Comments (2)
I have tried deleting my cache folder entirely and resetting everything by making a new manifest etc, following this tutorial here: https://allensdk.readthedocs.io/en/latest/_static/examples/nb/visual_behavior_neuropixels_LFP_analysis.html
I suspect it it my conda environment so I will try rebuilding it from the ground up without the .yml
from allensdk.
Ok so I fixed the problem by recreating the environment from scratch. This is a problem however because it means the .yml file I want to use to share the environment is not good enough to recreate my environment complete with other libraries I use in my code. This means my code is not shareable and if I were to try to publish my results would not be reproducible, which is something I want them to be.
So what is the problem with my .yml file, what are some solutions to this issue?
It is as follows:
name: allensdk_env
channels:
- edeno
- bioconda
- conda-forge
- r
- defaults
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=2_gnu
- brotli=1.1.0=hd590300_1
- brotli-bin=1.1.0=hd590300_1
- bzip2=1.0.8=hd590300_5
- ca-certificates=2023.11.17=hbcca054_0
- contourpy=1.2.0=py310hd41b1e2_0
- cycler=0.12.1=pyhd8ed1ab_0
- fonttools=4.45.0=py310h2372a71_0
- freetype=2.12.1=h267a509_2
- kiwisolver=1.4.5=py310hd41b1e2_1
- lcms2=2.15=hb7c19ff_3
- ld_impl_linux-64=2.40=h41732ed_0
- lerc=4.0.0=h27087fc_0
- libblas=3.9.0=19_linux64_openblas
- libbrotlicommon=1.1.0=hd590300_1
- libbrotlidec=1.1.0=hd590300_1
- libbrotlienc=1.1.0=hd590300_1
- libcblas=3.9.0=19_linux64_openblas
- libdeflate=1.19=hd590300_0
- libffi=3.4.2=h7f98852_5
- libgcc-ng=13.2.0=h807b86a_2
- libgfortran-ng=13.2.0=h69a702a_3
- libgfortran5=13.2.0=ha4646dd_3
- libgomp=13.2.0=h807b86a_2
- libjpeg-turbo=3.0.0=hd590300_1
- liblapack=3.9.0=19_linux64_openblas
- libnsl=2.0.1=hd590300_0
- libopenblas=0.3.24=pthreads_h413a1c8_0
- libpng=1.6.39=h753d276_0
- libsqlite=3.44.0=h2797004_0
- libstdcxx-ng=13.2.0=h7e041cc_3
- libtiff=4.6.0=ha9c0a0a_2
- libuuid=2.38.1=h0b41bf4_0
- libwebp-base=1.3.2=hd590300_0
- libxcb=1.15=h0b41bf4_0
- libzlib=1.2.13=hd590300_5
- matplotlib-base=3.8.2=py310h62c0568_0
- munkres=1.1.4=pyh9f0ad1d_0
- ncurses=6.4=h59595ed_2
- openjpeg=2.5.0=h488ebb8_3
- openssl=3.2.0=hd590300_0
- packaging=23.2=pyhd8ed1ab_0
- pip=23.3.1=pyhd8ed1ab_0
- piso=1.0.0=pyhd8ed1ab_0
- pthread-stubs=0.4=h36c2ea0_1001
- pyparsing=3.1.1=pyhd8ed1ab_0
- python=3.10.2=hc74c709_4_cpython
- python-dateutil=2.8.2=pyhd8ed1ab_0
- python-tzdata=2023.3=pyhd8ed1ab_0
- python_abi=3.10=4_cp310
- pytz=2023.3.post1=pyhd8ed1ab_0
- readline=8.2=h8228510_1
- ripple_detection=1.4.0=py_0
- scipy=1.11.3=py310hb13e2d6_1
- setuptools=68.2.2=pyhd8ed1ab_0
- six=1.16.0=pyh6c4a22f_0
- sqlite=3.44.0=h2c6b66d_0
- staircase=2.5.2=pyhd8ed1ab_0
- tk=8.6.13=noxft_h4845f30_101
- typing-extensions=4.8.0=hd8ed1ab_0
- typing_extensions=4.8.0=pyha770c72_0
- tzdata=2023c=h71feb2d_0
- unicodedata2=15.1.0=py310h2372a71_0
- wheel=0.41.3=pyhd8ed1ab_0
- xorg-libxau=1.0.11=hd590300_0
- xorg-libxdmcp=1.1.3=h7f98852_0
- xz=5.2.6=h166bdaf_0
- zstd=1.5.5=hfc55251_0
- pip:
- aiohttp==3.7.4
- allensdk==2.15.2
- argschema==3.0.4
- asttokens==2.4.1
- async-timeout==3.0.1
- attrs==23.1.0
- blosc2==2.3.1
- boto3==1.17.21
- botocore==1.20.112
- cachetools==4.2.4
- certifi==2023.7.22
- chardet==3.0.4
- charset-normalizer==3.3.2
- comm==0.2.0
- debugpy==1.8.0
- decorator==5.1.1
- distro==1.8.0
- exceptiongroup==1.1.3
- executing==2.0.1
- future==0.18.3
- glymur==0.8.19
- greenlet==3.0.1
- h5py==3.10.0
- hdmf==3.4.7
- idna==3.4
- imageio==2.32.0
- ipykernel==6.26.0
- ipython==8.17.2
- ipywidgets==8.1.1
- jedi==0.19.1
- jinja2==3.1.2
- jmespath==0.10.0
- jsonschema==4.19.2
- jsonschema-specifications==2023.7.1
- jupyter-client==8.6.0
- jupyter-core==5.5.0
- jupyterlab-widgets==3.0.9
- lazy-loader==0.3
- markupsafe==2.1.3
- marshmallow==3.20.1
- matplotlib==3.4.2
- matplotlib-inline==0.1.6
- msgpack==1.0.7
- multidict==6.0.4
- ndindex==1.7
- ndx-events==0.2.0
- nest-asyncio==1.5.8
- networkx==3.2.1
- numexpr==2.8.7
- numpy==1.23.5
- pandas==1.5.3
- parso==0.8.3
- patsy==0.5.3
- pexpect==4.8.0
- pillow==10.0.1
- platformdirs==4.0.0
- prompt-toolkit==3.0.41
- psutil==5.9.6
- psycopg2-binary==2.9.9
- ptyprocess==0.7.0
- pure-eval==0.2.2
- py-cpuinfo==9.0.0
- pygments==2.17.1
- pynrrd==0.4.3
- pynwb==2.2.0
- pyyaml==6.0.1
- pyzmq==25.1.1
- referencing==0.30.2
- requests==2.31.0
- requests-toolbelt==0.10.1
- rpds-py==0.12.0
- ruamel-yaml==0.18.5
- ruamel-yaml-clib==0.2.8
- s3transfer==0.3.7
- scikit-build==0.17.6
- scikit-image==0.22.0
- seaborn==0.13.0
- semver==3.0.2
- simpleitk==2.3.1
- simplejson==3.19.2
- sqlalchemy==2.0.23
- stack-data==0.6.3
- statsmodels==0.14.0
- tables==3.9.1
- tifffile==2023.9.26
- tomli==2.0.1
- tornado==6.3.3
- tqdm==4.66.1
- traitlets==5.13.0
- urllib3==1.26.18
- wcwidth==0.2.10
- widgetsnbextension==4.0.9
- xarray==2023.10.1
- yarl==1.9.2
prefix: /home/acampbell/miniconda3/envs/allensdk_env
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Related Issues (20)
- Request (Allen Brain Observatory Data): Access to ophys metadata as csv files
- Add 'quality' column to VBN units metadata table HOT 1
- how can I get the brain surface dorsal-ventral ccf coordinates for different probes?
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- Simultaneously importing `ecephys_project_cache` and `behavior_ecephys_session` breaks nwb file reading HOT 3
- incorrect task parameter value in session metadata for TRAINING_0 and TRAINING_1 HOT 1
- Cannot load both VisualCoding and VisualBehavior caches in the same Jupyter Notebook HOT 1
- DriftingGratings.get_response() does not explain what the ncells+1'th response corresponds to
- Error: pg_config executable not found. - Installing on Compute Canada HOT 2
- Update conda-forge package HOT 2
- Missing channels in LFP data, also is the LFP pre-scaled? HOT 1
- Broken .get_performance_metrics() method in VisualBehaviorNeuropixelsProjectCache.from_s3_cache(cache_dir=neuropixel_dataset_behavior) HOT 2
- The link to the latest source documentation is broken (google chrome, windows 11) HOT 1
- Does the Allen_sdk require openssl to be 3.1.4 or can it use a newer version as well?
- Creating drifting gratings (frame by frame)
- Unable to download cache files
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