update team task contributor section

.gitignore

@@ -13,3 +13,4 @@
 /site_libs
 *.rmarkdown
 /.luarc.json
+/tmp

team/_rerender_contributors.R

@@ -1,10 +1,15 @@
 library(rlang)
 
 repositories <- c(
-    "openproblems-bio/openproblems",
-    # "openproblems-bio/task_dimensionality_reduction",
-    # "openproblems-bio/task_spatially_variable_genes",
-    "openproblems-bio/task_perturbation_prediction"
+    "openproblems-bio/task_denoising",
+    "openproblems-bio/task_dimensionality_reduction",
+    "openproblems-bio/task_spatially_variable_genes",
+    "openproblems-bio/task_perturbation_prediction",
+    "openproblems-bio/task_batch_integration",
+    "openproblems-bio/task_cell_cell_communication",
+    "openproblems-bio/task_label_projection",
+    "openproblems-bio/task_spatial_decomposition",
+    "openproblems-bio/task_predict_modality"
 )
 
 cache_repository <- function(repo) {
@@ -20,20 +25,26 @@ cache_repository <- function(repo) {
     zzz <- processx::run("git", c("fetch", "--all"), wd = repo_dir)
 
     # reset the repository to the latest commit
-    zzz <- processx::run("git", c("pull", "origin", "main"), wd = repo_dir)
+    if (repo == "openproblems-bio/task_spatial_decomposition") {
+        zzz <- processx::run("git", c("pull", "origin", "add-missing-authors"), wd = repo_dir)
+    } else if (repo == "openproblems-bio/task_dimensionality_reduction") {
+        zzz <- processx::run("git", c("pull", "origin", "add_author"), wd = repo_dir)
+    } else {
+        zzz <- processx::run("git", c("pull", "origin", "main"), wd = repo_dir)
+    }
 
     # return the path to the repository
     return(repo_dir)
 }
 
 find_task_info <- function(repo_dir) {
     # find all authors in the repository
-    task_info <- list.files(repo_dir, pattern = "task_info.yaml", full.names = TRUE, recursive = TRUE)
-    task_info <- task_info[grep("/api/task_info.yaml", task_info)]
+    # task_info <- list.files(repo_dir, pattern = "task_info.yaml", full.names = TRUE, recursive = TRUE)
+    # task_info <- task_info[grep("/api/task_info.yaml", task_info)]
 
-    if (length(task_info) > 0) {
-        return(task_info)
-    }
+    # if (length(task_info) > 0) {
+    #     return(task_info)
+    # }
 
     viash_yaml <- list.files(repo_dir, pattern = "_viash.yaml", full.names = TRUE, recursive = TRUE)
 
@@ -52,8 +63,18 @@ render_author <- function(author) {
             email_clean <- tolower(stringr::str_trim(author$info$email))
             checksum <- digest::digest(email_clean, algo = "md5", serialize = FALSE)
             paste0("https://www.gravatar.com/avatar/", checksum)
-        } else {
+        } else if (file.exists("/images/avatar.svg")){
             "/images/avatar.svg"
+        } else {
+            # generate random avatar
+            name <- strsplit(author$name, " ")
+            url <- paste0("https://avatar.iran.liara.run/username?username=",name[[1]][[1]],"+",name[[1]][[2]])
+            output_dir <- file.path("tmp", gsub(" ", "_", author$name))
+            if (!dir.exists(output_dir)) {
+                dir.create(output_dir, recursive = TRUE)
+            }
+            download.file(url, file.path(output_dir, "avatar.png"), mode = "wb")
+            "avatar.png"
         }
 
     # process links
@@ -74,7 +95,7 @@ render_author <- function(author) {
         },
         orcid = function(value) {
             list(
-                icon = "fa-brands fa-orcid",
+                icon = "fa-brands--orcid",
                 text = "ORCID",
                 href = paste0("https://orcid.org/", value)
             )
@@ -98,8 +119,8 @@ render_author <- function(author) {
     out <- list(
         title = author$name,
         image = out_image,
-        # role = paste(stringr::str_to_title(author$roles), collapse = ", "),
-        role = "Task Contributor",
+        role = paste(stringr::str_to_title(author$roles), collapse = ", "),
+        # role = "Task Contributor",
         about = list(
             template = "jolla",
             links = out_links
@@ -162,18 +183,22 @@ for (task_name in names(tasks)) {
         author <- task$authors[[author_id]]
 
         txt <- render_author(author)
-        file_path <- file.path("team", "task_contributors", paste0(author_id, "/index.qmd"))
+        file_path <- file.path("team", "task_contributors", task_name, paste0(author_id, "/index.qmd"))
 
         if (!dir.exists(dirname(file_path))) {
             dir.create(dirname(file_path), recursive = TRUE)
         }
 
         writeLines(txt, file_path)
+
+        if (file.exists(file.path("tmp", gsub(" ", "_", author$name), "avatar.png"))) {
+            file.rename(file.path("tmp", gsub(" ", "_", author$name), "avatar.png"), file.path(dirname(file_path), "avatar.png"))
+        }
+
     }
 }
 
-teams <- list.dirs("team", full.names = FALSE, recursive = FALSE)
-teams <- teams[!teams %in% c("core_members", "scientific_advisors")]
+teams <- list.dirs("team/task_contributors", full.names = FALSE, recursive = FALSE)
 
 teams_headers <- paste0(
 "  - id: ", teams, "
@@ -183,7 +208,7 @@ teams_headers <- paste0(
     sort: ''"
 )
 teams_index <- paste0(
-"## ", stringr::str_to_title(gsub("_", " ", teams)), "
+"### ", stringr::str_to_title(gsub("_", " ", teams)), "
 
 :::{#", teams, "}
 :::
@@ -220,6 +245,8 @@ css: team.css
 :::{#scientific_advisors}
 :::
 
+## Task Contributors
+
 ", paste(teams_index, collapse = "\n"), "
 ")
 

team/core_members/burkhardt_daniel/index.qmd

@@ -21,7 +21,7 @@ about:
     - icon: bi-linkedin
       text: LinkedIn
       href: https://www.linkedin.com/in/daniel-burkhardt/
-    - icon: fa-brands fa-orcid
+    - icon: fa-brands--orcid
       text: ORCID
       href: https://orcid.org/0000-0001-7744-1363
 ---

team/core_members/cannoodt_robrecht/index.qmd

@@ -21,7 +21,7 @@ about:
     - icon: bi-linkedin
       text: LinkedIn
       href: https://www.linkedin.com/in/robrecht-cannoodt/
-    - icon: fa-brands fa-orcid
+    - icon: fa-brands--orcid
       text: ORCID
       href: https://orcid.org/0000-0003-3641-729X
 ---

team/core_members/gigante_scott/index.qmd

@@ -22,7 +22,7 @@ about:
     - icon: bi-linkedin
       text: LinkedIn
       href: https://www.linkedin.com/in/scottgigante/
-    - icon: fa-brands fa-orcid
+    - icon: fa-brands--orcid
       text: ORCID
       href: https://orcid.org/0000-0002-4544-2764
 ---

team/core_members/luecken_malte/index.qmd

@@ -21,7 +21,7 @@ about:
     - icon: bi-linkedin
       text: LinkedIn
       href: https://www.linkedin.com/in/malte-lücken-b8b21049/
-    - icon: fa-brands fa-orcid
+    - icon: fa-brands--orcid
       text: ORCID
       href: https://orcid.org/0000-0001-7464-7921
 ---

team/index.qmd

@@ -14,8 +14,48 @@ listing:
     type: grid
     template: members.ejs
     sort: ''
-  - id: task_contributors
-    contents: task_contributors/*/index.qmd
+  - id: batch_integration
+    contents: batch_integration/*/index.qmd
+    type: grid
+    template: members.ejs
+    sort: ''
+  - id: cell_cell_communication
+    contents: cell_cell_communication/*/index.qmd
+    type: grid
+    template: members.ejs
+    sort: ''
+  - id: denoising
+    contents: denoising/*/index.qmd
+    type: grid
+    template: members.ejs
+    sort: ''
+  - id: dimensionality_reduction
+    contents: dimensionality_reduction/*/index.qmd
+    type: grid
+    template: members.ejs
+    sort: ''
+  - id: label_projection
+    contents: label_projection/*/index.qmd
+    type: grid
+    template: members.ejs
+    sort: ''
+  - id: perturbation_prediction
+    contents: perturbation_prediction/*/index.qmd
+    type: grid
+    template: members.ejs
+    sort: ''
+  - id: predict_modality
+    contents: predict_modality/*/index.qmd
+    type: grid
+    template: members.ejs
+    sort: ''
+  - id: spatial_decomposition
+    contents: spatial_decomposition/*/index.qmd
+    type: grid
+    template: members.ejs
+    sort: ''
+  - id: spatially_variable_genes
+    contents: spatially_variable_genes/*/index.qmd
     type: grid
     template: members.ejs
     sort: ''
@@ -34,7 +74,47 @@ css: team.css
 
 ## Task Contributors
 
-:::{#task_contributors}
+### Batch Integration
+
+:::{#batch_integration}
+:::
+
+### Cell Cell Communication
+
+:::{#cell_cell_communication}
+:::
+
+### Denoising
+
+:::{#denoising}
+:::
+
+### Dimensionality Reduction
+
+:::{#dimensionality_reduction}
 :::
 
+### Label Projection
+
+:::{#label_projection}
+:::
 
+### Perturbation Prediction
+
+:::{#perturbation_prediction}
+:::
+
+### Predict Modality
+
+:::{#predict_modality}
+:::
+
+### Spatial Decomposition
+
+:::{#spatial_decomposition}
+:::
+
+### Spatially Variable Genes
+
+:::{#spatially_variable_genes}
+:::

team/task_contributors/daniel_strobl/index.qmd → team/task_contributors/batch_integration/daniel_strobl/index.qmd

@@ -1,12 +1,15 @@
 ---
 title: Daniel Strobl
 image: https://www.github.com/danielStrobl.png
-role: Task Contributor
+role: Author
 about:
   template: jolla
   links:
   - icon: bi-github
     text: GitHub
     href: https://github.com/danielStrobl
+  - icon: fa-brands--orcid
+    text: ORCID
+    href: https://orcid.org/0000-0002-5516-7057
 ---
 

team/task_contributors/kai_waldrant/index.qmd → team/task_contributors/batch_integration/kai_waldrant/index.qmd

@@ -1,14 +1,14 @@
 ---
 title: Kai Waldrant
 image: https://www.github.com/KaiWaldrant.png
-role: Task Contributor
+role: Contributor
 about:
   template: jolla
   links:
   - icon: bi-github
     text: GitHub
     href: https://github.com/KaiWaldrant
-  - icon: fa-brands fa-orcid
+  - icon: fa-brands--orcid
     text: ORCID
     href: https://orcid.org/0009-0003-8555-1361
 ---

team/task_contributors/batch_integration/malte_luecken/index.qmd

@@ -0,0 +1,15 @@
+---
+title: Malte Luecken
+image: https://www.github.com/LuckyMD.png
+role: Author
+about:
+  template: jolla
+  links:
+  - icon: bi-github
+    text: GitHub
+    href: https://github.com/LuckyMD
+  - icon: fa-brands--orcid
+    text: ORCID
+    href: https://orcid.org/0000-0001-7464-7921
+---
+

team/task_contributors/michaela_mueller/index.qmd → team/task_contributors/batch_integration/michaela_mueller/index.qmd

@@ -1,12 +1,15 @@
 ---
 title: Michaela Mueller
 image: https://www.github.com/mumichae.png
-role: Task Contributor
+role: Maintainer, Author
 about:
   template: jolla
   links:
   - icon: bi-github
     text: GitHub
     href: https://github.com/mumichae
+  - icon: fa-brands--orcid
+    text: ORCID
+    href: https://orcid.org/0000-0002-1401-1785
 ---
 

team/task_contributors/batch_integration/nartin_kim/index.qmd

@@ -0,0 +1,15 @@
+---
+title: Nartin Kim
+image: https://www.github.com/martinkim0.png
+role: Contributor
+about:
+  template: jolla
+  links:
+  - icon: bi-github
+    text: GitHub
+    href: https://github.com/martinkim0
+  - icon: fa-brands--orcid
+    text: ORCID
+    href: https://orcid.org/0009-0003-8555-1361
+---
+

team/task_contributors/cell_cell_communication/daniel_dimitrov/index.qmd

@@ -0,0 +1,12 @@
+---
+title: Daniel Dimitrov
+image: https://www.github.com/dbdimitrov.png
+role: Maintainer, Author
+about:
+  template: jolla
+  links:
+  - icon: bi-github
+    text: GitHub
+    href: https://github.com/dbdimitrov
+---
+

team/task_contributors/cell_cell_communication/vishnuvasan_raghuraman/index.qmd

@@ -0,0 +1,12 @@
+---
+title: Vishnuvasan Raghuraman
+image: https://www.github.com/vishnu-vasan.png
+role: Contributor
+about:
+  template: jolla
+  links:
+  - icon: bi-github
+    text: GitHub
+    href: https://github.com/vishnu-vasan
+---
+