[crystfel] 01/02: Imported Debian patch 0.5.3-1
Frédéric-Emmanuel Picca
picca at moszumanska.debian.org
Fri Jul 25 10:08:27 UTC 2014
This is an automated email from the git hooks/post-receive script.
picca pushed a commit to branch master
in repository crystfel.
commit 0595876da61805f2e09368b65a021369963a364f
Author: Valerio Mariani <valerio.mariani at gmail.com>
Date: Wed May 7 17:00:14 2014 +0100
Imported Debian patch 0.5.3-1
---
debian/changelog | 5 +
debian/compat | 1 +
debian/control | 111 ++++++++++++
debian/copyright | 41 +++++
debian/crystfel-dev.install | 3 +
debian/crystfel-doc.links | 1 +
debian/crystfel.install | 14 ++
debian/docs | 2 +
debian/libcrystfel-doc.install | 3 +
debian/libcrystfel4.install | 3 +
debian/libcrystfel4.symbols | 300 ++++++++++++++++++++++++++++++++
debian/patches/fix-man-pages.patch | 24 +++
debian/patches/fix-readme.patch | 22 +++
debian/patches/series | 3 +
debian/patches/skip-gpu-sim-check.patch | 41 +++++
debian/rules | 20 +++
debian/source/format | 1 +
17 files changed, 595 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..06b2132
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+crystfel (0.5.3-1) unstable; urgency=low
+
+ * Initial release (Closes: #743268)
+
+ -- Valerio Mariani <valerio.mariani at gmail.com> Wed, 7 May 2014 17:00:14 +0100
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..e080c5e
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,111 @@
+Source: crystfel
+Section: science
+Priority: extra
+Maintainer: Valerio Mariani <valerio.mariani at gmail.com>
+Build-Depends: debhelper (>= 8.0.0), autotools-dev, fftw3-dev, libhdf5-dev, zlib1g-dev, libgsl0-dev, libgtk2.0-dev, gtk-doc-tools, libncurses5-dev, ocl-icd-opencl-dev
+Standards-Version: 3.9.5
+Homepage: http://www.desy.de/~twhite/crystfel/
+Vcs-Git: git://git.bitwiz.org.uk/crystfel.git
+
+Package: crystfel
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Suite of programs for processing "serial" diffraction data "snapshots"
+ CrystFEL is a suite of programs for processing diffraction data acquired
+ "serially" in a "snapshot" manner. That means: a large number of individual
+ diffraction patterns, each corresponding to a random orientation of the
+ crystal, with little or no rotation or oscillation of the sample. This
+ is exactly the situation encountered when using the technique of Serial
+ Femtosecond Crystallography (SFX) with a free-electron laser source, which
+ is the application CrystFEL is primarily designed for. CrystFEL comprises
+ programs for indexing and integrating diffraction patterns, scaling and
+ merging intensities, simulating patterns, calculating figures of merit for
+ the data and visualising the results.
+ .
+ This version has been compiled with opencl support
+
+Package: libcrystfel4
+Architecture: any
+Multi-Arch: same
+Pre-Depends: ${misc:Pre-Depends}
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Replaces: libcrystfel2, libcrystfel3
+Description: Suite of programs for processing "serial" diffraction data "snapshots"
+ CrystFEL is a suite of programs for processing diffraction data acquired
+ "serially" in a "snapshot" manner. That means: a large number of individual
+ diffraction patterns, each corresponding to a random orientation of the
+ crystal, with little or no rotation or oscillation of the sample. This
+ is exactly the situation encountered when using the technique of Serial
+ Femtosecond Crystallography (SFX) with a free-electron laser source, which
+ is the application CrystFEL is primarily designed for. CrystFEL comprises
+ programs for indexing and integrating diffraction patterns, scaling and
+ merging intensities, simulating patterns, calculating figures of merit for
+ the data and visualising the results.
+ .
+ This version has been compiled with opencl support
+ .
+ This package contains the shared libraries used by the crystfel standard and
+ extra programs
+
+Package: crystfel-dev
+Architecture: any
+Depends: libcrystfel4 (= ${binary:Version}), ${misc:Depends}
+Suggests: libcrystfel-doc
+Description: Suite of programs for processing "serial" diffraction data "snapshots"
+ CrystFEL is a suite of programs for processing diffraction data acquired
+ "serially" in a "snapshot" manner. That means: a large number of individual
+ diffraction patterns, each corresponding to a random orientation of the
+ crystal, with little or no rotation or oscillation of the sample. This
+ is exactly the situation encountered when using the technique of Serial
+ Femtosecond Crystallography (SFX) with a free-electron laser source, which
+ is the application CrystFEL is primarily designed for. CrystFEL comprises
+ programs for indexing and integrating diffraction patterns, scaling and
+ merging intensities, simulating patterns, calculating figures of merit for
+ the data and visualising the results.
+ .
+ This version has been compiled with opencl support
+ .
+ This package contains header files and development information, which
+ is needed to build applications based on crystfel-opencl.
+
+Package: crystfel-doc
+Section: doc
+Depends: ${misc:Depends}
+Architecture: all
+Description: Suite of programs for processing "serial" diffraction data "snapshots"
+ CrystFEL is a suite of programs for processing diffraction data acquired
+ "serially" in a "snapshot" manner. That means: a large number of individual
+ diffraction patterns, each corresponding to a random orientation of the
+ crystal, with little or no rotation or oscillation of the sample. This
+ is exactly the situation encountered when using the technique of Serial
+ Femtosecond Crystallography (SFX) with a free-electron laser source, which
+ is the application CrystFEL is primarily designed for. CrystFEL comprises
+ programs for indexing and integrating diffraction patterns, scaling and
+ merging intensities, simulating patterns, calculating figures of merit for
+ the data and visualising the results.
+ .
+ This version has been compiled with opencl support
+ .
+ This package contains API documentation.
+
+Package: libcrystfel-dbg
+Section: debug
+Architecture: any
+Multi-Arch: same
+Depends: libcrystfel4 (= ${binary:Version}), ${misc:Depends}
+Description: Suite of programs for processing "serial" diffraction data "snapshots"
+ CrystFEL is a suite of programs for processing diffraction data acquired
+ "serially" in a "snapshot" manner. That means: a large number of individual
+ diffraction patterns, each corresponding to a random orientation of the
+ crystal, with little or no rotation or oscillation of the sample. This
+ is exactly the situation encountered when using the technique of Serial
+ Femtosecond Crystallography (SFX) with a free-electron laser source, which
+ is the application CrystFEL is primarily designed for. CrystFEL comprises
+ programs for indexing and integrating diffraction patterns, scaling and
+ merging intensities, simulating patterns, calculating figures of merit for
+ the data and visualising the results.
+ .
+ This version has been compiled with opencl support
+ .
+ This package contains the debugging symbols for libcrystfel3-opencl and
+ crystfel-opencl.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..523e718
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,41 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: crystfel
+Source: http://www.desy.de/~twhite/crystfel/download.html
+
+Files: *
+Copyright: 2012-2013 Deutsches Elektronen-Synchrotron DESY,
+ a research centre of the Helmholtz Association.
+License: GPLv3
+ CrystFEL has been released under the GNU GPLv3 (http://www.gnu.org/licenses/gpl-3.0.en.html). The full licence text has the legally binding details, but here is a brief summary:
+ .
+ You have the right to use CrystFEL on your own data, even if you're using it for commercial and/or proprietary gain. You have the right to study the source code and learn how it works, and to modify the source code to suit your own needs or to fix bugs. You also have the right to pass copies of original or modified versions to whomever you think might benefit from it.
+ .
+ However, these rights come with strings attached. Amongst other things, you are obliged to keep all the copyright notices and author information intact if you pass copies of CrystFEL on to other people. If you release a modified version of CrystFEL to the public, you must make the modified source code available as well. More importantly, if you release a program which links against CrystFEL's shared library libcrystfel, your program must also be distributed under the GNU GPL (version 3 [...]
+ .
+ Most importantly of all, CrystFEL comes with no warranty of any kind, not even the implied warranty of merchantability or fitness for a particular purpose. Like all software, CrystFEL contains bugs. The risk that CrystFEL will go crazy and delete all your data — or more realistically that you'll have to retract your Nobel prize winning structure because its analysis turned out to be wrong — rests entirely with you as the user. Fortunately, and in contrast many other software suites, you [...]
+ If you'd like to know more about the GNU General Public Licence and its implications, you could read the GPL FAQ (http://www.gnu.org/licenses/gpl-faq.html).
+ .
+ The licence conditions of CrystFEL do not free you from the normal rules of scientific conduct. That means that, although it's not required by the licence conditions, you should consider citing the following article if CrystFEL was important to the work described in your paper:
+ .
+ T. A. White, R. A. Kirian, A. V. Martin, A. Aquila, K. Nass, A. Barty and H. N. Chapman. "CrystFEL: a software suite for snapshot serial crystallography". J. Appl. Cryst. 45 (2012), p335–341. doi:10.1107/S0021889812002312
+ .
+ If you modified CrystFEL for your research, you should state that fact in your paper and give details of the modifications you made, whether or not you released the modified version to the public.
+
+Files: debian/*
+Copyright: 2014 Valerio Mariani <valerio.mariani at gmail.com>
+License: GPLv3
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
diff --git a/debian/crystfel-dev.install b/debian/crystfel-dev.install
new file mode 100644
index 0000000..3e52f58
--- /dev/null
+++ b/debian/crystfel-dev.install
@@ -0,0 +1,3 @@
+usr/include
+usr/lib/*/pkgconfig
+usr/lib/*/libcrystfel.so
diff --git a/debian/crystfel-doc.links b/debian/crystfel-doc.links
new file mode 100644
index 0000000..d21a156
--- /dev/null
+++ b/debian/crystfel-doc.links
@@ -0,0 +1 @@
+/usr/share/doc/crystfel/ /usr/share/gtk-doc/html/crystfel
diff --git a/debian/crystfel.install b/debian/crystfel.install
new file mode 100644
index 0000000..021b603
--- /dev/null
+++ b/debian/crystfel.install
@@ -0,0 +1,14 @@
+usr/bin
+usr/share/crystfel
+usr/share/man
+usr/share/doc/crystfel/cspad-feb2011.geom
+usr/share/doc/crystfel/lcls-cxi-9keV.beam
+usr/share/doc/crystfel/lcls-dec.beam
+usr/share/doc/crystfel/lcls-dec.geom
+usr/share/doc/crystfel/lcls-june.beam
+usr/share/doc/crystfel/lcls-june-r0013-r0128.geom
+usr/share/doc/crystfel/lcls-xpp-estimate.beam
+usr/share/doc/crystfel/lcls-xpp-estimate.geom
+usr/share/doc/crystfel/scripts
+usr/share/doc/crystfel/simple.geom
+usr/share/doc/crystfel/twin-calculator.pdf
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..50bd824
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1,2 @@
+NEWS
+README
diff --git a/debian/libcrystfel-doc.install b/debian/libcrystfel-doc.install
new file mode 100644
index 0000000..196f094
--- /dev/null
+++ b/debian/libcrystfel-doc.install
@@ -0,0 +1,3 @@
+usr/share/doc/crystfel/reference /usr/share/libcrystfel/
+doc/twin-calculator.odt /usr/share/doc/libcrystfel/
+
diff --git a/debian/libcrystfel4.install b/debian/libcrystfel4.install
new file mode 100644
index 0000000..4394c6a
--- /dev/null
+++ b/debian/libcrystfel4.install
@@ -0,0 +1,3 @@
+usr/lib/*/libcrystfel.a
+usr/lib/*/libcrystfel.so.4
+usr/lib/*/libcrystfel.so.4.0.0
diff --git a/debian/libcrystfel4.symbols b/debian/libcrystfel4.symbols
new file mode 100644
index 0000000..f0ae953
--- /dev/null
+++ b/debian/libcrystfel4.symbols
@@ -0,0 +1,300 @@
+libcrystfel.so.4 libcrystfel4 #MINVER#
+ add_copy_hdf5_field at Base 0.5.3
+ add_refl at Base 0.5.3
+ add_refl_to_list at Base 0.5.3
+ add_symop at Base 0.5.3
+ assplode at Base 0.5.3
+ asymmetric_indices at Base 0.5.3
+ bravais_lattice at Base 0.5.3
+ build_indexer_list at Base 0.5.3
+ cell_free at Base 0.5.3
+ cell_fudge_gslcblas at Base 0.5.3
+ cell_get_cartesian at Base 0.5.3
+ cell_get_centering at Base 0.5.3
+ cell_get_lattice_type at Base 0.5.3
+ cell_get_parameters at Base 0.5.3
+ cell_get_pointgroup at Base 0.5.3
+ cell_get_reciprocal at Base 0.5.3
+ cell_get_unique_axis at Base 0.5.3
+ cell_is_sensible at Base 0.5.3
+ cell_new at Base 0.5.3
+ cell_new_from_cell at Base 0.5.3
+ cell_new_from_direct_axes at Base 0.5.3
+ cell_new_from_parameters at Base 0.5.3
+ cell_new_from_reciprocal_axes at Base 0.5.3
+ cell_print at Base 0.5.3
+ cell_rep at Base 0.5.3
+ cell_rotate at Base 0.5.3
+ cell_set_cartesian at Base 0.5.3
+ cell_set_cartesian_a at Base 0.5.3
+ cell_set_cartesian_b at Base 0.5.3
+ cell_set_cartesian_c at Base 0.5.3
+ cell_set_centering at Base 0.5.3
+ cell_set_lattice_type at Base 0.5.3
+ cell_set_parameters at Base 0.5.3
+ cell_set_pointgroup at Base 0.5.3
+ cell_set_reciprocal at Base 0.5.3
+ cell_set_unique_axis at Base 0.5.3
+ cell_transform at Base 0.5.3
+ cell_transform_inverse at Base 0.5.3
+ check_list_symmetry at Base 0.5.3
+ check_prefix at Base 0.5.3
+ chomp at Base 0.5.3
+ cleanup_indexing at Base 0.5.3
+ close_stream at Base 0.5.3
+ copy_data at Base 0.5.3
+ copy_geom at Base 0.5.3
+ copy_hdf5_fields at Base 0.5.3
+ copy_reflist at Base 0.5.3
+ crystal_copy at Base 0.5.3
+ crystal_free at Base 0.5.3
+ crystal_get_cell at Base 0.5.3
+ crystal_get_image at Base 0.5.3
+ crystal_get_mosaicity at Base 0.5.3
+ crystal_get_num_saturated_reflections at Base 0.5.3
+ crystal_get_osf at Base 0.5.3
+ crystal_get_profile_radius at Base 0.5.3
+ crystal_get_reflections at Base 0.5.3
+ crystal_get_resolution_limit at Base 0.5.3
+ crystal_get_user_flag at Base 0.5.3
+ crystal_new at Base 0.5.3
+ crystal_set_cell at Base 0.5.3
+ crystal_set_image at Base 0.5.3
+ crystal_set_mosaicity at Base 0.5.3
+ crystal_set_num_saturated_reflections at Base 0.5.3
+ crystal_set_osf at Base 0.5.3
+ crystal_set_profile_radius at Base 0.5.3
+ crystal_set_reflections at Base 0.5.3
+ crystal_set_resolution_limit at Base 0.5.3
+ crystal_set_user_flag at Base 0.5.3
+ describe_symmetry at Base 0.5.3
+ dirax_cleanup at Base 0.5.3
+ dirax_prepare at Base 0.5.3
+ fill_in_beam_parameters at Base 0.5.3
+ fill_in_values at Base 0.5.3
+ filter_median at Base 0.5.3
+ filter_noise at Base 0.5.3
+ filters_fudge_gslcblas at Base 0.5.3
+ find_equiv_in_list at Base 0.5.3
+ find_intersections at Base 0.5.3
+ find_panel at Base 0.5.3
+ find_panel_by_name at Base 0.5.3
+ find_panel_number at Base 0.5.3
+ find_refl at Base 0.5.3
+ first_refl at Base 0.5.3
+ flat_noise at Base 0.5.3
+ forbidden_reflection at Base 0.5.3
+ free_all_crystals at Base 0.5.3
+ free_beam_parameters at Base 0.5.3
+ free_copy_hdf5_field_list at Base 0.5.3
+ free_detector_geometry at Base 0.5.3
+ free_symoplist at Base 0.5.3
+ free_symopmask at Base 0.5.3
+ gaussian_noise at Base 0.5.3
+ get_ambiguities at Base 0.5.3
+ get_asymm at Base 0.5.3
+ get_beam_parameters at Base 0.5.3
+ get_detector_geometry at Base 0.5.3
+ get_detector_pos at Base 0.5.3
+ get_equiv at Base 0.5.3
+ get_esd_intensity at Base 0.5.3
+ get_excitation_error at Base 0.5.3
+ get_indices at Base 0.5.3
+ get_intensity at Base 0.5.3
+ get_lorentz at Base 0.5.3
+ get_mean_bg at Base 0.5.3
+ get_partial at Base 0.5.3
+ get_partiality at Base 0.5.3
+ get_peak at Base 0.5.3
+ get_peaks at Base 0.5.3
+ get_phase at Base 0.5.3
+ get_pixel_extents at Base 0.5.3
+ get_pointgroup at Base 0.5.3
+ get_q at Base 0.5.3
+ get_q_for_panel at Base 0.5.3
+ get_redundancy at Base 0.5.3
+ get_refinable at Base 0.5.3
+ get_scalable at Base 0.5.3
+ get_status_label at Base 0.5.3
+ get_symmetric_indices at Base 0.5.3
+ get_temp1 at Base 0.5.3
+ get_temp2 at Base 0.5.3
+ get_tt at Base 0.5.3
+ get_value at Base 0.5.3
+ grainspotter_cleanup at Base 0.5.3
+ grainspotter_index at Base 0.5.3
+ grainspotter_prepare at Base 0.5.3
+ hdf5_read at Base 0.5.3
+ hdf5_write at Base 0.5.3
+ hdf5_write_image at Base 0.5.3
+ hdfile_close at Base 0.5.3
+ hdfile_get_string_value at Base 0.5.3
+ hdfile_is_scalar at Base 0.5.3
+ hdfile_open at Base 0.5.3
+ hdfile_read_group at Base 0.5.3
+ hdfile_set_first_image at Base 0.5.3
+ hdfile_set_image at Base 0.5.3
+ histogram_add_value at Base 0.5.3
+ histogram_free at Base 0.5.3
+ histogram_get_data at Base 0.5.3
+ histogram_get_max at Base 0.5.3
+ histogram_get_min at Base 0.5.3
+ histogram_get_num_bins at Base 0.5.3
+ histogram_init at Base 0.5.3
+ histogram_set_max at Base 0.5.3
+ histogram_set_min at Base 0.5.3
+ histogram_set_num_bins at Base 0.5.3
+ histogram_show at Base 0.5.3
+ image_add_crystal at Base 0.5.3
+ image_add_feature at Base 0.5.3
+ image_feature_closest at Base 0.5.3
+ image_feature_count at Base 0.5.3
+ image_feature_list_free at Base 0.5.3
+ image_feature_list_new at Base 0.5.3
+ image_get_feature at Base 0.5.3
+ image_remove_feature at Base 0.5.3
+ in_bad_region at Base 0.5.3
+ index_pattern at Base 0.5.3
+ indexer_str at Base 0.5.3
+ integrate_all at Base 0.5.3
+ integrate_all_2 at Base 0.5.3
+ integrate_peak at Base 0.5.3
+ integration_method at Base 0.5.3
+ intmat_copy at Base 0.5.3
+ intmat_det at Base 0.5.3
+ intmat_equals at Base 0.5.3
+ intmat_free at Base 0.5.3
+ intmat_get at Base 0.5.3
+ intmat_intmat_mult at Base 0.5.3
+ intmat_intvec_mult at Base 0.5.3
+ intmat_inverse at Base 0.5.3
+ intmat_is_identity at Base 0.5.3
+ intmat_is_inversion at Base 0.5.3
+ intmat_new at Base 0.5.3
+ intmat_print at Base 0.5.3
+ intmat_set at Base 0.5.3
+ is_centric at Base 0.5.3
+ is_centrosymmetric at Base 0.5.3
+ is_stream at Base 0.5.3
+ is_subgroup at Base 0.5.3
+ largest_q at Base 0.5.3
+ lattice_from_str at Base 0.5.3
+ load_cell_from_pdb at Base 0.5.3
+ lock_reflection at Base 0.5.3
+ make_BgMask at Base 0.5.3
+ map_all_peaks at Base 0.5.3
+ match_cell at Base 0.5.3
+ match_cell_ab at Base 0.5.3
+ max_intensity at Base 0.5.3
+ mosflm_cleanup at Base 0.5.3
+ mosflm_prepare at Base 0.5.3
+ new_copy_hdf5_field_list at Base 0.5.3
+ new_symopmask at Base 0.5.3
+ next_found_refl at Base 0.5.3
+ next_refl at Base 0.5.3
+ normalise_quaternion at Base 0.5.3
+ notrail at Base 0.5.3
+ num_equivs at Base 0.5.3
+ num_reflections at Base 0.5.3
+ open_stream_fd_for_write at Base 0.5.3
+ open_stream_for_read at Base 0.5.3
+ open_stream_for_write at Base 0.5.3
+ parse_symmetry_operations at Base 0.5.3
+ peak_sanity_check at Base 0.5.3
+ poisson_noise at Base 0.5.3
+ polarisation_correction at Base 0.5.3
+ prepare_indexing at Base 0.5.3
+ progress_bar at Base 0.5.3
+ quat_rot at Base 0.5.3
+ quaternion_modulus at Base 0.5.3
+ quaternion_valid at Base 0.5.3
+ random_flat at Base 0.5.3
+ random_quaternion at Base 0.5.3
+ read_chunk at Base 0.5.3
+ read_crystal at Base 0.5.3
+ read_reflections at Base 0.5.3
+ read_reflections_from_file at Base 0.5.3
+ reax_cleanup at Base 0.5.3
+ reax_index at Base 0.5.3
+ reax_prepare at Base 0.5.3
+ record_image at Base 0.5.3
+ reflection_free at Base 0.5.3
+ reflection_new at Base 0.5.3
+ reflist_free at Base 0.5.3
+ reflist_new at Base 0.5.3
+ render_scale at Base 0.5.3
+ res_cutoff at Base 0.5.3
+ resolution at Base 0.5.3
+ resolution_limits at Base 0.5.3
+ reverse_2d_mapping at Base 0.5.3
+ rewind_stream at Base 0.5.3
+ right_handed at Base 0.5.3
+ rotate_cell at Base 0.5.3
+ run_dirax at Base 0.5.3
+ run_mosflm at Base 0.5.3
+ run_threads at Base 0.5.3
+ run_xds at Base 0.5.3
+ safe_basename at Base 0.5.3
+ search_peaks at Base 0.5.3
+ select_intersections at Base 0.5.3
+ set_detector_pos at Base 0.5.3
+ set_esd_intensity at Base 0.5.3
+ set_intensity at Base 0.5.3
+ set_lorentz at Base 0.5.3
+ set_mean_bg at Base 0.5.3
+ set_partial at Base 0.5.3
+ set_partiality at Base 0.5.3
+ set_peak at Base 0.5.3
+ set_phase at Base 0.5.3
+ set_redundancy at Base 0.5.3
+ set_refinable at Base 0.5.3
+ set_scalable at Base 0.5.3
+ set_symmetric_indices at Base 0.5.3
+ set_symmetry_name at Base 0.5.3
+ set_temp1 at Base 0.5.3
+ set_temp2 at Base 0.5.3
+ show_matrix at Base 0.5.3
+ show_matrix_eqn at Base 0.5.3
+ simple_geometry at Base 0.5.3
+ smallest_q at Base 0.5.3
+ special_position at Base 0.5.3
+ stat_pearson_f_ignore at Base 0.5.3
+ stat_pearson_f_zero at Base 0.5.3
+ stat_pearson_i at Base 0.5.3
+ stat_r1_i at Base 0.5.3
+ stat_r1_ignore at Base 0.5.3
+ stat_r1_zero at Base 0.5.3
+ stat_r2 at Base 0.5.3
+ stat_rdiff_ignore at Base 0.5.3
+ stat_rdiff_intensity at Base 0.5.3
+ stat_rdiff_zero at Base 0.5.3
+ stat_scale_intensity at Base 0.5.3
+ stderr_lock at Base 0.5.3
+ str_lattice at Base 0.5.3
+ symmetry_name at Base 0.5.3
+ tfn_combine at Base 0.5.3
+ tfn_free at Base 0.5.3
+ tfn_from_intmat at Base 0.5.3
+ tfn_identity at Base 0.5.3
+ tfn_inverse at Base 0.5.3
+ tfn_print at Base 0.5.3
+ tfn_vector at Base 0.5.3
+ tree_depth at Base 0.5.3
+ twod_mapping at Base 0.5.3
+ uncenter_cell at Base 0.5.3
+ unlock_reflection at Base 0.5.3
+ update_partialities at Base 0.5.3
+ update_partialities_2 at Base 0.5.3
+ utils_fudge_gslcblas at Base 0.5.3
+ validate_cell at Base 0.5.3
+ validate_peaks at Base 0.5.3
+ write_chunk at Base 0.5.3
+ write_command at Base 0.5.3
+ write_detector_geometry at Base 0.5.3
+ write_line at Base 0.5.3
+ write_reflections_to_file at Base 0.5.3
+ write_reflist at Base 0.5.3
+ write_reflist_2 at Base 0.5.3
+ write_stream_header at Base 0.5.3
+ xds_cleanup at Base 0.5.3
+ xds_prepare at Base 0.5.3
diff --git a/debian/patches/fix-man-pages.patch b/debian/patches/fix-man-pages.patch
new file mode 100644
index 0000000..5d5cbd9
--- /dev/null
+++ b/debian/patches/fix-man-pages.patch
@@ -0,0 +1,24 @@
+diff -rupN crystfel-0.5.3_orig/doc/man/crystfel_geometry.5 crystfel-0.5.3/doc/man/crystfel_geometry.5
+--- crystfel-0.5.3_orig/doc/man/crystfel_geometry.5 2014-04-08 17:31:49.000000000 +0200
++++ crystfel-0.5.3/doc/man/crystfel_geometry.5 2014-04-22 09:58:20.945176355 +0200
+@@ -8,7 +8,7 @@
+
+ .TH CRYSTFEL\_GEOMETRY 5
+ .SH NAME
+-CRYSTFEL DETECTOR GEOMETRY AND BEAM DESCRIPTION FILES
++CRYSTFEL \- DETECTOR GEOMETRY AND BEAM DESCRIPTION FILES
+
+ See below for information about CrystFEL's beam description files.
+
+diff -rupN crystfel-0.5.3_orig/doc/man/get_hkl.1 crystfel-0.5.3/doc/man/get_hkl.1
+--- crystfel-0.5.3_orig/doc/man/get_hkl.1 2014-04-04 13:59:11.000000000 +0200
++++ crystfel-0.5.3/doc/man/get_hkl.1 2014-04-22 09:55:36.225177139 +0200
+@@ -77,7 +77,7 @@ In the first form, reflections with d (=
+ In the second form, anisotropic truncation will be performed with separate resolution limits \fIn1\fR, \fIn2\fR and \fIn3\fR along a*, b* and c* respectively. You must also specify \fB-p\fR or \fB--pdb\fR.
+
+ .PD 0
+-.IP \fB-p\fR \fIunitcell.pdb\fR
++.IP "\fB-p\fR \fIunitcell.pdb\fR"
+ .IP \fB--pdb=\fR\fIunitcell.pdb\fR
+ .PD
+ Specify the name of the PDB file containing at least a CRYST1 line describing the unit cell.
diff --git a/debian/patches/fix-readme.patch b/debian/patches/fix-readme.patch
new file mode 100644
index 0000000..a76b2b1
--- /dev/null
+++ b/debian/patches/fix-readme.patch
@@ -0,0 +1,22 @@
+diff -rupN crystfel-0.5.3_orig/README crystfel-0.5.3/README
+--- crystfel-0.5.3_orig/README 2014-04-09 16:07:02.000000000 +0200
++++ crystfel-0.5.3/README 2014-04-22 10:33:49.149166227 +0200
+@@ -99,6 +99,18 @@ documentation created using GTK-Doc.
+ Installation
+ ------------
+
++NOTE: CrystFEL relies on external programs to index patterns. If CCP4 is not
++already installed, and if you'd like to use MOSFLM indexing, calculate structure
++factors for simulation or convert data into a MTZ files, you'll need to install
++it. Go to the CCP4 website (http://www.ccp4.ac.uk/) and follow the instructions
++there. Check that CCP4 is installed and working properly by running ipmosflm on
++a command line. You should see a brief welcome message and a prompt, and no
++errors or warnings. If you'd like to index patterns using DirAx, you'll need to
++install it separately. Follow the instructions on the DirAx website.
++(http://www.crystal.chem.uu.nl/distr/dirax/). Check that DirAx is installed and
++working properly by running dirax on a command line. You should see a brief
++welcome message and a prompt, and no errors or warnings.
++
+ See the "INSTALL" file for the generic instructions on how to use the build
+ system. In short, it's the usual:
+
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..a741f43
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,3 @@
+fix-readme.patch
+fix-man-pages.patch
+skip-gpu-sim-check.patch
diff --git a/debian/patches/skip-gpu-sim-check.patch b/debian/patches/skip-gpu-sim-check.patch
new file mode 100644
index 0000000..5159c3a
--- /dev/null
+++ b/debian/patches/skip-gpu-sim-check.patch
@@ -0,0 +1,41 @@
+diff -rupN crystfel-0.5.3_orig/Makefile.in crystfel-0.5.3/Makefile.in
+--- crystfel-0.5.3_orig/Makefile.in 2014-04-09 16:17:51.000000000 +0200
++++ crystfel-0.5.3/Makefile.in 2014-04-15 14:42:24.024245651 +0200
+@@ -76,8 +76,8 @@ TESTS = tests/list_check$(EXEEXT) $(MERG
+ @BUILD_EXPLORER_TRUE at am__append_2 = src/cell_explorer
+ @HAVE_CAIRO_TRUE at am__append_3 = src/render_hkl
+ @HAVE_OPENCL_TRUE at am__append_4 = src/cl-utils.c src/diffraction-gpu.c
+- at HAVE_OPENCL_TRUE@am__append_5 = tests/gpu_sim_check
+- at HAVE_OPENCL_TRUE@am__append_6 = tests/gpu_sim_check
++#@HAVE_OPENCL_TRUE at am__append_5 = tests/gpu_sim_check
++#@HAVE_OPENCL_TRUE at am__append_6 = tests/gpu_sim_check
+ @HAVE_CAIRO_TRUE@@HAVE_PANGOCAIRO_TRUE@@HAVE_PANGO_TRUE at am__append_7 = src/scaling-report.c
+ subdir = .
+ DIST_COMMON = README $(am__configure_deps) $(srcdir)/Makefile.am \
+@@ -121,7 +121,7 @@ am__installdirs = "$(DESTDIR)$(bindir)"
+ "$(DESTDIR)$(man5dir)" "$(DESTDIR)$(man7dir)" \
+ "$(DESTDIR)$(crystfeldir)" "$(DESTDIR)$(crystfeldocdir)" \
+ "$(DESTDIR)$(scriptdir)"
+- at HAVE_OPENCL_TRUE@am__EXEEXT_4 = tests/gpu_sim_check$(EXEEXT)
++#@HAVE_OPENCL_TRUE at am__EXEEXT_4 = tests/gpu_sim_check$(EXEEXT)
+ PROGRAMS = $(bin_PROGRAMS) $(noinst_PROGRAMS)
+ am__dirstamp = $(am__leading_dot)dirstamp
+ am_src_ambigator_OBJECTS = src/ambigator.$(OBJEXT)
+@@ -224,7 +224,7 @@ tests_centering_check_DEPENDENCIES = $(t
+ $(top_builddir)/libcrystfel/libcrystfel.la
+ am__tests_gpu_sim_check_SOURCES_DIST = tests/gpu_sim_check.c \
+ src/diffraction.c src/diffraction-gpu.c src/cl-utils.c
+- at HAVE_OPENCL_TRUE@am_tests_gpu_sim_check_OBJECTS = \
++#@HAVE_OPENCL_TRUE at am_tests_gpu_sim_check_OBJECTS = \
+ @HAVE_OPENCL_TRUE@ tests/gpu_sim_check.$(OBJEXT) \
+ @HAVE_OPENCL_TRUE@ src/diffraction.$(OBJEXT) \
+ @HAVE_OPENCL_TRUE@ src/diffraction-gpu.$(OBJEXT) \
+@@ -726,7 +726,7 @@ LDADD = $(top_builddir)/lib/libgnu.la @I
+ src_partial_sim_SOURCES = src/partial_sim.c
+ src_pattern_sim_SOURCES = src/pattern_sim.c src/diffraction.c \
+ $(am__append_4)
+- at HAVE_OPENCL_TRUE@tests_gpu_sim_check_SOURCES = tests/gpu_sim_check.c src/diffraction.c \
++#@HAVE_OPENCL_TRUE at tests_gpu_sim_check_SOURCES = tests/gpu_sim_check.c src/diffraction.c \
+ @HAVE_OPENCL_TRUE@ src/diffraction-gpu.c src/cl-utils.c
+
+ src_process_hkl_SOURCES = src/process_hkl.c
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..cee1163
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,20 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+%:
+ dh $@ --with autotools-dev
+
+override_dh_auto_configure:
+ dh_auto_configure -- --enable-gtk-doc --with-opencl
+
+override_dh_strip:
+ dh_strip --dbg-package=libcrystfel-dbg
+
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-science/packages/crystfel.git
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