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Published 20 hours ago • verified publisher icon vitessce

`ContextualVersionConflict` when following getting started instructions ... but works on retry?

Open mccalluc opened this issue 4 years ago • 5 comments

I've followed the README instructions up to here:

git clone https://github.com/vitessce/vitessce-python.git
cd vitessce-python/
conda env create -f environment.yml
conda activate vitessce-jupyter-dev
pip install -e .

... and then I get this error:

pip._vendor.pkg_resources.ContextualVersionConflict: (pandas 0.25.1 (/opt/anaconda3/lib/python3.7/site-packages), Requirement.parse('pandas>=1.1.2'), {'vitessce'}) 
$ pip install -e .
Obtaining file:///Users/chuck/github/hubmap/vitessce-python
ERROR: Exception:
Traceback (most recent call last):
  File "/opt/anaconda3/lib/python3.7/site-packages/pip/_internal/req/req_install.py", line 407, in check_if_exists
    self.satisfied_by = pkg_resources.get_distribution(str(no_marker))
  File "/opt/anaconda3/lib/python3.7/site-packages/pip/_vendor/pkg_resources/__init__.py", line 481, in get_distribution
    dist = get_provider(dist)
  File "/opt/anaconda3/lib/python3.7/site-packages/pip/_vendor/pkg_resources/__init__.py", line 357, in get_provider
    return working_set.find(moduleOrReq) or require(str(moduleOrReq))[0]
  File "/opt/anaconda3/lib/python3.7/site-packages/pip/_vendor/pkg_resources/__init__.py", line 900, in require
    needed = self.resolve(parse_requirements(requirements))
  File "/opt/anaconda3/lib/python3.7/site-packages/pip/_vendor/pkg_resources/__init__.py", line 791, in resolve
    raise VersionConflict(dist, req).with_context(dependent_req)
pip._vendor.pkg_resources.ContextualVersionConflict: (pandas 0.25.1 (/opt/anaconda3/lib/python3.7/site-packages), Requirement.parse('pandas>=1.1.2'), {'vitessce'})

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/anaconda3/lib/python3.7/site-packages/pip/_internal/cli/base_command.py", line 188, in main
    status = self.run(options, args)
  File "/opt/anaconda3/lib/python3.7/site-packages/pip/_internal/commands/install.py", line 345, in run
    resolver.resolve(requirement_set)
  File "/opt/anaconda3/lib/python3.7/site-packages/pip/_internal/legacy_resolve.py", line 196, in resolve
    self._resolve_one(requirement_set, req)
  File "/opt/anaconda3/lib/python3.7/site-packages/pip/_internal/legacy_resolve.py", line 359, in _resolve_one
    abstract_dist = self._get_abstract_dist_for(req_to_install)
  File "/opt/anaconda3/lib/python3.7/site-packages/pip/_internal/legacy_resolve.py", line 291, in _get_abstract_dist_for
    req, self.require_hashes, self.use_user_site, self.finder,
  File "/opt/anaconda3/lib/python3.7/site-packages/pip/_internal/operations/prepare.py", line 255, in prepare_editable_requirement
    req.check_if_exists(use_user_site)
  File "/opt/anaconda3/lib/python3.7/site-packages/pip/_internal/req/req_install.py", line 418, in check_if_exists
    self.req.name
  File "/opt/anaconda3/lib/python3.7/site-packages/pip/_vendor/pkg_resources/__init__.py", line 481, in get_distribution
    dist = get_provider(dist)
  File "/opt/anaconda3/lib/python3.7/site-packages/pip/_vendor/pkg_resources/__init__.py", line 357, in get_provider
    return working_set.find(moduleOrReq) or require(str(moduleOrReq))[0]
  File "/opt/anaconda3/lib/python3.7/site-packages/pip/_vendor/pkg_resources/__init__.py", line 900, in require
    needed = self.resolve(parse_requirements(requirements))
  File "/opt/anaconda3/lib/python3.7/site-packages/pip/_vendor/pkg_resources/__init__.py", line 791, in resolve
    raise VersionConflict(dist, req).with_context(dependent_req)
pip._vendor.pkg_resources.ContextualVersionConflict: (pandas 0.25.1 (/opt/anaconda3/lib/python3.7/site-packages), Requirement.parse('pandas>=1.1.2'), {'vitessce'})

Poked around, didn't have any insights, tried again, and now it works:

$ pip install -e .
Obtaining file:///Users/chuck/github/hubmap/vitessce-python
Requirement already satisfied: ipywidgets>=7.0.0 in /opt/anaconda3/lib/python3.7/site-packages (from vitessce==0.1.0a10) (7.5.1)
Collecting hypercorn>=0.11.0 (from vitessce==0.1.0a10)
  Using cached https://files.pythonhosted.org/packages/68/53/9ceb193c35ce828936cb522b8759c99422b3453d3563ef0f0054ba3f9792/Hypercorn-0.11.2-py3-none-any.whl
Collecting ujson>=4.0.1 (from vitessce==0.1.0a10)
  Using cached https://files.pythonhosted.org/packages/32/49/84d979d75e4a01b92271b1451e31945eac0d5239bf481ba025af9ab271d7/ujson-4.0.2-cp37-cp37m-macosx_10_14_x86_64.whl
Collecting aiofiles>=0.6.0 (from vitessce==0.1.0a10)
  Downloading https://files.pythonhosted.org/packages/e7/61/007ac6f27fe1c2dc44d3a62f429a8440de1601428b4d0291eae1a3494d1f/aiofiles-0.7.0-py3-none-any.whl
Collecting starlette==0.14.0 (from vitessce==0.1.0a10)
  Using cached https://files.pythonhosted.org/packages/3b/48/c305e580e6584d8dd0c2c58238dac973f484345d9de4bc1aa5b162c86a54/starlette-0.14.0-py3-none-any.whl
Collecting zarr>=2.5.0 (from vitessce==0.1.0a10)
  Downloading https://files.pythonhosted.org/packages/95/57/9d4833535d11e8e83629e0a0a78fa1115deadf59532e226082346ee3e677/zarr-2.8.3-py3-none-any.whl (140kB)
     |████████████████████████████████| 143kB 4.4MB/s
Collecting numcodecs>=0.5.7 (from vitessce==0.1.0a10)
  Using cached https://files.pythonhosted.org/packages/bf/e6/2b34ce6db3dbb13c5b2e6e41d4b5a5bc98e0fc2f8e039249179b0a2c706b/numcodecs-0.7.3-cp37-cp37m-macosx_10_9_x86_64.whl
Requirement already satisfied: scipy>=1.2.1 in /opt/anaconda3/lib/python3.7/site-packages (from vitessce==0.1.0a10) (1.3.1)
Collecting negspy>=0.2.24 (from vitessce==0.1.0a10)
Collecting generate-tiff-offsets>=0.1.7 (from vitessce==0.1.0a10)
  Using cached https://files.pythonhosted.org/packages/a3/32/0b489c4d19e5b2cd06abbbdcbc0b0a330574d6d50fa024e188928e7a6f85/generate_tiff_offsets-0.1.7-py2.py3-none-any.whl
Collecting pandas>=1.1.2 (from vitessce==0.1.0a10)
  Using cached https://files.pythonhosted.org/packages/e2/01/d6ab319ffec641987d574ad2d1a9adee281389d5e24955f140d5e7c20283/pandas-1.2.4-cp37-cp37m-macosx_10_9_x86_64.whl
Requirement already satisfied: nbformat>=4.2.0 in /opt/anaconda3/lib/python3.7/site-packages (from ipywidgets>=7.0.0->vitessce==0.1.0a10) (4.4.0)
Requirement already satisfied: ipykernel>=4.5.1 in /opt/anaconda3/lib/python3.7/site-packages (from ipywidgets>=7.0.0->vitessce==0.1.0a10) (5.1.2)
Requirement already satisfied: widgetsnbextension~=3.5.0 in /opt/anaconda3/lib/python3.7/site-packages (from ipywidgets>=7.0.0->vitessce==0.1.0a10) (3.5.1)
Requirement already satisfied: traitlets>=4.3.1 in /opt/anaconda3/lib/python3.7/site-packages (from ipywidgets>=7.0.0->vitessce==0.1.0a10) (4.3.3)
Requirement already satisfied: ipython>=4.0.0; python_version >= "3.3" in /opt/anaconda3/lib/python3.7/site-packages (from ipywidgets>=7.0.0->vitessce==0.1.0a10) (7.8.0)
Collecting priority (from hypercorn>=0.11.0->vitessce==0.1.0a10)
  Using cached https://files.pythonhosted.org/packages/de/96/2f4b8da7be255cd41e825c398efd11a6706ff86e66ae198f012204aa2a4f/priority-1.3.0-py2.py3-none-any.whl
Collecting typing-extensions; python_version < "3.8" (from hypercorn>=0.11.0->vitessce==0.1.0a10)
  Downloading https://files.pythonhosted.org/packages/2e/35/6c4fff5ab443b57116cb1aad46421fb719bed2825664e8fe77d66d99bcbc/typing_extensions-3.10.0.0-py3-none-any.whl
Requirement already satisfied: toml in /opt/anaconda3/lib/python3.7/site-packages (from hypercorn>=0.11.0->vitessce==0.1.0a10) (0.10.2)
Collecting wsproto>=0.14.0 (from hypercorn>=0.11.0->vitessce==0.1.0a10)
  Using cached https://files.pythonhosted.org/packages/ea/25/0934b1d00f404d75335b144d4396e01998f25db8953bf54b4d6fe65b80ab/wsproto-1.0.0-py3-none-any.whl
Collecting h11 (from hypercorn>=0.11.0->vitessce==0.1.0a10)
  Using cached https://files.pythonhosted.org/packages/60/0f/7a0eeea938eaf61074f29fed9717f2010e8d0e0905d36b38d3275a1e4622/h11-0.12.0-py3-none-any.whl
Collecting h2>=3.1.0 (from hypercorn>=0.11.0->vitessce==0.1.0a10)
  Using cached https://files.pythonhosted.org/packages/bd/c2/5ffec707d0022208787908d9657f782ce35b653baa1e87abecf22a7cf513/h2-4.0.0-py3-none-any.whl
Requirement already satisfied: numpy>=1.7 in /opt/anaconda3/lib/python3.7/site-packages (from zarr>=2.5.0->vitessce==0.1.0a10) (1.17.2)
Collecting asciitree (from zarr>=2.5.0->vitessce==0.1.0a10)
Collecting fasteners (from zarr>=2.5.0->vitessce==0.1.0a10)
  Using cached https://files.pythonhosted.org/packages/78/20/c862d765287e9e8b29f826749ebae8775bdca50b2cb2ca079346d5fbfd76/fasteners-0.16-py2.py3-none-any.whl
Collecting tifffile==2020.10.1 (from generate-tiff-offsets>=0.1.7->vitessce==0.1.0a10)
  Using cached https://files.pythonhosted.org/packages/e8/8c/166c88fcbe3b3632dcf93a106f6d13892b1a2b822b61eb7cd9a5ab68b259/tifffile-2020.10.1-py3-none-any.whl
Requirement already satisfied: pytz>=2017.3 in /opt/anaconda3/lib/python3.7/site-packages (from pandas>=1.1.2->vitessce==0.1.0a10) (2019.3)
Requirement already satisfied: python-dateutil>=2.7.3 in /opt/anaconda3/lib/python3.7/site-packages (from pandas>=1.1.2->vitessce==0.1.0a10) (2.8.0)
Requirement already satisfied: ipython-genutils in /opt/anaconda3/lib/python3.7/site-packages (from nbformat>=4.2.0->ipywidgets>=7.0.0->vitessce==0.1.0a10) (0.2.0)
Requirement already satisfied: jsonschema!=2.5.0,>=2.4 in /opt/anaconda3/lib/python3.7/site-packages (from nbformat>=4.2.0->ipywidgets>=7.0.0->vitessce==0.1.0a10) (3.1.0)
Requirement already satisfied: jupyter-core in /opt/anaconda3/lib/python3.7/site-packages (from nbformat>=4.2.0->ipywidgets>=7.0.0->vitessce==0.1.0a10) (4.5.0)
Requirement already satisfied: tornado>=4.2 in /opt/anaconda3/lib/python3.7/site-packages (from ipykernel>=4.5.1->ipywidgets>=7.0.0->vitessce==0.1.0a10) (6.0.3)
Requirement already satisfied: jupyter-client in /opt/anaconda3/lib/python3.7/site-packages (from ipykernel>=4.5.1->ipywidgets>=7.0.0->vitessce==0.1.0a10) (5.3.3)
Requirement already satisfied: notebook>=4.4.1 in /opt/anaconda3/lib/python3.7/site-packages (from widgetsnbextension~=3.5.0->ipywidgets>=7.0.0->vitessce==0.1.0a10) (6.0.1)
Requirement already satisfied: six in /opt/anaconda3/lib/python3.7/site-packages (from traitlets>=4.3.1->ipywidgets>=7.0.0->vitessce==0.1.0a10) (1.12.0)
Requirement already satisfied: decorator in /opt/anaconda3/lib/python3.7/site-packages (from traitlets>=4.3.1->ipywidgets>=7.0.0->vitessce==0.1.0a10) (4.4.0)
Requirement already satisfied: pickleshare in /opt/anaconda3/lib/python3.7/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets>=7.0.0->vitessce==0.1.0a10) (0.7.5)
Requirement already satisfied: prompt-toolkit<2.1.0,>=2.0.0 in /opt/anaconda3/lib/python3.7/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets>=7.0.0->vitessce==0.1.0a10) (2.0.10)
Requirement already satisfied: backcall in /opt/anaconda3/lib/python3.7/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets>=7.0.0->vitessce==0.1.0a10) (0.1.0)
Requirement already satisfied: pygments in /opt/anaconda3/lib/python3.7/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets>=7.0.0->vitessce==0.1.0a10) (2.8.1)
Requirement already satisfied: setuptools>=18.5 in /opt/anaconda3/lib/python3.7/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets>=7.0.0->vitessce==0.1.0a10) (41.4.0)
Requirement already satisfied: appnope; sys_platform == "darwin" in /opt/anaconda3/lib/python3.7/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets>=7.0.0->vitessce==0.1.0a10) (0.1.0)
Requirement already satisfied: jedi>=0.10 in /opt/anaconda3/lib/python3.7/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets>=7.0.0->vitessce==0.1.0a10) (0.15.1)
Requirement already satisfied: pexpect; sys_platform != "win32" in /opt/anaconda3/lib/python3.7/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets>=7.0.0->vitessce==0.1.0a10) (4.7.0)
Collecting hyperframe<7,>=6.0 (from h2>=3.1.0->hypercorn>=0.11.0->vitessce==0.1.0a10)
  Using cached https://files.pythonhosted.org/packages/d7/de/85a784bcc4a3779d1753a7ec2dee5de90e18c7bcf402e71b51fcf150b129/hyperframe-6.0.1-py3-none-any.whl
Collecting hpack<5,>=4.0 (from h2>=3.1.0->hypercorn>=0.11.0->vitessce==0.1.0a10)
  Using cached https://files.pythonhosted.org/packages/d5/34/e8b383f35b77c402d28563d2b8f83159319b509bc5f760b15d60b0abf165/hpack-4.0.0-py3-none-any.whl
Requirement already satisfied: pyrsistent>=0.14.0 in /opt/anaconda3/lib/python3.7/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets>=7.0.0->vitessce==0.1.0a10) (0.15.4)
Requirement already satisfied: attrs>=17.4.0 in /opt/anaconda3/lib/python3.7/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets>=7.0.0->vitessce==0.1.0a10) (19.2.0)
Requirement already satisfied: importlib-metadata in /opt/anaconda3/lib/python3.7/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets>=7.0.0->vitessce==0.1.0a10) (0.23)
Requirement already satisfied: js-regex>=1.0.0 in /opt/anaconda3/lib/python3.7/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets>=7.0.0->vitessce==0.1.0a10) (1.0.1)
Requirement already satisfied: pyzmq>=13 in /opt/anaconda3/lib/python3.7/site-packages (from jupyter-client->ipykernel>=4.5.1->ipywidgets>=7.0.0->vitessce==0.1.0a10) (18.1.0)
Requirement already satisfied: nbconvert in /opt/anaconda3/lib/python3.7/site-packages (from notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets>=7.0.0->vitessce==0.1.0a10) (5.6.0)
Requirement already satisfied: terminado>=0.8.1 in /opt/anaconda3/lib/python3.7/site-packages (from notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets>=7.0.0->vitessce==0.1.0a10) (0.8.2)
Requirement already satisfied: jinja2 in /opt/anaconda3/lib/python3.7/site-packages (from notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets>=7.0.0->vitessce==0.1.0a10) (2.10.3)
Requirement already satisfied: Send2Trash in /opt/anaconda3/lib/python3.7/site-packages (from notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets>=7.0.0->vitessce==0.1.0a10) (1.5.0)
Requirement already satisfied: prometheus-client in /opt/anaconda3/lib/python3.7/site-packages (from notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets>=7.0.0->vitessce==0.1.0a10) (0.7.1)
Requirement already satisfied: wcwidth in /opt/anaconda3/lib/python3.7/site-packages (from prompt-toolkit<2.1.0,>=2.0.0->ipython>=4.0.0; python_version >= "3.3"->ipywidgets>=7.0.0->vitessce==0.1.0a10) (0.1.7)
Requirement already satisfied: parso>=0.5.0 in /opt/anaconda3/lib/python3.7/site-packages (from jedi>=0.10->ipython>=4.0.0; python_version >= "3.3"->ipywidgets>=7.0.0->vitessce==0.1.0a10) (0.5.1)
Requirement already satisfied: ptyprocess>=0.5 in /opt/anaconda3/lib/python3.7/site-packages (from pexpect; sys_platform != "win32"->ipython>=4.0.0; python_version >= "3.3"->ipywidgets>=7.0.0->vitessce==0.1.0a10) (0.6.0)
Requirement already satisfied: zipp>=0.5 in /opt/anaconda3/lib/python3.7/site-packages (from importlib-metadata->jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets>=7.0.0->vitessce==0.1.0a10) (0.6.0)
Collecting mistune<2,>=0.8.1 (from nbconvert->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets>=7.0.0->vitessce==0.1.0a10)
  Using cached https://files.pythonhosted.org/packages/09/ec/4b43dae793655b7d8a25f76119624350b4d65eb663459eb9603d7f1f0345/mistune-0.8.4-py2.py3-none-any.whl
Requirement already satisfied: bleach in /opt/anaconda3/lib/python3.7/site-packages (from nbconvert->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets>=7.0.0->vitessce==0.1.0a10) (3.1.0)
Requirement already satisfied: pandocfilters>=1.4.1 in /opt/anaconda3/lib/python3.7/site-packages (from nbconvert->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets>=7.0.0->vitessce==0.1.0a10) (1.4.2)
Requirement already satisfied: defusedxml in /opt/anaconda3/lib/python3.7/site-packages (from nbconvert->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets>=7.0.0->vitessce==0.1.0a10) (0.6.0)
Requirement already satisfied: entrypoints>=0.2.2 in /opt/anaconda3/lib/python3.7/site-packages (from nbconvert->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets>=7.0.0->vitessce==0.1.0a10) (0.3)
Requirement already satisfied: testpath in /opt/anaconda3/lib/python3.7/site-packages (from nbconvert->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets>=7.0.0->vitessce==0.1.0a10) (0.4.2)
Requirement already satisfied: MarkupSafe>=0.23 in /opt/anaconda3/lib/python3.7/site-packages (from jinja2->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets>=7.0.0->vitessce==0.1.0a10) (1.1.1)
Requirement already satisfied: more-itertools in /opt/anaconda3/lib/python3.7/site-packages (from zipp>=0.5->importlib-metadata->jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets>=7.0.0->vitessce==0.1.0a10) (7.2.0)
Requirement already satisfied: webencodings in /opt/anaconda3/lib/python3.7/site-packages (from bleach->nbconvert->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets>=7.0.0->vitessce==0.1.0a10) (0.5.1)
Installing collected packages: priority, typing-extensions, h11, wsproto, hyperframe, hpack, h2, hypercorn, ujson, aiofiles, starlette, numcodecs, asciitree, fasteners, zarr, negspy, tifffile, generate-tiff-offsets, pandas, vitessce, mistune
  Found existing installation: pandas 0.25.1
    Uninstalling pandas-0.25.1:
      Successfully uninstalled pandas-0.25.1
  Found existing installation: vitessce 0.1.0a10
    Can't uninstall 'vitessce'. No files were found to uninstall.
  Running setup.py develop for vitessce
Successfully installed aiofiles-0.7.0 asciitree-0.3.3 fasteners-0.16 generate-tiff-offsets-0.1.7 h11-0.12.0 h2-4.0.0 hpack-4.0.0 hypercorn-0.11.2 hyperframe-6.0.1 mistune-0.8.4 negspy-0.2.24 numcodecs-0.7.3 pandas-1.2.4 priority-1.3.0 starlette-0.14.0 tifffile-2020.10.1 typing-extensions-3.10.0.0 ujson-4.0.2 vitessce wsproto-1.0.0 zarr-2.8.3

mccalluc avatar May 30 '21 16:05 mccalluc

Can you provide your pip version? It looks like this may have been resolved recently based on this comment 14 days ago https://github.com/pypa/pip/issues/4537#issuecomment-839738231

keller-mark avatar Jun 01 '21 19:06 keller-mark 

$ pip --version
pip 19.2.3 from /opt/anaconda3/lib/python3.7/site-packages/pip (python 3.7)

mccalluc avatar Jun 02 '21 13:06 mccalluc

@mccalluc One thing that jumps out to me, and maybe @keller-mark can correct me since you seem to know conda better than me, is that your pip version is not localized to the environment. For example all of your paths are something like /opt/anaconda3/lib/ whereas when I have a conda environment, I get something like:

(bioformats) TecRef-LT-A0BC38:~ ilan_gold$ which pip
/usr/local/anaconda3/envs/bioformats/bin/pip

ilan-gold avatar Jun 02 '21 15:06 ilan-gold

@mccalluc had the vitessce-jupyter-dev environment been activated in your shell before you ran pip --version?

keller-mark avatar Jun 02 '21 17:06 keller-mark

@keller-mark Even the logs initially posted seem to have the same issue.

ilan-gold avatar Jun 02 '21 18:06 ilan-gold