Introduce teal_data class by gogonzo · Pull Request #171 · insightsengineering/teal.data

gogonzo · 2023-10-04T11:53:40Z

Part of insightsengineering/teal#937
Other PRs insightsengineering/teal#925 insightsengineering/teal.slice#440 insightsengineering/teal.gallery#75 insightsengineering/teal.code#153

install

staged.dependencies::dependency_table(
  project = "insightsengineering/teal@https://github.com",
  project_type = "repo@host",
  ref = "teal_data@main",
  verbose = 1
) |> staged.dependencies::install_deps()

teal_data class

teal_data class (teal_data-class.R) is en extension of qenv. teal_data contains extra slots datanames and join_keys. Besides, all teal.code methods works with teal_data object (eval_code, print etc.)
Old TealData$server returns teal_data now - to have single object type in teal (not in teal_module)
cdisc_data() and teal_data() return TealData or teal_data

ADSL <- synthetic_cdisc_data("latest")$adsl
ADTTE <- synthetic_cdisc_data("latest")$adtte
ADRS <- synthetic_cdisc_data("latest")$adrs

data <- cdisc_data(
  ADSL = ADSL,
  ADTTE = ADTTE,
  ADRS = ADRS,
  code = quote({
    ADSL <- synthetic_cdisc_data("latest")$adsl
    ADTTE <- synthetic_cdisc_data("latest")$adtte
    ADRS <- synthetic_cdisc_data("latest")$adrs
  })  
)

data |> eval_code(quote(a <- ADSL))

Co-authored-by: dinakar29 <26552821+dinakar29@users.noreply.github.com>

* the code related to `teal`'s data models moved from the original teal and teal.devel packages Related to insightsengineering/coredev-tasks#130

* fix vignette Co-authored-by: Dawid Kałędkowski <dawid.kaledkowski@gmail.com>

* refactored `is` to `inherits` * did some styling changes - someone really loved new lines when writing these tests Closes #11

* is to inherits

* update staged.deps * add tmh to downstream * Apply suggestions from code review * to_relational_data.TealData - to return TealData * Update R/to_relational_data.R Co-authored-by: Dawid Kałędkowski <dawid.kaledkowski@gmail.com>

* removed var_relabel * removed variable_labels and updated staged.dependencies * importFrom formatable var_labels * docs * removed extra space

* rename formatable into formatters * actions

* NEWS * Update NEWS.md

fixing preprocessing-data vignette

waiting for parser

preparing to use parser

teal_data no longer returns TealData when data are available.

fix

wrong package namespace for get_code

fixing R cmd check

github-actions · 2023-10-05T13:49:35Z

Unit Tests Summary

      1 files     27 suites 19s ⏱️
  365 tests   363 ✔️ 0 💤 0 ❌ 2 🔥
1 011 runs 1 009 ✔️ 0 💤 0 ❌ 2 🔥

For more details on these errors, see this check.

Results for commit 7cb1986.

♻️ This comment has been updated with latest results.

chlebowa · 2023-10-05T15:08:32Z

+#' @name new_teal_data
+#'
+#' @param code (`character(1)` or `language`) code to evaluate. Accepts and stores comments also.
+#' @param env (`list`) List of data.


Unless I am mistaken, we intend to always pass a list of datasets to this argument. The argument name is misleading then. Yes, the datasets will be list2env'ed and end up in the @env slot but it is not an environment that we pass. Can we name this more appropriately?

True, at this moment we have:

new_qenv(env = "environment", code = c("character", "language")) new_teal_data(env = "list", code = c("character", "language")) teal/cdisc_data(..., code = c("character", "language"))

According to our discussion two days ago, we plan to remove possibility to add env and code in new_qenv (we need to soft deprecate this). In the new_teal_data, i would change argument env to data (a list).

new_qenv() new_teal_data(env = "??", code = c("character", "language")) teal/cdisc_data(..., code = c("character", "language"))

Sounds great 👍

new_teal_data(env) new_teal_data(data)

fixing namespace warning

following changes in teal.code

fix

Part of insightsengineering/nestdevs-tasks#43

pawelru · 2023-10-11T12:45:18Z

vbump to 0.4.0?

What is the convention on @main to signal minor version bump? Should I set version from 0.3.0.9xxx 0.3.9.9xxx?

Set it to the target 0.4.0 value and merge the whole PR with [skip vbump]
@cicdguy please confirm

Correct. Bump to 0.4.0 for minor version.

The first digit is for major breaking changes.
The second for minor changes like features which do not break the core API.
The third digit is for patches and bugfixes.

So unless you're making a new release out of this, I'd say the new version is just a development version.

Can we do it now or shall we wait for the pre-release clean-ups? I think the latter as there might be other PRs merged in afterwards which will make it 0.4.0.9xxx and from there it would be problematic to "downgrade" into the target 0.4.0. So essentially we can address it during pre-release clean-up. Is that right?

Yes I would prefer doing it here instead of doing it later and downgrading it.

Sorry I wasn't clear. It is either:

do it now -> expect upcoming vbumps during standard dev cycle or hot-fixes -> downgrade during pre-release clean-ups

wait and do it later during pre-release clean-ups

Just clarified this - yes let's wait and do it later during pre-release cleanups (aka when the PR is being prepared for an upcoming release).

donyunardi · 2023-10-16T05:27:06Z

Please hold on merging this to main branch.
See discussion here:
insightsengineering/nestdevs-tasks#41

- Config/Needs/verdepcheck entries in new line - add `bioc::` for packages from Bioconductor Signed-off-by: Pawel Rucki <12943682+pawelru@users.noreply.github.com>

need higher version of teal.code - code slot is a character

update pkgdown

gogonzo · 2023-10-18T12:49:21Z

By accident I've closed this PR without a change to open again. New PR here #178

insights-engineering-bot and others added 30 commits March 2, 2022 13:08

Initial commit

3016bc9

CODEOWNERS removal and pre-commit config (#2)

60b0f0d

Co-authored-by: dinakar29 <26552821+dinakar29@users.noreply.github.com>

feat: initial feature commit

4c4fb9c

* the code related to `teal`'s data models moved from the original teal and teal.devel packages Related to insightsengineering/coredev-tasks#130

use moduleServer to fix bug (#7)

d73cbb8

* fix vignette Co-authored-by: Dawid Kałędkowski <dawid.kaledkowski@gmail.com>

[skip actions] Bump version to 0.0.0.9002

e9a64b0

miniACC (#8)

a874df1

[skip actions] Bump version to 0.0.0.9003

f975e04

add gitlab ci (#10)

2ab4d78

[skip actions] Bump version to 0.0.0.9004

7bcd8b6

fix: refactored tests in test-TealDatasetConnector.R (#12)

52970d9

* refactored `is` to `inherits` * did some styling changes - someone really loved new lines when writing these tests Closes #11

[skip actions] Bump version to 0.0.0.9005

8aaa750

dplyr to suggests (#9)

5dbde65

[skip actions] Bump version to 0.0.0.9006

6e9cea2

is to inherits (#15)

bc22dbc

* is to inherits

[skip actions] Bump version to 0.0.0.9007

b325f7b

Disable several workflows (#16)

ed64ebf

[skip actions] Bump version to 0.0.0.9008

1444c84

moved ddl articles from agileR to this package (#13)

5669a0f

[skip actions] Bump version to 0.0.0.9009

d1a92f2

update staged.deps (#17)

19b63cc

* update staged.deps * add tmh to downstream * Apply suggestions from code review * to_relational_data.TealData - to return TealData * Update R/to_relational_data.R Co-authored-by: Dawid Kałędkowski <dawid.kaledkowski@gmail.com>

[skip actions] Bump version to 0.0.0.9010

202fc83

news (#19)

3be6e2b

[skip actions] Bump version to 0.0.0.9011

03be7c7

removed var_relabel (#18)

b99b25a

* removed var_relabel * removed variable_labels and updated staged.dependencies * importFrom formatable var_labels * docs * removed extra space

[skip actions] Bump version to 0.0.0.9012

984f033

Fix reproducibility message (#20)

eaefa65

[skip actions] Bump version to 0.0.0.9013

60cab4d

rename formatable into formatters (#21)

d35b3b8

* rename formatable into formatters * actions

[skip actions] Bump version to 0.0.0.9014

6afa91d

NEWS (#1)

57e5fc3

* NEWS * Update NEWS.md

gogonzo added 8 commits October 5, 2023 11:41

f7204f4

fixing preprocessing-data vignette

67f96e4

waiting for parser

801bc72

preparing to use parser

7118d58

teal_data no longer returns TealData when data are available.

c461980

fix

75095ec

wrong package namespace for get_code

reverting breaking changes

36d4544

2fb8a39

fixing R cmd check

chlebowa reviewed Oct 5, 2023

View reviewed changes

gogonzo added 2 commits October 6, 2023 10:40

0e26f43

new_teal_data(env) new_teal_data(data)

e62f3a7

fixing namespace warning

kartikeyakirar reviewed Oct 6, 2023

View reviewed changes

Comment thread DESCRIPTION

gogonzo and others added 6 commits October 9, 2023 20:21

2680837

following changes in teal.code

[skip actions] Roxygen Man Pages Auto Update

4f26d55

75f0890

fix

[skip actions] Roxygen Man Pages Auto Update

2c0e3f7

add no_browser hook in pre-commit (#176)

50bae30

Part of insightsengineering/nestdevs-tasks#43

[skip actions] Bump version to 0.3.0.9006

3b32fac

pawelru reviewed Oct 11, 2023

View reviewed changes

pawelru and others added 5 commits October 16, 2023 13:02

Update DESCRIPTION (#175)

a0f98b6

- Config/Needs/verdepcheck entries in new line - add `bioc::` for packages from Bioconductor Signed-off-by: Pawel Rucki <12943682+pawelru@users.noreply.github.com>

[skip actions] Bump version to 0.3.0.9007

c04b7ed

Merge remote-tracking branch 'origin/main' into teal_data@main

7cb1986

55d0dbc

need higher version of teal.code - code slot is a character

9b3c303

update pkgdown

gogonzo changed the base branch from main to gh-pages October 18, 2023 12:27

gogonzo closed this Oct 18, 2023

donyunardi removed a link to an issue Oct 23, 2023

[summary] data refactor insightsengineering/teal#895

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teal_data class

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