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Alter dependency specification to avoid conflicts
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@baileythegreen
baileythegreen committed Dec 22, 2021
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2 changes: 1 addition & 1 deletion requirements.txt
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Expand Up @@ -7,7 +7,7 @@ numpy
openpyxl
pandas
Pillow
PyQt5
PyQt
scipy
seaborn
sqlalchemy==1.3.10
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5 comments on commit 0949a46

@peterjc
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@peterjc peterjc commented on 0949a46 Jan 5, 2022

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Hmm. Does this work in general?

$ python --version
Python 3.7.9
$ pip install PyQt
ERROR: Could not find a version that satisfies the requirement PyQt (from versions: none)
ERROR: No matching distribution found for PyQt
$ pip install PyQt5
Requirement already satisfied: PyQt5 in /.../apps/conda/lib/python3.7/site-packages (5.12.3)

@baileythegreen
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Hmm. Looks like there are differences in how pip and conda solve the dependency requirements. I see the same thing you do with pip, but when I tried conda this happened:

(with PyQt5 in requirements.txt)

(pyani_dev) ! conda config --add channels anaconda
(pyani_dev) ! make setup_env
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /Users/baileythegreen/Software/miniconda3/envs/pyani_dev

  added / updated specs:
    - bandit
    - black
    - blacken-docs
    - codecov
    - coverage
    - doc8
    - flake8
    - jinja2
    - mypy
    - pydocstyle
    - pylint
    - pytest
    - pytest-cov
    - rstcheck
    - sphinx


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    appdirs-1.4.4              |             py_0          13 KB  anaconda
    black-19.10b0              |             py_0          84 KB  anaconda
    ca-certificates-2020.10.14 |                0         127 KB  anaconda
    certifi-2020.6.20          |           py38_0         159 KB  anaconda
    codecov-2.1.10             |             py_0          20 KB  anaconda
    coverage-5.3               |   py38haf1e3a3_0         256 KB  anaconda
    jinja2-2.11.2              |             py_0          97 KB  anaconda
    pydocstyle-5.1.1           |             py_0          37 KB  anaconda
    pytest-cov-2.10.1          |             py_0          20 KB  anaconda
    regex-2020.10.15           |   py38haf1e3a3_0         349 KB  anaconda
    sphinx-3.2.1               |             py_0         1.4 MB  anaconda
    ------------------------------------------------------------
                                           Total:         2.6 MB

The following NEW packages will be INSTALLED:

  appdirs            anaconda/noarch::appdirs-1.4.4-py_0
  regex              anaconda/osx-64::regex-2020.10.15-py38haf1e3a3_0

The following packages will be SUPERSEDED by a higher-priority channel:

  black              conda-forge::black-21.12b0-pyhd8ed1ab~ --> anaconda::black-19.10b0-py_0
  ca-certificates    conda-forge::ca-certificates-2021.10.~ --> anaconda::ca-certificates-2020.10.14-0
  certifi            conda-forge::certifi-2021.10.8-py38h5~ --> anaconda::certifi-2020.6.20-py38_0
  codecov            conda-forge::codecov-2.1.11-pyhd3deb0~ --> anaconda::codecov-2.1.10-py_0
  coverage           conda-forge::coverage-6.2-py38h96a096~ --> anaconda::coverage-5.3-py38haf1e3a3_0
  jinja2             conda-forge::jinja2-3.0.3-pyhd8ed1ab_0 --> anaconda::jinja2-2.11.2-py_0
  pydocstyle         conda-forge::pydocstyle-6.1.1-pyhd8ed~ --> anaconda::pydocstyle-5.1.1-py_0
  pytest-cov         conda-forge::pytest-cov-3.0.0-pyhd8ed~ --> anaconda::pytest-cov-2.10.1-py_0
  sphinx             conda-forge::sphinx-4.3.2-pyh6c4a22f_0 --> anaconda::sphinx-3.2.1-py_0



Downloading and Extracting Packages
pydocstyle-5.1.1     | 37 KB     | ######################################################################### | 100% 
ca-certificates-2020 | 127 KB    | ######################################################################### | 100% 
regex-2020.10.15     | 349 KB    | ######################################################################### | 100% 
pytest-cov-2.10.1    | 20 KB     | ######################################################################### | 100% 
coverage-5.3         | 256 KB    | ######################################################################### | 100% 
codecov-2.1.10       | 20 KB     | ######################################################################### | 100% 
appdirs-1.4.4        | 13 KB     | ######################################################################### | 100% 
sphinx-3.2.1         | 1.4 MB    | ######################################################################### | 100% 
jinja2-2.11.2        | 97 KB     | ######################################################################### | 100% 
black-19.10b0        | 84 KB     | ######################################################################### | 100% 
certifi-2020.6.20    | 159 KB    | ######################################################################### | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

  - pyqt5

Current channels:

  - https://conda.anaconda.org/anaconda/osx-64
  - https://conda.anaconda.org/anaconda/noarch
  - https://conda.anaconda.org/conda-forge/osx-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://conda.anaconda.org/bioconda/osx-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.anaconda.com/pkgs/main/osx-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/osx-64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.


make: *** [setup_env] Error 1

(with PyQt in requirements.txt)

(pyani_dev) ! conda install -c anaconda pyqt
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /Users/baileythegreen/Software/miniconda3/envs/pyani_dev

  added / updated specs:
    - pyqt


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    dbus-1.13.18               |       h18a8e69_0         550 KB  anaconda
    expat-2.2.10               |       hb1e8313_2         127 KB  anaconda
    gettext-0.19.8.1           |       h15daf44_3         3.4 MB  anaconda
    glib-2.56.2                |       hd9629dc_0         4.7 MB  anaconda
    icu-58.2                   |       h0a44026_3        22.6 MB  anaconda
    jpeg-9b                    |       he5867d9_2         236 KB  anaconda
    libiconv-1.16              |       h1de35cc_0         1.3 MB  anaconda
    libpng-1.6.37              |       ha441bb4_0         325 KB  anaconda
    pcre-8.44                  |       hb1e8313_0         226 KB  anaconda
    pyqt-5.9.2                 |   py38h655552a_2         4.4 MB  anaconda
    qt-5.9.7                   |       h468cd18_1        76.8 MB  anaconda
    sip-4.19.8                 |   py38h0a44026_0         253 KB  anaconda
    ------------------------------------------------------------
                                           Total:       114.9 MB

The following NEW packages will be INSTALLED:

  dbus               anaconda/osx-64::dbus-1.13.18-h18a8e69_0
  expat              anaconda/osx-64::expat-2.2.10-hb1e8313_2
  gettext            anaconda/osx-64::gettext-0.19.8.1-h15daf44_3
  glib               anaconda/osx-64::glib-2.56.2-hd9629dc_0
  icu                anaconda/osx-64::icu-58.2-h0a44026_3
  jpeg               anaconda/osx-64::jpeg-9b-he5867d9_2
  libiconv           anaconda/osx-64::libiconv-1.16-h1de35cc_0
  libpng             anaconda/osx-64::libpng-1.6.37-ha441bb4_0
  pcre               anaconda/osx-64::pcre-8.44-hb1e8313_0
  pyqt               anaconda/osx-64::pyqt-5.9.2-py38h655552a_2
  qt                 anaconda/osx-64::qt-5.9.7-h468cd18_1
  sip                anaconda/osx-64::sip-4.19.8-py38h0a44026_0


Proceed ([y]/n)? y


Downloading and Extracting Packages
gettext-0.19.8.1     | 3.4 MB    | ######################################################################### | 100% 
glib-2.56.2          | 4.7 MB    | ######################################################################### | 100% 
icu-58.2             | 22.6 MB   | ######################################################################### | 100% 
sip-4.19.8           | 253 KB    | ######################################################################### | 100% 
jpeg-9b              | 236 KB    | ######################################################################### | 100% 
qt-5.9.7             | 76.8 MB   | ######################################################################### | 100% 
libiconv-1.16        | 1.3 MB    | ######################################################################### | 100% 
dbus-1.13.18         | 550 KB    | ######################################################################### | 100% 
libpng-1.6.37        | 325 KB    | ######################################################################### | 100% 
pyqt-5.9.2           | 4.4 MB    | ######################################################################### | 100% 
expat-2.2.10         | 127 KB    | ######################################################################### | 100% 
pcre-8.44            | 226 KB    | ######################################################################### | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

I will need to look into the best way to handle these not playing well together.

@peterjc
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Oh dear, that's be painful - I've been lucky to date, and not run into one of these namespaces clashes between pip and conda.

@widdowquinn
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The fundamental issue is that we're using CircleCI and pip exclusively to install packages, but pyqt/PyQt5 has different names in pip/conda, so we must choose one. pyqt installs OK with conda - but our CircleCI builds fail with that.

If we choose conda we either need to use miniconda/conda in our CircleCI config, or move to another CI (e.g. GitHub Actions) or similar.

The path of least resistance - while we still need to install via both conda and pip (which we do because some packages are in pip and not conda) - is the one chosen here, and that's perfectly fine.

We should try to keep this in mind though, should all the packages become available in conda and/or we swap to another CI, as we might want to revisit this, then.

@peterjc
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I suggest making it clear in the requirements.txt which system is being used (if sadly it cannot be both) with a human readable comment,

e.g. https://github.com/peterjc/thapbi-pict/blob/v0.11.2/requirements.txt

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