CaImAn
CaImAn copied to clipboard
Published
20 hours ago •
flatironinstitute
flatironinstitute
import error
import error caused by panel 0.12.6, which is the conda default. This issue was fixed 3 days ago with the release of 0.12.7, which is available on pypi
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
Input In [1], in <cell line: 23>()
20 except NameError:
21 pass
---> 23 import caiman as cm
24 from caiman.motion_correction import MotionCorrect
25 from caiman.source_extraction.cnmf import cnmf as cnmf
File ~/opt/miniconda3/envs/caiman/lib/python3.9/site-packages/caiman/__init__.py:4, in <module>
1 #!/usr/bin/env python
3 import pkg_resources
----> 4 from .base.movies import movie, load, load_movie_chain
5 from .base.timeseries import concatenate
6 from .cluster import start_server, stop_server
File ~/opt/miniconda3/envs/caiman/lib/python3.9/site-packages/caiman/base/movies.py:62, in <module>
59 from .traces import trace
61 from ..mmapping import load_memmap
---> 62 from ..utils import visualization
63 from .. import summary_images as si
64 from ..motion_correction import apply_shift_online, motion_correct_online
File ~/opt/miniconda3/envs/caiman/lib/python3.9/site-packages/caiman/utils/visualization.py:33, in <module>
31 from typing import Dict
32 from warnings import warn
---> 33 import holoviews as hv
34 import functools as fct
36 from ..base.rois import com
File ~/opt/miniconda3/envs/caiman/lib/python3.9/site-packages/holoviews/__init__.py:12, in <module>
8 __version__ = str(param.version.Version(fpath=__file__, archive_commit="$Format:%h$",
9 reponame="holoviews"))
11 from . import util # noqa (API import)
---> 12 from .annotators import annotate # noqa (API import)
13 from .core import archive, config # noqa (API import)
14 from .core.boundingregion import BoundingBox # noqa (API import)
File ~/opt/miniconda3/envs/caiman/lib/python3.9/site-packages/holoviews/annotators.py:10, in <module>
6 from inspect import getmro
8 import param
---> 10 from panel.pane import PaneBase
11 from panel.layout import Row, Tabs
12 from panel.util import param_name
File ~/opt/miniconda3/envs/caiman/lib/python3.9/site-packages/panel/__init__.py:1, in <module>
----> 1 from . import layout # noqa
2 from . import links # noqa
3 from . import pane # noqa
File ~/opt/miniconda3/envs/caiman/lib/python3.9/site-packages/panel/layout/__init__.py:1, in <module>
----> 1 from .accordion import Accordion # noqa
2 from .base import Column, ListLike, ListPanel, Panel, Row, WidgetBox # noqa
3 from .card import Card # noqa
File ~/opt/miniconda3/envs/caiman/lib/python3.9/site-packages/panel/layout/accordion.py:5, in <module>
1 import param
3 from bokeh.models import Column as BkColumn, CustomJS
----> 5 from .base import NamedListPanel
6 from .card import Card
9 class Accordion(NamedListPanel):
File ~/opt/miniconda3/envs/caiman/lib/python3.9/site-packages/panel/layout/base.py:11, in <module>
7 import param
9 from bokeh.models import Column as BkColumn, Row as BkRow
---> 11 from ..io.model import hold
12 from ..io.state import state
13 from ..reactive import Reactive
File ~/opt/miniconda3/envs/caiman/lib/python3.9/site-packages/panel/io/__init__.py:9, in <module>
6 import logging
7 import sys
----> 9 from ..config import config
11 from .callbacks import PeriodicCallback # noqa
12 from .embed import embed_state # noqa
File ~/opt/miniconda3/envs/caiman/lib/python3.9/site-packages/panel/config.py:21, in <module>
15 import param
17 from pyviz_comms import (
18 JupyterCommManager as _JupyterCommManager, extension as _pyviz_extension
19 )
---> 21 from .io.notebook import load_notebook
22 from .io.state import state
24 __version__ = str(param.version.Version(
25 fpath=__file__, archive_commit="$Format:%h$", reponame="panel"))
File ~/opt/miniconda3/envs/caiman/lib/python3.9/site-packages/panel/io/notebook.py:39, in <module>
37 from .embed import embed_state
38 from .model import add_to_doc, diff
---> 39 from .resources import Bundle, Resources, _env, bundle_resources
40 from .server import _server_url, _origin_url, get_server
41 from .state import state
File ~/opt/miniconda3/envs/caiman/lib/python3.9/site-packages/panel/io/resources.py:24, in <module>
22 from bokeh.resources import Resources as BkResources
23 from bokeh.settings import settings as _settings
---> 24 from jinja2 import Environment, Markup, FileSystemLoader
26 from ..util import url_path
27 from .state import state
ImportError: cannot import name 'Markup' from 'jinja2' (/Users/bendichter/opt/miniconda3/envs/caiman/lib/python3.9/site-packages/jinja2/__init__.py)
until conda updates the default, I don't think the current install instructions will work.You'll need to also
pip install -U panel
Do you mind checking to see if panel 0.12.1 has the issue? Or I wonder if pinning an older jinja2 would do the job.
It looks like jinja2 had 3.0.3 release 12 days ago; I wonder if that version has inadequate pinning.
# packages in environment at /Users/bendichter/opt/miniconda3/envs/caiman:
#
# Name Version Build Channel
abseil-cpp 20210324.2 he49afe7_0 conda-forge
absl-py 1.0.0 pyhd8ed1ab_0 conda-forge
aiohttp 3.8.1 py39h89e85a6_0 conda-forge
aiosignal 1.2.0 pyhd8ed1ab_0 conda-forge
aom 3.3.0 h96cf925_1 conda-forge
appnope 0.1.2 py39h6e9494a_2 conda-forge
argon2-cffi 21.3.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py39h89e85a6_1 conda-forge
asttokens 2.0.5 pyhd8ed1ab_0 conda-forge
astunparse 1.6.3 pyhd8ed1ab_0 conda-forge
async-timeout 4.0.2 pyhd8ed1ab_0 conda-forge
attrs 21.4.0 pyhd8ed1ab_0 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.1 pyhd3eb1b0_0
backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.10.0 pyha770c72_0 conda-forge
bleach 4.1.0 pyhd8ed1ab_0 conda-forge
blinker 1.4 py_1 conda-forge
blosc 1.21.0 he49afe7_0 conda-forge
bokeh 2.4.2 py39h6e9494a_0 conda-forge
brotli 1.0.9 h0d85af4_6 conda-forge
brotli-bin 1.0.9 h0d85af4_6 conda-forge
brotlipy 0.7.0 py39h89e85a6_1003 conda-forge
brunsli 0.1 h046ec9c_0 conda-forge
bzip2 1.0.8 h0d85af4_4 conda-forge
c-ares 1.18.1 h0d85af4_0 conda-forge
c-blosc2 2.0.4 ha1a4663_1 conda-forge
ca-certificates 2022.3.29 hecd8cb5_0
cachetools 4.2.4 pyhd8ed1ab_0 conda-forge
caiman 1.9.8 py39hbd61c47_0 conda-forge
cairo 1.16.0 he43a7df_1008 conda-forge
certifi 2021.10.8 py39h6e9494a_2 conda-forge
cffi 1.15.0 py39he338e87_0 conda-forge
cfitsio 4.1.0 h2c97ad1_0 conda-forge
charls 2.3.4 he49afe7_0 conda-forge
charset-normalizer 2.0.12 pyhd8ed1ab_0 conda-forge
click 8.1.1 py39h6e9494a_1 conda-forge
cloudpickle 2.0.0 pyhd8ed1ab_0 conda-forge
colorama 0.4.4 pyh9f0ad1d_0 conda-forge
colorcet 3.0.0 pyhd8ed1ab_0 conda-forge
cryptography 36.0.2 py39h1644bb1_0 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
cytoolz 0.11.2 py39h89e85a6_1 conda-forge
dask-core 2022.3.0 pyhd8ed1ab_0 conda-forge
dbus 1.13.18 h18a8e69_0
debugpy 1.5.1 py39h9fcab8e_0 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
entrypoints 0.4 pyhd8ed1ab_0 conda-forge
executing 0.8.3 pyhd8ed1ab_0 conda-forge
expat 2.4.8 h96cf925_0 conda-forge
ffmpeg 4.3.2 hbf27d7b_3 conda-forge
flit-core 3.7.1 pyhd8ed1ab_0 conda-forge
fontconfig 2.13.96 h676cef8_2 conda-forge
fonttools 4.31.2 py39h63b48b0_0 conda-forge
freetype 2.11.0 hd8bbffd_0
frozenlist 1.3.0 py39h89e85a6_0 conda-forge
fsspec 2022.2.0 pyhd8ed1ab_0 conda-forge
future 0.18.2 py39h6e9494a_4 conda-forge
gast 0.3.3 py_0 conda-forge
gettext 0.21.0 h7535e17_0
giflib 5.2.1 hbcb3906_2 conda-forge
glib 2.70.2 hcf210ce_4 conda-forge
glib-tools 2.70.2 hcf210ce_4 conda-forge
gmp 6.2.1 h2e338ed_0 conda-forge
gnutls 3.6.15 hed9c0bf_0
google-auth 1.35.0 pyh6c4a22f_0 conda-forge
google-auth-oauthlib 0.4.6 pyhd8ed1ab_0 conda-forge
google-pasta 0.2.0 pyh8c360ce_0 conda-forge
graphite2 1.3.14 h38d11af_0
grpc-cpp 1.37.1 h69eed7d_3 conda-forge
grpcio 1.37.1 py39hb974310_0 conda-forge
h5py 2.10.0 nompi_py39h1bb8402_106 conda-forge
harfbuzz 2.9.1 h159f659_1 conda-forge
hdf5 1.10.6 nompi_hc5d9132_1114 conda-forge
hdmf 2.2.0 pyh9f0ad1d_0 conda-forge
holoviews 1.14.8 pyhd8ed1ab_0 conda-forge
icu 68.2 he49afe7_0 conda-forge
idna 3.3 pyhd8ed1ab_0 conda-forge
imagecodecs 2022.2.22 py39ha3729fb_1 conda-forge
imageio 2.16.1 pyhcf75d05_0 conda-forge
importlib-metadata 4.11.3 py39h6e9494a_1 conda-forge
importlib_resources 5.6.0 pyhd8ed1ab_0 conda-forge
ipykernel 6.11.0 py39h71a6800_0 conda-forge
ipyparallel 8.2.0 pyhd8ed1ab_0 conda-forge
ipython 8.2.0 py39h6e9494a_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 7.7.0 pyhd8ed1ab_0 conda-forge
jasper 1.900.1 h636a363_1006 conda-forge
jbig 2.1 h0d85af4_2003 conda-forge
jedi 0.18.1 py39h6e9494a_0 conda-forge
jinja2 3.1.1 pyhd8ed1ab_0 conda-forge
joblib 1.1.0 pyhd8ed1ab_0 conda-forge
jpeg 9e h0d85af4_0 conda-forge
jsonschema 4.4.0 pyhd8ed1ab_0 conda-forge
jupyter 1.0.0 py39h6e9494a_7 conda-forge
jupyter_client 7.2.1 pyhd8ed1ab_0 conda-forge
jupyter_console 6.4.3 pyhd8ed1ab_0 conda-forge
jupyter_core 4.9.2 py39h6e9494a_0 conda-forge
jupyterlab_pygments 0.1.2 pyh9f0ad1d_0 conda-forge
jupyterlab_widgets 1.1.0 pyhd8ed1ab_0 conda-forge
jxrlib 1.1 h35c211d_2 conda-forge
keras-preprocessing 1.1.2 pyhd8ed1ab_0 conda-forge
kiwisolver 1.4.2 py39h7248d28_0 conda-forge
krb5 1.19.3 hb49756b_0 conda-forge
lame 3.100 h35c211d_1001 conda-forge
lcms2 2.12 h577c468_0 conda-forge
lerc 3.0 he49afe7_0 conda-forge
libaec 1.0.6 he49afe7_0 conda-forge
libavif 0.9.3 h5eb16cf_1 conda-forge
libblas 3.9.0 13_osx64_openblas conda-forge
libbrotlicommon 1.0.9 h0d85af4_6 conda-forge
libbrotlidec 1.0.9 h0d85af4_6 conda-forge
libbrotlienc 1.0.9 h0d85af4_6 conda-forge
libcblas 3.9.0 13_osx64_openblas conda-forge
libclang 11.1.0 default_he082bbe_1 conda-forge
libcurl 7.82.0 h9f20792_0 conda-forge
libcxx 13.0.1 hc203e6f_0 conda-forge
libdeflate 1.10 h0d85af4_0 conda-forge
libedit 3.1.20210910 hca72f7f_0
libev 4.33 haf1e3a3_1 conda-forge
libffi 3.4.2 h0d85af4_5 conda-forge
libgfortran 5.0.0 9_3_0_h6c81a4c_23 conda-forge
libgfortran5 9.3.0 h6c81a4c_23 conda-forge
libglib 2.70.2 hf1fb8c0_4 conda-forge
libiconv 1.16 haf1e3a3_0 conda-forge
libidn2 2.3.2 h0d85af4_0 conda-forge
liblapack 3.9.0 13_osx64_openblas conda-forge
liblapacke 3.9.0 13_osx64_openblas conda-forge
libllvm11 11.1.0 hd011deb_3 conda-forge
libnghttp2 1.47.0 h942079c_0 conda-forge
libopenblas 0.3.18 openmp_h3351f45_0 conda-forge
libopencv 4.5.2 py39h49f8dfa_0 conda-forge
libpng 1.6.37 h7cec526_2 conda-forge
libpq 13.5 hea3049e_1 conda-forge
libprotobuf 3.15.8 hcf210ce_1 conda-forge
libsodium 1.0.18 hbcb3906_1 conda-forge
libssh2 1.10.0 h52ee1ee_2 conda-forge
libtasn1 4.18.0 h0d85af4_0 conda-forge
libtiff 4.3.0 h17f2ce3_3 conda-forge
libunistring 0.9.10 h0d85af4_0 conda-forge
libwebp 1.2.2 h28dabe5_0 conda-forge
libwebp-base 1.2.2 h0d85af4_1 conda-forge
libxcb 1.13 h0d85af4_1004 conda-forge
libxml2 2.9.12 h93ec3fd_0 conda-forge
libzlib 1.2.11 h6c3fc93_1014 conda-forge
libzopfli 1.0.3 h046ec9c_0 conda-forge
llvm-openmp 13.0.1 hcb1a161_1 conda-forge
locket 0.2.1 py39hecd8cb5_2
lz4-c 1.9.3 he49afe7_1 conda-forge
markdown 3.3.6 pyhd8ed1ab_0 conda-forge
markupsafe 2.1.1 py39h63b48b0_1 conda-forge
matplotlib 3.5.1 py39h6e9494a_0 conda-forge
matplotlib-base 3.5.1 py39hb07454d_0 conda-forge
matplotlib-inline 0.1.3 pyhd8ed1ab_0 conda-forge
mistune 0.8.4 py39h89e85a6_1005 conda-forge
multidict 6.0.2 py39h89e85a6_0 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
mypy 0.942 py39h63b48b0_0 conda-forge
mypy_extensions 0.4.3 py39h6e9494a_4 conda-forge
mysql-common 8.0.28 hab7e275_2 conda-forge
mysql-libs 8.0.28 h2a44bf5_2 conda-forge
nbclient 0.5.13 pyhd8ed1ab_0 conda-forge
nbconvert 6.4.5 py39h6e9494a_0 conda-forge
nbformat 5.2.0 pyhd8ed1ab_0 conda-forge
ncurses 6.3 he49afe7_0 conda-forge
nest-asyncio 1.5.4 pyhd8ed1ab_0 conda-forge
nettle 3.7.3 h230ac6f_1
networkx 2.7.1 pyhd8ed1ab_1 conda-forge
nose 1.3.7 py_1006 conda-forge
notebook 6.4.10 pyha770c72_0 conda-forge
nspr 4.33 he9d5cce_0
nss 3.76 hfce436b_0 conda-forge
numpy 1.22.3 py39hf56e92f_0 conda-forge
oauthlib 3.2.0 pyhd8ed1ab_0 conda-forge
opencv 4.5.2 py39h6e9494a_0 conda-forge
openh264 2.1.1 hfd3ada9_0 conda-forge
openjpeg 2.4.0 h6e7aa92_1 conda-forge
openssl 1.1.1n h6c3fc93_0 conda-forge
opt_einsum 3.3.0 pyhd8ed1ab_1 conda-forge
packaging 21.3 pyhd8ed1ab_0 conda-forge
pandas 1.4.1 py39h4d6be9b_0 conda-forge
pandoc 2.17.1.1 h694c41f_0 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
panel 0.12.6 pyhd8ed1ab_0 conda-forge
param 1.12.0 pyh6c4a22f_0 conda-forge
parso 0.8.3 pyhd8ed1ab_0 conda-forge
partd 1.2.0 pyhd8ed1ab_0 conda-forge
pcre 8.45 he49afe7_0 conda-forge
peakutils 1.3.3 py_0 conda-forge
pexpect 4.8.0 pyh9f0ad1d_2 conda-forge
pickleshare 0.7.5 py39hde42818_1002 conda-forge
pillow 9.0.1 py39hd2c7aa1_2 conda-forge
pims 0.5 pyh9f0ad1d_1 conda-forge
pip 22.0.4 pyhd8ed1ab_0 conda-forge
pixman 0.40.0 hbcb3906_0 conda-forge
prometheus_client 0.13.1 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.27 pyha770c72_0 conda-forge
prompt_toolkit 3.0.27 hd8ed1ab_0 conda-forge
protobuf 3.15.8 py39h9fcab8e_0 conda-forge
psutil 5.9.0 py39h89e85a6_0 conda-forge
pthread-stubs 0.4 hc929b4f_1001 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge
py-opencv 4.5.2 py39h71a6800_0 conda-forge
pyasn1 0.4.8 py_0 conda-forge
pyasn1-modules 0.2.8 py_0
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pyct 0.4.6 py_0 conda-forge
pyct-core 0.4.6 py_0 conda-forge
pygments 2.11.2 pyhd8ed1ab_0 conda-forge
pyjwt 2.3.0 pyhd8ed1ab_1 conda-forge
pynwb 1.4.0 py39h6e9494a_1 conda-forge
pyopenssl 22.0.0 pyhd8ed1ab_0 conda-forge
pyparsing 3.0.7 pyhd8ed1ab_0 conda-forge
pyqt 5.12.3 py39h6e9494a_8 conda-forge
pyqt-impl 5.12.3 py39he44290a_8 conda-forge
pyqt5-sip 4.19.18 py39h15fb055_8 conda-forge
pyqtchart 5.12 py39he44290a_8 conda-forge
pyqtgraph 0.12.4 pyhd8ed1ab_0 conda-forge
pyqtwebengine 5.12.1 py39he44290a_8 conda-forge
pyrsistent 0.18.1 py39h89e85a6_0 conda-forge
pysocks 1.7.1 py39h6e9494a_4 conda-forge
python 3.9.12 h8b4d769_1_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-flatbuffers 1.12 pyhd8ed1ab_1 conda-forge
python_abi 3.9 2_cp39 conda-forge
pytz 2022.1 pyhd8ed1ab_0 conda-forge
pyu2f 0.1.5 pyhd8ed1ab_0 conda-forge
pyviz_comms 2.2.0 pyhd8ed1ab_0 conda-forge
pywavelets 1.3.0 py39h86b5767_0 conda-forge
pyyaml 6.0 py39h89e85a6_3 conda-forge
pyzmq 22.3.0 py39h7fec2f1_1 conda-forge
qt 5.12.9 h126340a_4 conda-forge
qtconsole 5.3.0 pyhd8ed1ab_0 conda-forge
qtconsole-base 5.3.0 pyhd8ed1ab_0 conda-forge
qtpy 2.0.1 pyhd8ed1ab_0 conda-forge
re2 2021.08.01 he49afe7_0 conda-forge
readline 8.1.2 hca72f7f_1
requests 2.27.1 pyhd8ed1ab_0 conda-forge
requests-oauthlib 1.3.1 pyhd8ed1ab_0 conda-forge
rsa 4.8 pyhd8ed1ab_0 conda-forge
ruamel.yaml 0.17.21 py39h89e85a6_0 conda-forge
ruamel.yaml.clib 0.2.6 py39h89e85a6_0 conda-forge
scikit-image 0.19.2 py39h4d6be9b_0 conda-forge
scikit-learn 1.0.2 py39hd4eea88_0 conda-forge
scipy 1.8.0 py39h056f1c0_1 conda-forge
send2trash 1.8.0 pyhd8ed1ab_0 conda-forge
setuptools 61.2.0 py39h6e9494a_3 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
slicerator 1.0.0 py_0 conda-forge
snappy 1.1.8 hb1e8313_3 conda-forge
soupsieve 2.3.1 pyhd8ed1ab_0 conda-forge
sqlite 3.38.2 h707629a_0
stack_data 0.2.0 pyhd8ed1ab_0 conda-forge
tensorboard 2.4.1 pyhd8ed1ab_1 conda-forge
tensorboard-plugin-wit 1.8.1 pyhd8ed1ab_0 conda-forge
tensorflow 2.4.1 py39h6e9494a_0 conda-forge
tensorflow-base 2.4.1 py39h9e0eb93_0 conda-forge
tensorflow-estimator 2.4.1 pyheb71bc4_0
termcolor 1.1.0 py_2 conda-forge
terminado 0.13.3 py39h6e9494a_0 conda-forge
testpath 0.6.0 pyhd8ed1ab_0 conda-forge
threadpoolctl 3.1.0 pyh8a188c0_0 conda-forge
tifffile 2022.3.25 pyhd8ed1ab_0 conda-forge
tk 8.6.12 h5dbffcc_0 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
toolz 0.11.2 pyhd8ed1ab_0 conda-forge
tornado 6.1 py39h89e85a6_2 conda-forge
tqdm 4.63.1 pyhd8ed1ab_0 conda-forge
traitlets 5.1.1 pyhd8ed1ab_0 conda-forge
typing-extensions 4.1.1 hd8ed1ab_0 conda-forge
typing_extensions 4.1.1 pyha770c72_0 conda-forge
tzdata 2022a h191b570_0 conda-forge
unicodedata2 14.0.0 py39h89e85a6_0 conda-forge
urllib3 1.26.9 pyhd8ed1ab_0 conda-forge
wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge
webencodings 0.5.1 py_1 conda-forge
werkzeug 2.0.3 pyhd8ed1ab_1 conda-forge
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
widgetsnbextension 3.6.0 py39h6e9494a_0 conda-forge
wrapt 1.14.0 py39h63b48b0_0 conda-forge
x264 1!161.3030 h0d85af4_1 conda-forge
xorg-libxau 1.0.9 h35c211d_0 conda-forge
xorg-libxdmcp 1.1.3 h35c211d_0 conda-forge
xz 5.2.5 haf1e3a3_1 conda-forge
yaml 0.2.5 h0d85af4_2 conda-forge
yarl 1.7.2 py39h89e85a6_1 conda-forge
z5py 2.0.15 py39h74502c3_0 conda-forge
zeromq 4.3.4 he49afe7_1 conda-forge
zfp 0.5.5 h4a89273_8 conda-forge
zipp 3.7.0 pyhd8ed1ab_1 conda-forge
zlib 1.2.11 h6c3fc93_1014 conda-forge
zstd 1.5.2 h582d3a0_0 conda-forge
>>> import caiman
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Users/bendichter/opt/miniconda3/envs/caiman/lib/python3.9/site-packages/caiman/__init__.py", line 4, in <module>
from .base.movies import movie, load, load_movie_chain
File "/Users/bendichter/opt/miniconda3/envs/caiman/lib/python3.9/site-packages/caiman/base/movies.py", line 57, in <module>
from ..utils import visualization
File "/Users/bendichter/opt/miniconda3/envs/caiman/lib/python3.9/site-packages/caiman/utils/visualization.py", line 33, in <module>
import holoviews as hv
File "/Users/bendichter/opt/miniconda3/envs/caiman/lib/python3.9/site-packages/holoviews/__init__.py", line 12, in <module>
from .annotators import annotate # noqa (API import)
File "/Users/bendichter/opt/miniconda3/envs/caiman/lib/python3.9/site-packages/holoviews/annotators.py", line 10, in <module>
from panel.pane import PaneBase
File "/Users/bendichter/opt/miniconda3/envs/caiman/lib/python3.9/site-packages/panel/__init__.py", line 1, in <module>
from . import layout # noqa
File "/Users/bendichter/opt/miniconda3/envs/caiman/lib/python3.9/site-packages/panel/layout/__init__.py", line 1, in <module>
from .accordion import Accordion # noqa
File "/Users/bendichter/opt/miniconda3/envs/caiman/lib/python3.9/site-packages/panel/layout/accordion.py", line 5, in <module>
from .base import NamedListPanel
File "/Users/bendichter/opt/miniconda3/envs/caiman/lib/python3.9/site-packages/panel/layout/base.py", line 11, in <module>
from ..io.model import hold
File "/Users/bendichter/opt/miniconda3/envs/caiman/lib/python3.9/site-packages/panel/io/__init__.py", line 9, in <module>
from ..config import config
File "/Users/bendichter/opt/miniconda3/envs/caiman/lib/python3.9/site-packages/panel/config.py", line 21, in <module>
from .io.notebook import load_notebook
File "/Users/bendichter/opt/miniconda3/envs/caiman/lib/python3.9/site-packages/panel/io/notebook.py", line 39, in <module>
from .resources import Bundle, Resources, _env, bundle_resources
File "/Users/bendichter/opt/miniconda3/envs/caiman/lib/python3.9/site-packages/panel/io/resources.py", line 24, in <module>
from jinja2 import Environment, Markup, FileSystemLoader
ImportError: cannot import name 'Markup' from 'jinja2' (/Users/bendichter/opt/miniconda3/envs/caiman/lib/python3.9/site-packages/jinja2/__init__.py)
Looks like 0.12.7 just made it onto conda-forge and a fresh-made environment gets me that.
@pgunn really? Because that's not what I am getting:
(base) MacBook-Pro-3:~ bendichter$ mamba create -n caiman -c conda-forge caiman
__ __ __ __
/ \ / \ / \ / \
/ \/ \/ \/ \
███████████████/ /██/ /██/ /██/ /████████████████████████
/ / \ / \ / \ / \ \____
/ / \_/ \_/ \_/ \ o \__,
/ _/ \_____/ `
|/
███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗
████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
██╔████╔██║███████║██╔████╔██║██████╔╝███████║
██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
mamba (0.15.3) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
Looking for: ['caiman']
pkgs/main/osx-64 [====================] (00m:00s) No change
pkgs/main/noarch [====================] (00m:00s) No change
pkgs/r/noarch [====================] (00m:00s) No change
conda-forge/osx-64 [====================] (00m:00s) No change
conda-forge/noarch [====================] (00m:00s) No change
pkgs/r/osx-64 [====================] (00m:00s) No change
Transaction
Prefix: /Users/bendichter/opt/miniconda3/envs/caiman
Updating specs:
- caiman
Package Version Build Channel Size
────────────────────────────────────────────────────────────────────────────────────────────────────────
Install:
────────────────────────────────────────────────────────────────────────────────────────────────────────
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+ pyrsistent 0.18.1 py39h89e85a6_0 conda-forge/osx-64 Cached
+ pysocks 1.7.1 py39h6e9494a_4 conda-forge/osx-64 Cached
+ python 3.9.12 h8b4d769_1_cpython conda-forge/osx-64 Cached
+ python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge/noarch Cached
+ python-flatbuffers 1.12 pyhd8ed1ab_1 conda-forge/noarch Cached
+ python_abi 3.9 2_cp39 conda-forge/osx-64 Cached
+ pytz 2022.1 pyhd8ed1ab_0 conda-forge/noarch Cached
+ pyu2f 0.1.5 pyhd8ed1ab_0 conda-forge/noarch Cached
+ pyviz_comms 2.2.0 pyhd8ed1ab_0 conda-forge/noarch Cached
+ pywavelets 1.3.0 py39h86b5767_0 conda-forge/osx-64 Cached
+ pyyaml 6.0 py39h89e85a6_3 conda-forge/osx-64 Cached
+ pyzmq 22.3.0 py39h7fec2f1_1 conda-forge/osx-64 Cached
+ qt 5.12.9 h126340a_4 conda-forge/osx-64 Cached
+ qtconsole 5.3.0 pyhd8ed1ab_0 conda-forge/noarch Cached
+ qtconsole-base 5.3.0 pyhd8ed1ab_0 conda-forge/noarch Cached
+ qtpy 2.0.1 pyhd8ed1ab_0 conda-forge/noarch Cached
+ re2 2021.08.01 he49afe7_0 conda-forge/osx-64 Cached
+ readline 8.1.2 hca72f7f_1 pkgs/main/osx-64 Cached
+ requests 2.27.1 pyhd8ed1ab_0 conda-forge/noarch Cached
+ requests-oauthlib 1.3.1 pyhd8ed1ab_0 conda-forge/noarch Cached
+ rsa 4.8 pyhd8ed1ab_0 conda-forge/noarch Cached
+ ruamel.yaml 0.17.21 py39h89e85a6_0 conda-forge/osx-64 Cached
+ ruamel.yaml.clib 0.2.6 py39h89e85a6_0 conda-forge/osx-64 Cached
+ scikit-image 0.19.2 py39h4d6be9b_0 conda-forge/osx-64 Cached
+ scikit-learn 1.0.2 py39hd4eea88_0 conda-forge/osx-64 Cached
+ scipy 1.8.0 py39h056f1c0_1 conda-forge/osx-64 Cached
+ send2trash 1.8.0 pyhd8ed1ab_0 conda-forge/noarch Cached
+ setuptools 61.2.0 py39h6e9494a_3 conda-forge/osx-64 Cached
+ six 1.16.0 pyh6c4a22f_0 conda-forge/noarch Cached
+ slicerator 1.0.0 py_0 conda-forge/noarch Cached
+ snappy 1.1.8 hb1e8313_3 conda-forge/osx-64 Cached
+ soupsieve 2.3.1 pyhd8ed1ab_0 conda-forge/noarch Cached
+ sqlite 3.38.2 h707629a_0 pkgs/main/osx-64 Cached
+ stack_data 0.2.0 pyhd8ed1ab_0 conda-forge/noarch Cached
+ tensorboard 2.4.1 pyhd8ed1ab_1 conda-forge/noarch Cached
+ tensorboard-plugin-wit 1.8.1 pyhd8ed1ab_0 conda-forge/noarch Cached
+ tensorflow 2.4.1 py39h6e9494a_0 conda-forge/osx-64 Cached
+ tensorflow-base 2.4.1 py39h9e0eb93_0 conda-forge/osx-64 Cached
+ tensorflow-estimator 2.4.1 pyheb71bc4_0 pkgs/main/noarch Cached
+ termcolor 1.1.0 py_2 conda-forge/noarch Cached
+ terminado 0.13.3 py39h6e9494a_0 conda-forge/osx-64 Cached
+ testpath 0.6.0 pyhd8ed1ab_0 conda-forge/noarch Cached
+ threadpoolctl 3.1.0 pyh8a188c0_0 conda-forge/noarch Cached
+ tifffile 2022.3.25 pyhd8ed1ab_0 conda-forge/noarch Cached
+ tk 8.6.12 h5dbffcc_0 conda-forge/osx-64 Cached
+ tomli 2.0.1 pyhd8ed1ab_0 conda-forge/noarch Cached
+ toolz 0.11.2 pyhd8ed1ab_0 conda-forge/noarch Cached
+ tornado 6.1 py39h89e85a6_2 conda-forge/osx-64 Cached
+ tqdm 4.63.1 pyhd8ed1ab_0 conda-forge/noarch Cached
+ traitlets 5.1.1 pyhd8ed1ab_0 conda-forge/noarch Cached
+ typing-extensions 4.1.1 hd8ed1ab_0 conda-forge/noarch Cached
+ typing_extensions 4.1.1 pyha770c72_0 conda-forge/noarch Cached
+ tzdata 2022a h191b570_0 conda-forge/noarch Cached
+ unicodedata2 14.0.0 py39h89e85a6_0 conda-forge/osx-64 Cached
+ urllib3 1.26.9 pyhd8ed1ab_0 conda-forge/noarch Cached
+ wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge/noarch Cached
+ webencodings 0.5.1 py_1 conda-forge/noarch Cached
+ werkzeug 2.0.3 pyhd8ed1ab_1 conda-forge/noarch Cached
+ wheel 0.37.1 pyhd8ed1ab_0 conda-forge/noarch Cached
+ widgetsnbextension 3.6.0 py39h6e9494a_0 conda-forge/osx-64 Cached
+ wrapt 1.14.0 py39h63b48b0_0 conda-forge/osx-64 Cached
+ x264 1!161.3030 h0d85af4_1 conda-forge/osx-64 Cached
+ xorg-libxau 1.0.9 h35c211d_0 conda-forge/osx-64 Cached
+ xorg-libxdmcp 1.1.3 h35c211d_0 conda-forge/osx-64 Cached
+ xz 5.2.5 haf1e3a3_1 conda-forge/osx-64 Cached
+ yaml 0.2.5 h0d85af4_2 conda-forge/osx-64 Cached
+ yarl 1.7.2 py39h89e85a6_1 conda-forge/osx-64 Cached
+ z5py 2.0.15 py39h74502c3_0 conda-forge/osx-64 Cached
+ zeromq 4.3.4 he49afe7_1 conda-forge/osx-64 Cached
+ zfp 0.5.5 h4a89273_8 conda-forge/osx-64 Cached
+ zipp 3.7.0 pyhd8ed1ab_1 conda-forge/noarch Cached
+ zlib 1.2.11 h6c3fc93_1014 conda-forge/osx-64 Cached
+ zstd 1.5.2 h582d3a0_0 conda-forge/osx-64 Cached
Summary:
Install: 294 packages
Total download: 0 B
────────────────────────────────────────────────────────────────────────────────────────────────────────
Confirm changes: [Y/n]
I wonder if this is an OS thing (seems a little unlikely) or if mamba is caching things it shouldn't.
0.12.7 is definitely on the server, and I definitely got it when I just built an environment. https://anaconda.org/conda-forge/panel/files
I wonder if mamba clean --all would clear a package/repo cache and get you the newer version. Can you try that?
I could do that, but it would only impact the environment.yml install route; I'd need to cut a new release to get people doing a pure package install covered (and it'd still mean not understanding whatever's causing this behaviour).
I assume that conda search -c conda-forge panel
Shows 0.12.7 for you?
I'm asking the conda-forge people if they have any ideas what's going on.
It's possible that just doing that search would force the repo index to update and change the package resolution.
