se-for-sci · henryiii · Jun 27, 2025 · Jun 23, 2025 · Jun 23, 2025
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -14,7 +14,7 @@ repos:
       - id: trailing-whitespace
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.13
+    rev: v0.12.0
     hooks:
       - id: ruff-format
         exclude: ^content/week01/cleanup_bessel\.ipynb$
@@ -31,7 +31,7 @@ repos:
       - id: nbstripout
 
   - repo: https://github.com/rbubley/mirrors-prettier
-    rev: "v3.5.3"
+    rev: "v3.6.0"
     hooks:
       - id: prettier
 

diff --git a/content/week02/intro.md b/content/week02/intro.md
@@ -8,7 +8,6 @@ system.
 Old school techniques are usually bad.
 
 - Version filenames is a disaster.
-
   - mythesis_v1.tex, mythesis_v2.tex, mythesis_last_v3.tex
   - creates clutter
   - Filenames rarely contain information other than chronology
@@ -17,7 +16,6 @@ Old school techniques are usually bad.
     but you have no idea where the error was introduced?
 
 - Sharing files with others is a disaster.
-
   - Emailing files sucks --- only magnifies the problems above
   - Track changes feature Google Docs or Word --- not so useful for anything
     complex
@@ -32,12 +30,10 @@ Modern version control techniques are usually great.
 Modern tools to promote collective intelligence.
 
 - Automated history of everything
-
   - not just files, but whole projects with folders and subfolders
   - who, what, when, and (most important) why
 
 - Automated sharing of everyone's latest edits
-
   - no more emailing files around
 
 - Easier disaster recovery with distributed VCSes like Git or Mercurial (see
@@ -46,7 +42,6 @@ Modern tools to promote collective intelligence.
 - Support for automated testing (we'll cover this in future lectures)
 
 - Infinite sandboxes for clutter-free, fear-free experimentation
-
   - this is where Git especially shines -- main topic today
 
 - CAVEAT 1: All of this works best with plain text files
@@ -63,11 +58,9 @@ Modern tools to promote collective intelligence.
 ![title](CVCS-vs-DVCS.png)
 
 - Local Version Control
-
   - Mainly just reduced clutter and automated tracking of chronology...
 
 - Centralized Version Control
-
   - Allows group work on the same files...
   - Single point of failure --- there is only a single "real" repository
   - Backing up is a separate process
@@ -108,7 +101,6 @@ Things to keep in mind during our exercise
 
 - Some git operations are of a "send it out" variety, while others are of a
   "bring it in" variety
-
   - important to keep straight which are of which flavor
 
 - Some git operations are repo-wise, while others are branch-wise

diff --git a/content/week10/debugging.md b/content/week10/debugging.md
@@ -12,7 +12,6 @@ In this lecture, we will:
 - learn tips and tricks from a lifelong experience in debugging
 
 - gain practical knowledge in
-
   - simple debugging techniques using compilers
   - simple debuggers for C/C++, Rust, and Python
   - more advanced graphical debuggers
@@ -38,7 +37,6 @@ When a code crashes it usually writes out a cryptic error message
 ### Typical error messages
 
 - `SIGFPE`: floating point exception
-
   - Often controlled by compiler options
   - division by zero
   - square root of a negative number
@@ -71,7 +69,6 @@ x[345] = 0.0; // panics at run-time
 
 - Make sure your shell “stack size limit” and "core size limit" are both set to
   “unlimited”
-
   - `ulimit -s unlimited` set stack memory to unlimited
   - `ulimit -c unlimited` set core file size to unlimited
   - `ulimit -a` show all limits
@@ -169,7 +166,6 @@ All compilers accept the `-g` option.
 ### Examples of useful compiler options
 
 - All compilers have options that try to detect potential bugs in the code
-
   - Array bounds check (gcc: -Warray-bounds)
     - Check for array subscripts and substrings out of bounds
     - Should be done on unoptimized code (-O0)
@@ -222,7 +218,6 @@ All compilers accept the `-g` option.
   MPI task in a parallel code)
 
 - No `core` file?
-
   - Check your shell limits: `ulimit –a` (bash) or `limit` (csh)
   - Look for `core file size` (bash) or `coredumpsize` (csh) > 0
 
@@ -301,7 +296,6 @@ gdb (1)              - The GNU Debugger
 - Online manual for gdb at `info gdb`
 
 - Can be used within the `emacs` editor
-
   - Can run gdb commands within the emacs source code window (e.g. `C-x SPC` to
     set a breakpoint)
 
@@ -546,7 +540,6 @@ $ rust-gdb ./example
 - Detective work starts
 
 - Try reducing the problem size and see if the error is still there
-
   - The smaller the better
   - Running with only 2 processes is ideal if your code is parallel
 
@@ -629,21 +622,18 @@ p expression
   restart a simulation from that point
 
 - Extremely important for codes that have long runtimes (> 1 hour)
-
   - Allows you to restart your simulation at the point of the latest checkpoint
   - Avoid losing hours of precious computer time
   - Especially important for parallel codes
 
 - Extremely important when you need to debug a code that crashes after a few
   hours!!
-
   - You can recompile the code with `–g` and start from the last checkpoint
   - Remember... `-g` slows down the code dramatically so you want to be as close
     to the crash as possible
 
 - When restarting a simulation from a checkpointed state, reproducibility is
   very important
-
   - Test by running the code to a certain point and saving its state at that
     point
   - Rerun the same case but split in 2 steps where the 2nd step uses restart
@@ -666,7 +656,6 @@ p expression
   (100,000+ processors)
 
 - The idea is simple:
-
   - Insert `print` statements at strategic locations in the code to gather
     information and try to pinpoint the faulty code line
   - Advantages over other forms of debugging:
@@ -689,7 +678,6 @@ p expression
   **standard output**
 
 - Write to **standard error** as much as possible since it is not buffered
-
   - `cerr <<` in C++
   - `eprint` in Rust
   - redirect output: `mpirun –np 1024 ./a.out 1> output.out 2> output.err`

diff --git a/notes/week3b.md b/notes/week3b.md
@@ -26,24 +26,20 @@ Design patterns in OOP
   - Composition - "has a" & restrict interface (you can't delete attributes with
     ) - verbose!
 - UML diagrams
-
   - Can show classes, interface, relationships
   - Several links to read more if interested
 
 - OOP Pattern 1: code injection
-
   - You can replace steps in a calculation via inheritance and overriding
 
 - OOP Pattern 2: Required interface (ABCs)
-
   - You can require an implementation to implement certain methods - called
     "abstract" (italics on a UML diagram)
   - Example: `content/week03/geom_example`
   - We did the dataclasses version in class (voted)
   - Example: `content/week03/integrator_example` (also in rendered notes)
 
 - SOLID:
-
   - S: modular
   - O: Open/closed API
   - Liskov substitution principle (like adding `power=` to `Geometry.area` but
@@ -52,17 +48,14 @@ Design patterns in OOP
   - D: Dependency inversion (low level depend on high level)
 
 - OOP Pattern 3: Functors
-
   - Not very native in Python, but common in some languages like C++
   - Can implement with function capture instead of classes
 
 - Separation of concerns
-
   - Some languages have techniques like multifile classes
   - Other ways to achieve, like mixins, dispatch (later), etc
 
 - OOP Pattern 4: eDSLs
-
   - Example with Path using division for joining
 
 - OOP Pattern 5: Mixins