Merge pull request #24 from sdevenes/feature/deploy_doc

Feature/deploy doc

.gitignore

@@ -7,3 +7,4 @@ public/*
 
 ### Python execution ###
 scripts/__pycache__/
+tests/output/

.travis.yml

@@ -0,0 +1,32 @@
+# From here: https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/use-conda-with-travis-ci.html
+language: python
+python:
+  # We don't actually use the Travis Python, but this keeps it organized.
+  - "3.7"
+  - "3.8"
+install:
+  # Install phase of our CI pipeline
+  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
+  - bash miniconda.sh -b -p $HOME/miniconda
+  - source "$HOME/miniconda/etc/profile.d/conda.sh"
+  - hash -r
+  - conda config --set always_yes yes --set changeps1 no
+  - conda update -q conda
+  - conda info -a
+  - conda create -q -n project python=$TRAVIS_PYTHON_VERSION -c plotly --file requirements.txt
+  - conda activate project
+
+script:
+  # Run phase of our CI pipeline
+  - make unitTests
+  - make doc
+
+deploy:
+  - provider: pages:git
+    verbose: true
+    edge: true
+    token: $GITHUB_TOKEN
+    local_dir: ./public/
+    on:
+        branch: master
+        condition: $TRAVIS_PYTHON_VERSION = 3.8

docs/Makefile

@@ -37,5 +37,6 @@ html: gendocs
 	mkdir -p $(OUTPUTDIR)/html/
 	cp -R $(BUILDDIR)/html/* $(OUTPUTDIR)
 	@echo "html files copied; the html files are in $(OUTPUTDIR)."
+	touch $(OUTPUTDIR)/.nojekyll
 
 

docs/source/modules.rst

@@ -8,4 +8,4 @@ scripts
    analysis
    database
    download_data
-   test
+   paper

docs/source/test.rst → docs/source/paper.rst

@@ -1,7 +1,7 @@
-test module
-===========
+paper module
+============
 
-.. automodule:: test
+.. automodule:: paper
    :members:
    :undoc-members:
    :show-inheritance:

makefile

@@ -0,0 +1,22 @@
+TESTDIR        = tests
+SCRIPTDIR      = scripts
+
+default:
+	echo "Welcome to M05 mini project"
+
+.PHONY: loadData
+loadData:
+	# todo
+
+.PHONY: unitTests
+unitTests: cleanTests
+	nosetests --nocapture -v "$(TESTDIR)/test.py"
+
+.PHONY: cleanTests
+cleanTests:
+	rm -rf "$(TESTDIR)/output"
+
+.PHONY: doc
+doc:
+	$(MAKE) -C docs clean
+	$(MAKE) -C docs html

requirements.txt

@@ -1,5 +1,6 @@
 requests
-sklearn
-plotly.express
+scikit-learn
+plotly_express==0.4.1
 sphinx
-sphinx_rtd_theme
+sphinx_rtd_theme
+nose

tests/test.py

@@ -0,0 +1,57 @@
+import os
+import sys
+sys.path.insert(0, os.path.dirname(os.path.realpath(__file__)) + "/../scripts/")
+
+import download_data
+import zipfile
+import requests
+
+import algorithm
+import analysis
+import numpy as np
+
+import nose.tools
+
+# Get the path of this file to easily build relative path
+base_path = os.path.dirname(os.path.realpath(__file__))
+
+def test_unzip_file_not_a_zip():
+    path_to_zip_file = base_path + "/inputs/not_a_zip.txt" # not a zip
+    directory_to_extract_to = base_path # extract here
+    nose.tools.assert_raises(zipfile.BadZipFile, download_data.unzip_file, path_to_zip_file, directory_to_extract_to)
+
+def test_unzip_file_invalid_zip_path():
+    path_to_zip_file = base_path + "/simpleZip.zip" # Invalid path
+    directory_to_extract_to = base_path # extract here
+    nose.tools.assert_raises(FileNotFoundError, download_data.unzip_file, path_to_zip_file, directory_to_extract_to)
+
+def test_unzip_file():
+    path_to_zip_file = base_path + "/inputs/simpleZip.zip"
+    directory_to_extract_to = base_path + "/output/" # extract here
+    download_data.unzip_file(path_to_zip_file, directory_to_extract_to)
+    nose.tools.ok_(os.path.isfile(base_path + "/output/f1.txt"), msg="SimpleZip not correctly unzipped")
+
+def test_download_url_invalid_url():
+    url = "https://invalid_url.zip"
+    save_path = base_path + "/output/invalid_dl.zip"
+    nose.tools.assert_raises(requests.exceptions.ConnectionError, download_data.download_url, url, save_path)
+
+def test_download_url():
+    url = "https://archive.ics.uci.edu/ml/machine-learning-databases/00405/Postures.zip" # Smaller zip to test
+    save_path = base_path + "/output/test_dl.zip"
+    download_data.download_url(url, save_path)
+    nose.tools.ok_(os.path.isfile(save_path), msg="Dataset not correctly downloaded")
+
+def test_make_labels():
+    X = [np.array([0, 1, 0]), np.array([2, 3]), np.array([7, 4, 6, 9])]
+    labels = algorithm.make_labels(X)
+    ref = np.array([0,0,0,1,1,2,2,2,2])
+    nose.tools.ok_((labels==ref).all(), msg="{} != {}".format(labels,ref))
+
+def test_get_confusion_matrix():
+    prediction = [1,2,3,1,2,2,3]
+    true_val = [1,2,3,1,2,3,2]
+    cm = analysis.get_confusion_matrix(prediction, true_val)
+    ref = np.array([[2, 0, 0],[0, 2, 1],[0, 1, 1]])
+    nose.tools.ok_((cm==ref).all(), msg="{} != {}".format(cm,ref))
+