Clean up of repo

.devcontainer/Dockerfile

@@ -1,7 +1,8 @@
 ################### BUILD AND RUN THIS DOCKER FILE ############################
 
 ### BUILD IMAGE
-# docker build -t rachelicr/env-pisca-v1 -f .devcontainer/Dockerfile .
+## docker build -t rachelicr/env-pisca-v1 -f .devcontainer/Dockerfile .
+# docker build -t env-pisca-v1 -f .devcontainer/Dockerfile .
 
 ### USE IMAGE
 # ctrl-sh-p in vscode and select the image

.vscode/launch.json

@@ -0,0 +1,28 @@
+{    
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Python:Streamlit",
+            "type": "python",
+            "request": "launch",
+            "module": "streamlit",
+            "args": [
+                 "run",
+                 "${file}",
+                 "--server.port",
+                 "8501"
+            ]
+        },
+        {
+            "name": "Python: Current File",
+            "type": "python",
+            "request": "launch",
+            "program": "${file}",
+            "console": "integratedTerminal",
+            "justMyCode": true
+        }
+    ]
+}
+
+
+

dev_docs/dev_1_container.md

@@ -0,0 +1,36 @@
+# Containerised Development
+
+Due to the complexity of the PISCA environment this project is designed to be developed and debugged in a container.  
+
+Thus, VSCode is the IDE of choice, as the ability use conatiners for development is integrated and free. It is also possible in a paid-foir version of pycharm.  
+You will need the Dev Containers extension installed.
+
+## The container
+The develoment container is defined in the `devcontainer.json` file. This file defines the container image to be used, the extensions to be installed and the settings to be used.
+
+The container image is defined in the `Dockerfile` file. This file defines the base image to be used and the additional packages to be installed.
+
+## Building the container
+- You should not need to build the container, it can pull down from docker automatically
+- Should you need to, the instructions for building are at the top of the Dockerfile
+
+## Using the container
+- ctrl-sh-p in vscode and select "Devcontainers: Repoen in container"
+
+You will see the file system much as before, this time in Workspaces/pisca-box a pseudo linux operating system.  
+It will feel a bit different to an ordinary dev environment as for example there is no virtual environment, that was all installed in the container.  
+
+If you find a need to add a python library or R library they need to go in the container and then it needs to be rebuilt and redistributed.
+
+Check it is as you would expect:  
+```R --version``` will give 4.3.2  
+```beast``` will throw java errors - but it is there  
+
+## Installations from the marketplace
+You will not have pulled in any of your markletplace extensions so they need re-installing: warning every time the container is rebuilt they need to be re-installed so don't get too comfortable.
+
+
+
+
+
+

dev_docs/dev_2_run_debug.md

@@ -0,0 +1,49 @@
+# Run the application
+
+Navigate 1 directory in then run the entry point:  
+```
+cd pisca-box-run
+streamlit run app/home.py
+```
+
+The application will pop up in [localhost 8501](http://localhost:8501/)
+
+# Debug the application
+https://stackoverflow.com/questions/60172282/how-to-run-debug-a-streamlit-application-from-an-ide
+the answer here that starts "If you're a VS Code user,"
+In summary, create a launch.json on the debugger (left side) in vscode. 
+Add to it this config below, navigate to the app/home.py page and choose to "run".
+```
+{    
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Python:Streamlit",
+            "type": "python",
+            "request": "launch",
+            "module": "streamlit",
+            "args": [
+                 "run",
+                 "${file}",
+                 "--server.port",
+                 "8501"
+            ]
+        },
+        {
+            "name": "Python: Current File",
+            "type": "python",
+            "request": "launch",
+            "program": "${file}",
+            "console": "integratedTerminal",
+            "justMyCode": true
+        }
+    ]
+}
+```
+when on the page you want to run, select python:streannlit and press play.
+
+
+
+
+
+

dev_docs/dev_3_build_application.md

@@ -0,0 +1,39 @@
+# Containerised Deployment
+
+Due to the complexity of the PISCA environment this project is designed to be deployed in a container.  
+
+## The application container
+The develoment container has already been explained. 
+The application container uses the development container as a base to minimise time spent building containers and replicating envirnments.
+
+The container image is defined in the `pisca-box-vue/Dockerfile` file.  
+It is fairly light and is mostly only an entry point into the copied code installation. 
+
+## Building the application container
+
+This is **NOT FROM INSIDE THE DEVCONTAINER** you want to go back to your local folder (ctrl-sh-p "Reopen in local folder").
+
+If you need to build and deploy the application container (you are probably in the ICR?) use the docker-compose.yml file.  
+This has the addition of the listening port, not necessary for manual running of the container, but necessary were it to be deployed on azure.
+
+You can use docker commands, or you can have the docker extenstion installed.  
+
+On the file pisca-box-vue/docker-compose.yml right click and select "Compose Up"  
+
+This will build the image and run it.
+
+## Test the image
+
+You can test the image by running it locally.
+```docker run --rm --name pisca-box -p 8002:8501 icrsc/pisca-box```
+[localhost:8002](http://localhost:8002) should show the app.
+
+## Push the image to docker hub
+
+You can find the image in the docker dashboard.
+
+Right-click and select push to upload to docker hub (you need access to be able to upload it to github).
+
+
+
+

dev_docs/test_1_regression.md

@@ -0,0 +1,11 @@
+
+# Regression Testing
+
+### In the development container (but not the app)
+Run the regression tests from pytests and the lint formatting:
+```
+pytest
+ruff --format=github --select=E9,F63,F7,F82 --target-version=py37 .
+ruff --format=github --target-version=py37 .
+```
+

testing.md → dev_docs/test_2_github.md

@@ -1,17 +1,5 @@
-# Testing Framework for pisca-box
 
-### Correctness
-The containerised app does not necessarily run on a workstation.
-
-### Before checkin
-from pisca-box$
-```
-ruff --format=github --select=E9,F63,F7,F82 --target-version=py37 .
-ruff --format=github --target-version=py37 .
-pytest
-```
-
-### Github Actions
+### Github Actions will run automatically on checkin
 - ruff is used as a linter and the tests created in tests directory are run when a push is made to github
 - Ruff can be installed from VSCode MarketPlace and will automatically execute contiunuously
   - The VSCode palette has Ruff: commands "quick fix" and "fix all" and "organize imports"

dev_docs/test_3_acceptance.md

@@ -0,0 +1,21 @@
+# Acceptance testing of a version
+
+**See below for what RUN CHECKS means**
+
+1. RUN CHECKS on the proposed application locally as a docker container before pushing to docker hub or github main
+2. Upload to docker hub and then RUN CHECKS on that docker image FROM ANOTHER MACHINE
+3. Upload to the public webserver and then RUN CHECKS from a non ICR laptop or at least not inside the ICR and not on the VPN
+4. RUN CHECKS from a mobile
+
+
+RUN CHECKS means:
+- The app is accessible
+- The app is responsive
+- The app runs
+  - beauti-box: test you can create a beauti xml file and download it
+  - pisca-box: test you can upload a beauti xml file and it is displayed
+  - tree-annotator: test you can annotate the previous trees file and download it
+  - plot-box: you can produce the plot from the above (or other files)
+- The app is performant
+  - all the above is not too slow
+