Move and restructure constants

.gitignore

@@ -149,7 +149,7 @@ dmypy.json
 *.gmt
 *.gmx
 
-data/
+# Directories to ignore
 figures/
 
 # OS specifics

analysis/[INITIALS]-[DATE]_sample_notebook.ipynb

@@ -82,7 +82,7 @@
    },
    "outputs": [],
    "source": [
-    "from fancypackage.ul import DATA_DIR"
+    "from fancypackage import FilePaths"
    ]
   },
   {
@@ -124,7 +124,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Any data should be stored in the `data` directory, or somewhere centrally on the cluster. The `data` directly is acessible from anywhere in this repo via `DATA_DIR`: "
+    "Any data should be stored in the `data` directory, or somewhere centrally on the cluster. The `data` directly is acessible from anywhere in this repo via `FilePaths`: "
    ]
   },
   {
@@ -136,12 +136,12 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "/nas/groups/treutlein/USERS/mlange/github/analysis_template/data\n"
+      "/nas/groups/treutlein/USERS/mlange/github/data\n"
      ]
     }
    ],
    "source": [
-    "print(DATA_DIR)"
+    "print(FilePaths.DATA)"
    ]
   },
   {
@@ -178,7 +178,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.10"
+   "version": "3.12.7"
   },
   "toc": {
    "base_numbering": 1,

src/fancypackage/__init__.py

@@ -1,6 +1,7 @@
 from importlib.metadata import version
 
 from . import pl, pp, tl, ul
+from ._constants import FilePaths
 
-__all__ = ["pl", "pp", "tl", "ul"]
+__all__ = ["pl", "pp", "tl", "ul", "FilePaths"]
 __version__ = version("fancypackage")

src/fancypackage/_constants.py

@@ -0,0 +1,11 @@
+from pathlib import Path
+
+
+class FilePaths:
+    """Paths to the data and figures directories."""
+
+    ROOT = Path(__file__).parents[3].resolve()
+
+    DATA = ROOT / "data"
+    FIGURES = ROOT / "figures"
+    DATASET_1 = DATA / "dataset_1"

src/fancypackage/ul/__init__.py

@@ -1 +1 @@
-from .constants import DATA_DIR, FIG_DIR
+from .basic import basic_utility

src/fancypackage/ul/basic.py

@@ -0,0 +1,17 @@
+from anndata import AnnData
+
+
+def basic_utility(adata: AnnData) -> int:
+    """Run a utility function
+
+    Parameters
+    ----------
+    adata
+        The AnnData object to do something with
+
+    Returns
+    -------
+    Some integer value.
+    """
+    print("Implement a utility function here.")
+    return 0