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APS-30ID-IXN / ipython-ixs

30-ID ipython configuration for bluesky (and other)
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create conda environment: bluesky_2021_1 #1

Closed prjemian closed 3 years ago

prjemian commented 3 years ago

Follow these instructions: https://github.com/BCDA-APS/use_bluesky/tree/main/python_installation#setup-custom-environment-for-bluesky

prjemian commented 3 years ago

Install keeps failing, with a core dump, even when commenting out certain packages such as happi, typhos, and pydm. Break this up into steps.

This worked:

conda create -n bluesky_2021_1 python=3.8
conda install -n bluesky_2021_1 anaconda black flake8
conda install -n bluesky_2021_1 bluesky databroker ophyd pyepics -c conda-forge
conda install -n bluesky_2021_1 pint  -c conda-forge
conda install -n bluesky_2021_1 aps-dm-api  -c aps-anl-tag -c nsls2forge
conda install -n bluesky_2021_1 apstools  -c aps-anl-tag -c nsls2forge
conda install -n bluesky_2021_1 punx -c nsls2forge
conda install -n bluesky_2021_1 pvview pydm -c aps-anl-tag -c pydm-tag
conda install -n bluesky_2021_1 area-detector-handlers databroker-pack -c nsls2forge
conda install -n bluesky_2021_1 hklpy gobject-introspection -c conda-forge -c nsls2forge
conda install -n bluesky_2021_1 hklpy -c conda-forge
conda install -n bluesky_2021_1 stdlogpj -c aps-anl-tag
conda activate bluesky_2021_1
pip install bluesky-live
conda install -n bluesky_2021_1 pandoc -c conda-forge
prjemian commented 3 years ago

installed packages:

# packages in environment at /home/beams/IXS/.conda/envs/bluesky_2021_1:
#
# Name                    Version                   Build  Channel
_anaconda_depends         2020.07                  py38_0  
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
alabaster                 0.7.12             pyhd3eb1b0_0  
anaconda                  custom                   py38_1  
anaconda-client           1.7.2                    py38_0  
anaconda-project          0.9.1              pyhd3eb1b0_1  
appdirs                   1.4.4                      py_0  
aps-dm-api                3.2.2                    py38_1    aps-anl-tag
apstools                  1.4.1                      py_0    aps-anl-tag
area-detector-handlers    0.0.8              pyhe636693_0    nsls2forge
argh                      0.26.2                   py38_0  
argon2-cffi               20.1.0           py38h7b6447c_1  
asciitree                 0.3.3                      py_2    conda-forge
asn1crypto                1.4.0                      py_0  
asteval                   0.9.16             pyh5ca1d4c_0    conda-forge
astroid                   2.4.2                    py38_0  
astropy                   4.2              py38h27cfd23_0  
async_generator           1.10               pyhd3eb1b0_0  
atomicwrites              1.4.0                      py_0  
attrs                     20.3.0             pyhd3eb1b0_0  
autopep8                  1.5.4                      py_0  
babel                     2.9.0              pyhd3eb1b0_0  
backcall                  0.2.0              pyhd3eb1b0_0  
backports                 1.0                pyhd3eb1b0_2  
backports.shutil_get_terminal_size 1.0.0              pyhd3eb1b0_3  
beautifulsoup4            4.9.3              pyha847dfd_0  
bitarray                  1.6.3            py38h27cfd23_1  
bkcharts                  0.2                      py38_0  
black                     19.10b0                    py_0  
blas                      1.0                         mkl  
bleach                    3.3.0              pyhd3eb1b0_0  
blosc                     1.20.1               hd408876_0  
bluesky                   1.6.7              pyhd8ed1ab_0    conda-forge
bluesky-live              0.0.7                    pypi_0    pypi
bokeh                     2.2.3                    py38_0  
boltons                   20.2.1             pyh9f0ad1d_0    conda-forge
boto                      2.49.0                   py38_0  
bottleneck                1.3.2            py38heb32a55_1  
brotli                    1.0.9                he6710b0_2  
brotlipy                  0.7.0           py38h27cfd23_1003  
brunsli                   0.1                  h2531618_0  
bzip2                     1.0.8                h7b6447c_0  
ca-certificates           2020.12.5            ha878542_0    conda-forge
cachetools                4.2.1              pyhd8ed1ab_0    conda-forge
cairo                     1.14.12              h8948797_3  
certifi                   2020.12.5        py38h578d9bd_1    conda-forge
cffi                      1.14.4           py38h261ae71_0  
chardet                   4.0.0           py38h06a4308_1003  
charls                    2.1.0                he6710b0_2  
click                     7.1.2              pyhd3eb1b0_0  
cloudpickle               1.6.0                      py_0  
clyent                    1.2.2                    py38_1  
colorama                  0.4.4              pyhd3eb1b0_0  
contextlib2               0.6.0.post1                py_0  
cryptography              2.9.2            py38h1ba5d50_0  
curl                      7.71.1               hbc83047_1  
cycler                    0.10.0                   py38_0  
cython                    0.29.21          py38h2531618_0  
cytoolz                   0.11.0           py38h7b6447c_0  
dask                      2021.1.1           pyhd3eb1b0_0  
dask-core                 2021.1.1           pyhd3eb1b0_0  
databroker                1.2.0              pyhd3deb0d_0    conda-forge
databroker-pack           0.3.0                      py_0    nsls2forge
dbus                      1.13.18              hb2f20db_0  
decorator                 4.4.2              pyhd3eb1b0_0  
defusedxml                0.6.0                      py_0  
deprecated                1.2.11             pyhd3eb1b0_0  
diff-match-patch          20200713                   py_0  
distributed               2021.1.1         py38h06a4308_1  
doct                      1.1.0                      py_0    conda-forge
docutils                  0.16                     py38_1  
entrypoints               0.3                      py38_0  
epics-base                7.0.4                h68659b9_0    conda-forge
et_xmlfile                1.0.1                   py_1001  
event-model               1.17.1             pyhd8ed1ab_0    conda-forge
expat                     2.2.10               he6710b0_2  
fastcache                 1.1.0            py38h7b6447c_0  
fasteners                 0.14.1                     py_3    conda-forge
filelock                  3.0.12             pyhd3eb1b0_1  
flake8                    3.8.4                      py_0  
flask                     1.1.2              pyhd3eb1b0_0  
fontconfig                2.13.1               h6c09931_0  
freetype                  2.10.4               h5ab3b9f_0  
fribidi                   1.0.10               h7b6447c_0  
fsspec                    0.8.3                      py_0  
future                    0.18.2                   py38_1  
get_terminal_size         1.0.0                haa9412d_0  
gettext                   0.19.8.1          h0b5b191_1005    conda-forge
gevent                    21.1.1           py38h27cfd23_1  
giflib                    5.1.4                h14c3975_1  
glib                      2.66.6               h9c3ff4c_3    conda-forge
glib-tools                2.66.6               h9c3ff4c_3    conda-forge
glob2                     0.7                pyhd3eb1b0_0  
gmp                       6.2.1                h2531618_2  
gmpy2                     2.0.8            py38hd5f6e3b_3  
gobject-introspection     1.66.1           py38h94476cb_0  
graphite2                 1.3.14               h23475e2_0  
greenlet                  1.0.0            py38h2531618_2  
gsl                       2.4                  h14c3975_4  
gst-plugins-base          1.14.0               h8213a91_2  
gstreamer                 1.14.0               h28cd5cc_2  
h5py                      2.10.0           py38h7918eee_0  
harfbuzz                  2.4.0                hca77d97_1  
hdf5                      1.10.4               hb1b8bf9_0  
heapdict                  1.0.1                      py_0  
historydict               1.2.3                      py_0    conda-forge
hkl                       5.0.0.2173       py38h17bde16_1    nsls2forge
hklpy                     0.3.15             pyhe636693_0    nsls2forge
html5lib                  1.1                        py_0  
humanize                  3.2.0              pyhd8ed1ab_0    conda-forge
icu                       58.2                 he6710b0_3  
idna                      2.10               pyhd3eb1b0_0  
imagecodecs               2021.1.11        py38h581e88b_1  
imageio                   2.9.0                      py_0  
imagesize                 1.2.0              pyhd3eb1b0_0  
importlib-metadata        2.0.0                      py_1  
importlib_metadata        2.0.0                         1  
importlib_resources       5.1.0            py38h578d9bd_0    conda-forge
iniconfig                 1.1.1              pyhd3eb1b0_0  
intake                    0.6.0                      py_0    conda-forge
intel-openmp              2020.2                      254  
intervaltree              3.1.0                      py_0  
ipykernel                 5.3.4            py38h5ca1d4c_0  
ipython                   7.20.0           py38hb070fc8_1  
ipython_genutils          0.2.0              pyhd3eb1b0_1  
ipywidgets                7.6.3              pyhd3eb1b0_1  
isort                     5.7.0              pyhd3eb1b0_0  
itsdangerous              1.1.0              pyhd3eb1b0_0  
jbig                      2.1                  hdba287a_0  
jdcal                     1.4.1                      py_0  
jedi                      0.17.2           py38h06a4308_1  
jeepney                   0.6.0              pyhd3eb1b0_0  
jinja2                    2.11.3             pyhd3eb1b0_0  
joblib                    1.0.0              pyhd3eb1b0_0  
jpeg                      9b                   h024ee3a_2  
json5                     0.9.5                      py_0  
jsonschema                3.2.0                      py_2  
jupyter                   1.0.0                    py38_7  
jupyter_client            6.1.7                      py_0  
jupyter_console           6.2.0                      py_0  
jupyter_core              4.7.1            py38h06a4308_0  
jupyterlab                2.2.6                      py_0  
jupyterlab_pygments       0.1.2                      py_0  
jupyterlab_server         1.2.0                      py_0  
jupyterlab_widgets        1.0.0              pyhd3eb1b0_1  
jxrlib                    1.1                  h7b6447c_2  
keyring                   22.0.1           py38h06a4308_0  
kiwisolver                1.3.1            py38h2531618_0  
krb5                      1.18.2               h173b8e3_0  
lazy-object-proxy         1.4.3            py38h27cfd23_2  
lcms2                     2.11                 h396b838_0  
ld_impl_linux-64          2.33.1               h53a641e_7  
lerc                      2.2.1                h2531618_0  
libaec                    1.0.4                he6710b0_1  
libarchive                3.4.2                h62408e4_0  
libcurl                   7.71.1               h20c2e04_1  
libdeflate                1.7                  h27cfd23_5  
libedit                   3.1.20191231         h14c3975_1  
libffi                    3.3                  he6710b0_2  
libgcc-ng                 9.3.0               h2828fa1_18    conda-forge
libgfortran-ng            7.3.0                hdf63c60_0  
libglib                   2.66.6               h1f3bc88_3    conda-forge
libgomp                   9.3.0               h2828fa1_18    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
liblief                   0.10.1               he6710b0_0  
libllvm10                 10.0.1               hbcb73fb_5  
libllvm9                  9.0.1                h4a3c616_1  
libpng                    1.6.37               hbc83047_0  
libsodium                 1.0.18               h7b6447c_0  
libspatialindex           1.9.3                he6710b0_0  
libssh2                   1.9.0                h1ba5d50_1  
libstdcxx-ng              9.3.0               h6de172a_18    conda-forge
libtiff                   4.1.0                h2733197_1  
libtool                   2.4.6             h7b6447c_1005  
libuuid                   1.0.3                h1bed415_2  
libwebp                   1.0.1                h8e7db2f_0  
libxcb                    1.14                 h7b6447c_0  
libxml2                   2.9.10               hb55368b_3  
libxslt                   1.1.34               hc22bd24_0  
libzopfli                 1.0.3                he6710b0_0  
llvmlite                  0.34.0           py38h269e1b5_4  
lmfit                     1.0.1                      py_1    conda-forge
locket                    0.2.1            py38h06a4308_1  
lxml                      4.6.2            py38h9120a33_0  
lz4-c                     1.9.3                h2531618_0  
lzo                       2.10                 h7b6447c_2  
markupsafe                1.1.1            py38h7b6447c_0  
matplotlib                3.3.2                h06a4308_0  
matplotlib-base           3.3.2            py38h817c723_0  
mccabe                    0.6.1                    py38_1  
mistune                   0.8.4           py38h7b6447c_1000  
mkl                       2020.2                      256  
mkl-service               2.3.0            py38he904b0f_0  
mkl_fft                   1.2.0            py38h23d657b_0  
mkl_random                1.1.1            py38h0573a6f_0  
mock                      4.0.3              pyhd3eb1b0_0  
mongoquery                1.3.5                      py_0    conda-forge
monotonic                 1.5                        py_0    conda-forge
more-itertools            8.6.0              pyhd3eb1b0_0  
mpc                       1.1.0                h10f8cd9_1  
mpfr                      4.0.2                hb69a4c5_1  
mpmath                    1.1.0                    py38_0  
msgpack-numpy             0.4.7.1            pyh9f0ad1d_0    conda-forge
msgpack-python            1.0.2            py38hff7bd54_1  
multipledispatch          0.6.0                    py38_0  
mypy_extensions           0.4.3                    py38_0  
nbclient                  0.5.1                      py_0  
nbconvert                 6.0.7                    py38_0  
nbformat                  5.1.2              pyhd3eb1b0_1  
ncurses                   6.2                  he6710b0_1  
nest-asyncio              1.4.3              pyhd3eb1b0_0  
networkx                  2.5                        py_0  
nltk                      3.5                        py_0  
nose                      1.3.7           pyhd3eb1b0_1006  
notebook                  6.2.0            py38h06a4308_0  
numba                     0.51.2           py38h0573a6f_1  
numcodecs                 0.7.3            py38h2531618_0  
numexpr                   2.7.2            py38hb2eb853_0  
numpy                     1.19.2           py38h54aff64_0  
numpy-base                1.19.2           py38hfa32c7d_0  
numpydoc                  1.1.0              pyhd3eb1b0_1  
olefile                   0.46                       py_0  
openjpeg                  2.3.0                h05c96fa_1  
openpyxl                  3.0.6              pyhd3eb1b0_0  
openssl                   1.1.1i               h7f98852_0    conda-forge
ophyd                     1.6.0              pyhd8ed1ab_0    conda-forge
packaging                 20.9               pyhd3eb1b0_0  
pandas                    1.2.1            py38ha9443f7_0  
pandoc                    2.11.4               h7f98852_0    conda-forge
pandocfilters             1.4.3            py38h06a4308_1  
pango                     1.45.3               hd140c19_0  
parso                     0.7.0                      py_0  
partd                     1.1.0                      py_0  
patchelf                  0.12                 h2531618_1  
path                      15.1.0           py38h06a4308_0  
path.py                   12.5.0                        0  
pathlib2                  2.3.5            py38h06a4308_2  
pathspec                  0.7.0                      py_0  
pathtools                 0.1.2                      py_1  
patsy                     0.5.1                    py38_0  
pcre                      8.44                 he6710b0_0  
pep8                      1.7.1                    py38_0  
perl                      5.32.0               h36c2ea0_0    conda-forge
pexpect                   4.8.0              pyhd3eb1b0_3  
pickleshare               0.7.5           pyhd3eb1b0_1003  
pillow                    8.1.0            py38he98fc37_0  
pims                      0.5                pyh9f0ad1d_1    conda-forge
pint                      0.16.1                     py_0    conda-forge
pip                       20.3.3           py38h06a4308_0  
pixman                    0.40.0               h7b6447c_0  
pkginfo                   1.7.0            py38h06a4308_0  
pluggy                    0.13.1                   py38_0  
ply                       3.11                     py38_0  
prettytable               2.0.0              pyhd8ed1ab_0    conda-forge
prometheus_client         0.9.0              pyhd3eb1b0_0  
prompt-toolkit            3.0.8                      py_0  
prompt_toolkit            3.0.8                         0  
psutil                    5.8.0            py38h27cfd23_1  
ptyprocess                0.7.0              pyhd3eb1b0_2  
punx                      0.2.5                      py_0    nsls2forge
pvview                    1.0.0                      py_0    aps-anl-tag
py                        1.10.0             pyhd3eb1b0_0  
py-lief                   0.10.1           py38h403a769_0  
pycairo                   1.19.1           py38h2a1e443_0  
pycodestyle               2.6.0                      py_0  
pycosat                   0.6.3            py38h7b6447c_1  
pycparser                 2.20                       py_2  
pycurl                    7.43.0.6         py38h1ba5d50_0  
pydm                      1.10.7                     py_0    pydm-tag
pydocstyle                5.1.1                      py_0  
pyepics                   3.4.3            py38h578d9bd_1    conda-forge
pyerfa                    1.7.1.1          py38h27cfd23_1  
pyflakes                  2.2.0              pyhd3eb1b0_0  
pygithub                  1.53                       py_0    nsls2forge
pygments                  2.7.4              pyhd3eb1b0_0  
pygobject                 3.38.0           py38h073a499_4    conda-forge
pyjwt                     2.0.1            py38h06a4308_0  
pylint                    2.6.0                    py38_0  
pyls-black                0.4.6                hd3eb1b0_0  
pyls-spyder               0.3.0              pyhd3eb1b0_0  
pymongo                   3.11.0           py38h348cfbe_4    conda-forge
pyodbc                    4.0.30           py38he6710b0_0  
pyopenssl                 20.0.1             pyhd3eb1b0_1  
pyparsing                 2.4.7              pyhd3eb1b0_0  
pyqt                      5.9.2            py38h05f1152_4  
pyqtgraph                 0.11.0                     py_0  
pyresttable               2020.0.3                   py_0    aps-anl-tag
pyrsistent                0.17.3           py38h7b6447c_0  
pysocks                   1.7.1            py38h06a4308_0  
pytables                  3.6.1            py38h9fd0a39_0  
pytest                    6.2.2            py38h06a4308_2  
python                    3.8.5                h7579374_1  
python-dateutil           2.8.1              pyhd3eb1b0_0  
python-jsonrpc-server     0.4.0                      py_0  
python-language-server    0.36.2             pyhd3eb1b0_0  
python-libarchive-c       2.9                pyhd3eb1b0_0  
python_abi                3.8                      1_cp38    conda-forge
pytz                      2021.1             pyhd3eb1b0_0  
pywavelets                1.1.1            py38h7b6447c_2  
pyxdg                     0.27               pyhd3eb1b0_0  
pyyaml                    5.4.1            py38h27cfd23_1  
pyzmq                     20.0.0           py38h2531618_1  
qdarkstyle                2.8.1                      py_0  
qt                        5.9.7                h5867ecd_1  
qtawesome                 1.0.1                      py_0  
qtconsole                 5.0.2              pyhd3eb1b0_0  
qtpy                      1.9.0                      py_0  
readline                  8.1                  h27cfd23_0  
regex                     2020.11.13       py38h27cfd23_0  
requests                  2.25.1             pyhd3eb1b0_0  
ripgrep                   12.1.1                        0  
rope                      0.18.0                     py_0  
rtree                     0.9.4                    py38_1  
ruamel_yaml               0.15.87          py38h7b6447c_1  
scikit-image              0.17.2           py38hdf5156a_0  
scikit-learn              0.23.2           py38h0573a6f_0  
scipy                     1.6.0            py38h91f5cce_0  
seaborn                   0.11.1             pyhd3eb1b0_0  
secretstorage             3.3.0            py38h06a4308_0  
send2trash                1.5.0              pyhd3eb1b0_1  
setuptools                52.0.0           py38h06a4308_0  
simplegeneric             0.8.1                    py38_2  
singledispatch            3.4.0.3                 py_1001  
sip                       4.19.13          py38he6710b0_0  
six                       1.15.0           py38h06a4308_0  
slicerator                1.0.0                      py_0    conda-forge
snappy                    1.1.8                he6710b0_0  
snowballstemmer           2.1.0              pyhd3eb1b0_0  
sortedcollections         2.1.0              pyhd3eb1b0_0  
sortedcontainers          2.3.0              pyhd3eb1b0_0  
soupsieve                 2.1                pyhd3eb1b0_0  
spec2nexus                2021.1.8             h39e3cac_0    aps-anl-tag
sphinx                    3.4.3              pyhd3eb1b0_0  
sphinxcontrib             1.0                      py38_1  
sphinxcontrib-applehelp   1.0.2              pyhd3eb1b0_0  
sphinxcontrib-devhelp     1.0.2              pyhd3eb1b0_0  
sphinxcontrib-htmlhelp    1.0.3              pyhd3eb1b0_0  
sphinxcontrib-jsmath      1.0.1              pyhd3eb1b0_0  
sphinxcontrib-qthelp      1.0.3              pyhd3eb1b0_0  
sphinxcontrib-serializinghtml 1.1.4              pyhd3eb1b0_0  
sphinxcontrib-websupport  1.2.4                      py_0  
spyder                    4.2.1            py38h06a4308_1  
spyder-kernels            1.10.1           py38h06a4308_0  
sqlalchemy                1.3.23           py38h27cfd23_0  
sqlite                    3.33.0               h62c20be_0  
statsmodels               0.12.1           py38h27cfd23_0  
stdlogpj                  1.0.3                      py_0    aps-anl-tag
suitcase-jsonl            0.2.0                      py_0    nsls2forge
suitcase-mongo            0.2.0              pyh9f0ad1d_0    conda-forge
suitcase-msgpack          0.2.4                      py_0    conda-forge
suitcase-utils            0.5.3              pyh9f0ad1d_0    conda-forge
super_state_machine       2.0.2                      py_0    conda-forge
sympy                     1.7.1            py38h06a4308_0  
tbb                       2020.3               hfd86e86_0  
tblib                     1.7.0                      py_0  
terminado                 0.9.2            py38h06a4308_0  
testpath                  0.4.4              pyhd3eb1b0_0  
textdistance              4.2.1              pyhd3eb1b0_0  
threadpoolctl             2.1.0              pyh5ca1d4c_0  
three-merge               0.1.1              pyhd3eb1b0_0  
tifffile                  2021.1.14          pyhd3eb1b0_1  
tk                        8.6.10               hbc83047_0  
toml                      0.10.1                     py_0  
toolz                     0.11.1             pyhd3eb1b0_0  
tornado                   6.1              py38h27cfd23_0  
tqdm                      4.56.0             pyhd3eb1b0_0  
traitlets                 5.0.5              pyhd3eb1b0_0  
typed-ast                 1.4.2            py38h27cfd23_1  
typing_extensions         3.7.4.3            pyh06a4308_0  
tzlocal                   2.1                pyh9f0ad1d_0    conda-forge
ujson                     4.0.2            py38h2531618_0  
uncertainties             3.1.5              pyhd8ed1ab_0    conda-forge
unicodecsv                0.14.1                   py38_0  
unixodbc                  2.3.9                h7b6447c_0  
urllib3                   1.26.3             pyhd3eb1b0_0  
watchdog                  1.0.2            py38h06a4308_1  
wcwidth                   0.2.5                      py_0  
webencodings              0.5.1                    py38_1  
werkzeug                  1.0.1              pyhd3eb1b0_0  
wheel                     0.36.2             pyhd3eb1b0_0  
widgetsnbextension        3.5.1                    py38_0  
wrapt                     1.11.2           py38h7b6447c_0  
wurlitzer                 2.0.1                    py38_0  
xarray                    0.16.2             pyhd8ed1ab_0    conda-forge
xlrd                      2.0.1              pyhd3eb1b0_0  
xlsxwriter                1.3.7              pyhd3eb1b0_0  
xlwt                      1.3.0                    py38_0  
xz                        5.2.5                h7b6447c_0  
yaml                      0.2.5                h7b6447c_0  
yapf                      0.30.0                     py_0  
zarr                      2.6.1              pyhd8ed1ab_0    conda-forge
zeromq                    4.3.3                he6710b0_3  
zfp                       0.5.5                h2531618_4  
zict                      2.0.0              pyhd3eb1b0_0  
zipp                      3.4.0              pyhd3eb1b0_0  
zlib                      1.2.11               h7b6447c_3  
zope                      1.0                      py38_1  
zope.event                4.5.0                    py38_0  
zope.interface            5.2.0            py38h27cfd23_0  
zstd                      1.4.5                h9ceee32_0