test automatic documentation with Sphinx

docs/Makefile

+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/conf.py

+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'Autoencoder BigData_Praktikum'
+copyright = '2023, Franziska Roepke, Harpreet Int-Veen, Paul Kühnel'
+author = 'Franziska Roepke, Harpreet Int-Veen, Paul Kühnel'
+release = '0.1'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = ['sphinx.ext.todo',
+              'sphinx.ext.duration',
+              'sphinx.ext.doctest',
+              'sphinx.ext.autodoc',
+              'sphinx.ext.viewcode',
+              'sphinx.ext.autosummary']
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', '*.loom', '.DS_Store']
+
+source_suffix = ['.rst', '.md']
+
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'alabaster'
+html_static_path = ['_static']

docs/source/index.rst

+.. Autoencoder BigData_Praktikum documentation master file, created by
+   sphinx-quickstart on Fri May 26 14:36:45 2023.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to Autoencoder BigData_Praktikum's documentation!
+=========================================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
+
+.. note::
+
+   This project is under active development.
+
+
+Development
+===========
+
+Notes
+-----
+
+Some notes during development:
+
+.. toctree::
+
+   Notizen
+
+
+Main documentation
+==================
+
+See API
+
+API
+===
+
+.. autosummary::
+   :toctree: generated
+
+   main_methods

main_methods.py

 import loompy
 import pandas as pd
+import os
 
 
 def loom_to_pandas_df(file_name="testfiles/test.loom"):
     """
-    :param file_name: the name of the loom file (default is: "testfiles/test.loom")
+    :param file_name: the name of the loom file (default is:
+    "testfiles/test.loom")
     :return: pandas DataFrame
     """
     df = pd.DataFrame  # Empty DataFrame - to return in case of wrong formatting
-
-    if file_name[-4:] != ".loom":
+    if file_name[-5:] != ".loom":
         print(f"{file_name} is not a valid file name. Only use '.loom' files!")
 
     with loompy.connect(file_name) as ds:
         try:
-            df = pd.DataFrame(data=ds[:, :], index=ds.ra.Gene, columns=ds.ca.input_name)
+            df = pd.DataFrame(data=ds[:, :],
+                              index=ds.ra.Gene,
+                              columns=ds.ca.input_name)
         except AttributeError or ValueError or OSError:
-            raise Exception(f"The loom file {file_name} does not exist or has no valid format!")
+            raise Exception(f"The loom file {file_name} does not exist or has "
+                            f"no valid format!")
 
     return df
+
+
+print(os.getcwd())
+os.chdir("testfiles")
+print(os.getcwd())
+# print(os.listdir())
+test_df = loom_to_pandas_df("AllelicExpressionPatterns-mouse-brain-SS2.loom")
+test_df.info()
+test_df.describe()
+print(".........")
+print(test_df)

testfiles/loom_test.py

 import loompy
 import pandas as pd
 
-ds = loompy.connect("test.loom")
-df = pd.DataFrame(data=ds[:, :], index=ds.ra.Gene, columns=ds.ca.input_name)
-ds.close()
+with loompy.connect("AllelicExpressionPatterns-mouse-brain-SS2.loom") as ds:
 
-df.info()
-df.describe()
\ No newline at end of file
+    #print(ds.ra.Gene)
+    print(ds.ca.input_name)
+    print(ds[0:10, 0:10])
+
+
+
+
+
+#ds = loompy.connect("test.loom")
+#df = pd.DataFrame(data=ds[:, :], index=ds.ra.Gene, columns=ds.ca.input_name)
+#ds.close()
+
+#df.info()
+#df.describe()