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  1. .gitattributes +37 -1
  2. flax_model/alphafold3/_data/libcifpp/components.cif +3 -0
  3. flax_model/alphafold3/_tools/hmmer/bin/alimask +3 -0
  4. flax_model/alphafold3/_tools/hmmer/bin/easel +3 -0
  5. flax_model/alphafold3/_tools/hmmer/bin/esl-afetch +3 -0
  6. flax_model/alphafold3/_tools/hmmer/bin/esl-alimanip +3 -0
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  8. flax_model/alphafold3/_tools/hmmer/bin/esl-alimask +3 -0
  9. flax_model/alphafold3/_tools/hmmer/bin/esl-alimerge +3 -0
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  11. flax_model/alphafold3/_tools/hmmer/bin/esl-alirev +3 -0
  12. flax_model/alphafold3/_tools/hmmer/bin/esl-alistat +3 -0
  13. flax_model/alphafold3/_tools/hmmer/bin/esl-compalign +3 -0
  14. flax_model/alphafold3/_tools/hmmer/bin/esl-compstruct +3 -0
  15. flax_model/alphafold3/_tools/hmmer/bin/esl-construct +3 -0
  16. flax_model/alphafold3/_tools/hmmer/bin/esl-histplot +3 -0
  17. flax_model/alphafold3/_tools/hmmer/bin/esl-mask +3 -0
  18. flax_model/alphafold3/_tools/hmmer/bin/esl-mixdchlet +3 -0
  19. flax_model/alphafold3/_tools/hmmer/bin/esl-reformat +3 -0
  20. flax_model/alphafold3/_tools/hmmer/bin/esl-seqrange +3 -0
  21. flax_model/alphafold3/_tools/hmmer/bin/esl-seqstat +3 -0
  22. flax_model/alphafold3/_tools/hmmer/bin/esl-sfetch +3 -0
  23. flax_model/alphafold3/_tools/hmmer/bin/esl-shuffle +3 -0
  24. flax_model/alphafold3/_tools/hmmer/bin/esl-ssdraw +3 -0
  25. flax_model/alphafold3/_tools/hmmer/bin/esl-translate +3 -0
  26. flax_model/alphafold3/_tools/hmmer/bin/esl-weight +3 -0
  27. flax_model/alphafold3/_tools/hmmer/bin/hmmalign +3 -0
  28. flax_model/alphafold3/_tools/hmmer/bin/hmmbuild +3 -0
  29. flax_model/alphafold3/_tools/hmmer/bin/hmmconvert +3 -0
  30. flax_model/alphafold3/_tools/hmmer/bin/hmmemit +3 -0
  31. flax_model/alphafold3/_tools/hmmer/bin/hmmfetch +3 -0
  32. flax_model/alphafold3/_tools/hmmer/bin/hmmlogo +3 -0
  33. flax_model/alphafold3/_tools/hmmer/bin/hmmpgmd +3 -0
  34. flax_model/alphafold3/_tools/hmmer/bin/hmmpgmd_shard +3 -0
  35. flax_model/alphafold3/_tools/hmmer/bin/hmmpress +3 -0
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  37. flax_model/alphafold3/_tools/hmmer/bin/hmmsearch +3 -0
  38. flax_model/alphafold3/_tools/hmmer/bin/hmmsim +3 -0
  39. flax_model/alphafold3/_tools/hmmer/bin/hmmstat +3 -0
  40. flax_model/alphafold3/_tools/hmmer/bin/jackhmmer +3 -0
  41. flax_model/alphafold3/_tools/hmmer/bin/makehmmerdb +3 -0
  42. flax_model/alphafold3/_tools/hmmer/bin/nhmmer +3 -0
  43. flax_model/alphafold3/_tools/hmmer/bin/nhmmscan +3 -0
  44. flax_model/alphafold3/_tools/hmmer/bin/phmmer +3 -0
  45. flax_model/alphafold3/constants/converters/ccd.pickle +3 -0
  46. flax_model/alphafold3/constants/converters/chemical_component_sets.pickle +3 -0
  47. flax_model/alphafold3/cpp.cpython-311-x86_64-linux-gnu.so +3 -0
  48. weight/_dep/Catch2.tar +3 -0
  49. weight/_dep/Catch2/docs/opensource-users.md +126 -0
  50. weight/_dep/Catch2/include/internal/benchmark/catch_benchmark.hpp +122 -0
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1
+ <a id="top"></a>
2
+ # Open Source projects using Catch
3
+
4
+ Catch is great for open source. With its [liberal license](../LICENSE.txt) and single-header, dependency-free, distribution
5
+ it's easy to just drop the header into your project and start writing tests - what's not to like?
6
+
7
+ As a result Catch is now being used in many Open Source projects, including some quite well known ones.
8
+ This page is an attempt to track those projects. Obviously it can never be complete.
9
+ This effort largely relies on the maintainers of the projects themselves updating this page and submitting a PR
10
+ (or, if you prefer contact one of the maintainers of Catch directly, use the
11
+ [forums](https://groups.google.com/forum/?fromgroups#!forum/catch-forum)), or raise an [issue](https://github.com/philsquared/Catch/issues) to let us know).
12
+ Of course users of those projects might want to update this page too. That's fine - as long you're confident the project maintainers won't mind.
13
+ If you're an Open Source project maintainer and see your project listed here but would rather it wasn't -
14
+ just let us know via any of the previously mentioned means - although I'm sure there won't be many who feel that way.
15
+
16
+ Listing a project here does not imply endorsement and the plan is to keep these ordered alphabetically to avoid an implication of relative importance.
17
+
18
+ ## Libraries & Frameworks
19
+
20
+ ### [ApprovalTests.cpp](https://github.com/approvals/ApprovalTests.cpp)
21
+ C++11 implementation of Approval Tests, for quick, convenient testing of legacy code.
22
+
23
+ ### [args](https://github.com/Taywee/args)
24
+ A simple header-only C++ argument parser library.
25
+
26
+ ### [Azmq](https://github.com/zeromq/azmq)
27
+ Boost Asio style bindings for ZeroMQ.
28
+
29
+ ### [Cataclysm: Dark Days Ahead](https://github.com/CleverRaven/Cataclysm-DDA)
30
+ Post-apocalyptic survival RPG.
31
+
32
+ ### [ChaiScript](https://github.com/ChaiScript/ChaiScript)
33
+ A, header-only, embedded scripting language designed from the ground up to directly target C++ and take advantage of modern C++ development techniques.
34
+
35
+ ### [ChakraCore](https://github.com/Microsoft/ChakraCore)
36
+ The core part of the Chakra JavaScript engine that powers Microsoft Edge.
37
+
38
+ ### [Clara](https://github.com/philsquared/Clara)
39
+ A, single-header-only, type-safe, command line parser - which also prints formatted usage strings.
40
+
41
+ ### [Couchbase-lite-core](https://github.com/couchbase/couchbase-lite-core)
42
+ The next-generation core storage and query engine for Couchbase Lite.
43
+
44
+ ### [cppcodec](https://github.com/tplgy/cppcodec)
45
+ Header-only C++11 library to encode/decode base64, base64url, base32, base32hex and hex (a.k.a. base16) as specified in RFC 4648, plus Crockford's base32.
46
+
47
+ ### [DtCraft](https://github.com/twhuang-uiuc/DtCraft)
48
+ A High-performance Cluster Computing Engine.
49
+
50
+ ### [forest](https://github.com/xorz57/forest)
51
+ Template Library of Tree Data Structures.
52
+
53
+ ### [Fuxedo](https://github.com/fuxedo/fuxedo)
54
+ Open source Oracle Tuxedo-like XATMI middleware for C and C++.
55
+
56
+ ### [Inja](https://github.com/pantor/inja)
57
+ A header-only template engine for modern C++.
58
+
59
+ ### [libcluon](https://github.com/chrberger/libcluon)
60
+ A single-header-only library written in C++14 to glue distributed software components (UDP, TCP, shared memory) supporting natively Protobuf, LCM/ZCM, MsgPack, and JSON for dynamic message transformations in-between.
61
+
62
+ ### [MNMLSTC Core](https://github.com/mnmlstc/core)
63
+ A small and easy to use C++11 library that adds a functionality set that will be available in C++14 and later, as well as some useful additions.
64
+
65
+ ### [nanodbc](https://github.com/lexicalunit/nanodbc/)
66
+ A small C++ library wrapper for the native C ODBC API.
67
+
68
+ ### [Nonius](https://github.com/libnonius/nonius)
69
+ A header-only framework for benchmarking small snippets of C++ code.
70
+
71
+ ### [polymorphic_value](https://github.com/jbcoe/polymorphic_value)
72
+ A polymorphic value-type for C++.
73
+
74
+ ### [Ppconsul](https://github.com/oliora/ppconsul)
75
+ A C++ client library for Consul. Consul is a distributed tool for discovering and configuring services in your infrastructure.
76
+
77
+ ### [Reactive-Extensions/ RxCpp](https://github.com/Reactive-Extensions/RxCpp)
78
+ A library of algorithms for values-distributed-in-time.
79
+
80
+ ### [SOCI](https://github.com/SOCI/soci)
81
+ The C++ Database Access Library.
82
+
83
+ ### [TextFlowCpp](https://github.com/philsquared/textflowcpp)
84
+ A small, single-header-only, library for wrapping and composing columns of text.
85
+
86
+ ### [thor](https://github.com/xorz57/thor)
87
+ Wrapper Library for CUDA.
88
+
89
+ ### [toml++](https://github.com/marzer/tomlplusplus)
90
+ A header-only TOML parser and serializer for modern C++.
91
+
92
+ ### [Trompeloeil](https://github.com/rollbear/trompeloeil)
93
+ A thread-safe header-only mocking framework for C++14.
94
+
95
+ ## Applications & Tools
96
+
97
+ ### [App Mesh](https://github.com/laoshanxi/app-mesh)
98
+ A high available cloud native micro-service application management platform implemented by modern C++.
99
+
100
+ ### [ArangoDB](https://github.com/arangodb/arangodb)
101
+ ArangoDB is a native multi-model database with flexible data models for documents, graphs, and key-values.
102
+
103
+ ### [Giada - Your Hardcore Loop Machine](https://github.com/monocasual/giada)
104
+ Minimal, open-source and cross-platform audio tool for live music production.
105
+
106
+ ### [MAME](https://github.com/mamedev/mame)
107
+ MAME originally stood for Multiple Arcade Machine Emulator.
108
+
109
+ ### [Newsbeuter](https://github.com/akrennmair/newsbeuter)
110
+ Newsbeuter is an open-source RSS/Atom feed reader for text terminals.
111
+
112
+ ### [PopHead](https://github.com/SPC-Some-Polish-Coders/PopHead)
113
+ A 2D, Zombie, RPG game which is being made on our own engine.
114
+
115
+ ### [raspigcd](https://github.com/pantadeusz/raspigcd)
116
+ Low level CLI app and library for execution of GCODE on Raspberry Pi without any additional microcontrolers (just RPi + Stepsticks).
117
+
118
+ ### [SpECTRE](https://github.com/sxs-collaboration/spectre)
119
+ SpECTRE is a code for multi-scale, multi-physics problems in astrophysics and gravitational physics.
120
+
121
+ ### [Standardese](https://github.com/foonathan/standardese)
122
+ Standardese aims to be a nextgen Doxygen.
123
+
124
+ ---
125
+
126
+ [Home](Readme.md#top)
weight/_dep/Catch2/include/internal/benchmark/catch_benchmark.hpp ADDED
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1
+ /*
2
+ * Created by Joachim on 16/04/2019.
3
+ * Adapted from donated nonius code.
4
+ *
5
+ * Distributed under the Boost Software License, Version 1.0. (See accompanying
6
+ * file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
7
+ */
8
+
9
+ // Benchmark
10
+ #ifndef TWOBLUECUBES_CATCH_BENCHMARK_HPP_INCLUDED
11
+ #define TWOBLUECUBES_CATCH_BENCHMARK_HPP_INCLUDED
12
+
13
+ #include "../catch_config.hpp"
14
+ #include "../catch_context.h"
15
+ #include "../catch_interfaces_reporter.h"
16
+ #include "../catch_test_registry.h"
17
+
18
+ #include "catch_chronometer.hpp"
19
+ #include "catch_clock.hpp"
20
+ #include "catch_environment.hpp"
21
+ #include "catch_execution_plan.hpp"
22
+ #include "detail/catch_estimate_clock.hpp"
23
+ #include "detail/catch_complete_invoke.hpp"
24
+ #include "detail/catch_analyse.hpp"
25
+ #include "detail/catch_benchmark_function.hpp"
26
+ #include "detail/catch_run_for_at_least.hpp"
27
+
28
+ #include <algorithm>
29
+ #include <functional>
30
+ #include <string>
31
+ #include <vector>
32
+ #include <cmath>
33
+
34
+ namespace Catch {
35
+ namespace Benchmark {
36
+ struct Benchmark {
37
+ Benchmark(std::string &&name)
38
+ : name(std::move(name)) {}
39
+
40
+ template <class FUN>
41
+ Benchmark(std::string &&name, FUN &&func)
42
+ : fun(std::move(func)), name(std::move(name)) {}
43
+
44
+ template <typename Clock>
45
+ ExecutionPlan<FloatDuration<Clock>> prepare(const IConfig &cfg, Environment<FloatDuration<Clock>> env) const {
46
+ auto min_time = env.clock_resolution.mean * Detail::minimum_ticks;
47
+ auto run_time = std::max(min_time, std::chrono::duration_cast<decltype(min_time)>(cfg.benchmarkWarmupTime()));
48
+ auto&& test = Detail::run_for_at_least<Clock>(std::chrono::duration_cast<ClockDuration<Clock>>(run_time), 1, fun);
49
+ int new_iters = static_cast<int>(std::ceil(min_time * test.iterations / test.elapsed));
50
+ return { new_iters, test.elapsed / test.iterations * new_iters * cfg.benchmarkSamples(), fun, std::chrono::duration_cast<FloatDuration<Clock>>(cfg.benchmarkWarmupTime()), Detail::warmup_iterations };
51
+ }
52
+
53
+ template <typename Clock = default_clock>
54
+ void run() {
55
+ IConfigPtr cfg = getCurrentContext().getConfig();
56
+
57
+ auto env = Detail::measure_environment<Clock>();
58
+
59
+ getResultCapture().benchmarkPreparing(name);
60
+ CATCH_TRY{
61
+ auto plan = user_code([&] {
62
+ return prepare<Clock>(*cfg, env);
63
+ });
64
+
65
+ BenchmarkInfo info {
66
+ name,
67
+ plan.estimated_duration.count(),
68
+ plan.iterations_per_sample,
69
+ cfg->benchmarkSamples(),
70
+ cfg->benchmarkResamples(),
71
+ env.clock_resolution.mean.count(),
72
+ env.clock_cost.mean.count()
73
+ };
74
+
75
+ getResultCapture().benchmarkStarting(info);
76
+
77
+ auto samples = user_code([&] {
78
+ return plan.template run<Clock>(*cfg, env);
79
+ });
80
+
81
+ auto analysis = Detail::analyse(*cfg, env, samples.begin(), samples.end());
82
+ BenchmarkStats<FloatDuration<Clock>> stats{ info, analysis.samples, analysis.mean, analysis.standard_deviation, analysis.outliers, analysis.outlier_variance };
83
+ getResultCapture().benchmarkEnded(stats);
84
+
85
+ } CATCH_CATCH_ALL{
86
+ if (translateActiveException() != Detail::benchmarkErrorMsg) // benchmark errors have been reported, otherwise rethrow.
87
+ std::rethrow_exception(std::current_exception());
88
+ }
89
+ }
90
+
91
+ // sets lambda to be used in fun *and* executes benchmark!
92
+ template <typename Fun,
93
+ typename std::enable_if<!Detail::is_related<Fun, Benchmark>::value, int>::type = 0>
94
+ Benchmark & operator=(Fun func) {
95
+ fun = Detail::BenchmarkFunction(func);
96
+ run();
97
+ return *this;
98
+ }
99
+
100
+ explicit operator bool() {
101
+ return true;
102
+ }
103
+
104
+ private:
105
+ Detail::BenchmarkFunction fun;
106
+ std::string name;
107
+ };
108
+ }
109
+ } // namespace Catch
110
+
111
+ #define INTERNAL_CATCH_GET_1_ARG(arg1, arg2, ...) arg1
112
+ #define INTERNAL_CATCH_GET_2_ARG(arg1, arg2, ...) arg2
113
+
114
+ #define INTERNAL_CATCH_BENCHMARK(BenchmarkName, name, benchmarkIndex)\
115
+ if( Catch::Benchmark::Benchmark BenchmarkName{name} ) \
116
+ BenchmarkName = [&](int benchmarkIndex)
117
+
118
+ #define INTERNAL_CATCH_BENCHMARK_ADVANCED(BenchmarkName, name)\
119
+ if( Catch::Benchmark::Benchmark BenchmarkName{name} ) \
120
+ BenchmarkName = [&]
121
+
122
+ #endif // TWOBLUECUBES_CATCH_BENCHMARK_HPP_INCLUDED