Merge pull request #582 from d3b-center/rokita/contributions-june5

remove gitignore til GHA works
d3b-center · Jul 7, 2024 · f60df8f · f60df8f
2 parents e289e49 + 203eb82
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diff --git a/analyses/count-contributions/02-format-contributions.Rmd b/analyses/count-contributions/02-format-contributions.Rmd
@@ -99,7 +99,8 @@ authors_rm <- c(
  "Bailey",
  "Ubuntu",
  "Teja Koganti",
- "Yuankun Zhu"
+ "Yuankun Zhu",
+ "Rocky Breslow"
 )
 ```
 

diff --git a/analyses/count-contributions/02-format-contributions.nb.html b/analyses/count-contributions/02-format-contributions.nb.html
diff --git a/analyses/count-contributions/03-set-authorship-order.nb.html b/analyses/count-contributions/03-set-authorship-order.nb.html
@@ -2910,14 +2910,14 @@ <h2>Set up</h2>
 <!-- rnb-source-begin eyJkYXRhIjoibGlicmFyeSh0aWR5dmVyc2UpIn0= -->
 <pre class="r"><code>library(tidyverse)</code></pre>
 <!-- rnb-source-end -->
-<!-- rnb-message-begin eyJkYXRhIjoi4pSA4pSAIEF0dGFjaGluZyBjb3JlIHRpZHl2ZXJzZSBwYWNrYWdlcyDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIAgdGlkeXZlcnNlIDIuMC4wIOKUgOKUgFxu4pyUIGRwbHlyICAgICAxLjEuNCAgICAg4pyUIHJlYWRyICAgICAyLjEuNVxu4pyUIGZvcmNhdHMgICAxLjAuMCAgICAg4pyUIHN0cmluZ3IgICAxLjUuMVxu4pyUIGdncGxvdDIgICAzLjUuMSAgICAg4pyUIHRpYmJsZSAgICAzLjIuMVxu4pyUIGx1YnJpZGF0ZSAxLjkuMyAgICAg4pyUIHRpZHlyICAgICAxLjMuMVxu4pyUIHB1cnJyICAgICAxLjAuMiAgICAgXG7ilIDilIAgQ29uZmxpY3RzIOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgOKUgCB0aWR5dmVyc2VfY29uZmxpY3RzKCkg4pSA4pSAXG7inJYgZHBseXI6OmZpbHRlcigpIG1hc2tzIHN0YXRzOjpmaWx0ZXIoKVxu4pyWIGRwbHlyOjpsYWcoKSAgICBtYXNrcyBzdGF0czo6bGFnKClcbuKEuSBVc2UgdGhlIGNvbmZsaWN0ZWQgcGFja2FnZSAoPGh0dHA6Ly9jb25mbGljdGVkLnItbGliLm9yZy8+KSB0byBmb3JjZSBhbGwgY29uZmxpY3RzIHRvIGJlY29tZSBlcnJvcnNcbiJ9 -->
-<pre><code>── Attaching core tidyverse packages ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 2.0.0 ──
+<!-- rnb-message-begin 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 -->
+<pre><code>── Attaching core tidyverse packages ──────────────────────────────────────────────────────────── tidyverse 2.0.0 ──
 ✔ dplyr 1.1.4 ✔ readr 2.1.5
 ✔ forcats 1.0.0 ✔ stringr 1.5.1
 ✔ ggplot2 3.5.1 ✔ tibble 3.2.1
 ✔ lubridate 1.9.3 ✔ tidyr 1.3.1
 ✔ purrr 1.0.2 
-── Conflicts ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
+── Conflicts ────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
 ✖ dplyr::filter() masks stats::filter()
 ✖ dplyr::lag() masks stats::lag()
 ℹ Use the conflicted package (&lt;http://conflicted.r-lib.org/&gt;) to force all conflicts to become errors</code></pre>
@@ -3030,9 +3030,9 @@ <h3>Code contributors</h3>
 <!-- rnb-source-begin eyJkYXRhIjoibW9kdWxlX2NvbnRyaWJ1dGlvbnNfZGYgPC0gcmVhZF90c3YobW9kdWxlX2NvbnRyaWJ1dGlvbnNfZmlsZSkifQ== -->
 <pre class="r"><code>module_contributions_df &lt;- read_tsv(module_contributions_file)</code></pre>
 <!-- rnb-source-end -->
-<!-- rnb-message-begin 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 -->
-<pre><code>Rows: 19 Columns: 2
-── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
+<!-- rnb-message-begin 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 -->
+<pre><code>Rows: 18 Columns: 2
+── Column specification ────────────────────────────────────────────────────────────────────────────────────────────
 Delimiter: &quot;\t&quot;
 chr (1): author
 dbl (1): num_modules
@@ -3114,7 +3114,7 @@ <h3>All positions and update metadata</h3>
 <!-- rnb-source-end -->
 <div data-pagedtable="false">
 <script data-pagedtable-source type="application/json">
-{"columns":[{"label":[""],"name":["_rn_"],"type":[""],"align":["left"]},{"label":["all_contributors_positions"],"name":[1],"type":["dbl"],"align":["right"]}],"data":[{"1":"1","_rn_":"Zhuangzhuang Geng"},{"1":"2","_rn_":"Eric Wafula"},{"1":"3","_rn_":"Yuanchao Zhang"},{"1":"4","_rn_":"Ryan J. Corbett"},{"1":"5","_rn_":"Run Jin"},{"1":"6","_rn_":"Krutika S. Gaonkar"},{"1":"7","_rn_":"Komal S. Rathi"},{"1":"8","_rn_":"Sangeeta Shukla"},{"1":"9","_rn_":"Dave Hill"},{"1":"10","_rn_":"Aditya Lahiri"},{"1":"11","_rn_":"Daniel P. Miller"},{"1":"12","_rn_":"Alex Sickler"},{"1":"13","_rn_":"Kelsey Keith"},{"1":"14","_rn_":"Christopher Blackden"},{"1":"15","_rn_":"Rocky Breslow"},{"1":"16","_rn_":"Antonia Chroni"},{"1":"17","_rn_":"Adam A. Kraya"},{"1":"18","_rn_":"Miguel A. Brown"},{"1":"19","_rn_":"Brian M. Ennis"},{"1":"20","_rn_":"Ammar S. Naqvi"},{"1":"21","_rn_":"Sharon J. Diskin"},{"1":"22","_rn_":"Bo Zhang"},{"1":"23","_rn_":"Joseph Dybas"},{"1":"24","_rn_":"Alvin Farrel"},{"1":"25","_rn_":"Jennifer L. Mason"},{"1":"26","_rn_":"Bailey K. Farrow"},{"1":"27","_rn_":"Yuankun Zhu"},{"1":"28","_rn_":"Matthew R. Lueder"},{"1":"29","_rn_":"Nicholas Van Kuren"},{"1":"30","_rn_":"Chuwei Zhong"},{"1":"31","_rn_":"Noel Coleman"},{"1":"32","_rn_":"Mariarita Santi"},{"1":"33","_rn_":"John M. Maris"},{"1":"34","_rn_":"Saksham Phul"},{"1":"35","_rn_":"Xiaoyan Huang"},{"1":"36","_rn_":"Asif T Chinwalla"},{"1":"37","_rn_":"Adam C. Resnick"},{"1":"38","_rn_":"Sarah Tasian"},{"1":"39","_rn_":"Deanne Taylor"},{"1":"40","_rn_":"Jo Lynne Rokita"}],"options":{"columns":{"min":{},"max":[10]},"rows":{"min":[10],"max":[10]},"pages":{}}}
+{"columns":[{"label":[""],"name":["_rn_"],"type":[""],"align":["left"]},{"label":["all_contributors_positions"],"name":[1],"type":["dbl"],"align":["right"]}],"data":[{"1":"1","_rn_":"Zhuangzhuang Geng"},{"1":"2","_rn_":"Eric Wafula"},{"1":"3","_rn_":"Yuanchao Zhang"},{"1":"4","_rn_":"Ryan J. Corbett"},{"1":"5","_rn_":"Run Jin"},{"1":"6","_rn_":"Krutika S. Gaonkar"},{"1":"7","_rn_":"Sangeeta Shukla"},{"1":"8","_rn_":"Komal S. Rathi"},{"1":"9","_rn_":"Dave Hill"},{"1":"10","_rn_":"Aditya Lahiri"},{"1":"11","_rn_":"Daniel P. Miller"},{"1":"12","_rn_":"Alex Sickler"},{"1":"13","_rn_":"Kelsey Keith"},{"1":"14","_rn_":"Christopher Blackden"},{"1":"15","_rn_":"Antonia Chroni"},{"1":"16","_rn_":"Miguel A. Brown"},{"1":"17","_rn_":"Adam A. Kraya"},{"1":"18","_rn_":"Bo Zhang"},{"1":"19","_rn_":"Asif T Chinwalla"},{"1":"20","_rn_":"Mariarita Santi"},{"1":"21","_rn_":"Carl J. Koschmann"},{"1":"22","_rn_":"Nicholas Van Kuren"},{"1":"23","_rn_":"Zied Abdullaev"},{"1":"24","_rn_":"Alvin Farrel"},{"1":"25","_rn_":"Weiping Ma"},{"1":"26","_rn_":"Yuankun Zhu"},{"1":"27","_rn_":"Adam C. Resnick"},{"1":"28","_rn_":"Jennifer L. Mason"},{"1":"29","_rn_":"Noel Coleman"},{"1":"30","_rn_":"Ammar S. Naqvi"},{"1":"31","_rn_":"Xiaoyan Huang"},{"1":"32","_rn_":"Sarah Tasian"},{"1":"33","_rn_":"Joseph Dybas"},{"1":"34","_rn_":"Brian M. Ennis"},{"1":"35","_rn_":"Sharon J. Diskin"},{"1":"36","_rn_":"Kenneth Aldape"},{"1":"37","_rn_":"John M. Maris"},{"1":"38","_rn_":"Bailey K. Farrow"},{"1":"39","_rn_":"Chuwei Zhong"},{"1":"40","_rn_":"Brian R. Rood"},{"1":"41","_rn_":"Matthew R. Lueder"},{"1":"42","_rn_":"Stephanie Stefankiewicz"},{"1":"43","_rn_":"Pei Wang"},{"1":"44","_rn_":"Saksham Phul"},{"1":"45","_rn_":"Deanne Taylor"},{"1":"46","_rn_":"Jo Lynne Rokita"}],"options":{"columns":{"min":{},"max":[10]},"rows":{"min":[10],"max":[10]},"pages":{}}}
  </script>
 </div>
 <!-- rnb-chunk-end -->

diff --git a/analyses/count-contributions/results/module_contribution_counts.tsv b/analyses/count-contributions/results/module_contribution_counts.tsv
@@ -14,7 +14,6 @@ Daniel P. Miller 3
 Alex Sickler 3
 Kelsey Keith 2
 Christopher Blackden 2
-Rocky Breslow 2
 Miguel A. Brown 1
 Adam A. Kraya 1
 Antonia Chroni 1
diff --git a/analyses/count-contributions/results/module_contributors.tsv b/analyses/count-contributions/results/module_contributors.tsv
@@ -29,7 +29,6 @@ focal-cn-file-preparation Jo Lynne Rokita
 focal-cn-file-preparation Krutika S. Gaonkar
 focal-cn-file-preparation Komal S. Rathi
 focal-cn-file-preparation Ryan J. Corbett
-focal-cn-file-preparation Rocky Breslow
 focal-cn-file-preparation Run Jin
 focal-cn-file-preparation Sangeeta Shukla
 focal-cn-file-preparation Zhuangzhuang Geng
@@ -58,7 +57,6 @@ gene-set-enrichment-analysis Krutika S. Gaonkar
 gene-set-enrichment-analysis Run Jin
 gene-set-enrichment-analysis Sangeeta Shukla
 gene_match Jo Lynne Rokita
-gene_match Rocky Breslow
 gene_match Run Jin
 gene_match Sangeeta Shukla
 independent-samples Eric Wafula

diff --git a/analyses/count-contributions/results/total_contributions_clean.tsv b/analyses/count-contributions/results/total_contributions_clean.tsv
@@ -1,9 +1,9 @@
 author num_commits
-Jo Lynne Rokita 1025
+Jo Lynne Rokita 1031
 Run Jin 576
 Eric Wafula 450
 Yuanchao Zhang 342
-Zhuangzhuang Geng 254
+Zhuangzhuang Geng 256
 Krutika S. Gaonkar 205
 Sangeeta Shukla 177
 Aditya Lahiri 176
@@ -18,4 +18,3 @@ Dave Hill 14
 Antonia Chroni 11
 Daniel P. Miller 6
 Alvin Farrel 2
-Rocky Breslow 1