Modify installation & models compilation for bioconda

[lkeegan]

• move rpbp_models dir to src/rpbp/models and add to MANIFEST.in
  • models are now installed to rpbp_install_dir/models
• get_default_models_base() now returns rpbp_install_dir/models
• compile_rpbp_models
  • checks if compiled exes exist, if so doesn't compile unless --force is specified
  • remove pbiotools dependency
  • this allows us to run rpbp-compile-models as part of bioconda recipe build
  • user gets pre-compiled stan models as part of rp-bp installation
• use compiled models instead of re-compiling
  • these functions would previously re-compile the stan files with every CmdStanModel instantiation:
  • orf_profile_construction/estimate_metagene_profile_bayes_factors.py
  • translation_prediction/estimate_orf_bayes_factors.py
  • specify exe_file instead of stan_file to avoid re-compiling them
  • call compile_rpbp_models.compile() to ensure exes are there before using them

Use bioconda dependencies in CI and test macos / different Python versions

• add MacOS CI jobs
  • use 1 cpu in tests on mac due to parallel processing issue #140
• test Python versions 3.7-3.10
• install all dependencies including pbiotools from bioconda
• use available cpus in tests instead of hard-coding num_cpus
• disable failing flake8 checks in pre-commit for now
• apply pre-commit fixes
• add missing import scipy.stats to estimate_orf_bayes_factors.py

[codecov[bot]]

Codecov Report

Merging #143 (6dfbd3e) into dev-ssciwr (c9bcf2e) will increase coverage by 3.48%. The diff coverage is 52.05%.

@@              Coverage Diff               @@
##           dev-ssciwr     #143      +/-   ##
==============================================
+ Coverage       45.39%   48.87%   +3.48%     
==============================================
  Files              33       34       +1     
  Lines            4060     4008      -52     
==============================================
+ Hits             1843     1959     +116     
+ Misses           2217     2049     -168     

Impacted Files	Coverage Δ
...n/dashboard/rpbp_profile_construction_dashboard.py	0.00% <ø> (ø)
...redictions/dashboard/rpbp_predictions_dashboard.py	0.00% <0.00%> (ø)
...sis/rpbp_predictions/summarize_rpbp_predictions.py	0.00% <0.00%> (ø)
...bp/orf_profile_construction/create_orf_profiles.py	94.95% <ø> (-0.13%)	:arrow_down:
.../translation_prediction/predict_translated_orfs.py	91.73% <ø> (-0.20%)	:arrow_down:
src/rpbp/ribo_utils/compile_rpbp_models.py	82.75% <82.75%> (ø)
...ruction/estimate_metagene_profile_bayes_factors.py	95.65% <100.00%> (-0.04%)	:arrow_down:
src/rpbp/ribo_utils/filenames.py	71.74% <100.00%> (+0.47%)	:arrow_up:
...anslation_prediction/estimate_orf_bayes_factors.py	90.44% <100.00%> (+35.03%)	:arrow_up:
src/rpbp/defaults.py	100.00% <0.00%> (+4.76%)	:arrow_up:
... and 3 more

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