bmcgough
commented
7 years ago This is the list of packages from Dirk's list that exist in Python3:
alabaster alembic appdirs APScheduler argh astroid awscli astropy autopep8 awscli Babel beautifulsoup4 beautifulsoup4 bitarray bitstring bokeh boto3 botocore burrito blaze bleach blessings blinker blist bokeh boto3 botocore bpython bz2file CacheControl certifi cffi chardet click cliff cliff colorama ConfigArgParse configobj contextlib2 cryptography cutadapt Cython cytoolz daemonize darkslide dbf deap debtcollector decorator distributed dnspython docutils dominate drmaa easygui easygui ecdsa enum34 fastcache fasteners Flask freezer funcsigs future gitdb2 GitPython google greenlet h5py html5lib HeapDict html5lib httplib2 idna inflection ipaddress ipdb ipykernel ipython iso8601 isort itsdangerous jedi Jinja2 jmespath jsonpatch jsonpointer jsonschema keystoneauth1 keyring keystoneauth1 lazr.uri ldap3 ldap3 locket lockfile lxml lxml Mako Markdown MarkupSafe matplotlib matplotlib mccabe mock monotonic mpi4py natsort natsort netaddr netifaces networkx nltk nose npyscreen numpy numpy numpydoc oauth olefile openstacksdk oslo.concurrency oslo.config oslo.context oslo.i18n odo olefile openstacksdk oslo.concurrency oslo.config oslo.context oslo.i18n oslo.log oslo.serialization oslo.utils oslo.serialization oslo.utils packaging pandas paramiko parse pathlib2 path.py pathtools patsy pbr pep8 pexpect pickleshare Pillow pip ply positional prettytable progressbar33 protobuf psutil psycopg2 ptyprocess py pyasn1 pycosat pycparser pycrypto pycurl pyflakes PyGithub Pygments PyGreSQL pyinotify pylint pymongo pymssql PyMySQL pyodbc pyOpenSSL pyparsing pyqi pysam pyserial pytest pytz PyVCF pyxdg PyYAML qcli qiime pyzmq qrcode QtAwesome qtconsole QtPy redis reportlab requests requests requestsexceptions rfc3986 rpy2 roman rsa s3transfer scandir scipy serializable setuptools shove SecretStorage setuptools simplegeneric simplejson singledispatch six smmap2 sortedcollections sortedcontainers Sphinx spyder SQLAlchemy stdeb stevedore stuf sympy tblib terminado toolz tornado traitlets ujson uritemplate urwid utils virtualenv visitor wadllib watchdog wheel WTForms xlrd xopen ZConfig zmq zope.interface
fizwit
just saw that a bunch of packages built for python2 have not made it into python3 (e.g. qiime scikit-learn)
petersen@rhino2:/home…-life-sciences$ diff -u /tmp/p2.list /tmp/p3.list --- /tmp/p2.list 2017-01-28 06:05:42.842944308 -0800 +++ /tmp/p3.list 2017-01-28 06:08:32.769380146 -0800 @@ -1,212 +1,283 @@ +abstract-rendering (0.5.1) +aenum (1.4.5) +alabaster (0.7.9) alembic (0.8.10) -alnvu (0.1.0) +anaconda-client (1.2.2) +apiwrapper (0.1.7) appdirs (1.4.0) APScheduler (3.3.1) +argcomplete (1.7.0) argh (0.26.2) astroid (1.4.9) -awscli (1.11.43) +astropy (1.3) +autopep8 (1.2.4) +awscli (1.11.35) Babel (2.3.4) backports.shutil-get-terminal-size (1.0.0) -bcbio-gff (0.6.4) -beautifulsoup4 (4.5.1) -biom-format (2.1.5) +beautifulsoup4 (4.5.3) biopython (1.68) +bitarray (0.8.1) bitstring (3.1.5) -bokeh (0.12.3) -boto3 (1.4.3) -botocore (1.5.6) -burrito (0.9.1) -burrito-fillings (0.1.1) +blaze (0.10.1) +bleach (1.5.0) +blessings (1.6) +blinker (1.4) +blist (1.3.6) +bokeh (0.12.4) +boto3 (1.4.4) +botocore (1.4.92) +bpython (0.16) +bz2file (0.98) +CacheControl (0.11.7) certifi (2017.1.23) cffi (1.9.1) +chardet (2.3.0) click (6.7) -cliff (2.3.0) +cliff (2.4.0) +cloudpickle (0.2.2) +clyent (1.2.1) cmd2 (0.6.9) -cogent (1.5.3) colorama (0.3.7) -colorbrewer (0.1.1) ConfigArgParse (0.11.0) +configobj (5.0.6) +contextlib2 (0.5.4) cryptography (1.7.1) +curtsies (0.2.11) cutadapt (1.12) cycler (0.10.0) Cython (0.25.2) +cytoolz (0.8.2) +daemonize (2.4.7) darkslide (2.3.3) -datacache (0.4.20) +dask (0.13.0) +datashape (0.5.2) +dbf (0.96.8) deap (1.0.2) debtcollector (1.10.0) decorator (4.0.10) deepTools (2.4.2) +distributed (1.15.0) +dnspython (1.15.0) docutils (0.13.1) dominate (2.3.1) drmaa (0.7.6) -easygui (0.98.0) +easygui (0.98.1) ecdsa (0.13) -emperor (0.9.60) -enum34 (1.1.6) +epydoc (3.0.1) +et-xmlfile (1.0.1) +fastcache (1.0.2) fasteners (0.14.1) Flask (0.12) flask-appconfig (0.11.1) -Flask-Bootstrap (3.3.7.0) +Flask-Bootstrap (3.3.7.1) +Flask-Cors (3.0.2) Flask-Debug (0.4.3) Flask-Migrate (2.0.2) flask-nav (0.6) Flask-Script (2.0.5) Flask-SQLAlchemy (2.1) -Flask-WTF (0.13.1) +Flask-WTF (0.14.2) freezer (4.0.0.0b2) funcsigs (1.0.2) -functools32 (3.2.3.post2) future (0.16.0) -futures (3.0.5) -gdata (2.0.18) -gitdb2 (2.0.0) -GitPython (2.1.1) -google (1.9.3) -gtfparse (0.0.6) +greenlet (0.4.11) h5py (2.7.0rc2) -html5lib (0.999999999) -HTSeq (0.6.1) +HeapDict (1.0.0) +html5lib (0.9999999) +httplib2 (0.9.2) idna (2.2) +imagesize (0.7.1) inflection (0.3.1) -ipaddress (1.0.18) +ip-associations-python-novaclient-ext (0.2) +ipdb (0.10.1) +ipykernel (4.5.2) ipython (5.1.0) ipython-genutils (0.1.0) iso8601 (0.1.11) +isort (4.2.5) itsdangerous (0.24) +jdcal (1.3) +jedi (0.9.0) Jinja2 (2.9.4) jmespath (0.9.0) +json2html (1.1.1) jsonpatch (1.15) jsonpointer (1.10) jsonschema (2.5.1) -keystoneauth1 (2.16.0) +keyring (10.1) +keystoneauth1 (2.18.0) +lazr.uri (1.0.3) lazy-object-proxy (1.2.2) -ldap3 (2.1.1) +ldap3 (2.2.0) liac-arff (2.1.0) +locket (0.2.0) lockfile (0.12.2) -lxml (3.7.2) +logilab-common (1.3.0) +lxml (3.7.1) Mako (1.0.6) Markdown (2.6.8) MarkupSafe (0.23) -matplotlib (2.0.0rc2) -memoized-property (1.0.3) +matplotlib (2.0.0) +mccabe (0.5.3) mincemeat (0.1.4) -misopy (0.5.3) +mistune (0.7.3) mock (2.0.0) monotonic (1.2) +moves (0.1) mpi4py (2.0.0) +mpmath (0.19) msgpack-python (0.4.8) -natsort (3.5.6) -ndg-httpsclient (0.4.2) +multipledispatch (0.4.9) +natsort (5.0.1) netaddr (0.7.18) netifaces (0.10.5) +networkx (1.11) +nltk (3.2.2) nose (1.3.7) +novaclient-auth-secretkey (0.1) npyscreen (4.10.5) Nuitka (0.5.25) -numpy (1.12.0rc1) +numexpr (2.6.1) +numpy (1.12.0) +numpydoc (0.6.0) oauth (1.0.1) -olefile (0.44) -openstacksdk (0.9.11) -os-client-config (1.24.0) -osc-lib (1.2.0) -oslo.concurrency (3.16.0) -oslo.config (3.21.0) -oslo.context (2.11.0) -oslo.i18n (3.11.0) +odo (0.5.0) +olefile (0.43) +openpyxl (2.4.1) +openstacksdk (0.9.13) +os-client-config (1.26.0) +os-diskconfig-python-novaclient-ext (0.1.3) +os-networksv2-python-novaclient-ext (0.26) +os-virtual-interfacesv2-python-novaclient-ext (0.20) +osc-lib (1.3.0) +oslo.concurrency (3.18.0) +oslo.config (3.22.0) +oslo.context (2.12.0) +oslo.i18n (3.12.0) oslo.log (3.19.0) -oslo.serialization (2.15.0) -oslo.utils (3.21.0) +oslo.serialization (2.16.0) +oslo.utils (3.22.0) packaging (16.8) pandas (0.19.2) +pandocfilters (1.4.1) paramiko (2.1.1) -parse (1.6.6) -pathlib2 (2.2.1) +path.py (10.1) pathtools (0.1.2) -paycheck (1.0.2) +patsy (0.4.1) pbr (1.10.0) +pep8 (1.7.0) pexpect (4.2.1) pickleshare (0.7.4) Pillow (4.0.0) pip (9.0.1) +ply (3.9) positional (1.1.1) +post-0 (0.0.0) prettytable (0.7.2) -progressbar33 (2.4) prompt-toolkit (1.0.9) +protobuf (3.2.0rc2) psutil (5.0.1) psycopg2 (2.6.2) ptyprocess (0.5.1) +public-0 (0.0.0) +py (1.4.32) +py2bit (0.2.0) pyasn1 (0.1.9) -pyastro (1.1) pyBigWig (0.3.2) PyClone (0.12.9) +pycosat (0.6.1) pycparser (2.17) pycrypto (2.6.1) pycurl (7.43.0) PyDP (0.2.2) -pyensembl (1.0.3) -pygithub3 (0.5.1) +pyflakes (1.4.0) +PyGithub (1.29) Pygments (2.2.0) +PyGreSQL (5.0.3) pyinotify (0.9.6) +pylint (1.6.4) pymongo (3.4.0) pymssql (2.1.3) PyMySQL (0.7.9) -pynast (1.2.2) +pyodbc (4.0.0) pyOpenSSL (16.2.0) pypandoc (1.3.3) pyparsing (2.1.10) -pyqi (0.3.2) +PyQtX (0.1.2) +pyrax (1.9.8) pysam (0.9.1.4) -python-cinderclient (1.9.0) +pyserial (3.2.1) +pytest (3.0.6) +python-cinderclient (1.10.0) python-dateutil (2.6.0) +python-debian (0.1.28) python-editor (1.0.3) python-freezerclient (1.1.0) -python-glanceclient (1.1.2) -python-keystoneclient (3.8.0) -python-memcached (1.58) +python-glanceclient (2.6.0) +python-hostlist (1.17) +python-keystoneclient (3.10.0) python-novaclient (7.0.0) -python-openstackclient (3.6.0) +python-openstackclient (3.7.0) python-pam (1.8.2) python-swiftclient (3.2.0) pytz (2016.10) -PyVCF (0.6.8) +pyxdg (0.25) PyYAML (3.12) -qcli (0.1.1) -qiime (1.9.1) -qiime-default-reference (0.1.3) +pyzmq (16.0.2) qrcode (5.3) +QtAwesome (0.4.3) +qtconsole (4.2.1) +QtPy (1.2.1) +rackspace-auth-openstack (1.3) +rackspace-novaclient (2.1) +rax-default-network-flags-python-novaclient-ext (0.4.0) +rax-scheduled-images-python-novaclient-ext (0.3.1) +redis (2.10.5) reportlab (3.3.0) -requests (2.12.4) +request-0 (0.0.0) +requests (2.13.0) requestsexceptions (1.1.3) rfc3986 (0.4.1) -rpy2 (2.8.5) +roman (2.0.0) rsa (3.4.2) +ruffus (2.6.3) +s3fs (0.0.8) s3transfer (0.1.10) scandir (1.4) -scikit-bio (0.2.3) -scikit-learn (0.18.1) scipy (0.18.1) -seqmagick (0.6.1) -serializable (0.1.1) -setuptools (32.2.0) -shove (0.6.6) +SecretStorage (2.3.1) +setuptools (28.8.0) simplegeneric (0.8.1) simplejson (3.10.0) singledispatch (3.4.0.3) six (1.10.0) -smmap2 (2.0.1) +snowballstemmer (1.2.1) +sockjs-tornado (1.0.3) +sortedcollections (0.4.2) +sortedcontainers (1.5.7) +Sphinx (1.5.2.dev20170126) +spyder (3.1.2) SQLAlchemy (1.1.5) +ssh-import-id (5.6) +stdeb (0.8.5) stevedore (1.19.1) -stuf (0.9.16) -subprocess32 (3.2.7) -tinytimer (0.0.0) +swiftly (2.6) +sympy (1.0) +tblib (1.3.0) +terminado (0.6) +toolz (0.8.2) +tornado (4.4.2) traitlets (4.3.1) twobitreader (3.1.4) -typechecks (0.0.2) tzlocal (1.3) +ujson (1.35) unicodecsv (0.14.1) uritemplate (3.0.0) urwid (1.3.1) +utils (0.9.0) virtualenv (15.1.0) visitor (0.1.3) +wadllib (1.3.2) warlock (1.3.0) watchdog (0.8.3) wcwidth (0.1.7) @@ -215,4 +286,10 @@ wheel (0.30.0a0) wrapt (1.10.8) WTForms (2.1) +xlrd (1.0.0) +XlsxWriter (0.9.6) xopen (0.1.1) +ZConfig (3.1.0) +zict (0.1.1) +zmq (0.0.0) +zope.interface (4.3.3)