Merge pull request #8 from biosustain/v1.2.x

V1.2.0

.gitignore

@@ -4,8 +4,7 @@
 *.so
 
 # Packages
-*.egg
-*.egg-info
+*.egg*
 dist
 build
 eggs
@@ -18,6 +17,7 @@ develop-eggs
 lib
 lib64
 __pycache__
+venv
 
 # Installer logs
 pip-log.txt
@@ -35,8 +35,9 @@ nosetests.xml
 .project
 .pydevproject
 
-# PyCharm
+# IDEs
 .idea
+.vscode
 
 # Test output
 test.*.pdf

.travis.yml

@@ -2,11 +2,12 @@ language: python
 cache:
   - pip: true
 python:
-  - "3.5"
+  - "3.6"
 before_install:
-  - | 
+  - |
     mkdir -p $HOME/.config/matplotlib && \
     echo 'backend: agg' > $HOME/.config/matplotlib/matplotlibrc
 install:
-  - "pip install ."
-script: python setup.py test
+  - pip install .
+  - pip install pytest
+script: pytest tests

croissance/__init__.py

@@ -1,15 +1,39 @@
-from croissance.estimation import Estimator
-from collections import namedtuple
+import pandas
 
-AnnotatedGrowthCurve = namedtuple('AnnotatedGrowthCurve', ('series', 'outliers', 'growth_phases'))
+import croissance.figures.plot
 
+from croissance.estimation import (
+    AnnotatedGrowthCurve,
+    GrowthEstimationParameters,
+    estimate_growth,
+)
+from croissance.estimation.util import normalize_time_unit
 
-def process_curve(curve: 'pandas.Series', **kwargs):
-    estimator = Estimator(**kwargs)
+
+__all__ = [
+    "plot_processed_curve",
+    "process_curve",
+]
+
+
+def process_curve(
+    curve: "pandas.Series",
+    segment_log_n0: bool = False,
+    constrain_n0: bool = False,
+    n0: float = 0.0,
+    unit: str = "hours",
+):
+    curve = normalize_time_unit(curve, unit)
     if curve.isnull().all():
         return AnnotatedGrowthCurve(curve, [], [])
-    return estimator.growth(curve)
 
+    params = GrowthEstimationParameters()
+    params.segment_log_n0 = segment_log_n0
+    params.constrain_n0 = constrain_n0
+    params.n0 = n0
 
+    return estimate_growth(curve, params=params)
 
 
+def plot_processed_curve(curve: AnnotatedGrowthCurve, yscale="both"):
+    return croissance.figures.plot.plot_processed_curve(curve=curve, yscale=yscale)