From 48e0823ea1818eba5710529bcc71b34bb80815b1 Mon Sep 17 00:00:00 2001 From: zackbatist Date: Wed, 18 Dec 2024 11:49:45 -0500 Subject: [PATCH] Implement github action for publishing on push. --- .github/workflows/publish.yml | 35 + _quarto.yml | 9 +- _site/LICENSE | 116 --- _site/about.html | 565 -------------- _site/context.html | 4 +- _site/context.pdf | Bin 6584 -> 0 bytes _site/glossary.html | 4 +- _site/glossary.pdf | Bin 4269 -> 0 bytes _site/images/openscapes_hex.png | Bin 27474 -> 0 bytes _site/index.html | 2 +- _site/index.pdf | Bin 8895 -> 0 bytes _site/posts.html | 8 +- _site/posts.pdf | Bin 3910 -> 0 bytes _site/posts.xml | 24 +- .../2023-12-11-technical-specs/index.html | 726 ------------------ .../2024-12-09-first-team-meeting/index.html | 4 +- _site/posts/2024-12-09-hello-world/index.html | 21 +- .../2024-12-11-technical-specs/index.html | 11 +- _site/project-documentation/Cases.pdf | Bin 32072 -> 0 bytes _site/project-documentation/cases.html | 6 +- .../coding-protocol.html | 4 +- .../project-documentation/coding-protocol.pdf | Bin 4605 -> 0 bytes .../data-management.html | 4 +- .../project-documentation/data-management.pdf | Bin 7237 -> 0 bytes .../ethics-protocol.html | 6 +- .../project-documentation/ethics-protocol.pdf | Bin 25414 -> 0 bytes .../interview-protocol.html | 4 +- .../research-protocol.html | 6 +- .../research-protocol.pdf | Bin 81229 -> 0 bytes _site/robots.txt | 2 +- _site/search.json | 465 ++++------- _site/site_libs/quarto-nav/headroom.min.js | 7 - _site/sitemap.xml | 104 +-- _site/styles.css | 1 - 34 files changed, 253 insertions(+), 1885 deletions(-) create mode 100644 .github/workflows/publish.yml delete mode 100644 _site/LICENSE delete mode 100644 _site/about.html delete mode 100644 _site/context.pdf delete mode 100644 _site/glossary.pdf delete mode 100644 _site/images/openscapes_hex.png delete mode 100644 _site/index.pdf delete mode 100644 _site/posts.pdf delete mode 100644 _site/posts/2023-12-11-technical-specs/index.html delete mode 100644 _site/project-documentation/Cases.pdf delete mode 100644 _site/project-documentation/coding-protocol.pdf delete mode 100644 _site/project-documentation/data-management.pdf delete mode 100644 _site/project-documentation/ethics-protocol.pdf delete mode 100644 _site/project-documentation/research-protocol.pdf delete mode 100644 _site/site_libs/quarto-nav/headroom.min.js delete mode 100644 _site/styles.css diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml new file mode 100644 index 0000000..eef1ad4 --- /dev/null +++ b/.github/workflows/publish.yml @@ -0,0 +1,35 @@ +on: + workflow_dispatch: + push: + branches: main + +name: Quarto Publish + +jobs: + build-deploy: + runs-on: ubuntu-latest + permissions: + contents: write + steps: + - name: Check out repository + uses: actions/checkout@v4 + + - name: Set up Quarto + uses: quarto-dev/quarto-actions/setup@v2 + + - name: Install R + uses: r-lib/actions/setup-r@v2 + with: + r-version: '4.2.0' + + - name: Install R Dependencies + uses: r-lib/actions/setup-renv@v2 + with: + cache-version: 1 + + - name: Render and Publish + uses: quarto-dev/quarto-actions/publish@v2 + with: + target: gh-pages + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} \ No newline at end of file diff --git a/_quarto.yml b/_quarto.yml index 4dc8cc0..685a1fa 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -1,10 +1,10 @@ project: type: website - + website: title: "CITF-Postdoc" - site-url: "https://zackbatist.info/MEDHI/" - repo-url: "https://github.com/zackbatist/MEDHI" + site-url: "https://zackbatist.info/CITF-Postdoc/" + repo-url: "https://github.com/zackbatist/CITF-Postdoc" repo-actions: [source] bread-crumbs: true page-navigation: false @@ -57,3 +57,6 @@ format: filters: - include-files.lua - quarto + +execute: + freeze: auto \ No newline at end of file diff --git a/_site/LICENSE b/_site/LICENSE deleted file mode 100644 index 670154e..0000000 --- a/_site/LICENSE +++ /dev/null @@ -1,116 +0,0 @@ -CC0 1.0 Universal - -Statement of Purpose - -The laws of most jurisdictions throughout the world automatically confer -exclusive Copyright and Related Rights (defined below) upon the creator and -subsequent owner(s) (each and all, an "owner") of an original work of -authorship and/or a database (each, a "Work"). - -Certain owners wish to permanently relinquish those rights to a Work for the -purpose of contributing to a commons of creative, cultural and scientific -works ("Commons") that the public can reliably and without fear of later -claims of infringement build upon, modify, incorporate in other works, reuse -and redistribute as freely as possible in any form whatsoever and for any -purposes, including without limitation commercial purposes. These owners may -contribute to the Commons to promote the ideal of a free culture and the -further production of creative, cultural and scientific works, or to gain -reputation or greater distribution for their Work in part through the use and -efforts of others. - -For these and/or other purposes and motivations, and without any expectation -of additional consideration or compensation, the person associating CC0 with a -Work (the "Affirmer"), to the extent that he or she is an owner of Copyright -and Related Rights in the Work, voluntarily elects to apply CC0 to the Work -and publicly distribute the Work under its terms, with knowledge of his or her -Copyright and Related Rights in the Work and the meaning and intended legal -effect of CC0 on those rights. - -1. Copyright and Related Rights. A Work made available under CC0 may be -protected by copyright and related or neighboring rights ("Copyright and -Related Rights"). 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Affirmer understands and acknowledges that Creative Commons is not a - party to this document and has no duty or obligation with respect to this - CC0 or use of the Work. - -For more information, please see - diff --git a/_site/about.html b/_site/about.html deleted file mode 100644 index 80c2ec9..0000000 --- a/_site/about.html +++ /dev/null @@ -1,565 +0,0 @@ - - - - - - - - - -About – CITF-Test - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-
- -
- -
- - - - -
- -
-
-

About

-
- - - -
- - - - -
- - - -
- - -

About this site

- - - -
- -
- - - - - \ No newline at end of file diff --git a/_site/context.html b/_site/context.html index e10df17..ec0ea45 100644 --- a/_site/context.html +++ b/_site/context.html @@ -331,7 +331,7 @@

Context

} var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//); var mailtoRegex = new RegExp(/^mailto:/); - var filterRegex = new RegExp("https:\/\/zackbatist\.info\/MEDHI\/"); + var filterRegex = new RegExp("https:\/\/zackbatist\.info\/CITF-Postdoc\/"); var isInternal = (href) => { return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href); } @@ -673,7 +673,7 @@

Context

  -
+

This page is built with ❤️ and Quarto.

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var mailtoRegex = new RegExp(/^mailto:/); - var filterRegex = new RegExp("https:\/\/zackbatist\.info\/MEDHI\/"); + var filterRegex = new RegExp("https:\/\/zackbatist\.info\/CITF-Postdoc\/"); var isInternal = (href) => { return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href); } @@ -672,7 +672,7 @@

Glossary

  -
+

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CITF-Postdoc

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Blog

- +   @@ -348,7 +348,7 @@

Blog

website - + Dec 9, 2024 @@ -359,7 +359,7 @@

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meeting notes, general thoughts - + Dec 9, 2024 @@ -468,7 +468,7 @@

Blog

} var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//); var mailtoRegex = new RegExp(/^mailto:/); - var filterRegex = new RegExp("https:\/\/zackbatist\.info\/MEDHI\/"); + var filterRegex = new RegExp("https:\/\/zackbatist\.info\/CITF-Postdoc\/"); var isInternal = (href) => { return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href); } diff --git a/_site/posts.pdf b/_site/posts.pdf deleted file mode 100644 index 882155f9c6a1ef3a5d203e9fa859341bd5de33ae..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 3910 zcmb7Hc{CL49u_egl3kg~5@QrGgRzfg23fNvS!c$KZ5VrY+1HR1S)<94kPzjQUCF*? ziEJ4(me0O-`|i2t)OWs4_ul`0=RNQFo#%bdvz%8@AEhn|y($G1oLgJo1^Aa(R zKm`Rcbq9hc&RtBMfcC_pa9E-(PD}^qV&`ek3xz=u2%v|jI}Ys(^clMwUk;>JVMhAb z^DDVx@!Q^ZTucnp?3D1u7In2N4BzVASU_dT0^#hwJ}Qk@Bh01U0=KJHeGezb8~h6N zxds&YSHw$_2cgmPku_Q1{`m7(9zD=W?UH3mn@zpfOX9e~gEDLi74qx?)Rm@MB%6X%Crma^_7i&Mp z`fgK1+sTw!TlL`?--BDp?R*TZ0mYAoUZug~ zSC{BH_&JHy#f^au{QKDT+8O)4Ncdf&alluU%>sR8QxlU-pF zr^1;4Pt6{N88?-f1hl>v)qX}(ofCk%78HDy$NA_FrSo0yy&k$G%5+NWjc*inPby=A z?Q%HdlFGa)oKoATM;0cP4aD!XbPUefhji6SUO>=N;slcWX$ajWpnKl0wj(b&0)(%0 zj9jfP6N+zXcMoaVy7T;6V2b`ALM!st@qx98rC4bu^?}q5MKZ9R-@i5N>e--O4vBj? z7t2@!BREpp-c3I*SK-(=)1&1<{R`q`e-LNnh4J)t#fc#`QR+k&Pvh^iIPy2nl9iSH zS(`YcKpl|R+2adGV{I`N8mUhsYCqEh@$Q2mqa*P~^jQIV+7rfb3#EithJKqXH%B!% zM__W^?6JLp2FeIIaMP#4eAFfLL7Sun&e@c-_|7EJICK19%jan{2E=yMypu={%n@46 zkoHXm&}a!Zi0hb};qai6NxSO#N9XJ+-hB`pG89IBV0Sa*4?&?>b?(81Ng_|rH*r|c zd>A75$|0+cdN@qLR3q*0?)%KgjQiZc=m&(@3Hfpz3*5X!404*2I?YbM-5b*Go2CeF>Ki3&MJHnFe&MvTq=P&Q=saD*_%i0A6VxoF>4l7#7 zLaXaKwZ)>o4{(A{hoqiX_VPFQJq%+~fAL09;Yi8u8^<%V(!Qk=F(0Vq8#<;;)S3!W zMRzVcJYvmk8+-9pm{~W!#5TsjvzRCF{7~Lq>)f*X;ySg?YxPguCnoaLcA55U)-ob^ zHnr7m+g=b3{%Z7D;nJ`{v8j|-NnXrmZWOnw@}l<6ioxpzp^5ILEEw+>!eDVWFcKr6 zWy%(pI3xe85W1I8I`W4}+cn>?u}PNnyk4B~Q@)h?Ku3}Mep2-u4U4g?HCH`Ig)p}k zpgR|Ul4ob=T;_QVuU6R6eC`~sPwh}vX(sLCSr{TP{1$V&YWL<6=84278=oN4A@~MK z;*&bdYJ$`olzHtW7e1dU**|fVLR`=enhYC+eCea?K#<)W*1V@S;EiDKS4P>rjemCR zBiwvk(-h=nd}Z*vf3_VOZla#Mh58W>o7bXqYc&)&@~8_E0SODIa39Lw&XTX??Q}8J zO?#wRK#IMB4CrWS`Kgh}Q#Y;j^p*DBEpcbHRtiN4SP{CQmfr~c?hZ9M{EuNUPEO)k zmrGUGj2sHJ<4Z~Efu@!9-K?fbM5M71%R+Yk4P)+^{LHau>kjk#dc%grY~0{pE0ul8 z#=aUEd~{oDLLbRVh>p}0M46#}Q~5Yat9M*3MeiFw7N$;qzxZPKZbur8PJQRx-R<{}%$hq*x}~&qDQq1I`<1qaAGPTY zi%?Sy9_?$Qj)|Mvt#&Nq{%@^yOO0;b3@C{%Q2%(EWVJw{FnZC2DO&PuPVY7}jF#G5 zhn%IXFij^Oo#q5R`bG4@pg$7iH!b|PsBp5evC+4&VYab%rJ@3SJ>mAxV1h~fSo{A5 zla%=1Dj#Q{V$Y_+o~8LJ297OJj7|dYaf$-*_bX!;x+0Coz%2drR@D=lFDc$alx|l4 zbpaH-7Jku>StZo(lp&C%EStSCj;oAc(Vrcb23+A^XbkpQ-SEjdvx*kbq{k|lmJW_2 zU^v%Dxt--AF%gcMopCAJ{rq=PbPUna8wTaPx}2JxDAMeM_VK+U4J9EX;qbNQ0lt;2 zJuS|rFQC`VhN%`PA%6NNC)3r)`oKVqdRNB#!ND#?gt*e8!8z{FmdP7?#cIQoRh9U- zWigu4nd&sUx z;_y-)cN?(ecqOnr*Cft#)%fe^`mJ)~36b_gL=;_x@>7dGM)PB_(R$SfX7aHip+#z8 z(V;Pq>D&6-cDLde-XPs%4hI`&w^Ivig1iggF-#ma$NTUEPx~p<8JKx*kywI{8w0nl zdK^klQVv$>z=p zS}NLNs@#9>gNpyy_g7PjUB@^Yc{+>f@j|7)cc#0CCodEV`%QbwK>ucmDq{oUfH-py z*>v~rjlx|@i(BY3tz|7US}b$y5gdwoKHVr%HeHb@qH(KU4anD0r*F*p$Tb0i)0q zuRx;%n5D;!7HJ!C5Q#(-YiZL^PfwEr<{z^OJz-HQF1AGz-uL871ff?%bIN8q&wDkK zK=Xa}o75)|ZC3`u>l_|1a>7fUd9Em@O>$$c;t-snS7J|RZD)#olr}DC8|=_EKqXQ_ z9iCcaL$esB3-ZfPyA9;4KlB(d&X9wiW*EE6HC{Ds=fizGlwaAxHk$ZC*#e$h-$NzM z6AIcSLelDc2J$=jW`w|9vzlH!)TN4@mH_wajY4>N$J_0%b|bcy?s7OFs=#1o5*%5^7wMps`VEHm6Q_16;S&0L;5ymSAu)Zt5L0myt# zaJ>(n%&vhJRr3d%_a|ULTqeWt{?m$I)GyOpa-eQS8mi32c}E;=;-ceGeIdkTZfnBZ zF-|+gQz_Xy*Js))Cp%_uo4zAj2g=Bn-Eb4$ocd&&!CxvIQ11NPtg8bznff}`Luubcq$g$4jrhTnAcScd zgq3CyKSD!w!`1>Hfo`x<%arOweiFTmjlKXWZev7$Ggw=Y7&B3~^iNleP5Tnj2q4vp zpbE-$Vn4G7+V@#+<6jg6xORSisQCZ`+NCkqFy+PqIVO-p6XkJBFFT=QQv=%tB0*v) z8P`AFZ>1zL9xCNt+qRu6tNgj|2Q zgM{?^3b1c6<|;%STjVZShv(fk3jk=af#m;bN!U+6s()MZrXdb5rin6FfTGb@SvS zF;jEs_Y;`q?;J1nbGQh8Xyi~9XGirtIyrr*ys9tyY9+2%Bn!e1BNJDA;{cC`shT0l z3$2&& CITF-Postdoc -https://zackbatist.info/MEDHI/posts.html - +https://zackbatist.info/CITF-Postdoc/posts.html + quarto-1.5.54 Mon, 09 Dec 2024 05:00:00 GMT Reflection on first team meeting - https://zackbatist.info/MEDHI/posts/2024-12-09-first-team-meeting/ + https://zackbatist.info/CITF-Postdoc/posts/2024-12-09-first-team-meeting/ Last week (2024/12/04) I finally met David, Tanya and Aklil in person. The meeting was meant to convey my vision for the project to the whole team, to align perspectives, and to articulate how this will actually work in practice.

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Last week (2024/12/04) I finally met with David Buckeridge, Tanya Murphy and Aklil Noza in person. The meeting was meant to convey my vision for the project to the whole team, to align perspectives, and to articulate how this will actually work in practice.

The gist is that I will be investigating the role of social and cultural factors in data-sharing initiatives such as CITF and other Maelstrom-affiliated projects, and how these relate to, overlap with, or conflict with technical and institutional/administrative factors. To be clear, these are all very important aspects of data-sharing, but we generally recognized that the social and cultural aspects are under-explored relative to their impact.

We briefly talked about how we will go about selecting cases, and I emphasized the importance of strategic case selection. This also involves carefully articulating the project’s goals so that the cases will complement them. We agreed that the dataset will likely comprise between 12-15 interviews of around 60-90 minutes in length with representatives from 4-5 cases (one of them being CITF), in addition to representatives of the Maelstrom team. Maelstrom will serve as a “fixed point” that limits the scope of the cases’ breadth and ensures that participants have a common frame of reference. It also potentially allows me to “offload” or “consolidate” reference to technical and administrative aspects of data-sharing through targeted interviews with Maelstrom personnel, instead of dealing with those things with the representatives for each case.

We discussed timelines and overlap with Aklil’s work, which will be more concerned with focus groups with CITF databank users. There is definitely overlap with the emphasis of my own work and we will coordinate data collection to enhance the potential for analytical alignment.

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]]> + ]]> introduction website - https://zackbatist.info/MEDHI/posts/2024-12-09-hello-world/ + https://zackbatist.info/CITF-Postdoc/posts/2024-12-09-hello-world/ Mon, 09 Dec 2024 05:00:00 GMT Technical specs for this website - https://zackbatist.info/MEDHI/posts/2024-12-11-technical-specs/ + https://zackbatist.info/CITF-Postdoc/posts/2024-12-11-technical-specs/ website - https://zackbatist.info/MEDHI/posts/2024-12-11-technical-specs/ - Wed, 18 Dec 2024 16:06:15 GMT + https://zackbatist.info/CITF-Postdoc/posts/2024-12-11-technical-specs/ + Wed, 18 Dec 2024 16:48:07 GMT diff --git a/_site/posts/2023-12-11-technical-specs/index.html b/_site/posts/2023-12-11-technical-specs/index.html deleted file mode 100644 index 87a5b3b..0000000 --- a/_site/posts/2023-12-11-technical-specs/index.html +++ /dev/null @@ -1,726 +0,0 @@ - - - - - - - - - - -Technical specs for this website – CITF-Postdoc - - - - - - - - - - - - - - - - - - - - - - - - - -
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I am using this website as a way to help organize and share key documents and resources. The research protocols are in flux at this stage in the project’s development, and this will make it easier to distribute up-to-date drafts with partners, while simultaneously enhancing transparency.

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This post outlines the technical specifications for this website and outlines a roadmap for its further development. It will therefore be continually updated as the site evolves.

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I initially created this website using Hugo. You can find an older version of this post reflecting that setup here: #2346852.

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Fundamentals

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This website is based on Quarto, a platform for writing and publishing scientific and technical writing. I had started off using Hugo, but there were too many limitations that Quarto was able to accomodate. I had used quarto before but without fully understanding it, and now I am starting to see its elegance.

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The site is hosted on GitHub Pages using a CI workflow to automatically generate the site files upon changes being pushed to the repo. The repo is located at https://github.com/zackbatist/CITF-Postdoc, though I’m making an effort to ensure that the site can be ported to another hosting provider if necessary.

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Generating PDFs

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As an avid user, I do not really want to abandon PDFs entirely. Thankfully, Quarto allows me to pass the markdown through a rendering engine and generate outputs in different formats with ease. I relied on this guide for assistance with this:

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These PDFs will be tracked with git and I’ll configure a latex template to generate timestamps and references to their corresponding web versions.

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Archiving and Version Control

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Every change is tracked using git. However I would also like to find a way to archive each research protocol in Zenodo so that they can be assigned stable DOIs and detailed metadata, which will make them easier to reference.

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I do not want to rely on Zenodo’s GitHub integration for two reasons: 1) I want this to be as platform-agnostic as possible, and 2) that system relies on GitHub’s release system which operates on the level of the whole repository rather than specific files. I might be able to write a custom CI workflow to archive specific files to Zenodo using their API. However, I want to be able to toggle this option, rather than have it occur for every single detected change. Maybe I can accomplish this by pushing the changes that I want to archive to a dedicated branch that the CI workflow is configured to operate on. Or it might be easier to simply do this manually, since I’m not sure I will be using it that often anyway.

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- - - - - - \ No newline at end of file diff --git a/_site/posts/2024-12-09-first-team-meeting/index.html b/_site/posts/2024-12-09-first-team-meeting/index.html index 1272d5b..50bef3c 100644 --- a/_site/posts/2024-12-09-first-team-meeting/index.html +++ b/_site/posts/2024-12-09-first-team-meeting/index.html @@ -347,7 +347,7 @@

Reflection on first team meeting

} var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//); var mailtoRegex = new RegExp(/^mailto:/); - var filterRegex = new RegExp("https:\/\/zackbatist\.info\/MEDHI\/"); + var filterRegex = new RegExp("https:\/\/zackbatist\.info\/CITF-Postdoc\/"); var isInternal = (href) => { return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href); } @@ -689,7 +689,7 @@

Reflection on first team meeting

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This page is built with ❤️ and Quarto.

diff --git a/_site/posts/2024-12-09-hello-world/index.html b/_site/posts/2024-12-09-hello-world/index.html index 423dd52..b128a26 100644 --- a/_site/posts/2024-12-09-hello-world/index.html +++ b/_site/posts/2024-12-09-hello-world/index.html @@ -6,10 +6,9 @@ - -Hello World! – Mediating Epidemiological Data Harmonization Initiatives +Hello World! – CITF-Postdoc