diff --git a/docs/source/conf.py b/docs/source/conf.py
index b0c41eeb89dacef71fd40a7258ccbdc25c78e8ab..351e3b5d2e6001513b6c2b799a7f204bdae4d767 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -35,10 +35,10 @@ release = "0.0.1"
# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
-extensions = ["myst_parser", "sphinx.ext.autodoc",'sphinx_tabs.tabs']
napoleon_google_docstring = False
-
+extensions = ["myst_parser", "sphinx.ext.autodoc","sphinx_tabs.tabs","sphinx.ext.napoleon","sphinx.ext.autodoc.typehints"]
+napoleosn_use_param=True
# Add any paths that contain templates here, relative to this directory.
templates_path = ["_templates"]
@@ -58,13 +58,13 @@ exclude_patterns = []
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = []
+html_static_path = ['_static']
sphinx_tabs_valid_builders = ['linkcheck']
sphinx_tabs_disable_tab_closing = True
-html_css_files=['https://raw.githack.com/ines/termynal/master/termynal.css']
+html_css_files=['https://raw.githack.com/Ganz1285/termynal/master/termynal.css']
sphinx_tabs_disable_css_loading = True
diff --git a/docs/source/getting_started/Installation.md b/docs/source/getting_started/Installation.md
index e1b4a2602f345b6aaa14994fc95e15c3f223fc67..055da84955e047fb8f8d243d56b6e01562cf40be 100644
--- a/docs/source/getting_started/Installation.md
+++ b/docs/source/getting_started/Installation.md
@@ -23,7 +23,7 @@ To Install **BiTIA** using pip, run this command:
-## Configuration
+## Configuration files
_TODO_: Order of searching configuration file.
diff --git a/docs/source/getting_started/Working.md b/docs/source/getting_started/Working.md
index 610e2527dd44e9651079e8757ac0a38d0a29ad87..f717293e7bfaae8a4959cf03eb93c183c879a7f3 100644
--- a/docs/source/getting_started/Working.md
+++ b/docs/source/getting_started/Working.md
@@ -1,4 +1,35 @@
-# Working with BiTIA CLI
+# WORKING WITH BiTIA
+
+To List available commands and options in bitia, execute `bitia --help`
+
+<div id="termynal" data-termynal>
+ <span data-ty="input">python -m bitia --help </span>
+ <span data-ty>Usage: python -m bitia [OPTIONS] COMMAND [ARGS]...
+
+ <b>Callback</b>
+
+<b><i>Options</i></b> <br><br>
+<b>--verbose</b> [debug|info|warning] [default: VerbosityLevel.warning]<br>
+<b>--plain</b> --no-plain [default: no-plain] <br>
+<b>--server</b> TEXT [default: None] <br>
+<b>--install-completion</b> Install completion for the current shell. <br>
+<b>--show-completion</b> Show completion for the current shell, to copy it or customize the installation. <br>
+<b>--help </b> Show this message and exit. <br>
+
+ <b><i>Commands</i></b> <br><br>
+
+ <b>checksum</b> value that represents the number of bits in a transmission message<br>
+ <b>create-container</b> Create container for the pipeline. The container starts running immediately on the server. Use command `logs` to stream the output. <br>
+ <b>list-container</b> List the remote server associated with the pipeline. <br>
+ <b>logs</b> Stream logs for the most recent run of a given pipeline. <br>
+ <b>run</b> Run a pipeline <br>
+ <b>submit</b> Submit your pipelin (url, directory, zip_file). <br>
+ <b>version</b> version information <br>
+
+</span>
+
+</div>
+
The three commands that are the core of BiTIA's functionality are:
- run
- submit
@@ -7,11 +38,27 @@ The three commands that are the core of BiTIA's functionality are:
<link type="text/css" href="../_static/./css/termynal.css" />
-### Bitia run can be employed in the following ways:
+## Bitia run
+
+<div id="termynal1" data-termynal>
+ <span data-ty="input"><b>python -m bitia run --help</span>
+ <span data-ty>
+Usage: python -m bitia run [OPTIONS] USER_INPUT<br>
+
+ Run a pipeline<br>
+
+ <b><i>Arguments</i></b> <br><br>
+ \* <b>user_input</b> TEXT [default: None] [required]<br><br>
+<i><b>Options</i></b> <br><br>
+<b>--rerun</b> --no-rerun [default: no-rerun]
+<b>--output-lines </b> TEXT<
+<b>--help </b> Show this message and exit.
+</span>
+</div>
-#### 1. Running commands
+### 1. Running commands
-<div id="termynal" data-termynal>
+<div id="termynal2" data-termynal>
<span data-ty="input">bitia run "samtools convert <foo.fa|http://y.com/foo.fa>"</span>
<span data-ty="progress"></span>
</div>
@@ -30,9 +77,9 @@ The above code will:
- Display the resulting output to the user console
-#### 2. Running Pipelines
+### 2. Running Pipelines
-<div id="termynal1" data-termynal>
+<div id="termynal3" data-termynal>
<span data-ty="input">bitia run pipeline.sh</span>
<span data-ty="progress"></span>
</div>
@@ -61,10 +108,10 @@ The above code will:
- executing the commands given in the pipeline
- Displays the resulting output to the user console
-#### 3. Running Directories with multiple required files
+### 3. Running Directories with multiple required files
-<div id="termynal3" data-termynal>
+<div id="termynal4" data-termynal>
<span data-ty="input">bitia run work/</span>
<span data-ty="progress"></span>
</div>
@@ -106,6 +153,6 @@ The above code will:
- Displays the resulting output to the user console
-<script type="text/javascript" src="https://raw.githack.com/tiangolo/fastapi/master/docs/en/docs/js/termynal.js" data-termynal-container="#termynal|#termynal1|#termynal3"></script>
-
+<script type="text/javascript" src="https://raw.githack.com/tiangolo/fastapi/master/docs/en/docs/js/termynal.js" data-termynal-container="#termynal|#termynal1|#termynal2|#termynal3|#termynal4"></script>
+
diff --git a/docs/source/index.md b/docs/source/index.md
index 22c99710ba8838eca8beaaea0f7ff09ddb67d39a..eb85c99bb8caee17659722fcad4c521a5b3f9f33 100644
--- a/docs/source/index.md
+++ b/docs/source/index.md
@@ -62,9 +62,5 @@ If you want to learn how to use BiTIA and installation, check out the following
- To Understand working with BiTIA, refer [Working with BiTIA CLI](getting_started/Working.md)
-<!--
-```{eval-rst}
-.. automodule:: bitia
-``` -->