From 857c74dc61295beb23e98f0c6cf81c768788fa62 Mon Sep 17 00:00:00 2001 From: Donald Campbell <125581724+donaldcampbelljr@users.noreply.github.com> Date: Thu, 2 Oct 2025 13:44:59 -0600 Subject: [PATCH] fix a bunch of typos --- autodoc.py | 2 +- docs/eido/code/cli.md | 2 +- docs/eido/nunjucks.js | 2 +- docs/geofetch/gse-finder.md | 2 +- docs/looper/advanced-guide/advanced-metadata.md | 2 +- docs/looper/changelog.md | 2 +- docs/pephub/changelog.md | 2 +- docs/pephub/developer/changelog.md | 2 +- docs/pephub/user/version-control.md | 2 +- docs/pephub/user/views.md | 2 +- docs/peppy/code/tutorial.md | 2 +- docs/pipestat/code/python-tutorial.md | 2 +- docs/pipestat/pipestat-schema.md | 2 +- docs/pipestat/summarize.md | 2 +- docs/pypiper/cli.md | 2 +- docs/pypiper/code/python-api.md | 2 +- docs/spec/howto-multi-value-attributes.md | 2 +- 17 files changed, 17 insertions(+), 17 deletions(-) diff --git a/autodoc.py b/autodoc.py index 5231f588..f926834f 100644 --- a/autodoc.py +++ b/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") diff --git a/docs/eido/code/cli.md b/docs/eido/code/cli.md index 0bdfc283..511e53e9 100644 --- a/docs/eido/code/cli.md +++ b/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 diff --git a/docs/eido/nunjucks.js b/docs/eido/nunjucks.js index 1f0d873d..5898ecd3 100644 --- a/docs/eido/nunjucks.js +++ b/docs/eido/nunjucks.js @@ -7356,7 +7356,7 @@ function defined(value) { exports.defined = defined; /** - * Returns `true` if the operand (one) is divisble by the test's argument + * Returns `true` if the operand (one) is divisible by the test's argument * (two). * @param { number } one * @param { number } two diff --git a/docs/geofetch/gse-finder.md b/docs/geofetch/gse-finder.md index b6d6f436..352f0d56 100644 --- a/docs/geofetch/gse-finder.md +++ b/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() diff --git a/docs/looper/advanced-guide/advanced-metadata.md b/docs/looper/advanced-guide/advanced-metadata.md index b93fe5eb..242ec9cb 100644 --- a/docs/looper/advanced-guide/advanced-metadata.md +++ b/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). diff --git a/docs/looper/changelog.md b/docs/looper/changelog.md index 82748d60..f5e8cac2 100644 --- a/docs/looper/changelog.md +++ b/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 diff --git a/docs/pephub/changelog.md b/docs/pephub/changelog.md index ce93ce6c..6ac72729 100644 --- a/docs/pephub/changelog.md +++ b/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 diff --git a/docs/pephub/developer/changelog.md b/docs/pephub/developer/changelog.md index 7c39b03c..272f6eda 100644 --- a/docs/pephub/developer/changelog.md +++ b/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 diff --git a/docs/pephub/user/version-control.md b/docs/pephub/user/version-control.md index e7859593..98043909 100644 --- a/docs/pephub/user/version-control.md +++ b/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) diff --git a/docs/pephub/user/views.md b/docs/pephub/user/views.md index 88b94936..822f0c4b 100644 --- a/docs/pephub/user/views.md +++ b/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 diff --git a/docs/peppy/code/tutorial.md b/docs/peppy/code/tutorial.md index bc2c0332..8cedf886 100644 --- a/docs/peppy/code/tutorial.md +++ b/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: diff --git a/docs/pipestat/code/python-tutorial.md b/docs/pipestat/code/python-tutorial.md index 50780e03..dd1b5557 100644 --- a/docs/pipestat/code/python-tutorial.md +++ b/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. diff --git a/docs/pipestat/pipestat-schema.md b/docs/pipestat/pipestat-schema.md index d10c3507..95e4d00e 100644 --- a/docs/pipestat/pipestat-schema.md +++ b/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 diff --git a/docs/pipestat/summarize.md b/docs/pipestat/summarize.md index dd31f6b2..751257a9 100644 --- a/docs/pipestat/summarize.md +++ b/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 diff --git a/docs/pypiper/cli.md b/docs/pypiper/cli.md index 67537d5a..0764e9f5 100644 --- a/docs/pypiper/cli.md +++ b/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: diff --git a/docs/pypiper/code/python-api.md b/docs/pypiper/code/python-api.md index a90c6ca4..101c7ffa 100644 --- a/docs/pypiper/code/python-api.md +++ b/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. diff --git a/docs/spec/howto-multi-value-attributes.md b/docs/spec/howto-multi-value-attributes.md index 39dc42e2..be7c1fe3 100644 --- a/docs/spec/howto-multi-value-attributes.md +++ b/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: