Antonio

Python3 support

7

Hi all. @cryos, will Avogadro ever support Python3? Is Avogadro still under development or your efforts are entirely for Avogadro2?

[seqan 2.4.0] app_test_fiona failed

3

Hi all. `app_test_fiona` test is failing on `Fedora` with following error on `x86_64` architecture only: ``` Start 3: app_test_fiona 3: Test command: /usr/bin/python2 "/builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/tests/run_tests.py" "/builddir/build/BUILD/seqan-seqan-v2.4.0" "/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release" 3: Test timeout computed...

Sphinx 5.0.2 is failing with SCons 4.4.0

7

Hi all. **Describe the bug** ``` Running Sphinx v5.0.2 WARNING: html_static_path entry '_static' does not exist [autosummary] generating autosummary for: SCons.Node.rst, SCons.Platform.rst, SCons.Scanner.rst, SCons.Script.rst, SCons.Tool.rst, SCons.Variables.rst, SCons.compat.rst, SCons.rst, index.rst building...

Hi all. Linker fails to compile the `test_fsunlinsol_*' tests when i use LTO flags (**-flto=auto -ffat-lto-objects -fexceptions**) ``` [ 81%] Linking Fortran executable test_fsunlinsol_sptfqmr_mod_serial cd /home/sagitter/rpmbuild/BUILD/sundials-6.0.0/sundials-6.0.0/build/examples/sunlinsol/sptfqmr/serial && /usr/bin/cmake -E cmake_link_script...

openbabel-python.i:79: Error: Syntax error in input

1

Hi all. [x ] I believe this to be a bug with Open Babel ## Environment Information Open Babel version: 3.1.1 Operating system and version: CentOS 7 Python-3.8.6 swig-2.0.10 ##...

Hi all. **Describe the bug** `pythonTestDbCLI` test is failing with following errors: ``` /builddir/build/BUILD/cmake-3.23.0-rc2/Source/CTest/cmCTestRunTest.cxx:1062 176/182 Test #176: pythonTestDbCLI ........................ /builddir/build/BUILD/cmake-3.23.0-rc2/Source/CTest/cmCTestRunTest.cxx:1065 Testing pythonTestDbCLI ... /builddir/build/BUILD/cmake-3.23.0-rc2/Source/CTest/cmCTestRunTest.cxx:259 ***Failed 2.92 sec /builddir/build/BUILD/cmake-3.23.0-rc2/Source/CTest/cmCTestRunTest.cxx:263 FFFFFFFFFFFF ======================================================================...

appdata file

4

Please, add an appdata file in the source archive; something like: ``` antimony.desktop CC0-1.0 MIT Computer-aided design CAD tool Science Antimony is a computer-aided design (CAD) tool from a parallel...

Hi, 2 tests failed by compiling latest Preprocess-1.2.2 under Python3: http://fpaste.org/272764/ ``` ====================================================================== FAIL: preprocess_inputs/preprocessinputs/recursive_include_a.py ---------------------------------------------------------------------- Traceback (most recent call last): File "./test_preprocess_inputs.py", line 103, in testFunction = lambda self,...

Hi all. `SystemTest_Converters_Correctness` test is not running with this error: ``` + /usr/bin/ctest --output-on-failure --force-new-ctest-process -j6 --V Test project /builddir/build/BUILD/percolator-rel-3-06/converters Start 1: SystemTest_Converters_Correctness 1/1 Test #1: SystemTest_Converters_Correctness ...***Failed 0.04 sec...

BGZF compression test failures

9

Hi all. ### Setup I am reporting a problem with Biopython version, Python version, and operating system as follows: Fedora 40 x86_64 Python-3.12.1 biopython-1.82 ### Expected behaviour No errors ###...