[med-svn] [Git][med-team/iitii][master] Respect https://lists.debian.org/debian-med/2020/06/msg00065.html - but this...
Andreas Tille
gitlab at salsa.debian.org
Tue Jun 9 13:45:33 BST 2020
Andreas Tille pushed to branch master at Debian Med / iitii
Commits:
f6815e30 by Andreas Tille at 2020-06-09T12:02:51+02:00
Respect https://lists.debian.org/debian-med/2020/06/msg00065.html - but this does not lead to a successful compilation
- - - - -
7 changed files:
- debian/control
- + debian/missing-sources/ctpl/LICENSE
- + debian/missing-sources/ctpl/ctpl_stl.h
- + debian/missing-sources/ctpl/get
- + debian/missing-sources/htslib/README
- debian/patches/use_debian_packages_libs_in_test.patch
- debian/rules
Changes:
=====================================
debian/control
=====================================
@@ -12,7 +12,7 @@ Build-Depends: debhelper-compat (= 13),
catch2 <!nocheck>,
pkg-config <!nocheck>,
libhts-dev <!nocheck>,
- libctpl-dev <!nocheck>
+ libglib2.0-dev <!nocheck>
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/iitii
Vcs-Git: https://salsa.debian.org/med-team/iitii.git
=====================================
debian/missing-sources/ctpl/LICENSE
=====================================
@@ -0,0 +1,191 @@
+Apache License
+ Version 2.0, January 2004
+ http://www.apache.org/licenses/
+
+ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
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+ 5. Submission of Contributions. Unless You explicitly state otherwise,
+ any Contribution intentionally submitted for inclusion in the Work
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+ 7. Disclaimer of Warranty. Unless required by applicable law or
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+ 8. Limitation of Liability. In no event and under no legal theory,
+ whether in tort (including negligence), contract, or otherwise,
+ unless required by applicable law (such as deliberate and grossly
+ negligent acts) or agreed to in writing, shall any Contributor be
+ liable to You for damages, including any direct, indirect, special,
+ incidental, or consequential damages of any character arising as a
+ result of this License or out of the use or inability to use the
+ Work (including but not limited to damages for loss of goodwill,
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+ 9. Accepting Warranty or Additional Liability. While redistributing
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+ END OF TERMS AND CONDITIONS
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+
+ Copyright (C) 2014 by Vitaliy Vitsentiy
+
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
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+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
=====================================
debian/missing-sources/ctpl/ctpl_stl.h
=====================================
@@ -0,0 +1,251 @@
+/*********************************************************
+*
+* Copyright (C) 2014 by Vitaliy Vitsentiy
+*
+* Licensed under the Apache License, Version 2.0 (the "License");
+* you may not use this file except in compliance with the License.
+* You may obtain a copy of the License at
+*
+* http://www.apache.org/licenses/LICENSE-2.0
+*
+* Unless required by applicable law or agreed to in writing, software
+* distributed under the License is distributed on an "AS IS" BASIS,
+* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+* See the License for the specific language governing permissions and
+* limitations under the License.
+*
+*********************************************************/
+
+
+#ifndef __ctpl_stl_thread_pool_H__
+#define __ctpl_stl_thread_pool_H__
+
+#include <functional>
+#include <thread>
+#include <atomic>
+#include <vector>
+#include <memory>
+#include <exception>
+#include <future>
+#include <mutex>
+#include <queue>
+
+
+
+// thread pool to run user's functors with signature
+// ret func(int id, other_params)
+// where id is the index of the thread that runs the functor
+// ret is some return type
+
+
+namespace ctpl {
+
+ namespace detail {
+ template <typename T>
+ class Queue {
+ public:
+ bool push(T const & value) {
+ std::unique_lock<std::mutex> lock(this->mutex);
+ this->q.push(value);
+ return true;
+ }
+ // deletes the retrieved element, do not use for non integral types
+ bool pop(T & v) {
+ std::unique_lock<std::mutex> lock(this->mutex);
+ if (this->q.empty())
+ return false;
+ v = this->q.front();
+ this->q.pop();
+ return true;
+ }
+ bool empty() {
+ std::unique_lock<std::mutex> lock(this->mutex);
+ return this->q.empty();
+ }
+ private:
+ std::queue<T> q;
+ std::mutex mutex;
+ };
+ }
+
+ class thread_pool {
+
+ public:
+
+ thread_pool() { this->init(); }
+ thread_pool(int nThreads) { this->init(); this->resize(nThreads); }
+
+ // the destructor waits for all the functions in the queue to be finished
+ ~thread_pool() {
+ this->stop(true);
+ }
+
+ // get the number of running threads in the pool
+ int size() { return static_cast<int>(this->threads.size()); }
+
+ // number of idle threads
+ int n_idle() { return this->nWaiting; }
+ std::thread & get_thread(int i) { return *this->threads[i]; }
+
+ // change the number of threads in the pool
+ // should be called from one thread, otherwise be careful to not interleave, also with this->stop()
+ // nThreads must be >= 0
+ void resize(int nThreads) {
+ if (!this->isStop && !this->isDone) {
+ int oldNThreads = static_cast<int>(this->threads.size());
+ if (oldNThreads <= nThreads) { // if the number of threads is increased
+ this->threads.resize(nThreads);
+ this->flags.resize(nThreads);
+
+ for (int i = oldNThreads; i < nThreads; ++i) {
+ this->flags[i] = std::make_shared<std::atomic<bool>>(false);
+ this->set_thread(i);
+ }
+ }
+ else { // the number of threads is decreased
+ for (int i = oldNThreads - 1; i >= nThreads; --i) {
+ *this->flags[i] = true; // this thread will finish
+ this->threads[i]->detach();
+ }
+ {
+ // stop the detached threads that were waiting
+ std::unique_lock<std::mutex> lock(this->mutex);
+ this->cv.notify_all();
+ }
+ this->threads.resize(nThreads); // safe to delete because the threads are detached
+ this->flags.resize(nThreads); // safe to delete because the threads have copies of shared_ptr of the flags, not originals
+ }
+ }
+ }
+
+ // empty the queue
+ void clear_queue() {
+ std::function<void(int id)> * _f;
+ while (this->q.pop(_f))
+ delete _f; // empty the queue
+ }
+
+ // pops a functional wrapper to the original function
+ std::function<void(int)> pop() {
+ std::function<void(int id)> * _f = nullptr;
+ this->q.pop(_f);
+ std::unique_ptr<std::function<void(int id)>> func(_f); // at return, delete the function even if an exception occurred
+ std::function<void(int)> f;
+ if (_f)
+ f = *_f;
+ return f;
+ }
+
+ // wait for all computing threads to finish and stop all threads
+ // may be called asynchronously to not pause the calling thread while waiting
+ // if isWait == true, all the functions in the queue are run, otherwise the queue is cleared without running the functions
+ void stop(bool isWait = false) {
+ if (!isWait) {
+ if (this->isStop)
+ return;
+ this->isStop = true;
+ for (int i = 0, n = this->size(); i < n; ++i) {
+ *this->flags[i] = true; // command the threads to stop
+ }
+ this->clear_queue(); // empty the queue
+ }
+ else {
+ if (this->isDone || this->isStop)
+ return;
+ this->isDone = true; // give the waiting threads a command to finish
+ }
+ {
+ std::unique_lock<std::mutex> lock(this->mutex);
+ this->cv.notify_all(); // stop all waiting threads
+ }
+ for (int i = 0; i < static_cast<int>(this->threads.size()); ++i) { // wait for the computing threads to finish
+ if (this->threads[i]->joinable())
+ this->threads[i]->join();
+ }
+ // if there were no threads in the pool but some functors in the queue, the functors are not deleted by the threads
+ // therefore delete them here
+ this->clear_queue();
+ this->threads.clear();
+ this->flags.clear();
+ }
+
+ template<typename F, typename... Rest>
+ auto push(F && f, Rest&&... rest) ->std::future<decltype(f(0, rest...))> {
+ auto pck = std::make_shared<std::packaged_task<decltype(f(0, rest...))(int)>>(
+ std::bind(std::forward<F>(f), std::placeholders::_1, std::forward<Rest>(rest)...)
+ );
+ auto _f = new std::function<void(int id)>([pck](int id) {
+ (*pck)(id);
+ });
+ this->q.push(_f);
+ std::unique_lock<std::mutex> lock(this->mutex);
+ this->cv.notify_one();
+ return pck->get_future();
+ }
+
+ // run the user's function that excepts argument int - id of the running thread. returned value is templatized
+ // operator returns std::future, where the user can get the result and rethrow the catched exceptins
+ template<typename F>
+ auto push(F && f) ->std::future<decltype(f(0))> {
+ auto pck = std::make_shared<std::packaged_task<decltype(f(0))(int)>>(std::forward<F>(f));
+ auto _f = new std::function<void(int id)>([pck](int id) {
+ (*pck)(id);
+ });
+ this->q.push(_f);
+ std::unique_lock<std::mutex> lock(this->mutex);
+ this->cv.notify_one();
+ return pck->get_future();
+ }
+
+
+ private:
+
+ // deleted
+ thread_pool(const thread_pool &);// = delete;
+ thread_pool(thread_pool &&);// = delete;
+ thread_pool & operator=(const thread_pool &);// = delete;
+ thread_pool & operator=(thread_pool &&);// = delete;
+
+ void set_thread(int i) {
+ std::shared_ptr<std::atomic<bool>> flag(this->flags[i]); // a copy of the shared ptr to the flag
+ auto f = [this, i, flag/* a copy of the shared ptr to the flag */]() {
+ std::atomic<bool> & _flag = *flag;
+ std::function<void(int id)> * _f;
+ bool isPop = this->q.pop(_f);
+ while (true) {
+ while (isPop) { // if there is anything in the queue
+ std::unique_ptr<std::function<void(int id)>> func(_f); // at return, delete the function even if an exception occurred
+ (*_f)(i);
+ if (_flag)
+ return; // the thread is wanted to stop, return even if the queue is not empty yet
+ else
+ isPop = this->q.pop(_f);
+ }
+ // the queue is empty here, wait for the next command
+ std::unique_lock<std::mutex> lock(this->mutex);
+ ++this->nWaiting;
+ this->cv.wait(lock, [this, &_f, &isPop, &_flag](){ isPop = this->q.pop(_f); return isPop || this->isDone || _flag; });
+ --this->nWaiting;
+ if (!isPop)
+ return; // if the queue is empty and this->isDone == true or *flag then return
+ }
+ };
+ this->threads[i].reset(new std::thread(f)); // compiler may not support std::make_unique()
+ }
+
+ void init() { this->nWaiting = 0; this->isStop = false; this->isDone = false; }
+
+ std::vector<std::unique_ptr<std::thread>> threads;
+ std::vector<std::shared_ptr<std::atomic<bool>>> flags;
+ detail::Queue<std::function<void(int id)> *> q;
+ std::atomic<bool> isDone;
+ std::atomic<bool> isStop;
+ std::atomic<int> nWaiting; // how many threads are waiting
+
+ std::mutex mutex;
+ std::condition_variable cv;
+ };
+
+}
+
+#endif // __ctpl_stl_thread_pool_H__
=====================================
debian/missing-sources/ctpl/get
=====================================
@@ -0,0 +1,4 @@
+#!/bin/sh
+# see https://lists.debian.org/debian-med/2020/06/msg00065.html
+wget https://raw.githubusercontent.com/vit-vit/CTPL/master/ctpl_stl.h
+wget https://raw.githubusercontent.com/vit-vit/CTPL/master/LICENSE
=====================================
debian/missing-sources/htslib/README
=====================================
@@ -0,0 +1,10 @@
+These header files are part of the private interface of htslib and not
+shipped in the libhts-dev package. The files in this directory are
+a copy of the files found in the source package
+
+ htslib (1.10.2-3) unstable; urgency=medium
+
+Since these are only used for testing but not in the actual program
+it should be OK to simply ship this copy here.
+
+ -- Andreas Tille <tille at debian.org> Fri, 05 Jun 2020 17:53:54 +0200
=====================================
debian/patches/use_debian_packages_libs_in_test.patch
=====================================
@@ -46,14 +46,3 @@ Description: Use Debian packaged libraries also in tests
target_link_libraries(gnomad_benchmark libhts libz.a libbz2.a liblzma.a)
include(CTest)
---- a/test/util.h
-+++ b/test/util.h
-@@ -8,7 +8,7 @@
- #include <assert.h>
- #include "kstring.h"
- #include "tbx.h"
--#include "ctpl_stl.h"
-+#include "ctpl/ctpl.h"
- #include "iitii.h"
-
- using namespace std;
=====================================
debian/rules
=====================================
@@ -16,5 +16,6 @@ CMAKE_EXTRA_FLAGS += -DDEBIAN_BUILD=1
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
cp $(CURDIR)/debian/missing-sources/htslib/* test
+ cp $(CURDIR)/debian/missing-sources/ctpl/*.h test
cd test && cmake . && make
endif
View it on GitLab: https://salsa.debian.org/med-team/iitii/-/commit/f6815e30b606070760ac57b23fb14ba1ed760b3e
--
View it on GitLab: https://salsa.debian.org/med-team/iitii/-/commit/f6815e30b606070760ac57b23fb14ba1ed760b3e
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