Adjusted estimation process, reorganized promotion section and the tr…

…avis test setup

.gitignore

@@ -2,5 +2,6 @@
 __pxcache__/
 *.pyc
 .idea/
-docs/_build
+docs/build
+promotion/
 

.pre-commit-config.yaml

@@ -1,20 +1,22 @@
 repos:
 -   repo: https://github.com/ambv/black
-    rev: stable
+    rev: 19.3b0
     hooks:
     - id: black
       language_version: python3.6
+      exclude: ^docs/
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v1.2.3
     hooks:
     - id: flake8
-- repo: https://github.com/timothycrosley/isort
-  rev: v4.3.20
-  hooks:
+-   repo: https://github.com/timothycrosley/isort
+    rev: 4.3.20
+    hooks:
     - id: isort
-    - name: isort
-    - entry: isort
-    - require_serial: true
-    - language: python
-    - types: [python]
+      name: isort
+      exclude: ^docs/
+      entry: isort
+      require_serial: true
+      language: python
+      types: [python]
 

.travis.yml

@@ -1,14 +1,27 @@
 language: python
+
 python:
   - "3.6"
 
 install:
-    - pip install -r requirements.txt
-    - pip install pytest-cov
-    - pip install codecov
+  - sudo apt-get update
+  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
+  - bash miniconda.sh -b -p $HOME/miniconda
+  - PATH="$HOME/miniconda/bin:$PATH"
+  - conda env create -f environment.yml
+  - source activate grmpy
+
+before_script:
+  - export PYTHONPATH=$PYTHONPATH:$(pwd)
 
 script:
-    - py.test --cov=grmpy
+    - py.test
+    - bash utils/run_sphinx_build.sh
+    - travis_wait python utils/travis_runner.py
+    - python -c "import grmpy; grmpy.test()"
 
 after_success:
     - codecov
+
+notifications:
+  email: false

development/tests/regression/draft.py

@@ -1,57 +1,61 @@
-"""The test provides a regression test battery. In the first step it loops over 100 different seeds,
-generates a random init file for each seed, simulates the resulting dataframe, sums it up and saves
-the sum and the generated dictionary in /grmpy/test/resources/ as a json file. In the second step it
-reads the json file, and loops over all entries. For each element it prints an init file, simulates
-the dataframe, sums it up again and compares the sum from the first step with the one from the
-second step.
+"""The test provides a regression test battery. In the first step it loops over 100
+different seeds, generates a random init file for each seed, simulates the resulting
+dataframe, sums it up and saves the sum and the generated dictionary in
+/grmpy/test/resources/ as a json file. In the second step it reads the json file, and
+loops over all entries. For each element it prints an init file, simulates the dataframe,
+sums it up again and compares the sum from the first step with the one from the second
+step.
  """
 
 import json
 import os
 
 import numpy as np
 
-from grmpy.estimate.estimate_auxiliary import calculate_criteria
-from grmpy.estimate.estimate_auxiliary import start_values
-from grmpy.test.random_init import generate_random_dict
-from grmpy.test.random_init import print_dict
+from grmpy.estimate.estimate_auxiliary import (
+    calculate_criteria,
+    process_data,
+    start_values,
+)
+from grmpy.read.read import read
 from grmpy.simulate.simulate import simulate
 from grmpy.test.auxiliary import cleanup
-from grmpy.read.read import read
+from grmpy.test.random_init import generate_random_dict, print_dict
 
 NUM_TESTS = 100
 
 np.random.seed(1234235)
 seeds = np.random.randint(0, 1000, size=NUM_TESTS)
 directory = os.path.dirname(__file__)
-file_dir = os.path.join(directory, 'old_regression_vault.grmpy.json')
+file_dir = os.path.join(directory, "old_regression_vault.grmpy.json")
 
 if True:
     tests = []
     for seed in seeds:
         np.random.seed(seed)
         constr = dict()
-        constr['DETERMINISTIC'], constr['CATEGORICAL'] = False, False
+        constr["DETERMINISTIC"], constr["CATEGORICAL"] = False, False
         dict_ = generate_random_dict(constr)
-        df = simulate('test.grmpy.ini')
+        df = simulate("test.grmpy.yml")
         stat = np.sum(df.sum())
-        init_dict = read('test.grmpy.ini')
-        start = start_values(init_dict, df, 'init')
-        criteria = calculate_criteria(init_dict, df, start)
+        init_dict = read("test.grmpy.yml")
+        start = start_values(init_dict, df, "init")
+        _, X1, X0, Z1, Z0, Y1, Y0 = process_data(df, init_dict)
+        criteria = calculate_criteria(init_dict, X1, X0, Z1, Z0, Y1, Y0, start)
         tests += [(stat, dict_, criteria)]
-    json.dump(tests, open(file_dir, 'w'))
+    json.dump(tests, open(file_dir, "w"))
 
 if True:
-    tests = json.load(open(file_dir, 'r'))
+    tests = json.load(open(file_dir, "r"))
 
     for test in tests:
         stat, dict_, criteria = test
         print_dict(dict_)
-        init_dict = read('test.grmpy.yml')
-        df = simulate('test.grmpy.yml')
-        start = start_values(init_dict, df, 'init')
+        init_dict = read("test.grmpy.yml")
+        df = simulate("test.grmpy.yml")
+        start = start_values(init_dict, df, "init")
         criteria_ = calculate_criteria(init_dict, df, start)
         np.testing.assert_array_almost_equal(criteria, criteria_)
         np.testing.assert_almost_equal(np.sum(df.sum()), stat)
 
-cleanup('regression')
+cleanup("regression")

development/tests/regression/run.py

@@ -1,29 +1,41 @@
 #!/usr/bin/env python
-"""The test provides the basic capabilities to work with the regression tests of the package."""
+"""The test provides the basic capabilities to work with the regression tests of the
+package.
+"""
 import argparse
 import json
 import os
 
 import numpy as np
-import grmpy
 
-from grmpy.test.random_init import generate_random_dict
-from grmpy.test.random_init import print_dict
+import grmpy
+from grmpy.estimate.estimate_auxiliary import (
+    calculate_criteria,
+    process_data,
+    start_values,
+)
+from grmpy.read.read import read
 from grmpy.simulate.simulate import simulate
-from grmpy.test.auxiliary import cleanup
+from grmpy.test.auxiliary import cleanup, dict_transformation
+from grmpy.test.random_init import generate_random_dict, print_dict
 
 
 def process_arguments(parser):
     """This function parses the input arguments."""
     args = parser.parse_args()
-
     # Distribute input arguments
     request = args.request
+    if "num_tests" in args:
+        num_tests = int(args.num_tests)
+    else:
+        num_tests = None
 
     # Test validity of input arguments
-    assert request in ['check', 'create']
-
-    return request
+    if request not in ["check", "create"]:
+        raise AssertionError()
+    if num_tests not in [i for i in np.arange(1001)]:
+        raise AssertionError(9)
+    return request, num_tests
 
 
 def create_vault(num_tests=100, seed=123):
@@ -33,39 +45,83 @@ def create_vault(num_tests=100, seed=123):
     tests = []
     for _ in range(num_tests):
         dict_ = generate_random_dict()
-        df = simulate('test.grmpy.ini')
+        init_dict = read("test.grmpy.yml")
+        df = simulate("test.grmpy.yml")
+        _, X1, X0, Z1, Z0, Y1, Y0 = process_data(df, init_dict)
+        x0 = start_values(init_dict, df, "init")
+        criteria = calculate_criteria(init_dict, X1, X0, Z1, Z0, Y1, Y0, x0)
         stat = np.sum(df.sum())
-        tests += [(stat, dict_)]
+        tests += [(stat, dict_, criteria)]
         cleanup()
 
-    json.dump(tests, open('old_regression_vault.grmpy.json', 'w'))
+    json.dump(tests, open("regression_vault.grmpy.json", "w"))
 
 
-def check_vault():
-    """This function checks the complete regression vault that is distributed as part of the
-    package.
+def check_vault(num_tests=100):
+    """This function checks the complete regression vault that is distributed as part of
+    the package.
     """
-    fname = os.path.dirname(grmpy.__file__) + '/test/resources/old_regression_vault.grmpy.json'
+    fname = (
+        os.path.dirname(grmpy.__file__)
+        + "/test/resources/old_regression_vault.grmpy.json"
+    )
     tests = json.load(open(fname))
 
+    if num_tests > len(tests):
+        print(
+            "The specified number of evaluations is larger than the number"
+            " of entries in the regression_test vault.\n"
+            "Therefore the test runs the complete test battery."
+        )
+    else:
+        tests = [tests[i] for i in np.random.choice(len(tests), num_tests)]
+
     for test in tests:
         stat, dict_, criteria = test
-        print_dict(dict_)
-        df = simulate('test.grmpy.ini')
+        print_dict(dict_transformation(dict_))
+        init_dict = read("test.grmpy.yml")
+        df = simulate("test.grmpy.yml")
+        _, X1, X0, Z1, Z0, Y1, Y0 = process_data(df, init_dict)
+        x0 = start_values(init_dict, df, "init")
+        criteria_ = calculate_criteria(init_dict, X1, X0, Z1, Z0, Y1, Y0, x0)
+        np.testing.assert_almost_equal(criteria_, criteria)
         np.testing.assert_almost_equal(np.sum(df.sum()), stat)
-        cleanup('regression')
-
-
-if __name__ == '__main__':
-
-    parser = argparse.ArgumentParser(description='Work with regression tests for package.')
-
-    parser.add_argument('--request', action='store', dest='request', required=True,
-                        choices=['check', 'create'], help='request')
-
-    request = process_arguments(parser)
-
-    if request == 'check':
-        check_vault()
-    elif request == 'create':
-        create_vault()
+        cleanup("regression")
+
+
+if __name__ == "__main__":
+
+    parser = argparse.ArgumentParser(
+        description="Work with regression tests for package."
+    )
+
+    parser.add_argument(
+        "--request",
+        action="store",
+        dest="request",
+        required=True,
+        choices=["check", "create"],
+        help="request",
+    )
+
+    parser.add_argument(
+        "--num_tests",
+        action="store",
+        dest="num_tests",
+        required=False,
+        choices=[str(i) for i in np.arange(1001)],
+        help="num_tests",
+    )
+
+    request, num_tests = process_arguments(parser)
+
+    if request == "check":
+        if num_tests is None:
+            check_vault()
+        else:
+            check_vault(num_tests)
+    elif request == "create":
+        if num_tests is None:
+            create_vault()
+        else:
+            create_vault(num_tests)

development/tests/replication/replication.grmpy.yml

@@ -13,6 +13,8 @@ ESTIMATION:
     indicator: state
     comparison: 0
     output_file: est.grmpy.info
+    print_output: est.grmpy.info
+
 TREATED:
     params:
     - 1.0