more cleanup, add usage documenter script

docs/geofetch/usage.md → docs/geofetch/code/usage.md

@@ -1,11 +1,13 @@
-# <img src="./img/geofetch_logo.svg" class="img-header">  usage reference
+# <img src="../../img/geofetch_logo.svg" class="img-header" style="height:70px">  usage reference
 
 `geofetch` command-line usage instructions:
 
 
 
 `geofetch --help`
-```{console}
+
+
+```console
 usage: geofetch [<args>]
 
 The example how to use geofetch (to download GSE573030 just metadata):
@@ -16,7 +18,7 @@ To download all processed data of GSE57303:
 
 Automatic GEO and SRA data downloader
 
-options:
+optional arguments:
   -h, --help            show this help message and exit
   -V, --version         show program's version number and exit
   -i INPUT, --input INPUT
@@ -124,4 +126,5 @@ raw:
                         out metadata.
   --add-convert-modifier
                         Add looper SRA convert modifier to config file.
+
 ```

docs/geofetch/usage-template.md.tpl

@@ -0,0 +1,4 @@
+# <img src="../../img/geofetch_logo.svg" class="img-header" style="height:70px">  usage reference
+
+`geofetch` command-line usage instructions:
+

docs/looper/sample-annotation-sheet.md

@@ -23,7 +23,7 @@ It specifies the source of data for the sample (e.g. ATAC-seq, RNA-seq, RRBS).
 - `data_source` - This column is used by default to specify the location of the input data file.
 Usually you want your annotation sheet to specify the locations of files corresponding to each sample.
 You can use this to simplify pointing to file locations with a neat string-replacement method that keeps things clean and portable.
-For more details, see the [derived columns page](derived-columns.md).
+For more details, see the [derived columns section](#derived-columns).
 Really, you just need any column specifying at least 1 data file for input. This is **required** for `looper` to submit job(s) for a `Sample`.
 - `toggle` - If the value of this column is not 1, `looper` will not submit the pipeline for that sample.
 This enables you to submit a subset of samples.

docs/pephub/README.md

@@ -20,7 +20,7 @@ docker build -t pephub.databio.org .
 
 ### Run
 
-PEPhub requires many parameters to run. You can read more about those [here](https://github.com/pepkit/pephub/blob/master/docs/server-settings.md). These must be injected as environment variables. You can manually do this and inject one-by-one. There is an example script in this repo called [launch_docker.sh](launch_docker.sh).
+PEPhub requires many parameters to run. You can read more about those [here](https://github.com/pepkit/pephub/blob/master/docs/server-settings.md). These must be injected as environment variables. You can manually do this and inject one-by-one. There is an example script in the repo called `launch_docker.sh`.
 
 ```
 launch_docker.sh

docs/pephub/pepdbagent/README.md

@@ -139,4 +139,5 @@ NamespaceReturnModel(count=1,
 
 
 # Example PEPs
-To populate database with example peps use function written in manual tests: [Manual test](../manual_tests.py)
+
+To populate database with example peps use function written in `manual_tests.py`.

docs/pipestat/code/python-api.md

@@ -668,7 +668,7 @@ Pipestat standardizes reporting of pipeline results and pipeline status manageme
 
 
 ```python
-def __init__(self, project_name: Union[str, NoneType]=None, record_identifier: Union[str, NoneType]=None, schema_path: Union[str, NoneType]=None, results_file_path: Union[str, NoneType]=None, database_only: Union[bool, NoneType]=True, config_file: Union[str, NoneType]=None, config_dict: Union[dict, NoneType]=None, flag_file_dir: Union[str, NoneType]=None, show_db_logs: bool=False, pipeline_type: Union[str, NoneType]=None, pipeline_name: Union[str, NoneType]='default_pipeline_name', result_formatter: staticmethod=<function default_formatter at 0x7f2b10515b80>, multi_pipelines: bool=False, output_dir: Union[str, NoneType]=None)
+def __init__(self, project_name: Union[str, NoneType]=None, record_identifier: Union[str, NoneType]=None, schema_path: Union[str, NoneType]=None, results_file_path: Union[str, NoneType]=None, database_only: Union[bool, NoneType]=True, config_file: Union[str, NoneType]=None, config_dict: Union[dict, NoneType]=None, flag_file_dir: Union[str, NoneType]=None, show_db_logs: bool=False, pipeline_type: Union[str, NoneType]=None, pipeline_name: Union[str, NoneType]='default_pipeline_name', result_formatter: staticmethod=<function default_formatter at 0x7f2df0115d30>, multi_pipelines: bool=False, output_dir: Union[str, NoneType]=None)
 ```
 
 Initialize the PipestatManager object