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apsbss: warning messages #386

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prjemian opened this issue Jul 28, 2020 · 9 comments · Fixed by #400
Closed

apsbss: warning messages #386

prjemian opened this issue Jul 28, 2020 · 9 comments · Fixed by #400
Labels
bug documentation
Milestone
1.3.4

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@prjemian
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@jkirchman emails:

I began using your apsbss tools yesterday and I'm encountering a python
warning message for a number of subcommands:

519 jkirchman@s27bcda dm>  apsbss update 27id:dm:
/APSshare/anaconda3/Bluesky/lib/python3.7/site-packages/pims/image_reader.py:26: 
RuntimeWarning: PIMS image_reader.py could not find scikit-image. 
Falling back to matplotlib's imread(), which uses floats instead of 
integers. This may break your scripts.
(To ignore this warning, include the line 
"warnings.simplefilter("ignore", RuntimeWarning)" in your script.)
   warnings.warn(RuntimeWarning(ski_preferred))

I have updated my path to include the apsbss python script. Do I instead
need to activate a virtual environment? Or is there a different method
to address this warning?

BTW, I think you must have changed the parameters needed for current subcommand. The example at https://apstools.readthedocs.io/en/latest/applications/apsbss.html#what-proposal-and-esaf-id-numbers-to-use shows the proper use as:

    $ apsbss current 9id:bss: 9-ID-B,C

but it only works for me when I omit the IOC prefix parameter:

    $ apsbss current 9-ID-B,C
@prjemian prjemian added this to the 1.3.4 milestone Jul 28, 2020
@prjemian
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prjemian commented Jul 28, 2020 •
edited
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@jkirchman: Since apsbss does not use imaging (so no PIMS, scikit-image, or matplotlib), I'm guessing this happens due to other factors, most likely environment. If you are using apsbss from /APSshare/anaconda3/Bluesky/bin/apsbss (which should use /APSshare/anaconda3/Bluesky/bin/python`) and you get this error, then maybe it would help if you sourced a virtual environment first. Try this:

bash
export PYTHONPATH=
source /APSshare/anaconda3/Bluesky/bin/activate base
apsbss update 27id:dm:

Same problem?

@prjemian
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Also, do you have a PYTHONPATH environment variable set? Might help to unset that. Amending my previous comment for this.

@prjemian
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prjemian commented Aug 8, 2020

@jkirchman: Is there a PYTHONPATH variable?

@prjemian
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prjemian commented Aug 8, 2020

I'm also suspicious of package versions installed in /APSshare/anaconda3/Bluesky/. I'll compare with the bluesky_2020_5 environment for the USAXS instrument.

prjemian added a commit that referenced this issue Aug 8, 2020
@prjemian
DOC #386
76c3201
@prjemian prjemian mentioned this issue Aug 8, 2020
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@prjemian
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prjemian commented Aug 8, 2020

Compare packages on /APSshare and the USAXS custom environment:

============================= ================ ================== ================ ======================== ================== ================
package                       APSshare version APSshare build     APSshare channel USAXS version            USAXS build        USAXS channel   
============================= ================ ================== ================ ======================== ================== ================
_libgcc_mutex                 0.1              main                                0.1                      main
alabaster                                                                          0.7.12                   pypi_0             pypi
appdirs                       1.4.3            py37h28b3542_0                      1.4.3                    py37h28b3542_0
aps-dm-api                    3.2.2            py37_1             aps-anl-tag      3.2.2                    py37_1             aps-anl-tag
apstools                      1.3.3            py_0               aps-anl-tag      1.3.3                    py_0               aps-anl-tag
area-detector-handlers        0.0.4            py_0               nsls2forge       0.0.4                    py_0               nsls2forge
asciitree                     0.3.3            py_2                                0.3.3                    py_2
asteval                       0.9.18           pyh5ca1d4c_0       nsls2forge       0.9.16                   pyh5ca1d4c_0       conda-forge
astroid                       2.4.2            py37_0                              2.4.2                    py37_0
astropy                                                                            4.0.1.post1              pypi_0             pypi
astroscrappy                                                                       1.0.8                    pypi_0             pypi
attrs                         19.3.0           py_0                                19.3.0                   py_0
babel                                                                              2.8.0                    pypi_0             pypi
backcall                      0.2.0            py_0                                0.2.0                    py_0
blas                          1.0              mkl                                 1.0                      mkl
bleach                        3.1.5            py_0                                3.1.5                    py_0
bluesky                       1.6.4            py_0               nsls2forge       1.6.4                    py_0               conda-forge
bokeh                         2.1.1            py37_0                              2.1.1                    py37_0
boltons                       19.1.0           py_0               nsls2forge       20.2.0                   pyh9f0ad1d_0       conda-forge
brotlipy                      0.7.0            py37h7b6447c_1000
ca-certificates               2020.6.24        0                                   2020.6.24                0
cachetools                    4.1.0            py_1                                4.1.0                    py_1
cairo                         1.14.12          h8948797_3                          1.14.12                  h8948797_3
certifi                       2020.6.20        py37_0                              2020.6.20                py37_0
cffi                          1.14.0           py37h2e261b9_0                      1.14.0                   py37h2e261b9_0
chardet                       3.0.4            py37_1003                           3.0.4                    py37_1003
click                         7.1.2            py_0                                7.1.2                    py_0
cloudpickle                   1.5.0            py_0                                1.5.0                    py_0
coloredlogs                   10.0             py37_0                              10.0                     py37_0
conda                         4.8.3            py37_0
conda-package-handling        1.6.1            py37h7b6447c_0
contexter                                                                          0.1.4                    pypi_0             pypi
coverage                      5.0              py37h7b6447c_0                      5.1                      pypi_0             pypi
coveralls                     1.5.1            py37_0
cryptography                  2.9.2            py37h1ba5d50_0                      2.9.2                    py37h1ba5d50_0
cycler                        0.10.0           py37_0                              0.10.0                   py37_0
cytoolz                       0.10.1           py37h7b6447c_0                      0.10.1                   py37h7b6447c_0
dask                          2.20.0           py_0                                2.20.0                   py_0
dask-core                     2.20.0           py_0                                2.20.0                   py_0
databroker                    1.0.6            py_0               nsls2forge       1.0.6                    py_0               nsls2forge
dbus                          1.13.16          hb2f20db_0                          1.13.16                  hb2f20db_0
decorator                     4.4.2            py_0                                4.4.2                    py_0
defusedxml                    0.6.0            py_0                                0.6.0                    py_0
deprecated                    1.2.9            pypi_0             pypi             1.2.7                    py_0
dill                                                                               0.3.1.1                  pypi_0             pypi
distlib                                                                            0.3.0                    pypi_0             pypi
distributed                   2.20.0           py37_0                              2.20.0                   py37_0
docopt                        0.6.2            py37_0
doct                          1.1.0            py_0               nsls2forge       1.1.0                    py_0               conda-forge
docutils                                                                           0.16                     pypi_0             pypi
entrypoints                   0.3              py37_0                              0.3                      py37_0
epics-base                    7.0.4            pl526_1            aps-anl-tag      7.0.4                    pl526_1            aps-anl-tag
epicscorelibs                 7.0.3.99.2.0     py37h68659b9_0     conda-forge      7.0.3.99.2.0             py37h68659b9_0     conda-forge
event-model                   1.15.2           py_0               nsls2forge       1.15.0                   py_0               conda-forge
expat                         2.2.9            he6710b0_2                          2.2.9                    he6710b0_2
fabio                                                                              0.10.0                   pypi_0             pypi
fasteners                     0.15             py_0                                0.15                     py_0
filelock                                                                           3.0.12                   pypi_0             pypi
fontconfig                    2.13.0           h9420a91_0                          2.13.0                   h9420a91_0
freetype                      2.10.2           h5ab3b9f_0                          2.10.2                   h5ab3b9f_0
fsspec                        0.7.4            py_0                                0.7.4                    py_0
future                                                                             0.18.2                   py37_1
gitdb                                                                              4.0.5                    pypi_0             pypi
gitpython                                                                          0.3.6                    pypi_0             pypi
glib                          2.63.1           h5a9c865_0                          2.63.1                   h5a9c865_0
gobject-introspection         1.56.1           py37hbc4ca2d_2                      1.56.1                   py37hbc4ca2d_2
gsl                           2.4              h14c3975_4                          2.4                      h14c3975_4
gst-plugins-base              1.14.0           hbbd80ab_1                          1.14.0                   hbbd80ab_1
gstreamer                     1.14.0           hb453b48_1                          1.14.0                   hb453b48_1
h5py                          2.10.0           py37h7918eee_0                      2.10.0                   py37h7918eee_0
happi                         1.6.0            py_0               conda-forge      1.6.0                    py_0               conda-forge
hdf5                          1.10.4           hb1b8bf9_0                          1.10.4                   hb1b8bf9_0
heapdict                      1.0.1            py_0                                1.0.1                    py_0
helpdev                                                                            0.7.1                    pypi_0             pypi
historydict                   1.2.3            py_0               nsls2forge       1.2.3                    py_0               conda-forge
hkl                           5.0.0.2173       py37_6             lightsource2-tag 5.0.0.2173               py37h17bde16_1     nsls2forge
hklpy                         0.3.13           py37_0             lightsource2-tag 0.3.13                   py37_0             lightsource2-tag
humanfriendly                 8.2              py37_0                              8.2                      py37_0
humanize                      0.5.1            py37_1                              0.5.1                    py37_1
icu                           58.2             he6710b0_3                          58.2                     he6710b0_3
idna                          2.10             py_0                                2.9                      py_1
imagecodecs-lite              2019.12.3        py37h8f50634_0     conda-forge      2019.12.3                py37h8f50634_0     conda-forge
imageio                                                                            2.8.0                    pypi_0             pypi
imagesize                                                                          1.2.0                    pypi_0             pypi
importlib-metadata            1.7.0            py37_0                              1.7.0                    py37_0
importlib_metadata            1.7.0            0                                   1.7.0                    0
intake                        0.6.0            py_0                                0.6.0                    py_0
intel-openmp                  2020.1           217                                 2020.1                   217
ipykernel                     5.3.2            py37h5ca1d4c_0                      5.3.2                    py37h5ca1d4c_0
ipython                       7.13.0           py37h5ca1d4c_0                      7.13.0                   py37h5ca1d4c_0
ipython_genutils              0.2.0            py37_0                              0.2.0                    py37_0
ipywidgets                    7.5.1            py_0                                7.5.1                    py_0
isort                         4.3.21           py37_0                              4.3.21                   py37_0
jedi                          0.17.1           py37_0                              0.17.1                   py37_0
jinja2                        2.11.2           py_0                                2.11.2                   py_0
jpeg                          9b               h024ee3a_2                          9b                       h024ee3a_2
json5                                                                              0.9.5                    py_0
jsonschema                    3.2.0            py37_1                              3.2.0                    py37_1
jupyter                       1.0.0            py37_7                              1.0.0                    py37_7
jupyter_client                6.1.6            py_0                                6.1.6                    py_0
jupyter_console               6.1.0            py_0                                6.1.0                    py_0
jupyter_core                  4.6.3            py37_0                              4.6.3                    py37_0
jupyterlab                                                                         1.2.6                    pyhf63ae98_0
jupyterlab_server                                                                  1.2.0                    py_0
kiwisolver                    1.2.0            py37hfd86e86_0                      1.2.0                    py37hfd86e86_0
lazy-object-proxy             1.4.3            py37h7b6447c_0                      1.4.3                    py37h7b6447c_0
lcms2                         2.11             h396b838_0                          2.11                     h396b838_0
ld_impl_linux-64              2.33.1           h53a641e_7                          2.33.1                   h53a641e_7
libedit                       3.1.20191231     h14c3975_1                          3.1.20191231             h14c3975_1
libffi                        3.2.1            hd88cf55_4                          3.2.1                    hd88cf55_4
libgcc-ng                     9.1.0            hdf63c60_0                          9.1.0                    hdf63c60_0
libgfortran-ng                7.3.0            hdf63c60_0                          7.3.0                    hdf63c60_0
libiconv                      1.15             h63c8f33_5                          1.15                     h63c8f33_5
libpng                        1.6.37           hbc83047_0                          1.6.37                   hbc83047_0
libsodium                     1.0.18           h7b6447c_0                          1.0.18                   h7b6447c_0
libstdcxx-ng                  9.1.0            hdf63c60_0                          9.1.0                    hdf63c60_0
libtiff                       4.1.0            h2733197_1                          4.1.0                    h2733197_1
libuuid                       1.0.3            h1bed415_2                          1.0.3                    h1bed415_2
libxcb                        1.14             h7b6447c_0                          1.14                     h7b6447c_0
libxml2                       2.9.10           he19cac6_1                          2.9.10                   he19cac6_1
libxslt                       1.1.34           hc22bd24_0                          1.1.34                   hc22bd24_0
lmfit                         1.0.0            py_1               nsls2forge       1.0.0                    py_0               conda-forge
locket                        0.2.0            py37_1                              0.2.0                    py37_1
lxml                          4.5.0            py37hefd8a0e_0                      4.5.0                    py37hefd8a0e_0
lz4-c                         1.9.2            he6710b0_0                          1.9.2                    he6710b0_0
markupsafe                    1.1.1            py37h14c3975_1                      1.1.1                    py37h14c3975_1
matplotlib                    3.2.2            0                                   3.2.2                    0
matplotlib-base               3.2.2            py37hef1b27d_0                      3.2.2                    py37hef1b27d_0
mccabe                        0.6.1            py37_1                              0.6.1                    py37_1
mistune                       0.8.4            py37h14c3975_1001                   0.8.4                    py37h14c3975_1001
mkl                           2020.1           217                                 2020.1                   217
mkl-service                   2.3.0            py37he904b0f_0                      2.3.0                    py37he904b0f_0
mkl_fft                       1.1.0            py37h23d657b_0                      1.1.0                    py37h23d657b_0
mkl_random                    1.1.1            py37h0573a6f_0                      1.1.1                    py37h0573a6f_0
mongoquery                    1.1.0            py_0               nsls2forge       1.3.5                    py_0               conda-forge
monotonic                     1.5              py_0                                1.5                      py_0
msgpack-numpy                 0.4.4.3          py_0                                0.4.4.3                  py_0
msgpack-python                1.0.0            py37hfd86e86_1                      1.0.0                    py37hfd86e86_1
nbconvert                     5.6.1            py37_1                              5.6.1                    py37_1
nbformat                      5.0.7            py_0                                5.0.7                    py_0
ncurses                       6.2              he6710b0_1                          6.2                      he6710b0_1
networkx                      2.4              py_1                                2.4                      py_1
nose                                                                               1.3.7                    pypi_0             pypi
notebook                      6.0.3            py37_0                              6.0.3                    py37_0
numcodecs                     0.6.4            py37he6710b0_0                      0.6.4                    py37he6710b0_0
numexpr                                                                            2.7.1                    pypi_0             pypi
numpy                         1.18.5           py37ha1c710e_0                      1.18.5                   py37ha1c710e_0
numpy-base                    1.18.5           py37hde5b4d6_0                      1.18.5                   py37hde5b4d6_0
olefile                       0.46             py37_0                              0.46                     py37_0
openssl                       1.1.1g           h7b6447c_0                          1.1.1g                   h7b6447c_0
ophyd                         1.5.2            py_0               nsls2forge       1.5.1                    py_0               conda-forge
packaging                     20.4             py_0                                20.4                     py_0
pandas                        1.0.5            py37h0573a6f_0                      1.0.5                    py37h0573a6f_0
pandoc                        2.10             0                                   2.10                     0
pandocfilters                 1.4.2            py37_1                              1.4.2                    py37_1
parso                         0.7.0            py_0                                0.7.0                    py_0
partd                         1.1.0            py_0                                1.1.0                    py_0
pathlib                                                                            1.0.1                    pypi_0             pypi
pcre                          8.44             he6710b0_0                          8.44                     he6710b0_0
perl                          5.26.2           h14c3975_0                          5.26.2                   h14c3975_0
pexpect                       4.8.0            py37_1                              4.8.0                    py37_1
pickleshare                   0.7.5            py37_1001                           0.7.5                    py37_1001
pillow                        7.2.0            py37hb39fc2d_0                      7.2.0                    py37hb39fc2d_0
pims                          0.5              py_1                                0.5                      py_1
pip                           20.1.1           py37_1                              20.1.1                   py37_1
pixman                        0.40.0           h7b6447c_0                          0.40.0                   h7b6447c_0
prettytable                   0.7.2            py_0               nsls2forge       0.7.2                    py_3               conda-forge
prometheus_client             0.8.0            py_0                                0.8.0                    py_0
prompt-toolkit                3.0.5            py_0                                3.0.5                    py_0
prompt_toolkit                3.0.5            0                                   3.0.5                    0
psutil                        5.7.0            py37h7b6447c_0                      5.7.0                    py37h7b6447c_0
ptyprocess                    0.6.0            py37_0                              0.6.0                    py37_0
punx                          0.2.2            pypi_0             pypi             0.2.5                    pypi_0             pypi
pvview                        1.0.0            py_0               aps-anl-tag      1.0.0                    py_0               aps-anl-tag
pycairo                       1.19.1           py37h2a1e443_0                      1.19.1                   py37h2a1e443_0
pycosat                       0.6.3            py37h7b6447c_0
pycparser                     2.20             py_2                                2.20                     py_2
pydm                          1.10.1           pyh9f0ad1d_0       conda-forge      1.10.1                   pyh9f0ad1d_0       conda-forge
pyepics                       3.4.2            py37_0             nsls2forge       3.4.2                    py37hc8dfbb8_0     conda-forge
pyfai                                                                              0.19.0                   pypi_0             pypi
pygithub                      1.51             pypi_0             pypi             1.43.6                   py37hc8dfbb8_1     conda-forge
pygments                      2.6.1            py_0                                2.6.1                    py_0
pygobject                     3.30.5           py37hfc86313_1     conda-forge      3.30.5                   py37hfc86313_1     conda-forge
pyjwt                         1.7.1            pypi_0             pypi             1.7.1                    py37_0
pylint                        2.5.0            py37_1                              2.5.0                    py37_1
pymongo                       3.9.0            py37he6710b0_0                      3.9.0                    py37he6710b0_0
pyopenssl                     19.1.0           py_1                                19.1.0                   py_1
pyparsing                     2.4.7            py_0                                2.4.7                    py_0
pypi-publisher                                                                     0.0.4                    pypi_0             pypi
pyqt                          5.9.2            py37h05f1152_2                      5.9.2                    py37h05f1152_2
pyqt5                                                                              5.14.2                   pypi_0             pypi
pyqt5-sip                                                                          12.7.2                   pypi_0             pypi
pyqtgraph                     0.11.0           py_0                                0.11.0                   py_0
pyresttable                   2020.0.2         py_0               aps-anl-tag      2020.0.2                 py_0               aps-anl-tag
pyrsistent                    0.16.0           py37h7b6447c_0                      0.16.0                   py37h7b6447c_0
pysocks                       1.7.1            py37_1                              1.7.1                    py37_1
python                        3.7.7            hcf32534_0_cpython                  3.7.7                    hcf32534_0_cpython
python-dateutil               2.8.1            py_0                                2.8.1                    py_0
python_abi                    3.7              1_cp37m            conda-forge      3.7                      1_cp37m            conda-forge
pytz                          2020.1           py_0                                2020.1                   py_0
pywavelets                                                                         1.1.1                    pypi_0             pypi
pyyaml                        5.3.1            py37h7b6447c_1                      5.3.1                    py37h7b6447c_1
pyzmq                         19.0.1           py37he6710b0_1                      19.0.1                   py37he6710b0_1
qdarkstyle                                                                         2.8.1                    pypi_0             pypi
qt                            5.9.7            h5867ecd_1                          5.9.7                    h5867ecd_1
qtconsole                     4.7.5            py_0                                4.7.5                    py_0
qtmodern                                                                           0.2.0                    pypi_0             pypi
qtpy                          1.9.0            py_0                                1.9.0                    py_0
readline                      8.0              h7b6447c_0                          8.0                      h7b6447c_0
requests                      2.24.0           py_0                                2.23.0                   py37_0
ruamel_yaml                   0.15.87          py37h7b6447c_1
sasmodels                                                                          1.0.2                    pypi_0             pypi
scandir                                                                            1.10.0                   pypi_0             pypi
scikit-beam                                                                        0.0.21                   pypi_0             pypi
scikit-image                                                                       0.16.2                   pypi_0             pypi
scipy                         1.5.0            py37h0b6359f_0                      1.5.0                    py37h0b6359f_0
send2trash                    1.5.0            py37_0                              1.5.0                    py37_0
setuptools                    49.2.0           py37_0                              49.2.0                   py37_0
signalslot                                                                         0.1.2                    pypi_0             pypi
silx                                                                               0.12.0                   pypi_0             pypi
simplejson                    3.17.0           py37h7b6447c_0                      3.17.0                   py37h7b6447c_0
sip                           4.19.8           py37hf484d3e_0                      4.19.8                   py37hf484d3e_0
six                           1.15.0           py_0                                1.15.0                   py_0
slicerator                    1.0.0            py_0                                1.0.0                    py_0
smmap                                                                              3.0.4                    pypi_0             pypi
snowballstemmer                                                                    2.0.0                    pypi_0             pypi
sortedcontainers              2.2.2            py_0                                2.2.2                    py_0
spec2nexus                    2021.1.7         h39e3cac_0         aps-anl-tag      2021.1.7                 h39e3cac_0         aps-anl-tag
sphinx                                                                             3.0.3                    pypi_0             pypi
sphinx-rtd-theme                                                                   0.4.3                    pypi_0             pypi
sphinxcontrib-applehelp                                                            1.0.2                    pypi_0             pypi
sphinxcontrib-devhelp                                                              1.0.2                    pypi_0             pypi
sphinxcontrib-htmlhelp                                                             1.0.3                    pypi_0             pypi
sphinxcontrib-jsmath                                                               1.0.1                    pypi_0             pypi
sphinxcontrib-qthelp                                                               1.0.3                    pypi_0             pypi
sphinxcontrib-serializinghtml                                                      1.1.4                    pypi_0             pypi
sqlite                        3.32.3           h62c20be_0                          3.32.3                   h62c20be_0
stdlogpj                      1.0.3            py_0               aps-anl-tag      1.0.3                    py_0               aps-anl-tag
suitcase-mongo                0.2.0            py_0               nsls2forge       0.2.0                    py_0               nsls2forge
suitcase-msgpack              0.2.4            py_0               nsls2forge       0.2.4                    py_0               nsls2forge
suitcase-utils                0.5.0            py_2               nsls2forge       0.5.0                    py_2               nsls2forge
super_state_machine           2.0.2            py_0               nsls2forge       2.0.2                    py37_1000          conda-forge
tblib                         1.6.0            py_0                                1.6.0                    py_0
terminado                     0.8.3            py37_0                              0.8.3                    py37_0
testpath                      0.4.4            py_0                                0.4.4                    py_0
tifffile                      0.15.1           py37heb32a55_2                      0.15.1                   py37heb32a55_2
tk                            8.6.10           hbc83047_0                          8.6.10                   hbc83047_0
toml                          0.10.1           py_0                                0.10.1                   py_0
toolz                         0.10.0           py_0                                0.10.0                   py_0
tornado                       6.0.4            py37h7b6447c_1                      6.0.4                    py37h7b6447c_1
tqdm                          4.47.0           py_0                                4.47.0                   py_0
traitlets                     4.3.3            py37_0                              4.3.3                    py37_0
typed-ast                     1.4.1            py37h7b6447c_0                      1.4.1                    py37h7b6447c_0
typing_extensions             3.7.4.2          py_0                                3.7.4.2                  py_0
tzlocal                       2.0.0            py37_0                              2.0.0                    py37_0
uncertainties                 3.1.2            py_0               nsls2forge       3.1.4                    py_0               conda-forge
urllib3                       1.25.9           py_0                                1.25.8                   py37_0
virtualenv                                                                         20.0.20                  pypi_0             pypi
wcwidth                       0.2.5            py_0                                0.2.5                    py_0
weakrefmethod                                                                      1.0.3                    pypi_0             pypi
webencodings                  0.5.1            py37_1                              0.5.1                    py37_1
wheel                         0.34.2           py37_0                              0.34.2                   py37_0
widgetsnbextension            3.5.1            py37_0                              3.5.1                    py37_0
wrapt                         1.11.2           py37h7b6447c_0                      1.11.2                   py37h7b6447c_0
xarray                        0.16.0           py_0                                0.16.0                   py_0
xicam                                                                              0+untagged.1367.gcfad222 pypi_0             pypi
xicam-saxs                                                                         0.1.0                    pypi_0             pypi
xicam-xpcs                                                                         1.1.0                    pypi_0             pypi
xlrd                          1.2.0            py37_0                              1.2.0                    py37_0
xz                            5.2.5            h7b6447c_0                          5.2.5                    h7b6447c_0
yaml                          0.2.5            h7b6447c_0                          0.2.5                    h7b6447c_0
zarr                          2.3.2            py_0                                2.3.2                    py_0
zeromq                        4.3.2            he6710b0_2                          4.3.2                    he6710b0_2
zict                          2.0.0            py_0                                2.0.0                    py_0
zipp                          3.1.0            py_0                                3.1.0                    py_0
zlib                          1.2.11           h7b6447c_3                          1.2.11                   h7b6447c_3
zstd                          1.4.5            h0b5b093_0                          1.4.5                    h0b5b093_0
============================= ================ ================== ================ ======================== ================== ================

@prjemian
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prjemian commented Aug 8, 2020

Notably:

USAXS has scikit-beam 0.0.21 and scikit-image 0.16.2 installed via pip, APSshare has neither. This is likely the problem.

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prjemian commented Aug 8, 2020

Will pip install scikit-beam and pip install scikit-image in /APSshare/anaconda3/Bluesky

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prjemian commented Aug 8, 2020

BTW, here is the code to compare two conda environments (that generated the table above):


from collections import defaultdict
import os
import pyRestTable
# import sys

SUITE = dict(
    # These files contain the output of ``conda list``
    APSshare="APSshare.txt", 
    USAXS="USAXS.txt"
    )


def main():
    path = os.path.dirname(__file__)
    db = defaultdict(lambda: {})
    for env, fname in SUITE.items():
        with open(os.path.join(path, fname), "r") as fp:
            for line in fp.readlines():
                if line.startswith("#"):
                    continue
                parts = line.strip().split()
                if len(parts) not in (3, 4):
                    continue
                elif len(parts) == 3:
                    parts.append("")
                package, version, build, channel = parts
                db[package][env] = (version, build, channel)

    table = pyRestTable.Table()
    table.addLabel("package")
    for env in sorted(SUITE.keys()):
        table.addLabel(f"{env} version")
        table.addLabel(f"{env} build")
        table.addLabel(f"{env} channel")
    for package, pkg_info in sorted(db.items()):
        row = [package,]
        for env in sorted(SUITE.keys()):
            if env in pkg_info:
                row += pkg_info[env]
            else:
                row += ["", "", ""]
        table.addRow(row)
    print(table)


if __name__ == "__main__":
    main()

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prjemian commented Aug 8, 2020

open new issue if problem recurs

@prjemian prjemian closed this as completed Aug 8, 2020
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resolve warnings and example documentation inconsistency BCDA-APS/apstools
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@prjemian