prior_pred: Initial module and rough stability test

[garland-culbreth]

@bradbell @ntemiq @garland-culbreth

In this we've made the module for copying a node's dismod.db and emptying its data table to then run fit and sample to predict from the priors alone.

The next steps we've planned are:

1. Get at_cascade/csv/predict_prior.py to produce the output fit_predict.csv and sam_predict.csv files storing the prior predictions.
2. Build out the initial stability test in example/csv/prior_pred.py into a full test
3. Add a flag to at_cascade/csv/predict.py and its downstream modules to tell them whether we want prior predictions; default False to leave regular functionality unaffected
4. Add conditionals where needed in that module tree to invoke at_cascade/csv/predict_prior.py when flagged

Much of example/csv/prior_pred.py is still duplicated from example/csv/break_fit_pred.py, this is because right now it's being used as a very rough stability test (ie, does the script run without failing); once we get to (2) that step will involve changing the rest of that file to align with what we're actually using it for as well.

[bradbell]

In the at_cascade.git directory, please try running

bin/check_all.sh

[garland-culbreth]

Adding the output of the bin/check_all.sh command in this text file: log.txt

[bradbell]

Adding the output of the bin/check_all.sh command in this text file: log.txt

The key here is the last line of log.txt:

check_all.sh: OK

If that does not appear, then something went wrong.

[bradbell]

I tried to run bin/check_all.sh and got the output below. I suspect that xrst is not in your execution path so testing bin/run_xrst.sh was skipped on your system:

at_cascade.git>bin/check_all.sh
bin/check_copy.sh
bin/check_copy.sh: OK
bin/check_invisible.sh
check_invisible.sh: OK
bin/check_tab.sh
check_tab.sh: OK
bin/check_version.sh
check_version.sh OK
bin/run_xrst.sh
xrst --local_toc --target html --html_theme sphinx_rtd_theme --index_page_name at_cascade 
xrst: Error
The file at_cascade/csv/predict_prior.py
used in a toc_table command does not contain any begin commands.
project_directory = /home/bradbell/repo/at_cascade.git
page = csv.module
file = at_cascade/csv/__init__.py
line = 123

Since we plan to eventually make predicting from the priors an option to csv.predict, I suspect the best thing to do is to remove predict_prior.py from the toc_table command (and to install xrst on your system so the documentation gets built).

[bradbell]

One way to handle this problem is to change {xrst_begin and {xrst_end to {xrst_comment in the offending file; i.e., tell xrst that this is not intended to be processed.

at_cascade.git>bin/check_all.sh
bin/check_copy.sh
bin/check_copy.sh: OK
bin/check_invisible.sh
check_invisible.sh: OK
bin/check_tab.sh
check_tab.sh: OK
bin/check_version.sh
check_version.sh OK
bin/run_xrst.sh
xrst --local_toc --target html --html_theme sphinx_rtd_theme --index_page_name at_cascade 

warning: group_name = default
The following files have pages with the empty group name
but they are not in any xrst_toc commands starting at the root_file for the default group
   example/csv/prior_pred.py
Using following input_files: git ls-files
sphinx-build -b html -j 1 build/rst build/html
rm -r build/html/_sources
cp -r build/rst/_sources build/html/_sources
xrst: See warnings above
run_xrst.sh: aboring due to xrst errors above
at_cascade.git>

[garland-culbreth]

I've been running into issues with the scripts in /bin, specifically check_invisible.sh and check_version.sh, due to syntactic differences with OSX. This discussion covers the issue I encountered

[garland-culbreth]

Closing this PR and opening a new one with the same changes but cleaner files