te.getVersionInfo() fails on latest release

hsauro commented 4 years ago

If i type te.getVersionInfo() I get:

te.getVersionInfo() Traceback (most recent call last):

File "", line 1, in te.getVersionInfo()

File "C:\Tellurium-Winpython-3.7\python-3.7.7.amd64\lib\site-packages\tellurium\tellurium.py", line 212, in getVersionInfo ('antimony', antimony.version),

AttributeError: module 'antimony' has no attribute 'version'

evilnose commented 4 years ago

I found that this issue is present on linux as well. I've rebuilt and reuploaded antimony for linux. The fix was to add a module-level attribute __version__ in __init__.py.

For future antimony builds, I suggest having __init__.py automatically fetch the version string using the code provided in this SO post.

However te.getVersionInfo() still doesn't work right now since the tesedml wheels were built incorrectly. I'll rebuild those now.

hsauro commented 4 years ago

ok thanks!

H

On Thu, Aug 6, 2020 at 2:00 PM Gary Geng notifications@github.com wrote:

I found that this issue is present on linux as well. I've rebuilt and reuploaded antimony for linux. The fix was to add a module-level attribute version in init.py.

For future antimony builds, I suggest having init.py automatically fetch the version string using the code provided in this https://stackoverflow.com/a/17638236/9171534 SO post.

However te.getVersionInfo() still doesn't work right now since the tesedml wheels were built incorrectly. I'll rebuild those now.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/sys-bio/tellurium/issues/465#issuecomment-670188525, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAIBSDRDYHPJUFG4SITZUNLR7MKQDANCNFSM4PW4DINQ .

-- Herbert Sauro, Professor University of Washington, Bioengineering 206-685-2119, www.sys-bio.org hsauro@uw.edu Books: http://books.analogmachine.org/

hsauro commented 4 years ago

PS If you want to update the way we handle version go ahead. I think I used what you suggested in a recent package I helped write.

H

On Thu, Aug 6, 2020 at 2:39 PM Herbert M Sauro hsauro@uw.edu wrote:

ok thanks!

H

On Thu, Aug 6, 2020 at 2:00 PM Gary Geng notifications@github.com wrote:

I found that this issue is present on linux as well. I've rebuilt and reuploaded antimony for linux. The fix was to add a module-level attribute version in init.py.

For future antimony builds, I suggest having init.py automatically fetch the version string using the code provided in this https://stackoverflow.com/a/17638236/9171534 SO post.

However te.getVersionInfo() still doesn't work right now since the tesedml wheels were built incorrectly. I'll rebuild those now.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/sys-bio/tellurium/issues/465#issuecomment-670188525, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAIBSDRDYHPJUFG4SITZUNLR7MKQDANCNFSM4PW4DINQ .

-- Herbert Sauro, Professor University of Washington, Bioengineering 206-685-2119, www.sys-bio.org hsauro@uw.edu Books: http://books.analogmachine.org/

-- Herbert Sauro, Professor University of Washington, Bioengineering 206-685-2119, www.sys-bio.org hsauro@uw.edu Books: http://books.analogmachine.org/

evilnose commented 4 years ago

Sure, I'll do that. Also I think phrasedml is suffering from the same issue.

However, I don't think I have access to the sourceforge svn repo. Lucian, can you give me access? Or I can detail the changes I made and you can push it.

hsauro commented 4 years ago

I'll need a new linux pip installer once you're ready.

Herbert

On Thu, Aug 6, 2020 at 3:42 PM Gary Geng notifications@github.com wrote:

Sure, I'll do that. Also I think phrasedml is suffering from the same issue.

However, I don't think I have access to the sourceforge svn repo. Lucian, can you give me access? Or I can detail the changes I made and you can push it.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/sys-bio/tellurium/issues/465#issuecomment-670226843, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAIBSDQWMM4RZS72FOZ2OHTR7MWVJANCNFSM4PW4DINQ .

-- Herbert Sauro, Professor University of Washington, Bioengineering 206-685-2119, www.sys-bio.org hsauro@uw.edu Books: http://books.analogmachine.org/

luciansmith commented 4 years ago

I'm more than happy to get you access to svn's phrasedml. However, as I discovered today, there are actually two versions out there, because at some point, phrasedml was copied over to github/sys-bio, and further updates were made there. I was just working on the mac release of that, and made some updates to let it compile there.

Also, that version has a fixed init.py file anyway, so let's move away from the sf version. If you don't have access to the github/phrasedml version, let me know!

-Lucian

On Thu, Aug 6, 2020 at 3:43 PM Gary Geng notifications@github.com wrote:

Sure, I'll do that. Also I think phrasedml is suffering from the same issue.

However, I don't think I have access to the sourceforge svn repo. Lucian, can you give me access? Or I can detail the changes I made and you can push it.

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/sys-bio/tellurium/issues/465#issuecomment-670226843, or unsubscribe https://github.com/notifications/unsubscribe-auth/AANH3VURFGI7F5VOGEMPQHLR7MWVJANCNFSM4PW4DINQ .

evilnose commented 4 years ago

That'll work, thanks!

I also need to modify antimony; I've added only two lines to __init__.py, so I think it might be easier for me to send it to you?

Also, I don't think I've worked with a tellurium installer. Where should I go to build that after the fixes are made?

luciansmith commented 4 years ago

The good news here is that Tellurium itself doesn't need to be re-installed: it's pure python, so it only needs to be build/uploaded in one place. And the failing function was calling the library functions, so when those libraries are updated, the function will Just Work.

Herbert, I have now uploaded new Windows versions of everything that didn't have a version attribute. You can get the new ones by entering (inside Spyder, even):


pip install --upgrade antimony tesbml tesedml tecombine tenuml

evilnose commented 4 years ago

The linux versions should work now as well.

hsauro commented 4 years ago

Ok great try the Linux version. I’ve got a browser web page to talk to tellurium in a docker image. This is for work with Veronica.

JingWui commented 4 years ago

Hi,

I am working with Tellurium package and the te.getVersionInfo() still doesn't work for the tesedml with the following error E AttributeError: module 'tesedml' has no attribute 'version'. However It works on Windows, Python 3.7.1. and Python 3.8.3, and my installed Tellurium package is 2.1.6 and tesedml is 0.4.5.2. But it fails on the ubuntu platform when tested on Travis CI.

Is there a way for me to resolve the issue? Thank you so much.

luciansmith commented 4 years ago

Hi, JingWiu! I have tested this on a running VM of ubuntu, and 'getVersionInfo' works there, which means that there must be something different in your Travis CI setup that is the source of the problem.

Can you send us (or copy into a comment) the contents of your .travis.yml file (or the relevant bits from it) so we can test ourselves? Thank you!

JingWui commented 4 years ago

Hi Lucian,

Please find attached the information when running Travis CI. The error appeared as follows when we tried to use the exportInlineOmex function from Tellurium. def VersionDict(): '''Return dict of version strings.''' import tesbml, tesedml, tecombine return { 'tellurium': getTelluriumVersion(), 'roadrunner': roadrunner.getVersionStr(roadrunner.VERSIONSTR_BASIC), 'antimony': antimony.version, 'phrasedml': phrasedml.version, 'tesbml': libsbml.getLibSBMLDottedVersion(),

      'tesedml': tesedml.__version__,
'tecombine': tecombine.version } E AttributeError: module 'tesedml' has no attribute 'version'

FYI, I managed to run without error on my own computer (Windows). Please find attached the pip list for your reference.

On Wed, Oct 28, 2020 at 4:58 AM Lucian Smith notifications@github.com wrote:

Hi, JingWiu! I have tested this on a running VM of ubuntu, and 'getVersionInfo' works there, which means that there must be something different in your Travis CI setup that is the source of the problem.

Can you send us (or copy into a comment) the contents of your .travis.yml file (or the relevant bits from it) so we can test ourselves? Thank you!

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/sys-bio/tellurium/issues/465#issuecomment-717534935, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHXBYKKEFWV4ORDLGVUFMTTSM4X6VANCNFSM4PW4DINQ .

Package Version Location

alabaster 0.7.12 anaconda-client 1.7.2 anaconda-navigator 1.9.12 anaconda-project 0.8.3 antimony 2.12.0.3 appdirs 1.4.4 argh 0.26.2 asn1crypto 1.3.0 astroid 2.4.2 astropy 4.0.1.post1 atomicwrites 1.4.0 attrs 19.3.0 autopep8 1.5.3 Babel 2.8.0 backcall 0.2.0 backports.functools-lru-cache 1.6.1 backports.shutil-get-terminal-size 1.0.0 backports.tempfile 1.0 backports.weakref 1.0.post1 bcrypt 3.1.7 beautifulsoup4 4.9.1 biopython 1.78 bitarray 1.4.0 bkcharts 0.2 bleach 3.1.5 bokeh 2.1.1 boto 2.49.0 Bottleneck 1.3.2 brotlipy 0.7.0 certifi 2020.6.20 cffi 1.14.0 chardet 3.0.4 click 7.1.2 cloudpickle 1.5.0 clyent 1.2.2 colorama 0.4.3 comtypes 1.1.7 conda 4.8.3 conda-build 3.18.11 conda-package-handling 1.7.0 conda-verify 3.4.2 contextlib2 0.6.0.post1 cryptography 2.9.2 cycler 0.10.0 Cython 0.29.21 cytoolz 0.10.1 dask 2.20.0 decorator 4.4.2 defusedxml 0.6.0 diff-match-patch 20200713 distributed 2.20.0 dnaplotlib 1.0 docutils 0.16 entrypoints 0.3 et-xmlfile 1.0.1 fastcache 1.1.0 filelock 3.0.12 flake8 3.8.3 Flask 1.1.2 fsspec 0.7.4 future 0.18.2 fuzzywuzzy 0.18.0 gevent 20.6.2 glob2 0.7 gmpy2 2.0.8 greenlet 0.4.16 h5py 2.10.0 HeapDict 1.0.1 html5lib 1.1 idna 2.10 imageio 2.9.0 imagesize 1.2.0 importlib-metadata 1.7.0 intervaltree 3.0.2 ipykernel 5.3.2 ipython 7.16.1 ipython-genutils 0.2.0 ipywidgets 7.5.1 isort 4.3.21 itsdangerous 1.1.0 jdcal 1.4.1 jedi 0.17.1 Jinja2 2.11.2 joblib 0.16.0 json5 0.9.5 jsonschema 3.2.0 jupyter 1.0.0 jupyter-client 6.1.6 jupyter-console 6.1.0 jupyter-core 4.6.3 jupyterlab 2.1.5 jupyterlab-server 1.2.0 keyring 21.2.1 kiwisolver 1.2.0 lazy-object-proxy 1.4.3 libarchive-c 2.9 libroadrunner 2.0.0 llvmlite 0.33.0+1.g022ab0f locket 0.2.0 lxml 4.5.2 MarkupSafe 1.1.1 matplotlib 3.2.2 mccabe 0.6.1 menuinst 1.4.16 mistune 0.8.4 mkl-fft 1.1.0 mkl-random 1.1.1 mkl-service 2.3.0 mock 4.0.2 more-itertools 8.4.0 mpmath 1.1.0 msgpack 1.0.0 multipledispatch 0.6.0 navigator-updater 0.2.1 nbconvert 5.6.1 nbformat 5.0.7 networkx 2.4 nltk 3.5 nose 1.3.7 notebook 6.0.3 numba 0.50.1 numexpr 2.7.1 numpy 1.19.2 numpydoc 1.1.0 olefile 0.46 openpyxl 3.0.4 packaging 20.4 pandas 1.0.5 pandocfilters 1.4.2 paramiko 2.7.1 parso 0.7.0 partd 1.1.0 path 13.1.0 pathlib2 2.3.5 pathtools 0.1.2 patsy 0.5.1 pep8 1.7.1 pexpect 4.8.0 phrasedml 1.0.10 pickleshare 0.7.5 Pillow 7.2.0 pip 20.1.1 pkginfo 1.5.0.1 plotly 4.11.0 pluggy 0.13.1 ply 3.11 prometheus-client 0.8.0 prompt-toolkit 3.0.5 psutil 5.7.0 py 1.9.0 pycodestyle 2.6.0 pycosat 0.6.3 pycparser 2.20 pycurl 7.43.0.5 pydocstyle 5.0.2 pyflakes 2.2.0 Pygments 2.6.1 pylint 2.5.3 PyNaCl 1.4.0 pyodbc 4.0.0-unsupported pyOpenSSL 19.1.0 pyparsing 2.4.7 pyreadline 2.1 pyrsistent 0.16.0 PySocks 1.7.1 pytest 5.4.3 python-dateutil 2.8.1 python-jsonrpc-server 0.3.4 python-language-server 0.34.1 pytz 2020.1 PyWavelets 1.1.1 pywin32 227 pywin32-ctypes 0.2.0 pywinpty 0.5.7 PyYAML 5.3.1 pyzmq 19.0.1 QDarkStyle 2.8.1 QtAwesome 0.7.2 qtconsole 4.7.5 QtPy 1.9.0 regex 2020.6.8 reportlab 3.5.54 requests 2.24.0 retrying 1.3.3 rope 0.17.0 Rtree 0.9.4 ruamel-yaml 0.15.87 SALib 1.3.11 sbml2matlab 1.2.3 scikit-image 0.16.2 scikit-learn 0.23.1 scipy 1.5.3 seaborn 0.10.1 Send2Trash 1.5.0 setuptools 49.2.0.post20200714 simplegeneric 0.8.1 singledispatch 3.4.0.3 sip 4.19.13 six 1.15.0 snowballstemmer 2.0.0 sortedcollections 1.2.1 sortedcontainers 2.2.2 soupsieve 2.0.1 Sphinx 3.1.2 sphinxcontrib-applehelp 1.0.2 sphinxcontrib-devhelp 1.0.2 sphinxcontrib-htmlhelp 1.0.3 sphinxcontrib-jsmath 1.0.1 sphinxcontrib-qthelp 1.0.3 sphinxcontrib-serializinghtml 1.1.4 sphinxcontrib-websupport 1.2.3 spyder 4.1.4 spyder-kernels 1.9.2 SQLAlchemy 1.3.18 statsmodels 0.11.1 sympy 1.6.1 synbiopython 0.0.1 c:\users\jingwui\dropbox\post_doc_documents\git_synbiopython_revised2\synbiopython tables 3.6.1 tblib 1.6.0 tecombine 0.2.7.0 tellurium 2.1.6 tenuml 1.1.1.4 terminado 0.8.3 tesbml 5.18.1.2 tesedml 0.4.5.2 testpath 0.4.4 threadpoolctl 2.1.0 toml 0.10.1 toolz 0.10.0 tornado 6.0.4 tqdm 4.47.0 traitlets 4.3.3 typing-extensions 3.7.4.2 ujson 1.35 unicodecsv 0.14.1 urllib3 1.25.9 watchdog 0.10.3 wcwidth 0.2.5 webencodings 0.5.1 Werkzeug 1.0.1 wheel 0.34.2 widgetsnbextension 3.5.1 win-inet-pton 1.1.0 win-unicode-console 0.5 wincertstore 0.2 wrapt 1.11.2 xlrd 1.2.0 XlsxWriter 1.2.9 xlwings 0.19.5 xlwt 1.3.0 xmltodict 0.12.0 yapf 0.30.0 zict 2.0.0 zipp 3.1.0 zope.event 4.4 zope.interface 4.7.1

Build system information Build language: python Build dist: xenial Build id: 193487276 Job id: 410224012 Runtime kernel version: 4.15.0-1077-gcp travis-build version: acd5a925 Build image provisioning date and time Wed Jun 24 13:36:52 UTC 2020 Operating System Details Distributor ID: Ubuntu Description: Ubuntu 16.04.6 LTS Release: 16.04 Codename: xenial Systemd Version systemd 229 Cookbooks Version 3f92a99 https://github.com/travis-ci/travis-cookbooks/tree/3f92a99 git version git version 2.27.0 bash version GNU bash, version 4.3.48(1)-release (x86_64-pc-linux-gnu) gcc version gcc (Ubuntu 5.4.0-6ubuntu1~16.04.12) 5.4.0 20160609 docker version Client: Version: 18.06.0-ce API version: 1.38 Go version: go1.10.3 Git commit: 0ffa825 Built: Wed Jul 18 19:11:02 2018 OS/Arch: linux/amd64 Experimental: false Server: Engine: Version: 18.06.0-ce API version: 1.38 (minimum version 1.12) Go version: go1.10.3 Git commit: 0ffa825 Built: Wed Jul 18 19:09:05 2018 OS/Arch: linux/amd64 Experimental: false clang version clang version 7.0.0 (tags/RELEASE_700/final) jq version jq-1.5 bats version Bats 0.4.0 shellcheck version 0.7.0 shfmt version v2.6.3 ccache version 3.2.4 cmake version cmake version 3.12.4 heroku version heroku/7.42.1 linux-x64 node-v12.16.2 imagemagick version Version: ImageMagick 6.8.9-9 Q16 x86_64 2019-11-12 http://www.imagemagick.org md5deep version 4.4 mercurial version version 4.8 mysql version mysql Ver 14.14 Distrib 5.7.30, for Linux (x86_64) using EditLine wrapper openssl version OpenSSL 1.0.2g 1 Mar 2016 packer version 1.3.3 postgresql client version psql (PostgreSQL) 10.13 (Ubuntu 10.13-1.pgdg16.04+1) ragel version Ragel State Machine Compiler version 6.8 Feb 2013 sudo version 1.8.16 gzip version gzip 1.6 zip version Zip 3.0 vim version VIM - Vi IMproved 7.4 (2013 Aug 10, compiled Mar 18 2020 14:06:17) iptables version iptables v1.6.0 curl version curl 7.47.0 (x86_64-pc-linux-gnu) libcurl/7.47.0 GnuTLS/3.4.10 zlib/1.2.8 libidn/1.32 librtmp/2.3 wget version GNU Wget 1.17.1 built on linux-gnu. rsync version rsync version 3.1.1 protocol version 31 gimme version v1.5.4 nvm version 0.35.3 perlbrew version /home/travis/perl5/perlbrew/bin/perlbrew - App::perlbrew/0.88 phpenv version rbenv 1.1.2-30-gc879cb0 rvm version rvm 1.29.10 (latest) by Michal Papis, Piotr Kuczynski, Wayne E. Seguin [https://rvm.io] default ruby version ruby 2.5.3p105 (2018-10-18 revision 65156) [x86_64-linux] CouchDB version couchdb 1.6.1 ElasticSearch version 5.5.0 Installed Firefox version firefox 63.0.1 MongoDB version MongoDB 4.0.19 PhantomJS version 2.1.1 Pre-installed PostgreSQL versions 9.4.26 9.5.22 9.6.18 Redis version redis-server 6.0.5 Pre-installed Go versions 1.11.1 ant version Apache Ant(TM) version 1.9.6 compiled on July 20 2018 mvn version Apache Maven 3.6.3 (cecedd343002696d0abb50b32b541b8a6ba2883f) gradle version Gradle 5.1.1! lein version Leiningen 2.9.3 on Java 11.0.2 OpenJDK 64-Bit Server VM Pre-installed Node.js versions v10.21.0 v11.0.0 v12.18.1 v4.9.1 v6.17.1 v8.12.0 v8.17.0 v8.9 phpenv versions system 5.6 5.6.40 7.1 7.1.27 7.2

7.2.15 (set by /home/travis/.phpenv/version) hhvm hhvm-stable composer --version Composer version 1.8.4 2019-02-11 10:52:10 Pre-installed Ruby versions ruby-2.3.8 ruby-2.4.5 ruby-2.5.3 0.02s0.01s0.51s0.28s0.07s0.00s0.06s0.00s0.01s0.01s0.01s0.02s0.01s0.00s0.00s0.03s0.01s0.02s0.49s0.00s0.00s0.00s0.01s0.00s0.12s0.01s0.94s0.00s0.00s6.04s0.00s3.01s0.00s2.53s docker_mtu resolvconf Downloading archive: https://storage.googleapis.com/travis-ci-language-archives/python/binaries/ubuntu/16.04/x86_64/python-3.8.3.tar.bz2 0.47s$ curl -sSf --retry 5 -o python-3.8.3.tar.bz2 ${archive_url} 11.83s$ sudo tar xjf python-3.8.3.tar.bz2 --directory /

$ source ~/virtualenv/python3.8.3/bin/activate $ python --version Python 3.8.3 $ pip --version pip 20.1 from /home/travis/virtualenv/python3.8.3/lib/python3.8/site-packages/pip (python 3.8)

$ pip install --upgrade pip Collecting pip Downloading pip-20.2.4-py2.py3-none-any.whl (1.5 MB) Installing collected packages: pip Attempting uninstall: pip Found existing installation: pip 20.1 Uninstalling pip-20.1: Successfully uninstalled pip-20.1 Successfully installed pip-20.2.4

$ pip install --upgrade coveralls pytest-cov pytest Collecting coveralls Downloading coveralls-2.1.2-py2.py3-none-any.whl (13 kB) Collecting pytest-cov Downloading pytest_cov-2.10.1-py2.py3-none-any.whl (19 kB) Collecting pytest Downloading pytest-6.1.1-py3-none-any.whl (272 kB) Collecting requests>=1.0.0 Downloading requests-2.24.0-py2.py3-none-any.whl (61 kB) Collecting coverage<6.0,>=4.1 Downloading coverage-5.3-cp38-cp38-manylinux1_x86_64.whl (230 kB) Collecting docopt>=0.6.1 Downloading docopt-0.6.2.tar.gz (25 kB) Collecting py>=1.8.2 Downloading py-1.9.0-py2.py3-none-any.whl (99 kB) Requirement already satisfied, skipping upgrade: pluggy<1.0,>=0.12 in /home/travis/virtualenv/python3.8.3/lib/python3.8/site-packages (from pytest) (0.13.1) Collecting toml Downloading toml-0.10.1-py2.py3-none-any.whl (19 kB) Collecting iniconfig Downloading iniconfig-1.1.1-py2.py3-none-any.whl (5.0 kB) Requirement already satisfied, skipping upgrade: attrs>=17.4.0 in /home/travis/virtualenv/python3.8.3/lib/python3.8/site-packages (from pytest) (19.3.0) Requirement already satisfied, skipping upgrade: packaging in /home/travis/virtualenv/python3.8.3/lib/python3.8/site-packages (from pytest) (20.3) Collecting idna<3,>=2.5 Downloading idna-2.10-py2.py3-none-any.whl (58 kB) Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 Downloading urllib3-1.25.11-py2.py3-none-any.whl (127 kB) Collecting chardet<4,>=3.0.2 Downloading chardet-3.0.4-py2.py3-none-any.whl (133 kB) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /home/travis/virtualenv/python3.8.3/lib/python3.8/site-packages (from requests>=1.0.0->coveralls) (2020.4.5.1) Requirement already satisfied, skipping upgrade: six in /home/travis/virtualenv/python3.8.3/lib/python3.8/site-packages (from packaging->pytest) (1.14.0) Requirement already satisfied, skipping upgrade: pyparsing>=2.0.2 in /home/travis/virtualenv/python3.8.3/lib/python3.8/site-packages (from packaging->pytest) (2.4.7) Building wheels for collected packages: docopt Building wheel for docopt (setup.py) ... done Created wheel for docopt: filename=docopt-0.6.2-py2.py3-none-any.whl size=13704 sha256=d43c504f561bf73b0c6fd6c3d85b1d22666d562bb2bbf821e0c79016b18e07e7 Stored in directory: /home/travis/.cache/pip/wheels/56/ea/58/ead137b087d9e326852a851351d1debf4ada529b6ac0ec4e8c Successfully built docopt Installing collected packages: idna, urllib3, chardet, requests, coverage, docopt, coveralls, py, toml, iniconfig, pytest, pytest-cov Attempting uninstall: py Found existing installation: py 1.8.1 Uninstalling py-1.8.1: Successfully uninstalled py-1.8.1 Attempting uninstall: pytest Found existing installation: pytest 5.4.2 Uninstalling pytest-5.4.2: Successfully uninstalled pytest-5.4.2 Successfully installed chardet-3.0.4 coverage-5.3 coveralls-2.1.2 docopt-0.6.2 idna-2.10 iniconfig-1.1.1 py-1.9.0 pytest-6.1.1 pytest-cov-2.10.1 requests-2.24.0 toml-0.10.1 urllib3-1.25.11

$ pip install -e . Collecting pandas>=0.22 Downloading pandas-1.1.3-cp38-cp38-manylinux1_x86_64.whl (9.3 MB) Collecting fuzzywuzzy Downloading fuzzywuzzy-0.18.0-py2.py3-none-any.whl (18 kB) Collecting dnaplotlib Downloading dnaplotlib-1.0.tar.gz (17 kB) Collecting tellurium Downloading tellurium-2.1.6-py3-none-any.whl (117 kB) Collecting tesbml Downloading tesbml-5.18.1.2-cp38-cp38-manylinux2014_x86_64.whl (6.3 MB) Collecting biopython Downloading biopython-1.78-cp38-cp38-manylinux1_x86_64.whl (2.3 MB) Collecting reportlab Downloading reportlab-3.5.54-cp38-cp38-manylinux2010_x86_64.whl (2.6 MB) Collecting nbgitpuller Downloading nbgitpuller-0.9.0-py2.py3-none-any.whl (14 kB) Requirement already satisfied: numpy>=1.15.4 in /home/travis/virtualenv/python3.8.3/lib/python3.8/site-packages (from pandas>=0.22->synbiopython==0.0.1) (1.18.4) Collecting pytz>=2017.2 Downloading pytz-2020.1-py2.py3-none-any.whl (510 kB) Collecting python-dateutil>=2.7.3 Downloading python_dateutil-2.8.1-py2.py3-none-any.whl (227 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kB) Collecting ipython-genutils Downloading ipython_genutils-0.2.0-py2.py3-none-any.whl (26 kB) Collecting ptyprocess>=0.5 Downloading ptyprocess-0.6.0-py2.py3-none-any.whl (39 kB) Requirement already satisfied: wcwidth in /home/travis/virtualenv/python3.8.3/lib/python3.8/site-packages (from prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0->ipython->tellurium->synbiopython==0.0.1) (0.1.9) Collecting parso<0.8.0,>=0.7.0 Downloading parso-0.7.1-py2.py3-none-any.whl (109 kB) Collecting cffi>=1.0.0 Downloading cffi-1.14.3-cp38-cp38-manylinux1_x86_64.whl (410 kB) Collecting pandocfilters>=1.4.1 Downloading pandocfilters-1.4.3.tar.gz (16 kB) Collecting jupyterlab-pygments Downloading jupyterlab_pygments-0.1.2-py2.py3-none-any.whl (4.6 kB) Collecting bleach Downloading bleach-3.2.1-py2.py3-none-any.whl (145 kB) Collecting mistune<2,>=0.8.1 Downloading mistune-0.8.4-py2.py3-none-any.whl (16 kB) Collecting testpath Downloading testpath-0.4.4-py2.py3-none-any.whl (163 kB) Collecting defusedxml 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sha256=d2b4ce180b9dc596e24b7bde2581c2fd21b08d780319a493d9257b789da47ef2 Stored in directory: /home/travis/.cache/pip/wheels/8f/ce/3d/1e72484b51e74993b8933b3c145ef81cfd70a56d30d1228267 Building wheel for tornado (setup.py) ... done Created wheel for tornado: filename=tornado-6.0.4-cp38-cp38-linux_x86_64.whl size=423023 sha256=ce878e60d5afc6b98a77571a41b738d0da37830cb12a84d0171f4d628f5711b5 Stored in directory: /home/travis/.cache/pip/wheels/88/79/e5/598ba17e85eccf2626eab62e4ee8452895636cd542650d450d Building wheel for retrying (setup.py) ... done Created wheel for retrying: filename=retrying-1.3.3-py3-none-any.whl size=11430 sha256=eebbcfaebbeed5c947ea26e198898ef08c31c85f390b416df25071d0b7f985fd Stored in directory: /home/travis/.cache/pip/wheels/c4/a7/48/0a434133f6d56e878ca511c0e6c38326907c0792f67b476e56 Building wheel for pandocfilters (setup.py) ... done Created wheel for pandocfilters: filename=pandocfilters-1.4.3-py3-none-any.whl size=7991 sha256=75e170d0e11461e605f5e5d5ff3beb05947e8e15cb9de487ae994b0822c8ffe0 Stored in directory: /home/travis/.cache/pip/wheels/fc/39/52/8d6f3cec1cca4ceb44d658427c35711b19d89dbc4914af657f Building wheel for pyrsistent (setup.py) ... done Created wheel for pyrsistent: filename=pyrsistent-0.17.3-cp38-cp38-linux_x86_64.whl size=114308 sha256=9316d510bd917f1b5629b7656f5c8528defab2865d8c510dd4cec86aa31476ec Stored in directory: /home/travis/.cache/pip/wheels/3d/22/08/7042eb6309c650c7b53615d5df5cc61f1ea9680e7edd3a08d2 Successfully built dnaplotlib tornado retrying pandocfilters pyrsistent Installing collected packages: pytz, python-dateutil, pandas, fuzzywuzzy, dnaplotlib, scipy, pyzmq, tornado, ipython-genutils, traitlets, jupyter-core, jupyter-client, ptyprocess, pexpect, decorator, pygments, backcall, prompt-toolkit, parso, jedi, pickleshare, ipython, ipykernel, tenuml, libroadrunner, tesbml, antimony, MarkupSafe, jinja2, tesedml, phrasedml, pillow, kiwisolver, cycler, matplotlib, tecombine, retrying, plotly, sbml2matlab, tellurium, biopython, reportlab, prometheus-client, pycparser, cffi, argon2-cffi, pandocfilters, pyrsistent, jsonschema, nbformat, jupyterlab-pygments, webencodings, bleach, mistune, testpath, defusedxml, nest-asyncio, async-generator, nbclient, entrypoints, nbconvert, Send2Trash, terminado, notebook, nbgitpuller, synbiopython Running setup.py develop for synbiopython ERROR: After October 2020 you may experience errors when installing or updating packages. This is because pip will change the way that it resolves dependency conflicts. We recommend you use --use-feature=2020-resolver to test your packages with the new resolver before it becomes the default.

libroadrunner 2.0.0 requires numpy>=1.19, but you'll have numpy 1.18.4 which is incompatible. matplotlib 3.3.2 requires certifi>=2020.06.20, but you'll have certifi 2020.4.5.1 which is incompatible. tellurium 2.1.6 requires numpy>=1.19.0, but you'll have numpy 1.18.4 which is incompatible.

Successfully installed MarkupSafe-1.1.1 Send2Trash-1.5.0 antimony-2.12.0.2 argon2-cffi-20.1.0 async-generator-1.10 backcall-0.2.0 biopython-1.78 bleach-3.2.1 cffi-1.14.3 cycler-0.10.0 decorator-4.4.2 defusedxml-0.6.0 dnaplotlib-1.0 entrypoints-0.3 fuzzywuzzy-0.18.0 ipykernel-5.3.4 ipython-7.18.1 ipython-genutils-0.2.0 jedi-0.17.2 jinja2-2.11.2 jsonschema-3.2.0 jupyter-client-6.1.7 jupyter-core-4.6.3 jupyterlab-pygments-0.1.2 kiwisolver-1.2.0 libroadrunner-2.0.0 matplotlib-3.3.2 mistune-0.8.4 nbclient-0.5.1 nbconvert-6.0.7 nbformat-5.0.8 nbgitpuller-0.9.0 nest-asyncio-1.4.2 notebook-6.1.4 pandas-1.1.3 pandocfilters-1.4.3 parso-0.7.1 pexpect-4.8.0 phrasedml-1.0.10.3 pickleshare-0.7.5 pillow-8.0.1 plotly-4.12.0 prometheus-client-0.8.0 prompt-toolkit-3.0.8 ptyprocess-0.6.0 pycparser-2.20 pygments-2.7.2 pyrsistent-0.17.3 python-dateutil-2.8.1 pytz-2020.1 pyzmq-19.0.2 reportlab-3.5.54 retrying-1.3.3 sbml2matlab-1.2.3.1 scipy-1.5.3 synbiopython tecombine-0.2.7.0 tellurium-2.1.6 tenuml-1.1.1.4 terminado-0.9.1 tesbml-5.18.1.2 tesedml-0.4.5.3 testpath-0.4.4 tornado-6.0.4 traitlets-5.0.5 webencodings-0.5.1

../../../virtualenv/python3.8.3/lib/python3.8/site-packages/tellurium/tellurium.py:695: in exportInlineOmex saveInlineOMEX(inline_omex, export_location) ../../../virtualenv/python3.8.3/lib/python3.8/site-packages/tellurium/teconverters/inline_omex.py:27: in saveInlineOMEX omex = inlineOmex.fromString(omex_str) ../../../virtualenv/python3.8.3/lib/python3.8/site-packages/tellurium/teconverters/inline_omex.py:199: in fromString return inlineOmex(sources) ../../../virtualenv/python3.8.3/lib/python3.8/site-packages/tellurium/teconverters/inline_omex.py:52: in init description=DumpJSONInfo(), ../../../virtualenv/python3.8.3/lib/python3.8/site-packages/tellurium/tellurium.py:1077: in DumpJSONInfo 'version_info': VersionDict()})

def VersionDict():
    '''Return dict of version strings.'''
    import tesbml, tesedml, tecombine
    return {
        'tellurium': getTelluriumVersion(),
        'roadrunner': roadrunner.getVersionStr(roadrunner.VERSIONSTR_BASIC),
        'antimony': antimony.__version__,
        'phrasedml': phrasedml.__version__,
        'tesbml': libsbml.getLibSBMLDottedVersion(),

      'tesedml': tesedml.__version__,
'tecombine': tecombine.version } E AttributeError: module 'tesedml' has no attribute 'version'

veghp commented 4 years ago

Hi @luciansmith , thank you for looking into this and for developing this package. We intend to use it in synbiopython and here are the contents of the travis.yml:

language: python
python:
  - "3.8.3"

# command to install dependencies
before_install:
  - pip --version
  - pip install --upgrade pip
  - pip --version
  - pip install --upgrade pytest pytest-cov coveralls
install:
  - pip install -e .
# command to run tests
script:
  - python -m pytest -v --cov synbiopython --cov-report term-missing

after_success:
  - coveralls

This build passed on Travis on June 1 (with this travis.yml), but not now, which means tesedml or tellurium had a new release which breaks the build: https://pypi.org/project/tesedml/#history

I hope these help. Thanks

JingWui commented 4 years ago

Hi @luciansmith,

With the provided details, do you have an idea of how we can resolve the issue? Let us know if any more information required.

Your advice on this matter would be greatly appreciated. Thank you.

luciansmith commented 4 years ago

OK! I think I figured out the problem.

Somewhere in your own code, you define a function called "VersionDict". From your description earlier I thought you were getting errors from tellurium's 'getVersionInfo()', but I don't think you are:

    def VersionDict():
        '''Return dict of version strings.'''
        import tesbml, tesedml, tecombine
        return {
            'tellurium': getTelluriumVersion(),
            'roadrunner': roadrunner.getVersionStr(roadrunner.VERSIONSTR_BASIC),
            'antimony': antimony.__version__,
            'phrasedml': phrasedml.__version__,
            'tesbml': libsbml.getLibSBMLDottedVersion(),
           'tesedml': tesedml.__version__,
           'tecombine': tecombine.__version__
            }

The problem is that version was indeed not defined for tesedml: instead, you need to call the same thing that was used in tesbml: 'getLibSEDMLDottedVersion()'.

You can check what we use to find the version information from tellurium's 'getVersionInfo()', at line 204 of https://github.com/sys-bio/tellurium/blob/develop/tellurium/tellurium.py :

def getVersionInfo():
    """ Returns version information for tellurium included packages.
    :returns: list of tuples (package, version)
    """
    versions = [
        ('tellurium', getTelluriumVersion()),
        ('roadrunner', roadrunner.__version__),
        ('antimony', antimony.__version__),
    ]
    if libsbml:
        versions.append(('libsbml', libsbml.getLibSBMLDottedVersion()))
    if libsedml:
        versions.append(('libsedml', libsedml.getLibSEDMLDottedVersion()))
    if phrasedml:
        versions.append(('phrasedml', phrasedml.__version__))
    if sbol:
        versions.append(('pySBOL', sbol.__version__))
    return versions

veghp commented 4 years ago

Thank you for your reply! Actually, VersionDict() is defined in tellurium.py, not our code: https://github.com/sys-bio/tellurium/blob/bf853af081d33ce950ebccd2d32615203ea8fb01/tellurium/tellurium.py#L1066

Are you intending to retire VersionDict()?

luciansmith commented 4 years ago

Oh! One of the disadvantages of coming to the code late in its life is that there are all sorts of surprises like this buried in different places ;-)

So, yes, I will fix VersionDict(), and in the meantime, feel free to use getVersionInfo() instead, or to edit the code yourself to become:

def VersionDict():
    '''Return dict of version strings.'''
    import tesbml, tesedml, tecombine
    return {
        'tellurium': getTelluriumVersion(),
        'roadrunner': roadrunner.getVersionStr(roadrunner.VERSIONSTR_BASIC),
        'antimony': antimony.__version__,
        'phrasedml': phrasedml.__version__,
        'tesbml': libsbml.getLibSBMLDottedVersion(),
        'tesedml': tesedml.getLibSEDMLDottedVersion(),
        'tecombine': tecombine.getLibCombineDottedVersion(),
        }

(As it turned out, the same problem existed with tecombine.)

JingWui commented 4 years ago

It is working now! @luciansmith Thank you so much for fixing that!

luciansmith commented 4 years ago

Great Thanks @JingWui for bringing it to our attention.

sys-bio / tellurium

te.getVersionInfo() fails on latest release #465