fix a bunch of typos

autodoc.py

@@ -86,7 +86,7 @@
 else:
     print("Skipping usage documentation")
 
-# # Render Juptyer notebooks to markdown
+# # Render Jupyter notebooks to markdown
 if args["x_jupyter"] is False and "jupyter" in cfg:
     for item in cfg["jupyter"]:
         files = glob.glob(f"docs/{item['in']}/*.ipynb")

docs/eido/code/cli.md

@@ -42,7 +42,7 @@ eido inspect peppro_paper.yaml
     Sections: name, pep_version, sample_table, looper, sample_modifiers
 
 
- - To inspect a specific sample, one needs to provide the sample name (via `-n`/`--sample-name` oprional argument)
+ - To inspect a specific sample, one needs to provide the sample name (via `-n`/`--sample-name` optional argument)
 
 
 ```bash

docs/geofetch/gse-finder.md

@@ -11,7 +11,7 @@ is a geofetch class that provides functions to find and retrieve a list of GSE (
 ___
 ## Tutorial
 
-0) Initiale Finder object. 
+0) Initial Finder object. 
 ```python
 from geofetch import Finder
 gse_obj = Finder()

docs/looper/advanced-guide/advanced-metadata.md

@@ -2,7 +2,7 @@
 
 We already covered how you can specify sample metadata using either a [simple csv file](../user-tutorial/initialize.md) or a [PEP](../user-tutorial/metadata.md).
 But in that tutorial we covered only the basic features of PEPs.
-PEPs are actually a lot more powerful, and many of those featuers are useful for looper projects.
+PEPs are actually a lot more powerful, and many of those features are useful for looper projects.
 Here, we'll show you a few of the more advanced features of PEPs and explain how they can be useful with looper. 
 We still won't cover everything here, though.
 If you want to see *all* the features of PEP, you should consult the [detailed PEP documentation](../../spec/simple-example.md).

docs/looper/changelog.md

@@ -127,7 +127,7 @@ This release breaks backwards compatibility for Looper versions < 2.0.0
 - fix `looper table` failing without `sample.protocol`
 
 ### Changed
-- correct `--looper_conifg` to `--looper-config`
+- correct `--looper_config` to `--looper-config`
 
 ## [1.5.0] -- 2023-08-09
 

docs/pephub/changelog.md

@@ -153,7 +153,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ### Fixed
 
 - sample table would exhibit odd, erratic behavior if column names were left blank
-- alnding page styling was not otpimal
+- alnding page styling was not optimal
 
 ## [0.9.6] - 07-20-2023
 

docs/pephub/developer/changelog.md

@@ -72,7 +72,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ### Fixed
 
 - sample table would exhibit odd, erratic behavior if column names were left blank
-- alnding page styling was not otpimal
+- landing page styling was not optimal
 
 ## [0.9.6] - 2023-07-20
 

docs/pephub/user/version-control.md

@@ -8,7 +8,7 @@ PEPhub automatically records a history of your files whenever changes are made.
 
 ![alt text](../img/menu-history.png)
 
-Selecting this option will bring up the *History Interface*, which will provide buttons allowing you to view or delete entries from your history table. If you choose the `View` button for an entry, it will show you the PEP at that point in history. It also opens a new interface that will allow you to click `Restore` to overwright your current PEP with the historical version you are currently viewing, or you can `Download` the table as it was at that point in history.
+Selecting this option will bring up the *History Interface*, which will provide buttons allowing you to view or delete entries from your history table. If you choose the `View` button for an entry, it will show you the PEP at that point in history. It also opens a new interface that will allow you to click `Restore` to overwrite your current PEP with the historical version you are currently viewing, or you can `Download` the table as it was at that point in history.
 
 ![alt text](../img/history-interface.png)
 

docs/pephub/user/views.md

@@ -2,7 +2,7 @@
 
 ## What are views?
 
-Large tables (*e.g.* >5,000 rows) can be unweildy with PEPhup. It can be hard to find the elements you're looking for. To address this, PEPhub provides the *Views* feature. Views provide a way to look at a subset of a large table (basically, a filtered table).
+Large tables (*e.g.* >5,000 rows) can be unwieldy with PEPhup. It can be hard to find the elements you're looking for. To address this, PEPhub provides the *Views* feature. Views provide a way to look at a subset of a large table (basically, a filtered table).
 
 ## How to create a view
 

docs/peppy/code/tutorial.md

@@ -1,6 +1,6 @@
 # Basic PEP example
 
-This vignette will show you a simple example PEP-formatted project, and how to read it into python using the `peppy` package. This example comes from the [example_peps repsitory](https://github.com/pepkit/example_peps) in the [example_basic](https://github.com/pepkit/example_peps/tree/master/example_basic) folder.
+This vignette will show you a simple example PEP-formatted project, and how to read it into python using the `peppy` package. This example comes from the [example_peps repository](https://github.com/pepkit/example_peps) in the [example_basic](https://github.com/pepkit/example_peps/tree/master/example_basic) folder.
 
 
 Start by importing `peppy`, and then let's take a look at the configuration file that defines our project:

docs/pipestat/code/python-tutorial.md

@@ -23,7 +23,7 @@ The changes reported using the `report` method of `PipestatManger` will be secur
 2. a **PostgreSQL database** (pass a path to the pipestat config to the constructor)
 This option gives the user the possibility to use a fully fledged database to back `PipestatManager`. 
 
-3. a **PEP on PEPhub** (pass a pep path to the constructior, e.g. `psm = PipestatManager(pephub_path=pephubpath)`)
+3. a **PEP on PEPhub** (pass a pep path to the constructor, e.g. `psm = PipestatManager(pephub_path=pephubpath)`)
 This option gives the user the possibility to use PEPhub as a backend for results. 
 
 

docs/pipestat/pipestat-schema.md

@@ -3,7 +3,7 @@
 ## Introduction
 Pipestat requires a schema, in which all the results that the pipeline can report are specified. 
 
-It is written in [JSON schema](https://cswr.github.io/JsonSchema/spec/basic_types/) which definines specific data types:
+It is written in [JSON schema](https://cswr.github.io/JsonSchema/spec/basic_types/) which defines specific data types:
 
 ### Data types
 

docs/pipestat/summarize.md

@@ -17,7 +17,7 @@ psm.summarize(output_dir="/home/output_dir",portable= True )
 ```
 
 
-Simiarly this can be accomplished via the CLI:
+Similarly this can be accomplished via the CLI:
 
 ```shell
 

docs/pypiper/cli.md

@@ -49,7 +49,7 @@ With that said, there are a few universal (Pypiper-added) options that are frequ
 ## Customizing `add_pypiper_args()`
 
 
-There are two ways to modulate the arguments added by `add_pypiper_args()` function: the `groups` argument, which lets you add argument groups; or the `args` argument, which lets you add arguments indvidually. By default, `add_pypiper_args()` add all arguments listed in the `pypiper` group. You may instead pass a list of one or more of these groups of arguments (to `groups`) or individual arguments (to `args`) to customize exactly the set of built-in options your pipeline implements.
+There are two ways to modulate the arguments added by `add_pypiper_args()` function: the `groups` argument, which lets you add argument groups; or the `args` argument, which lets you add arguments individually. By default, `add_pypiper_args()` add all arguments listed in the `pypiper` group. You may instead pass a list of one or more of these groups of arguments (to `groups`) or individual arguments (to `args`) to customize exactly the set of built-in options your pipeline implements.
 
 For example, `parser.add_pypiper_args(parser, groups=['pypiper', 'common'])` will add all arguments listed under `pypiper` and `common` below:
 

docs/pypiper/code/python-api.md

@@ -349,7 +349,7 @@ provides some logging output.
 - `target` (`str | Sequence[str]`):  Output file(s) to produce, optional.If all target files exist, the command will not be run. If no target is given, a lock_name must be provided.
 - `lock_name` (`str`):  Name of lock file. Optional.
 - `shell` (`bool`):  If command requires should be run in its own shell.Optional. Default: None --will try to determine whether the command requires a shell.
-- `nofail` (`bool`):  Whether the pipeline proceed past a nonzero return froma process, default False; nofail can be used to implement non-essential parts of the pipeline; if a 'nofail' command fails, the pipeline is free to continue execution.
+- `nofail` (`bool`):  Whether the pipeline proceed past a nonzero return from process, default False; nofail can be used to implement non-essential parts of the pipeline; if a 'nofail' command fails, the pipeline is free to continue execution.
 - `clean` (`bool`):  True means the target file will be automatically addedto an auto cleanup list. Optional.
 - `follow` (`callable`):  Function to call after executing (each) command.
 - `container` (`str`):  Name for Docker container in which to run commands.

docs/spec/howto-multi-value-attributes.md

@@ -38,7 +38,7 @@ sample_table: annotation.csv
 subsample_table: subsample_table.csv
 ```
 
-Make sure the `sample_name` column of this table matche the `sample_name` column in your sample_table, and then include any columns that require multiple values. `PEP` will automatically include all of these values as appropriate. 
+Make sure the `sample_name` column of this table match the `sample_name` column in your sample_table, and then include any columns that require multiple values. `PEP` will automatically include all of these values as appropriate. 
 
 Here's a simple example of a PEP that uses subsamples. If you define `annotation.csv` like this: