From babfa9c38c7b2fac9f5af6d64e856ce0faae8d6a Mon Sep 17 00:00:00 2001 From: Lars Vilhuber Date: Sun, 31 Dec 2023 04:33:00 -0500 Subject: [PATCH] Updates for an even simpler first step --- 01_run_it_again.md | 14 ++++++++++++++ 01_hands_off_running.md => 02_hands_off_running.md | 3 ++- 02_environments.md => 10_environments.md | 0 3 files changed, 16 insertions(+), 1 deletion(-) create mode 100644 01_run_it_again.md rename 01_hands_off_running.md => 02_hands_off_running.md (99%) rename 02_environments.md => 10_environments.md (100%) diff --git a/01_run_it_again.md b/01_run_it_again.md new file mode 100644 index 0000000..bcf4534 --- /dev/null +++ b/01_run_it_again.md @@ -0,0 +1,14 @@ +# Run it all again + +The very first test is that your code must run, beginning to end, top to bottom, without error, and ideally without any user intervention. This should in principle (re)create all figures, tables, and numbers you include in your paper. + + +## Exceptions + +### Code runs for a very long time + +What happens when some of these re-runs are very long? See later in this chapter for how to handle this. + +### Making the code run takes you a very long time + +While the code, once set to run, can do so on its own, *you* might need to spend a lot of time getting all the various pieces to run. This should be a warning sign: if it takes you a long time to get it to run, or to manually reproduce the results, it might take others even longer. Furthermore, it may suggest that you haven't been able to re-run your own code very often, which can be correlated with fragility or even lack of reproducibility. We address this partially in the [next section](hands-off-running). diff --git a/01_hands_off_running.md b/02_hands_off_running.md similarity index 99% rename from 01_hands_off_running.md rename to 02_hands_off_running.md index 5f400e1..3c95ac1 100644 --- a/01_hands_off_running.md +++ b/02_hands_off_running.md @@ -1,3 +1,4 @@ +(hands-off-running)= # Hands-off running The very first test is that your code must run, beginning to end, top to bottom, without error, and ideally without any user intervention. This should in principle (re)create all figures, tables, and numbers you include in your paper. @@ -8,7 +9,7 @@ Many users may not be set up to run in one single top-to-bottom run. It helps to We have seen users who appear to highlight code and to run it interactively, in pieces, using the program file as a kind of notepad. This is not reproducible, and should be avoided. It is fine for debugging. ``` -## Some simple examples of main files +## Examples diff --git a/02_environments.md b/10_environments.md similarity index 100% rename from 02_environments.md rename to 10_environments.md