Project/1.0 cleanup

[WardBrian]

Submission Checklist

• Run unit tests
• Declare copyright holder and open-source license: see below

Summary

This closes up a couple tiny issues (seconds in filenames, a show_versions command) and fixes our tests failing if cmdstan isn't installed in ~/.cmdstan[py]

sample(), generate_quantities() et al now accept a time_fmt string which is passed to RunSet for the time format of the csv files. It defaults to "%Y%m%d%H%M%S", which is the same as before but with seconds appended.

Output of show_versions is based on what xarray does for it's method of the same name, but it is simpler than their use case. It looks like:

INSTALLED VERSIONS
---------------------
python: 3.9.5 | packaged by conda-forge | (default, Jun 19 2021, 00:32:32) 
[GCC 9.3.0]
python-bits: 64
OS: Linux
OS-release: 5.11.0-27-generic
machine: x86_64
processor: x86_64
byteorder: little
LC_ALL: None
LANG: en_US.UTF-8
LOCALE: ('en_US', 'UTF-8')
cmdstan_folder: /home/brian/miniconda3/envs/stan/cmdstan-2.27.0/
cmdstanpy: 0.9.77
pandas: 1.3.1
xarray: 0.18.2
tdqm: None
numpy: 1.21.0
ujson: 4.0.2

Copyright and Licensing

Please list the copyright holder for the work you are submitting (this will be you or your assignee, such as a university or company):
Simons Foundation

By submitting this pull request, the copyright holder is agreeing to license the submitted work under the following licenses:

• Code: BSD 3-clause (https://opensource.org/licenses/BSD-3-Clause)

[codecov-commenter]

Codecov Report

Merging #449 (6072d26) into develop (38932eb) will decrease coverage by 0.80%.
The diff coverage is n/a.

@@             Coverage Diff             @@
##           develop     #449      +/-   ##
===========================================
- Coverage    76.96%   76.15%   -0.81%     
===========================================
  Files           27       27              
  Lines         8664     8760      +96     
===========================================
+ Hits          6668     6671       +3     
- Misses        1996     2089      +93     

Impacted Files	Coverage Δ
a/cmdstanpy/cmdstanpy/cmdstanpy/utils.py	71.67% <0.00%> (-3.59%)	⬇️
cmdstanpy/cmdstanpy/utils.py	68.32% <0.00%> (-3.42%)	⬇️
...runner/work/cmdstanpy/cmdstanpy/cmdstanpy/utils.py	68.32% <0.00%> (-3.42%)	⬇️
cmdstanpy/cmdstanpy/stanfit.py	92.28% <0.00%> (ø)
cmdstanpy/cmdstanpy/__init__.py	86.36% <0.00%> (ø)
a/cmdstanpy/cmdstanpy/cmdstanpy/stanfit.py	92.05% <0.00%> (ø)
a/cmdstanpy/cmdstanpy/cmdstanpy/__init__.py	86.36% <0.00%> (ø)
...nner/work/cmdstanpy/cmdstanpy/cmdstanpy/stanfit.py	92.28% <0.00%> (ø)
...ner/work/cmdstanpy/cmdstanpy/cmdstanpy/__init__.py	86.36% <0.00%> (ø)
cmdstanpy/cmdstanpy/model.py	78.32% <0.00%> (+0.40%)	⬆️
... and 2 more

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