Merge branch 'JOSS_pythonSubmit' of github.com:avigna/COMPAS-1 into JOSS_pythonSubmit

Author: avigna

docs/compasHPC.md

@@ -79,7 +79,7 @@ to your `~/.bash_profile` or equivalent.
   Make a copy of the `stroopwafelInterface.py` file in the `defaults/` folder into your current directory, and set the `run_on_helios` parameter to `True`.
   Set any other stroopwafel parameters as you see fit.
 
-  If you have many non-default COMPAS arguments, you are encouraged to set them in a `pythonSubmit.py` file in the same directory, 
+  If you have many non-default COMPAS arguments, you are encouraged to set them in a `runSubmit.py` file in the same directory, 
   and set the `usePythonSubmit` parameter to `True`.
 
   See sampling.md for details.

docs/docker.md

@@ -41,22 +41,22 @@ To see all available versions, go to the TeamCOMPAS docker hub page [here](https
 
 ### Running
 
-COMPAS can still be configured via command line arguments passed to the COMPAS executable or via a `pythonSubmit.py` file.
+COMPAS can still be configured via command line arguments passed to the COMPAS executable or via a `runSubmit.py` file.
 
-#### Run pythonSubmit.py
+#### Execute runSubmit.py
 
-To run COMPAS via a `pythonSubmit.py` file, the command is a little more complex.
+To run COMPAS via a `runSubmit.py` file, the command is a little more complex.
 
 ```
 docker run                                                  \
     --rm                                                    \
     -it                                                     \
     -v $(pwd)/compas-logs:/app/COMPAS/logs                  \
-    -v $(pwd)/pythonSubmit.py:/app/starts/pythonSubmit.py   \
+    -v $(pwd)/runSubmit.py:/app/starts/runSubmit.py   \
     -e COMPAS_EXECUTABLE_PATH=/app/COMPAS/bin/COMPAS        \
     -e COMPAS_LOGS_OUTPUT_DIR_PATH=/app/COMPAS/logs         \
     teamcompas/compas                                       \
-    python3 /app/starts/pythonSubmit.py                     
+    python3 /app/starts/runSubmit.py                     
 ```
 
 Breaking down this command:
@@ -74,7 +74,7 @@ short for [-i and -t](https://docs.docker.com/engine/reference/run/#foreground)
 `-v <path-on-host>:<path-in-container>`
 [Bind mounts](https://docs.docker.com/storage/bind-mounts/)
 mount `<path-on-host>` to `<path-in-container`>
-This time we not only want to get the output from COMPAS on the host machine, we also want to supply a `pythonSubmit.py` to the container from the host machine.
+This time we not only want to get the output from COMPAS on the host machine, we also want to supply a `runSubmit.py` to the container from the host machine.
 
 `-e VAR_NAME=value`
 [Environment variables](https://docs.docker.com/engine/reference/run/#env-environment-variables)
@@ -83,13 +83,13 @@ set the environment variable `VAR_VAME` to `value`
 `teamcompas/compas`
 the image to run
 
-`python3 /app/starts/pythonSubmit.py`
+`python3 /app/starts/runSubmit.py`
 the command to run when the container starts
 
 
 #### Run the COMPAS executable
 
-To run the COMPAS executable directly (i.e. without `pythonSubmit.py`)
+To run the COMPAS executable directly (i.e. without `runSubmit.py`)
 ```
 docker run                                  \
     --rm                                    \
@@ -136,12 +136,12 @@ More info on `docker run` [here](https://docs.docker.com/engine/reference/run/)
 
 NOTE 1:
 
-Two new environment variables have been added, both of these apply to `pythonSubmit.py` only and are non-breaking changes.
+Two new environment variables have been added, both of these apply to `runSubmit.py` only and are non-breaking changes.
 
-`COMPAS_EXECUTABLE_PATH` is an addition to the default `pythonSubmit.py` that overrides where `pythonSubmit.py` looks for the compiled COMPAS.
+`COMPAS_EXECUTABLE_PATH` is an addition to the default `runSubmit.py` that overrides where `runSubmit.py` looks for the compiled COMPAS.
 This override exists purely for ease-of-use from the command line.
 
-`COMPAS_LOGS_OUTPUT_DIR_PATH` is also an addition to the default `pythonSubmit.py` that overrides where logs are placed.
+`COMPAS_LOGS_OUTPUT_DIR_PATH` is also an addition to the default `runSubmit.py` that overrides where logs are placed.
 The override exists because the mounted directory (option `-v`) is created before COMPAS runs. COMPAS sees that the directory where it's supposed to put logs already exists, so it created a different (i.e. non-mapped) directory to deposit logs in.
 
 
@@ -154,16 +154,16 @@ All container output will be hidden.
 An example where this would be useful is if you were running 4 instances of COMPAS at once.
 You could copy/paste the following into the terminal...
 ```
-docker run --rm -d -v $(pwd)/compas-logs/run_0:/app/COMPAS/logs -v $(pwd)/pythonSubmitMMsolar_01.py:/app/starts/pythonSubmit.py teamcompas/compas python3 /app/starts/pythonSubmit.py &
+docker run --rm -d -v $(pwd)/compas-logs/run_0:/app/COMPAS/logs -v $(pwd)/runSubmitMMsolar_01.py:/app/starts/runSubmit.py teamcompas/compas python3 /app/starts/runSubmit.py &
 
-docker run --rm -d -v $(pwd)/compas-logs/run_1:/app/COMPAS/logs -v $(pwd)/pythonSubmitMMsolar_02.py:/app/starts/pythonSubmit.py teamcompas/compas python3 /app/starts/pythonSubmit.py &
+docker run --rm -d -v $(pwd)/compas-logs/run_1:/app/COMPAS/logs -v $(pwd)/runSubmitMMsolar_02.py:/app/starts/runSubmit.py teamcompas/compas python3 /app/starts/runSubmit.py &
 
-docker run --rm -d -v $(pwd)/compas-logs/run_2:/app/COMPAS/logs -v $(pwd)/pythonSubmitMMsolar_03.py:/app/starts/pythonSubmit.py teamcompas/compas python3 /app/starts/pythonSubmit.py &
+docker run --rm -d -v $(pwd)/compas-logs/run_2:/app/COMPAS/logs -v $(pwd)/runSubmitMMsolar_03.py:/app/starts/runSubmit.py teamcompas/compas python3 /app/starts/runSubmit.py &
 
-docker run --rm -d -v $(pwd)/compas-logs/run_3:/app/COMPAS/logs -v $(pwd)/pythonSubmitMMsolar_04.py:/app/starts/pythonSubmit.py teamcompas/compas python3 /app/starts/pythonSubmit.py
+docker run --rm -d -v $(pwd)/compas-logs/run_3:/app/COMPAS/logs -v $(pwd)/runSubmitMMsolar_04.py:/app/starts/runSubmit.py teamcompas/compas python3 /app/starts/runSubmit.py
 ```
 
-...which would run 4 separate instances of COMPAS, each with its own `pythonSubmit.py` file and logging directory, and all console output supressed.
+...which would run 4 separate instances of COMPAS, each with its own `runSubmit.py` file and logging directory, and all console output supressed.
 
 You may want to check the console output to see how far into the run COMPAS is.
 The command for this is `docker logs <container_id>`.
@@ -235,7 +235,7 @@ Make COMPAS using a specific makefile (more below) and as many cores as possible
 [RUN](https://docs.docker.com/engine/reference/builder/#run) docs
 
 Dockerfiles will usually end with a `CMD` directive that specifies what command should run when the container is started.
-COMPAS doesn't have a `CMD` directive because some users will want to run the executable directly and some will want to use `pythonSubmit.`.
+COMPAS doesn't have a `CMD` directive because some users will want to run the executable directly and some will want to use `runSubmit.`.
 [CMD](https://docs.docker.com/engine/reference/builder/#cmd) docs