remove init_chunks in docs #31

denisovan31415 · 2022-05-12T17:02:03Z

closes #30

removed all mentions of init_chunks
tidy up wording

github-actions · 2022-05-12T17:04:52Z

Code Coverage Summary

Filename                Stmts    Miss  Cover    Missing
--------------------  -------  ------  -------  ----------------------------------------------------------------------------------------------------------------------------------------
R/chunk.R                 150       3  98.00%   363-369
R/chunks_pipe.R            28      25  10.71%   16-48
R/chunks.R                402      40  90.05%   334, 424, 430-433, 439, 466-467, 484-491, 500, 506-515, 561, 587, 593-594, 596, 612, 621, 630, 672, 675, 698-703, 1029, 1050, 1104, 1155
R/get_eval_details.R      113     113  0.00%    15-178
R/include_css_js.R          7       7  0.00%    12-19
R/utils.R                  24      19  20.83%   13, 17-38
TOTAL                     724     207  71.41%

Results for commit: e972667

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

github-actions · 2022-05-12T17:05:39Z

Unit Tests Summary

    1 files     3 suites 3s ⏱️
  42 tests   42 ✔️ 0 💤 0 ❌
294 runs 294 ✔️ 0 💤 0 ❌

Results for commit 397f05f.

♻️ This comment has been updated with latest results.

Polkas

This PR should not be merged till the function is at least depreciated.

I will start from scratch

gogonzo · 2022-05-13T08:27:45Z

@Polkas I don't agree. We shouldn't mention this function at all in the vignette to encourage anyone using this. I don't recommend having init_chunks in the vignette and possibly fix possible occurrences of init_chunks outside of our repos after we fix this.
There might be big new user of our chunks and should we encurange them to use init_chunks? I don't think so

Polkas

First round of the review, I think we could make it even better.

Polkas · 2022-05-13T08:21:28Z

vignettes/basic_chunks.Rmd


 The next sections will explain what a chunk is and how it is evaluated.

 # What is a chunk?

-A quoted R expression is a necessary step to create a **chunk** object. Quoted R expressions can be created in three different ways:
+A quoted R expression is a necessary step to create a **chunk** object, which is an R6 object of class `chunk_call`. Quoted R expressions can be created in three different ways:


MAJOR AND IMPORTANT
at least 4 ways, we should point to substitute which we use almost everywhere.
What about rlang functions which could be used interchangeably. I think it will be nice to give at least one example with rlang next to the base solution.

And with bquote it was not used its biggest advantage, the .()

We have to assume that end users do not understand the meta programming idea.
We could think of a reference to Advanced R Programming (old version) to the proper chapter like http://adv-r.had.co.nz/Computing-on-the-language.html and http://adv-r.had.co.nz/Expressions.html

We don't need to print the class and I think this markdown-chunk can be limited to this:

A quoted R expression is a necessary step to create a chunk object, which is an R6 object of class chunk_call. Quoted R expressions can be created in several ways:

quote when a call is composed as-is.

substitute when a call is composed basing on variables.

Alternatively, one can use bquote or rlang::expr or any function which returns a language (call, expression or name).

# when call is composed as is quote(a <- 2) # when call is composed basing on values substitute(x <- 2, list(x = as.name(a)))

Polkas · 2022-05-13T08:24:49Z

vignettes/basic_chunks.Rmd

@@ -59,13 +59,8 @@ print(b)
 eval(expr_c)
 ```

-A `chunk` object is an R6 object of class `chunk_call` which can be created and evaluated using the expressions above  as follows:
+Now `chunk` objects can be created and evaluated using the expressions above as follows:


The chunk objects can be created ...

It was always like that

Polkas · 2022-05-13T09:17:02Z

vignettes/basic_chunks.Rmd

-As already said the chunks in the container will never throw an error upon execution. Errors are caught and stored in the `chunks` object. The most important function to check if everything went fine is `teal.code::chunks_is_ok`. It will return `TRUE` in the case where everything was fine.
+A chunks container object also has its own `eval` method. The function `teal.code::chunks_safe_eval` is merely a wrapper of this method. It is named `"safe_eval"` because it performs an additional step to handle errors by calling another method of the chunks container object, `validate_is_ok`. If any error occurs during the evaluation of expressions pushed into the chunks container, the error is handled and stored in the `chunk` object that contains the expression, and thus no error is thrown to the calling environment.
+
+The most important function to check if everything went fine is `teal.code::chunks_is_ok`. It will return `TRUE` in the case where everything was fine.


"everything went fine" what it means. we should be more explicit.

Polkas · 2022-05-13T09:28:00Z

vignettes/basic_chunks.Rmd

 ```
 <img src="images/get_rcode.png" alt="get_rcode" style="width: 100%;"/>

 ## Feature 4: `eval` - evaluating the code

-The `eval` function is responsible to run the code inside the chunks container. The `eval` function of a chunks container is called `teal.code::chunks_safe_eval`. It evaluates all chunks inside the container in the order they were pushed. It is not possible to change the order or run just pieces of the code. The chunks will not throw an error when being evaluated. See below for further details.
+The `eval` function is responsible to run the code inside the chunks container. The `eval` function of a chunks container is called `teal.code::chunks_safe_eval`. It evaluates all chunks inside the container in the order they were pushed. It is not possible to change the order or run just pieces of the code.


It is not clear, and conflict with the chapter 5

e.g. you use the function which is not yet introduced.

Polkas · 2022-05-13T09:36:10Z

vignettes/basic_chunks.Rmd

@@ -11,20 +11,20 @@ vignette: >

 # The chunks container

-The main concept behind the code chunks is the chunks container. This container consists of two elements:
+The main concept behind code reproducibility is the chunks container object. This object consists of two elements:


I think it is too general now.

Suggested change

The main concept behind code reproducibility is the chunks container object. This object consists of two elements:

The main concept behind teal code reproducibility is the chunks container object. This object consists of two elements:

Suggested change

The main concept behind code reproducibility is the chunks container object. This object consists of two elements:

The main concept behind code reproducibility is the chunks container object. This object consists of two elements:

Polkas · 2022-05-13T09:37:54Z

vignettes/basic_chunks.Rmd

-Normally as a module developer the chunks container will be used within the `server` function of a shiny/teal module. This enables storing the chunks container inside the shiny session. For simplicity reasons this feature will be used in the tutorial. To store a container inside the shiny session simply use the call `init_chunks()` and the `chunks` R6 object will be stored in `session$userData$<MODULENAME>$chunks`. After using `init_chunks()`, the functions dealing with chunks container can be used. Those are recommended. If for any reasons you want to use your own chunks container, it is possible. Please see the last section of this article for more information. So for now, we just call `teal.code::init_chunks()`.
-
-As a simulation of the teal environment the `init_session` function is provided:
+Normally as a module developer the chunks container will be used within the `server` function of a shiny/teal module. To create a chunks container object, call the R6 class `new` method:


It is expected that the regular usage ..

gogonzo

Contentwise vignette is fine. Just little details addressed by Maciej and highlighted in my suggestions. We should avoid using bquote in the examples as 1-year ago we made a refactor of the modules to change bquote->substitute. We can mention several ways of making calls but we should focus on base::quote and base::substitute.

gogonzo · 2022-05-13T10:09:27Z

vignettes/basic_chunks.Rmd

-
---
-
-## Implementation of code chunks containers
-
-There are two ways to initialize the code chunks inside shiny modules:
-
- Using R6 implementation: `session_chunks <- chunks$new()`.
-
- Using `teal.code` wrappers: `teal.code::init_chunks()`.
-
-The `teal.code` functions can be used in both cases:
-
-
-```{r}
-session <- init_session()
-teal.code::init_chunks()
-a <- 1
-b <- 2
-
-# set a & b in env
-teal.code::chunks_reset()
-# push to chunks
-teal.code::chunks_push(expression = bquote(a <- a + 1))
-# eval gives return value
-teal.code::chunks_safe_eval()
-stopifnot(teal.code::chunks_get_var("a") == 2)
-
-teal.code::chunks_push(expression = bquote(c <- a + b))
-teal.code::chunks_safe_eval()
-stopifnot(teal.code::chunks_get_var("c") == 4)
-teal.code::chunks_push(expression = quote(a + b + c))
-stopifnot(teal.code::chunks_safe_eval() == 8)
-# create a new chunks objet explicitly
-chunks2 <- teal.code::chunks$new()
-# push into this object
-teal.code::chunks_push(bquote(d <- 1), chunks = chunks2)
-# push the whole of chunks2 into our main chunks object
-teal.code::chunks_push_chunks(chunks2)
-# evaluate and get results
-teal.code::chunks_safe_eval()
-teal.code::chunks_get_var("d")
-```
-
-The _default_ `chunks` object in many `teal.code` functions is the `chunks` object coupled to the shiny session. But as shown above it is possible to use other `chunk` objects with these functions using their `chunks` argument. The `chunks` object is an R6 object and consult the function documentation for details of its explicit methods.


I agree that this should be in advanced

gogonzo · 2022-05-13T10:21:51Z

vignettes/basic_chunks.Rmd


 The next sections will explain what a chunk is and how it is evaluated.

 # What is a chunk?

-A quoted R expression is a necessary step to create a **chunk** object. Quoted R expressions can be created in three different ways:
+A quoted R expression is a necessary step to create a **chunk** object, which is an R6 object of class `chunk_call`. Quoted R expressions can be created in three different ways:


We don't need to print the class and I think this markdown-chunk can be limited to this:

A quoted R expression is a necessary step to create a chunk object, which is an R6 object of class chunk_call. Quoted R expressions can be created in several ways:

quote when a call is composed as-is.

substitute when a call is composed basing on variables.

Alternatively, one can use bquote or rlang::expr or any function which returns a language (call, expression or name).

# when call is composed as is quote(a <- 2) # when call is composed basing on values substitute(x <- 2, list(x = as.name(a)))

denisovan31415 · 2022-05-13T19:19:44Z

@Polkas @gogonzo

I think I have address all of your comments.

In addition, I removed the gif summary at the end because it is now outdated and it was difficult to follow.

Polkas

LGTM. Thanks for the update.

denisovan31415 added 2 commits May 12, 2022 11:26

porting over changes

b51e402

removed init_chunks

0630195

denisovan31415 added documentation 📃 documentation core labels May 12, 2022

Polkas self-assigned this May 13, 2022

Polkas previously requested changes May 13, 2022

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gogonzo reviewed May 13, 2022

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major refactor

0833022

denisovan31415 added 2 commits May 13, 2022 14:38

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Polkas approved these changes May 16, 2022

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Merge branch 'main' into 30_remove_init_chunks_doc@main

397f05f

denisovan31415 merged commit be0f5ea into main May 16, 2022

denisovan31415 deleted the 30_remove_init_chunks_doc@main branch May 16, 2022 12:03

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remove init_chunks in docs #31

remove init_chunks in docs #31

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	The main concept behind code reproducibility is the chunks container object. This object consists of two elements:
	The main concept behind teal code reproducibility is the chunks container object. This object consists of two elements:

remove init_chunks in docs #31

remove init_chunks in docs #31

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