Add option `allow-tcp-connections-on-replica`, set to true by default.

This option corresponds to `skip-networking` in mariadb configuration.
Changing it only takes effect the next time mariadb is restarted; this
does not occur automatically. Instead a script is provided to shutdown
mariadb: bin/mariadb-shutdown-gracefully. Mariadb will then be started
by SlapOS the next time the instance is processed (even when master is
offline).

TODO: This is currently sub-optimal because the promise will trigger a
bang of the partition when allow-tcp-connections-on-replica is enabled
and mariadb has not been restarted, but as SlapOS will not restart the
mariadb service automatically, the partition is processed needlessly.

Leaving this option set currently limits the ability to takoever fully
as a part of the service of a mariadb instance, without SlapOS action:
the value of skip-networking will be controlled by SlapOS, rather than
by the user interacting with the mariadb service.

Deactivate zope promises when the neo is expected to be BACKINGUP,
as this makes the zope process crash, which is currently expected.

Deactivating the zope process entirely in that case is not desired
because reactivating it would require updating instance parameters
and reprocessing the partition. Instead, ideally, the zope service
should adapt to the state of the neo.

Also, move zope service from etc/service to etc/run to make it not
be "on-watch", so that when the neo is BACKINGUP and zope crashes,
the partition does not bang and reprocess continuously. This seems
ok because the promise already asserts the service is running.

Add scripts in bin directory that can be called manually to apply a
new primary-url (after having edited it in the instance parameters)
by turning a primary into a replica or by making a replica follow a
new primary, all without deleting existing data - so this is useful
when the existing data does not diverge from the new primary.

Being able to start replicating from a new primary without deleting
existing data is convenient, but maybe it's better or sufficient or
both to only be able to tell a mariadb to just destroy its existing
data and re-bootstrap from scratch.

Being able to delete all existing data and start from scratch seems
necessary in any case, but it's not clear that a special feature is
needed for this: maybe it's completely enough to be able to destroy
and re-request the instance through standard slapos operations.

Questions remain for automated usage:

1. One option is to provide a url the user may simply interact with
   (clickable button ...) to call the appropriate script. This kind
   of interaction could also be used to trigger the deletion of all
   existing data for a fresh bootstrap.

2. Another option is that editing the primary-url in the parameters
   results in the appropriate script being called. This makes sense
   as a way to remain in sync with given parameters, although there
   are some drawbacks: the uncertain propagation time, and the fact
   there is no guarantee that the existing data can converge to the
   state of the new primary. This might be grounds to keep all this
   strictly manual.

In any case, this relies already on the propagation of the instance
parameters to input the new primary-url, so it may not be useful at
all for any use-case, manual or automated.

Add a script in bin directory that can be called manually to turn a
replica into a primary. Being able to turn a replica into a primary
is an absolutely necessary feature of replication. It's a necessary
step of a takoever procedure.

Questions remain for automatisation. One option is to provide a url
the user may simply interact with (clickable button ...) to trigger
the script, that may also be used automatically as part of a larger
takoever procedure.

Triggering the change to primary by editing the instance parameters
- such as by removing the replication-related parameters - does not
seem best: one immediate drawback is the uncertain propagation time
of instance parameters; another is the reliance on the availability
of the SlapOS master to trigger a usually time-sensitive operation.

1. Remove mariadb_update service.
   Instead, initialize databases and users on creation, and run updater
   and apply timezones info on every (re)start. This covers the actions
   that mariadb_update used to handle.

2. Allow requesting a mariadb set-up to replicate another mariadb,
   using parameters of the form:

   ```
   'replication': {
     'bootstrap-url': 'http(s)://<recent-backup-of-primary>
     'primary-url': 'mysql://<replication-user>:<password>@<ip>:<port>'
     'seconds-behind-master-threshold': <integer, defaults to 0>
   }
   ```

   This takes effect on mariadb database creation - when no data exists
   yet. That way existing data cannot be deleted by setting or changing
   the replication parameters after the fact.

   A promise checks that the state of the running mariadb matches the
   requested state (replica/primary, replication source); but if not,
   the mariadb database will not automatically converge without human
   intervention once ~/srv/mariadb directory exists.

   The bootstrap-url may be omitted: this skips replication bootstrap
   and requires that all binlogs be still available on the primary.
   This is useful when the primary is recent and may not have a ready
   backup for bootstrap yet.

To facilitate these changes, component/mariadb now exposes a template
script for the mariadbd service, with ready hooks to take actions on
database creation and on database (re)start.

Use a generated password and publish its url.

When upstream-cluster and upstream-masters are given, also pass --backup
to the neo master so that it converges automatically to BACKINGUP state.

Remove

```
[gcc:python2]
part = gcc-8.5
```

from neoppod/software-common.cfg and dream/software.cfg as it causes
gcc being pinned to a different version before and after rebootstrap
when the initial python version is not Python2.

This reverts dc91e5d4.

When use-ipv6 is enabled, make mariadb publish an url of the form:
  `mysql://user:password@[ipv6]:port/database`

instead of:
  `mysql://user:password@ipv6:port/database`

which results in the zope instances crashing during processing
due to urlparse.urlsplit failing to parse the url.

The `which` command is not always available, so we use `command -v`
instead. An issue was opened upstream in
https://github.com/GNUAspell/aspell-lang/issues/3 , and a PR was
proposed but not yet accepted.

See merge request !1761

Due to disk usage on my production server, I had to move the theia's
backup to a different file system. I bind mount this other fs on:

slappart0/srv/backup/theia

Mounting on "slappart0/srv/backup" would make logrogate
complain (logrotate is used in the "backup" cron, triggering the
resiliency process). So "slappart0/srv/backup/theia" was the 2nd best
idea. Unfortunately for my case, os.rename raises if the src and dest
filesystems are different, as it os.rename guarantees the atomicity of
the operation. As atomicity is not that important for copying the
signature file, it can be replaced by shutil.move.

In case if there is a problem the output allows to understand the underlying
cause.

In case of correct run, no output is shown.

It's never used, and that's not the repetetive nor deploy-like way of doing
development in the end.

This part is unit tested against slapproxy, but unfortunately other
implementations of SlapOS Master might return None in such case failing
fully the profile.

Fix it without test, but with marking the problem.

Thanks to this tool allowing incremental checksum calculation increase of
backup size does not result with increase of backup time spend on checksum
calculation.

The statsmodels 0.14.4 needs upgraded version of slapos.toolbox. Also
fix mmonitor stack eggs version.

See merge request !1757

The value can already be accessed from the buildout parameters.
No need to do one http query to read the value.

See merge request !1756

See merge request !1749

The previous approach was ingesting uless "Time" lines sometimes

the default is 128 lines which is sometimes not enough

After previous patch the build of this test passes further than buildout rebootstrap but fails with

    Installing software release /srv/slapgrid/slappart5/srv/project/slapos/component/ZODB/test-zodb4-wc2.cfg ...
    ...
    Installing persistent-repository.
    Warning: "branch" parameter with value "master" is ignored. Checking out to revision 4.6.4-0-g7ed95cf.
    Cloning into '/srv/slapgrid/slappart5/srv/runner/software/04a9ddca848c1bb62254aab83f212066/parts/persistent'...
    HEAD is now at 7ed95cf Preparing release 4.6.4
    Updating python-cffi.
    Updating persistent.
    DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support pip 21.0 will remove support for this functionality.
    Installing BTrees.
    networkcache: Trying to download pypi:persistent=4.9.3 from network cache...
    Getting distribution for 'persistent==4.9.3'.
        ERROR: Command errored out with exit status 1:
         command: /srv/slapgrid/slappart5/srv/runner/shared/python2.7/474396ed0d332179d494b6d9d3f28ef5/bin/python2.7 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-kywY6K/setup.py'"'"'; __file__='"'"'/tmp/pip-req-build-kywY6K/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-LeIkZV
             cwd: /tmp/pip-req-build-kywY6K/
        Complete output (25 lines):
        DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support pip 21.0 will remove support for this functionality.
        WARNING: Url 'file:///dev/null/cffi/' is ignored: it is neither a file nor a directory.
        ERROR: Could not find a version that satisfies the requirement cffi (from versions: none)
        ERROR: No matching distribution found for cffi
        Traceback (most recent call last):
          File "<string>", line 1, in <module>
          File "/tmp/pip-req-build-kywY6K/setup.py", line 149, in <module>
            entry_points={})
          File "/srv/slapgrid/slappart5/srv/runner/software/04a9ddca848c1bb62254aab83f212066/eggs/setuptools-44.1.1-py2.7.egg/setuptools/__init__.py", line 161, in setup
            _install_setup_requires(attrs)
          File "/srv/slapgrid/slappart5/srv/runner/software/04a9ddca848c1bb62254aab83f212066/eggs/setuptools-44.1.1-py2.7.egg/setuptools/__init__.py", line 156, in _install_setup_requires
            dist.fetch_build_eggs(dist.setup_requires)
          File "/srv/slapgrid/slappart5/srv/runner/software/04a9ddca848c1bb62254aab83f212066/eggs/setuptools-44.1.1-py2.7.egg/setuptools/dist.py", line 721, in fetch_build_eggs
            replace_conflicting=True,
          File "/srv/slapgrid/slappart5/srv/runner/software/04a9ddca848c1bb62254aab83f212066/eggs/setuptools-44.1.1-py2.7.egg/pkg_resources/__init__.py", line 782, in resolve
            replace_conflicting=replace_conflicting
          File "/srv/slapgrid/slappart5/srv/runner/software/04a9ddca848c1bb62254aab83f212066/eggs/setuptools-44.1.1-py2.7.egg/pkg_resources/__init__.py", line 1065, in best_match
            return self.obtain(req, installer)
          File "/srv/slapgrid/slappart5/srv/runner/software/04a9ddca848c1bb62254aab83f212066/eggs/setuptools-44.1.1-py2.7.egg/pkg_resources/__init__.py", line 1077, in obtain
            return installer(requirement)
          File "/srv/slapgrid/slappart5/srv/runner/software/04a9ddca848c1bb62254aab83f212066/eggs/setuptools-44.1.1-py2.7.egg/setuptools/dist.py", line 777, in fetch_build_egg
            return fetch_build_egg(self, req)
          File "/srv/slapgrid/slappart5/srv/runner/software/04a9ddca848c1bb62254aab83f212066/eggs/setuptools-44.1.1-py2.7.egg/setuptools/installer.py", line 130, in fetch_build_egg
            raise DistutilsError(str(e))
        distutils.errors.DistutilsError: Command '['/srv/slapgrid/slappart5/srv/runner/shared/python2.7/474396ed0d332179d494b6d9d3f28ef5/bin/python2.7', '-m', 'pip', '--disable-pip-version-check', 'wheel', '--no-deps', '-w', '/tmp/tmptaQnzb', '--quiet', '--index-url', 'file:///dev/null', 'cffi']' returned non-zero exit status 1
        ----------------------------------------
    ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
    While:
      Installing BTrees.
      Base installation request: 'persistent'
      Getting distribution for 'persistent==4.9.3'.

    An internal error occurred due to a bug in either zc.buildout or in a
    recipe being used:
    Traceback (most recent call last):
      File "/srv/slapgrid/slappart5/srv/runner/software/04a9ddca848c1bb62254aab83f212066/eggs/zc.buildout-3.0.1+slapos009-py2.7.egg/zc/buildout/buildout.py", line 2664, in main
        getattr(buildout, command)(args)
      File "/srv/slapgrid/slappart5/srv/runner/software/04a9ddca848c1bb62254aab83f212066/eggs/zc.buildout-3.0.1+slapos009-py2.7.egg/zc/buildout/buildout.py", line 855, in install
        self._install_parts(install_args)
      File "/srv/slapgrid/slappart5/srv/runner/software/04a9ddca848c1bb62254aab83f212066/eggs/zc.buildout-3.0.1+slapos009-py2.7.egg/zc/buildout/buildout.py", line 1026, in _install_parts
        installed_files = self[part]._call(recipe.install)
      File "/srv/slapgrid/slappart5/srv/runner/software/04a9ddca848c1bb62254aab83f212066/eggs/zc.buildout-3.0.1+slapos009-py2.7.egg/zc/buildout/buildout.py", line 1948, in _call
        return f()
      File "/srv/slapgrid/slappart5/srv/runner/software/04a9ddca848c1bb62254aab83f212066/eggs/zc.recipe.egg-2.0.8.dev0+slapos009-py2.7.egg/zc/recipe/egg/custom.py", line 79, in install
        self._install_setup_eggs()
      File "/srv/slapgrid/slappart5/srv/runner/software/04a9ddca848c1bb62254aab83f212066/eggs/zc.recipe.egg-2.0.8.dev0+slapos009-py2.7.egg/zc/recipe/egg/custom.py", line 119, in _install_setup_eggs
        newest=self.newest,
      File "/srv/slapgrid/slappart5/srv/runner/software/04a9ddca848c1bb62254aab83f212066/eggs/zc.buildout-3.0.1+slapos009-py2.7.egg/zc/buildout/easy_install.py", line 1178, in install
        return installer.install(specs, working_set, patch_dict=patch_dict)
      File "/srv/slapgrid/slappart5/srv/runner/software/04a9ddca848c1bb62254aab83f212066/eggs/zc.buildout-3.0.1+slapos009-py2.7.egg/zc/buildout/easy_install.py", line 835, in install
        for dist in self._get_dist(requirement, ws):
      File "/srv/slapgrid/slappart5/srv/runner/software/04a9ddca848c1bb62254aab83f212066/eggs/zc.buildout-3.0.1+slapos009-py2.7.egg/zc/buildout/easy_install.py", line 711, in _get_dist
        dists = [_move_to_eggs_dir_and_compile(dist, self._dest, self)]
      File "/srv/slapgrid/slappart5/srv/runner/software/04a9ddca848c1bb62254aab83f212066/eggs/zc.buildout-3.0.1+slapos009-py2.7.egg/zc/buildout/easy_install.py", line 2205, in _move_to_eggs_dir_and_compile
        [tmp_loc] = call_pip_wheel(dist.location, tmp_dest, options)
      File "/srv/slapgrid/slappart5/srv/runner/software/04a9ddca848c1bb62254aab83f212066/eggs/zc.buildout-3.0.1+slapos009-py2.7.egg/zc/buildout/easy_install.py", line 2100, in call_pip_wheel
        call_pip_command(['wheel', '-w', dest], [spec], options)
      File "/srv/slapgrid/slappart5/srv/runner/software/04a9ddca848c1bb62254aab83f212066/eggs/zc.buildout-3.0.1+slapos009-py2.7.egg/zc/buildout/easy_install.py", line 2038, in call_pip_command
        subprocess.check_call(args, env=env)
      File "/srv/slapgrid/slappart5/srv/runner/shared/python2.7/474396ed0d332179d494b6d9d3f28ef5/lib/python2.7/subprocess.py", line 190, in check_call
        raise CalledProcessError(retcode, cmd)
    CalledProcessError: Command '['/srv/slapgrid/slappart5/srv/runner/shared/python2.7/474396ed0d332179d494b6d9d3f28ef5/bin/python2.7', '-m', 'pip', 'wheel', '-w', '/srv/slapgrid/slappart5/srv/runner/software/04a9ddca848c1bb62254aab83f212066/eggs/tmpmfO6r5', '--no-deps', '-q', '--no-index', '--no-build-isolation', '--no-python-version-warning', '--no-cache-dir', '/tmp/tmpbuYU1zget_dist/persistent-4.9.3.tar.gz']' returned non-zero exit status 1
    2025-03-03 06:25:33 slapos[1517575] ERROR Failed to run buildout profile in directory '/srv/slapgrid/slappart5/srv/runner/software/04a9ddca848c1bb62254aab83f212066'
    2025-03-03 06:25:33 slapos[1517575] INFO Finished software releases.

What happens here is that test-zodb4-wc2.cfg installs persistent via git clone
but at 4.6.4 version, while the version of wanted egg in ZODB/buildout.cfg
[versions] is 4.9.3. This way when buildout sees that BTrees needs persistent as
the dependency, it looks for "whether we already have persistent==4.9.3
installed", determines the answer as "no" (as we have persistent 4.6.4), and
tries to install persistent by itself, and fails somewhere around cffi which we
also provide via zc.recipe.egg:custom.

The cffi error is only a consequence of original problem of mismatched
persistent versions.

-> Fix BTrees/persistent build by keeping used persistent versions in sync in between buildout.cfg and test-zodb4-wc2.cfg

As test-zodb4-wc2.cfg explains

    we need persistent to be a git checkout because persistent tests want to
    discover in-tree files that are not present in persistent egg when it is
    installed in non-development mode:

      https://erp5.nexedi.net/test_result_module/20201123-3F859E35/7
      (look for "AssertionError: could not find my setup.py")

      https://github.com/zopefoundation/persistent/blob/4.6.4-0-g7ed95cf/persistent/tests/test_docs.py#L37-L43

and on the other hand we do not use git checkout way uniformly because people
wanted to use plain eggs when component/ZODB was bootstrapped.

This way we have to use both egg and git checkout and keep their versions in sync.

After this patch the build of test-zodb4-wc2 is recovered.

/cc @xavier_thompson
/reviewed-by @kazuhiko, @levin.zimmermann
/helped-and-reviewed-by @jerome
/reviewed-on !1752

Since c170fe3e (ZODB: Provide ZODB4-wc2 which backports MVCC approach from
ZODB5) we have a custom version of ZODB4 with backports from ZODB5 so that
wendelin.core can work in environments where we still use ZODB4.

In 2022 this test got broken after SlapOS transitioned to use python3 by
default and fixed in 5cb11e9e (component/ZODB: keep running the test on
python3). Then fixed in 2024 again in e742508b (! component/openssl: add
OpenSSL-3.0.13, still using OpenSSL-1.1 for python 2.).

However as of today building this test fails with

    slapos.rebootstrap:
    ************ REBOOTSTRAP: IMPORTANT NOTICE ************
    bin/buildout is being reinstalled right now, as new python:
      /srv/slapgrid/slappart5/srv/runner/shared/python2.7/b8880e7ab7f4124a466ecb817efb447c/bin/python2.7
    is available, and buildout is using another python:
      /opt/slapos/parts/python3/bin/python3
    Buildout will be restarted automatically to have this change applied.
    ************ REBOOTSTRAP: IMPORTANT NOTICE ************

    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/srv/slapgrid/slappart5/srv/runner/software/04a9ddca848c1bb62254aab83f212066/eggs/zc.buildout-3.0.1+slapos009-py3.7.egg/zc/__init__.py", line 1, in <module>
        __import__('pkg_resources').declare_namespace(__name__)
      File "/srv/slapgrid/slappart5/srv/runner/software/04a9ddca848c1bb62254aab83f212066/eggs/setuptools-67.8.0-py3.7.egg/pkg_resources/__init__.py", line 1423
        local = f"sanitized.{_safe_segment(rest)}".strip(".")
                                                 ^
    SyntaxError: invalid syntax
    While:
      Installing.

    An internal error occurred due to a bug in either zc.buildout or in a
    recipe being used:
    Traceback (most recent call last):
      File "/srv/slapgrid/slappart5/srv/runner/software/04a9ddca848c1bb62254aab83f212066/eggs/zc.buildout-3.0.1+slapos009-py3.7.egg/zc/buildout/buildout.py", line 2664, in main
        getattr(buildout, command)(args)
      File "/srv/slapgrid/slappart5/srv/runner/software/04a9ddca848c1bb62254aab83f212066/eggs/zc.buildout-3.0.1+slapos009-py3.7.egg/zc/buildout/buildout.py", line 855, in install
        self._install_parts(install_args)
      File "/srv/slapgrid/slappart5/srv/runner/software/04a9ddca848c1bb62254aab83f212066/eggs/zc.buildout-3.0.1+slapos009-py3.7.egg/zc/buildout/buildout.py", line 870, in _install_parts
        self._setup_directories()
      File "/srv/slapgrid/slappart5/srv/runner/software/04a9ddca848c1bb62254aab83f212066/eggs/slapos.rebootstrap-4.7-py3.7.egg/slapos/rebootstrap/__init__.py", line 58, in wrapper
        return getattr(self, attr)(*args, **kw)
      File "/srv/slapgrid/slappart5/srv/runner/software/04a9ddca848c1bb62254aab83f212066/eggs/slapos.rebootstrap-4.7-py3.7.egg/slapos/rebootstrap/__init__.py", line 108, in _setup_directories
        "zc.buildout.buildout.main()" % (paths, args + ['bootstrap'])])
      File "/opt/slapos/parts/python3/lib/python3.7/subprocess.py", line 363, in check_call
        raise CalledProcessError(retcode, cmd)
    subprocess.CalledProcessError: Command '['/srv/slapgrid/slappart5/srv/runner/shared/python2.7/b8880e7ab7f4124a466ecb817efb447c/bin/python2.7', '-c', "import sys ; sys.path[0:0]=['/srv/slapgrid/slappart5/srv/runner/software/04a9ddca848c1bb62254aab83f212066/eggs/slapos.libnetworkcache-0.25-py3.7.egg', '/srv/slapgrid/slappart5/srv/runner/software/04a9ddca848c1bb62254aab83f212066/eggs/zc.buildout-3.0.1+slapos009-py3.7.egg', '/srv/slapgrid/slappart5/srv/runner/software/04a9ddca848c1bb62254aab83f212066/eggs/setuptools-67.8.0-py3.7.egg', '/srv/slapgrid/slappart5/srv/runner/software/04a9ddca848c1bb62254aab83f212066/eggs/wheel-0.41.2-py3.7.egg', '/srv/slapgrid/slappart5/srv/runner/software/04a9ddca848c1bb62254aab83f212066/eggs/pip-23.2.1-py3.7.egg'] ; import zc.buildout.buildout ; sys.argv[1:1]=['buildout:extends-cache=/tmp/tmpdx2upamb', 'buildout:directory=/srv/slapgrid/slappart5/srv/runner/software/04a9ddca848c1bb62254aab83f212066', 'bootstrap'] ; zc.buildout.buildout.main()"]' returned non-zero exit status 1.

The problem here is that even though we use py2 for the software, the used
version of setuptools is py3 only and so it breaks.

This problem was already cared in f5b80301 (Downgrade pip, wheel and setuptools
in python2 SRs), but that commit missed to update test-zodb4-wc2.cfg .

-> Fix that.

After this patch the build of component/ZODB/test-zodb4-wc2.cfg becomes
recovered in the sense that it passes further than rebootstrap, but breaks at
the build of persistent / BTrees eggs. We will fix this in the next patch.

/cc @xavier_thompson
/reviewed-by @jerome, @kazuhiko, @levin.zimmermann
/reviewed-on !1752