Bump certifi

[ttung]

It seems like Docker build can't deal with requests to install older versions of certifi other than is installed by travis by default.

[ttung]

@joshmoore any idea why this is necessary?

here's the log from a failed run.

[joshmoore]

any idea why this is necessary?

This last time I looked into this, I think I got dug long enough to find out that "conda and pip don't work flawlessly together". (cF. pypa/pip#5247)

This is where the --ignore-installed in #713 came from. What's changed here is that we now have a call to pip in environment.yml. I've had some success with adding flags to environment.yml files. I'd suggest trying:

  - pip:
    - --ignore-installed
    - ...

Another option would be to try to force conda use the version of certifi that pip is expecting.

---

NB: something I found while searching around that might be worth a second look -- https://picky-conda.readthedocs.io/en/latest/

[codecov-io]

Codecov Report

Merging #1080 into master will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master    #1080   +/-   ##
=======================================
  Coverage   90.81%   90.81%           
=======================================
  Files         164      164           
  Lines        6151     6151           
=======================================
  Hits         5586     5586           
  Misses        565      565

---

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[ttung]

Looks like flags in the pip section of environment.yml is not supported.

further confirmed with https://travis-ci.com/spacetx/starfish/builds/104144068

[joshmoore]

No objections to the bump, but I'm not completely aware of possible impact to existing virtualenvs/condas. Would it be an option to filter this out of the strict list?

Another alternative I've found is to use a pip config file:

$ head *
==> config <==
[install]
ignore-installed = true

==> Dockerfile <==
FROM continuumio/miniconda3
RUN useradd -m starfish
USER starfish

# Set up the initial conda environment
COPY --chown=starfish:starfish environment.yml /src/environment.yml
COPY --chown=starfish:starfish REQUIREMENTS* /src/
COPY --chown=starfish:starfish config /src/
WORKDIR /src
ENV PIP_CONFIG_FILE=/src/config

==> environment.yml <==
name: test
channels:
- defaults
dependencies:
- python>=3.6
- pip:
  - -r REQUIREMENTS.txt

==> REQUIREMENTS.txt <==
certifi==2018.11.29

[ttung]

I prefer this approach.

[ttung]

Closing in favor of #1085