make release-tag: Merge branch 'master' into stable

pvk-developer · pvk-developer · commit addba6cb0c8a · 2021-01-26T22:16:00.000+01:00
diff --git a/.travis.yml b/.travis.yml
diff --git a/HISTORY.md b/HISTORY.md
@@ -1,6 +1,6 @@
 # History
 
-## 0.0.1 - 2020-11-30
+## 0.0.1 - 2021-01-26
 
 First release to PyPI.
 
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -3,6 +3,7 @@ include CONTRIBUTING.md
 include HISTORY.md
 include LICENSE
 include README.md
+include sigpro/data/demo_timeseries.csv
 
 recursive-include tests *
 recursive-exclude * __pycache__
diff --git a/Makefile b/Makefile
@@ -81,48 +81,51 @@ install-test: clean-build clean-pyc ## install the package and test dependencies
 install-develop: clean-build clean-pyc ## install the package in editable mode and dependencies for development
 	pip install -e .[dev]
 
-MINIMUM := $(shell sed -n '/install_requires = \[/,/]/p' setup.py | head -n-1 | tail -n+2 | sed 's/ *\(.*\),$?$$/\1/g' | tr '>' '=')
-
-.PHONY: install-minimum
-install-minimum: ## install the minimum supported versions of the package dependencies
-	pip install $(MINIMUM)
 
 # LINT TARGETS
 
 .PHONY: lint
 lint: ## check style with flake8 and isort
-	flake8 sigpro
-	flake8 tests --ignore=D
-	isort -c --recursive sigpro tests
-	pylint sigpro --rcfile=setup.cfg
+	invoke lint
 
 .PHONY: fix-lint
 fix-lint: ## fix lint issues using autoflake, autopep8, and isort
-	find sigpro tests -name '*.py' | xargs autoflake --in-place --remove-all-unused-imports --remove-unused-variables
-	autopep8 --in-place --recursive --aggressive sigpro tests
-	isort --apply --atomic --recursive sigpro tests
+	find sigpro -name '*.py' | xargs autoflake --in-place --remove-all-unused-imports --remove-unused-variables
+	autopep8 --in-place --recursive --aggressive sigpro
+	isort --apply --atomic --recursive sigpro
 
+	find tests -name '*.py' | xargs autoflake --in-place --remove-all-unused-imports --remove-unused-variables
+	autopep8 --in-place --recursive --aggressive tests
+	isort --apply --atomic --recursive tests
 
 # TEST TARGETS
 
 .PHONY: test-unit
 test-unit: ## run tests quickly with the default Python
-	python -m pytest --cov=sigpro
+	invoke pytest
 
 .PHONY: test-readme
 test-readme: ## run the readme snippets
-	rm -rf tests/readme_test && mkdir tests/readme_test
-	cd tests/readme_test && rundoc run --single-session python3 -t python3 ../../README.md
-	rm -rf tests/readme_test
+	invoke readme
+
+
+.PHONY: test-tutorials
+test-tutorials: ## run the tutorial notebooks
+	invoke tutorials
+
 
 .PHONY: test
-test: test-unit test-readme ## test everything that needs test dependencies
+test: test-unit test-readme test-tutorials ## test everything that needs test dependencies
+
+.PHONY: check-dependencies
+check-dependencies: ## test if there are any broken dependencies
+	pip check
 
 .PHONY: test-devel
-test-devel: lint docs ## test everything that needs development dependencies
+test-devel: check-dependencies lint docs ## test everything that needs development dependencies
 
 .PHONY: test-all
-test-all: ## test using tox
+test-all:
 	tox -r
 
 .PHONY: coverage
@@ -132,12 +135,11 @@ coverage: ## check code coverage quickly with the default Python
 	coverage html
 	$(BROWSER) htmlcov/index.html
 
-
 # DOCS TARGETS
 
 .PHONY: docs
 docs: clean-docs ## generate Sphinx HTML documentation, including API docs
-	sphinx-apidoc --separate --no-toc -o docs/api/ sigpro
+	sphinx-apidoc --module-first --separate -T -o docs/api/ sigpro
 	$(MAKE) -C docs html
 
 .PHONY: view-docs
@@ -146,7 +148,7 @@ view-docs: docs ## view docs in browser
 
 .PHONY: serve-docs
 serve-docs: view-docs ## compile the docs watching for changes
-	watchmedo shell-command -W -R -D -p '*.rst;*.md' -c '$(MAKE) -C docs html' docs
+	watchmedo shell-command -W -R -D -p '*.rst;*.md' -c '$(MAKE) -C docs html' .
 
 
 # RELEASE TARGETS
@@ -170,7 +172,7 @@ publish-test: dist publish-confirm ## package and upload a release on TestPyPI
 
 .PHONY: publish
 publish: dist publish-confirm ## package and upload a release
-	twine upload --repository-url https://pypi.dailab.ml:8080 dist/*
+	twine upload dist/*
 
 .PHONY: bumpversion-release
 bumpversion-release: ## Merge master to stable and bumpversion release
diff --git a/README.md b/README.md
@@ -5,8 +5,7 @@
 
 [![Development Status](https://img.shields.io/badge/Development%20Status-2%20--%20Pre--Alpha-yellow)](https://pypi.org/search/?c=Development+Status+%3A%3A+2+-+Pre-Alpha)
 [![PyPi Shield](https://img.shields.io/pypi/v/SigPro.svg)](https://pypi.python.org/pypi/SigPro)
-[![Travis CI Shield](https://travis-ci.org/signals-dev/SigPro.svg?branch=master)](https://travis-ci.org/signals-dev/SigPro)
-[![Coverage Status](https://codecov.io/gh/signals-dev/SigPro/branch/master/graph/badge.svg)](https://codecov.io/gh/signals-dev/SigPro)
+[![Tests](https://github.com/signals-dev/SigPro/workflows/Run%20Tests/badge.svg)](https://github.com/signals-dev/SigPro/actions?query=workflow%3A%22Run+Tests%22+branch%3Amaster)
 [![Downloads](https://pepy.tech/badge/sigpro)](https://pepy.tech/project/sigpro)
 
 
diff --git a/setup.cfg b/setup.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.0.1
+current_version = 0.0.1.dev1
 commit = True
 tag = True
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\.(?P<release>[a-z]+)(?P<candidate>\d+))?
diff --git a/setup.py b/setup.py
@@ -12,9 +12,9 @@
     history = history_file.read()
 
 install_requires = [
-    'mlblocks>=0.3.4,<0.4',
+    'mlblocks>=0.4.0,<0.5',
     'pandas>=1,<2',
-    'numpy>=1.15.4,<2',
+    'numpy>=1.17.4,<1.19',
     'scipy>=1.3.3,<2',
 ]
 
@@ -61,6 +61,7 @@
     'coverage>=4.5.1,<6',
     'tox>=2.9.1,<4',
     'importlib-metadata<2,>=0.12',
+    'invoke',
 ]
 
 setup(
@@ -99,6 +100,6 @@
     test_suite='tests',
     tests_require=tests_require,
     url='https://github.com/signals-dev/SigPro',
-    version='0.0.1',
+    version='0.0.1.dev1',
     zip_safe=False,
 )
diff --git a/sigpro/__init__.py b/sigpro/__init__.py
@@ -4,7 +4,7 @@
 
 __author__ = """MIT Data To AI Lab"""
 __email__ = 'dailabmit@gmail.com'
-__version__ = '0.0.1'
+__version__ = '0.0.1.dev1'
 
 import os
 
diff --git a/sigpro/aggregations/frequency/band.py b/sigpro/aggregations/frequency/band.py
@@ -0,0 +1,30 @@
+"""Band Module."""
+
+import numpy as np
+
+
+def band_mean(amplitude_values, frequency_values, min_frequency, max_frequency):
+    """Compute the mean values for a specific band.
+
+    Filter between a high and low band and compute the mean value for this specific band.
+
+    Args:
+        amplitude_values (np.ndarray):
+            A numpy array with the signal values.
+        frequency_values (np.ndarray):
+            A numpy array with the frequency values.
+        min_frequency (int or float):
+            Band minimum.
+        max_frequency (int or float):
+            Band maximum.
+
+    Returns:
+        float:
+            Mean value for the given band.
+    """
+    lower_frequency_than = frequency_values <= max_frequency
+    higher_frequency_than = frequency_values >= min_frequency
+    selected_idx = np.where(higher_frequency_than & lower_frequency_than)
+    selected_values = amplitude_values[selected_idx]
+
+    return np.mean(selected_values)
diff --git a/sigpro/primitives/sigpro/aggregations/frequency/band/band_mean.json b/sigpro/primitives/sigpro/aggregations/frequency/band/band_mean.json
@@ -0,0 +1,37 @@
+{
+    "name": "sigpro.aggregations.frequency.band.band_mean",
+    "primitive": "sigpro.aggregations.frequency.band.band_mean",
+    "classifiers": {
+        "type": "aggregation",
+        "subtype": "frequency"
+    },
+    "produce": {
+        "args": [
+            {
+                "name": "amplitude_values",
+                "type": "numpy.ndarray"
+            },
+            {
+                "name": "frequency_values",
+                "type": "numpy.ndarray"
+            }
+        ],
+        "output": [
+            {
+                "name": "value",
+                "type": "float"
+            }
+        ]
+    },
+    "hyperparameters": {
+        "fixed": {
+            "min_frequency": {
+                "type": "float"
+            },
+            "max_frequency": {
+                "type": "float"
+            }
+        },
+        "tunable": {}
+    }
+}
diff --git a/tasks.py b/tasks.py
@@ -0,0 +1,92 @@
+import glob
+import os
+import re
+import shutil
+import stat
+from pathlib import Path
+
+from invoke import task
+
+
+@task
+def pytest(c):
+    c.run('python -m pytest --cov=sigpro')
+
+
+@task
+def install_minimum(c):
+    with open('setup.py', 'r') as setup_py:
+        lines = setup_py.read().splitlines()
+
+    versions = []
+    started = False
+    for line in lines:
+        if started:
+            if line == ']':
+                break
+
+            line = line.strip()
+            line = re.sub(r',?<=?[\d.]*,?', '', line)
+            line = re.sub(r'>=?', '==', line)
+            line = re.sub(r"""['",]""", '', line)
+            versions.append(line)
+
+        elif line.startswith('install_requires = ['):
+            started = True
+
+    c.run(f'python -m pip install {" ".join(versions)}')
+
+
+@task
+def minimum(c):
+    install_minimum(c)
+    c.run('python -m pip check')
+    c.run('python -m pytest')
+
+
+@task
+def readme(c):
+    test_path = Path('tests/readme_test')
+    if test_path.exists() and test_path.is_dir():
+        shutil.rmtree(test_path)
+
+    cwd = os.getcwd()
+    os.makedirs(test_path, exist_ok=True)
+    shutil.copy('README.md', test_path / 'README.md')
+    os.chdir(test_path)
+    c.run('rundoc run --single-session python3 -t python3 README.md')
+    os.chdir(cwd)
+    shutil.rmtree(test_path)
+
+
+@task
+def tutorials(c):
+    for ipynb_file in glob.glob('tutorials/*.ipynb') + glob.glob('tutorials/**/*.ipynb'):
+        if '.ipynb_checkpoints' not in ipynb_file:
+            c.run((
+                'jupyter nbconvert --execute --ExecutePreprocessor.timeout=3600 '
+                f'--to=html --stdout {ipynb_file}'
+            ), hide='out')
+
+
+@task
+def lint(c):
+    c.run('flake8 sigpro')
+    c.run('flake8 tests --ignore=D,SFS2')
+    c.run('isort -c --recursive sigpro tests')
+    # c.run('pydocstyle sigpro')
+    c.run('pylint sigpro --rcfile=setup.cfg')
+
+
+def remove_readonly(func, path, _):
+    "Clear the readonly bit and reattempt the removal"
+    os.chmod(path, stat.S_IWRITE)
+    func(path)
+
+
+@task
+def rmdir(c, path):
+    try:
+        shutil.rmtree(path, onerror=remove_readonly)
+    except PermissionError:
+        pass
diff --git a/tests/unit/aggregations/frequency/__init__.py b/tests/unit/aggregations/frequency/__init__.py
diff --git a/tests/unit/aggregations/frequency/test_band.py b/tests/unit/aggregations/frequency/test_band.py
@@ -0,0 +1,21 @@
+# -*- coding: utf-8 -*-
+
+"""Tests for sigpro.aggregations.frequency.band package."""
+
+import numpy as np
+
+from sigpro.aggregations.frequency.band import band_mean
+
+AMPLITUDE_VALUES = np.arange(200)
+FREQUENCY_VALUES = np.arange(200)
+
+
+def test_band_mean():
+    # setup
+    expected = 15  # we computed previoulsy
+
+    # run
+    result = band_mean(AMPLITUDE_VALUES, FREQUENCY_VALUES, min_frequency=10, max_frequency=20)
+
+    # assert
+    assert result == expected
diff --git a/tox.ini b/tox.ini
