clean up docs in preparation for refactor of style

Signed-off-by: vsoch <vsoch@users.noreply.github.com>

0-index.md

@@ -25,7 +25,7 @@ docker run -p 80:80 vanessa/expfactory-surveys start
 docker run -p 80:80 vanessa/expfactory-experiments start
 ```
 
-If you want a more gentle introduction, start with reading some [background](pages/0-background.md) on containers and why the Experiment Factory exists in the first place. Then move on to our quick start to [generate](https://expfactory.github.io/generate#quick-start) your own experiment container. Please [give feedback](https://www.github.com/expfactory/expfactory/issues) about your needs to further develop the software. The [library](https://expfactory.github.io/experiments/) will show you a selection to choose from, including all experiments, surveys, and games migrated from [the legacy Expfactory](https://www.github.com/expfactory/expfactory-experiments). If you have web-based experiments to contribute, please [reach out](https://www.github.com/expfactory/expfactory/issues)! Your contributions and feedback are greatly appreciated!
+If you want a more gentle introduction, start with reading some [background](pages/0-background.md) on containers and why the Experiment Factory exists in the first place. Then move on to our quick start to [generate](https://expfactory.github.io/generate#quick-start) your own experiment container. Please [give feedback](https://github.com/expfactory/expfactory/issues) about your needs to further develop the software. The [library](https://expfactory.github.io/experiments/) will show you a selection to choose from, including all experiments, surveys, and games migrated from [the legacy Expfactory](https://github.com/expfactory/expfactory-experiments). If you have web-based experiments to contribute, please [reach out](https://github.com/expfactory/expfactory/issues)! Your contributions and feedback are greatly appreciated!
 
 ## User Guide
 
@@ -37,7 +37,7 @@ If you want a more gentle introduction, start with reading some [background](pag
 
 ## Developer Guide
 
- - [Contribute](pages/5-contribute.md) an experiment to the [library](https://www.github.com/expfactory/experiments) for others to use.
+ - [Contribute](pages/5-contribute.md) an experiment to the [library](https://github.com/expfactory/experiments) for others to use.
  - [Interactive Development](pages/6-develop.md) suggested practice to develop and debug an experiment interactively in the container
 
 ## Library
@@ -72,13 +72,13 @@ You'll notice a little eliipsis (<i class="fa fa-ellipsis-h"></i>) next to each
 
 We are here for you! You can ask a question directly or open an issue for:
 
- - [Experiment Factory Core](https://www.github.com/expfactory/expfactory/issues) 
- - [Experiment Library](https://www.github.com/expfactory/experiments/issues)
- - [Survey Generator](https://www.github.com/expfactory/survey-generator/issues)
- - [Expfactory Builder](https://www.github.com/expfactory/expfactory-builder/issues)
- - [Expfactory Robots](https://www.github.com/expfactory/expfactory-robots/issues)
+ - [Experiment Factory Core](https://github.com/expfactory/expfactory/issues) 
+ - [Experiment Library](https://github.com/expfactory/experiments/issues)
+ - [Survey Generator](https://github.com/expfactory/survey-generator/issues)
+ - [Expfactory Builder](https://github.com/expfactory/expfactory-builder/issues)
+ - [Expfactory Robots](https://github.com/expfactory/expfactory-robots/issues)
 
-If your issue is for a particular experiment, open the issue at the respective repository for the [expfactory-experiments](https://www.github.com/expfactory-experiments) organization.
+If your issue is for a particular experiment, open the issue at the respective repository for the [expfactory-experiments](https://github.com/expfactory-experiments) organization.
 
 <div>
     <a href="/generate"><button class="next-button btn btn-primary"><i class="fa fa-chevron-right"></i> </button></a>

_config.yml

@@ -2,7 +2,7 @@
 title:        The Experiment Factory
 tagline:      ""
 baseurl:      "/"
-repo:       "https://www.github.com/expfactory/expfactory.github.io"
+repo:       "https://github.com/expfactory/expfactory.github.io"
 
 # About/contact
 author:

_includes/page-footer.html

@@ -5,6 +5,6 @@
   <span style="float:right">
     <a href="{{ site.repo }}" target="_blank"><i style="margin-right:5px" class="fa fa-github fa-2x"></i></a>
     <a href="/pdf" target="_blank"><i style="margin-right:5px" class="fa fa-save fa-2x"></i></a>
-    <a href="https://www.github.com/expfactory-experiments">Experiments</a>
+    <a href="https://github.com/expfactory-experiments">Experiments</a>
   </span>
 </footer>

pages/0-background.md

@@ -26,9 +26,9 @@ This general workflow using the experiment factory builder means that you could
  - go back and use the same version of the builder to re-create your experiment container, or a slight derivation of it
  - (developers) contribute to the core expfactory Python software to enhance the builder, or [another integration or tool](/integrations).
 
-If you have not heard of Docker we recommend that you [read about it first](https://www.docker.com/what-container) and go through a [getting started](https://docs.docker.com/get-started/) tutorial. When you are ready, come back here and try out the quick start. If you have any questions, [please don't hesitate to ask](https://www.github.com/expfactory/expfactory/issues).
+If you have not heard of Docker we recommend that you [read about it first](https://www.docker.com/what-container) and go through a [getting started](https://docs.docker.com/get-started/) tutorial. When you are ready, come back here and try out the quick start. If you have any questions, [please don't hesitate to ask](https://github.com/expfactory/expfactory/issues).
 
-Do you have more questions? Please [post an issue](https://www.github.com/expfactory/expfactory/issues).
+Do you have more questions? Please [post an issue](https://github.com/expfactory/expfactory/issues).
 
 <div>
     <a href="/"><button class="previous-button btn btn-primary"><i class="fa fa-chevron-left"></i> </button></a>

pages/1-generate.md

@@ -33,10 +33,13 @@ What experiments do you want in your container? Let's see the ones that are avai
 docker run quay.io/vanessa/expfactory-builder list
 ```
 
-Cool, I like `digit-span`, `spatial-span`, `test-task`, and `tower-of-london`.
+Cool, I like `digit-span`, `spatial-span`, `test-task`, and `tower-of-london`. Notice here
+that we are running as our user so the resulting files don't have permissions issues.
 
 ```
-docker run -v $PWD:/data quay.io/vanessa/expfactory-builder build digit-span spatial-span tower-of-london test-task 
+docker run -v $PWD:/data --user "$(id -u):$(id -g)" \ 
+    quay.io/vanessa/expfactory-builder build \
+    digit-span spatial-span tower-of-london test-task 
 ```
 
 Let's build the container from the Dockerfile! We are going to name it `expfactory/experiments`
@@ -58,6 +61,7 @@ Open your browser to localhost ([http://127.0.0.1](http://127.0.0.1)) to see the
 
 
 # Detailed Start
+
 The generation of a container comes down to adding the experiments to a text file that records all the commands to generate your container. Since we are using Docker, this file will be the Dockerfile, and you should [install Docker](https://docs.docker.com/engine/installation/) first and be comfortable with the basic usage. In these sections, we will be building your container from a customized file. You will be doing the following:
 
  - generating a recipe with (reproducible) steps to build a custom container
@@ -67,6 +71,7 @@ Note that if you want to deploy a container with https, you should read our [htt
 
 
 ## The Expfactory Builder Image
+
 Both of these steps start with the expfactory builder container. 
 We've [provided an image](https://quay.io/repository/vanessa/expfactory-builder?tab=tags) that will generate a Dockerfile, and from it you can build your Docker image.  
 Note that bases for expfactory were initially provided on [Docker Hub](https://hub.docker.com/r/vanessa/expfactory-builder/tags) and have moved to [Quay.io](https://quay.io/repository/vanessa/expfactory-builder?tab=tags). Dockerfiles in the repository that use the expfactory-builder are also updated. If you need a previous version, please see the tags on the original Docker Hub. We don't build the image within the same 
@@ -98,26 +103,27 @@ docker run quay.io/vanessa/expfactory-builder list
 
 Expfactory Version: 3.0
 Experiments
-1  adaptive-n-back	https://www.github.com/expfactory-experiments/adaptive-n-back
-2  breath-counting-task	https://www.github.com/expfactory-experiments/breath-counting-task
-3  dospert-eb-survey	https://www.github.com/expfactory-experiments/dospert-eb-survey
-4  dospert-rp-survey	https://www.github.com/expfactory-experiments/dospert-rp-survey
-5  dospert-rt-survey	https://www.github.com/expfactory-experiments/dospert-rt-survey
-6  test-task	https://www.github.com/expfactory-experiments/test-task
-7  tower-of-london	https://www.github.com/expfactory-experiments/tower-of-london
+1  adaptive-n-back	https://github.com/expfactory-experiments/adaptive-n-back
+2  breath-counting-task	https://github.com/expfactory-experiments/breath-counting-task
+3  dospert-eb-survey	https://github.com/expfactory-experiments/dospert-eb-survey
+4  dospert-rp-survey	https://github.com/expfactory-experiments/dospert-rp-survey
+5  dospert-rt-survey	https://github.com/expfactory-experiments/dospert-rt-survey
+6  test-task	https://github.com/expfactory-experiments/test-task
+7  tower-of-london	https://github.com/expfactory-experiments/tower-of-london
 ```
 
 Try using grep if you want to search for a term in the name or url
 
 ```
 docker run quay.io/vanessa/expfactory-builder list | grep survey
-2  alcohol-drugs-survey	https://www.github.com/expfactory-experiments/alcohol-drugs-survey
-4  dospert-eb-survey	https://www.github.com/expfactory-experiments/dospert-eb-survey
-5  dospert-rp-survey	https://www.github.com/expfactory-experiments/dospert-rp-survey
-6  dospert-rt-survey	https://www.github.com/expfactory-experiments/dospert-rt-survey
+2  alcohol-drugs-survey	https://github.com/expfactory-experiments/alcohol-drugs-survey
+4  dospert-eb-survey	https://github.com/expfactory-experiments/dospert-eb-survey
+5  dospert-rp-survey	https://github.com/expfactory-experiments/dospert-rp-survey
+6  dospert-rt-survey	https://github.com/expfactory-experiments/dospert-rt-survey
 ```
 
 ## Local Experiment Selection
+
 If you have experiments on your local machine where an experiment is defined based on [these criteria](/contribute#experiment-pre-reqs) or more briefly:
 
  - the config.json has all required fields
@@ -190,7 +196,7 @@ This is really great! Now we can add the `Dockerfile` and `startscript.sh` to ou
 
 LABEL EXPERIMENT_test-task /scif/apps/test-task
 WORKDIR /scif/apps
-RUN expfactory install https://www.github.com/expfactory-experiments/test-task
+RUN expfactory install https://github.com/expfactory-experiments/test-task
 
 LABEL EXPERIMENT_test-task-two /scif/apps/test-task-two
 ADD test-task-two /scif/apps/test-task-two
@@ -487,22 +493,22 @@ url again? Let's ask...
 expfactory list
 Expfactory Version: 3.0
 Experiments
-1  adaptive-n-back	https://www.github.com/expfactory-experiments/adaptive-n-back
-2  alcohol-drugs-survey	https://www.github.com/expfactory-experiments/alcohol-drugs-survey
-3  breath-counting-task	https://www.github.com/expfactory-experiments/breath-counting-task
-4  digit-span	https://www.github.com/expfactory-experiments/digit-span
-5  dospert-eb-survey	https://www.github.com/expfactory-experiments/dospert-eb-survey
-6  dospert-rp-survey	https://www.github.com/expfactory-experiments/dospert-rp-survey
-7  dospert-rt-survey	https://www.github.com/expfactory-experiments/dospert-rt-survey
-8  spatial-span	https://www.github.com/expfactory-experiments/spatial-span
-9  test-task	https://www.github.com/expfactory-experiments/test-task
-10 tower-of-london	https://www.github.com/expfactory-experiments/tower-of-london
+1  adaptive-n-back	https://github.com/expfactory-experiments/adaptive-n-back
+2  alcohol-drugs-survey	https://github.com/expfactory-experiments/alcohol-drugs-survey
+3  breath-counting-task	https://github.com/expfactory-experiments/breath-counting-task
+4  digit-span	https://github.com/expfactory-experiments/digit-span
+5  dospert-eb-survey	https://github.com/expfactory-experiments/dospert-eb-survey
+6  dospert-rp-survey	https://github.com/expfactory-experiments/dospert-rp-survey
+7  dospert-rt-survey	https://github.com/expfactory-experiments/dospert-rt-survey
+8  spatial-span	https://github.com/expfactory-experiments/spatial-span
+9  test-task	https://github.com/expfactory-experiments/test-task
+10 tower-of-london	https://github.com/expfactory-experiments/tower-of-london
 ```
 
 Ah yes, let's install test-task:
 
 ```
-$ expfactory install https://www.github.com/expfactory-experiments/test-task
+$ expfactory install https://github.com/expfactory-experiments/test-task
 Expfactory Version: 3.0
 Cloning into '/tmp/tmp5xn6oc4v/test-task'...
 remote: Counting objects: 62, done.
@@ -528,7 +534,7 @@ You then should have the new experiment installed in the container! Remember, yo
 docker run -v $PWD:/data quay.io/vanessa/expfactory-builder build digit-span test-task 
 ```
 
-If you have any questions about the above, or want more detail, please [get in touch](https://www.github.com/expfactory/issues) as I am looking to develop this.
+If you have any questions about the above, or want more detail, please [get in touch](https://github.com/expfactory/issues) as I am looking to develop this.
 
 
 Now that you are comfortable generating your container, check out how to [customize it](/customize).

pages/2-customize.md

@@ -105,7 +105,7 @@ The next set are relevant for installation.
 Note that bases for expfactory were initially provided on [Docker Hub](https://hub.docker.com/r/vanessa/expfactory-builder/tags) and have moved to [Quay.io](https://quay.io/repository/vanessa/expfactory-builder?tab=tags). Dockerfiles in the repository that use the expfactory-builder are also updated. If you need a previous version, please see the tags on the original Docker Hub.
 
 ## Expfactory wants Your Feedback!
-The customization process is very important, because it will mean allowing you to select variable stimuli, lengths, or anything to make a likely general experiment specific to your use case. To help with this, please [let us know](https://www.github.com/expfactory/expfactory/issues) your thoughts.
+The customization process is very important, because it will mean allowing you to select variable stimuli, lengths, or anything to make a likely general experiment specific to your use case. To help with this, please [let us know](https://github.com/expfactory/expfactory/issues) your thoughts.
 
 <div>
     <a href="/generate"><button class="previous-button btn btn-primary"><i class="fa fa-chevron-left"></i> </button></a>

pages/3-usage.md

@@ -163,9 +163,8 @@ and export the environment variable in the container to the file. Make sure to o
 
 For a complete tutorial of the above, see the [test-parse-url repository](https://github.com/expfactory-experiments/test-parse-url/tree/master/docker).
 
-
-
 ## Start a Headless Experiment Container
+
 "Headless" refers to the idea that you going to be running your experiment with remote participants, and you will need to send them to a different portal that has them login first. In order to do this, you need to start the container with the `--headless` flag, and then issue a command to pre-generate these users.
 
 First we can start the container (notice that we are giving it a name to easily reference it by) with `--headless` mode.
@@ -189,10 +188,10 @@ docker run -p 80:80 -d --name experiments -v /tmp/data:/scif/data <container> \
                     --experiments test-task,tower-of-london start
 ```
 
-If you ask for non random order without giving a list, you will present the experiments in the order listed on the filesystem. See [pre-set-experiments](#pre-set-experiments) for more information.
-
+If you ask for non random order without giving a list, you will present the experiments in the order listed on the filesystem. See [pre-set-experiments](#pre-set-experiments) for more information. 
 
 ### Generate tokens
+
 A "token" is basically a subject id that is intended to be used once, and can be sent securely to your participants to access the experiments. The token can be refreshed, revoked, or active. You will need to generate them, and briefly it looks like this:
 
 
@@ -219,9 +218,18 @@ And of course it follows that if you enter a bad token, you cannot enter.
 </div>
 
 Once entry is given, the user can continue normally to complete the experiments in the protocol. 
+If you want to provide the pre-generated URL to your participants to skip the login, you can have them navigate to this url
+
+```
+https://<your-server>/login?token=<token>
+https://<your-server>/login?token=a34d4512-1841-4219-873d-2b9d1727a37a
+```
+
+**Important** since this is sending data with a GET request, this is not recommended to do without https.
 
 
 ### Headless Finish
+
 When the user finishes the protocol, the user will have the token revoked so an additional attempt to do the experiments will not work. You would need to generate a new session with token (the `--new` command above) or restart the participant to rewrite the previously generated data.
 
 
@@ -851,7 +859,7 @@ A few questions for you!
 
  - Would password protection of the portal be desired?
 
-To best develop the software for different deployment, it's important to discuss these issues. Please [post an issue](https://www.github.com/expfactory/expfactory/issues) to give feedback.
+To best develop the software for different deployment, it's important to discuss these issues. Please [post an issue](https://github.com/expfactory/expfactory/issues) to give feedback.
 
 
 <br>