Housekeeping for v1.0

[ethho]

Clean up repository for an official v1.0 release. This will involve:

• [x] Version pin

  $ rg -g '!examples/**' -g '!logs/**' -g '!poetry*' version
  tox.ini
  12:    gsl-config --version
  
  setup.py
  38:    containing GSL version, library dir, and include dir.
  41:        'version': shell_call(['gsl-config', '--version']).split('.'),
  62:    assert int(gsl_config['version'][0]) > 0
  96:# Create version file
  98:with open(os.path.join(pkg_dir,'version.py'), 'w') as VF:
  99:    cnt = """# THIS FILE IS GENERATED FROM SETUP.PY\nversion = '%s'"""
  115:    version=VERSION,  # Required
  132:    # Supported python versions
  
  README.md
  62:    gsl-config --version
  80:    gsl-config --version
  86:        gsl-config --version
  
  catchment_census_tract_overlap.ipynb
  260:    "version": 3
  267:   "version": "3.7.9"
  
  pyproject.toml
  3:version = "0.1.0"
  11:scipy = { version = "^1.6.2",  python = ">=3.8,<3.10" }
  15:dask = {extras = ["dataframe", "distributed"], version = "^2021.4.0"} 
  
  Makefile
  11:VERSION = $(shell python setup.py --version)
  
  20210511_DemoPartitionProcess.ipynb
  1244:    "The older version of the contact matrix is incorrect because of some bugs in my logic for contact partitioning."
  1940:    "version": 3
  1947:   "version": "3.7.9"
  
  episimlab/version.py
  2:version = '0.1.0'
  
  episimlab/io/config.py
  14:    """Reads model input variables from a version 1.0 configuration file.

  • [x] pyproject.toml
  • [x] episimlab.version
  • [x] git tag
• [x] Package
  • [x] partition submodule, much of which is unused
  • [x] network submodule, all of which is unused
  • [x] model submodule
• [ ] Build
  • [x] Makefile
  • [ ] Possible switch to poetry, if cythonize supports
    • This SO post indicates that this is an undocumented feature
• [ ] Misc.
  • [ ] Check TODO and DEBUG tags
  • [ ] Ensure all tests passing
• [ ] Version tick
  • [ ] pyproject.toml
  • [ ] episimlab.version
  • [ ] git tag HEAD
• [ ] Kick off CI/CD if enabled

[ethho]

Clean up Episimlab repo

[ethho]

TODO Tags

• [ ] NaN checks