Re: openbabel-3.1* in Rawhide
IQmol isn't compatible with openbabel3. Latest 2.15.0 release (compiled in Fedora) is missing in upstream's repository (but available for Windows/Mac, Linux abandoned?) On 11/6/21 14:01, Antonio T. sagitter wrote: side-tag: f36-build-side-47471 On 11/5/21 21:33, Alexander Ploumistos wrote: On Fri, Nov 5, 2021 at 9:23 PM Antonio T. sagitter wrote: On 10/24/21 15:11, Alexander Ploumistos wrote: Hello Antonio, On Sun, Oct 24, 2021 at 3:05 PM Antonio T. sagitter wrote: We are ready to push openbabel3 in Rawhide Will it be just Rawhide? Will you please let us know when the build is done in order to rebuild dependent packages? Within 24 hours i will create a side-tag in Rawhide. -- --- Antonio Trande Fedora Project mailto: sagit...@fedoraproject.org GPG key: 0xCC1CFEF30920C8AE GPG key server: https://keyserver1.pgp.com/ OpenPGP_0xCC1CFEF30920C8AE.asc Description: OpenPGP public key OpenPGP_signature Description: OpenPGP digital signature ___ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure
Re: openbabel-3.1* in Rawhide
side-tag: f36-build-side-47471 On 11/5/21 21:33, Alexander Ploumistos wrote: On Fri, Nov 5, 2021 at 9:23 PM Antonio T. sagitter wrote: On 10/24/21 15:11, Alexander Ploumistos wrote: Hello Antonio, On Sun, Oct 24, 2021 at 3:05 PM Antonio T. sagitter wrote: We are ready to push openbabel3 in Rawhide Will it be just Rawhide? Will you please let us know when the build is done in order to rebuild dependent packages? Within 24 hours i will create a side-tag in Rawhide. Thanks Antonio, I'll probably be able to do the rebuild on Sunday night. -- --- Antonio Trande Fedora Project mailto: sagit...@fedoraproject.org GPG key: 0xCC1CFEF30920C8AE GPG key server: https://keyserver1.pgp.com/ OpenPGP_0xCC1CFEF30920C8AE.asc Description: OpenPGP public key OpenPGP_signature Description: OpenPGP digital signature ___ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure
Re: openbabel-3.1* in Rawhide
On Fri, Nov 5, 2021 at 9:23 PM Antonio T. sagitter wrote: > > On 10/24/21 15:11, Alexander Ploumistos wrote: > > Hello Antonio, > > > > On Sun, Oct 24, 2021 at 3:05 PM Antonio T. sagitter > > wrote: > >> > >> We are ready to push openbabel3 in Rawhide > > > > Will it be just Rawhide? Will you please let us know when the build is > > done in order to rebuild dependent packages? > > Within 24 hours i will create a side-tag in Rawhide. Thanks Antonio, I'll probably be able to do the rebuild on Sunday night. ___ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure
Re: openbabel-3.1* in Rawhide
On 10/24/21 15:11, Alexander Ploumistos wrote: Hello Antonio, On Sun, Oct 24, 2021 at 3:05 PM Antonio T. sagitter wrote: We are ready to push openbabel3 in Rawhide Will it be just Rawhide? Will you please let us know when the build is done in order to rebuild dependent packages? Within 24 hours i will create a side-tag in Rawhide. Are we saying goodbye to Avogadro 1.x? Thank you for all the work you've put into this, A. ___ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure -- --- Antonio Trande Fedora Project mailto: sagit...@fedoraproject.org GPG key: 0xCC1CFEF30920C8AE GPG key server: https://keyserver1.pgp.com/ OpenPGP_0xCC1CFEF30920C8AE.asc Description: OpenPGP public key OpenPGP_signature Description: OpenPGP digital signature ___ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure
Re: openbabel-3.1* in Rawhide
On 10/24/21 15:11, Alexander Ploumistos wrote: Hello Antonio, Hi Alexander. On Sun, Oct 24, 2021 at 3:05 PM Antonio T. sagitter wrote: We are ready to push openbabel3 in Rawhide Will it be just Rawhide? Yes. Will you please let us know when the build is done in order to rebuild dependent packages? Not before one week at least. I will mail you again just before i have created a side-tag in Rawhide. Are we saying goodbye to Avogadro 1.x? Well, Avogadro 1 is no longer under active development since September 2021. We have Avogadro 2 now. Thank you for all the work you've put into this, A. ___ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure -- --- Antonio Trande Fedora Project mailto: sagit...@fedoraproject.org GPG key: 0xCC1CFEF30920C8AE GPG key server: https://keyserver1.pgp.com/ OpenPGP_0xCC1CFEF30920C8AE.asc Description: OpenPGP public key OpenPGP_signature Description: OpenPGP digital signature ___ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure
Re: openbabel-3.1* in Rawhide
Hello Antonio, On Sun, Oct 24, 2021 at 3:05 PM Antonio T. sagitter wrote: > > We are ready to push openbabel3 in Rawhide Will it be just Rawhide? Will you please let us know when the build is done in order to rebuild dependent packages? Are we saying goodbye to Avogadro 1.x? Thank you for all the work you've put into this, A. ___ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure
Re: openbabel-3.1* in Rawhide
Hi all. We are ready to push openbabel3 in Rawhide, all packages (except chemtool that requires openbabel in runtime) have been rebuilt: https://copr.fedorainfracloud.org/coprs/sagitter/Openbabel-3/builds/ -- --- Antonio Trande Fedora Project mailto: sagit...@fedoraproject.org GPG key: 0xCC1CFEF30920C8AE GPG key server: https://keyserver1.pgp.com/ OpenPGP_0xCC1CFEF30920C8AE.asc Description: OpenPGP public key OpenPGP_signature Description: OpenPGP digital signature ___ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure
Re: openbabel-3.1* in Rawhide
Hi all. Even Kalzium (new release) is rebuilt against openbabel3 -- --- Antonio Trande Fedora Project mailto: sagit...@fedoraproject.org GPG key: 0x29FBC85D7A51CC2F GPG key server: https://keyserver1.pgp.com/ OpenPGP_0x29FBC85D7A51CC2F.asc Description: OpenPGP public key OpenPGP_signature Description: OpenPGP digital signature ___ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure
Re: openbabel-3.1* in Rawhide
On 9/26/21 05:07, Jerry James wrote:
> On Sat, Sep 25, 2021 at 5:10 PM Alexander Ploumistos
> wrote:
>> I built the latest avogadro2 and avogadro2-libs from the srpm in your
>> copr for F34 and I hit some graphical glitches again. On Wayland,
>> Avogadro2 for X11 has a transparent canvas, whereas the other one (I
>> guess Wayland) doesn't, but as soon as I add a fourth atom to the
>> drawing, it crashes:
>>
>> /usr/include/c++/11/bits/stl_vector.h:1045: std::vector<_Tp,
>> _Alloc>::reference std::vector<_Tp,
>> _Alloc>::operator[](std::vector<_Tp, _Alloc>::size_type) [with _Tp =
>> Eigen::Matrix; _Alloc =
>> std::allocator >; std::vector<_Tp,
>> _Alloc>::reference = Eigen::Matrix&; std::vector<_Tp,
>> _Alloc>::size_type = long unsigned int]: Assertion '__n <
>> this->size()' failed.
>> Aborted (core dumped)
>
> I don't know if this is the same as the inchi-related abort, but that
> one is caused by this code, on lines 178-180 of molecule_smiles.cpp,
> in Molecule::ToInChI():
>
> std::string s = ostream.str();
> s[s.length() - 1] = '\0'; // Abort happens here
> return ( QString( s.c_str() ) );
>
> The abort happens because s is the empty string, so s.length() == 0,
> and assigning to s[-1] just isn't a good idea. I'm pretty sure that
> line isn't needed anyway. Isn't s.c_str() guaranteed to provide a
> null-terminated C string?
In addition to .c_str() providing a null-terminated C string, the above
code is wrong also in another sense: s.length() is the length of the
string EXCLUDING THE TERMINATOR so that code is in fact removing the
last letter of the string which can't be the purpose.
You can easily verify this behavior with
#include
#include
int main ()
{
std::string str1(""), str2("c");
std::cout << "str1.length()= " << str1.length() << ", str2.length()= "
<< str2.length() << std::endl;
return 0;
}
which prints out
$ ./a.out
str1.length()= 0, str2.length()= 1
--
Susi Lehtola
Fedora Project Contributor
jussileht...@fedoraproject.org
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Re: openbabel-3.1* in Rawhide
On Sun, Sep 26, 2021 at 12:59 PM Antonio T. sagitter wrote: > > On 9/26/21 10:22, Antonio T. sagitter wrote: > > I moved the openbabel's libraries under a private lib directory. > > 'desktop' files are modified for working in this sense. > > Sorry, i meant gchemistry's libraries under a private lib directory. > > > > Let me check again Avogadro2. My mistake about gnome-chemistry-utils, after the failure to open some cif files in F35, in F34 I kept launching the programs from the terminal. They do work (with the same problems they had with Open Babel 2). Avogadro launched with the right backend only suffers from the crash after the addition of a fourth atom. The Wayland backend works also on X11, whereas the X11 one shows a transparent canvas on Wayland. I am using your last copr build. ___ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure
Re: openbabel-3.1* in Rawhide
On 9/26/21 10:22, Antonio T. sagitter wrote: On 9/26/21 01:10, Alexander Ploumistos wrote: On Sat, Sep 25, 2021 at 5:05 PM Alexander Ploumistos wrote: I will try with a Fedora 34 VM later and report back. I got pretty much the same results on F34. I think xdrawchem works better with Open Babel 3 than it does with Open Babel 2, at least as far as structure cleanup goes (I installed the current version in F34). With Open Babel 2, SMILES output is also asterisks and trying InChi output crashes the program, so nothing changed there. gnome-chemistry-utils programs can't find the required shared object files in F34 either. I moved the openbabel's libraries under a private lib directory. 'desktop' files are modified for working in this sense. Sorry, i meant gchemistry's libraries under a private lib directory. Let me check again Avogadro2. ___ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure -- --- Antonio Trande Fedora Project mailto: sagit...@fedoraproject.org GPG key: 0x29FBC85D7A51CC2F GPG key server: https://keyserver1.pgp.com/ OpenPGP_0x29FBC85D7A51CC2F.asc Description: OpenPGP public key OpenPGP_signature Description: OpenPGP digital signature ___ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure
Re: openbabel-3.1* in Rawhide
I have rebuilt Avogadro2* against openbabel3 The package provides two desktop files, for Wayland and x11 with different environment variables. That was a bug: https://github.com/OpenChemistry/avogadroapp/issues/167 I will apply the patch and try again. On 9/25/21 17:05, Alexander Ploumistos wrote: Hello Antonio, * Avogadro2: Avogadro appears to be working, but I can't see anything on the canvas, it displays whatever window is behind it on the screen, or the wallpaper if there's nothing else there. Maybe a Wayland bug? I will try with a Fedora 34 VM later and report back. -- --- Antonio Trande Fedora Project mailto: sagit...@fedoraproject.org GPG key: 0x29FBC85D7A51CC2F GPG key server: https://keyserver1.pgp.com/ OpenPGP_0x29FBC85D7A51CC2F.asc Description: OpenPGP public key OpenPGP_signature Description: OpenPGP digital signature ___ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure
Re: openbabel-3.1* in Rawhide
On 9/26/21 01:10, Alexander Ploumistos wrote: On Sat, Sep 25, 2021 at 5:05 PM Alexander Ploumistos wrote: I will try with a Fedora 34 VM later and report back. I got pretty much the same results on F34. I think xdrawchem works better with Open Babel 3 than it does with Open Babel 2, at least as far as structure cleanup goes (I installed the current version in F34). With Open Babel 2, SMILES output is also asterisks and trying InChi output crashes the program, so nothing changed there. gnome-chemistry-utils programs can't find the required shared object files in F34 either. I moved the openbabel's libraries under a private lib directory. 'desktop' files are modified for working in this sense. Let me check again Avogadro2. -- --- Antonio Trande Fedora Project mailto: sagit...@fedoraproject.org GPG key: 0x29FBC85D7A51CC2F GPG key server: https://keyserver1.pgp.com/ OpenPGP_0x29FBC85D7A51CC2F.asc Description: OpenPGP public key OpenPGP_signature Description: OpenPGP digital signature ___ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure
Re: openbabel-3.1* in Rawhide
On Sat, Sep 25, 2021 at 08:07:20PM -0600, Jerry James wrote: > On Sat, Sep 25, 2021 at 5:10 PM Alexander Ploumistos > wrote: > > I built the latest avogadro2 and avogadro2-libs from the srpm in your > > copr for F34 and I hit some graphical glitches again. On Wayland, > > Avogadro2 for X11 has a transparent canvas, whereas the other one (I > > guess Wayland) doesn't, but as soon as I add a fourth atom to the > > drawing, it crashes: > > > > /usr/include/c++/11/bits/stl_vector.h:1045: std::vector<_Tp, > > _Alloc>::reference std::vector<_Tp, > > _Alloc>::operator[](std::vector<_Tp, _Alloc>::size_type) [with _Tp = > > Eigen::Matrix; _Alloc = > > std::allocator >; std::vector<_Tp, > > _Alloc>::reference = Eigen::Matrix&; std::vector<_Tp, > > _Alloc>::size_type = long unsigned int]: Assertion '__n < > > this->size()' failed. > > Aborted (core dumped) > > I don't know if this is the same as the inchi-related abort, but that > one is caused by this code, on lines 178-180 of molecule_smiles.cpp, > in Molecule::ToInChI(): > > std::string s = ostream.str(); > s[s.length() - 1] = '\0'; // Abort happens here > return ( QString( s.c_str() ) ); > > The abort happens because s is the empty string, so s.length() == 0, > and assigning to s[-1] just isn't a good idea. I'm pretty sure that > line isn't needed anyway. Isn't s.c_str() guaranteed to provide a > null-terminated C string? Yes, this is guaranteed: > Returns a pointer to an array that contains a null-terminated > sequence of characters (i.e., a C-string) representing the current > value of the string object. Zbyszek ___ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure
Re: openbabel-3.1* in Rawhide
On Sat, Sep 25, 2021 at 5:10 PM Alexander Ploumistos wrote: > I built the latest avogadro2 and avogadro2-libs from the srpm in your > copr for F34 and I hit some graphical glitches again. On Wayland, > Avogadro2 for X11 has a transparent canvas, whereas the other one (I > guess Wayland) doesn't, but as soon as I add a fourth atom to the > drawing, it crashes: > > /usr/include/c++/11/bits/stl_vector.h:1045: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, > _Alloc>::operator[](std::vector<_Tp, _Alloc>::size_type) [with _Tp = > Eigen::Matrix; _Alloc = > std::allocator >; std::vector<_Tp, > _Alloc>::reference = Eigen::Matrix&; std::vector<_Tp, > _Alloc>::size_type = long unsigned int]: Assertion '__n < > this->size()' failed. > Aborted (core dumped) I don't know if this is the same as the inchi-related abort, but that one is caused by this code, on lines 178-180 of molecule_smiles.cpp, in Molecule::ToInChI(): std::string s = ostream.str(); s[s.length() - 1] = '\0'; // Abort happens here return ( QString( s.c_str() ) ); The abort happens because s is the empty string, so s.length() == 0, and assigning to s[-1] just isn't a good idea. I'm pretty sure that line isn't needed anyway. Isn't s.c_str() guaranteed to provide a null-terminated C string? -- Jerry James http://www.jamezone.org/ ___ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure
Re: openbabel-3.1* in Rawhide
On Sat, Sep 25, 2021 at 5:05 PM Alexander Ploumistos wrote: > > I will try with a Fedora 34 VM later and report back. I got pretty much the same results on F34. I think xdrawchem works better with Open Babel 3 than it does with Open Babel 2, at least as far as structure cleanup goes (I installed the current version in F34). With Open Babel 2, SMILES output is also asterisks and trying InChi output crashes the program, so nothing changed there. gnome-chemistry-utils programs can't find the required shared object files in F34 either. I built the latest avogadro2 and avogadro2-libs from the srpm in your copr for F34 and I hit some graphical glitches again. On Wayland, Avogadro2 for X11 has a transparent canvas, whereas the other one (I guess Wayland) doesn't, but as soon as I add a fourth atom to the drawing, it crashes: /usr/include/c++/11/bits/stl_vector.h:1045: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](std::vector<_Tp, _Alloc>::size_type) [with _Tp = Eigen::Matrix; _Alloc = std::allocator >; std::vector<_Tp, _Alloc>::reference = Eigen::Matrix&; std::vector<_Tp, _Alloc>::size_type = long unsigned int]: Assertion '__n < this->size()' failed. Aborted (core dumped) However, when given a badly drawn propene or propane molecule, the structure optimization works fine. On X, I did not get the transparent canvas, but I got the crash at the fourth atom. I was able to open some of my existing files though, with up to several thousand atoms and the structure optimization worked fine after I had deformed them. At least any issues are not from Open Babel 3 (I guess). ___ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure
Re: openbabel-3.1* in Rawhide
Hello Antonio,
On Fri, Sep 24, 2021 at 7:50 PM Antonio T. sagitter
wrote:
>
> Even the porting to openbabel3 of 'xdrawchem' is done.
> Please, can anyone that uses these software test them?
I spun up a Fedora 35 VM and installed everything from your copr,
didn't mess with any system settings. Here's what I've got.
* xdrawchem:
I hadn't used it since Molsketch was revived a few years ago and I'm
not sure if everything was working as expected. My guess was that
structure refinement ("clean up molecule") and the SMILES/InChi output
had to do with Open Babel, so I tried those. For SMILES, regardless of
the atom type, I always get an asterisk, e.g. for butane. Double
bonds and such are correctly placed in the star-filled strings though.
InChi crashed the program:
==
*** Open Babel Warning in InChI code
#1 :Unsupported in this mode element '*'
==
*** Open Babel Error in InChI code
InChI generation failed
/usr/include/c++/11/bits/basic_string.h:1058:
std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::reference
std::__cxx11::basic_string<_CharT, _Traits,
_Alloc>::operator[](std::__cxx11::basic_string<_CharT, _Traits,
_Alloc>::size_type) [with _CharT = char; _Traits =
std::char_traits; _Alloc = std::allocator;
std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::reference =
char&; std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type
= long unsigned int]: Assertion '__pos <= size()' failed.
Aborted (core dumped)
Structure cleanup sort of works, but as 2D projections of the actual
3D structures, which is not that great-looking for a 2D drawing
program.
* gnome-chemistry-utils:
While the (right) gnome-chemistry-utils-libs package is installed, I
could not get the individual programs to start, e.g.
$ gcrystal
gcrystal: error while loading shared libraries: libgcu-0.14.so.0:
cannot open shared object file: No such file or directory
$ gchemcalc
gchemcalc: error while loading shared libraries: libgcugtk-0.14.so.0:
cannot open shared object file: No such file or directory
* Avogadro2:
Avogadro appears to be working, but I can't see anything on the
canvas, it displays whatever window is behind it on the screen, or the
wallpaper if there's nothing else there. Maybe a Wayland bug?
I will try with a Fedora 34 VM later and report back.
P.S.: I have never used ghemical, so I didn't try it.
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Re: openbabel-3.1* in Rawhide
Even the porting to openbabel3 of 'xdrawchem' is done. Please, can anyone that uses these software test them? https://copr.fedorainfracloud.org/coprs/sagitter/Openbabel-3/builds/ On 9/1/21 10:35, Mamoru TASAKA wrote:> xdrawchem https://github.com/bryanherger/xdrawchem/pull/17 Best regards. -- --- Antonio Trande Fedora Project mailto: sagit...@fedoraproject.org GPG key: 0x29FBC85D7A51CC2F GPG key server: https://keyserver1.pgp.com/ OpenPGP_0x29FBC85D7A51CC2F.asc Description: OpenPGP public key OpenPGP_signature Description: OpenPGP digital signature ___ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure
Re: openbabel-3.1* in Rawhide
'ghemical' and 'libghemical' should be okay, too. On 9/1/21 10:35, Mamoru TASAKA wrote: On 8/31/21 8:05 PM, Alexander Ploumistos wrote: On Tue, Aug 31, 2021 at 6:08 PM Antonio T. sagitter wrote: On 8/31/21 5:27 PM, Alexander Ploumistos wrote: We must decide if go forward with most recent software or stay stationary. Which software are not ready for openbabel-3 yet? Almost two years ago (how time flies!), when the subject had been first broached, Dominik provided this list: Link-time dependencies: IQmol avogadro ghemical Okay with debian patch: https://sources.debian.org/src/ghemical/3.0.0-5/debian/patches/openbabel3.patch/ I've applied this to Fedora git source. -- --- Antonio Trande Fedora Project mailto: sagit...@fedoraproject.org GPG key: 0x29FBC85D7A51CC2F GPG key server: https://keyserver1.pgp.com/ OpenPGP_0x29FBC85D7A51CC2F.asc Description: OpenPGP public key OpenPGP_signature Description: OpenPGP digital signature ___ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure
Re: openbabel-3.1* in Rawhide
I have not used this patch for getting 'gnome-chemistry-utils' working
in x11 and Wayland:
diff --git a/programs/3d/main.cc b/programs/3d/main.cc
index 9bd59a4..aa18e3e 100644
--- a/programs/3d/main.cc
+++ b/programs/3d/main.cc
@@ -58,6 +58,7 @@ int main(int argc, char *argv[])
GError *error = NULL;
GOptionContext *context;
+ gdk_set_allowed_backends ("wayland,x11");
gtk_init (, );
gcu::Element::LoadBODR ();
diff --git a/programs/crystal/main.cc b/programs/crystal/main.cc
index e688c3d..55fd8b9 100644
--- a/programs/crystal/main.cc
+++ b/programs/crystal/main.cc
@@ -63,6 +63,7 @@ int main(int argc, char *argv[])
GOptionContext *context;
GError *error = NULL;
+ gdk_set_allowed_backends ("wayland,x11");
gtk_init (, );
Element::LoadRadii ();
if (argc > 1 && argv[1][0] == '-') {
because i don't know if it's correct. Some tools need to be ran by
setting the GDK_BACKEND environment variable.
On 9/24/21 07:41, Alexander Ploumistos wrote:
On Thu, Sep 23, 2021 at 3:37 PM Antonio T. sagitter
wrote:
gnome-chemistry-utils is ready for openbabel3; it's in my Copr project.
Well done Antonio!
I will give it a try this weekend.
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Re: openbabel-3.1* in Rawhide
On Thu, Sep 23, 2021 at 3:37 PM Antonio T. sagitter wrote: > > gnome-chemistry-utils is ready for openbabel3; it's in my Copr project. Well done Antonio! I will give it a try this weekend. ___ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure
Re: openbabel-3.1* in Rawhide
gnome-chemistry-utils is ready for openbabel3; it's in my Copr project. On 9/1/21 10:35, Mamoru TASAKA wrote: gnome-chemistry-utils debian says only a small modification is needed: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=946263#20 -- --- Antonio Trande Fedora Project mailto: sagit...@fedoraproject.org GPG key: 0x29FBC85D7A51CC2F GPG key server: https://keyserver1.pgp.com/ OpenPGP_0x29FBC85D7A51CC2F.asc Description: OpenPGP public key OpenPGP_signature Description: OpenPGP digital signature ___ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure
Re: openbabel-3.1* in Rawhide
Hello Antonio, On Fri, Sep 3, 2021 at 2:32 PM Antonio T. sagitter wrote: > > Links of Copr projects to get srpms for testing: > > openbabel3-3.1.1: > https://copr.fedorainfracloud.org/coprs/sagitter/Openbabel-3/ As expected, Molsketch had no problem with 3.1.1, it built fine. I also played with the binaries in /usr/bin/ a bit, not much difference from what I saw two years ago, some small bugs were fixed in the meantime and I was able to recreate some of the bugs reported upstream. I'd really love to say that I'd help with porting the other packages, but until March my spare time will be severely limited and I could use every second spent away from a computer screen. However, if you decide to move forward I'll at least try to lend a hand. ___ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure
Re: openbabel-3.1* in Rawhide
Hi Antonio, On Wed, Sep 1, 2021 at 8:11 PM Antonio T. sagitter wrote: > > 'openbabel2' and 'openbabel3' cannot co-exist if installed because they > have same binary files, it's a "binary name conflicts". > > Is it acceptable an openbabel2/openbabel(3) conflict in Fedora? I think that the people you'd be catering to by providing both packages are also the ones more likely to be bitten by the conflict between them. Taking Avogadro as an example, there are people who use both Avogadro and Avogadro2, because of their different feature sets. If one day these people are notified that they can't have both Avogadro and Avogadro2 installed at the same time, I don't suppose they're going to be much less displeased than when they'd find out that Avogadro had been deprecated. In my view, the way forward is for maintainers to patch what can be patched to work with Open Babel 3 and lay the others to rest. Less work for you and slightly less or equal amount of frustration for the users. At least now that enough time has passed since the 3.x release, as Mamoru pointed out, a lot of the work required has already been done by other distros. ___ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure
Re: openbabel-3.1* in Rawhide
'openbabel2' and 'openbabel3' cannot co-exist if installed because they have same binary files, it's a "binary name conflicts". Is it acceptable an openbabel2/openbabel(3) conflict in Fedora? On 9/1/21 10:35 AM, Mamoru TASAKA wrote: Antonio T. sagitter wrote on 2021/09/01 16:58: You're right, i underestimated the issue. Probably, Avogadro is not compatible with openbabel3 but Avogadro2 should be. I try to keep a separated 'openbabel2' package as new rpm, and then upgrade current 'openbabel' to the release 3+ Thank you. There is useful information on debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=946263 -- --- Antonio Trande Fedora Project mailto: sagit...@fedoraproject.org GPG key: 0x29FBC85D7A51CC2F GPG key server: https://keyserver1.pgp.com/ OpenPGP_0x29FBC85D7A51CC2F.asc Description: OpenPGP public key OpenPGP_signature Description: OpenPGP digital signature ___ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure
Re: openbabel-3.1* in Rawhide
Antonio T. sagitter wrote on 2021/09/01 16:58: You're right, i underestimated the issue. Probably, Avogadro is not compatible with openbabel3 but Avogadro2 should be. I try to keep a separated 'openbabel2' package as new rpm, and then upgrade current 'openbabel' to the release 3+ Thank you. There is useful information on debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=946263 On 8/31/21 8:05 PM, Alexander Ploumistos wrote: On Tue, Aug 31, 2021 at 6:08 PM Antonio T. sagitter wrote: On 8/31/21 5:27 PM, Alexander Ploumistos wrote: We must decide if go forward with most recent software or stay stationary. Which software are not ready for openbabel-3 yet? Almost two years ago (how time flies!), when the subject had been first broached, Dominik provided this list: Link-time dependencies: IQmol avogadro ghemical Okay with debian patch: https://sources.debian.org/src/ghemical/3.0.0-5/debian/patches/openbabel3.patch/ I've applied this to Fedora git source. gnome-chemistry-utils debian says only a small modification is needed: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=946263#20 kalzium molsketch xdrawchem https://github.com/bryanherger/xdrawchem/pull/17 Run-time dependencies: avogadro2 chemtool molsketch At the time, I think only Molsketch was compatible with Open Babel 3. After getting version 3.1.1 to build[1], I spent a few weekends trying to modify gnome-chemistry-utils, but due to lack of time I didn't go very far and looking at the code in my files, I'm not really sure what I've actually done, I don't remember much. Personally, I use avogadro* a lot, which you maintain (and therefore I don't worry about it ;) ) and GChemCalc (almost daily) and sometimes GSpectrum from g-c-u, neither of which is indispensable, though both are quite handy. I haven't checked any of the other programs on that list recently, but about a year ago, not much had changed. I can leave to you an openbabel-3 srpm or Copr builds of it for your tests. One week is a minimal time, no problem if you need more time. As far as I can tell, Molsketch will use whichever version of Open Babel is installed on the system and users of a couple of other distros have been building it against v3 without any problems, so I don't expect any either. Just please let me know when you've built it in Rawhide and I'll do the rebuild then - hopefully the new version will also be out by that time. Best regards, A. 1. https://copr.fedorainfracloud.org/coprs/alexpl/openbabel/builds/ ___ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure ___ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure
Re: openbabel-3.1* in Rawhide
You're right, i underestimated the issue. Probably, Avogadro is not compatible with openbabel3 but Avogadro2 should be. I try to keep a separated 'openbabel2' package as new rpm, and then upgrade current 'openbabel' to the release 3+ Thank you. On 8/31/21 8:05 PM, Alexander Ploumistos wrote: On Tue, Aug 31, 2021 at 6:08 PM Antonio T. sagitter wrote: On 8/31/21 5:27 PM, Alexander Ploumistos wrote: We must decide if go forward with most recent software or stay stationary. Which software are not ready for openbabel-3 yet? Almost two years ago (how time flies!), when the subject had been first broached, Dominik provided this list: Link-time dependencies: IQmol avogadro ghemical gnome-chemistry-utils kalzium molsketch xdrawchem Run-time dependencies: avogadro2 chemtool molsketch At the time, I think only Molsketch was compatible with Open Babel 3. After getting version 3.1.1 to build[1], I spent a few weekends trying to modify gnome-chemistry-utils, but due to lack of time I didn't go very far and looking at the code in my files, I'm not really sure what I've actually done, I don't remember much. Personally, I use avogadro* a lot, which you maintain (and therefore I don't worry about it ;) ) and GChemCalc (almost daily) and sometimes GSpectrum from g-c-u, neither of which is indispensable, though both are quite handy. I haven't checked any of the other programs on that list recently, but about a year ago, not much had changed. I can leave to you an openbabel-3 srpm or Copr builds of it for your tests. One week is a minimal time, no problem if you need more time. As far as I can tell, Molsketch will use whichever version of Open Babel is installed on the system and users of a couple of other distros have been building it against v3 without any problems, so I don't expect any either. Just please let me know when you've built it in Rawhide and I'll do the rebuild then - hopefully the new version will also be out by that time. Best regards, A. 1. https://copr.fedorainfracloud.org/coprs/alexpl/openbabel/builds/ -- --- Antonio Trande Fedora Project mailto: sagit...@fedoraproject.org GPG key: 0x29FBC85D7A51CC2F GPG key server: https://keyserver1.pgp.com/ OpenPGP_0x29FBC85D7A51CC2F.asc Description: OpenPGP public key OpenPGP_signature Description: OpenPGP digital signature ___ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure
Re: openbabel-3.1* in Rawhide
On Tue, Aug 31, 2021 at 6:08 PM Antonio T. sagitter wrote: > > On 8/31/21 5:27 PM, Alexander Ploumistos wrote: > > > > We must decide if go forward with most recent software or stay stationary. > Which software are not ready for openbabel-3 yet? Almost two years ago (how time flies!), when the subject had been first broached, Dominik provided this list: Link-time dependencies: IQmol avogadro ghemical gnome-chemistry-utils kalzium molsketch xdrawchem Run-time dependencies: avogadro2 chemtool molsketch At the time, I think only Molsketch was compatible with Open Babel 3. After getting version 3.1.1 to build[1], I spent a few weekends trying to modify gnome-chemistry-utils, but due to lack of time I didn't go very far and looking at the code in my files, I'm not really sure what I've actually done, I don't remember much. Personally, I use avogadro* a lot, which you maintain (and therefore I don't worry about it ;) ) and GChemCalc (almost daily) and sometimes GSpectrum from g-c-u, neither of which is indispensable, though both are quite handy. I haven't checked any of the other programs on that list recently, but about a year ago, not much had changed. > I can leave to you an openbabel-3 srpm or Copr builds of it for your tests. > > One week is a minimal time, no problem if you need more time. > As far as I can tell, Molsketch will use whichever version of Open Babel is installed on the system and users of a couple of other distros have been building it against v3 without any problems, so I don't expect any either. Just please let me know when you've built it in Rawhide and I'll do the rebuild then - hopefully the new version will also be out by that time. Best regards, A. 1. https://copr.fedorainfracloud.org/coprs/alexpl/openbabel/builds/ ___ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure
Re: openbabel-3.1* in Rawhide
On 8/31/21 5:27 PM, Alexander Ploumistos wrote: Hello Antonio, Hi Alexander. On Tue, Aug 31, 2021 at 5:03 PM Antonio T. sagitter wrote: openbabel-3.1.1 is ready for Rawhide branch. 'libopenbabel' soname is updated from 5 to 7, all dependent packages will need a rebuild at least: What about the packages that haven't been ported to work with Open Babel 3.* yet? We must decide if go forward with most recent software or stay stationary. Which software are not ready for openbabel-3 yet? > Do you intend to keep v2 around in some form? No. $ repoquery --whatrequires openbabel-devel --disablerepo=* --enablerepo=*-source molsketch-0:0.7.2-1.fc34.src I'm waiting for Hendrik to release a new version sometime soon, at worst let it FTBFS and I'll deal with it in time. I can leave to you an openbabel-3 srpm or Copr builds of it for your tests. One week is a minimal time, no problem if you need more time. All the best, A. ___ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure -- --- Antonio Trande Fedora Project mailto: sagit...@fedoraproject.org GPG key: 0x29FBC85D7A51CC2F GPG key server: https://keyserver1.pgp.com/ OpenPGP_0x29FBC85D7A51CC2F.asc Description: OpenPGP public key OpenPGP_signature Description: OpenPGP digital signature ___ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure
Re: openbabel-3.1* in Rawhide
Hello Antonio, On Tue, Aug 31, 2021 at 5:03 PM Antonio T. sagitter wrote: > > openbabel-3.1.1 is ready for Rawhide branch. 'libopenbabel' soname is > updated from 5 to 7, all dependent packages will need a rebuild at least: What about the packages that haven't been ported to work with Open Babel 3.* yet? Do you intend to keep v2 around in some form? > $ repoquery --whatrequires openbabel-devel --disablerepo=* > --enablerepo=*-source > > molsketch-0:0.7.2-1.fc34.src I'm waiting for Hendrik to release a new version sometime soon, at worst let it FTBFS and I'll deal with it in time. All the best, A. ___ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure
