EFF Reduce the size of shared objects of the C-extensions generated by Cython

### Context

scikit-learn uses C-extensions in critical part of its implementations via Cython.

Each C-entension is build from one or several Cython translation unit (a `.pyx` file with a potential `.pxd` companion file). 

In scikit-learn, each C-extension build consists of a single Cython translation which is transpilled to a C or C++ translation unit, which is then compiled to a shared object file.

The resulting C or C++ translation unit contains the code translation from Cython to C and large preambule and epylogue of macros, functions, structs, global variables such as virtual tables, Python module definition, etc.

For instance, while the code of [`sklearn/utils/_heap.pyx`](https://github.com/scikit-learn/scikit-learn/blob/main/sklearn/utils/_heap.pyx) only consists of less than 100 lines for a single function, the resulting `sklearn/utils/heap.c` file consists of more than 3500 lines, most of being the preambule's and the epilogue's injected by Cython:

<details>
<summary> Content of the generated <code>sklearn/utils/heap.c</code> </summary>

```

▾ macros
   -CYTHON_ABI
   -CYTHON_ASSUME_SAFE_MACROS
   -CYTHON_ASSUME_SAFE_MACROS
   -CYTHON_ASSUME_SAFE_MACROS
   -CYTHON_ASSUME_SAFE_MACROS
   -CYTHON_AVOID_BORROWED_REFS
   -CYTHON_AVOID_BORROWED_REFS
   -CYTHON_AVOID_BORROWED_REFS
   -CYTHON_AVOID_BORROWED_REFS
   -CYTHON_COMPILING_IN_CPYTHON
   -CYTHON_COMPILING_IN_CPYTHON
   -CYTHON_COMPILING_IN_CPYTHON
   -CYTHON_COMPILING_IN_CPYTHON
   -CYTHON_COMPILING_IN_NOGIL
   -CYTHON_COMPILING_IN_NOGIL
   -CYTHON_COMPILING_IN_NOGIL
   -CYTHON_COMPILING_IN_NOGIL
   -CYTHON_COMPILING_IN_PYPY
   -CYTHON_COMPILING_IN_PYPY
   -CYTHON_COMPILING_IN_PYPY
   -CYTHON_COMPILING_IN_PYPY
   -CYTHON_COMPILING_IN_PYSTON
   -CYTHON_COMPILING_IN_PYSTON
   -CYTHON_COMPILING_IN_PYSTON
   -CYTHON_COMPILING_IN_PYSTON
   -CYTHON_FALLTHROUGH
   -CYTHON_FALLTHROUGH
   -CYTHON_FALLTHROUGH
   -CYTHON_FALLTHROUGH
   -CYTHON_FALLTHROUGH
   -CYTHON_FALLTHROUGH
   -CYTHON_FAST_PYCALL
   -CYTHON_FAST_PYCALL
   -CYTHON_FAST_PYCALL
   -CYTHON_FAST_PYCALL
   -CYTHON_FAST_PYCCALL
   -CYTHON_FAST_THREAD_STATE
   -CYTHON_FAST_THREAD_STATE
   -CYTHON_FAST_THREAD_STATE
   -CYTHON_FAST_THREAD_STATE
   -CYTHON_FAST_THREAD_STATE
   -CYTHON_FORMAT_SSIZE_T
   -CYTHON_FUTURE_DIVISION
   -CYTHON_HEX_VERSION
   -CYTHON_INLINE
   -CYTHON_INLINE
   -CYTHON_INLINE
   -CYTHON_INLINE
   -CYTHON_INLINE
   -CYTHON_MAYBE_UNUSED_VAR(x)
   -CYTHON_NCP_UNUSED
   -CYTHON_NCP_UNUSED
   -CYTHON_PEP393_ENABLED
   -CYTHON_PEP393_ENABLED
   -CYTHON_PEP489_MULTI_PHASE_INIT
   -CYTHON_PEP489_MULTI_PHASE_INIT
   -CYTHON_PEP489_MULTI_PHASE_INIT
   -CYTHON_PEP489_MULTI_PHASE_INIT
   -CYTHON_PEP489_MULTI_PHASE_INIT
   -CYTHON_REFNANNY
   -CYTHON_RESTRICT
   -CYTHON_RESTRICT
   -CYTHON_RESTRICT
   -CYTHON_RESTRICT
   -CYTHON_SMALL_CODE
   -CYTHON_SMALL_CODE
   -CYTHON_SMALL_CODE
   -CYTHON_UNPACK_METHODS
   -CYTHON_UNPACK_METHODS
   -CYTHON_UNPACK_METHODS
   -CYTHON_UNPACK_METHODS
   -CYTHON_UNUSED
   -CYTHON_UNUSED
   -CYTHON_UNUSED
   -CYTHON_UNUSED
   -CYTHON_UPDATE_DESCRIPTOR_DOC
   -CYTHON_UPDATE_DESCRIPTOR_DOC
   -CYTHON_UPDATE_DESCRIPTOR_DOC
   -CYTHON_USE_ASYNC_SLOTS
   -CYTHON_USE_ASYNC_SLOTS
   -CYTHON_USE_ASYNC_SLOTS
   -CYTHON_USE_ASYNC_SLOTS
   -CYTHON_USE_ASYNC_SLOTS
   -CYTHON_USE_ASYNC_SLOTS
   -CYTHON_USE_DICT_VERSIONS
   -CYTHON_USE_DICT_VERSIONS
   -CYTHON_USE_DICT_VERSIONS
   -CYTHON_USE_DICT_VERSIONS
   -CYTHON_USE_EXC_INFO_STACK
   -CYTHON_USE_EXC_INFO_STACK
   -CYTHON_USE_EXC_INFO_STACK
   -CYTHON_USE_EXC_INFO_STACK
   -CYTHON_USE_EXC_INFO_STACK
   -CYTHON_USE_PYLIST_INTERNALS
   -CYTHON_USE_PYLIST_INTERNALS
   -CYTHON_USE_PYLIST_INTERNALS
   -CYTHON_USE_PYLIST_INTERNALS
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   -CYTHON_USE_PYLONG_INTERNALS
   -CYTHON_USE_PYLONG_INTERNALS
   -CYTHON_USE_PYLONG_INTERNALS
   -CYTHON_USE_PYLONG_INTERNALS
   -CYTHON_USE_PYTYPE_LOOKUP
   -CYTHON_USE_PYTYPE_LOOKUP
   -CYTHON_USE_PYTYPE_LOOKUP
   -CYTHON_USE_PYTYPE_LOOKUP
   -CYTHON_USE_PYTYPE_LOOKUP
   -CYTHON_USE_TP_FINALIZE
   -CYTHON_USE_TP_FINALIZE
   -CYTHON_USE_TP_FINALIZE
   -CYTHON_USE_TP_FINALIZE
   -CYTHON_USE_TYPE_SLOTS
   -CYTHON_USE_TYPE_SLOTS
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   -CYTHON_USE_UNICODE_INTERNALS
   -CYTHON_USE_UNICODE_INTERNALS
   -CYTHON_USE_UNICODE_INTERNALS
   -CYTHON_USE_UNICODE_INTERNALS
   -CYTHON_USE_UNICODE_WRITER
   -CYTHON_USE_UNICODE_WRITER
   -CYTHON_USE_UNICODE_WRITER
   -CYTHON_USE_UNICODE_WRITER
   -CYTHON_USE_UNICODE_WRITER
   -CYTHON_WITHOUT_ASSERTIONS
   -DL_EXPORT(t)
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   -PY_LONG_LONG
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▾-__anonf7ac09720103 : enum
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▾-__anonf7ac09720208 : struct
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▾-__anonf7ac09720308 : struct
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```

</details>

### Problem

Currently the uncompressed size of scikit-learn is around 48.8MB, 20MB of which are shared object files. As reported by @rth in https://github.com/pyodide/pyodide/issues/4289, while shared object files are optimized for Emscripten quite heavily, they still accounts for most of the size of scikit-learn on this stack.

<details>
<summary>Extensions' shared object sizes on Linux</summary>

```bash
find . -name \*.so -exec du -h {} \; | sort -h --reverse
```

```
2,1M	./sklearn/_loss/_loss.cpython-312-x86_64-linux-gnu.so
712K	./sklearn/utils/sparsefuncs_fast.cpython-312-x86_64-linux-gnu.so
672K	./sklearn/neighbors/_kd_tree.cpython-312-x86_64-linux-gnu.so
672K	./sklearn/neighbors/_ball_tree.cpython-312-x86_64-linux-gnu.so
624K	./sklearn/tree/_tree.cpython-312-x86_64-linux-gnu.so
608K	./sklearn/metrics/_dist_metrics.cpython-312-x86_64-linux-gnu.so
520K	./sklearn/datasets/_svmlight_format_fast.cpython-312-x86_64-linux-gnu.so
504K	./sklearn/preprocessing/_target_encoder_fast.cpython-312-x86_64-linux-gnu.so
476K	./sklearn/svm/_libsvm.cpython-312-x86_64-linux-gnu.so
448K	./sklearn/svm/_libsvm_sparse.cpython-312-x86_64-linux-gnu.so
448K	./sklearn/metrics/_pairwise_distances_reduction/_middle_term_computer.cpython-312-x86_64-linux-gnu.so
440K	./sklearn/metrics/_pairwise_distances_reduction/_datasets_pair.cpython-312-x86_64-linux-gnu.so
440K	./sklearn/linear_model/_cd_fast.cpython-312-x86_64-linux-gnu.so
404K	./sklearn/cluster/_k_means_elkan.cpython-312-x86_64-linux-gnu.so
396K	./sklearn/utils/_cython_blas.cpython-312-x86_64-linux-gnu.so
396K	./sklearn/cluster/_k_means_common.cpython-312-x86_64-linux-gnu.so
384K	./sklearn/preprocessing/_csr_polynomial_expansion.cpython-312-x86_64-linux-gnu.so
352K	./sklearn/metrics/_pairwise_distances_reduction/_radius_neighbors.cpython-312-x86_64-linux-gnu.so
340K	./sklearn/tree/_splitter.cpython-312-x86_64-linux-gnu.so
340K	./sklearn/cluster/_hdbscan/_tree.cpython-312-x86_64-linux-gnu.so
324K	./sklearn/metrics/_pairwise_distances_reduction/_argkmin.cpython-312-x86_64-linux-gnu.so
324K	./sklearn/linear_model/_sgd_fast.cpython-312-x86_64-linux-gnu.so
312K	./sklearn/tree/_criterion.cpython-312-x86_64-linux-gnu.so
312K	./sklearn/cluster/_k_means_lloyd.cpython-312-x86_64-linux-gnu.so
308K	./sklearn/ensemble/_hist_gradient_boosting/splitting.cpython-312-x86_64-linux-gnu.so
308K	./sklearn/cluster/_hdbscan/_reachability.cpython-312-x86_64-linux-gnu.so
304K	./sklearn/cluster/_hierarchical_fast.cpython-312-x86_64-linux-gnu.so
292K	./sklearn/metrics/_pairwise_distances_reduction/_base.cpython-312-x86_64-linux-gnu.so
280K	./sklearn/linear_model/_sag_fast.cpython-312-x86_64-linux-gnu.so
276K	./sklearn/ensemble/_hist_gradient_boosting/histogram.cpython-312-x86_64-linux-gnu.so
272K	./sklearn/svm/_liblinear.cpython-312-x86_64-linux-gnu.so
268K	./sklearn/utils/_seq_dataset.cpython-312-x86_64-linux-gnu.so
264K	./sklearn/neighbors/_quad_tree.cpython-312-x86_64-linux-gnu.so
260K	./sklearn/metrics/_pairwise_distances_reduction/_radius_neighbors_classmode.cpython-312-x86_64-linux-gnu.so
256K	./sklearn/_isotonic.cpython-312-x86_64-linux-gnu.so
252K	./sklearn/cluster/_k_means_minibatch.cpython-312-x86_64-linux-gnu.so
248K	./sklearn/utils/_fast_dict.cpython-312-x86_64-linux-gnu.so
248K	./sklearn/tree/_utils.cpython-312-x86_64-linux-gnu.so
248K	./sklearn/metrics/_pairwise_fast.cpython-312-x86_64-linux-gnu.so
244K	./sklearn/decomposition/_online_lda_fast.cpython-312-x86_64-linux-gnu.so
240K	./sklearn/metrics/_pairwise_distances_reduction/_argkmin_classmode.cpython-312-x86_64-linux-gnu.so
232K	./sklearn/utils/_typedefs.cpython-312-x86_64-linux-gnu.so
232K	./sklearn/utils/_isfinite.cpython-312-x86_64-linux-gnu.so
220K	./sklearn/utils/arrayfuncs.cpython-312-x86_64-linux-gnu.so
220K	./sklearn/ensemble/_gradient_boosting.cpython-312-x86_64-linux-gnu.so
216K	./sklearn/ensemble/_hist_gradient_boosting/utils.cpython-312-x86_64-linux-gnu.so
212K	./sklearn/utils/_random.cpython-312-x86_64-linux-gnu.so
212K	./sklearn/utils/murmurhash.cpython-312-x86_64-linux-gnu.so
212K	./sklearn/ensemble/_hist_gradient_boosting/_predictor.cpython-312-x86_64-linux-gnu.so
212K	./sklearn/decomposition/_cdnmf_fast.cpython-312-x86_64-linux-gnu.so
212K	./sklearn/cluster/_hdbscan/_linkage.cpython-312-x86_64-linux-gnu.so
204K	./sklearn/metrics/cluster/_expected_mutual_info_fast.cpython-312-x86_64-linux-gnu.so
204K	./sklearn/manifold/_barnes_hut_tsne.cpython-312-x86_64-linux-gnu.so
192K	./sklearn/utils/_weight_vector.cpython-312-x86_64-linux-gnu.so
184K	./sklearn/manifold/_utils.cpython-312-x86_64-linux-gnu.so
184K	./sklearn/ensemble/_hist_gradient_boosting/_gradient_boosting.cpython-312-x86_64-linux-gnu.so
184K	./sklearn/cluster/_dbscan_inner.cpython-312-x86_64-linux-gnu.so
180K	./sklearn/ensemble/_hist_gradient_boosting/_bitset.cpython-312-x86_64-linux-gnu.so
180K	./sklearn/ensemble/_hist_gradient_boosting/_binning.cpython-312-x86_64-linux-gnu.so
128K	./sklearn/utils/_vector_sentinel.cpython-312-x86_64-linux-gnu.so
112K	./sklearn/ensemble/_hist_gradient_boosting/common.cpython-312-x86_64-linux-gnu.so
80K	    ./sklearn/feature_extraction/_hashing_fast.cpython-312-x86_64-linux-gnu.so
48K	    ./sklearn/utils/_openmp_helpers.cpython-312-x86_64-linux-gnu.so
32K	    ./sklearn/svm/_newrand.cpython-312-x86_64-linux-gnu.so
28K	    ./sklearn/utils/_sorting.cpython-312-x86_64-linux-gnu.so
28K	    ./sklearn/neighbors/_partition_nodes.cpython-312-x86_64-linux-gnu.so
24K	    ./sklearn/utils/_heap.cpython-312-x86_64-linux-gnu.so
24K	    ./sklearn/__check_build/_check_build.cpython-312-x86_64-linux-gnu.so
```

</details>

### Possible solutions

#### Strip all symbols and optimize for size

This can be done by adding `-Wl,--strip-all` to `extra_link_args` and `-Os -g0` to `extra_compile_args`.

In practice, it can significantly shrink shared object (up to nearly 50% size reduction):

<details>

<summary>Extensions' shared object sizes on Linux after striping all symbols and optimizing for size</summary>

```
find . -name \*.so -exec du -h {} \; | sort -h --reverse
```

```
1,2M	sklearn/_loss/_loss.cpython-312-x86_64-linux-gnu.so
560K	sklearn/tree/_tree.cpython-312-x86_64-linux-gnu.so
468K	sklearn/neighbors/_kd_tree.cpython-312-x86_64-linux-gnu.so
468K	sklearn/neighbors/_ball_tree.cpython-312-x86_64-linux-gnu.so
460K	sklearn/utils/sparsefuncs_fast.cpython-312-x86_64-linux-gnu.so
460K	sklearn/metrics/_dist_metrics.cpython-312-x86_64-linux-gnu.so
380K	sklearn/datasets/_svmlight_format_fast.cpython-312-x86_64-linux-gnu.so
376K	sklearn/svm/_libsvm.cpython-312-x86_64-linux-gnu.so
352K	sklearn/svm/_libsvm_sparse.cpython-312-x86_64-linux-gnu.so
336K	sklearn/tree/_splitter.cpython-312-x86_64-linux-gnu.so
320K	sklearn/preprocessing/_target_encoder_fast.cpython-312-x86_64-linux-gnu.so
320K	sklearn/metrics/_pairwise_distances_reduction/_middle_term_computer.cpython-312-x86_64-linux-gnu.so
316K	sklearn/metrics/_pairwise_distances_reduction/_datasets_pair.cpython-312-x86_64-linux-gnu.so
312K	sklearn/utils/_cython_blas.cpython-312-x86_64-linux-gnu.so
308K	sklearn/linear_model/_cd_fast.cpython-312-x86_64-linux-gnu.so
300K	sklearn/tree/_criterion.cpython-312-x86_64-linux-gnu.so
280K	sklearn/preprocessing/_csr_polynomial_expansion.cpython-312-x86_64-linux-gnu.so
280K	sklearn/metrics/_pairwise_distances_reduction/_radius_neighbors.cpython-312-x86_64-linux-gnu.so
280K	sklearn/cluster/_k_means_elkan.cpython-312-x86_64-linux-gnu.so
276K	sklearn/cluster/_k_means_common.cpython-312-x86_64-linux-gnu.so
252K	sklearn/linear_model/_sgd_fast.cpython-312-x86_64-linux-gnu.so
248K	sklearn/cluster/_hdbscan/_tree.cpython-312-x86_64-linux-gnu.so
244K	sklearn/metrics/_pairwise_distances_reduction/_argkmin.cpython-312-x86_64-linux-gnu.so
240K	sklearn/tree/_utils.cpython-312-x86_64-linux-gnu.so
240K	sklearn/ensemble/_hist_gradient_boosting/splitting.cpython-312-x86_64-linux-gnu.so
236K	sklearn/cluster/_hierarchical_fast.cpython-312-x86_64-linux-gnu.so
236K	sklearn/cluster/_hdbscan/_reachability.cpython-312-x86_64-linux-gnu.so
232K	sklearn/svm/_liblinear.cpython-312-x86_64-linux-gnu.so
228K	sklearn/cluster/_k_means_lloyd.cpython-312-x86_64-linux-gnu.so
224K	sklearn/metrics/_pairwise_distances_reduction/_base.cpython-312-x86_64-linux-gnu.so
212K	sklearn/neighbors/_quad_tree.cpython-312-x86_64-linux-gnu.so
208K	sklearn/linear_model/_sag_fast.cpython-312-x86_64-linux-gnu.so
204K	sklearn/ensemble/_hist_gradient_boosting/histogram.cpython-312-x86_64-linux-gnu.so
200K	sklearn/utils/_seq_dataset.cpython-312-x86_64-linux-gnu.so
196K	sklearn/utils/_fast_dict.cpython-312-x86_64-linux-gnu.so
196K	sklearn/metrics/_pairwise_distances_reduction/_radius_neighbors_classmode.cpython-312-x86_64-linux-gnu.so
196K	sklearn/_isotonic.cpython-312-x86_64-linux-gnu.so
196K	sklearn/decomposition/_online_lda_fast.cpython-312-x86_64-linux-gnu.so
196K	sklearn/cluster/_k_means_minibatch.cpython-312-x86_64-linux-gnu.so
192K	sklearn/utils/_isfinite.cpython-312-x86_64-linux-gnu.so
192K	sklearn/metrics/_pairwise_fast.cpython-312-x86_64-linux-gnu.so
192K	sklearn/metrics/_pairwise_distances_reduction/_argkmin_classmode.cpython-312-x86_64-linux-gnu.so
184K	sklearn/utils/_typedefs.cpython-312-x86_64-linux-gnu.so
180K	sklearn/utils/arrayfuncs.cpython-312-x86_64-linux-gnu.so
180K	sklearn/ensemble/_hist_gradient_boosting/utils.cpython-312-x86_64-linux-gnu.so
180K	sklearn/ensemble/_gradient_boosting.cpython-312-x86_64-linux-gnu.so
172K	sklearn/utils/_random.cpython-312-x86_64-linux-gnu.so
168K	sklearn/utils/murmurhash.cpython-312-x86_64-linux-gnu.so
168K	sklearn/ensemble/_hist_gradient_boosting/_predictor.cpython-312-x86_64-linux-gnu.so
168K	sklearn/decomposition/_cdnmf_fast.cpython-312-x86_64-linux-gnu.so
168K	sklearn/cluster/_hdbscan/_linkage.cpython-312-x86_64-linux-gnu.so
160K	sklearn/metrics/cluster/_expected_mutual_info_fast.cpython-312-x86_64-linux-gnu.so
160K	sklearn/manifold/_barnes_hut_tsne.cpython-312-x86_64-linux-gnu.so
152K	sklearn/utils/_weight_vector.cpython-312-x86_64-linux-gnu.so
152K	sklearn/manifold/_utils.cpython-312-x86_64-linux-gnu.so
152K	sklearn/ensemble/_hist_gradient_boosting/_gradient_boosting.cpython-312-x86_64-linux-gnu.so
152K	sklearn/cluster/_dbscan_inner.cpython-312-x86_64-linux-gnu.so
148K	sklearn/ensemble/_hist_gradient_boosting/_bitset.cpython-312-x86_64-linux-gnu.so
144K	sklearn/ensemble/_hist_gradient_boosting/_binning.cpython-312-x86_64-linux-gnu.so
112K	sklearn/utils/_vector_sentinel.cpython-312-x86_64-linux-gnu.so
96K	sklearn/ensemble/_hist_gradient_boosting/common.cpython-312-x86_64-linux-gnu.so
68K	sklearn/feature_extraction/_hashing_fast.cpython-312-x86_64-linux-gnu.so
44K	sklearn/utils/_openmp_helpers.cpython-312-x86_64-linux-gnu.so
32K	sklearn/svm/_newrand.cpython-312-x86_64-linux-gnu.so
28K	sklearn/utils/_sorting.cpython-312-x86_64-linux-gnu.so
28K	sklearn/neighbors/_partition_nodes.cpython-312-x86_64-linux-gnu.so
24K	sklearn/utils/_heap.cpython-312-x86_64-linux-gnu.so
24K	sklearn/__check_build/_check_build.cpython-312-x86_64-linux-gnu.so
```
</details>

#### Group several translation units within C extensions (and use interprocedural optimization)

So as to reuse duplicated symbols in shared objects and perform optimization over several translation units (such as inlining functions, etc.)

COMMENT:
> However it's still rather large with likely some duplicate objects between .so (aside from the exported symbols).

Inter-procedural optimizations (such as link-time optimization) might help reducing the size of shared objects since it generally remove objects' duplication in between translation unit for each shared object.

Ideally, objects' duplication must not be present across shared objects. Resolving https://github.com/cython/cython/issues/2356 seems relevant in this regard, but I do not know of other mitigations.

I am afraid I do not have time to have a look at this issue right now. I'll try to see if I can explore solutions soon.

Labels: Build / CI, cython, C/C++