@ -84,7 +93,7 @@
    "source": [
     "# import single-cell packages\n",
     "import scanpy as sc\n",
-    "from fancypackage import DATA_DIR, FIG_DIR"
+    "from fancypackage.ul import DATA_DIR, FIG_DIR"
    ]
   },
   {
@@ -96,14 +105,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Running Scanpy 1.9.3, on 2024-04-24 17:16.\n"
+      "Running Scanpy 1.10.3, on 2024-10-16 17:32.\n"
      ]
     }
    ],
@@ -120,7 +129,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -158,14 +167,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "/Users/mlange/Projects/analysis_template/data\n"
+      "/nas/groups/treutlein/USERS/mlange/github/analysis_template/data\n"
      ]
     }
    ],
@@ -188,7 +197,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "py310",
+   "display_name": "analysis_template",
    "language": "python",
    "name": "python3"
   },
@@ -202,7 +211,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.12"
+   "version": "3.11.10"
   },
   "toc": {
    "base_numbering": 1,

src/fancypackage/__init__.py

@@ -1,3 +1,6 @@
-from .core import DATA_DIR, FIG_DIR
+from importlib.metadata import version
 
-__all__ = ["DATA_DIR", "FIG_DIR"]
+from . import pl, pp, tl, ul
+
+__all__ = ["pl", "pp", "tl", "ul"]
+__version__ = version("fancypackage")

src/fancypackage/pl/__init__.py

@@ -0,0 +1 @@
+from .basic import BasicClass, basic_plot

src/fancypackage/pl/basic.py

@@ -0,0 +1,63 @@
+from anndata import AnnData
+
+
+def basic_plot(adata: AnnData) -> int:
+    """Generate a basic plot for an AnnData object.
+
+    Parameters
+    ----------
+    adata
+        The AnnData object to preprocess.
+
+    Returns
+    -------
+    Some integer value.
+    """
+    print("Import matplotlib and implement a plotting function here.")
+    return 0
+
+
+class BasicClass:
+    """A basic class.
+
+    Parameters
+    ----------
+    adata
+        The AnnData object to preprocess.
+    """
+
+    my_attribute: str = "Some attribute."
+    my_other_attribute: int = 0
+
+    def __init__(self, adata: AnnData):
+        print("Implement a class here.")
+
+    def my_method(self, param: int) -> int:
+        """A basic method.
+
+        Parameters
+        ----------
+        param
+            A parameter.
+
+        Returns
+        -------
+        Some integer value.
+        """
+        print("Implement a method here.")
+        return 0
+
+    def my_other_method(self, param: str) -> str:
+        """Another basic method.
+
+        Parameters
+        ----------
+        param
+            A parameter.
+
+        Returns
+        -------
+        Some integer value.
+        """
+        print("Implement a method here.")
+        return ""

src/fancypackage/pp/__init__.py

@@ -0,0 +1 @@
+from .basic import basic_preproc

src/fancypackage/pp/basic.py

@@ -0,0 +1,17 @@
+from anndata import AnnData
+
+
+def basic_preproc(adata: AnnData) -> int:
+    """Run a basic preprocessing on the AnnData object.
+
+    Parameters
+    ----------
+    adata
+        The AnnData object to preprocess.
+
+    Returns
+    -------
+    Some integer value.
+    """
+    print("Implement a preprocessing function here.")
+    return 0

src/fancypackage/tl/__init__.py

@@ -0,0 +1 @@
+from .basic import basic_tool

src/fancypackage/tl/basic.py

@@ -0,0 +1,17 @@
+from anndata import AnnData
+
+
+def basic_tool(adata: AnnData) -> int:
+    """Run a tool on the AnnData object.
+
+    Parameters
+    ----------
+    adata
+        The AnnData object to preprocess.
+
+    Returns
+    -------
+    Some integer value.
+    """
+    print("Implement a tool to run on the AnnData object.")
+    return 0

src/fancypackage/ul/__init__.py

@@ -0,0 +1 @@
+from .constants import DATA_DIR, FIG_DIR