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Dependency issue in setup.py as of 8/26/2020 #178

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asparke2 opened this issue Aug 26, 2020 · 3 comments · Fixed by #179
Closed

Dependency issue in setup.py as of 8/26/2020 #178

asparke2 opened this issue Aug 26, 2020 · 3 comments · Fixed by #179
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@asparke2
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Describe the bug
Dependency issue when building environment as of 8/26/2020

To Reproduce
Steps to reproduce the behavior:

  1. Clone the repo
  2. Create a conda environment
  3. upgrade pip
  4. pip install -e .

Expected behavior
No dependency issues

Logs

Here's the output of step 4:

(fix-postproc-errs) [aparker@el1 buildstockbatch-fix-postproc-errs]$ pip install -e .
Obtaining file:///lustre/eaglefs/projects/comstock/repos/buildstockbatch-fix-postproc-errs
Requirement already satisfied: pyyaml in /lustre/eaglefs/shared-projects/buildstock/envs/fix-postproc-errs/lib/python3.7/site-packages (from buildstock-batch==0.18) (5.3.1)
Collecting requests
  Using cached requests-2.24.0-py2.py3-none-any.whl (61 kB)
Requirement already satisfied: numpy>=1.11 in /lustre/eaglefs/shared-projects/buildstock/envs/fix-postproc-errs/lib/python3.7/site-packages (from buildstock-batch==0.18) (1.19.1)
Requirement already satisfied: pandas!=1.0.4,>=1.0.0 in /lustre/eaglefs/shared-projects/buildstock/envs/fix-postproc-errs/lib/python3.7/site-packages (from buildstock-batch==0.18) (1.1.1)
Collecting joblib
  Using cached joblib-0.16.0-py3-none-any.whl (300 kB)
Requirement already satisfied: pyarrow>=0.14.1 in /lustre/eaglefs/shared-projects/buildstock/envs/fix-postproc-errs/lib/python3.7/site-packages (from buildstock-batch==0.18) (1.0.1)
Requirement already satisfied: dask[complete]>=2.1.0 in /lustre/eaglefs/shared-projects/buildstock/envs/fix-postproc-errs/lib/python3.7/site-packages (from buildstock-batch==0.18) (2.24.0)
Collecting docker
  Using cached docker-4.3.1-py2.py3-none-any.whl (145 kB)
Collecting boto3>=1.10.44
  Downloading boto3-1.14.48-py2.py3-none-any.whl (129 kB)
     |████████████████████████████████| 129 kB 911 kB/s
Collecting s3fs>=0.4.0
  Using cached s3fs-0.5.0-py3-none-any.whl (21 kB)
Requirement already satisfied: fsspec>=0.6.0 in /lustre/eaglefs/shared-projects/buildstock/envs/fix-postproc-errs/lib/python3.7/site-packages (from buildstock-batch==0.18) (0.8.0)
Collecting docutils<0.15,>=0.10
  Using cached docutils-0.14-py3-none-any.whl (543 kB)
Processing /home/aparker/.cache/pip/wheels/26/51/78/d8eafd10407e5822f792def21f9a477168a24933fe10ea9b48/yamale-3.0.3-py3-none-any.whl
Collecting ruamel.yaml>=0.15.0
  Using cached ruamel.yaml-0.16.10-py2.py3-none-any.whl (111 kB)
Collecting testfixtures
  Using cached testfixtures-6.14.1-py2.py3-none-any.whl (89 kB)
Collecting awsretry
  Using cached awsretry-1.0.1-py2.py3-none-any.whl (6.5 kB)
Requirement already satisfied: certifi>=2017.4.17 in /lustre/eaglefs/shared-projects/buildstock/envs/fix-postproc-errs/lib/python3.7/site-packages (from requests->buildstock-batch==0.18) (2020.6.20)
Collecting chardet<4,>=3.0.2
  Using cached chardet-3.0.4-py2.py3-none-any.whl (133 kB)
Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1
  Using cached urllib3-1.25.10-py2.py3-none-any.whl (127 kB)
Collecting idna<3,>=2.5
  Using cached idna-2.10-py2.py3-none-any.whl (58 kB)
Requirement already satisfied: python-dateutil>=2.7.3 in /lustre/eaglefs/shared-projects/buildstock/envs/fix-postproc-errs/lib/python3.7/site-packages (from pandas!=1.0.4,>=1.0.0->buildstock-batch==0.18) (2.8.1)
Requirement already satisfied: pytz>=2017.2 in /lustre/eaglefs/shared-projects/buildstock/envs/fix-postproc-errs/lib/python3.7/site-packages (from pandas!=1.0.4,>=1.0.0->buildstock-batch==0.18) (2020.1)
Requirement already satisfied: distributed>=2.0; extra == "complete" in /lustre/eaglefs/shared-projects/buildstock/envs/fix-postproc-errs/lib/python3.7/site-packages (from dask[complete]>=2.1.0->buildstock-batch==0.18) (2.24.0)
Requirement already satisfied: bokeh>=1.0.0; extra == "complete" in /lustre/eaglefs/shared-projects/buildstock/envs/fix-postproc-errs/lib/python3.7/site-packages (from dask[complete]>=2.1.0->buildstock-batch==0.18) (2.2.0)
Requirement already satisfied: cloudpickle>=0.2.2; extra == "complete" in /lustre/eaglefs/shared-projects/buildstock/envs/fix-postproc-errs/lib/python3.7/site-packages (from dask[complete]>=2.1.0->buildstock-batch==0.18) (1.6.0)
Requirement already satisfied: partd>=0.3.10; extra == "complete" in /lustre/eaglefs/shared-projects/buildstock/envs/fix-postproc-errs/lib/python3.7/site-packages (from dask[complete]>=2.1.0->buildstock-batch==0.18) (1.1.0)
Requirement already satisfied: toolz>=0.8.2; extra == "complete" in /lustre/eaglefs/shared-projects/buildstock/envs/fix-postproc-errs/lib/python3.7/site-packages (from dask[complete]>=2.1.0->buildstock-batch==0.18) (0.10.0)
Collecting websocket-client>=0.32.0
  Using cached websocket_client-0.57.0-py2.py3-none-any.whl (200 kB)
Requirement already satisfied: six>=1.4.0 in /lustre/eaglefs/shared-projects/buildstock/envs/fix-postproc-errs/lib/python3.7/site-packages (from docker->buildstock-batch==0.18) (1.15.0)
Collecting jmespath<1.0.0,>=0.7.1
  Using cached jmespath-0.10.0-py2.py3-none-any.whl (24 kB)
Collecting s3transfer<0.4.0,>=0.3.0
  Using cached s3transfer-0.3.3-py2.py3-none-any.whl (69 kB)
Collecting botocore<1.18.0,>=1.17.48
  Using cached botocore-1.17.48-py2.py3-none-any.whl (6.5 MB)
Collecting aiobotocore>=1.0.1
  Using cached aiobotocore-1.1.0-py3-none-any.whl (43 kB)
Collecting ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.9"
  Using cached ruamel.yaml.clib-0.2.0-cp37-cp37m-manylinux1_x86_64.whl (547 kB)
Collecting boto
  Using cached boto-2.49.0-py2.py3-none-any.whl (1.4 MB)
Requirement already satisfied: click>=6.6 in /lustre/eaglefs/shared-projects/buildstock/envs/fix-postproc-errs/lib/python3.7/site-packages (from distributed>=2.0; extra == "complete"->dask[complete]>=2.1.0->buildstock-batch==0.18) (7.1.2)
Requirement already satisfied: zict>=0.1.3 in /lustre/eaglefs/shared-projects/buildstock/envs/fix-postproc-errs/lib/python3.7/site-packages (from distributed>=2.0; extra == "complete"->dask[complete]>=2.1.0->buildstock-batch==0.18) (2.0.0)
Requirement already satisfied: tblib>=1.6.0 in /lustre/eaglefs/shared-projects/buildstock/envs/fix-postproc-errs/lib/python3.7/site-packages (from distributed>=2.0; extra == "complete"->dask[complete]>=2.1.0->buildstock-batch==0.18) (1.6.0)
Requirement already satisfied: sortedcontainers!=2.0.0,!=2.0.1 in /lustre/eaglefs/shared-projects/buildstock/envs/fix-postproc-errs/lib/python3.7/site-packages (from distributed>=2.0; extra == "complete"->dask[complete]>=2.1.0->buildstock-batch==0.18) (2.2.2)
Requirement already satisfied: msgpack>=0.6.0 in /lustre/eaglefs/shared-projects/buildstock/envs/fix-postproc-errs/lib/python3.7/site-packages (from distributed>=2.0; extra == "complete"->dask[complete]>=2.1.0->buildstock-batch==0.18) (1.0.0)
Requirement already satisfied: psutil>=5.0 in /lustre/eaglefs/shared-projects/buildstock/envs/fix-postproc-errs/lib/python3.7/site-packages (from distributed>=2.0; extra == "complete"->dask[complete]>=2.1.0->buildstock-batch==0.18) (5.7.2)
Requirement already satisfied: tornado>=5; python_version < "3.8" in /lustre/eaglefs/shared-projects/buildstock/envs/fix-postproc-errs/lib/python3.7/site-packages (from distributed>=2.0; extra == "complete"->dask[complete]>=2.1.0->buildstock-batch==0.18) (6.0.4)
Requirement already satisfied: setuptools in /lustre/eaglefs/shared-projects/buildstock/envs/fix-postproc-errs/lib/python3.7/site-packages (from distributed>=2.0; extra == "complete"->dask[complete]>=2.1.0->buildstock-batch==0.18) (49.6.0.post20200814)
Requirement already satisfied: Jinja2>=2.7 in /lustre/eaglefs/shared-projects/buildstock/envs/fix-postproc-errs/lib/python3.7/site-packages (from bokeh>=1.0.0; extra == "complete"->dask[complete]>=2.1.0->buildstock-batch==0.18) (2.11.2)
Requirement already satisfied: typing-extensions>=3.7.4 in /lustre/eaglefs/shared-projects/buildstock/envs/fix-postproc-errs/lib/python3.7/site-packages (from bokeh>=1.0.0; extra == "complete"->dask[complete]>=2.1.0->buildstock-batch==0.18) (3.7.4.2)
Requirement already satisfied: pillow>=7.1.0 in /lustre/eaglefs/shared-projects/buildstock/envs/fix-postproc-errs/lib/python3.7/site-packages (from bokeh>=1.0.0; extra == "complete"->dask[complete]>=2.1.0->buildstock-batch==0.18) (7.2.0)
Requirement already satisfied: packaging>=16.8 in /lustre/eaglefs/shared-projects/buildstock/envs/fix-postproc-errs/lib/python3.7/site-packages (from bokeh>=1.0.0; extra == "complete"->dask[complete]>=2.1.0->buildstock-batch==0.18) (20.4)
Requirement already satisfied: locket in /lustre/eaglefs/shared-projects/buildstock/envs/fix-postproc-errs/lib/python3.7/site-packages (from partd>=0.3.10; extra == "complete"->dask[complete]>=2.1.0->buildstock-batch==0.18) (0.2.0)
Processing /home/aparker/.cache/pip/wheels/62/76/4c/aa25851149f3f6d9785f6c869387ad82b3fd37582fa8147ac6/wrapt-1.12.1-cp37-cp37m-linux_x86_64.whl
Collecting aiohttp>=3.3.1
  Using cached aiohttp-3.6.2-cp37-cp37m-manylinux1_x86_64.whl (1.2 MB)
Collecting aioitertools>=0.5.1
  Using cached aioitertools-0.7.0-py3-none-any.whl (20 kB)
Requirement already satisfied: heapdict in /lustre/eaglefs/shared-projects/buildstock/envs/fix-postproc-errs/lib/python3.7/site-packages (from zict>=0.1.3->distributed>=2.0; extra == "complete"->dask[complete]>=2.1.0->buildstock-batch==0.18) (1.0.1)
Requirement already satisfied: MarkupSafe>=0.23 in /lustre/eaglefs/shared-projects/buildstock/envs/fix-postproc-errs/lib/python3.7/site-packages (from Jinja2>=2.7->bokeh>=1.0.0; extra == "complete"->dask[complete]>=2.1.0->buildstock-batch==0.18) (1.1.1)
Requirement already satisfied: pyparsing>=2.0.2 in /lustre/eaglefs/shared-projects/buildstock/envs/fix-postproc-errs/lib/python3.7/site-packages (from packaging>=16.8->bokeh>=1.0.0; extra == "complete"->dask[complete]>=2.1.0->buildstock-batch==0.18) (2.4.7)
Collecting yarl<2.0,>=1.0
  Using cached yarl-1.5.1-cp37-cp37m-manylinux1_x86_64.whl (258 kB)
Collecting multidict<5.0,>=4.5
  Using cached multidict-4.7.6-cp37-cp37m-manylinux1_x86_64.whl (149 kB)
Collecting attrs>=17.3.0
  Using cached attrs-20.1.0-py2.py3-none-any.whl (49 kB)
Collecting async-timeout<4.0,>=3.0
  Using cached async_timeout-3.0.1-py3-none-any.whl (8.2 kB)
Installing collected packages: chardet, urllib3, idna, requests, joblib, websocket-client, docker, jmespath, docutils, botocore, s3transfer, boto3, wrapt, multidict, yarl, attrs, async-timeout, aiohttp, aioitertools, aiobotocore, s3fs,  Running setup.py develop for buildstock-batchtures, boto, awsretry, buildstock-batch
ERROR: After October 2020 you may experience errors when installing or updating packages. This is because pip will change the way that it resolves dependency conflicts.

We recommend you use --use-feature=2020-resolver to test your packages with the new resolver before it becomes the default.

aiobotocore 1.1.0 requires botocore<1.17.45,>=1.17.44, but you'll have botocore 1.17.48 which is incompatible.
Successfully installed aiobotocore-1.1.0 aiohttp-3.6.2 aioitertools-0.7.0 async-timeout-3.0.1 attrs-20.1.0 awsretry-1.0.1 boto-2.49.0 boto3-1.14.48 botocore-1.17.48 buildstock-batch chardet-3.0.4 docker-4.3.1 docutils-0.14 idna-2.10 jmespath-0.10.0 joblib-0.16.0 multidict-4.7.6 requests-2.24.0 ruamel.yaml-0.16.10 ruamel.yaml.clib-0.2.0 s3fs-0.5.0 s3transfer-0.3.3 testfixtures-6.14.1 urllib3-1.25.10 websocket-client-0.57.0 wrapt-1.12.1 yamale-3.0.3 yarl-1.5.1

And here's the output of pipdeptree

(fix-postproc-errs) [aparker@el1 buildstockbatch-fix-postproc-errs]$ pipdeptree
Warning!!! Possibly conflicting dependencies found:
* aiobotocore==1.1.0
 - botocore [required: >=1.17.44,<1.17.45, installed: 1.17.48]
------------------------------------------------------------------------
bokeh==2.2.0
  - Jinja2 [required: >=2.7, installed: 2.11.2]
    - MarkupSafe [required: >=0.23, installed: 1.1.1]
  - numpy [required: >=1.11.3, installed: 1.19.1]
  - packaging [required: >=16.8, installed: 20.4]
    - pyparsing [required: >=2.0.2, installed: 2.4.7]
    - six [required: Any, installed: 1.15.0]
  - pillow [required: >=7.1.0, installed: 7.2.0]
  - python-dateutil [required: >=2.1, installed: 2.8.1]
    - six [required: >=1.5, installed: 1.15.0]
  - PyYAML [required: >=3.10, installed: 5.3.1]
  - tornado [required: >=5.1, installed: 6.0.4]
  - typing-extensions [required: >=3.7.4, installed: 3.7.4.2]
buildstock-batch==0.18
  - awsretry [required: Any, installed: 1.0.1]
    - boto [required: Any, installed: 2.49.0]
    - boto3 [required: Any, installed: 1.14.48]
      - botocore [required: >=1.17.48,<1.18.0, installed: 1.17.48]
        - docutils [required: >=0.10,<0.16, installed: 0.14]
        - jmespath [required: >=0.7.1,<1.0.0, installed: 0.10.0]
        - python-dateutil [required: >=2.1,<3.0.0, installed: 2.8.1]
          - six [required: >=1.5, installed: 1.15.0]
        - urllib3 [required: >=1.20,<1.26, installed: 1.25.10]
      - jmespath [required: >=0.7.1,<1.0.0, installed: 0.10.0]
      - s3transfer [required: >=0.3.0,<0.4.0, installed: 0.3.3]
        - botocore [required: >=1.12.36,<2.0a.0, installed: 1.17.48]
          - docutils [required: >=0.10,<0.16, installed: 0.14]
          - jmespath [required: >=0.7.1,<1.0.0, installed: 0.10.0]
          - python-dateutil [required: >=2.1,<3.0.0, installed: 2.8.1]
            - six [required: >=1.5, installed: 1.15.0]
          - urllib3 [required: >=1.20,<1.26, installed: 1.25.10]
    - botocore [required: Any, installed: 1.17.48]
      - docutils [required: >=0.10,<0.16, installed: 0.14]
      - jmespath [required: >=0.7.1,<1.0.0, installed: 0.10.0]
      - python-dateutil [required: >=2.1,<3.0.0, installed: 2.8.1]
        - six [required: >=1.5, installed: 1.15.0]
      - urllib3 [required: >=1.20,<1.26, installed: 1.25.10]
  - boto3 [required: >=1.10.44, installed: 1.14.48]
    - botocore [required: >=1.17.48,<1.18.0, installed: 1.17.48]
      - docutils [required: >=0.10,<0.16, installed: 0.14]
      - jmespath [required: >=0.7.1,<1.0.0, installed: 0.10.0]
      - python-dateutil [required: >=2.1,<3.0.0, installed: 2.8.1]
        - six [required: >=1.5, installed: 1.15.0]
      - urllib3 [required: >=1.20,<1.26, installed: 1.25.10]
    - jmespath [required: >=0.7.1,<1.0.0, installed: 0.10.0]
    - s3transfer [required: >=0.3.0,<0.4.0, installed: 0.3.3]
      - botocore [required: >=1.12.36,<2.0a.0, installed: 1.17.48]
        - docutils [required: >=0.10,<0.16, installed: 0.14]
        - jmespath [required: >=0.7.1,<1.0.0, installed: 0.10.0]
        - python-dateutil [required: >=2.1,<3.0.0, installed: 2.8.1]
          - six [required: >=1.5, installed: 1.15.0]
        - urllib3 [required: >=1.20,<1.26, installed: 1.25.10]
  - dask [required: >=2.1.0, installed: 2.24.0]
    - pyyaml [required: Any, installed: 5.3.1]
  - docker [required: Any, installed: 4.3.1]
    - requests [required: >=2.14.2,!=2.18.0, installed: 2.24.0]
      - certifi [required: >=2017.4.17, installed: 2020.6.20]
      - chardet [required: >=3.0.2,<4, installed: 3.0.4]
      - idna [required: >=2.5,<3, installed: 2.10]
      - urllib3 [required: >=1.21.1,<1.26,!=1.25.1,!=1.25.0, installed: 1.25.10]
    - six [required: >=1.4.0, installed: 1.15.0]
    - websocket-client [required: >=0.32.0, installed: 0.57.0]
      - six [required: Any, installed: 1.15.0]
  - docutils [required: >=0.10,<0.15, installed: 0.14]
  - fsspec [required: >=0.6.0, installed: 0.8.0]
  - joblib [required: Any, installed: 0.16.0]
  - numpy [required: >=1.11, installed: 1.19.1]
  - pandas [required: >=1.0.0,!=1.0.4, installed: 1.1.1]
    - numpy [required: >=1.15.4, installed: 1.19.1]
    - python-dateutil [required: >=2.7.3, installed: 2.8.1]
      - six [required: >=1.5, installed: 1.15.0]
    - pytz [required: >=2017.2, installed: 2020.1]
  - pyarrow [required: >=0.14.1, installed: 1.0.1]
    - numpy [required: >=1.14, installed: 1.19.1]
  - pyyaml [required: Any, installed: 5.3.1]
  - requests [required: Any, installed: 2.24.0]
    - certifi [required: >=2017.4.17, installed: 2020.6.20]
    - chardet [required: >=3.0.2,<4, installed: 3.0.4]
    - idna [required: >=2.5,<3, installed: 2.10]
    - urllib3 [required: >=1.21.1,<1.26,!=1.25.1,!=1.25.0, installed: 1.25.10]
  - ruamel.yaml [required: >=0.15.0, installed: 0.16.10]
    - ruamel.yaml.clib [required: >=0.1.2, installed: 0.2.0]
  - s3fs [required: >=0.4.0, installed: 0.5.0]
    - aiobotocore [required: >=1.0.1, installed: 1.1.0]
      - aiohttp [required: >=3.3.1, installed: 3.6.2]
        - async-timeout [required: >=3.0,<4.0, installed: 3.0.1]
        - attrs [required: >=17.3.0, installed: 20.1.0]
        - chardet [required: >=2.0,<4.0, installed: 3.0.4]
        - multidict [required: >=4.5,<5.0, installed: 4.7.6]
        - yarl [required: >=1.0,<2.0, installed: 1.5.1]
          - idna [required: >=2.0, installed: 2.10]
          - multidict [required: >=4.0, installed: 4.7.6]
          - typing-extensions [required: >=3.7.4, installed: 3.7.4.2]
      - aioitertools [required: >=0.5.1, installed: 0.7.0]
        - typing-extensions [required: >=3.7, installed: 3.7.4.2]
      - botocore [required: >=1.17.44,<1.17.45, installed: 1.17.48]
        - docutils [required: >=0.10,<0.16, installed: 0.14]
        - jmespath [required: >=0.7.1,<1.0.0, installed: 0.10.0]
        - python-dateutil [required: >=2.1,<3.0.0, installed: 2.8.1]
          - six [required: >=1.5, installed: 1.15.0]
        - urllib3 [required: >=1.20,<1.26, installed: 1.25.10]
      - wrapt [required: >=1.10.10, installed: 1.12.1]
    - fsspec [required: >=0.8.0, installed: 0.8.0]
  - testfixtures [required: Any, installed: 6.14.1]
  - yamale [required: >=2.0, installed: 3.0.3]
    - pyyaml [required: Any, installed: 5.3.1]
cytoolz==0.10.1
  - toolz [required: >=0.8.0, installed: 0.10.0]
distributed==2.24.0
  - click [required: >=6.6, installed: 7.1.2]
  - cloudpickle [required: >=1.5.0, installed: 1.6.0]
  - dask [required: >=2.9.0, installed: 2.24.0]
    - pyyaml [required: Any, installed: 5.3.1]
  - msgpack [required: >=0.6.0, installed: 1.0.0]
  - psutil [required: >=5.0, installed: 5.7.2]
  - pyyaml [required: Any, installed: 5.3.1]
  - setuptools [required: Any, installed: 49.6.0.post20200814]
  - sortedcontainers [required: !=2.0.1,!=2.0.0, installed: 2.2.2]
  - tblib [required: >=1.6.0, installed: 1.6.0]
  - toolz [required: >=0.8.2, installed: 0.10.0]
  - tornado [required: >=5, installed: 6.0.4]
  - zict [required: >=0.1.3, installed: 2.0.0]
    - heapdict [required: Any, installed: 1.0.1]
olefile==0.46
partd==1.1.0
  - locket [required: Any, installed: 0.2.0]
  - toolz [required: Any, installed: 0.10.0]
pipdeptree==1.0.0
  - pip [required: >=6.0.0, installed: 20.2.2]
wheel==0.35.1

Possible Resolution
Looks like s3fs released a version 0.5.0, but the buildstock-0.18 used 0.4.2. Here's the dependency tree in question:

  - s3fs [required: >=0.4.0, installed: 0.5.0]
    - aiobotocore [required: >=1.0.1, installed: 1.1.0]
      - botocore [required: >=1.17.44,<1.17.45, installed: 1.17.48]

I think the resolution is changing the setup.py file to:
's3fs>=0.4.0,<0.5.0',

Platform (please complete the following information):

  • Simulation platform: Eagle
  • BuildStockBatch version, branch, or sha: develop as of 8.26.2020
  • Local Desktop OS: Windows
@asparke2 asparke2 added the bug Something isn't working label Aug 26, 2020
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@nmerket FYI

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nmerket commented Aug 26, 2020

Yeah, it's either that or downgrading to a version of boto3 that uses an older version of botocore.

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nmerket commented Aug 26, 2020

Also, I wasn't aware of pipdeptree. Very handy!

@nmerket nmerket mentioned this issue Aug 26, 2020
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Fixing dependency issue on Eagle installation NREL/buildstockbatch
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@asparke2 @nmerket