[med-svn] [Git][med-team/sina][master] 10 commits: New upstream version 1.6.1

Steffen Möller gitlab at salsa.debian.org
Mon Jun 8 17:54:48 BST 2020



Steffen Möller pushed to branch master at Debian Med / sina


Commits:
f4cde295 by Steffen Moeller at 2020-06-08T18:27:39+02:00
New upstream version 1.6.1
- - - - -
c287bcbc by Steffen Moeller at 2020-06-08T18:27:39+02:00
routine-update: New upstream version

- - - - -
1b4f4f67 by Steffen Moeller at 2020-06-08T18:27:40+02:00
Update upstream source from tag 'upstream/1.6.1'

Update to upstream version '1.6.1'
with Debian dir d0f4ea13f98effaad3d80615a04e0693dca4df35
- - - - -
aecd5cb6 by Steffen Moeller at 2020-06-08T18:27:40+02:00
routine-update: Standards-Version: 4.5.0

- - - - -
daea071a by Steffen Moeller at 2020-06-08T18:27:40+02:00
routine-update: debhelper-compat 13

- - - - -
d11d11c2 by Steffen Moeller at 2020-06-08T18:27:44+02:00
routine-update: Remove trailing whitespace in debian/changelog

- - - - -
50b087c1 by Steffen Moeller at 2020-06-08T18:27:44+02:00
routine-update: Add salsa-ci file

- - - - -
7937f146 by Steffen Moeller at 2020-06-08T18:27:45+02:00
routine-update: Rules-Requires-Root: no

- - - - -
d14df3aa by Steffen Moeller at 2020-06-08T18:27:48+02:00
Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.

Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html


Fixes: lintian: upstream-metadata-missing-repository
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html

- - - - -
053aad36 by Steffen Moeller at 2020-06-08T18:54:27+02:00
Still running into compilation issue - libtbb kills it

- - - - -


18 changed files:

- .bumpversion.cfg
- .travis.yml
- configure.ac
- debian/changelog
- − debian/compat
- debian/control
- + debian/patches/configure.patch
- debian/patches/series
- debian/rules
- + debian/salsa-ci.yml
- debian/upstream/metadata
- 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])


=====================================
debian/changelog
=====================================
@@ -1,10 +1,18 @@
-sina (1.6.0-1) UNRELEASED; urgency=medium
+sina (1.6.1-1) UNSTABLE; urgency=medium
 
+  [ Andreas Tille ]
   * Initial release (Closes: #<bug>)
-  TODO: Needs libarb
-     https://salsa.debian.org/med-team/libarb
-  
+
   TODO: test_data directory is required to run build-time tests. It is not
      included into the upstream tarball.
 
- -- Andreas Tille <tille at debian.org>  Thu, 13 Jun 2019 08:25:26 +0200
+  [ Steffen Moeller ]
+  * Standards-Version: 4.5.0 (routine-update)
+  * debhelper-compat 13 (routine-update)
+  * Remove trailing whitespace in debian/changelog (routine-update)
+  * Add salsa-ci file (routine-update)
+  * Rules-Requires-Root: no (routine-update)
+  * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
+    Repository-Browse.
+
+ -- Steffen Moeller <moeller at debian.org>  Mon, 08 Jun 2020 18:27:48 +0200


=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-12


=====================================
debian/control
=====================================
@@ -4,7 +4,7 @@ Uploaders: Andreas Tille <tille at debian.org>,
            Liubov Chuprikova <chuprikovalv at gmail.com>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 12~),
+Build-Depends: debhelper-compat (= 13),
                pkg-config,
                libboost-filesystem-dev,
                libboost-iostreams-dev,
@@ -18,10 +18,11 @@ Build-Depends: debhelper (>= 12~),
                zlib1g-dev,
                libarb-dev,
                python3-sphinx
-Standards-Version: 4.3.0
+Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/sina
 Vcs-Git: https://salsa.debian.org/med-team/sina.git
 Homepage: https://github.com/epruesse/SINA
+Rules-Requires-Root: no
 
 Package: sina
 Architecture: any


=====================================
debian/patches/configure.patch
=====================================
@@ -0,0 +1,54 @@
+Index: sina/configure.ac
+===================================================================
+--- sina.orig/configure.ac
++++ sina/configure.ac
+@@ -179,22 +179,22 @@ if test x"$GLIB_LIBS" = x""; then
+ fi
+ 
+ AX_LIB_ARBDB
+-if test x"$ARB_LIBS" = x""; then
+-  missing_libs="$missing_libs
+-  ARB libraries (libARBDB)"
+-fi
++#if test x"$ARB_LIBS" = x""; then
++#  missing_libs="$missing_libs
++#  ARB libraries (libARBDB)"
++#fi
+ 
+ AX_LIB_ARB_PROBE
+-if test x"$ARB_PROBE_LIBS" = x""; then
+-  missing_libs="$missing_libs
+-  ARB PROBE library (PROBE_COM/client.a)"
+-fi
++#if test x"$ARB_PROBE_LIBS" = x""; then
++#  missing_libs="$missing_libs
++#  ARB PROBE library (PROBE_COM/client.a)"
++#fi
+ 
+ AX_LIB_ARB_HELIX
+-if test x"$ARB_HELIX_LIBS" = x""; then
+-  missing_libs="$missing_libs
+-  ARB HELIX library (SL/HELIX/HELIX.a)"
+-fi
++#if test x"$ARB_HELIX_LIBS" = x""; then
++#  missing_libs="$missing_libs
++#  ARB HELIX library (SL/HELIX/HELIX.a)"
++#fi
+ 
+ AX_ARB_CHECK_FUNC([GBT_FIND_SEQUENCE], [GBT_find_sequence(NULL, NULL)])
+ AX_ARB_STATUS_RETURN_TYPE
+@@ -228,10 +228,10 @@ done
+ AC_SUBST(ARB_FILES)
+ 
+ AX_LIB_TBB
+-if test x"$TBB_LIB" = x""; then
+-  missing_libs="$missing_libs
+-  Intel Threading Building Blocks (libtbb)"
+-fi
++#if test x"$TBB_LIB" = x""; then
++#  missing_libs="$missing_libs
++#  Intel Threading Building Blocks (libtbb)"
++#fi
+ 
+ AX_LIB_TBB_MALLOC
+ 


=====================================
debian/patches/series
=====================================
@@ -1 +1,2 @@
 fix_libs.patch
+configure.patch


=====================================
debian/rules
=====================================
@@ -12,10 +12,16 @@ include /usr/share/dpkg/default.mk
 	dh $@
 
 override_dh_auto_configure:
-	dh_auto_configure -- --with-arbhome=/usr/lib/x86_64-linux-gnu/arb
+	dh_auto_configure -- --with-arbhome=/usr/lib/arb \
+	  --without-tbb --disable-static
 
 ### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected
 override_dh_auto_test:
 #ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 #	do_stuff_for_testing
 #endif
+
+override_dh_auto_clean:
+	dh_auto_clean
+	rm -f config.log
+	rm -f doc/doctrees/CHANGELOG.doctree doc/doctrees/README.doctree doc/doctrees/commandline.doctree doc/doctrees/environment.pickle doc/doctrees/index.doctree doc/doctrees/install.doctree doc/build.stamp config.status src/sina.o


=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml


=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,5 @@
+Bug-Database: https://github.com/epruesse/SINA/issues
+Bug-Submit: https://github.com/epruesse/SINA/issues/new
 Reference:
  - Author: Elmar Pruesse and Jörg Peplies and Frank Oliver Glöckner
    Title: >
@@ -20,3 +22,5 @@ Registry:
    Entry: sina
  - Name: bio.tools
    Entry: sina
+Repository: https://github.com/epruesse/SINA.git
+Repository-Browse: https://github.com/epruesse/SINA


=====================================
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/-/compare/e313b6932046e54f575c06ad1de7058292b321bc...053aad3633182b6619a9d93cd52135455e0b7cc4

-- 
View it on GitLab: https://salsa.debian.org/med-team/sina/-/compare/e313b6932046e54f575c06ad1de7058292b321bc...053aad3633182b6619a9d93cd52135455e0b7cc4
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