📝 update docs

.gitignore

@@ -107,6 +107,8 @@ _build
 docs/pytometry.*
 lamin_sphinx
 docs/conf.py
+docs/_static/logo.svg
 
 # data
 docs/tutorials/*.fcs
+docs/tutorials/*.h5ad

README.md

@@ -1,5 +1,6 @@
+[![Stars](https://img.shields.io/github/stars/buettnerlab/pytometry?logo=GitHub&color=yellow)](https://github.com/buettnerlab/pytometry/stargazers)
 <a href="https://gitmoji.dev">
-  <img src="https://img.shields.io/badge/gitmoji-%20😜%20😍-FFDD67.svg?style=flat-square" alt="Gitmoji">
+<img src="https://img.shields.io/badge/gitmoji-%20😜%20😍-FFDD67.svg?style=flat-square" alt="Gitmoji">
 </a>
 
 # Pytometry: Flow & mass cytometry analytics

docs/conf.py

@@ -29,7 +29,7 @@
 }
 
 html_logo = (
-    "https://raw.githubusercontent.com/laminlabs/lamin-profile/main/assets/logo.svg"
+    "https://raw.githubusercontent.com/buettnerlab/pytometry/main/_static/logo.svg"
 )
 html_favicon = "../lamin_sphinx/_static/img/favicon.ico"
 templates_path = ["_templates", "../lamin_sphinx/_templates"]

docs/examples/index.md

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

docs/guides/index.md

@@ -1,9 +1,9 @@
 # Guides
 
-These are guides on specific problems. The notebooks get executed in CI for testing.
+These are guides on specific problems. The notebooks are executed in CI for testing.
 
 ```{toctree}
 :maxdepth: 1
 
-curate-data
+
 ```

docs/notes/index.md

@@ -1,13 +1,10 @@
 # Notes
 
-These are any notes on design decisions, prototypes, background that don't make it into the package.
-
-They can be the material for a blog post or paper later on!
+These are any notes on design decisions, prototypes, background that do not make it into the package.
 
 ```{toctree}
 :maxdepth: 1
 :glob:
 :reversed:
 
-*
 ```

docs/tutorials/quickstart.ipynb

@@ -15,7 +15,17 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from pytometry import ExampleClass, example_function"
+    "import pytometry as pm\n",
+    "import readfcs\n",
+    "import anndata"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "e40e3302",
+   "metadata": {},
+   "source": [
+    "Read fcs file example from the `readfcs` package."
    ]
   },
   {
@@ -25,7 +35,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "example_function(\"A\")"
+    "from urllib.request import urlretrieve\n",
+    "\n",
+    "path_data, _ = urlretrieve(readfcs.datasets.example(), \"example.fcs\")"
    ]
   },
   {
@@ -35,7 +47,25 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ex = ExampleClass(1)"
+    "adata = pm.io.read_fcs(path_data)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8d571a05",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "assert isinstance(adata, anndata._core.anndata.AnnData)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "995de332",
+   "metadata": {},
+   "source": [
+    "Save data to `HDF5` file format."
    ]
   },
   {
@@ -45,13 +75,13 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "assert ex.bar() == \"hello\""
+    "adata.write(\"example.h5ad\")"
    ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "Python 3.9.7 ('pyto_dev')",
    "language": "python",
    "name": "python3"
   },
@@ -65,7 +95,12 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.12"
+   "version": "3.9.7"
+  },
+  "vscode": {
+   "interpreter": {
+    "hash": "48c3c4927e81daf79217bae0bb1c93e3ab00a11990990ff2e155253980f357b0"
+   }
   }
  },
  "nbformat": 4,

pytometry/__init__.py

@@ -7,15 +7,23 @@
 This is the complete API reference:
 
 .. autosummary::
+   :recursive:
    :toctree: .
 
-   example_function
-   ExampleClass
+   read_write.read_fcs
+   preprocessing.split_signal
+   preprocessing.compensate
+   preprocessing.find_indexes
+   tools.normalize_arcsinh
+   tools.normalize_logicle
+   tools.normalize_biExp
+
 """
 
 __version__ = "0.0.1"  # denote a pre-release for 0.1.0 with 0.1a1
 
 from . import preprocessing as pp
 from . import read_write as io
 from . import tools as tl
-from ._core import ExampleClass, example_function  # noqa
+
+# from ._core import ExampleClass, example_function  # noqa

pytometry/preprocessing/_process_data.py

@@ -1,11 +1,9 @@
-import math
 import re
+from typing import Optional
 
 import numpy as np
 import pandas as pd
 import seaborn as sb
-
-# import FlowCytometryTools as fct
 from anndata import AnnData
 from matplotlib import pyplot as plt
 from matplotlib import rcParams
@@ -16,7 +14,7 @@
 # import os.path
 
 
-def create_comp_mat(spillmat, relevant_data=""):
+def create_comp_mat(spillmat: pd.DataFrame, relevant_data: str = "") -> pd.DataFrame:
     """Creates a compensation matrix from a spillover matrix.
 
     Args:
@@ -25,7 +23,7 @@ def create_comp_mat(spillmat, relevant_data=""):
             Defaults to ''.
 
     Returns:
-        pd.DataFrame: Compensation matrix as pandas dataframe.
+        pd.DataFrame of the compensation matrix.
     """
     if relevant_data == "":
         comp_mat = np.linalg.inv(spillmat)
@@ -43,11 +41,11 @@ def find_indexes(
     key_added="signal_type",
     data_type="facs",
     copy: bool = False,
-):
+) -> Optional[AnnData]:
     """Find channels of interest for computing compensation.
 
     Args:
-        adata (AnnData): anndata object
+        adata (AnnData): AnnData object
         var_key (str, optional): key where to check if a feature is an area,
              height etc. type of value. Use `var_names` if None.
         key_added (str, optional): key where result vector is added to the adata.var.
@@ -108,7 +106,7 @@ def compensate(
     comp_matrix=None,
     matrix_type="spillover",
     copy: bool = False,
-):
+) -> Optional[AnnData]:
     """Computes compensation for data channels.
 
     Args:
@@ -186,7 +184,7 @@ def split_signal(
     option="area",
     data_type="facs",
     copy: bool = False,
-):
+) -> Optional[AnnData]:
     """Method to filter out height or area data.
 
     Args:
@@ -290,7 +288,7 @@ def plotdata(
     number = len(names)
 
     columns = 3
-    rows = math.ceil(number / columns)
+    rows = np.ceil(number / columns)
 
     fig = plt.figure()
     fig.subplots_adjust(hspace=0.4, wspace=0.6)