Small updates

Author: Llannelongue

_data/navigation.yml

@@ -27,6 +27,9 @@ training:
   - title: Ten Simple Rules
     url: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009324
   - title: "Recordings"
+    children:
+      - title: "EMBL-EBI webinar"
+        url: https://www.ebi.ac.uk/training/events/environmental-impact-computational-biology/
 
 talks:
   - title: "To jump straight to the latest recordings and slides:"

_pages/GA4HPC/GA4HPC.md

@@ -31,15 +31,15 @@ At this stage, the script works on any HPC server using [SLURM](https://slurm.sc
 
 ## How to install it
 
-It doesn't require any particular permissions, you just need to copy the GitHub repository on your HPC drive, enter some information about your data centre, and you're good to go! [Tutorial here](/GA4HPC/install)
+It doesn't require any particular permissions, you just need to copy the GitHub repository on your HPC drive, enter some information about your data centre, and you're good to go! [Tutorial here]({% link _pages/GA4HPC/GA4HPC_installation.md %})
 
 ## How to use it
 
 Anyone with access to `the_shared_directory` where the script is located can run the calculator,
 by running the same command, with various options available:
 
 ```
-usage: GreenAlgorithms_global.py [-h] [-S STARTDAY] [-E ENDDAY] [--filterCWD]
+usage: myCarbonFootprint.sh      [-h] [-S STARTDAY] [-E ENDDAY] [--filterCWD]
                                  [--filterJobIDs FILTERJOBIDS]
                                  [--filterAccount FILTERACCOUNT] [--reportBug]
                                  [--reportBugHere]
@@ -61,6 +61,16 @@ optional arguments:
                         Comma seperated list of Job IDs you want to filter on.
   --filterAccount FILTERACCOUNT
                         Only consider jobs charged under this account
+  --customSuccessStates CUSTOMSUCCESSSTATES
+                        Comma-separated list of job states. By default, only
+                        jobs that exit with status CD or COMPLETED are
+                        considered succesful (PENDING, RUNNING and REQUEUD are
+                        ignored). Jobs with states listed here will be
+                        considered successful as well (best to list both
+                        2-letter and full-length codes. Full list of job
+                        states:
+                        https://slurm.schedmd.com/squeue.html#SECTION_JOB-
+                        STATE-CODES
   --reportBug           In case of a bug, this flag logs jobs informations so
                         that we can fix it. Note that this will write out some
                         basic information about your jobs, such as runtime,
@@ -78,8 +88,10 @@ optional arguments:
 ### Limitations to keep in mind
 
  - The workload manager doesn't alway log the exact CPU usage time, and when this information is missing, we assume that all cores are used at 100%.
- - For now, we assume that GPU jobs only use 1 GPU and the GPU is used at 100% (as the information needed for more accurate measurement is not available)
+ - For now, we assume that GPU jobs only use 1 GPU and the GPU is used at 100%, as the information needed for more accurate measurement is not always available.
+
  (both of these may lead to slightly overestimated carbon footprints, although the order of magnitude is likely to be correct)
+
  - Conversely, the wasted energy due to memory overallocation may be largely underestimated, as the information needed is not always logged.
 
 ## Report bugs
@@ -88,7 +100,7 @@ If you spot any bugs, or would like new features, just [open a new issue on GitH
 
 ## How to modify the script for my cluster?
 
-See the ["Edit code and contribute"](/GA4HPC/edit) page on how to modify the code and share your improvements with other users.
+See the ["Edit code and contribute"]({% link _pages/GA4HPC/GA4HPC_editCode.md %}) page on how to modify the code and share your improvements with other users.
 
 ## Licence
 

_pages/GA4HPC/GA4HPC_editCode.md

@@ -9,7 +9,7 @@ toc: true
 ---
 
 You may need to edit the tool, either to make it work with the specifities of your cluster, or just to add new features.
-Eitherway, please consider submitting some pull requests to the GitHub to share these edits with other users!
+Eitherway, please consider submitting some pull requests to [the GitHub](https://github.com/GreenAlgorithms/GreenAlgorithms4HPC) to share these edits with other users!
 
 There are some example of intermediary files [here](https://github.com/GreenAlgorithms/GreenAlgorithms4HPC/tree/main/example_files/).
 

_pages/Training/training.md

@@ -22,22 +22,34 @@ blog_articles:
   url: /training/
   btn_label: "Learn more"
   btn_class: "btn--primary"
+
+feature_row_1:
+- image_path: assets/images/EMBL-EBI webinar.png
+  alt: "The carbon footprint of computational biology, an EMBL-EBI training webinar."
+  title: "A training webinar with EMBL-EBI"
+  excerpt: "We did a webinar with EMBL-EBI's training team, it's still available with the slides!"
+  url: "https://www.ebi.ac.uk/training/events/environmental-impact-computational-biology/"
+  btn_label: "Learn more"
+  btn_class: "btn--primary"
 ---
 
 We regroup here resources that can be used to learn more about green computing.
 
 If you just want a summary of what you can do today, __check out our [Ten Simple Rules article](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009324)__!
 {: .notice--info}
 
+<!-- :hourglass: &nbsp; More coming soon &nbsp; :hourglass:
+{: .notice--warning} -->
+
+{% include feature_row id="feature_row_1" type="left"%}
+
 <!-- # Tutorials
 
 {% include feature_row id="blog_articles" type="left"  %} -->
 
-:hourglass: &nbsp; More coming soon &nbsp; :hourglass:
-{: .notice--warning}
-
 ## Other resources available online
 
 - You can check the carbon intensity of a location live on [electricitymaps.com](https://app.electricitymaps.com/map).
 - To tackle the carbon footprint of "wet" labs, there is the [LEAF framework](https://www.ucl.ac.uk/sustainable/leaf/take-part-leaf).
+- The [1point5 lab](https://labos1point5.org/) initiative is an international, cross-disciplinary collective of French academics who share a common goal: to better understand and reduce the environmental impact of research.
 - Curious about the energy usage of Bitcoin? There is a tool for that [here](https://ccaf.io/cbeci/index).

_pages/app_userGuide.md

@@ -28,7 +28,7 @@ sidebar:
 
 ## Methods and data
 
-The methodology behind the Green Algorithms project is described in [our publication](https://onlinelibrary.wiley.com/doi/10.1002/advs.202100707) (go [here](/publications/) for the full list of publications related to this project).
+The methodology behind the Green Algorithms project is described in [our publication](https://onlinelibrary.wiley.com/doi/10.1002/advs.202100707) (go [here]({% link _pages/publications.md %}) for the full list of publications related to this project).
 
 All the data used for the calculator are in the [`/data`](https://github.com/GreenAlgorithms/green-algorithms-tool/tree/master/data) directory on GitHub.
 

_pages/talks.md

@@ -3,19 +3,24 @@ permalink: /talks/
 
 title: Talks
 
+header:
+  overlay_image: assets/images/stripes_banner_1.png
+  overlay_filter: linear-gradient(rgba(255, 255,255, 0), 20%, rgba(255, 255, 255, 1))
+  text_color: rgb(80, 80, 80)
+
 sidebar:
   nav: talks
 
-toc: true 
+toc: true
 ---
 
 List of talks about the Green Algorithms projects, with links to slide decks and recording when available.
 
 ## 2022
 
-- __AI-2022__ British Computer Society's International Conference on Artificial Intelligence: talk at the [_Sustainability & AI_ workshop](http://bcs-sgai.org/ai2022/?section=workshops) (December 2022). Slides [here](https://drive.google.com/file/d/15KP3gxyuu23MW6WaNAW867Ti4RBBZClP/view?usp=share_link).
+- __AI-2022__ British Computer Society's International Conference on Artificial Intelligence - [_Sustainability & AI_ workshop](http://bcs-sgai.org/ai2022/?section=workshops) (December 2022). [\[slides\]](https://drive.google.com/file/d/15KP3gxyuu23MW6WaNAW867Ti4RBBZClP/view?usp=share_link).
 
-- __EMBL-EBI webinar__ on the carbon footprint footprint of computational biology (November 2022). Recording [here](https://www.ebi.ac.uk/training/events/environmental-impact-computational-biology/) or [here on YouTube](https://www.youtube.com/watch?v=Kl64yn1eDUo) and slides [here](https://drive.google.com/file/d/1pklCNNXAFadjVwCMj0draIt8nL_89Tx0/view?usp=share_link).
+- __EMBL-EBI webinar__ on the carbon footprint footprint of computational biology (November 2022). [\[recording\]](https://www.ebi.ac.uk/training/events/environmental-impact-computational-biology/) [\[YouTube\]](https://www.youtube.com/watch?v=Kl64yn1eDUo) [\[slides\]](https://drive.google.com/file/d/1pklCNNXAFadjVwCMj0draIt8nL_89Tx0/view?usp=share_link).
 
 ## 2021
 

assets/images/EMBL-EBI webinar.png

@@ -25,7 +25,7 @@ feature_row_1:
 - image_path: /assets/images/GAapp_16x9.jpg
   alt: "Screenshot of the green algorithms calculator."
   title: "The online calculator"
-  excerpt: "A tool to easily estimate the carbon footprint of a project."
+  excerpt: "A tool to easily estimate the carbon footprint of a computation."
   url: "/app-user-guide/"
   btn_label: "Learn more"
   btn_class: "btn--primary"
@@ -65,12 +65,14 @@ gallery_logos:
 __Are you looking for the online calculator?__ It's been moved to [calculator.green-algorithms.org](http://calculator.green-algorithms.org)
 {: .notice--success}
 
-__:hourglass: This website is a work in progress, and we will keep adding content in the coming weeks!__
+__:hourglass: This website is a work in progress, and we will keep adding content in the coming weeks/months!__ Comments/suggestions can be made [here](https://github.com/GreenAlgorithms/GreenAlgorithms.github.io/issues).
 {: .notice--warning}
 
 The Green Algorithms project aims at promoting more environmentally sustainable computational science. It regroups calculators that researchers can use to estimate the carbon footprint of their projects, tips on how to be more environmentally friendly, training material, past talks etc.
 
+<!-- TODO add news -->
 
+<!-- TODO do the google SEO -->
 
 <!-- ## Estimating the carbon footprint of algorithms -->