[med-svn] [Git][med-team/sina][upstream] New upstream version 1.6.1
Steffen Möller
gitlab at salsa.debian.org
Mon Jun 8 17:54:56 BST 2020
Steffen Möller pushed to branch upstream at Debian Med / sina
Commits:
f4cde295 by Steffen Moeller at 2020-06-08T18:27:39+02:00
New upstream version 1.6.1
- - - - -
10 changed files:
- .bumpversion.cfg
- .travis.yml
- configure.ac
- doc/source/CHANGELOG.rst
- doc/source/install.rst
- src/kmer_search.cpp
- src/progress.h
- src/query_arb.cpp
- src/search_filter.cpp
- src/sina.cpp
Changes:
=====================================
.bumpversion.cfg
=====================================
@@ -1,5 +1,5 @@
[bumpversion]
-current_version = 1.6.0
+current_version = 1.6.1
parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<stage>(dev|rc)))?(\.(?P<again>\d+))?
serialize =
{major}.{minor}.{patch}-{stage}.{again}
=====================================
.travis.yml
=====================================
@@ -19,7 +19,6 @@ install:
- ./ci_scripts/install_conda.sh
- source $BASH_ENV
- conda list
- - find $MINICONDA -name '*.la' -print0 | xargs -0 rm
- export LDFLAGS="$LDFLAGS -Wl,-rpath -Wl,$MINICONDA/lib"
- case "$(uname)" in
Linux) OSNAME=linux;;
=====================================
configure.ac
=====================================
@@ -1,6 +1,6 @@
# Init
-AC_INIT([SINA],[1.6.0],[elmar at pruesse.net],,[http://github.com/epruesse/SINA])
+AC_INIT([SINA],[1.6.1],[elmar at pruesse.net],,[http://github.com/epruesse/SINA])
AC_COPYRIGHT([Copyright (c) 2005-2018 Elmar Pruesse])
AC_CONFIG_AUX_DIR([build-aux])
AC_CONFIG_MACRO_DIR([m4])
=====================================
doc/source/CHANGELOG.rst
=====================================
@@ -3,6 +3,10 @@
Changelog
=========
+Version 1.6.1:
+--------------
+ - fix progress bar not honoring verbosity (:issue:`85`)
+
Version 1.6.0:
--------------
- make internal kmer engine the default (:issue:`23`)
=====================================
doc/source/install.rst
=====================================
@@ -71,16 +71,16 @@ are available on the `SINA releases`_ page at Github. Head on over
there and download the Linux or Macos one. Inside the folder created
by unpacking the archive, you should find a `sina` executable::
- tar xf ~/Downloads/sina-1.6.0-linux.tar.gz
- ~/Downloads/sina-1.6.0-linux/sina --help
+ tar xf ~/Downloads/sina-1.6.1-linux.tar.gz
+ ~/Downloads/sina-1.6.1-linux/sina --help
To install SINA system wide, place the contents of the archive in
`/opt` and create symlinks into `/usr/local/bin`::
- wget https://github.com/epruesse/SINA/releases/download/v1.6.0/sina-1.5.0-linux.tar.gz
- sudo tar xf sina-1.6.0-linux.tar.gz -C /opt
- rm sina-1.6.0-linux.tar.gz
- sudo ln -s /opt/sina-1.6.0-linux /opt/sina
+ wget https://github.com/epruesse/SINA/releases/download/v1.6.1/sina-1.5.0-linux.tar.gz
+ sudo tar xf sina-1.6.1-linux.tar.gz -C /opt
+ rm sina-1.6.1-linux.tar.gz
+ sudo ln -s /opt/sina-1.6.1-linux /opt/sina
sudo ln -s /opt/sina/bin/sina /usr/local/bin/sina
.. _`SINA releases`: https://github.com/epruesse/SINA/releases
=====================================
src/kmer_search.cpp
=====================================
@@ -152,7 +152,7 @@ unsigned int kmer_search::size() const { return pimpl->n_sequences; }
class IndexBuilder {
kmer_search::impl *idx;
- Progress *p;
+ logger_progress *p;
public:
std::vector<vlimap*> kmer_idx;
@@ -205,7 +205,7 @@ public:
{
}
- IndexBuilder(kmer_search::impl *idx_, Progress *p_)
+ IndexBuilder(kmer_search::impl *idx_, logger_progress *p_)
: idx(idx_), p(p_), kmer_idx(idx->n_kmers, nullptr)
{
}
@@ -243,7 +243,7 @@ kmer_search::impl::build() {
sequence_names = arbdb->getSequenceNames();
n_sequences = sequence_names.size();
- Progress p("Building Index", n_sequences);
+ logger_progress p(logger, "Building Index", n_sequences);
IndexBuilder bi(this, &p);
tbb::parallel_reduce(tbb::blocked_range<size_t>(0, n_sequences), bi);
=====================================
src/progress.h
=====================================
@@ -51,6 +51,8 @@ static const char* bar_syms_ascii[] = {
};
+/* abstract base rendering progress bar
+ * needs show_progress() filled in */
class base_progress {
public:
using clock_t = std::chrono::steady_clock;
@@ -63,9 +65,7 @@ public:
_bar_syms(ascii?bar_syms_ascii:bar_syms_unicode),
_nsyms(ascii?std::extent<decltype(bar_syms_ascii)>::value
:std::extent<decltype(bar_syms_unicode)>::value)
- {
- //show_progress();
- }
+ {}
void restart(std::string desc="", unsigned int total=0) {
_n = 0;
@@ -204,6 +204,7 @@ private:
const std::string nototal_fmt = "{desc}: {n} [{elapsed:%T}]{eol}";
};
+/* Progress monitor writing directly to a file */
class Progress final : public base_progress {
public:
Progress(std::string desc="", unsigned int total=0, bool ascii=false,
@@ -227,6 +228,8 @@ public:
}
void show_progress(timepoint_t now=clock_t::now()) override final {
+ // called from base_progress when it decided the progress bar needs
+ // to be printed again
fmt::memory_buffer buf;
render_progress(now, _width, buf);
std::copy(term_move_up.begin(), term_move_up.end(), std::back_inserter(buf));
@@ -239,63 +242,72 @@ private:
FILE* _file;
};
-class status_msg;
+/****** spdlog integration ****/
+
+class status_line;
-class status_msg_sink {
+class status_line_registry {
public:
- virtual ~status_msg_sink() {}
+ virtual ~status_line_registry() {}
- void add_status(status_msg *msg) {
- _status_messages.push_back(msg);
+ void add_status_line(status_line *msg) {
+ _status_lines.push_back(msg);
}
- void remove_status(status_msg *msg) {
- _status_messages.erase(
- std::remove(_status_messages.begin(), _status_messages.end(), msg),
- _status_messages.end());
+ void remove_status_line(status_line *msg) {
+ _status_lines.erase(
+ std::remove(_status_lines.begin(), _status_lines.end(), msg),
+ _status_lines.end());
+ }
+ const std::vector<status_line*>& get_status_lines() {
+ return _status_lines;
}
- virtual void print_status_message(status_msg* msg) = 0;
-
- int update_messages(fmt::memory_buffer& buf, unsigned int width);
+ virtual void print_status_line_registry() = 0;
private:
- std::vector<status_msg*> _status_messages;
+ std::vector<status_line*> _status_lines;
+ int _change_since_last_print{0};
};
-class status_msg {
+class status_line {
public:
- status_msg(std::shared_ptr<spdlog::logger> logger,
+ status_line(std::shared_ptr<spdlog::logger> logger,
spdlog::level::level_enum level)
: _logger(logger), _level(level)
{
+ /* on creation, register it with all sinks that understand about us */
for (auto &sink : _logger->sinks()) {
- auto ptr = dynamic_cast<status_msg_sink*>(sink.get());
+ auto ptr = dynamic_cast<status_line_registry*>(sink.get());
if (ptr) {
- ptr->add_status(this);
+ ptr->add_status_line(this);
}
}
}
- ~status_msg() {
+ ~status_line() {
+ /* on deletion, deregister from all sinks */
for (auto &sink : _logger->sinks()) {
- auto ptr = dynamic_cast<status_msg_sink*>(sink.get());
+ auto ptr = dynamic_cast<status_line_registry*>(sink.get());
if (ptr) {
- ptr->remove_status(this);
+ ptr->remove_status_line(this);
}
}
}
- void trigger_message_print() {
+ /* trigger (re)print of this status line */
+ void trigger_print_status_lines() {
for (auto &sink : _logger->sinks()) {
- auto ptr = dynamic_cast<status_msg_sink*>(sink.get());
- if (ptr) {
- ptr->print_status_message(this);
+ if (sink->should_log(get_level())) {
+ auto ptr = dynamic_cast<status_line_registry*>(sink.get());
+ if (ptr) {
+ ptr->print_status_line_registry();
+ }
}
}
}
- virtual void update_message(fmt::memory_buffer &buf, unsigned int width) = 0;
+ virtual void render_status_line(fmt::memory_buffer &buf, unsigned int width) = 0;
static const char* magic_filename() {
static const char* file = "PROGRESS MONITOR";
@@ -304,14 +316,17 @@ public:
bool should_log() {
return _logger->should_log(_level);
}
+ spdlog::level::level_enum get_level() {
+ return _level;
+ }
- void log(fmt::memory_buffer &buf) {
+ void send_log_msg(fmt::memory_buffer &buf) {
using spdlog::details::fmt_helper::to_string_view;
spdlog::source_loc loc;
loc.filename = magic_filename();
spdlog::details::log_msg msg{loc, &_logger->name(), _level, to_string_view(buf)};
for (auto &sink : _logger->sinks()) {
- if (sink->should_log(_level)) {
+ if (sink->should_log(get_level())) {
sink->log(msg);
}
}
@@ -319,15 +334,9 @@ public:
private:
std::shared_ptr<spdlog::logger> _logger;
- spdlog::level::level_enum _level;
+ spdlog::level::level_enum _level{spdlog::level::off};
};
-inline int status_msg_sink::update_messages(fmt::memory_buffer &buf, unsigned int width) {
- for (auto msg : _status_messages) {
- msg->update_message(buf, width);
- }
- return _status_messages.size();
-}
class sigwinch_mixin {
protected:
@@ -391,9 +400,9 @@ private:
template<typename TargetStream, class ConsoleMutex>
-class terminal_sink
+class terminal_sink final
: public spdlog::sinks::ansicolor_sink<TargetStream, ConsoleMutex>,
- public status_msg_sink, public sigwinch_mixin {
+ public status_line_registry, public sigwinch_mixin {
public:
using super = spdlog::sinks::ansicolor_sink<TargetStream, ConsoleMutex>;
using mutex_t = typename ConsoleMutex::mutex_t;
@@ -405,27 +414,52 @@ public:
}
~terminal_sink() override = default;
- void log(const spdlog::details::log_msg &msg) override {
- if (not super::should_do_colors_) {
- super::log(msg);
+ // normal log message coming in
+ void log(const spdlog::details::log_msg &msg) override final {
+ _print(&msg);
+ }
+
+ // update to status coming in
+ void print_status_line_registry() override final {
+ _print(nullptr);
+ }
+
+ void _print(const spdlog::details::log_msg *msg) {
+ if (not super::should_do_colors_) { // not a tty
+ if (msg != nullptr) { // got a msg
+ super::log(*msg); // pass it upstream
+ }
return;
}
- if (msg.source.filename == status_msg::magic_filename()) {
- return; // special messages handled elsewhere
- }
- fmt::memory_buffer messages;
- int nlines = update_messages(messages, _ncols);
+
if (check_got_sigwinch()) {
update_term_width();
}
+
+ // render status lines
+ fmt::memory_buffer status_text;
+ int nlines = 0;
+ for (auto line : get_status_lines()) {
+ if (this->should_log(line->get_level())) {
+ line->render_status_line(status_text, _ncols);
+ ++ nlines;
+ }
+ }
+
+ // move back up to last log line
std::lock_guard<mutex_t> lock(super::mutex_);
- for (int i=0; i < nlines; ++i) {
+ for (int i=0; i < _last_status_lines; ++i) {
fwrite(term_move_up.data(), 1, term_move_up.size(), super::target_file_);
}
+ _last_status_lines = nlines;
- fwrite(term_clear_line.data(), 1, term_clear_line.size(), super::target_file_);
- super::log(msg);
- fwrite(messages.data(), 1, messages.size(), super::target_file_);
+ // print message if we have one and it's not an update for other sinks
+ if (msg != nullptr && msg->source.filename != status_line::magic_filename()) {
+ fwrite(term_clear_line.data(), 1, term_clear_line.size(), super::target_file_);
+ super::log(*msg);
+ }
+
+ fwrite(status_text.data(), 1, status_text.size(), super::target_file_);
fflush(super::target_file_);
}
@@ -438,26 +472,11 @@ public:
}
}
- void print_status_message(status_msg*) override {
- if (not super::should_do_colors_) {
- return;
- }
- fmt::memory_buffer messages;
- int nlines = update_messages(messages, _ncols);
- if (check_got_sigwinch()) {
- update_term_width();
- }
- std::lock_guard<mutex_t> lock(super::mutex_);
- for (int i=0; i < nlines; ++i) {
- fwrite(term_move_up.data(), 1, term_move_up.size(), super::target_file_);
- }
- fwrite(messages.data(), 1, messages.size(), super::target_file_);
- fflush(super::target_file_);
- }
const std::string term_move_up = "\x1B[A";
const std::string term_clear_line = "\x1B[K";
private:
- unsigned int _ncols;
+ unsigned int _ncols{60};
+ unsigned int _last_status_lines{0};
};
using terminal_stdout_sink_mt = terminal_sink<spdlog::details::console_stdout, spdlog::details::console_mutex>;
@@ -477,7 +496,7 @@ inline std::shared_ptr<spdlog::logger> stderr_terminal_mt(const std::string &log
}
-class logger_progress final : public base_progress, status_msg {
+class logger_progress final : public base_progress, status_line {
public:
logger_progress(std::shared_ptr<spdlog::logger> logger,
std::string desc="", unsigned int total=0, bool ascii=false,
@@ -485,28 +504,30 @@ public:
spdlog::level::level_enum level=spdlog::level::warn
)
: base_progress(desc, total, ascii),
- status_msg(logger, level)
+ status_line(logger, level)
{
}
~logger_progress() {
}
void show_progress(timepoint_t now=clock_t::now()) override final {
- if (!should_log()) return;
- duration_t delta_time = now - _last_update;
- if (delta_time < _mininterval) {
- trigger_message_print();
+ if (!should_log()) {
+ // early quit if our logger has loglevel below ourselves
return;
}
- _last_update = now;
+ duration_t delta_time = now - _last_update;
+ status_line::trigger_print_status_lines();
+ if (delta_time > _mininterval) {
+ _last_update = now;
- fmt::memory_buffer buf;
- render_progress(now, 60, buf);
- log(buf);
+ fmt::memory_buffer buf;
+ base_progress::render_progress(now, 60, buf);
+ status_line::send_log_msg(buf);
+ }
}
- void update_message(fmt::memory_buffer &buf, unsigned int width) override final {
- render_progress(clock_t::now(), width, buf);
+ void render_status_line(fmt::memory_buffer &buf, unsigned int width) override final {
+ base_progress::render_progress(clock_t::now(), width, buf);
}
private:
=====================================
src/query_arb.cpp
=====================================
@@ -264,9 +264,7 @@ query_arb::query_arb(const fs::path& arbfile)
logger->info("Loading names map... (for {})", data->filename);
- logger_progress q(logger, "Scanning", spec_count);
-
- Progress p("Scanning", spec_count);
+ logger_progress p(logger, "Scanning", spec_count);
for ( GBDATA* gbspec = GBT_first_species(data->gbmain);
gbspec != nullptr; gbspec = GBT_next_species(gbspec)) {
data->gbdata_cache[GBT_read_name(gbspec)] = gbspec;
=====================================
src/search_filter.cpp
=====================================
@@ -189,7 +189,7 @@ search_filter::search_filter()
data->arb = query_arb::getARBDB(opts->pt_database);
if (opts->search_all) {
- Progress p("Caching Sequences", data->arb->getSeqCount());
+ logger_progress p(logger, "Caching Sequences", data->arb->getSeqCount());
vector<string> names = data->arb->getSequenceNames();
for (string& name: names) {
data->sequences.push_back(&data->arb->getCseq(name));
=====================================
src/sina.cpp
=====================================
@@ -396,7 +396,7 @@ int real_main(int argc, char** argv) {
tbb::task_scheduler_init init(vm["threads"].as<unsigned int>());
tf::graph g; // Main data flow graph (pipeline)
- logger_progress p(logger, "Processing", 0, false);
+ logger_progress p(logger, "Processing");
vector<std::unique_ptr<tf::graph_node>> nodes; // Nodes (for cleanup)
tf::sender<tray> *last_node; // Last tray producing node
View it on GitLab: https://salsa.debian.org/med-team/sina/-/commit/f4cde295b116d95e1b2af159d5dc2523365a954e
--
View it on GitLab: https://salsa.debian.org/med-team/sina/-/commit/f4cde295b116d95e1b2af159d5dc2523365a954e
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