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Training #24

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merged 120 commits into from
Aug 30, 2023
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59ac77a
add training materials; few enhancements
pawelru Jun 19, 2023
6c9381c
move up entry
pawelru Jun 19, 2023
982b47b
correct date; add thank you slide
pawelru Jun 19, 2023
e0dcb4d
add pdf
pawelru Jun 19, 2023
4f5d639
Merge branch 'main' into training
pawelru Jun 19, 2023
e0bd3e4
add more discussion on min strategy
pawelru Jun 20, 2023
66576fc
pdf
pawelru Jun 20, 2023
9d1b5a4
Merge remote-tracking branch 'origin/training' into training
pawelru Jun 20, 2023
2d70c4b
remove code that has been introduced after merge
pawelru Jun 20, 2023
ccee2ce
redesign min strategy
pawelru Jun 26, 2023
d08bc0c
docs
pawelru Jun 26, 2023
1d662c9
rm min_direct; rename _cohorts into _isolated; move ppm logic into ob…
pawelru Jul 5, 2023
d4a0cc8
Merge branch 'main' into training
pawelru Jul 5, 2023
11188af
typo
pawelru Jul 5, 2023
36278df
update training
pawelru Jul 6, 2023
3c15ab6
fix: should use host only
averissimo Jul 13, 2023
5c99daf
test: update test logic to new solve_ip()
averissimo Jul 13, 2023
031f118
test: adds github testing that was failing to new framework
averissimo Jul 13, 2023
0fd3869
test: converts remmaining tests
averissimo Jul 13, 2023
91ffcef
tests: adds documentation on new functions
averissimo Jul 13, 2023
1b65bfc
test: adds Config/Needs/verdepcheck to temporary DESCRIPTION
averissimo Jul 13, 2023
f7ef8c6
docs: adds comment with reason of testing if package exists
averissimo Jul 14, 2023
ed42d20
Update tests/testthat/helper.R
averissimo Jul 14, 2023
6046b67
fix: corrects variable name
averissimo Jul 14, 2023
a0dab4c
Merge pull request #27 from insightsengineering/tests-update
averissimo Jul 17, 2023
8a238bf
Merge a0dab4cdbd71d775dbdff8d706b922baaf854bca into d1cf34c3bbe4f2d2c…
pawelru Jul 17, 2023
c433994
[skip actions] Restyle files
github-actions[bot] Jul 17, 2023
d86414e
(min_isolatd): enforce Rcpp min version and select min version duplicate
averissimo Jul 10, 2023
aad9662
docs: typo
averissimo Jul 10, 2023
261ed9b
fix: minor bugs and keeps only minimum version of packages
averissimo Jul 10, 2023
c7d2368
fix: typo
averissimo Jul 10, 2023
81dcef0
remove duplicate packages with same version
averissimo Jul 10, 2023
3edf4e6
fix: keep primary dependency version
averissimo Jul 10, 2023
37b6748
docs: move function to utils
averissimo Jul 10, 2023
9821383
fix: improve code on keeping primary dependency version
averissimo Jul 10, 2023
c9f98e5
fix: keep primary dependency min version
averissimo Jul 11, 2023
4352850
remove Rcpp enforment
averissimo Jul 11, 2023
d940853
revert minimal version enforcement
averissimo Jul 11, 2023
0579af9
feat: shows error log from package building
averissimo Jul 11, 2023
c2d4b99
fix: account for multiple dates from gh query
averissimo Jul 12, 2023
89f3b76
feat: supports github only dependencies
averissimo Jul 12, 2023
f65c8b3
docs: remove documentation for deleted function
averissimo Jul 13, 2023
e58166a
fix: improve on graphql query and adds unit test
averissimo Jul 14, 2023
33e7277
chore: adds documentation and compare dates that come from GH GraphQL
averissimo Jul 14, 2023
846f5b0
chore: adds if clause for examples
averissimo Jul 14, 2023
a470d97
fix: solution for Remotes conflicts in version and key (ref)
averissimo Jul 17, 2023
9796b12
fix: Applied Remotes cleanup to min_cohort too
averissimo Jul 17, 2023
5a3a6d9
Adds verbose message to exception that is not self-descriptive
averissimo Jul 18, 2023
0f6b80e
Update R/get_ref.R
averissimo Jul 18, 2023
ac12fea
PR feedback: useless expression corrected, code/msg improvement
averissimo Jul 18, 2023
31ff448
text: Improves on message
averissimo Jul 18, 2023
5370242
fix: Avoid identical calls to resolve_ppm_snapshot
averissimo Jul 19, 2023
7ae7b72
cleanup: remove parent column
averissimo Jul 19, 2023
109db00
chore: replace tab with spaces
averissimo Jul 19, 2023
047d3f2
fix: keep only top version on resolution table to correct non-converg…
averissimo Jul 20, 2023
bf166cd
Merge pull request #26 from insightsengineering/training-improvements
averissimo Jul 24, 2023
d484a30
Merge bf166cd796211d3eecd3f15c308e7112afb8a195 into d1cf34c3bbe4f2d2c…
pawelru Jul 24, 2023
ad404d1
[skip actions] Restyle files
github-actions[bot] Jul 24, 2023
a80dbc2
chore: add reusable function to determine package version from descri…
averissimo Jul 24, 2023
f1adec1
chore: cleanup and documentation improvement
averissimo Jul 25, 2023
b6c8ddd
fix: test compatibility with current strategies
averissimo Jul 17, 2023
3ab80f7
tests: Adds encapsulation tests for min_isolated strategy
averissimo Jul 17, 2023
78352d9
chore: reverts suppress messages and correct CHECK problems with subset
averissimo Jul 17, 2023
793f21d
chore: lint corrections
averissimo Jul 18, 2023
7a2e65d
chore: simplifies code
averissimo Jul 25, 2023
11c267b
chore: remove browser() call and update logic to use already implemen…
averissimo Jul 25, 2023
6cc7222
use numeric package versioning to be more permissible
averissimo Jul 25, 2023
5c27947
feat: add functions that test the install of multiple versions of a p…
averissimo Jul 25, 2023
776134f
fix: cohort problem with Bioc pkgs not having a published date
averissimo Jul 26, 2023
c93644b
fix: adds httr dep and uses official metadata from bioc
averissimo Jul 26, 2023
6453e8a
fix: replace bioc general release by last modified date from source
averissimo Jul 26, 2023
b0ec8d8
chore: refactor desc_field cleanup so it depends only on desc
averissimo Aug 1, 2023
ecce629
chore: adds tests for local_description and documentation
averissimo Aug 1, 2023
bb91882
chore: added 1 more test
averissimo Aug 1, 2023
2a63d94
ci: test check ci, to be reverted
averissimo Aug 1, 2023
535b7b0
Revert "ci: test check ci, to be reverted"
averissimo Aug 1, 2023
0bd24ee
fix: corrects a bunch of problems with R CMD check
averissimo Aug 1, 2023
38c06cb
ci: test check ci, to be reverted
averissimo Aug 1, 2023
ecde252
Merge 38c06cb1e44a54cddda898bccc961df9ad53257c into ad404d1ed6495f556…
averissimo Aug 1, 2023
999714e
[skip actions] Restyle files
github-actions[bot] Aug 1, 2023
1bbd883
chore: correct spelling and replace rlang call
averissimo Aug 1, 2023
70f6869
cleanup: remove feature from branch
averissimo Aug 1, 2023
1c957af
chore: cleanup
averissimo Aug 2, 2023
03bc473
[skip actions] Roxygen Man Pages Auto Update
github-actions[bot] Aug 2, 2023
e3a18d4
clean: cleanup of function that is only called once
averissimo Aug 8, 2023
5b71394
Apply suggestions from code review
averissimo Aug 8, 2023
7a094f2
[skip actions] Roxygen Man Pages Auto Update
github-actions[bot] Aug 8, 2023
a5be19b
chore: update examples to use dplyr/rlang
averissimo Aug 8, 2023
e3ffda0
dplyr in examples; pre-commit
pawelru Aug 8, 2023
fc94e3d
chore: remove bioc download method in favor of fallback to latest CRAN
averissimo Aug 12, 2023
157b6ad
fix: defaults to latest snapshot for Bioc packages
averissimo Aug 16, 2023
b3f7de2
fix: fix naming convention of function
averissimo Aug 16, 2023
bc0730b
tests: adds test suites and fixes a hardcoded string
averissimo Aug 16, 2023
16929bf
Merge bc0730be249aa70389125ac64373d9b1870ffc87 into ad404d1ed6495f556…
averissimo Aug 16, 2023
eec97b1
[skip actions] Restyle files
github-actions[bot] Aug 16, 2023
a9926e3
fix: corrects bugs found during tests
averissimo Aug 16, 2023
0819cbd
chore: document
averissimo Aug 17, 2023
49e4e8b
chore: remove httr dependency
averissimo Aug 17, 2023
783d755
fix: corrects typo on test
averissimo Aug 17, 2023
bd256b8
alphabetical order in pre-commit config
pawelru Aug 17, 2023
4a3236c
remove duplicates prior solving min_isolated
pawelru Aug 17, 2023
0719bdd
fix: issue in test_common and code cleanup
averissimo Aug 18, 2023
28b2dca
fix: bunch of corrections on cohort and code
averissimo Aug 18, 2023
74332e0
clean-up importFrom; add withr to pkg imports
pawelru Aug 21, 2023
6d22e75
add stats::na.omit to namespace
pawelru Aug 21, 2023
2074a76
fix: failure to resolve package should raise error later in the process
averissimo Aug 21, 2023
7ce8e09
chore: remove unnecessary parameter
averissimo Aug 21, 2023
99b0dc2
Apply suggestions from code review
averissimo Aug 21, 2023
95f7989
chore: change order of arguments and tests update
averissimo Aug 21, 2023
d72747d
chore: change order of arguments and tests update
averissimo Aug 21, 2023
fce38e3
chore: remove unnecessary NA as argument can be of length 0 or a date
averissimo Aug 21, 2023
d11385b
fix: small improvement on dealing with NA dates
averissimo Aug 21, 2023
9190f74
fix: enforce class on get_release_date methods output
averissimo Aug 22, 2023
826ddf5
add withr to pre-commit
pawelru Aug 24, 2023
68cb7eb
use map_key_character in other places
pawelru Aug 24, 2023
a0b01a5
add Andre to authors; Roche cph and fnd; LICENSE
pawelru Aug 24, 2023
ecbdc98
fix DESCRIPTION file
pawelru Aug 24, 2023
cfabadf
Merge pull request #28 from insightsengineering/training-cleanup
averissimo Aug 28, 2023
939d598
Merge branch 'main' into training
pawelru Aug 28, 2023
1fd5899
docs
pawelru Aug 28, 2023
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1 change: 1 addition & 0 deletions .pre-commit-config.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,7 @@ repos:
exclude: >
(?x)^(
data/.*|
inst/.*|
(.*/|)\.Rprofile|
(.*/|)\.Renviron|
(.*/|)\.gitignore|
Expand Down
31 changes: 29 additions & 2 deletions NAMESPACE
Original file line number Diff line number Diff line change
Expand Up @@ -6,21 +6,48 @@ S3method(get_ref_min,remote_ref_github)
S3method(get_ref_min,remote_ref_standard)
S3method(get_ref_min_incl_cran,remote_ref)
S3method(get_ref_min_incl_cran,remote_ref_github)
S3method(get_release_date,remote_ref)
S3method(get_release_date,remote_ref_cran)
S3method(get_release_date,remote_ref_github)
S3method(get_release_date,remote_ref_standard)
S3method(solve_ip,deps_installation_proposal)
S3method(solve_ip,min_isolated_deps_installation_proposal)
export(check_ip)
export(download_ip)
export(execute_ip)
export(get_ref_max)
export(get_ref_min)
export(get_ref_min_incl_cran)
export(get_ref_release)
export(get_release_date)
export(install_ip)
export(max_deps_check)
export(min_deps_check)
export(min_cohort_deps_check)
export(min_isolated_deps_check)
export(new_max_deps_installation_proposal)
export(new_min_deps_installation_proposal)
export(new_min_cohort_deps_installation_proposal)
export(new_min_isolated_deps_installation_proposal)
export(new_release_deps_installation_proposal)
export(release_deps_check)
export(solve_ip)
importFrom(cli,cli_progress_bar)
importFrom(cli,cli_progress_update)
importFrom(cli,col_green)
importFrom(cli,pb_current)
importFrom(cli,pb_elapsed)
importFrom(cli,pb_eta)
importFrom(cli,pb_extra)
importFrom(cli,pb_spin)
importFrom(cli,pb_total)
importFrom(cli,symbol)
importFrom(desc,desc)
importFrom(gh,gh)
importFrom(gh,gh_gql)
importFrom(pkgcache,cran_archive_list)
importFrom(pkgcache,meta_cache_list)
importFrom(pkgcache,ppm_repo_url)
importFrom(pkgcache,ppm_snapshots)
importFrom(pkgdepends,as_pkg_dependencies)
importFrom(pkgdepends,new_pkg_deps)
importFrom(pkgdepends,new_pkg_installation_proposal)
importFrom(pkgdepends,parse_pkg_ref)
Expand Down
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