*: version up many python packages

mostly packages with known vulnerabilities or causing failures/warnings
in the tests.

This also cleanup duplicates version definitions, sometimes the test
profiles overloaded some versions from stack/slapos.cfg

component/jupyter-py2/buildout.cfg

@@ -79,7 +79,6 @@ mistune = 0.7.3
 nbformat = 4.3.0
 notebook = 4.4.1
 pandas = 0.19.2
-plone.recipe.command = 1.1
 prompt-toolkit = 1.0.13
 ptyprocess = 0.5.1
 pyzmq = 16.0.2
@@ -92,7 +91,6 @@ tornado = 4.4.2
 widgetsnbextension = 2.0.0
 # numpy >= 1.13.1 is required for numpy.core.multiarray
 numpy = 1.13.1
-certifi = 2020.6.20
 
 # nbconvert 4.2.0 depends on entrypoints egg that is not available as tar/zip source.
 nbconvert = 4.1.0

software/jupyter/software.cfg

@@ -72,7 +72,6 @@ notebook = 6.1.5
 numpy = 1.14.6
 pandas = 0.25.3
 pandocfilters = 1.4.3
-plone.recipe.command = 1.1
 prompt-toolkit = 1.0.13
 ptyprocess = 0.5.1
 pyzmq = 20.0.0
@@ -86,7 +85,6 @@ tornado = 6.1
 traitlets = 5.0.5
 webencodings = 0.5.1
 widgetsnbextension = 2.0.0
-certifi = 2020.6.20
 Send2Trash = 1.5.0
 argon2-cffi = 20.1.0
 nbconvert = 6.0.7

software/neoppod/software-common.cfg

@@ -129,6 +129,5 @@ coverage = 4.5.1
 ecdsa = 0.13
 mysqlclient = 1.3.12
 pycrypto = 2.6.1
-pycurl = 7.43.0
 cython-zstd = 0.2
 funcsigs = 1.0.2

software/slapos-sr-testing/software.cfg

@@ -394,28 +394,21 @@ tests =
 [versions]
 # slapos.core is used from the clone always
 slapos.core =
+
 # Various needed versions
-Pillow = 5.3.0
-PyNaCl = 1.3.0
-bcrypt = 3.1.4
+Pillow = 9.2.0
 forcediphttpsadapter = 1.0.1
-httplib2 = 0.11.3
+httplib2 = 0.20.4
 image = 1.5.25
-paramiko = 2.4.2
 plantuml = 0.3.0:whl
 pysftp = 0.2.9
 requests-toolbelt = 0.8.0
 selenium = 3.141.0
-
-# Patched eggs
-PyPDF2 = 1.26.0+SlapOSPatched001
-
-# Django 1.11 is python 2 compatible
-Django = 1.11
-
 testfixtures = 6.11.0
-funcsigs = 1.0.2
-mysqlclient = 1.3.12
+mysqlclient = 2.1.1
 pexpect = 4.8.0
 ptyprocess = 0.6.0
 psycopg2 = 2.8.6
+
+# Patched eggs
+PyPDF2 = 1.26.0+SlapOSPatched001

software/slapos-testing/software.cfg

@@ -244,19 +244,12 @@ slapos.toolbox =
 rubygemsrecipe =
 
 # All other depencies should be pinned.
-Pygments = 2.1.3
-zc.lockfile = 1.4
-bcrypt = 3.1.4
-dnspython = 1.15.0
-funcsigs = 1.0.2
+Pygments = 2.13.0
 httmock = 1.2.6
 manuel = 1.9.0
-mock = 2.0.0:whl
 testfixtures = 6.11.0
-pycurl = 7.43.0.2
 pyflakes = 2.0.0
 zope.testing = 4.6.2
-urllib3 = 1.24.1
 pathlib = 1.0.1
 psycopg2 = 2.8.6
 iniparse = 0.5

stack/caucase/buildout.cfg

@@ -37,4 +37,7 @@ depends = ${caucase-jinja2-library-eggs:eggs}
 [versions]
 caucase = 0.9.12
 pem = 21.1.0
+PyJWT = 2.4.0
+
+[versions:python2]
 PyJWT = 1.7.1

stack/erp5/buildout.cfg

@@ -59,6 +59,8 @@ extends =
   ../../component/wendelin.core/buildout.cfg
   ../../component/jupyter-py2/buildout.cfg
   ../../component/pygolang/buildout.cfg
+  ../../component/bcrypt/buildout.cfg
+  ../../component/python-pynacl/buildout.cfg
   ../../stack/caucase/buildout.cfg
   ../../software/neoppod/software-common.cfg
 # keep neoppod extends last
@@ -475,6 +477,8 @@ eggs = ${neoppod:eggs}
   mock
   oauthlib
   objgraph
+  ${python-pynacl:egg}
+  ${bcrypt:egg}
   paramiko
   ply
   pyflakes
@@ -701,7 +705,6 @@ pprofile = 2.0.4
 pyasn1-modules = 0.0.8
 pycountry = 17.1.8
 pycrypto = 2.6.1
-pycurl = 7.43.0
 pyflakes = 1.5.0
 python-memcached = 1.58
 pytracemalloc = 1.2
@@ -726,7 +729,6 @@ dask = 0.18.1
 toolz = 0.9.0
 zope.globalrequest = 1.5
 waitress = 1.4.4
-xlrd = 1.1.0
 
 Products.ZSQLMethods = 2.13.5
 fpconst = 0.7.2
@@ -736,11 +738,8 @@ python-libmilter = 1.0.3
 zope.app.debug = 3.4.1
 zope.app.dependable = 3.5.1
 zope.app.form = 4.0.2
-et-xmlfile = 1.0.1
-h5py = 2.7.1
 mpmath = 0.19
 openpyxl = 2.4.8
-sympy = 1.1.1
 jdcal = 1.3
 deepdiff = 3.3.0
 unidiff = 0.5.5

stack/slapos.cfg

@@ -167,7 +167,7 @@ importlib-metadata = 1.7.0:whl
 inotify-simple = 1.1.1
 itsdangerous = 0.24
 lock-file = 2.0
-lxml = 4.6.5
+lxml = 4.9.1
 meld3 = 1.0.2
 mock = 3.0.5
 more-itertools = 5.0.0
@@ -179,7 +179,7 @@ plone.recipe.command = 1.1
 prettytable = 0.7.2
 psutil = 5.8.0
 pluggy = 0.13.1:whl
-py = 1.9.0:whl
+py = 1.11.0:whl
 pyOpenSSL = 19.1.0
 pyparsing = 3.0.9:whl
 py-mld = 1.0.3
@@ -208,12 +208,14 @@ unicodecsv = 0.14.1
 wcwidth = 0.2.5
 wheel = 0.35.1:whl
 xml-marshaller = 1.0.2
-zc.lockfile = 1.0.2
+zc.lockfile = 1.4
 zdaemon = 4.2.0
 zipp = 1.2.0:whl
 zodburi = 2.5.0
 zope.event = 3.5.2
-paramiko = 2.1.3
+paramiko = 2.11.0
+PyNaCl = 1.3.0
+bcrypt = 3.1.4
 CacheControl = 0.12.6:whl
 msgpack = 0.6.2
 Flask = 1.1.2
@@ -235,7 +237,6 @@ pytest-runner = 5.2:whl
 ipaddress = 1.0.23
 jsonschema = 3.0.2:whl
 lockfile = 0.12.2:whl
-# XXX 'slapos node format' raises an exception with netifaces 0.10.5.
 netifaces = 0.10.7
 packaging = 16.8
 passlib = 1.7.1