python-pymol-3.1.0-bp160.1.10

- changes to .spec file:
  * to make build work on leap 15.6, add sle15_python_module_pythons
    and conditional BuildRequires: gcc12-c++
  * drop skip_python2 and oldpython

- update to 3.1.0
  * File Support
  - BCIF import support
  - gzipped-compressed SDF (SDFGZ) import support
  * Python API
  - "delete_states" command (removal of one or more states)
  - "declare_command" extension for improved ergonomics of introducing
    and customizing PyMOL functionality
  - "cell_color" setting for altering unit cell colors
  * Developer & Infrastructure
  - Migration from distutils to setuptools

- Add reproducible.patch to normalize build date (boo#1047218)
- Remove no-build-date.patch

- Update to version 3.0.0+git.1725549602.9d3061c:
  * Symbol renaming in molfile_plugin and internal linkage
  * New command: delete_states
  * mark bind() calls with override where needed
  * Separate CGO to VBO logic out into functions
  * Remove unused returnData
  * Use vector for memory alloc
  * Use struct for total vert counts in CGO.cpp
  * Remove _PYMOL_IOS (Discontinued; prep for MVK)
  * Python 3.12 TypeError: convert progress to int for progress bar
  * Fix ray/draw panel error when modifying units
- Remove upstream patches:
  * pymol3-version-compare.patch
  * no-o3.patch
  * pymol3-numpy2.patch

- add patches:
  * pymol3-numpy2.patch:  add numpy-2 compatability
  * pymol3-version-compare.patch:  fix tests/helpers/test_utils.py

- update to 3.0.0
  * Panels
  - Nucleic Acid Builder supported
  - Scenes Panel (Basic version)
  - Improved APBS electrostatics plugin integrated
  * Distance/Bonding detection
  - Halogen-bond detection and display
  * Python API
  - "fnab" command (sequence to nucleic acid chain)
  - Improved CGO builder API
  - get_sasa_relative() "subsele" argument added
  - new clip modes/API
  - iterate() adds "explicit_valence" and "explicit_degree"
  - "cell_centered" setting added
  - by grid-cell background gradient "bg_gradient=2"
  - look_at() added
  - experimental "curve_new" / "move_on_curve"
  * Developer
  - C++17 required
  - pymol-testing integrated
  - pytest introduced
  - Github Actions CI
  * And many other fixes and small additions provided by
    developers and the community...
- spec file:
  * re-add test related stuff as upstream introduced a pytest
    based testing
  * drop TestExporting.testglTF - requires an executable from
    Schrodinger
  * on Leap, drop / tweak some tests to fit old package versions

- update to 2.5.0
  * File Import/Export
  - DX binary map import (*dxbin)
  - PDB/MMTF export: symmetry information now added
  - Improved FASTA import
  - Support for map.gz and mrc.gz extensions
  * Builder & Panels
  - Improved Fuse command (disallows hypervalent bonds,
    substitute monovalent atoms instead of attaching to them)
  - Customizable keyboard shortcut menu
  - Properties inspector now supports unsetting settings with
    “Delete” key
  * Graphics & Visualization
  - Ray interior colors now match primitives with
    `set ray_interior_color, atomic`
  - Isomesh transparency support
  - `sphere_mode` 5 removed (9 as replacement)
  - Curved cartoon cylindrical helices
  - Isosurface generation via marching cubes with setting
    `isosurface_algorithm, (0, 1)` (0 requires VTKm)
  * PBC Handling
  - Periodic boundary conditions supported in rebond, smooth,
    and intra_fit
  * Python API
  - Python 2 support removed
  - pbc argument added to rebond, smooth, and intra_fit
  - png(None) returns bytes
  - scene_order() allows list for `names`
  - pbc_wrap() and pbc_unwrap added
  - matrix_reset() supports `state=0` for all states
  - editing_ring() added
  - unset now restores the default value for global settings
  - load_traj now uses state=1 by default
  - get_area command and dots representation: Exclude
    “flag ignore” atoms
- no-o3.patch: adapt to 2.5.0
- spec file:
  * some tweaks to adapt to 2.5.0
  * remove test related stuff; test run commands are removed
    from 2.5.0 as unmaintained and useless

- Remove the execute bit from some test scripts to remove a spurious
  requirement.

- Skip python3.6 because numpy no longer support it.
- Add mmtf-cpp-devel and use msgpackc.
- Attempt to get the test to run.
  * Use _service to download pymol-testing for test data.
  * Use bcond to enable/disable testing arguments.
  * Pymol seems to need itself to test.
  * Add %check section.

- Update to 2.4.0:
  * load_traj
  - support netcdf format
  - support `selection` argument with all file formats
  * CCP4/MRC Map Support
  - Distinguish .ccp4 and .mrc extensions (regarding origin)
  - .map extension: auto-detect the format
  * New distance mode 8
  * MMTF export: Consider `pdb_retain_ids` setting
  * GLTF export (based on collada2gltf)
  * New `internal_gui_name_color_mode` setting
  * MPEG4 Movie export: Apply `movie_fps` setting to exported
    file
  * Python API
  - Improved error handling with exceptions
  - New: cmd.rebond()
  - New: cmd.get_capabilities()
  - Fix: cmd.get_bonds() state off by one
  - cmd.fit() et al.: raise on error
  * Launch Options
  - Restore `-V` launch argument for external GUI height
  - macOS: `open` event opens new window

- Remove glew runtime dependency (only contains debug tools and
  documentation).
- Remove freeglut build dependency (unused unless enabled with
  '--glut' setup.py option).
- Use https for URL.

- Upgrade to 2.3.0:
  * atom-level cartoon_transparency
  * aln export for Nucleic Acids
  * new API function: cmd.set_raw_alignment()
  * fetch async=0 by default
  * fast MMTF export (requires mmtf-cpp)
  * new setting: seq_view_gap_mode

- Update to version 2.2.0+git.1544795767.c481a7c1:
  * fix SettingUniqueFromPyList w/ float3
  * remove pymol::Image::Image(T&& vec, ...)
  * refactor: pymol::Image tweaks
  * rewrite "get_raw_alignment"
  * refactor: pymol::vla::operator->() usage
  * fix #16 pymol::vla::operator[] for VS2015 32bit
  * fix pymol::vla::operator+ for VS2015
  * pymol::Image::pixels()
  * fix build
  * fix macOS build
- Switch off msgpackc as we don't have mmtf-cpp packaged.

- Version update to 2.2.0:
  * Switch devel links to github
  * No finegraned news file see ChangeLog for commit info
- Rebase patch no-o3.patch

- Fix fdupes call
- Install license and docu files

- Trim marketing words from description.

- Update to normal release that was released on 2018-03-19, 2 commits
  changing tiny stuff compared to svn rev 4187
- Rename pymol to python-pymol to respect the packaging guidelines
- Fix qt5 devel python dependency to pull py3 and py2 both
- Obey system optflags instead of passing -O3
  * no-o3.patch

- update to svn rev 4187
  * PyQt interface (2.1.0)
  * stick_round_nub for COLLADA export
  * UTF-8 in feedback
  * display_scale_factor (ported from Incentive PyMOL)
  * dx map import: support "type float" and skewed delta
  * new selection keywords: polymer.protein polymer.nucleic
  * new command: multifilesave
  * MMTF export (requires simplemmtf python module)
  * select: present, state -1 -> current object state
  * create: source_state = -1 -> current
    (was: source_state = -1/0 -> all)
  * cif: support quoted '?' and '.' as values
    cif_get_array -> None instead of empty string for ? and .
  * fix copy discrete object w/o coords
  * fix loading pdbqr AutoDock 4 atom types
  * fix get_model('none') and get_str('mol', 'none')
  * h_add refactored: 5x faster, support discrete objects-

- update to svn rev 4184
  * Python 3.7 support (https://sf.net/p/pymol/bugs/197/)
  * enable align with alt-codes
  - allow matching of non-alt-code to alt-code atoms in alignments
  - swap sorting priority of 'name' and 'alt' identifiers
  - sort empty 'alt' before non-empty 'alt'
  * flags 6 and 7 for protein and nucleic acid
  * mmCIF: read _atom_site.pdbx_formal_charge
  * improve coordinate loading from mmcif chem_comp files
  - ignore columns with all ? (missing) values
  - select columns with "chem_comp_cartn_use" setting
  * fix h_add: skip missing coordinates
  * Python API: New "auto library mode". Automatically start a
    non-GUI PyMOL instance if the pymol.cmd API is used without
    running pymol.launch() first
  * pdb_echo_tags for mmCIF and MMTF
  * command parser: improve exception handling
  * fix some PSE export memory leaks
  * pymol2.cmd2: eliminate (non-weak) circular references
  * movie making: reinterpolate after add_nutate/add_roll etc.
  * support "module:callable" in loadfunctions/safefunctions
  * yellow state indicator for discrete objects
  * mpng modal draw improvements
  * fix elements from .gro files (pymol/bugs/196, r4181 regression)
  * save .mtl: raise exception
  * Python 3:
  - fix "GUI Font Size" dialog (pmw/bugs/47)
  - fix COLLADA export
  * some elements wrong from SDF and XYZ
  * pse_export_version support with Python 3

- 1.9.0.0
  * L > residues (oneletter)
  * fix py3 crash in "A > copy to object"
  * fix scene object visibility with hidden groups
  * fix "ending" after loading movie session

- update to svn rev 4177
  * expose "oneletter" to label/iterate
  * sequence viewer: MSE=M SEC=U
  * wire/licorice rep aliases
  * menu: A > copy to object
  * new commands: copy_to, uniquify
  * fix slow 'extract' performance

- obsolete and provide pymol

- move to python singlespec

- 1.8.7.0
  * support "not ..." and "enabled" in name patterns (e.g.: delete not enabled)
  * improve/fix unicode+utf-8 handling for labels
  * iterate color settings: type int (e.g.: iterate all, print(s.sphere_color))
  * fix cmd.load with contents https://sf.net/p/pymol/mailman/message/35966326/
  * fix ray tracing of stick_ball + valence https://sf.net/p/pymol/mailman/message/35928857/
  * web.pymolhttpd -> pymol.pymolhttpd
    Generic "web" name conflicts with webpy
    https://sf.net/p/pymol/bugs/148/
  * make build reproducible
    https://sf.net/p/pymol/patches/12/
  * delete obsolete packaging files
  * internal command line: consistent behavior across platforms
  * new "label" selection operator
  * alter_state: remove restriction on x/y/z/flags
  * iterate/label: expose "state" for discrete atoms
  * CTRL+L drag/click -> move/center in 3-Button-Viewing mode
  * auto-detect $PREFIX/share/pymol as $PYMOL_PATH
  * locale LC_NUMERIC=C float parsing/formatting
  * Python 3: fix wrong PyCapsule_New destructor
  * PSE compatibility between Python 2 and 3

- 1.8.6.1 fixes
  * Python 3.6 fixes
  * Python 3: fix builder bond order buttons (Red Hat Bug 1442127)
  * fix MAE export PDB residue/atom names
  * restored "scene_animation" setting (1.7.6 regression)
  * restored "import cmd" prevention (1.8.6.0 regression)

- remove explicity library dependency

- remove explicity library dependency

- require libmsgpack

- 1.8.4.0 release

- update to svn rev 4161
  * pse_export_version: legacy scenes support
  * use ignore_case setting with set_name command
  * setup.py: detect anaconda prefix

- update to svn rev 4160
  * experimental MMTF load support
  * map export in CCP4 format
  * SDF V3000 import/export support
  * refactor molecular file formats export: Unified handling of PDB, PQR, mmCIF, MOL2, SDF, XYZ, MAE
  * PLY geometry import (as CGO)
  * new command: unset_deep
  * new setting: cartoon_all_alt: Create cartoon for every alt code
  * stick_h_scale: default=1.0 (was: 0.4) but remove dependency on negative stick_radius
  * auto_show_classified: Visualize small (< 50 atoms) polymer classified molecules like organic
  * bymol selection operator: ignore zero-order bonds
  * menu: isomesh/surface negative color
  * improve alignment of residues with unknown resn (e.g. ligands):
    give a match score of 5 to perfect matches of unknown residue codes.
    Previously, those got match score -1.
  * remove broken and obsolete "PMO" file support
  * use "label_digits" setting with "label" command
  * do not resize window when loading a session file
  * fix ignored SCALE w/ identity rotation (e.g. 1WAP)
  * fix "scene auto, clear" (Scene > Delete)
  * new setting: pick_shading: do flat shading for programmable image color analysis
  * experimental cmd.raw_image_callback: post cmd.draw() callback