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Update documentation toolchain so that it compiles again #480

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The draft documentation can be viewed here https://empirical--480.org.readthedocs.build/en/480/

The main topic we need to decide on is how tightly we want to strip out changes unrelated to documentation.
If we want to have this PR be strictly doc-related, mostly nonfunctional changes only, there will be some diffs that need to get ripped out.
I labeled a few diffs that look like they might have leaked in from other work.

Miscellanea:

  • Do we want to link here in the side bar?
  • Is disabling the "namespace" component of this page or moving it to the end very hard to do? May be worth considering.
  • Do we want to keep "Page Hierarchy" here. The todo and deprecated lists are useful. But I think this is kind of a weird way to open the API section.
  • we probably should update the example file header docstring on this page
  • do we want to update anything on this page given the extensive documentation overhaul we've done? It might be worth brain dumping some how things are now working behind the scenes for posterity while we still remember.

Additional, non-necessary clean up that might be nice:

include/emp/Evolve/SystematicsAnalysis.hpp Show resolved Hide resolved
include/emp/Evolve/SystematicsAnalysis.hpp Show resolved Hide resolved
}

/// Returns the total number of times a mutation of type @param type
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why @param -> \c?

include/emp/Evolve/World.hpp Show resolved Hide resolved
include/emp/Evolve/World.hpp Show resolved Hide resolved
@@ -1089,7 +1089,7 @@ namespace emp {

template <size_t NUM_BITS, bool ZERO_LEFT>
bool BitArray<NUM_BITS,ZERO_LEFT>::Get(size_t index) const {
emp_assert(index >= 0 && index < NUM_BITS);
emp_assert(index < NUM_BITS);
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inadvertently leaked-in off topic diff?

@@ -1026,7 +1026,7 @@ namespace emp {
const size_t from_bit
) {
// Only check for same-ness if the two types are the same.
if constexpr (FROM_BITS == NUM_BITS) emp_assert(&from_array != this);
if constexpr (FROM_BITS == NUM_BITS) { emp_assert(&from_array != this); }
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inadvertently leaked-in off topic diff?

for (size_t i = 0; i < NUM_BITS; i++) Set(i, bitset[i]);
return *this;
}

/// Assignment operator from a string of '0's and '1's.
template <size_t NUM_BITS, bool ZERO_LEFT>
BitArray<NUM_BITS,ZERO_LEFT> &
BitArray<NUM_BITS,ZERO_LEFT>::operator=(const std::string & bitstring) {
BitArray<NUM_BITS,ZERO_LEFT>::operator=(const std::string & bitstring) & {
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inadvertently leaked-in off topic diff?

@@ -997,15 +997,15 @@ namespace emp {
/// Assignment operator from a std::bitset.
template <size_t NUM_BITS, bool ZERO_LEFT>
BitArray<NUM_BITS,ZERO_LEFT> &
BitArray<NUM_BITS,ZERO_LEFT>::operator=(const std::bitset<NUM_BITS> & bitset) {
BitArray<NUM_BITS,ZERO_LEFT>::operator=(const std::bitset<NUM_BITS> & bitset) & {
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inadvertently leaked-in off topic diff?

/// Set a range of bits to one: [start, stop)
BitVector & SetRange(size_t start, size_t stop)
{ return ApplyRange([](field_t){ return FIELD_ALL; }, start, stop); }
/// Set a range of bits to value (default one): [start, stop)
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inadvertently leaked-in off topic diff?

@mmore500
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mmore500 commented Dec 8, 2023

Closing, superseded by #484

@mmore500 mmore500 closed this Dec 8, 2023
@mmore500 mmore500 deleted the fix-docs branch December 8, 2023 00:04
@mmore500 mmore500 restored the fix-docs branch December 8, 2023 00:56
mmore500 added a commit that referenced this pull request Dec 8, 2023
Isolate docs changes from MABE changes in #480
@mmore500 mmore500 deleted the fix-docs branch December 8, 2023 20:44
@mmore500 mmore500 restored the fix-docs branch December 8, 2023 21:50
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4 participants