Merge pull request #452 from web4bio/development

Development

.github/dependabot.yml

@@ -0,0 +1,9 @@
+version: 2
+updates:
+  - package-ecosystem: "npm"
+    directory: "/"
+    schedule:
+      interval: "daily"
+    # Update the npm manifest file to relax
+    # the version requirements
+    target-branch: "development"

README.md

@@ -24,32 +24,33 @@ This is a public, open-source project, as well as a project that students may re
 5. Study the [GDC API](https://docs.gdc.cancer.gov/API/Users_Guide/Getting_Started/) and note how easy it is to retrieve data. The next step is to start doing just that in the middle of your own notes. Have a [look at mine](https://beta.observablehq.com/@jonasalmeida/webgen).
 6. Study the [FireBrowse API](http://firebrowse.org).
 7. Report issues or requests for new features.
-8. Create a fork or a branch, and make a pull request.
+8. Create a fork or a branch off of the **development branch**, and make a pull request.
 
 ## Participants
 
 | Name & GitHub ID  | Individual folder or notebook | Observable | Other links|
 | --- | --- | --- | --- |
 | [Richard Moffitt](https://github.com/rmoffitt) | [Folder](/archive/richard/), [js Sandbox](/archive/richard/richard.html) | [Notebook homepage](https://observablehq.com/@rmoffitt?tab=notebooks), [WebGen page](https://observablehq.com/@rmoffitt/webgen), [Simple GDC query tool](https://observablehq.com/@rmoffitt/tcgaplots) | [Faculty website](https://bmi.stonybrookmedicine.edu/people/moffitt_richard) |
 | [Jonas Almeida](http://www.github.com/jonasalmeida) | [Folder](https://github.com/web4bio/webgen/tree/master/archive/jonas), [js Sandbox](https://web4bio.github.io/webgen/archive/jonas/) | [Sandbox](https://beta.observablehq.com/@jonasalmeida/webgen)    | [Firebrowse](https://github.com/episphere/firebrowse) |
-| [Carolyn Bremer](http://www.github.com/cgbrem) | [Fall 2019 Log](https://docs.google.com/document/d/1z0pNNcCbAV8Sb0JKBMMoaw0-78mEdBKtLWa6WKW4ijk/edit), [Spring 2020 Log](https://docs.google.com/document/d/1l8UgEMjIHbWd9m8RNZy4ZXpysO4Gtk0Kf0olnhbPtXc/edit), [Fall 2020 Log](https://docs.google.com/document/d/1edAH_tN2WeVNjC3mCg7IkX6jSyO3aI1f7iU3Gv-LSeA/edit?usp=sharing), [Spring 2021 Log](https://docs.google.com/document/d/1L6ftHoj4R18iJfqCTJRlqUCQMmHICYqdOtm2SskLXxY/edit?usp=sharing) |[Sandbox](https://observablehq.com/@cgbrem/web-gen-fall-19) |   |
+| [Adit Anand](https://github.com/19aanand) | [Spring 2020 Log](https://docs.google.com/document/d/1K6yBJq7C4XOlkl4Hm5smnPiY-lj_lJ2miwV6pRl-KEU/edit?usp=sharing), [Fall 2020 Log](https://docs.google.com/document/d/1g1pkQcqoDTa40BUXveAWDokW_1Q-spkC_0n6xB5vTO8/edit), [Spring 2021 Log](https://docs.google.com/document/d/1UBOF3QSd02kix0n5uzxW3Eqs1lzMZXHmorj1T8GJ8Cw/edit?usp=sharing), [Fall 2021 Log](https://docs.google.com/document/d/13BsRrLdiGLRID1_ujppGLsEVq2g1U1ffXv8c4kDbia4/edit?usp=sharing) | [Observable](https://observablehq.com/@19aanand), [Spring 2022 Log](https://docs.google.com/document/d/1sAw29x8wT0yNvueq61pPnCzOpuv3ls3LPKOYm_D2UMM/edit?usp=sharing) |   |
+| [Eric Ruan](https://github.com/ericr491) | [Fall 2020 Log](https://docs.google.com/document/d/1RldOmYmN9yAjB2dhHcvPQdRe_WidyJhlccK51Nb8tL8/edit?usp=sharing) [Spring 2021 Log](https://docs.google.com/document/d/1E57BM8ln0ewCxISpZ9LQnRqD4SuqdmNj42SgI5eLKD4/edit?usp=sharing) [Fall 2021 Log](https://docs.google.com/document/d/1OpXK8qwvS5juWyJMlgKuINEAMhm28c85loT4u1oMrnc/edit?usp=sharing) [Spring 2022 Log](https://docs.google.com/document/d/1Q3xe8NNM8B3HeSc85a-9e3fAH4NEztp-zrs_Sj0x67o/edit?usp=sharing)| [Sandbox](https://observablehq.com/@ericr491/webgen) | |
+| [Purva Shenoy](https://github.com/prvshenoy01) |[Spring 2021 Log,](https://docs.google.com/document/d/1vo6JgeLybK2bQZVbIQKpvwXKHdMI1QGGGrPGXOzRIrA/edit?usp=sharing) [Fall 2021 Log,](https://docs.google.com/document/d/1Ku6s_Y_XVSa5IFjgfgdrf_9WD64o_77Q7NmDrRIk_FA/edit?usp=sharing) [Spring 2022 Log](https://docs.google.com/document/d/1Mpy5ksn_UF-2igpojq4JGo0o4BnprAND6CMBtpMlM9w/edit?usp=sharing)| |
+| [Jie Xi Li](https://github.com/jli0980) | [Spring 2022 Log](https://docs.google.com/document/d/1NPfO22X5CkfYnU697NwupE9xVAoyIRRuVZ5tCBRg3BI/edit?usp=sharing)  |[Observable](https://observablehq.com/@39a49c172bedfa3c/webgen-spring-2022)| |
+| [Amara Im](https://github.com/amaraim22) | [Spring 2021 Log](https://docs.google.com/document/d/1L9jJvpQX5DLRC43ajV3Sk4Cll0koJPJI6Uu3oediN1Y/edit?usp=sharing) [Fall 2021 Log](https://docs.google.com/document/d/19PlE5GM0VXGWPHi2ZcMEAkKjnqIVjut4E2i2n13-ghk/edit?usp=sharing) | [Sandbox](https://observablehq.com/@amaraim22/webgen) | |
 | [Erika Nemeth](http://www.github.com/enemeth19) | [Fall 2019 Log](https://docs.google.com/document/d/1yCoHM8SleFvwsuQzfcO19oCWE36EUJ482bX38X8a7xY/edit?usp=sharing), [Spring 2020 Log](https://docs.google.com/document/d/11f0B8j0gTE6leyFeDKHd6onu2LOnVyqPDmGc-vt5d_c/edit?usp=sharing), [Fall 2020 Log](https://docs.google.com/document/d/18d5oB-Uft5nBskVxnZuEcaXHDPE291y2PBzQtcPZXVo/edit?usp=sharing), [Spring 2021 Log](https://docs.google.com/document/d/1aWkkX9PEcEZWaK37F5n0_LABoo1JIj8OS-mkj4k5Ras/edit?usp=sharing) | [WebGen Background](https://observablehq.com/@enemeth19/webgen) | [Interactive Plots](https://episphere.github.io/mortalitytracker/board/) |
 | [Zhenghao (Kevin) Zhu](https://github.com/ZhenghaoZhu) | [Spring 2020 Log](https://docs.google.com/document/d/1x_UYj9iuYBXwfJBVzOtyGaZJc6LOymu_gvBZ-CIJt2U/edit?usp=sharing), [Fall 2020 Log](https://docs.google.com/document/d/1HMWPe9dYiMrsONfoxObnglpwDLDVDa-Hu2AnJ0bcJmE/edit?usp=sharing) | [Sandbox](https://observablehq.com/@zhenghaozhu/webgen) |   |
-| [Adit Anand](https://github.com/19aanand) | [Spring 2020 Log](https://docs.google.com/document/d/1K6yBJq7C4XOlkl4Hm5smnPiY-lj_lJ2miwV6pRl-KEU/edit?usp=sharing), [Fall 2020 Log](https://docs.google.com/document/d/1g1pkQcqoDTa40BUXveAWDokW_1Q-spkC_0n6xB5vTO8/edit), [Spring 2021 Log](https://docs.google.com/document/d/1UBOF3QSd02kix0n5uzxW3Eqs1lzMZXHmorj1T8GJ8Cw/edit?usp=sharing), [Fall 2021 Log](https://docs.google.com/document/d/13BsRrLdiGLRID1_ujppGLsEVq2g1U1ffXv8c4kDbia4/edit?usp=sharing) | [Observable](https://observablehq.com/@19aanand) |   |
-| [Yuwei Zhang](https://github.com/Yuw-zhang) | [Fall 2020 Log](https://docs.google.com/document/d/1INk8iqLC-mqNpSYvK5mgmly7jMlk3Mwc3l4ylU-H-SU/edit?usp=sharing) |[Histology Sandbox](https://observablehq.com/@yuw-zhang/webgen) | | 
-| [Luke Torre-Healy](https://github.com/lthealy) | [Fall 2020 Log](https://docs.google.com/document/d/14CbEL9a69vw59s9eNWlebVGBgKQDJclhiaY-yZLjRyU/edit?usp=sharing)| [Sandbox](https://observablehq.com/@lthealy/webgen-doc)| [SBU](https://renaissance.stonybrookmedicine.edu/mstp/people/Torre-Healy) |
-| [Kevin Murgas](https://github.com/kevin-murgas) | | [Sandbox](https://observablehq.com/@kevin-murgas/webgen) | |
-| [Soma Kobayashi](https://github.com/skobayashi0417) | [Fall 2020 Log](https://docs.google.com/document/d/14oeMCzMhF3AISCIlZo9wm0hmrjTOgVGnp8jB4ZF-lS8/edit?usp=sharing) | [Histology Sandbox](https://observablehq.com/@skobayashi0417/test) | |
-| [Eric Ruan](https://github.com/ericr491) | [Fall 2020 Log](https://docs.google.com/document/d/1RldOmYmN9yAjB2dhHcvPQdRe_WidyJhlccK51Nb8tL8/edit?usp=sharing) [Spring 2021 Log](https://docs.google.com/document/d/1E57BM8ln0ewCxISpZ9LQnRqD4SuqdmNj42SgI5eLKD4/edit?usp=sharing) [Fall 2021 Log](https://docs.google.com/document/d/1OpXK8qwvS5juWyJMlgKuINEAMhm28c85loT4u1oMrnc/edit?usp=sharing) | [Sandbox](https://observablehq.com/@ericr491/webgen) | |
-| [Jillian Unkenholz](https://github.com/jillianunk32)  | [Fall 2020 Log](https://docs.google.com/document/d/1c1T6mJisOjjH_uQheGSuq5BtZTJ1u-04OMFvhlM-PAY/edit?usp=sharing), [Spring 2021 Log](https://docs.google.com/document/d/1t9JfmrQJ7Xjy29iUG4icd3QaqzZ0-LQQeVNzT-IzbxI/edit?usp=sharing)|[Sandbox](https://observablehq.com/@jillianunk32/webgen) | |
-| [Chowdhury An-Noor](https://github.com/chowdhuryannoor) |[Fall 2020 Log, ](https://docs.google.com/document/d/1LGMLUeRYprQLJjIqrcAhkt0rZmliiRqFKP8AvuWq1z0/edit?usp=sharing)[Spring 2021 Log,](https://docs.google.com/document/d/1ulA40p_Nqh7AGBdE8e7HqRGJ7oboAYh47FGu6tK0Gpc/edit?usp=sharing) |[Sandbox](https://observablehq.com/@chowdhuryannoor/webgen-chowdhury) | |
-| [Amara Im](https://github.com/amaraim22) | [Spring 2021 Log](https://docs.google.com/document/d/1L9jJvpQX5DLRC43ajV3Sk4Cll0koJPJI6Uu3oediN1Y/edit?usp=sharing) [Fall 2021 Log](https://docs.google.com/document/d/19PlE5GM0VXGWPHi2ZcMEAkKjnqIVjut4E2i2n13-ghk/edit?usp=sharing) | [Sandbox](https://observablehq.com/@amaraim22/webgen) | |
-| [Purva Shenoy](https://github.com/prvshenoy01) |[Spring 2021 Log,](https://docs.google.com/document/d/1vo6JgeLybK2bQZVbIQKpvwXKHdMI1QGGGrPGXOzRIrA/edit?usp=sharing) [Fall 2021 Log](https://docs.google.com/document/d/1Ku6s_Y_XVSa5IFjgfgdrf_9WD64o_77Q7NmDrRIk_FA/edit?usp=sharing)| |
-| [Shiying Lin](https://github.com/20shiy) |[Fall 2021 Log](https://docs.google.com/document/d/1xkBotug4-K3Upo4yEUmWYy8Q_rqnIYvnKAIYZWFdnIE/edit?usp=sharing) |[Observable](https://observablehq.com/@20shiy/webgen-fall-2021) | |
-| [Will Li](https://github.com/liwll) | [Fall 2021 Log](https://docs.google.com/document/d/1aVD6soq5g_a9s8o1ztR4pKyPgkiOnK4EhEHu-d7oBe8/edit?usp=sharing) | [Sandbox](https://observablehq.com/@liwll/webgen) | |
-| [Joshua Mathew](https://github.com/jmath908) | [Fall 2021 Log](https://docs.google.com/document/d/1gBdkrxdAwOR24T8fhQzn2UaAR5ME5rdTozyNG81Amf8/edit?usp=sharing)  | |
 
 #### Alumni
+  * [Kevin Murgas](https://github.com/kevin-murgas)
+  * [Luke Torre-Healy](https://github.com/lthealy)
+  * [Chowdhury An-Noor](https://github.com/chowdhuryannoor)
+  * [Yuwei Zhang](https://github.com/Yuw-zhang)
+  * [Soma Kobayashi](https://github.com/skobayashi0417)
+  * [Jillian Unkenholz](https://github.com/jillianunk32)
+  * [Joshua Mathew](https://github.com/jmath908)
+  * [Will Li](https://github.com/liwll)
+  * [Shiying Lin](https://github.com/20shiy)
+  * [Carolyn Bremer](http://www.github.com/cgbrem) :[Sandbox](https://observablehq.com/@cgbrem/web-gen-fall-19)
   * [Ethan Earlie](https://github.com/Ethan-Earlie): [Sandbox](https://observablehq.com/@ethan-earlie/webgen), [Web App](https://web4bio.github.io/webgen/main/) 
   * [Hunter Jimenez](https://github.com/hunterjimenezsbu): [Histology Sandbox](https://observablehq.com/@huntsmna817/webgen)
   * [Ki Oh](https://github.com/KO-BMI): [Sandbox](https://observablehq.com/@fluffyshoes/web-gen-fall-19) 

conf.json

@@ -3,6 +3,7 @@
   "recurseDepth": 10,
   "source": {
       "include": ["./main/js/"],
+      "exclude": ["./main/js/smartCache/"],
       "includePattern": ".+\\.js(doc|x)?$",
       "excludePattern": "(^|\\/|\\\\)_"
   },

main/css/style.css

@@ -60,6 +60,14 @@
     }
 }
 
+#load{
+    width:100%;
+    height:100%;
+    position:fixed;
+    z-index:9999;
+    background:url("loading-icon-image.gif") no-repeat center center rgba(0,0,0,0.25)
+}
+
 /* ///////////////////////////////////////////////////////////////////////////////////////////////////////////////// */
 /* ///////////////////////////////////////////////////////////////////////////////////////////////////////////////// */
 /* ///////////////////////////////////////////////////////////////////////////////////////////////////////////////// */