Instalation of pdfgetx3 2.1.1
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Rodrigo Uchida Ichikawa
Oct 25, 2020, 1:21:21 PM10/25/20
to diffpy-users
Dear all,
I installed pdfgetx3 2.1.1 on Windows and when I hit the command 'pdfgetx3 --version' the follwing message appeared:
(base) C:\>pdfgetx3 --version
Traceback (most recent call last):
File "C:\Users\Rodrigo\anaconda3\Scripts\pdfgetx3-script.py", line 33, in <module>
sys.exit(load_entry_point('diffpy.pdfgetx==2.1.1', 'console_scripts', 'pdfgetx3')())
File "C:\Users\Rodrigo\anaconda3\Scripts\pdfgetx3-script.py", line 25, in importlib_load_entry_point
return next(matches).load()
File "C:\Users\Rodrigo\anaconda3\lib\importlib\metadata.py", line 77, in load
module = import_module(match.group('module'))
File "C:\Users\Rodrigo\anaconda3\lib\importlib\__init__.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1014, in _gcd_import
File "<frozen importlib._bootstrap>", line 991, in _find_and_load
File "<frozen importlib._bootstrap>", line 961, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "<frozen importlib._bootstrap>", line 1014, in _gcd_import
File "<frozen importlib._bootstrap>", line 991, in _find_and_load
File "<frozen importlib._bootstrap>", line 961, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "<frozen importlib._bootstrap>", line 1014, in _gcd_import
File "<frozen importlib._bootstrap>", line 991, in _find_and_load
File "<frozen importlib._bootstrap>", line 961, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "<frozen importlib._bootstrap>", line 1014, in _gcd_import
File "<frozen importlib._bootstrap>", line 991, in _find_and_load
File "<frozen importlib._bootstrap>", line 973, in _find_and_load_unlocked
ModuleNotFoundError: No module named 'diffpy'
I then tried to install diffpy-cmi following the steps in 'https://www.diffpy.org/products/diffpycmi/index.html' but i got another message:
(py37) C:\>conda config --add channels diffpy
Warning: 'diffpy' already in 'channels' list, moving to the top
(py37) C:\>conda install diffpy-cmi
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
PackagesNotFoundError: The following packages are not available from current channels:
- diffpy-cmi
Current channels:
To search for alternate channels that may provide the conda package you're
looking for, navigate to
and use the search bar at the top of the page.
I tried to look for another channels but didn't find any.
Any suggestions about how to run the pdfgetx3?
Thank you.
Rodrigo Uchida Ichikawa.
Songsheng Tao
Oct 25, 2020, 1:44:57 PM10/25/20
to diffpy...@googlegroups.com
Dear Rodrigo:
Could you try the following steps?
(1) In your terminal, do
``conda activate base``
``conda list diffpy.pdfgetx``
If you find the ``diffpy.pdfgetx`` package in the base environment:
something is wrong with the build process of pdfgetx and we will release a new version to fix it.
else:
diffpy.pdfgetx is not installed correctly in the base environment.
(2) To install the diffpy.pdfgetx
First you need a conda environment that has python and pip.
``conda activate base``
``conda list pip``
To make sure pip showing up in your base environment.
If not, ``conda install pip`` to install the pip.
then, do
``which pip``
The path to pip will show in your terminal. Make sure the path contains the path "anaconda3/bin/pip". It means that your pip is in the base conda environment.
``pip install ./diffpy.pdfgetx-VERSION.whl``
Substitute the "./diffpy.pdfgetx-VERSION.whl" to the path to the .whl file on your computer.
(3) About diffpy-cmi, there is no release for windows and it is not required to run diffpy.pdfgetx.
Sincerely,
Songsheng
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|
Rodrigo Uchida Ichikawa
Oct 25, 2020, 2:53:25 PM10/25/20
to diffpy-users
Dear Songsheng,
Thank you for your answer.
I did what you asked in step 1 and got:
(base) C:\>conda list diffpy.pdfgetx
# packages in environment at C:\Users\Rodrigo\anaconda3:
#
# Name Version Build Channel
diffpy-pdfgetx 2.1.1 pypi_0 pypi
Then, I tried to call 'pdfgetx3 --version' and got:
So, maybe is something is wrong with the build process?
Thank you again.
Rodrigo.
Songsheng Tao
Oct 25, 2020, 3:16:34 PM10/25/20
to diffpy...@googlegroups.com
I suspect that it is a build problem. We will look into it. Could you do ``conda list`` and paste the output (a list of packages and their version) here? It will help us to identify the bug. Thank you.
To view this discussion on the web visit https://groups.google.com/d/msgid/diffpy-users/d0669917-f2e9-4718-97a0-0b85d851a79dn%40googlegroups.com.
Rodrigo Uchida Ichikawa
Oct 25, 2020, 3:26:12 PM10/25/20
to diffpy-users
Sure, please find the output below:
(base) C:\Users\Rodrigo>conda list
# packages in environment at C:\Users\Rodrigo\anaconda3:
#
# Name Version Build Channel
_ipyw_jlab_nb_ext_conf 0.1.0 py38_0
alabaster 0.7.12 py_0
anaconda 2020.07 py38_0
anaconda-client 1.7.2 py38_0
anaconda-navigator 1.9.12 py38_0
anaconda-project 0.8.4 py_0
argh 0.26.2 py38_0
asn1crypto 1.3.0 py38_0
astroid 2.4.2 py38_0
astropy 4.0.1.post1 py38he774522_1
atomicwrites 1.4.0 py_0
attrs 19.3.0 py_0
autopep8 1.5.3 py_0
babel 2.8.0 py_0
backcall 0.2.0 py_0
backports 1.0 py_2
backports.functools_lru_cache 1.6.1 py_0
backports.shutil_get_terminal_size 1.0.0 py38_2
backports.tempfile 1.0 py_1
backports.weakref 1.0.post1 py_1
bcrypt 3.1.7 py38he774522_1
beautifulsoup4 4.9.1 py38_0
bitarray 1.4.0 py38he774522_0
bkcharts 0.2 py38_0
blas 1.0 mkl
bleach 3.1.5 py_0
blosc 1.19.0 h7bd577a_0
bokeh 2.1.1 py38_0
boto 2.49.0 py38_0
bottleneck 1.3.2 py38h2a96729_1
brotlipy 0.7.0 py38he774522_1000
bzip2 1.0.8 he774522_0
ca-certificates 2020.6.24 0
certifi 2020.6.20 py38_0
cffi 1.14.0 py38h7a1dbc1_0
chardet 3.0.4 py38_1003
click 7.1.2 py_0
cloudpickle 1.5.0 py_0
clyent 1.2.2 py38_1
colorama 0.4.3 py_0
comtypes 1.1.7 py38_1001
conda 4.9.0 py38_0
conda-build 3.18.11 py38_1
conda-env 2.6.0 1
conda-package-handling 1.7.2 py38h76e460a_0
conda-verify 3.4.2 py_1
console_shortcut 0.1.1 4
contextlib2 0.6.0.post1 py_0
cryptography 2.9.2 py38h7a1dbc1_0
curl 7.71.1 h2a8f88b_1
cycler 0.10.0 py38_0
cython 0.29.21 py38ha925a31_0
cytoolz 0.10.1 py38he774522_0
dask 2.20.0 py_0
dask-core 2.20.0 py_0
decorator 4.4.2 py_0
defusedxml 0.6.0 py_0
diff-match-patch 20200713 py_0
diffpy-pdfgetx 2.0.0 pypi_0 pypi
distributed 2.20.0 py38_0
docutils 0.16 py38_1
entrypoints 0.3 py38_0
et_xmlfile 1.0.1 py_1001
fastcache 1.1.0 py38he774522_0
filelock 3.0.12 py_0
flake8 3.8.3 py_0
flask 1.1.2 py_0
freetype 2.10.2 hd328e21_0
fsspec 0.7.4 py_0
future 0.18.2 py38_1
get_terminal_size 1.0.0 h38e98db_0
gevent 20.6.2 py38he774522_0
glob2 0.7 py_0
gmpy2 2.0.8 py38h7edee0f_3
greenlet 0.4.16 py38he774522_0
h5py 2.10.0 py38h5e291fa_0
hdf5 1.10.4 h7ebc959_0
heapdict 1.0.1 py_0
html5lib 1.1 py_0
icc_rt 2019.0.0 h0cc432a_1
icu 58.2 ha925a31_3
idna 2.10 py_0
imageio 2.9.0 py_0
imagesize 1.2.0 py_0
importlib-metadata 1.7.0 py38_0
importlib_metadata 1.7.0 0
intel-openmp 2020.1 216
intervaltree 3.0.2 py_1
ipykernel 5.3.2 py38h5ca1d4c_0
ipython 7.16.1 py38h5ca1d4c_0
ipython_genutils 0.2.0 py38_0
ipywidgets 7.5.1 py_0
isort 4.3.21 py38_0
itsdangerous 1.1.0 py_0
jdcal 1.4.1 py_0
jedi 0.17.1 py38_0
jinja2 2.11.2 py_0
joblib 0.16.0 py_0
jpeg 9b hb83a4c4_2
json5 0.9.5 py_0
jsonschema 3.2.0 py38_0
jupyter 1.0.0 py38_7
jupyter_client 6.1.6 py_0
jupyter_console 6.1.0 py_0
jupyter_core 4.6.3 py38_0
jupyterlab 2.1.5 py_0
jupyterlab_server 1.2.0 py_0
keyring 21.2.1 py38_0
kiwisolver 1.2.0 py38h74a9793_0
krb5 1.18.2 hc04afaa_0
lazy-object-proxy 1.4.3 py38he774522_0
libarchive 3.4.2 h5e25573_0
libcurl 7.71.1 h2a8f88b_1
libiconv 1.15 h1df5818_7
liblief 0.10.1 ha925a31_0
libllvm9 9.0.1 h21ff451_0
libpng 1.6.37 h2a8f88b_0
libsodium 1.0.18 h62dcd97_0
libspatialindex 1.9.3 h33f27b4_0
libssh2 1.9.0 h7a1dbc1_1
libtiff 4.1.0 h56a325e_1
libxml2 2.9.10 h464c3ec_1
libxslt 1.1.34 he774522_0
llvmlite 0.33.0 py38ha925a31_0
locket 0.2.0 py38_1
lxml 4.5.2 py38h1350720_0
lz4-c 1.9.2 h62dcd97_0
lzo 2.10 he774522_2
m2w64-gcc-libgfortran 5.3.0 6
m2w64-gcc-libs 5.3.0 7
m2w64-gcc-libs-core 5.3.0 7
m2w64-gmp 6.1.0 2
m2w64-libwinpthread-git 5.0.0.4634.697f757 2
markupsafe 1.1.1 py38he774522_0
matplotlib 3.2.2 0
matplotlib-base 3.2.2 py38h64f37c6_0
mccabe 0.6.1 py38_1
menuinst 1.4.16 py38he774522_1
mistune 0.8.4 py38he774522_1000
mkl 2020.1 216
mkl-service 2.3.0 py38hb782905_0
mkl_fft 1.1.0 py38h45dec08_0
mkl_random 1.1.1 py38h47e9c7a_0
mock 4.0.2 py_0
more-itertools 8.4.0 py_0
mpc 1.1.0 h7edee0f_1
mpfr 4.0.2 h62dcd97_1
mpir 3.0.0 hec2e145_1
mpmath 1.1.0 py38_0
msgpack-python 1.0.0 py38h74a9793_1
msys2-conda-epoch 20160418 1
multipledispatch 0.6.0 py38_0
navigator-updater 0.2.1 py38_0
nbconvert 5.6.1 py38_0
nbformat 5.0.7 py_0
networkx 2.4 py_1
nltk 3.5 py_0
nose 1.3.7 py38_2
notebook 6.0.3 py38_0
numba 0.50.1 py38h47e9c7a_0
numexpr 2.7.1 py38h25d0782_0
numpy 1.18.5 py38h6530119_0
numpy-base 1.18.5 py38hc3f5095_0
numpydoc 1.1.0 py_0
olefile 0.46 py_0
openpyxl 3.0.4 py_0
openssl 1.1.1g he774522_0
packaging 20.4 py_0
pandas 1.0.5 py38h47e9c7a_0
pandoc 2.10 0
pandocfilters 1.4.2 py38_1
paramiko 2.7.1 py_0
parso 0.7.0 py_0
partd 1.1.0 py_0
path 13.1.0 py38_0
path.py 12.4.0 0
pathlib2 2.3.5 py38_0
pathtools 0.1.2 py_1
patsy 0.5.1 py38_0
pep8 1.7.1 py38_0
pexpect 4.8.0 py38_0
pickleshare 0.7.5 py38_1000
pillow 7.2.0 py38hcc1f983_0
pip 20.1.1 py38_1
pkginfo 1.5.0.1 py38_0
pluggy 0.13.1 py38_0
ply 3.11 py38_0
powershell_shortcut 0.0.1 3
prometheus_client 0.8.0 py_0
prompt-toolkit 3.0.5 py_0
prompt_toolkit 3.0.5 0
psutil 5.7.0 py38he774522_0
py 1.9.0 py_0
py-lief 0.10.1 py38ha925a31_0
pycodestyle 2.6.0 py_0
pycosat 0.6.3 py38he774522_0
pycparser 2.20 py_2
pycurl 7.43.0.5 py38h7a1dbc1_0
pydocstyle 5.0.2 py_0
pyflakes 2.2.0 py_0
pygments 2.6.1 py_0
pylint 2.5.3 py38_0
pynacl 1.4.0 py38h62dcd97_1
pyodbc 4.0.30 py38ha925a31_0
pyopenssl 19.1.0 py_1
pyparsing 2.4.7 py_0
pyqt 5.9.2 py38ha925a31_4
pyreadline 2.1 py38_1
pyrsistent 0.16.0 py38he774522_0
pysocks 1.7.1 py38_0
pytables 3.6.1 py38ha5be198_0
pytest 5.4.3 py38_0
python 3.8.3 he1778fa_2
python-dateutil 2.8.1 py_0
python-jsonrpc-server 0.3.4 py_1
python-language-server 0.34.1 py38_0
python-libarchive-c 2.9 py_0
pytz 2020.1 py_0
pywavelets 1.1.1 py38he774522_0
pywin32 227 py38he774522_1
pywin32-ctypes 0.2.0 py38_1000
pywinpty 0.5.7 py38_0
pyyaml 5.3.1 py38he774522_1
pyzmq 19.0.1 py38ha925a31_1
qdarkstyle 2.8.1 py_0
qt 5.9.7 vc14h73c81de_0
qtawesome 0.7.2 py_0
qtconsole 4.7.5 py_0
qtpy 1.9.0 py_0
regex 2020.6.8 py38he774522_0
requests 2.24.0 py_0
rope 0.17.0 py_0
rtree 0.9.4 py38h21ff451_1
ruamel_yaml 0.15.87 py38he774522_1
scikit-image 0.16.2 py38h47e9c7a_0
scikit-learn 0.23.1 py38h25d0782_0
scipy 1.5.0 py38h9439919_0
seaborn 0.10.1 py_0
send2trash 1.5.0 py38_0
setuptools 49.2.0 py38_0
simplegeneric 0.8.1 py38_2
singledispatch 3.4.0.3 py38_0
sip 4.19.13 py38ha925a31_0
six 1.15.0 py_0
snappy 1.1.8 h33f27b4_0
snowballstemmer 2.0.0 py_0
sortedcollections 1.2.1 py_0
sortedcontainers 2.2.2 py_0
soupsieve 2.0.1 py_0
sphinx 3.1.2 py_0
sphinxcontrib 1.0 py38_1
sphinxcontrib-applehelp 1.0.2 py_0
sphinxcontrib-devhelp 1.0.2 py_0
sphinxcontrib-htmlhelp 1.0.3 py_0
sphinxcontrib-jsmath 1.0.1 py_0
sphinxcontrib-qthelp 1.0.3 py_0
sphinxcontrib-serializinghtml 1.1.4 py_0
sphinxcontrib-websupport 1.2.3 py_0
spyder 4.1.4 py38_0
spyder-kernels 1.9.2 py38_0
sqlalchemy 1.3.18 py38he774522_0
sqlite 3.32.3 h2a8f88b_0
statsmodels 0.11.1 py38he774522_0
sympy 1.6.1 py38_0
tbb 2020.0 h74a9793_0
tblib 1.6.0 py_0
terminado 0.8.3 py38_0
testpath 0.4.4 py_0
threadpoolctl 2.1.0 pyh5ca1d4c_0
tk 8.6.10 he774522_0
toml 0.10.1 py_0
toolz 0.10.0 py_0
tornado 6.0.4 py38he774522_1
tqdm 4.47.0 py_0
traitlets 4.3.3 py38_0
typing_extensions 3.7.4.2 py_0
ujson 1.35 py38he774522_0
unicodecsv 0.14.1 py38_0
urllib3 1.25.9 py_0
vc 14.1 h0510ff6_4
vs2015_runtime 14.16.27012 hf0eaf9b_3
watchdog 0.10.3 py38_0
wcwidth 0.2.5 py_0
webencodings 0.5.1 py38_1
werkzeug 1.0.1 py_0
wheel 0.34.2 py38_0
widgetsnbextension 3.5.1 py38_0
win_inet_pton 1.1.0 py38_0
win_unicode_console 0.5 py38_0
wincertstore 0.2 py38_0
winpty 0.4.3 4
wrapt 1.11.2 py38he774522_0
xlrd 1.2.0 py_0
xlsxwriter 1.2.9 py_0
xlwings 0.19.5 py38_0
xlwt 1.3.0 py38_0
xmltodict 0.12.0 py_0
xz 5.2.5 h62dcd97_0
yaml 0.2.5 he774522_0
yapf 0.30.0 py_0
zeromq 4.3.2 ha925a31_2
zict 2.0.0 py_0
zipp 3.1.0 py_0
zlib 1.2.11 h62dcd97_4
zope 1.0 py38_1
zope.event 4.4 py38_0
zope.interface 4.7.1 py38he774522_0
zstd 1.4.5 ha9fde0e_0
Best.
Rodrigo.
Songsheng Tao
Oct 25, 2020, 4:02:40 PM10/25/20
to diffpy...@googlegroups.com, Hung Vuong
I found that in the result, it showed that:
It is version 2.0.0. However, when you run "pdfgetx3 --version":
File "C:\Users\Rodrigo\anaconda3\Scripts\pdfgetx3-script.py", line 33, in <module>
sys.exit(load_entry_point('diffpy.pdfgetx==2.1.1', 'console_scripts', 'pdfgetx3')())
sys.exit(load_entry_point('diffpy.pdfgetx==2.1.1', 'console_scripts', 'pdfgetx3')())
the system tried to look for 2.1.1. Could you try to install the diffpy.pdfgetx in a clean new environment?
1. create a new conda environment with the requirements.
conda create -n pdfgetx_env pip setuptools six numpy matplotlib ipython python=3.8
2. activate the environment
conda activate pdfgetx_env
3. install the pdfgetx
pip install <diffpy.pdfgetx-VERSION.whl>
4. run
pdfgetx3 --version
At the same time, we will check the build problem on windows.
To view this discussion on the web visit https://groups.google.com/d/msgid/diffpy-users/8b22aa4d-1add-4975-ba29-1d178b6ff5dfn%40googlegroups.com.
Rodrigo Uchida Ichikawa
Oct 25, 2020, 4:20:43 PM10/25/20
to diffpy-users
Perfect!
It worked!
Thanks a lot.
Best.
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