Feature/v0.9.9 (#14)

* support methylprep v1.5.6 manifest changes; exposing two genome builds and X/Y chrome to DMP function * pandas install error on circleci * circleci to force downloading new manifests * fixed diff_meth_pos bugs * working volcano plots again * working volcano plots again * v1.0 circleci/coverall/codacy fix * coveralls badge * working DMR functions. needs some tidying and unit testing * v1.0 features are there, plus some unit test coverage, though not complete * circleci didn't like git in reqs.txt * testing git in setup.py on circleci * testing git in setup.py on circleci * v0.9.9 local tests pass * increases test coverage, adding a no_sync mode to fetch_genes because the tables are checked in to repo and could be used without DB * fixing unit tests * fixed bonferoni bug * tests OK. features complete. Adding docs next * working on updated docs
FoxoTech · Oct 14, 2021 · 780eb80 · 780eb80
1 parent 601def1
commit 780eb80
Show file tree

Hide file tree

Showing 33 changed files with 13,016 additions and 102 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -30,7 +30,6 @@ jobs:
             pipenv run pytest tests --junit-xml=htmlcov/junit.xml # rerun tests to collect test-results
             pipenv run coverage report
             pipenv run coverage html
-            pipenv run coverage xml
             pipenv run coveralls
             # set COVERALLS_REPO_TOKEN=<...> in ENVIRONMENT variables in circleci
             # pipenv run coverage run --omit '*tests*','*/home/*' setup.py test

diff --git a/README.md b/README.md
@@ -1,11 +1,11 @@
 `methylize` is a python package for analyzing output from Illumina methylation arrays. It complements `methylprep` and `methylcheck`. View on [ReadTheDocs.](https://life-epigenetics-methylize.readthedocs-hosted.com/en/latest/)
 
-[![Readthedocs](https://readthedocs.com/projects/life-epigenetics-methylize/badge/?version=latest)](https://life-epigenetics-methylize.readthedocs-hosted.com/en/latest/) [![image](https://img.shields.io/pypi/l/pipenv.svg)](https://python.org/pypi/pipenv)  [![CircleCI](https://circleci.com/gh/FOXOBioScience/methylize.svg?style=shield&circle-token=6a80b317c9e581e0969cdc73cc3233b3c70b9dbd)](https://circleci.com/gh/FOXOBioScience/methylize)  [![Codacy Badge](https://api.codacy.com/project/badge/Grade/36c282629145444facdd2d96b4462afa)](https://www.codacy.com?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=FOXOBioScience/methylize&amp;utm_campaign=Badge_Grade)
-[![Coverage Status](https://coveralls.io/repos/github/FOXOBioScience/methylize/badge.svg?t=uf7qX4)](https://coveralls.io/github/FOXOBioScience/methylize)
+[![Readthedocs](https://readthedocs.com/projects/life-epigenetics-methylize/badge/?version=latest)](https://life-epigenetics-methylize.readthedocs-hosted.com/en/latest/) [![image](https://img.shields.io/pypi/l/pipenv.svg)](https://python.org/pypi/pipenv) [![CircleCI](https://circleci.com/gh/FoxoTech/methylize/tree/master.svg?style=shield)](https://circleci.com/gh/FoxoTech/methylize/tree/master) [![Codacy Badge](https://app.codacy.com/project/badge/Grade/099d26465bd64c2387afa063810a13e6)](https://www.codacy.com/gh/FoxoTech/methylize/dashboard?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=FOXOBioScience/methylize&amp;utm_campaign=Badge_Grade) [![Coverage Status](https://coveralls.io/repos/github/FoxoTech/methylize/badge.svg?branch=master)](https://coveralls.io/github/FoxoTech/methylize?branch=master)
+
 
 1. [Overview](README.md)
 2. [Demonstrating differentially methylated probe (DMP) detection (volcano plot) and mapping to chrosomes (manhattan plot)](docs/demo_diff_meth_pos.ipynb)
-3. [About BumpHunter](docs/bumphunter.md)
+3. [differentially methylated regions](docs/diff_meth_regions.md)
 
 ## Methylize Package
 
@@ -14,12 +14,12 @@ The `methylize` package contains both high-level APIs for processing data from l
 `Methylize` allows you to run linear or logistic regression on all probes and identify points of interest in the methylome where DNA is differentially modified. Then you can use these regression results to create *volcano plots* and *manhattan plots*.
 
 ### Sample Manhattan Plot
-![Manhattan Plot](https://github.com/FOXOBioScience/methylize/blob/master/docs/manhattan_example.png?raw=true)
+![Manhattan Plot](https://github.com/FoxoTech/methylize/blob/master/docs/manhattan_example.png?raw=true)
 
-![Manhattan Plot (alternate coloring)](https://github.com/FOXOBioScience/methylize/blob/master/docs/manhattan_example2.png?raw=true)
+![Manhattan Plot (alternate coloring)](https://github.com/FoxoTech/methylize/blob/master/docs/manhattan_example2.png?raw=true)
 
 ### Sample Volcano Plot
-![Volcano Plot](https://github.com/FOXOBioScience/methylize/blob/master/docs/volcano_example.png?raw=true)
+![Volcano Plot](https://github.com/FoxoTech/methylize/blob/master/docs/volcano_example.png?raw=true)
 
 Customizable: Plot size, color palette, and cutoff p-value lines can be set by the user.
 Exporting: You can export all probe statistics, or just the significant probes as CSV or python pickled DataFrame.

diff --git a/conf.py b/conf.py
@@ -24,9 +24,9 @@
 author = 'FOXO Bioscience'
 
 # The short X.Y version
-version = '0.9.3'
+version = '1.0.0'
 # The full version, including alpha/beta/rc tags
-release = '0.9'
+release = '1.0'
 
 
 # -- General configuration ---------------------------------------------------

diff --git a/docs/demo_diff_meth_pos.ipynb b/docs/demo_diff_meth_pos.ipynb
@@ -632,7 +632,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.3"
+   "version": "3.8.8"
   }
  },
  "nbformat": 4,

diff --git a/docs/example_data/test_sample_betas_450k.pkl b/docs/example_data/test_sample_betas_450k.pkl
diff --git a/docs/example_data/test_sample_betas_450k_phenotype.pkl b/docs/example_data/test_sample_betas_450k_phenotype.pkl
diff --git a/docs/example_data/test_sample_betas_epicplus_30k.pkl b/docs/example_data/test_sample_betas_epicplus_30k.pkl
diff --git a/docs/filtering_probes_with_dmp.ipynb b/docs/filtering_probes_with_dmp.ipynb
@@ -350,7 +350,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.3"
+   "version": "3.8.8"
   }
  },
  "nbformat": 4,