[med-svn] [Git][med-team/relion][debian/master] 6 commits: disable dbgsym packages on ci builds
Andreas Beckmann (@anbe)
gitlab at salsa.debian.org
Thu Sep 29 12:58:31 BST 2022
Andreas Beckmann pushed to branch debian/master at Debian Med / relion
Commits:
25012c3e by Andreas Beckmann at 2022-09-26T22:22:15+02:00
disable dbgsym packages on ci builds
to avoid failures due to excessively large artifacts
- - - - -
759a9237 by Andreas Beckmann at 2022-09-28T18:39:57+02:00
build for Architecture: any
- - - - -
a33c4b3f by Andreas Beckmann at 2022-09-28T18:45:59+02:00
use different synopsis
- - - - -
412e78c5 by Andreas Beckmann at 2022-09-28T18:47:16+02:00
Standards-Version: 4.6.1
- - - - -
55fbf0ad by Andreas Beckmann at 2022-09-28T22:27:46+02:00
fix some typos found by Lintian
- - - - -
dd23a813 by Andreas Beckmann at 2022-09-29T13:27:19+02:00
release relion (3.1.3-2) to unstable
- - - - -
6 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/patches/series
- + debian/patches/typos.patch
- debian/salsa-ci.yml
Changes:
=====================================
debian/changelog
=====================================
@@ -1,14 +1,18 @@
-relion (3.1.3-2) UNRELEASED; urgency=medium
-
- [ Andreas Tille ]
- * Enable uscan to create a sensible download name
+relion (3.1.3-2) unstable; urgency=medium
[ Andreas Beckmann ]
+ * Team upload.
* Cherry-pick upstream fixes related to cub. (Closes: #995224)
* Simplify debian/rules.
* Fix missing hardening flags.
+ * Build for Architecture: any.
+ * Standards-Version: 4.6.1.
+ * Fix some typos found by Lintian.
+
+ [ Andreas Tille ]
+ * Enable uscan to create a sensible download name
- -- Andreas Tille <tille at debian.org> Wed, 20 Oct 2021 09:02:12 +0200
+ -- Andreas Beckmann <anbe at debian.org> Thu, 29 Sep 2022 13:27:08 +0200
relion (3.1.3-1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -11,14 +11,14 @@ Build-Depends: cmake,
libopenmpi-dev,
libtiff-dev,
fluid
-Standards-Version: 4.6.0
+Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/relion
Vcs-Git: https://salsa.debian.org/med-team/relion.git
Homepage: https://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page
Rules-Requires-Root: no
Package: relion
-Architecture: amd64 i386
+Architecture: any
Depends: openmpi-gcc | openmpi-bin,
${misc:Depends},
${shlibs:Depends},
@@ -43,9 +43,9 @@ Description: toolkit for 3D reconstructions in cryo-electron microscopy
CUDA/GPU support.
Package: relion-gui
-Architecture: amd64 i386
-Depends: openmpi-gcc | openmpi-bin,
- relion,
+Architecture: any
+Depends:
+ relion (= ${binary:Version}),
${misc:Depends},
${shlibs:Depends},
Breaks: relion-bin,
@@ -57,7 +57,7 @@ Replaces: relion-bin,
relion-bin+mpi,
relion-bin+mpi+gui,
Conflicts: relion-cuda-gui,
-Description: parallel toolkit for 3D reconstructions in cryo-electron microscopy
+Description: toolkit for 3D reconstructions in cryo-electron microscopy (gui apps)
RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone
computer program for Maximum A Posteriori refinement of (multiple) 3D
reconstructions or 2D class averages in cryo-electron microscopy.
=====================================
debian/copyright
=====================================
@@ -9,6 +9,7 @@ License: GPL-2+
Files: debian/*
Copyright: 2014-2020, Q-Leap Networks GmbH <info at q-leap.de>
+ © 2022 Andreas Beckmann <anbe at debian.org>
License: GPL-2+
Files: src/CPlot2D.cpp
=====================================
debian/patches/series
=====================================
@@ -1 +1,2 @@
0001-Repair-wrong-comment-sign-pointed-out-by-Alexey-Roma.patch
+typos.patch
=====================================
debian/patches/typos.patch
=====================================
@@ -0,0 +1,131 @@
+Author: Andreas Beckmann <anbe at debian.org>
+Description: fix typos found by Lintian
+
+--- a/src/acc/cuda/custom_allocator.cuh
++++ b/src/acc/cuda/custom_allocator.cuh
+@@ -301,7 +301,7 @@ private:
+ {
+ char *mangled_name = 0, *offset_begin = 0, *offset_end = 0;
+
+- // find parantheses and +address offset surrounding mangled name
++ // find parentheses and +address offset surrounding mangled name
+ for (char *p = messages[i]; *p; ++p)
+ {
+ if (*p == '(')
+--- a/src/args.cpp
++++ b/src/args.cpp
+@@ -412,7 +412,7 @@ void IOParser::writeUsageOneSection(int
+
+ void IOParser::writeUsage(std::ostream &out)
+ {
+- out << "+++ RELION: command line arguments (with defaults for optional ones between parantheses) +++"<<std::endl;
++ out << "+++ RELION: command line arguments (with defaults for optional ones between parentheses) +++"<<std::endl;
+
+ for (int section = 0; section < section_names.size(); section++)
+ {
+--- a/src/args.h
++++ b/src/args.h
+@@ -211,7 +211,7 @@ public:
+ * , delimited for threads within each rank
+ * and outputs a rank-major array which supplies
+ * a mapping as input for distribution of ranks
+- * and threads over the availiable/specfied GPUs.
++ * and threads over the available/specified GPUs.
+ */
+ void untangleDeviceIDs(std::string &tangled, std::vector < std::vector < std::string > > &untangled);
+
+--- a/src/autopicker.cpp
++++ b/src/autopicker.cpp
+@@ -105,7 +105,7 @@ void AutoPicker::read(int argc, char **a
+ do_read_fom_maps = parser.checkOption("--read_fom_maps", "Skip probability calculations, re-read precalculated maps from disc");
+ do_optimise_scale = !parser.checkOption("--skip_optimise_scale", "Skip the optimisation of the micrograph scale for better prime factors in the FFTs. This runs slower, but at exactly the requested resolution.");
+ do_only_unfinished = parser.checkOption("--only_do_unfinished", "Only autopick those micrographs for which the coordinate file does not yet exist");
+- do_gpu = parser.checkOption("--gpu", "Use GPU acceleration when availiable");
++ do_gpu = parser.checkOption("--gpu", "Use GPU acceleration when available");
+ gpu_ids = parser.getOption("--gpu", "Device ids for each MPI-thread","default");
+ #ifndef CUDA
+ if(do_gpu)
+--- a/src/gpu_utils/cuda_mem_utils.h
++++ b/src/gpu_utils/cuda_mem_utils.h
+@@ -441,7 +441,7 @@ private:
+ {
+ char *mangled_name = 0, *offset_begin = 0, *offset_end = 0;
+
+- // find parantheses and +address offset surrounding mangled name
++ // find parentheses and +address offset surrounding mangled name
+ for (char *p = messages[i]; *p; ++p)
+ {
+ if (*p == '(')
+--- a/src/metadata_label.h
++++ b/src/metadata_label.h
+@@ -867,7 +867,7 @@ private:
+ EMDL::addLabel(EMDL_OPTIMISER_DO_HELICAL_REFINE, EMDL_BOOL, "rlnDoHelicalRefine", "Flag to indicate that helical refinement should be performed");
+ EMDL::addLabel(EMDL_OPTIMISER_IGNORE_HELICAL_SYMMETRY, EMDL_BOOL, "rlnIgnoreHelicalSymmetry", "Flag to indicate that helical symmetry is ignored in 3D reconstruction");
+ EMDL::addLabel(EMDL_OPTIMISER_FOURIER_MASK, EMDL_STRING, "rlnFourierMask", "Name of an FFTW-centred Fourier mask to be applied to the Projector for refinement.");
+- EMDL::addLabel(EMDL_OPTIMISER_HELICAL_TWIST_INITIAL, EMDL_DOUBLE, "rlnHelicalTwistInitial", "The intial helical twist (rotation per subunit) in degrees before refinement");
++ EMDL::addLabel(EMDL_OPTIMISER_HELICAL_TWIST_INITIAL, EMDL_DOUBLE, "rlnHelicalTwistInitial", "The initial helical twist (rotation per subunit) in degrees before refinement");
+ EMDL::addLabel(EMDL_OPTIMISER_HELICAL_RISE_INITIAL, EMDL_DOUBLE, "rlnHelicalRiseInitial", "The initial helical rise (translation per subunit) in Angstroms before refinement");
+ EMDL::addLabel(EMDL_OPTIMISER_HELICAL_Z_PERCENTAGE, EMDL_DOUBLE, "rlnHelicalCentralProportion", "Only expand this central fraction of the Z axis when imposing real-space helical symmetry");
+ EMDL::addLabel(EMDL_OPTIMISER_HELICAL_NSTART, EMDL_INT, "rlnNrHelicalNStart", "The N-number for an N-start helix");
+--- a/src/ml_optimiser_mpi.cpp
++++ b/src/ml_optimiser_mpi.cpp
+@@ -568,7 +568,7 @@ void MlOptimiserMpi::initialiseWorkLoad(
+ if (node->size <= 2)
+ REPORT_ERROR("MlOptimiserMpi::initialiseWorkLoad: at least 3 MPI processes are required when splitting data into random halves");
+ if (node->size % 2 == 0)
+- REPORT_ERROR("MlOptimiserMpi::initialiseWorkLoad: the number of MPI processes must be an odd number when gold-standard seperation is applied.");
++ REPORT_ERROR("MlOptimiserMpi::initialiseWorkLoad: the number of MPI processes must be an odd number when gold-standard separation is applied.");
+ }
+ else if (node->size <= 1)
+ REPORT_ERROR("MlOptimiserMpi::initialiseWorkLoad: at least 2 MPI processes are required, otherwise use the sequential program");
+--- a/src/particle_subtractor.cpp
++++ b/src/particle_subtractor.cpp
+@@ -293,7 +293,7 @@ void ParticleSubtractor::revert()
+ }
+
+ obsModel.save(MD, fn_out + "original.star");
+- std::cout << "Writen " << (fn_out + "original.star") << std::endl;
++ std::cout << "Written " << (fn_out + "original.star") << std::endl;
+ }
+
+ void ParticleSubtractor::run()
+--- a/src/pipeline_jobs.cpp
++++ b/src/pipeline_jobs.cpp
+@@ -1092,7 +1092,7 @@ Note that for importing coordinate files
+ Also note that micrographs, movies and coordinate files all need to be in the same directory (with the same rootnames, e.g.mic1 in the example above) in order to be imported correctly. 3D masks or references can be imported from anywhere. \n \n \
+ Note that movie-particle STAR files cannot be imported from a previous version of RELION, as the way movies are handled has changed in RELION-2.0. \n \n \
+ For the import of a particle, 2D references or micrograph STAR file or of a 3D reference or mask, only a single file can be imported at a time. \n \n \
+-Note that due to a bug in a fltk library, you cannot import from directories that contain a substring of the current directory, e.g. dont important from /home/betagal if your current directory is called /home/betagal_r2. In this case, just change one of the directory names.");
++Note that due to a bug in a fltk library, you cannot import from directories that contain a substring of the current directory, e.g. don't import from /home/betagal if your current directory is called /home/betagal_r2. In this case, just change one of the directory names.");
+
+ joboptions["node_type"] = JobOption("Node type:", job_nodetype_options, 0, "Select the type of Node this is.");
+ joboptions["optics_group_particles"] = JobOption("Rename optics group for particles:", (std::string)"", "Only for the import of a particles STAR file with a single, or no, optics groups defined: rename the optics group for the imported particles to this string.");
+@@ -1300,7 +1300,7 @@ void RelionJob::initialiseMotioncorrJob(
+ joboptions["patch_x"] = JobOption("Number of patches X:", std::string("1"), "Number of patches (in X and Y direction) to apply motioncor2.");
+ joboptions["patch_y"] = JobOption("Number of patches Y:", std::string("1"), "Number of patches (in X and Y direction) to apply motioncor2.");
+ joboptions["group_frames"] = JobOption("Group frames:", 1, 1, 5, 1, "Average together this many frames before calculating the beam-induced shifts.");
+- joboptions["bin_factor"] = JobOption("Binning factor:", 1, 1, 2, 1, "Bin the micrographs this much by a windowing operation in the Fourier Tranform. Binning at this level is hard to un-do later on, but may be useful to down-scale super-resolution images. Float-values may be used. Do make sure though that the resulting micrograph size is even.");
++ joboptions["bin_factor"] = JobOption("Binning factor:", 1, 1, 2, 1, "Bin the micrographs this much by a windowing operation in the Fourier Transform. Binning at this level is hard to un-do later on, but may be useful to down-scale super-resolution images. Float-values may be used. Do make sure though that the resulting micrograph size is even.");
+ joboptions["fn_gain_ref"] = JobOption("Gain-reference image:", "", "*.mrc", ".", "Location of the gain-reference file to be applied to the input micrographs. Leave this empty if the movies are already gain-corrected.");
+ joboptions["gain_rot"] = JobOption("Gain rotation:", job_gain_rotation_options, 0, "Rotate the gain reference by this number times 90 degrees clockwise in relion_display. This is the same as -RotGain in MotionCor2. Note that MotionCor2 uses a different convention for rotation so it says 'counter-clockwise'. Valid values are 0, 1, 2 and 3.");
+ joboptions["gain_flip"] = JobOption("Gain flip:", job_gain_flip_options, 0, "Flip the gain reference after rotation. This is the same as -FlipGain in MotionCor2. 0 means do nothing, 1 means flip Y (upside down) and 2 means flip X (left to right).");
+@@ -4587,7 +4587,7 @@ void RelionJob::initialisePostprocessJob
+
+ joboptions["do_auto_bfac"] = JobOption("Estimate B-factor automatically?", true, "If set to Yes, then the program will use the automated procedure described by Rosenthal and Henderson (2003, JMB) to estimate an overall B-factor for your map, and sharpen it accordingly. \
+ Note that your map must extend well beyond the lowest resolution included in the procedure below, which should not be set to resolutions much lower than 10 Angstroms. ");
+- joboptions["autob_lowres"] = JobOption("Lowest resolution for auto-B fit (A):", 10, 8, 15, 0.5, "This is the lowest frequency (in Angstroms) that will be included in the linear fit of the Guinier plot as described in Rosenthal and Henderson (2003, JMB). Dont use values much lower or higher than 10 Angstroms. If your map does not extend beyond 10 Angstroms, then instead of the automated procedure use your own B-factor.");
++ joboptions["autob_lowres"] = JobOption("Lowest resolution for auto-B fit (A):", 10, 8, 15, 0.5, "This is the lowest frequency (in Angstroms) that will be included in the linear fit of the Guinier plot as described in Rosenthal and Henderson (2003, JMB). Don't use values much lower or higher than 10 Angstroms. If your map does not extend beyond 10 Angstroms, then instead of the automated procedure use your own B-factor.");
+ joboptions["do_adhoc_bfac"] = JobOption("Use your own B-factor?", false, "Instead of using the automated B-factor estimation, provide your own value. Use negative values for sharpening the map. \
+ This option is useful if your map does not extend beyond the 10A needed for the automated procedure, or when the automated procedure does not give a suitable value (e.g. in more disordered parts of the map).");
+ joboptions["adhoc_bfac"] = JobOption("User-provided B-factor:", -1000, -2000, 0, -50, "Use negative values for sharpening. Be careful: if you over-sharpen your map, you may end up interpreting noise for signal!");
+--- a/src/tiff_converter.cpp
++++ b/src/tiff_converter.cpp
+@@ -318,7 +318,7 @@ void TIFFConverter::initialise(int _rank
+ total_ranks = _total_ranks;
+
+ if (do_estimate && total_ranks != 1)
+- REPORT_ERROR("MPI parallelisation is not avaialble for --estimate_gain");
++ REPORT_ERROR("MPI parallelisation is not available for --estimate_gain");
+
+ if (fn_out[fn_out.size() - 1] != '/')
+ fn_out += "/";
=====================================
debian/salsa-ci.yml
=====================================
@@ -2,3 +2,6 @@
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
+
+variables:
+ DEB_BUILD_OPTIONS: "noautodbgsym"
View it on GitLab: https://salsa.debian.org/med-team/relion/-/compare/5984c17623398d4b826e33537bca0e060a086147...dd23a813e863f8b944a70237445f6b27505a3b27
--
View it on GitLab: https://salsa.debian.org/med-team/relion/-/compare/5984c17623398d4b826e33537bca0e060a086147...dd23a813e863f8b944a70237445f6b27505a3b27
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