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reduce the amount of spelling issues / WORDLIST #210

Merged
merged 8 commits into from
Jun 26, 2023
Merged

reduce the amount of spelling issues / WORDLIST #210

merged 8 commits into from
Jun 26, 2023

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m7pr
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@m7pr m7pr commented Jun 20, 2023

The follow-up after https://github.com/insightsengineering/coredev-tasks/issues/235

Work in progress - the current output of spelling::spell_check_package()

  WORD                   FOUND IN
Armen                  hermes.Rmd:43
Benjamini              h_diff_expr_deseq2.Rd:19
                       h_diff_expr_voom.Rd:19
BioConductor           hermes.Rmd:54,56,79
BioMart                connect_biomart.Rd:9,30
                       h_ensembl_to_entrez_ids.Rd:20
                       h_get_annotation_biomart.Rd:5,13
                       h_get_granges_by_id.Rd:5
                       h_get_size_biomart.Rd:13,24
                       h_strip_prefix.Rd:26
                       query.Rd:38
                       description:5
                       hermes.Rmd:84,235
Bové                  hermes-package.Rd:20
CDISC                  inner_join_cdisc.Rd:5,17,29
cloneable              GeneSpec.Rd:182
cpm                    description:8
CPM                    control_quality.Rd:15,19,22
                       normalize.Rd:55,66,77
                       quality_flags.Rd:44,47
                       hermes.Rmd:274,337
DESeq                  h_diff_expr_deseq2.Rd:5
                       description:9
dichotomize            draw_barplot.Rd:29
dispersions            diff_expression.Rd:71
Ensembl                connect_biomart.Rd:16,30
                       h_ensembl_to_entrez_ids.Rd:5,10,20
                       h_get_annotation_biomart.Rd:11
                       h_get_granges_by_id.Rd:13
                       h_get_size_biomart.Rd:11
                       query.Rd:39
Entrez                 expression_set.Rd:9
                       h_ensembl_to_entrez_ids.Rd:5,15,20
                       h_get_annotation_biomart.Rd:11
                       h_get_size_biomart.Rd:11
                       h_strip_prefix.Rd:25
                       hermes_data.Rd:9
                       multi_assay_experiment.Rd:11
                       summarized_experiment.Rd:9
funder                 hermes-package.Rd:42
getter                 quality_flags.Rd:55
Hochberg               h_diff_expr_deseq2.Rd:19
                       h_diff_expr_voom.Rd:19
Hoffmann               hermes-package.Rd:42
homoskedastic          normalize.Rd:71,72
Karapetyan             hermes.Rmd:43
Kilobase               normalize.Rd:58,79
kilobases              normalize.Rd:59
Marbach                hermes.Rmd:43
Midori                 hermes-package.Rd:29
Obenchain              hermes.Rmd:43
pandoc                 hermes.Rmd:508
pre                    description:3
quartile               control_quality.Rd:26
repo                   README.md:20,31
                       README.Rmd:23,29
reproducibility        connect_biomart.Rd:31
Rmd                    hermes.Rmd:477
RNAseq                 hermes.Rmd:43,79,83,473,504
rpkm                   description:9
RPKM                   normalize.Rd:58,62,63,64,79
                       hermes.Rmd:337
RStudio                hermes.Rmd:476
Sabanés               hermes-package.Rd:20
SummarizedExperiment   description:4
templated              NEWS.md:72
                       README.md:54
                       README.Rmd:46
                       hermes.Rmd:90
testthat               assertion_arguments.Rd:18
                       check_proportion.Rd:35
tpm                    description:9
TPM                    normalize.Rd:62,81
                       hermes.Rmd:337
voom                   description:9
VOOM                   normalize.Rd:66,83
yaml                   hermes.Rmd:478
Zhang                  hermes-package.Rd:29,36

@m7pr m7pr self-assigned this Jun 20, 2023
@m7pr m7pr added documentation Improvements or additions to documentation core labels Jun 20, 2023
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m7pr commented Jun 21, 2023

hi @danielinteractive - this is not yet done, this is just Draft. There is still a bunch of list I'd like to fix in spelling. Once I'm done, I'll change this Draft to a PR and will ask you for a review. Is that OK? Or you just expressed your faith, that it's gonna be fine whathever I propose :)?

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Thanks @m7pr yep then just re-request review once final :-) I just meant to say any wordlist updates will be great.

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m7pr commented Jun 23, 2023

The final spelling check list is below. Most of the words are surnames, named-entities or shortcodes in DESCRIPTION file, or software-development like terms that are not yet in standard dictionaries used by hunspell.

spelling:::spell_check_package()
  WORD                   FOUND IN
Armen                  hermes.Rmd:43
Benjamini              h_diff_expr_deseq2.Rd:19
                       h_diff_expr_voom.Rd:19
BioMart                description:5
Bové                  hermes-package.Rd:20
cloneable              GeneSpec.Rd:182
cpm                    description:8
DESeq                  description:9
dichotomize            draw_barplot.Rd:29
dispersions            diff_expression.Rd:71
funder                 hermes-package.Rd:42
Hochberg               h_diff_expr_deseq2.Rd:19
                       h_diff_expr_voom.Rd:19
Hoffmann               hermes-package.Rd:42
homoskedastic          normalize.Rd:71,72
Karapetyan             hermes.Rmd:43
Kilobase               normalize.Rd:58,79
kilobases              normalize.Rd:59
Marbach                hermes.Rmd:43
Midori                 hermes-package.Rd:29
Obenchain              hermes.Rmd:43
pre                    description:3
quartile               control_quality.Rd:26
repo                   README.md:20,31
                       README.Rmd:23,29
reproducibility        connect_biomart.Rd:31
rpkm                   description:9
Sabanés               hermes-package.Rd:20
SummarizedExperiment   description:4
templated              NEWS.md:72
                       README.md:54
                       README.Rmd:46
                       hermes.Rmd:90
tpm                    description:9
voom                   description:9
Zhang                  hermes-package.Rd:29,36

@m7pr m7pr marked this pull request as ready for review June 23, 2023 14:12
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m7pr commented Jun 23, 2023

Hey @danielinteractive - it's ready for your review

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github-actions bot commented Jun 23, 2023 •
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badge

Code Coverage Summary

Filename                   Stmts    Miss  Cover    Missing
-----------------------  -------  ------  -------  ------------------------
R/assertthat.R                19       1  94.74%   149
R/calc_cor.R                  25       0  100.00%
R/checkmate.R                  4       0  100.00%
R/connections.R              143     125  12.59%   27-161, 215-287, 356-381
R/differential.R             101       3  97.03%   190, 193, 196
R/dplyr_compatibility.R        3       1  66.67%   23
R/draw_barplot.R              34       0  100.00%
R/draw_boxplot.R              71       5  92.96%   81, 88-89, 106, 109
R/draw_heatmap.R              35       1  97.14%   71
R/draw_scatterplot.R          32       4  87.50%   73-74, 87, 93
R/GeneSpec-class.R            68       0  100.00%
R/graphs.R                   107       3  97.20%   107-109
R/HermesData-class.R          35       4  88.57%   134-137
R/HermesData-methods.R       194       0  100.00%
R/HermesData-validate.R       44       0  100.00%
R/join_cdisc.R                37       0  100.00%
R/normalization.R            100       2  98.00%   194, 223
R/pca_cor_samplevar.R         59       0  100.00%
R/pca.R                       28       0  100.00%
R/quality.R                   75       3  96.00%   109-112
R/top_genes.R                 51       0  100.00%
R/utils.R                     98       0  100.00%
TOTAL                       1363     152  88.85%

Diff against main

Filename      Stmts    Miss  Cover
----------  -------  ------  --------
TOTAL             0       0  +100.00%

Results for commit: 1b54358

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

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github-actions bot commented Jun 26, 2023 •
edited
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Unit Tests Summary

    1 files    23 suites   2m 3s ⏱️
273 tests 256 ✔️ 17 💤 0 ❌
847 runs  824 ✔️ 23 💤 0 ❌

Results for commit bc07bbf.

♻️ This comment has been updated with latest results.

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m7pr commented Jun 26, 2023

Hey @danielinteractive I did re-request your review as I made 2 changes/reverts after your comments. Thanks for the input!

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danielinteractive approved these changes Jun 26, 2023
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Thanks @m7pr - I appreciate the effort from your side. I would suggest for the future, before jumping into any changes on our packages, let's have a quick chat to discuss the value of these changes so that we can optimize the efforts

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m7pr commented Jun 26, 2023

will do, thanks for the cooperation

@m7pr m7pr merged commit 08c751c into main Jun 26, 2023
@m7pr m7pr deleted the update_wordlist@main branch June 26, 2023 13:04
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