Tables & h5py dependency error #76
Description
I followed the instructions to install merlin. I have also created the appropriate .env file with the path to parameters, data and analysis folder. I wanted to test the setup using the code structure mentioned in the documentation
$ merlin -a analysis.json -m microscope_parameters.json -o dataorganization.csv -c codebook_0_M22E1_0.csv -n 5 testdata
The code when run shows error when importing the tables module
File "C:\ProgramData\Anaconda3\envs\merfish2\Scripts\merlin-script.py", line 33, in <module>
sys.exit(load_entry_point('merlin', 'console_scripts', 'merlin')())
File "C:\ProgramData\Anaconda3\envs\merfish2\Scripts\merlin-script.py", line 25, in importlib_load_entry_point
return next(matches).load()
File "C:\ProgramData\Anaconda3\envs\merfish2\lib\site-packages\importlib_metadata\__init__.py", line 194, in load
module = import_module(match.group('module'))
File "C:\ProgramData\Anaconda3\envs\merfish2\lib\importlib\__init__.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 994, in _gcd_import
File "<frozen importlib._bootstrap>", line 971, in _find_and_load
File "<frozen importlib._bootstrap>", line 941, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "<frozen importlib._bootstrap>", line 994, in _gcd_import
File "<frozen importlib._bootstrap>", line 971, in _find_and_load
File "<frozen importlib._bootstrap>", line 955, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 665, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 678, in exec_module
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "c:\users\dpant\downloads\merlin\merlin\__init__.py", line 8, in <module>
from merlin.core import dataset
File "c:\users\dpant\downloads\merlin\merlin\core\dataset.py", line 20, in <module>
import tables
File "C:\ProgramData\Anaconda3\envs\merfish2\lib\site-packages\tables\__init__.py", line 99, in <module>
from .utilsextension import (
ImportError: DLL load failed: The specified module could not be found.
Here are the lsit of packages I have installed
$ conda list
# packages in environment at C:\ProgramData\Anaconda3\envs\merfish2:
#
# Name Version Build Channel
alabaster 0.7.12 pypi_0 pypi
appdirs 1.4.4 pypi_0 pypi
atomicwrites 1.4.0 pypi_0 pypi
attrs 21.2.0 pypi_0 pypi
babel 2.9.1 pypi_0 pypi
blas 1.0 mkl
blosc 1.21.0 h19a0ad4_0
boto3 1.20.3 pypi_0 pypi
botocore 1.23.3 pypi_0 pypi
bzip2 1.0.8 he774522_0
cached-property 1.5.2 pypi_0 pypi
cachetools 4.2.4 pypi_0 pypi
certifi 2021.5.30 py36haa95532_0
charset-normalizer 2.0.7 pypi_0 pypi
colorama 0.4.4 pypi_0 pypi
configargparse 1.5.3 pypi_0 pypi
connection-pool 0.0.3 pypi_0 pypi
coverage 6.1.2 pypi_0 pypi
cycler 0.11.0 pypi_0 pypi
cython 0.29.24 pypi_0 pypi
datrie 0.8.2 pypi_0 pypi
decorator 4.4.2 pypi_0 pypi
docutils 0.15.2 pypi_0 pypi
filelock 3.3.2 pypi_0 pypi
gitdb 4.0.9 pypi_0 pypi
gitpython 3.1.18 pypi_0 pypi
google-api-core 2.2.2 pypi_0 pypi
google-auth 2.3.3 pypi_0 pypi
google-cloud-core 2.2.1 pypi_0 pypi
google-cloud-storage 1.42.3 pypi_0 pypi
google-crc32c 1.3.0 pypi_0 pypi
google-resumable-media 2.1.0 pypi_0 pypi
googleapis-common-protos 1.53.0 pypi_0 pypi
h5py 2.10.0 py36h5e291fa_0
hdf5 1.10.4 h7ebc959_0
icc_rt 2019.0.0 h0cc432a_1
idna 3.3 pypi_0 pypi
imageio 2.10.3 pypi_0 pypi
imagesize 1.3.0 pypi_0 pypi
importlib-metadata 4.8.2 pypi_0 pypi
iniconfig 1.1.1 pypi_0 pypi
intel-openmp 2021.4.0 haa95532_3556
ipython-genutils 0.2.0 pypi_0 pypi
jinja2 3.0.3 pypi_0 pypi
jmespath 0.10.0 pypi_0 pypi
joblib 1.1.0 pypi_0 pypi
jsonschema 3.2.0 pypi_0 pypi
jupyter-core 4.9.1 pypi_0 pypi
kiwisolver 1.3.1 pypi_0 pypi
libspatialindex 1.9.3 h6c2663c_0
lz4-c 1.9.3 h2bbff1b_1
lzo 2.10 he774522_2
markupsafe 2.0.1 pypi_0 pypi
matplotlib 3.3.4 pypi_0 pypi
merlin 0.1.6 dev_0 <develop>
mkl 2020.2 256
mkl-service 2.3.0 py36h196d8e1_0
mkl_fft 1.3.0 py36h46781fe_0
mkl_random 1.1.1 py36h47e9c7a_0
mock 4.0.3 pyhd3eb1b0_0
nbformat 5.1.3 pypi_0 pypi
networkx 2.5.1 pypi_0 pypi
numexpr 2.7.3 py36hcbcaa1e_0
numpy 1.19.5 pypi_0 pypi
numpy-base 1.19.2 py36ha3acd2a_0
opencv-python 4.5.4.58 pypi_0 pypi
packaging 21.2 pypi_0 pypi
pandas 1.1.5 pypi_0 pypi
pillow 8.4.0 pypi_0 pypi
pip 21.2.2 py36haa95532_0
pluggy 1.0.0 pypi_0 pypi
protobuf 3.19.1 pypi_0 pypi
psutil 5.8.0 pypi_0 pypi
pulp 2.5.1 pypi_0 pypi
py 1.11.0 pypi_0 pypi
pyasn1 0.4.8 pypi_0 pypi
pyasn1-modules 0.2.8 pypi_0 pypi
pyclustering 0.10.1.2 pypi_0 pypi
pygments 2.10.0 pypi_0 pypi
pyparsing 2.4.7 pypi_0 pypi
pyqt5 5.15.6 pypi_0 pypi
pyqt5-qt5 5.15.2 pypi_0 pypi
pyqt5-sip 12.9.0 pypi_0 pypi
pyreadline 2.1 py36_1
pyrsistent 0.18.0 pypi_0 pypi
pytables 3.6.1 py36h1da0976_0
pytest 6.2.5 pypi_0 pypi
pytest-cov 3.0.0 pypi_0 pypi
python 3.6.13 h3758d61_0
python-dateutil 2.8.2 pypi_0 pypi
python-dotenv 0.19.2 pypi_0 pypi
pytz 2021.3 pypi_0 pypi
pywavelets 1.1.1 pypi_0 pypi
pywin32 302 pypi_0 pypi
pyyaml 6.0 pypi_0 pypi
ratelimiter 1.2.0.post0 pypi_0 pypi
requests 2.26.0 pypi_0 pypi
rsa 4.7.2 pypi_0 pypi
rtree 0.9.7 py36h2eaa2aa_1
s3transfer 0.5.0 pypi_0 pypi
scikit-image 0.17.2 pypi_0 pypi
scikit-learn 0.24.2 pypi_0 pypi
scipy 1.5.4 pypi_0 pypi
seaborn 0.11.2 pypi_0 pypi
setuptools 58.0.4 py36haa95532_0
shapely 1.5.9 pypi_0 pypi
six 1.16.0 pyhd3eb1b0_0
smart-open 5.2.1 pypi_0 pypi
smmap 5.0.0 pypi_0 pypi
snakemake 6.10.0 pypi_0 pypi
snowballstemmer 2.1.0 pypi_0 pypi
sphinx 4.3.0 pypi_0 pypi
sphinx-rtd-theme 1.0.0 pypi_0 pypi
sphinxcontrib-applehelp 1.0.2 pypi_0 pypi
sphinxcontrib-devhelp 1.0.2 pypi_0 pypi
sphinxcontrib-htmlhelp 2.0.0 pypi_0 pypi
sphinxcontrib-jsmath 1.0.1 pypi_0 pypi
sphinxcontrib-qthelp 1.0.3 pypi_0 pypi
sphinxcontrib-serializinghtml 1.1.5 pypi_0 pypi
sqlite 3.36.0 h2bbff1b_0
stopit 1.1.2 pypi_0 pypi
tables 3.6.1 pypi_0 pypi
tabulate 0.8.9 pypi_0 pypi
threadpoolctl 3.0.0 pypi_0 pypi
tifffile 2020.9.3 pypi_0 pypi
toml 0.10.2 pypi_0 pypi
tomli 1.2.2 pypi_0 pypi
toposort 1.7 pypi_0 pypi
traitlets 4.3.3 pypi_0 pypi
typing-extensions 3.10.0.2 pypi_0 pypi
urllib3 1.26.7 pypi_0 pypi
vc 14.2 h21ff451_1
vs2015_runtime 14.27.29016 h5e58377_2
wheel 0.37.0 pyhd3eb1b0_1
wincertstore 0.2 py36h7fe50ca_0
wrapt 1.13.3 pypi_0 pypi
xmltodict 0.12.0 pypi_0 pypi
zipp 3.6.0 pypi_0 pypi
zlib 1.2.11 h62dcd97_4
zstd 1.4.9 h19a0ad4_0