$ conda create -n pangraphviewer python=3.10
Channels:
- conda-forge
- bioconda
- defaults
Platform: osx-64
Collecting package metadata (repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /Users/waterhop/miniconda3/envs/pangraphviewer
added / updated specs:
- python=3.10
The following packages will be downloaded:
package | build
---------------------------|-----------------
bzip2-1.0.8 | hfdf4475_7 131 KB conda-forge
ca-certificates-2024.7.4 | h8857fd0_0 151 KB conda-forge
libffi-3.4.2 | h0d85af4_5 50 KB conda-forge
libsqlite-3.46.0 | h1b8f9f3_0 887 KB conda-forge
libzlib-1.3.1 | h87427d6_1 56 KB conda-forge
ncurses-6.5 | h5846eda_0 804 KB conda-forge
openssl-3.3.1 | h87427d6_2 2.4 MB conda-forge
pip-24.2 | pyhd8ed1ab_0 1.2 MB conda-forge
python-3.10.14 |h00d2728_0_cpython 11.3 MB conda-forge
readline-8.2 | h9e318b2_1 250 KB conda-forge
setuptools-72.1.0 | pyhd8ed1ab_0 1.4 MB conda-forge
tk-8.6.13 | h1abcd95_1 3.1 MB conda-forge
tzdata-2024a | h0c530f3_0 117 KB conda-forge
wheel-0.44.0 | pyhd8ed1ab_0 57 KB conda-forge
xz-5.2.6 | h775f41a_0 233 KB conda-forge
------------------------------------------------------------
Total: 22.1 MB
The following NEW packages will be INSTALLED:
bzip2 conda-forge/osx-64::bzip2-1.0.8-hfdf4475_7
ca-certificates conda-forge/osx-64::ca-certificates-2024.7.4-h8857fd0_0
libffi conda-forge/osx-64::libffi-3.4.2-h0d85af4_5
libsqlite conda-forge/osx-64::libsqlite-3.46.0-h1b8f9f3_0
libzlib conda-forge/osx-64::libzlib-1.3.1-h87427d6_1
ncurses conda-forge/osx-64::ncurses-6.5-h5846eda_0
openssl conda-forge/osx-64::openssl-3.3.1-h87427d6_2
pip conda-forge/noarch::pip-24.2-pyhd8ed1ab_0
python conda-forge/osx-64::python-3.10.14-h00d2728_0_cpython
readline conda-forge/osx-64::readline-8.2-h9e318b2_1
setuptools conda-forge/noarch::setuptools-72.1.0-pyhd8ed1ab_0
tk conda-forge/osx-64::tk-8.6.13-h1abcd95_1
tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0
wheel conda-forge/noarch::wheel-0.44.0-pyhd8ed1ab_0
xz conda-forge/osx-64::xz-5.2.6-h775f41a_0
Proceed ([y]/n)? y
Downloading and Extracting Packages:
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate pangraphviewer
#
# To deactivate an active environment, use
#
# $ conda deactivate
(base) C02W40N4J1GQ:panGraphViewerWeb waterhop$ conda activate pangraphviewer
(pangraphviewer) C02W40N4J1GQ:panGraphViewerWeb waterhop$ pip install -r requirements.txt
Collecting Django==3.1.3 (from -r requirements.txt (line 1))
Using cached Django-3.1.3-py3-none-any.whl.metadata (3.7 kB)
Collecting django-bootstrap4 (from -r requirements.txt (line 2))
Using cached django_bootstrap4-24.3-py3-none-any.whl.metadata (5.5 kB)
Collecting requests (from -r requirements.txt (line 3))
Downloading requests-2.32.3-py3-none-any.whl.metadata (4.6 kB)
Collecting django-environ (from -r requirements.txt (line 4))
Using cached django_environ-0.11.2-py2.py3-none-any.whl.metadata (11 kB)
Collecting djangorestframework (from -r requirements.txt (line 5))
Using cached djangorestframework-3.15.2-py3-none-any.whl.metadata (10 kB)
Collecting configparser (from -r requirements.txt (line 6))
Using cached configparser-7.1.0-py3-none-any.whl.metadata (5.4 kB)
Collecting natsort (from -r requirements.txt (line 7))
Using cached natsort-8.4.0-py3-none-any.whl.metadata (21 kB)
Collecting networkx (from -r requirements.txt (line 8))
Using cached networkx-3.3-py3-none-any.whl.metadata (5.1 kB)
Collecting fontawesome-free==5.15 (from -r requirements.txt (line 9))
Using cached fontawesome_free-5.15.0-py3-none-any.whl.metadata (1.6 kB)
Collecting bokeh==2.2.3 (from -r requirements.txt (line 10))
Using cached bokeh-2.2.3.tar.gz (8.8 MB)
Preparing metadata (setup.py) ... done
Collecting dna_features_viewer (from -r requirements.txt (line 11))
Downloading dna_features_viewer-3.1.3-py3-none-any.whl.metadata (2.0 kB)
Collecting pysam (from -r requirements.txt (line 12))
Downloading pysam-0.22.1-cp310-cp310-macosx_10_9_x86_64.whl.metadata (1.5 kB)
Collecting pandas (from -r requirements.txt (line 13))
Downloading pandas-2.2.2-cp310-cp310-macosx_10_9_x86_64.whl.metadata (19 kB)
Collecting whitenoise (from -r requirements.txt (line 14))
Downloading whitenoise-6.7.0-py3-none-any.whl.metadata (3.7 kB)
Collecting jinja2==3.0 (from -r requirements.txt (line 15))
Downloading Jinja2-3.0.0-py3-none-any.whl.metadata (3.5 kB)
Collecting asgiref<4,>=3.2.10 (from Django==3.1.3->-r requirements.txt (line 1))
Downloading asgiref-3.8.1-py3-none-any.whl.metadata (9.3 kB)
Collecting pytz (from Django==3.1.3->-r requirements.txt (line 1))
Downloading pytz-2024.1-py2.py3-none-any.whl.metadata (22 kB)
Collecting sqlparse>=0.2.2 (from Django==3.1.3->-r requirements.txt (line 1))
Downloading sqlparse-0.5.1-py3-none-any.whl.metadata (3.9 kB)
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Collecting numpy>=1.11.3 (from bokeh==2.2.3->-r requirements.txt (line 10))
Downloading numpy-2.1.0-cp310-cp310-macosx_10_9_x86_64.whl.metadata (60 kB)
Collecting pillow>=7.1.0 (from bokeh==2.2.3->-r requirements.txt (line 10))
Downloading pillow-10.4.0-cp310-cp310-macosx_10_10_x86_64.whl.metadata (9.2 kB)
Collecting packaging>=16.8 (from bokeh==2.2.3->-r requirements.txt (line 10))
Downloading packaging-24.1-py3-none-any.whl.metadata (3.2 kB)
Collecting tornado>=5.1 (from bokeh==2.2.3->-r requirements.txt (line 10))
Downloading tornado-6.4.1-cp38-abi3-macosx_10_9_x86_64.whl.metadata (2.5 kB)
Collecting typing_extensions>=3.7.4 (from bokeh==2.2.3->-r requirements.txt (line 10))
Downloading typing_extensions-4.12.2-py3-none-any.whl.metadata (3.0 kB)
Collecting MarkupSafe>=2.0.0rc2 (from jinja2==3.0->-r requirements.txt (line 15))
Downloading MarkupSafe-2.1.5-cp310-cp310-macosx_10_9_x86_64.whl.metadata (3.0 kB)
INFO: pip is looking at multiple versions of django-bootstrap4 to determine which version is compatible with other requirements. This could take a while.
Collecting django-bootstrap4 (from -r requirements.txt (line 2))
Downloading django_bootstrap4-24.2-py3-none-any.whl.metadata (5.5 kB)
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Collecting beautifulsoup4>=4.8.0 (from django-bootstrap4->-r requirements.txt (line 2))
Downloading beautifulsoup4-4.12.3-py3-none-any.whl.metadata (3.8 kB)
Collecting django-bootstrap4 (from -r requirements.txt (line 2))
Downloading django_bootstrap4-23.1-py3-none-any.whl.metadata (3.5 kB)
Downloading django_bootstrap4-22.3-py3-none-any.whl.metadata (3.4 kB)
INFO: pip is still looking at multiple versions of django-bootstrap4 to determine which version is compatible with other requirements. This could take a while.
Downloading django_bootstrap4-22.2-py3-none-any.whl.metadata (3.4 kB)
Downloading django_bootstrap4-22.1-py3-none-any.whl.metadata (3.5 kB)
Collecting charset-normalizer<4,>=2 (from requests->-r requirements.txt (line 3))
Downloading charset_normalizer-3.3.2-cp310-cp310-macosx_10_9_x86_64.whl.metadata (33 kB)
Collecting idna<4,>=2.5 (from requests->-r requirements.txt (line 3))
Downloading idna-3.7-py3-none-any.whl.metadata (9.9 kB)
Collecting urllib3<3,>=1.21.1 (from requests->-r requirements.txt (line 3))
Downloading urllib3-2.2.2-py3-none-any.whl.metadata (6.4 kB)
Collecting certifi>=2017.4.17 (from requests->-r requirements.txt (line 3))
Downloading certifi-2024.7.4-py3-none-any.whl.metadata (2.2 kB)
INFO: pip is looking at multiple versions of djangorestframework to determine which version is compatible with other requirements. This could take a while.
Collecting djangorestframework (from -r requirements.txt (line 5))
Downloading djangorestframework-3.15.1-py3-none-any.whl.metadata (11 kB)
Collecting matplotlib>=3 (from dna_features_viewer->-r requirements.txt (line 11))
Downloading matplotlib-3.9.2-cp310-cp310-macosx_10_12_x86_64.whl.metadata (11 kB)
Collecting Biopython (from dna_features_viewer->-r requirements.txt (line 11))
Downloading biopython-1.84-cp310-cp310-macosx_10_9_x86_64.whl.metadata (12 kB)
Collecting tzdata>=2022.7 (from pandas->-r requirements.txt (line 13))
Downloading tzdata-2024.1-py2.py3-none-any.whl.metadata (1.4 kB)
Collecting soupsieve>1.2 (from beautifulsoup4>=4.8.0->django-bootstrap4->-r requirements.txt (line 2))
Downloading soupsieve-2.6-py3-none-any.whl.metadata (4.6 kB)
Collecting contourpy>=1.0.1 (from matplotlib>=3->dna_features_viewer->-r requirements.txt (line 11))
Downloading contourpy-1.2.1-cp310-cp310-macosx_10_9_x86_64.whl.metadata (5.8 kB)
Collecting cycler>=0.10 (from matplotlib>=3->dna_features_viewer->-r requirements.txt (line 11))
Downloading cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB)
Collecting fonttools>=4.22.0 (from matplotlib>=3->dna_features_viewer->-r requirements.txt (line 11))
Downloading fonttools-4.53.1-cp310-cp310-macosx_10_9_universal2.whl.metadata (162 kB)
Collecting kiwisolver>=1.3.1 (from matplotlib>=3->dna_features_viewer->-r requirements.txt (line 11))
Downloading kiwisolver-1.4.5-cp310-cp310-macosx_10_9_x86_64.whl.metadata (6.4 kB)
Collecting pyparsing>=2.3.1 (from matplotlib>=3->dna_features_viewer->-r requirements.txt (line 11))
Downloading pyparsing-3.1.2-py3-none-any.whl.metadata (5.1 kB)
Collecting six>=1.5 (from python-dateutil>=2.1->bokeh==2.2.3->-r requirements.txt (line 10))
Downloading six-1.16.0-py2.py3-none-any.whl.metadata (1.8 kB)
WARNING: The candidate selected for download or install is a yanked version: 'fontawesome-free' candidate (version 5.15.0 at https://files.pythonhosted.org/packages/6f/3a/98383624239a75c57f37c8846e627e32848b67c50da18b5b6c5a3c02131b/fontawesome_free-5.15.0-py3-none-any.whl (from https://pypi.org/simple/fontawesome-free/))
Reason for being yanked: <none given>
Downloading Django-3.1.3-py3-none-any.whl (7.8 MB)
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Downloading whitenoise-6.7.0-py3-none-any.whl (19 kB)
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Building wheels for collected packages: bokeh
Building wheel for bokeh (setup.py) ... done
Created wheel for bokeh: filename=bokeh-2.2.3-py3-none-any.whl size=9296296 sha256=6a3242376e0f5a6ded69088d7a751ff515302a2ce42cc0f2e1ac521aac5e9d87
Stored in directory: /Users/waterhop/Library/Caches/pip/wheels/86/f1/67/388682ddb04b452e8d906d18765d5732dff873c5f63717e96a
Successfully built bokeh
Installing collected packages: pytz, fontawesome-free, whitenoise, urllib3, tzdata, typing_extensions, tornado, sqlparse, soupsieve, six, PyYAML, pysam, pyparsing, pillow, packaging, numpy, networkx, natsort, MarkupSafe, kiwisolver, idna, fonttools, django-environ, cycler, configparser, charset-normalizer, certifi, requests, python-dateutil, jinja2, contourpy, Biopython, beautifulsoup4, asgiref, pandas, matplotlib, Django, bokeh, dna_features_viewer, djangorestframework, django-bootstrap4
Successfully installed Biopython-1.84 Django-3.1.3 MarkupSafe-2.1.5 PyYAML-6.0.2 asgiref-3.8.1 beautifulsoup4-4.12.3 bokeh-2.2.3 certifi-2024.7.4 charset-normalizer-3.3.2 configparser-7.1.0 contourpy-1.2.1 cycler-0.12.1 django-bootstrap4-22.1 django-environ-0.11.2 djangorestframework-3.15.1 dna_features_viewer-3.1.3 fontawesome-free-5.15.0 fonttools-4.53.1 idna-3.7 jinja2-3.0.0 kiwisolver-1.4.5 matplotlib-3.9.2 natsort-8.4.0 networkx-3.3 numpy-2.1.0 packaging-24.1 pandas-2.2.2 pillow-10.4.0 pyparsing-3.1.2 pysam-0.22.1 python-dateutil-2.9.0.post0 pytz-2024.1 requests-2.32.3 six-1.16.0 soupsieve-2.6 sqlparse-0.5.1 tornado-6.4.1 typing_extensions-4.12.2 tzdata-2024.1 urllib3-2.2.2 whitenoise-6.7.0
(pangraphviewer) C02W40N4J1GQ:panGraphViewerWeb waterhop$ ./run.sh
Starting server ....
Performing system checks...
Exception in thread django-main-thread:
Traceback (most recent call last):
File "/Users/waterhop/miniconda3/envs/pangraphviewer/lib/python3.10/threading.py", line 1016, in _bootstrap_inner
self.run()
File "/Users/waterhop/miniconda3/envs/pangraphviewer/lib/python3.10/threading.py", line 953, in run
self._target(*self._args, **self._kwargs)
File "/Users/waterhop/miniconda3/envs/pangraphviewer/lib/python3.10/site-packages/django/utils/autoreload.py", line 53, in wrapper
fn(*args, **kwargs)
File "/Users/waterhop/miniconda3/envs/pangraphviewer/lib/python3.10/site-packages/django/core/management/commands/runserver.py", line 118, in inner_run
self.check(display_num_errors=True)
File "/Users/waterhop/miniconda3/envs/pangraphviewer/lib/python3.10/site-packages/django/core/management/base.py", line 392, in check
all_issues = checks.run_checks(
File "/Users/waterhop/miniconda3/envs/pangraphviewer/lib/python3.10/site-packages/django/core/checks/registry.py", line 70, in run_checks
new_errors = check(app_configs=app_configs, databases=databases)
File "/Users/waterhop/miniconda3/envs/pangraphviewer/lib/python3.10/site-packages/django/core/checks/urls.py", line 13, in check_url_config
return check_resolver(resolver)
File "/Users/waterhop/miniconda3/envs/pangraphviewer/lib/python3.10/site-packages/django/core/checks/urls.py", line 23, in check_resolver
return check_method()
File "/Users/waterhop/miniconda3/envs/pangraphviewer/lib/python3.10/site-packages/django/urls/resolvers.py", line 408, in check
for pattern in self.url_patterns:
File "/Users/waterhop/miniconda3/envs/pangraphviewer/lib/python3.10/site-packages/django/utils/functional.py", line 48, in __get__
res = instance.__dict__[self.name] = self.func(instance)
File "/Users/waterhop/miniconda3/envs/pangraphviewer/lib/python3.10/site-packages/django/urls/resolvers.py", line 589, in url_patterns
patterns = getattr(self.urlconf_module, "urlpatterns", self.urlconf_module)
File "/Users/waterhop/miniconda3/envs/pangraphviewer/lib/python3.10/site-packages/django/utils/functional.py", line 48, in __get__
res = instance.__dict__[self.name] = self.func(instance)
File "/Users/waterhop/miniconda3/envs/pangraphviewer/lib/python3.10/site-packages/django/urls/resolvers.py", line 582, in urlconf_module
return import_module(self.urlconf_name)
File "/Users/waterhop/miniconda3/envs/pangraphviewer/lib/python3.10/importlib/__init__.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1050, in _gcd_import
File "<frozen importlib._bootstrap>", line 1027, in _find_and_load
File "<frozen importlib._bootstrap>", line 1006, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 688, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 883, in exec_module
File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
File "/Users/waterhop/Downloads/panGraphViewer/panGraphViewerWeb/pangraph/urls.py", line 22, in <module>
re_path(r'^', include('pangraphviewer.urls')),
File "/Users/waterhop/miniconda3/envs/pangraphviewer/lib/python3.10/site-packages/django/urls/conf.py", line 34, in include
urlconf_module = import_module(urlconf_module)
File "/Users/waterhop/miniconda3/envs/pangraphviewer/lib/python3.10/importlib/__init__.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1050, in _gcd_import
File "<frozen importlib._bootstrap>", line 1027, in _find_and_load
File "<frozen importlib._bootstrap>", line 1006, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 688, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 883, in exec_module
File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
File "/Users/waterhop/Downloads/panGraphViewer/panGraphViewerWeb/pangraphviewer/urls.py", line 3, in <module>
from . import views
File "/Users/waterhop/Downloads/panGraphViewer/panGraphViewerWeb/pangraphviewer/views.py", line 15, in <module>
from pangraphviewer.panGraphWeb import *
File "/Users/waterhop/Downloads/panGraphViewer/panGraphViewerWeb/pangraphviewer/panGraphWeb.py", line 1, in <module>
from pangraphviewer.panGraph import *
File "/Users/waterhop/Downloads/panGraphViewer/panGraphViewerWeb/pangraphviewer/panGraph.py", line 17, in <module>
from bokeh.embed import file_html
File "/Users/waterhop/miniconda3/envs/pangraphviewer/lib/python3.10/site-packages/bokeh/embed/__init__.py", line 23, in <module>
from .server import server_document, server_session
File "/Users/waterhop/miniconda3/envs/pangraphviewer/lib/python3.10/site-packages/bokeh/embed/server.py", line 26, in <module>
from ..resources import DEFAULT_SERVER_HTTP_URL
File "/Users/waterhop/miniconda3/envs/pangraphviewer/lib/python3.10/site-packages/bokeh/resources.py", line 43, in <module>
from .model import Model
File "/Users/waterhop/miniconda3/envs/pangraphviewer/lib/python3.10/site-packages/bokeh/model.py", line 30, in <module>
from .core.properties import Any, Dict, Instance, List, String
File "/Users/waterhop/miniconda3/envs/pangraphviewer/lib/python3.10/site-packages/bokeh/core/properties.py", line 254, in <module>
from .property.auto import Auto; Auto
File "/Users/waterhop/miniconda3/envs/pangraphviewer/lib/python3.10/site-packages/bokeh/core/property/auto.py", line 22, in <module>
from .enum import Enum
File "/Users/waterhop/miniconda3/envs/pangraphviewer/lib/python3.10/site-packages/bokeh/core/property/enum.py", line 24, in <module>
from .primitive import String
File "/Users/waterhop/miniconda3/envs/pangraphviewer/lib/python3.10/site-packages/bokeh/core/property/primitive.py", line 34, in <module>
bokeh_bool_types += (np.bool8,)
File "/Users/waterhop/miniconda3/envs/pangraphviewer/lib/python3.10/site-packages/numpy/__init__.py", line 414, in __getattr__
raise AttributeError("module {!r} has no attribute "
AttributeError: module 'numpy' has no attribute 'bool8'. Did you mean: 'bool'?
Hi,
I got
AttributeError: module 'numpy' has no attribute 'bool8'. Did you mean: 'bool'?when trying to run it on MacOS:What did I miss?