🎨 Simplify read function and datasets calls

docs/examples/YYYY-MM-DD-task-slug.ipynb

@@ -0,0 +1,48 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "1d7b3b73-75f9-468d-8783-873ebadcab9b",
+   "metadata": {},
+   "source": [
+    "# My task description"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "97ec6631-8473-4a2d-b488-def921bb83de",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import pytometry"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3.9.13 64-bit",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.13"
+  },
+  "vscode": {
+   "interpreter": {
+    "hash": "b0fa6594d8f4cbf19f97940f81e996739fb7646882a419484c72d19e05852a7e"
+   }
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

docs/examples/index.md

@@ -9,4 +9,5 @@ The notebooks do **not** get executed in CI for testing because they involve lar
 :glob:
 :reversed:
 
+*
 ```

docs/guides/curate-data.ipynb

@@ -0,0 +1,60 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "0a9571ac-9c68-437f-ba51-95d06e283cac",
+   "metadata": {},
+   "source": [
+    "# How to curate data"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "0abfc3c7",
+   "metadata": {},
+   "source": [
+    "```{note}\n",
+    "Any guide notebook is automatically run for testing! If a cell fails, the tests will fail! Try changing the assert statement below to observe.\n",
+    "\n",
+    "Note that task notebooks are neither tested, nor being built!\n",
+    "```"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "bcc0c374-0224-4935-b862-0b013c624375",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "assert 1 == 1"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3.9.13 64-bit",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.13"
+  },
+  "vscode": {
+   "interpreter": {
+    "hash": "b0fa6594d8f4cbf19f97940f81e996739fb7646882a419484c72d19e05852a7e"
+   }
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

docs/guides/index.md

@@ -5,5 +5,5 @@ These are guides on specific problems. The notebooks are executed in CI for test
 ```{toctree}
 :maxdepth: 1
 
-
+curate-data
 ```

docs/index.md

@@ -9,8 +9,8 @@
 
 tutorials/index
 api
+examples/index
 guides/index
 notes/index
-examples/index
 changelog
 ```

docs/notes/YYYY-MM-DD-my-design-choice.ipynb

@@ -0,0 +1,43 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "1d7b3b73-75f9-468d-8783-873ebadcab9b",
+   "metadata": {},
+   "source": [
+    "# My design choice"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "97ec6631-8473-4a2d-b488-def921bb83de",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import pytometry"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.7"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

docs/notes/index.md

@@ -7,4 +7,5 @@ These are any notes on design decisions, prototypes, background that do not make
 :glob:
 :reversed:
 
+*
 ```

docs/tutorials/preprocessing.ipynb

@@ -47,9 +47,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from urllib.request import urlretrieve\n",
-    "\n",
-    "path_data, _ = urlretrieve(readfcs.datasets.example(), \"example.fcs\")"
+    "path_data = readfcs.datasets.example()"
    ]
   },
   {
@@ -236,11 +234,8 @@
   }
  ],
  "metadata": {
-  "interpreter": {
-   "hash": "48c3c4927e81daf79217bae0bb1c93e3ab00a11990990ff2e155253980f357b0"
-  },
   "kernelspec": {
-   "display_name": "Python 3.9.7 ('pyto_dev')",
+   "display_name": "Python 3.9.13 64-bit",
    "language": "python",
    "name": "python3"
   },
@@ -254,7 +249,12 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.7"
+   "version": "3.9.13"
+  },
+  "vscode": {
+   "interpreter": {
+    "hash": "b0fa6594d8f4cbf19f97940f81e996739fb7646882a419484c72d19e05852a7e"
+   }
   }
  },
  "nbformat": 4,

docs/tutorials/quickstart.ipynb

@@ -35,9 +35,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from urllib.request import urlretrieve\n",
-    "\n",
-    "path_data, _ = urlretrieve(readfcs.datasets.example(), \"example.fcs\")"
+    "path_data = readfcs.datasets.example()"
    ]
   },
   {
@@ -81,7 +79,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3.9.7 ('pyto_dev')",
+   "display_name": "Python 3.9.13 64-bit",
    "language": "python",
    "name": "python3"
   },
@@ -95,11 +93,11 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.7"
+   "version": "3.9.13"
   },
   "vscode": {
    "interpreter": {
-    "hash": "48c3c4927e81daf79217bae0bb1c93e3ab00a11990990ff2e155253980f357b0"
+    "hash": "b0fa6594d8f4cbf19f97940f81e996739fb7646882a419484c72d19e05852a7e"
    }
   }
  },

docs/tutorials/read_fcs.ipynb

@@ -25,20 +25,19 @@
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": null,
+   "cell_type": "markdown",
    "metadata": {},
-   "outputs": [],
    "source": [
-    "%load_ext autoreload\n",
-    "%autoreload 2"
+    "Read data from `readfcs` package example."
    ]
   },
   {
-   "cell_type": "markdown",
+   "cell_type": "code",
+   "execution_count": null,
    "metadata": {},
+   "outputs": [],
    "source": [
-    "Read data from `readfcs` package example."
+    "path_data = readfcs.datasets.example()"
    ]
   },
   {
@@ -47,9 +46,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from urllib.request import urlretrieve\n",
-    "\n",
-    "path_data, _ = urlretrieve(readfcs.datasets.example(), \"example.fcs\")"
+    "adata = pm.io.read_fcs(path_data)"
    ]
   },
   {
@@ -58,7 +55,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "adata = pm.io.read_fcs(path_data)"
+    "adata"
    ]
   },
   {
@@ -67,7 +64,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "adata"
+    "adata.var"
    ]
   },
   {
@@ -104,11 +101,8 @@
   }
  ],
  "metadata": {
-  "interpreter": {
-   "hash": "48c3c4927e81daf79217bae0bb1c93e3ab00a11990990ff2e155253980f357b0"
-  },
   "kernelspec": {
-   "display_name": "Python 3.9.7 ('pyto_dev')",
+   "display_name": "Python 3.9.13 ('py39')",
    "language": "python",
    "name": "python3"
   },
@@ -122,7 +116,12 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.7"
+   "version": "3.9.13"
+  },
+  "vscode": {
+   "interpreter": {
+    "hash": "ae1fefc8646a06dd2e75004cd934adda7c5727b046986a772e3b44b0ffba9754"
+   }
   }
  },
  "nbformat": 4,

pytometry/read_write/_readfcs.py

@@ -1,5 +1,3 @@
-from pathlib import PosixPath
-
 import readfcs
 from anndata import AnnData
 
@@ -8,27 +6,10 @@ def read_fcs(path: str) -> AnnData:
     """Read FCS file and convert into AnnData format.
 
     Args:
-        path (str): path or Path
+        path: str or Path
             location of fcs file to parse
 
     Returns:
         an AnnData object of the fcs file
     """
-    if isinstance(path, PosixPath):
-        path = path.as_posix()
-
-    adata = readfcs.read(path)
-
-    # move marker name to index. Then merging data becomes easier
-    if "marker" in adata.var_keys():
-        adata.var["channel"] = adata.var_names.values
-        # check in "marker" column that all cells have a value
-        # otherwise, copy from "channel"
-        marker_val = adata.var["marker"].values
-        for idx, marker in enumerate(marker_val):
-            if marker in ["", " "]:
-                marker_val[idx] = adata.var["channel"][idx]
-        adata.var_names = marker_val
-        del adata.var["marker"]
-
-    return adata
+    return readfcs.read(path)

tests/test_base.py

@@ -5,14 +5,6 @@
 
 
 def test_read_fcs():
-    from urllib.request import urlretrieve
-
-    path_data, _ = urlretrieve(readfcs.datasets.example(), "example.fcs")
+    path_data = readfcs.datasets.example()
     adata = read_fcs(path_data)
     assert isinstance(adata, anndata._core.anndata.AnnData)
-
-
-# def test_dummy():
-#    assert example_function("A") == "a"
-#    ex = ExampleClass(1)
-#    assert ex.bar() == "hello"